diff --git a/pvactools/lib/fasta_generator.py b/pvactools/lib/fasta_generator.py
index 81ded11b..3bba14d9 100644
--- a/pvactools/lib/fasta_generator.py
+++ b/pvactools/lib/fasta_generator.py
@@ -402,8 +402,8 @@ def execute(self):
                             if right_clip_length > first_position:
                                 warnings.add("Clipping {} amino acids off the start of peptide {} would clip the best peptide. Skipping.".format(right_clip_length, seq2))
                                 continue
-                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length):(len(seq1_seq) - left_clip_length)]
-                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length]
+                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length - left_clip_length):(len(seq1_seq) - left_clip_length)]
+                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length + right_clip_length]
 
                         if self.spacer != 'None':
                             seq_ID = "{}|{}|{}|{}|{}".format(seq1, left_clip_length, self.spacer, right_clip_length, seq2)
diff --git a/tests/test_data/fasta_generator/output_pvacvector.fasta b/tests/test_data/fasta_generator/output_pvacvector.fasta
index eb87e7bf..d4c33e82 100644
--- a/tests/test_data/fasta_generator/output_pvacvector.fasta
+++ b/tests/test_data/fasta_generator/output_pvacvector.fasta
@@ -1,538 +1,540 @@
 >1
-CNHLKKHHAKAKQY
+AGKKLKEHHDGTWICR
 >2
-CNHLKKHHDGTWICR
+AGKKLKEHHFGAPAWS
 >3
-CNHLKKHHFGAPAWS
+AGKKLKEHHGAPAWSQ
 >4
-CNHLKKHHGAPAWS
+AGKKLKEHHGTWICRF
 >5
-CNHLKKHHGTWICR
+AGKKLKEHHGYVWFRF
 >6
-CNHLKKHHHPRWEIL
+AGKKLKEHHHPRWEIL
 >7
-CNHLKKHHKLGILFG
+AGKKLKEHHKLGILFG
 >8
-CNHLKKHHKQSQWMT
+AGKKLKEHHKQSQWMT
 >9
-CNHLKKHHKTTWQVW
+AGKKLKEHHKTTWQVW
 >10
-CNHLKKHHLAKAKQY
+AGKKLKEHHLASTLSP
 >11
-CNHLKKHHLASTLS
+AGKKLKEHHLGILFGR
 >12
-CNHLKKHHLGILFG
+AGKKLKEHHPRWEILI
 >13
-CNHLKKHHPRWEIL
+AGKKLKEHHQSQWMTE
 >14
-CNHLKKHHQSQWMT
+AGKKLKEHHRTGLIAH
 >15
-CNHLKKHHRTGLIAH
+AGKKLKEHHSLASTLS
 >16
-CNHLKKHHSLASTLS
+AGKKLKEHHTGLIAHF
 >17
-CNHLKKHHTGLIAH
+AGKKLKEHHTTWQVWL
 >18
-CNHLKKHHTTWQVW
+AGKKLKEHHYVWFRFV
 >19
-CNHLKKLHHAKAKQY
+CNHLKKLHHAKAKQYR
 >20
-CNHLKKLHHGAPAWS
+CNHLKKLHHGAPAWSQ
 >21
-CNHLKKLHHGTWICR
+CNHLKKLHHGTWICRF
 >22
-CNHLKKLHHLASTLS
+CNHLKKLHHLASTLSP
 >23
-CNHLKKLHHLGILFG
+CNHLKKLHHLGILFGR
 >24
-CNHLKKLHHPRWEIL
+CNHLKKLHHPRWEILI
 >25
-CNHLKKLHHQSQWMT
+CNHLKKLHHQSQWMTE
 >26
-CNHLKKLHHTGLIAH
+CNHLKKLHHTGLIAHF
 >27
-CNHLKKLHHTTWQVW
+CNHLKKLHHTTWQVWL
 >28
-CSRSDGHHAKAKQY
+CSRSDGLHHAKAKQYR
 >29
-CSRSDGHHDGTWICR
+CSRSDGLHHGAPAWSQ
 >30
-CSRSDGHHFGAPAWS
+CSRSDGLHHGTWICRF
 >31
-CSRSDGHHGAPAWS
+CSRSDGLHHLASTLSP
 >32
-CSRSDGHHGTWICR
+CSRSDGLHHLGILFGR
 >33
-CSRSDGHHGYVWFRF
+CSRSDGLHHPRWEILI
 >34
-CSRSDGHHHPRWEIL
+CSRSDGLHHTGLIAHF
 >35
-CSRSDGHHKLGILFG
+CSRSDGLHHTTWQVWL
 >36
-CSRSDGHHKTTWQVW
+CSRSDGLHHYVWFRFV
 >37
-CSRSDGHHLAKAKQY
+DGALSLRHHAKAKQYR
 >38
-CSRSDGHHLASTLS
+DGALSLRHHGAPAWSQ
 >39
-CSRSDGHHLGILFG
+DGALSLRHHGTWICRF
 >40
-CSRSDGHHPRWEIL
+DGALSLRHHLASTLSP
 >41
-CSRSDGHHRTGLIAH
+DGALSLRHHPRWEILI
 >42
-CSRSDGHHSLASTLS
+DGALSLRHHQSQWMTE
 >43
-CSRSDGHHTGLIAH
+DGALSLRHHTGLIAHF
 >44
-CSRSDGHHTTWQVW
+DGALSLRHHTTWQVWL
 >45
-CSRSDGHHYVWFRF
+DGALSLRHHYVWFRFV
 >46
-CSRSDGLHHAKAKQY
+EEFDFILHHAKAKQYR
 >47
-CSRSDGLHHGAPAWS
+EEFDFILHHDGTWICR
 >48
-CSRSDGLHHGTWICR
+EEFDFILHHFGAPAWS
 >49
-CSRSDGLHHLASTLS
+EEFDFILHHGAPAWSQ
 >50
-CSRSDGLHHLGILFG
+EEFDFILHHGTWICRF
 >51
-CSRSDGLHHPRWEIL
+EEFDFILHHGYVWFRF
 >52
-CSRSDGLHHTGLIAH
+EEFDFILHHHPRWEIL
 >53
-CSRSDGLHHTTWQVW
+EEFDFILHHKLGILFG
 >54
-CSRSDGLHHYVWFRF
+EEFDFILHHKQSQWMT
 >55
-DGALSLHHAKAKQY
+EEFDFILHHLAKAKQY
 >56
-DGALSLHHDGTWICR
+EEFDFILHHLASTLSP
 >57
-DGALSLHHFGAPAWS
+EEFDFILHHLGILFGR
 >58
-DGALSLHHGAPAWS
+EEFDFILHHPRWEILI
 >59
-DGALSLHHGTWICR
+EEFDFILHHQSQWMTE
 >60
-DGALSLHHGYVWFRF
+EEFDFILHHRTGLIAH
 >61
-DGALSLHHHPRWEIL
+EEFDFILHHSLASTLS
 >62
-DGALSLHHKQSQWMT
+EEFDFILHHTGLIAHF
 >63
-DGALSLHHKTTWQVW
+EEFDFILHHYVWFRFV
 >64
-DGALSLHHLAKAKQY
+EFDFILPHHAKAKQYR
 >65
-DGALSLHHLASTLS
+EFDFILPHHGAPAWSQ
 >66
-DGALSLHHPRWEIL
+EFDFILPHHGTWICRF
 >67
-DGALSLHHQSQWMT
+EFDFILPHHLASTLSP
 >68
-DGALSLHHRTGLIAH
+EFDFILPHHLGILFGR
 >69
-DGALSLHHSLASTLS
+EFDFILPHHPRWEILI
 >70
-DGALSLHHTGLIAH
+EFDFILPHHQSQWMTE
 >71
-DGALSLHHTTWQVW
+EFDFILPHHTGLIAHF
 >72
-DGALSLHHYVWFRF
+EFDFILPHHYVWFRFV
 >73
-DGALSLRHHAKAKQY
+FCNHLKKHHAKAKQYR
 >74
-DGALSLRHHGAPAWS
+FCNHLKKHHDGTWICR
 >75
-DGALSLRHHGTWICR
+FCNHLKKHHFGAPAWS
 >76
-DGALSLRHHLASTLS
+FCNHLKKHHGAPAWSQ
 >77
-DGALSLRHHPRWEIL
+FCNHLKKHHGTWICRF
 >78
-DGALSLRHHQSQWMT
+FCNHLKKHHHPRWEIL
 >79
-DGALSLRHHTGLIAH
+FCNHLKKHHKLGILFG
 >80
-DGALSLRHHTTWQVW
+FCNHLKKHHKQSQWMT
 >81
-DGALSLRHHYVWFRF
+FCNHLKKHHKTTWQVW
 >82
-EFDFILHHAKAKQY
+FCNHLKKHHLAKAKQY
 >83
-EFDFILHHDGTWICR
+FCNHLKKHHLASTLSP
 >84
-EFDFILHHFGAPAWS
+FCNHLKKHHLGILFGR
 >85
-EFDFILHHGAPAWS
+FCNHLKKHHPRWEILI
 >86
-EFDFILHHGTWICR
+FCNHLKKHHQSQWMTE
 >87
-EFDFILHHGYVWFRF
+FCNHLKKHHRTGLIAH
 >88
-EFDFILHHHPRWEIL
+FCNHLKKHHSLASTLS
 >89
-EFDFILHHKLGILFG
+FCNHLKKHHTGLIAHF
 >90
-EFDFILHHKQSQWMT
+FCNHLKKHHTTWQVWL
 >91
-EFDFILHHLAKAKQY
+FSGGAATHHAKAKQYR
 >92
-EFDFILHHLASTLS
+FSGGAATHHDGTWICR
 >93
-EFDFILHHLGILFG
+FSGGAATHHGTWICRF
 >94
-EFDFILHHPRWEIL
+FSGGAATHHGYVWFRF
 >95
-EFDFILHHQSQWMT
+FSGGAATHHHPRWEIL
 >96
-EFDFILHHRTGLIAH
+FSGGAATHHKLGILFG
 >97
-EFDFILHHSLASTLS
+FSGGAATHHKQSQWMT
 >98
-EFDFILHHTGLIAH
+FSGGAATHHKTTWQVW
 >99
-EFDFILHHYVWFRF
+FSGGAATHHLAKAKQY
 >100
-EFDFILPHHAKAKQY
+FSGGAATHHLASTLSP
 >101
-EFDFILPHHGAPAWS
+FSGGAATHHLGILFGR
 >102
-EFDFILPHHGTWICR
+FSGGAATHHPRWEILI
 >103
-EFDFILPHHLASTLS
+FSGGAATHHQSQWMTE
 >104
-EFDFILPHHLGILFG
+FSGGAATHHRTGLIAH
 >105
-EFDFILPHHPRWEIL
+FSGGAATHHSLASTLS
 >106
-EFDFILPHHQSQWMT
+FSGGAATHHTGLIAHF
 >107
-EFDFILPHHTGLIAH
+FSGGAATHHTTWQVWL
 >108
-EFDFILPHHYVWFRF
+FSGGAATHHYVWFRFV
 >109
-GKKLKEGHHGAPAWS
+GKKLKEGHHGAPAWSQ
 >110
-GKKLKEGHHGTWICR
+GKKLKEGHHGTWICRF
 >111
-GKKLKEGHHLASTLS
+GKKLKEGHHLASTLSP
 >112
-GKKLKEGHHLGILFG
+GKKLKEGHHLGILFGR
 >113
-GKKLKEGHHPRWEIL
+GKKLKEGHHPRWEILI
 >114
-GKKLKEGHHQSQWMT
+GKKLKEGHHQSQWMTE
 >115
-GKKLKEGHHTGLIAH
+GKKLKEGHHTGLIAHF
 >116
-GKKLKEGHHTTWQVW
+GKKLKEGHHTTWQVWL
 >117
-GKKLKEGHHYVWFRF
+GKKLKEGHHYVWFRFV
 >118
-GKKLKEHHDGTWICR
+KREAKTKHHAKAKQYR
 >119
-GKKLKEHHFGAPAWS
+KREAKTKHHGAPAWSQ
 >120
-GKKLKEHHGAPAWS
+KREAKTKHHGTWICRF
 >121
-GKKLKEHHGTWICR
+KREAKTKHHLASTLSP
 >122
-GKKLKEHHGYVWFRF
+KREAKTKHHLGILFGR
 >123
-GKKLKEHHHPRWEIL
+KREAKTKHHQSQWMTE
 >124
-GKKLKEHHKLGILFG
+KREAKTKHHTGLIAHF
 >125
-GKKLKEHHKQSQWMT
+KREAKTKHHTTWQVWL
 >126
-GKKLKEHHKTTWQVW
+KREAKTKHHYVWFRFV
 >127
-GKKLKEHHLASTLS
+LDGALSLHHAKAKQYR
 >128
-GKKLKEHHLGILFG
+LDGALSLHHDGTWICR
 >129
-GKKLKEHHPRWEIL
+LDGALSLHHFGAPAWS
 >130
-GKKLKEHHQSQWMT
+LDGALSLHHGAPAWSQ
 >131
-GKKLKEHHRTGLIAH
+LDGALSLHHGTWICRF
 >132
-GKKLKEHHSLASTLS
+LDGALSLHHGYVWFRF
 >133
-GKKLKEHHTGLIAH
+LDGALSLHHHPRWEIL
 >134
-GKKLKEHHTTWQVW
+LDGALSLHHKQSQWMT
 >135
-GKKLKEHHYVWFRF
+LDGALSLHHKTTWQVW
 >136
-KREAKTHHAKAKQY
+LDGALSLHHLAKAKQY
 >137
-KREAKTHHDGTWICR
+LDGALSLHHLASTLSP
 >138
-KREAKTHHFGAPAWS
+LDGALSLHHPRWEILI
 >139
-KREAKTHHGAPAWS
+LDGALSLHHQSQWMTE
 >140
-KREAKTHHGTWICR
+LDGALSLHHRTGLIAH
 >141
-KREAKTHHGYVWFRF
+LDGALSLHHSLASTLS
 >142
-KREAKTHHKLGILFG
+LDGALSLHHTGLIAHF
 >143
-KREAKTHHKQSQWMT
+LDGALSLHHTTWQVWL
 >144
-KREAKTHHKTTWQVW
+LDGALSLHHYVWFRFV
 >145
-KREAKTHHLAKAKQY
+LRRLPDDHHAKAKQYR
 >146
-KREAKTHHLASTLS
+LRRLPDDHHDGTWICR
 >147
-KREAKTHHLGILFG
+LRRLPDDHHFGAPAWS
 >148
-KREAKTHHQSQWMT
+LRRLPDDHHGAPAWSQ
 >149
-KREAKTHHRTGLIAH
+LRRLPDDHHGTWICRF
 >150
-KREAKTHHSLASTLS
+LRRLPDDHHGYVWFRF
 >151
-KREAKTHHTGLIAH
+LRRLPDDHHHPRWEIL
 >152
-KREAKTHHTTWQVW
+LRRLPDDHHKLGILFG
 >153
-KREAKTHHYVWFRF
+LRRLPDDHHKQSQWMT
 >154
-KREAKTKHHAKAKQY
+LRRLPDDHHKTTWQVW
 >155
-KREAKTKHHGAPAWS
+LRRLPDDHHLAKAKQY
 >156
-KREAKTKHHGTWICR
+LRRLPDDHHLASTLSP
 >157
-KREAKTKHHLASTLS
+LRRLPDDHHLGILFGR
 >158
-KREAKTKHHLGILFG
+LRRLPDDHHPRWEILI
 >159
-KREAKTKHHQSQWMT
+LRRLPDDHHQSQWMTE
 >160
-KREAKTKHHTGLIAH
+LRRLPDDHHSLASTLS
 >161
-KREAKTKHHTTWQVW
+LRRLPDDHHTTWQVWL
 >162
-KREAKTKHHYVWFRF
+LRRLPDDHHYVWFRFV
 >163
-LTNGVPHHAKAKQY
+LTNGVPIHHAKAKQYR
 >164
-LTNGVPHHFGAPAWS
+LTNGVPIHHGAPAWSQ
 >165
-LTNGVPHHGAPAWS
+LTNGVPIHHLASTLSP
 >166
-LTNGVPHHGYVWFRF
+LTNGVPIHHLGILFGR
 >167
-LTNGVPHHHPRWEIL
+LTNGVPIHHPRWEILI
 >168
-LTNGVPHHKLGILFG
+LTNGVPIHHQSQWMTE
 >169
-LTNGVPHHKQSQWMT
+LTNGVPIHHTGLIAHF
 >170
-LTNGVPHHKTTWQVW
+LTNGVPIHHTTWQVWL
 >171
-LTNGVPHHLAKAKQY
+LTNGVPIHHYVWFRFV
 >172
-LTNGVPHHLASTLS
+PSSYLPPHHAKAKQYR
 >173
-LTNGVPHHLGILFG
+PSSYLPPHHDGTWICR
 >174
-LTNGVPHHPRWEIL
+PSSYLPPHHFGAPAWS
 >175
-LTNGVPHHQSQWMT
+PSSYLPPHHGAPAWSQ
 >176
-LTNGVPHHRTGLIAH
+PSSYLPPHHGTWICRF
 >177
-LTNGVPHHSLASTLS
+PSSYLPPHHGYVWFRF
 >178
-LTNGVPHHTGLIAH
+PSSYLPPHHHPRWEIL
 >179
-LTNGVPHHTTWQVW
+PSSYLPPHHKLGILFG
 >180
-LTNGVPHHYVWFRF
+PSSYLPPHHKQSQWMT
 >181
-LTNGVPIHHAKAKQY
+PSSYLPPHHKTTWQVW
 >182
-LTNGVPIHHGAPAWS
+PSSYLPPHHLAKAKQY
 >183
-LTNGVPIHHLASTLS
+PSSYLPPHHLGILFGR
 >184
-LTNGVPIHHLGILFG
+PSSYLPPHHPRWEILI
 >185
-LTNGVPIHHPRWEIL
+PSSYLPPHHQSQWMTE
 >186
-LTNGVPIHHQSQWMT
+PSSYLPPHHRTGLIAH
 >187
-LTNGVPIHHTGLIAH
+PSSYLPPHHTGLIAHF
 >188
-LTNGVPIHHTTWQVW
+PSSYLPPHHTTWQVWL
 >189
-LTNGVPIHHYVWFRF
+PSSYLPPHHYVWFRFV
 >190
-RRLPDDHHAKAKQY
+RCSRSDGHHAKAKQYR
 >191
-RRLPDDHHDGTWICR
+RCSRSDGHHDGTWICR
 >192
-RRLPDDHHFGAPAWS
+RCSRSDGHHFGAPAWS
 >193
-RRLPDDHHGAPAWS
+RCSRSDGHHGAPAWSQ
 >194
-RRLPDDHHGTWICR
+RCSRSDGHHGTWICRF
 >195
-RRLPDDHHGYVWFRF
+RCSRSDGHHGYVWFRF
 >196
-RRLPDDHHHPRWEIL
+RCSRSDGHHHPRWEIL
 >197
-RRLPDDHHKLGILFG
+RCSRSDGHHKLGILFG
 >198
-RRLPDDHHKQSQWMT
+RCSRSDGHHKTTWQVW
 >199
-RRLPDDHHKTTWQVW
+RCSRSDGHHLAKAKQY
 >200
-RRLPDDHHLAKAKQY
+RCSRSDGHHLASTLSP
 >201
-RRLPDDHHLASTLS
+RCSRSDGHHLGILFGR
 >202
-RRLPDDHHLGILFG
+RCSRSDGHHPRWEILI
 >203
-RRLPDDHHPRWEIL
+RCSRSDGHHRTGLIAH
 >204
-RRLPDDHHQSQWMT
+RCSRSDGHHSLASTLS
 >205
-RRLPDDHHSLASTLS
+RCSRSDGHHTGLIAHF
 >206
-RRLPDDHHTTWQVW
+RCSRSDGHHTTWQVWL
 >207
-RRLPDDHHYVWFRF
+RCSRSDGHHYVWFRFV
 >208
-RRLPDDKHHAKAKQY
+RRLPDDKHHAKAKQYR
 >209
-RRLPDDKHHGAPAWS
+RRLPDDKHHGAPAWSQ
 >210
-RRLPDDKHHGTWICR
+RRLPDDKHHGTWICRF
 >211
-RRLPDDKHHLASTLS
+RRLPDDKHHLASTLSP
 >212
-RRLPDDKHHLGILFG
+RRLPDDKHHLGILFGR
 >213
-RRLPDDKHHPRWEIL
+RRLPDDKHHPRWEILI
 >214
-RRLPDDKHHQSQWMT
+RRLPDDKHHQSQWMTE
 >215
-RRLPDDKHHTTWQVW
+RRLPDDKHHTTWQVWL
 >216
-RRLPDDKHHYVWFRF
+RRLPDDKHHYVWFRFV
 >217
-SGGAATHHAKAKQY
+SGGAATSHHAKAKQYR
 >218
-SGGAATHHDGTWICR
+SGGAATSHHGTWICRF
 >219
-SGGAATHHGTWICR
+SGGAATSHHLASTLSP
 >220
-SGGAATHHGYVWFRF
+SGGAATSHHLGILFGR
 >221
-SGGAATHHHPRWEIL
+SGGAATSHHPRWEILI
 >222
-SGGAATHHKLGILFG
+SGGAATSHHQSQWMTE
 >223
-SGGAATHHKQSQWMT
+SGGAATSHHTGLIAHF
 >224
-SGGAATHHKTTWQVW
+SGGAATSHHTTWQVWL
 >225
-SGGAATHHLAKAKQY
+SGGAATSHHYVWFRFV
 >226
-SGGAATHHLASTLS
+SLTNGVPHHAKAKQYR
 >227
-SGGAATHHLGILFG
+SLTNGVPHHFGAPAWS
 >228
-SGGAATHHPRWEIL
+SLTNGVPHHGAPAWSQ
 >229
-SGGAATHHQSQWMT
+SLTNGVPHHGYVWFRF
 >230
-SGGAATHHRTGLIAH
+SLTNGVPHHHPRWEIL
 >231
-SGGAATHHSLASTLS
+SLTNGVPHHKLGILFG
 >232
-SGGAATHHTGLIAH
+SLTNGVPHHKQSQWMT
 >233
-SGGAATHHTTWQVW
+SLTNGVPHHKTTWQVW
 >234
-SGGAATHHYVWFRF
+SLTNGVPHHLAKAKQY
 >235
-SGGAATSHHAKAKQY
+SLTNGVPHHLASTLSP
 >236
-SGGAATSHHGTWICR
+SLTNGVPHHLGILFGR
 >237
-SGGAATSHHLASTLS
+SLTNGVPHHPRWEILI
 >238
-SGGAATSHHLGILFG
+SLTNGVPHHQSQWMTE
 >239
-SGGAATSHHPRWEIL
+SLTNGVPHHRTGLIAH
 >240
-SGGAATSHHQSQWMT
+SLTNGVPHHSLASTLS
 >241
-SGGAATSHHTGLIAH
+SLTNGVPHHTGLIAHF
 >242
-SGGAATSHHTTWQVW
+SLTNGVPHHTTWQVWL
 >243
-SGGAATSHHYVWFRF
+SLTNGVPHHYVWFRFV
 >244
-SSYLPPHHAKAKQY
+SSYLPPHHHAKAKQYR
 >245
-SSYLPPHHDGTWICR
+SSYLPPHHHGAPAWSQ
 >246
-SSYLPPHHFGAPAWS
+SSYLPPHHHGTWICRF
 >247
-SSYLPPHHGAPAWS
+SSYLPPHHHLGILFGR
 >248
-SSYLPPHHGTWICR
+SSYLPPHHHPRWEILI
 >249
-SSYLPPHHGYVWFRF
+SSYLPPHHHQSQWMTE
 >250
-SSYLPPHHHAKAKQY
+SSYLPPHHHTGLIAHF
 >251
-SSYLPPHHHGAPAWS
+SSYLPPHHHTTWQVWL
 >252
-SSYLPPHHHGTWICR
+SSYLPPHHHYVWFRFV
 >253
-SSYLPPHHHLGILFG
+YKREAKTHHAKAKQYR
 >254
-SSYLPPHHHPRWEIL
+YKREAKTHHDGTWICR
 >255
-SSYLPPHHHQSQWMT
+YKREAKTHHFGAPAWS
 >256
-SSYLPPHHHTGLIAH
+YKREAKTHHGAPAWSQ
 >257
-SSYLPPHHHTTWQVW
+YKREAKTHHGTWICRF
 >258
-SSYLPPHHHYVWFRF
+YKREAKTHHGYVWFRF
 >259
-SSYLPPHHKLGILFG
+YKREAKTHHKLGILFG
 >260
-SSYLPPHHKQSQWMT
+YKREAKTHHKQSQWMT
 >261
-SSYLPPHHKTTWQVW
+YKREAKTHHKTTWQVW
 >262
-SSYLPPHHLAKAKQY
+YKREAKTHHLAKAKQY
 >263
-SSYLPPHHLGILFG
+YKREAKTHHLASTLSP
 >264
-SSYLPPHHPRWEIL
+YKREAKTHHLGILFGR
 >265
-SSYLPPHHQSQWMT
+YKREAKTHHQSQWMTE
 >266
-SSYLPPHHRTGLIAH
+YKREAKTHHRTGLIAH
 >267
-SSYLPPHHTGLIAH
+YKREAKTHHSLASTLS
 >268
-SSYLPPHHTTWQVW
+YKREAKTHHTGLIAHF
 >269
-SSYLPPHHYVWFRF
+YKREAKTHHTTWQVWL
+>270
+YKREAKTHHYVWFRFV
diff --git a/tests/test_data/fasta_generator/output_pvacvector.key b/tests/test_data/fasta_generator/output_pvacvector.key
index ed34e291..969f6847 100644
--- a/tests/test_data/fasta_generator/output_pvacvector.key
+++ b/tests/test_data/fasta_generator/output_pvacvector.key
@@ -1,39 +1,39 @@
 1:
-- MT.CASP10.S654R|1|HH|1|MT.DTX3L.G501R
+- MT.DTX3L.G501R|1|HH|0|MT.NRCAM.P838H
 2:
-- MT.CASP10.S654R|1|HH|0|MT.NRCAM.P838H
+- MT.DTX3L.G501R|1|HH|0|MT.POM121C.G3107R
 3:
-- MT.CASP10.S654R|1|HH|0|MT.POM121C.G3107R
+- MT.DTX3L.G501R|1|HH|1|MT.POM121C.G3107R
 4:
-- MT.CASP10.S654R|1|HH|1|MT.POM121C.G3107R
+- MT.DTX3L.G501R|1|HH|1|MT.NRCAM.P838H
 5:
-- MT.CASP10.S654R|1|HH|1|MT.NRCAM.P838H
+- MT.DTX3L.G501R|1|HH|0|MT.CASP10.S654R
 6:
-- MT.CASP10.S654R|1|HH|0|MT.ACSL3.S345N
+- MT.DTX3L.G501R|1|HH|0|MT.ACSL3.S345N
 7:
-- MT.CASP10.S654R|1|HH|0|MT.SUMF2.G23A
+- MT.DTX3L.G501R|1|HH|0|MT.SUMF2.G23A
 8:
-- MT.CASP10.S654R|1|HH|0|MT.TP53.R157H
+- MT.DTX3L.G501R|1|HH|0|MT.TP53.R157H
 9:
-- MT.CASP10.S654R|1|HH|0|MT.PEX1.V356I
+- MT.DTX3L.G501R|1|HH|0|MT.PEX1.V356I
 10:
-- MT.CASP10.S654R|1|HH|0|MT.DTX3L.G501R
+- MT.DTX3L.G501R|1|HH|1|MT.FAT3.R4848T
 11:
-- MT.CASP10.S654R|1|HH|1|MT.FAT3.R4848T
+- MT.DTX3L.G501R|1|HH|1|MT.SUMF2.G23A
 12:
-- MT.CASP10.S654R|1|HH|1|MT.SUMF2.G23A
+- MT.DTX3L.G501R|1|HH|1|MT.ACSL3.S345N
 13:
-- MT.CASP10.S654R|1|HH|1|MT.ACSL3.S345N
+- MT.DTX3L.G501R|1|HH|1|MT.TP53.R157H
 14:
-- MT.CASP10.S654R|1|HH|1|MT.TP53.R157H
+- MT.DTX3L.G501R|1|HH|0|MT.PRDM15.G654W
 15:
-- MT.CASP10.S654R|1|HH|0|MT.PRDM15.G654W
+- MT.DTX3L.G501R|1|HH|0|MT.FAT3.R4848T
 16:
-- MT.CASP10.S654R|1|HH|0|MT.FAT3.R4848T
+- MT.DTX3L.G501R|1|HH|1|MT.PRDM15.G654W
 17:
-- MT.CASP10.S654R|1|HH|1|MT.PRDM15.G654W
+- MT.DTX3L.G501R|1|HH|1|MT.PEX1.V356I
 18:
-- MT.CASP10.S654R|1|HH|1|MT.PEX1.V356I
+- MT.DTX3L.G501R|1|HH|1|MT.CASP10.S654R
 19:
 - MT.CASP10.S654R|0|HH|1|MT.DTX3L.G501R
 20:
@@ -53,167 +53,167 @@
 27:
 - MT.CASP10.S654R|0|HH|1|MT.PEX1.V356I
 28:
-- MT.TP53.R157H|1|HH|1|MT.DTX3L.G501R
+- MT.TP53.R157H|0|HH|1|MT.DTX3L.G501R
 29:
-- MT.TP53.R157H|1|HH|0|MT.NRCAM.P838H
+- MT.TP53.R157H|0|HH|1|MT.POM121C.G3107R
 30:
-- MT.TP53.R157H|1|HH|0|MT.POM121C.G3107R
+- MT.TP53.R157H|0|HH|1|MT.NRCAM.P838H
 31:
-- MT.TP53.R157H|1|HH|1|MT.POM121C.G3107R
+- MT.TP53.R157H|0|HH|1|MT.FAT3.R4848T
 32:
-- MT.TP53.R157H|1|HH|1|MT.NRCAM.P838H
+- MT.TP53.R157H|0|HH|1|MT.SUMF2.G23A
 33:
-- MT.TP53.R157H|1|HH|0|MT.CASP10.S654R
+- MT.TP53.R157H|0|HH|1|MT.ACSL3.S345N
 34:
-- MT.TP53.R157H|1|HH|0|MT.ACSL3.S345N
+- MT.TP53.R157H|0|HH|1|MT.PRDM15.G654W
 35:
-- MT.TP53.R157H|1|HH|0|MT.SUMF2.G23A
+- MT.TP53.R157H|0|HH|1|MT.PEX1.V356I
 36:
-- MT.TP53.R157H|1|HH|0|MT.PEX1.V356I
+- MT.TP53.R157H|0|HH|1|MT.CASP10.S654R
 37:
-- MT.TP53.R157H|1|HH|0|MT.DTX3L.G501R
+- MT.SUMF2.G23A|0|HH|1|MT.DTX3L.G501R
 38:
-- MT.TP53.R157H|1|HH|1|MT.FAT3.R4848T
+- MT.SUMF2.G23A|0|HH|1|MT.POM121C.G3107R
 39:
-- MT.TP53.R157H|1|HH|1|MT.SUMF2.G23A
+- MT.SUMF2.G23A|0|HH|1|MT.NRCAM.P838H
 40:
-- MT.TP53.R157H|1|HH|1|MT.ACSL3.S345N
+- MT.SUMF2.G23A|0|HH|1|MT.FAT3.R4848T
 41:
-- MT.TP53.R157H|1|HH|0|MT.PRDM15.G654W
+- MT.SUMF2.G23A|0|HH|1|MT.ACSL3.S345N
 42:
-- MT.TP53.R157H|1|HH|0|MT.FAT3.R4848T
+- MT.SUMF2.G23A|0|HH|1|MT.TP53.R157H
 43:
-- MT.TP53.R157H|1|HH|1|MT.PRDM15.G654W
+- MT.SUMF2.G23A|0|HH|1|MT.PRDM15.G654W
 44:
-- MT.TP53.R157H|1|HH|1|MT.PEX1.V356I
+- MT.SUMF2.G23A|0|HH|1|MT.PEX1.V356I
 45:
-- MT.TP53.R157H|1|HH|1|MT.CASP10.S654R
+- MT.SUMF2.G23A|0|HH|1|MT.CASP10.S654R
 46:
-- MT.TP53.R157H|0|HH|1|MT.DTX3L.G501R
+- MT.PEX1.V356I|1|HH|1|MT.DTX3L.G501R
 47:
-- MT.TP53.R157H|0|HH|1|MT.POM121C.G3107R
+- MT.PEX1.V356I|1|HH|0|MT.NRCAM.P838H
 48:
-- MT.TP53.R157H|0|HH|1|MT.NRCAM.P838H
+- MT.PEX1.V356I|1|HH|0|MT.POM121C.G3107R
 49:
-- MT.TP53.R157H|0|HH|1|MT.FAT3.R4848T
+- MT.PEX1.V356I|1|HH|1|MT.POM121C.G3107R
 50:
-- MT.TP53.R157H|0|HH|1|MT.SUMF2.G23A
+- MT.PEX1.V356I|1|HH|1|MT.NRCAM.P838H
 51:
-- MT.TP53.R157H|0|HH|1|MT.ACSL3.S345N
+- MT.PEX1.V356I|1|HH|0|MT.CASP10.S654R
 52:
-- MT.TP53.R157H|0|HH|1|MT.PRDM15.G654W
+- MT.PEX1.V356I|1|HH|0|MT.ACSL3.S345N
 53:
-- MT.TP53.R157H|0|HH|1|MT.PEX1.V356I
+- MT.PEX1.V356I|1|HH|0|MT.SUMF2.G23A
 54:
-- MT.TP53.R157H|0|HH|1|MT.CASP10.S654R
+- MT.PEX1.V356I|1|HH|0|MT.TP53.R157H
 55:
-- MT.SUMF2.G23A|1|HH|1|MT.DTX3L.G501R
+- MT.PEX1.V356I|1|HH|0|MT.DTX3L.G501R
 56:
-- MT.SUMF2.G23A|1|HH|0|MT.NRCAM.P838H
+- MT.PEX1.V356I|1|HH|1|MT.FAT3.R4848T
 57:
-- MT.SUMF2.G23A|1|HH|0|MT.POM121C.G3107R
+- MT.PEX1.V356I|1|HH|1|MT.SUMF2.G23A
 58:
-- MT.SUMF2.G23A|1|HH|1|MT.POM121C.G3107R
+- MT.PEX1.V356I|1|HH|1|MT.ACSL3.S345N
 59:
-- MT.SUMF2.G23A|1|HH|1|MT.NRCAM.P838H
+- MT.PEX1.V356I|1|HH|1|MT.TP53.R157H
 60:
-- MT.SUMF2.G23A|1|HH|0|MT.CASP10.S654R
+- MT.PEX1.V356I|1|HH|0|MT.PRDM15.G654W
 61:
-- MT.SUMF2.G23A|1|HH|0|MT.ACSL3.S345N
+- MT.PEX1.V356I|1|HH|0|MT.FAT3.R4848T
 62:
-- MT.SUMF2.G23A|1|HH|0|MT.TP53.R157H
+- MT.PEX1.V356I|1|HH|1|MT.PRDM15.G654W
 63:
-- MT.SUMF2.G23A|1|HH|0|MT.PEX1.V356I
+- MT.PEX1.V356I|1|HH|1|MT.CASP10.S654R
 64:
-- MT.SUMF2.G23A|1|HH|0|MT.DTX3L.G501R
+- MT.PEX1.V356I|0|HH|1|MT.DTX3L.G501R
 65:
-- MT.SUMF2.G23A|1|HH|1|MT.FAT3.R4848T
+- MT.PEX1.V356I|0|HH|1|MT.POM121C.G3107R
 66:
-- MT.SUMF2.G23A|1|HH|1|MT.ACSL3.S345N
+- MT.PEX1.V356I|0|HH|1|MT.NRCAM.P838H
 67:
-- MT.SUMF2.G23A|1|HH|1|MT.TP53.R157H
+- MT.PEX1.V356I|0|HH|1|MT.FAT3.R4848T
 68:
-- MT.SUMF2.G23A|1|HH|0|MT.PRDM15.G654W
+- MT.PEX1.V356I|0|HH|1|MT.SUMF2.G23A
 69:
-- MT.SUMF2.G23A|1|HH|0|MT.FAT3.R4848T
+- MT.PEX1.V356I|0|HH|1|MT.ACSL3.S345N
 70:
-- MT.SUMF2.G23A|1|HH|1|MT.PRDM15.G654W
+- MT.PEX1.V356I|0|HH|1|MT.TP53.R157H
 71:
-- MT.SUMF2.G23A|1|HH|1|MT.PEX1.V356I
+- MT.PEX1.V356I|0|HH|1|MT.PRDM15.G654W
 72:
-- MT.SUMF2.G23A|1|HH|1|MT.CASP10.S654R
+- MT.PEX1.V356I|0|HH|1|MT.CASP10.S654R
 73:
-- MT.SUMF2.G23A|0|HH|1|MT.DTX3L.G501R
+- MT.CASP10.S654R|1|HH|1|MT.DTX3L.G501R
 74:
-- MT.SUMF2.G23A|0|HH|1|MT.POM121C.G3107R
+- MT.CASP10.S654R|1|HH|0|MT.NRCAM.P838H
 75:
-- MT.SUMF2.G23A|0|HH|1|MT.NRCAM.P838H
+- MT.CASP10.S654R|1|HH|0|MT.POM121C.G3107R
 76:
-- MT.SUMF2.G23A|0|HH|1|MT.FAT3.R4848T
+- MT.CASP10.S654R|1|HH|1|MT.POM121C.G3107R
 77:
-- MT.SUMF2.G23A|0|HH|1|MT.ACSL3.S345N
+- MT.CASP10.S654R|1|HH|1|MT.NRCAM.P838H
 78:
-- MT.SUMF2.G23A|0|HH|1|MT.TP53.R157H
+- MT.CASP10.S654R|1|HH|0|MT.ACSL3.S345N
 79:
-- MT.SUMF2.G23A|0|HH|1|MT.PRDM15.G654W
+- MT.CASP10.S654R|1|HH|0|MT.SUMF2.G23A
 80:
-- MT.SUMF2.G23A|0|HH|1|MT.PEX1.V356I
+- MT.CASP10.S654R|1|HH|0|MT.TP53.R157H
 81:
-- MT.SUMF2.G23A|0|HH|1|MT.CASP10.S654R
+- MT.CASP10.S654R|1|HH|0|MT.PEX1.V356I
 82:
-- MT.PEX1.V356I|1|HH|1|MT.DTX3L.G501R
+- MT.CASP10.S654R|1|HH|0|MT.DTX3L.G501R
 83:
-- MT.PEX1.V356I|1|HH|0|MT.NRCAM.P838H
+- MT.CASP10.S654R|1|HH|1|MT.FAT3.R4848T
 84:
-- MT.PEX1.V356I|1|HH|0|MT.POM121C.G3107R
+- MT.CASP10.S654R|1|HH|1|MT.SUMF2.G23A
 85:
-- MT.PEX1.V356I|1|HH|1|MT.POM121C.G3107R
+- MT.CASP10.S654R|1|HH|1|MT.ACSL3.S345N
 86:
-- MT.PEX1.V356I|1|HH|1|MT.NRCAM.P838H
+- MT.CASP10.S654R|1|HH|1|MT.TP53.R157H
 87:
-- MT.PEX1.V356I|1|HH|0|MT.CASP10.S654R
+- MT.CASP10.S654R|1|HH|0|MT.PRDM15.G654W
 88:
-- MT.PEX1.V356I|1|HH|0|MT.ACSL3.S345N
+- MT.CASP10.S654R|1|HH|0|MT.FAT3.R4848T
 89:
-- MT.PEX1.V356I|1|HH|0|MT.SUMF2.G23A
+- MT.CASP10.S654R|1|HH|1|MT.PRDM15.G654W
 90:
-- MT.PEX1.V356I|1|HH|0|MT.TP53.R157H
+- MT.CASP10.S654R|1|HH|1|MT.PEX1.V356I
 91:
-- MT.PEX1.V356I|1|HH|0|MT.DTX3L.G501R
+- MT.POM121C.G3107R|1|HH|1|MT.DTX3L.G501R
 92:
-- MT.PEX1.V356I|1|HH|1|MT.FAT3.R4848T
+- MT.POM121C.G3107R|1|HH|0|MT.NRCAM.P838H
 93:
-- MT.PEX1.V356I|1|HH|1|MT.SUMF2.G23A
+- MT.POM121C.G3107R|1|HH|1|MT.NRCAM.P838H
 94:
-- MT.PEX1.V356I|1|HH|1|MT.ACSL3.S345N
+- MT.POM121C.G3107R|1|HH|0|MT.CASP10.S654R
 95:
-- MT.PEX1.V356I|1|HH|1|MT.TP53.R157H
+- MT.POM121C.G3107R|1|HH|0|MT.ACSL3.S345N
 96:
-- MT.PEX1.V356I|1|HH|0|MT.PRDM15.G654W
+- MT.POM121C.G3107R|1|HH|0|MT.SUMF2.G23A
 97:
-- MT.PEX1.V356I|1|HH|0|MT.FAT3.R4848T
+- MT.POM121C.G3107R|1|HH|0|MT.TP53.R157H
 98:
-- MT.PEX1.V356I|1|HH|1|MT.PRDM15.G654W
+- MT.POM121C.G3107R|1|HH|0|MT.PEX1.V356I
 99:
-- MT.PEX1.V356I|1|HH|1|MT.CASP10.S654R
+- MT.POM121C.G3107R|1|HH|0|MT.DTX3L.G501R
 100:
-- MT.PEX1.V356I|0|HH|1|MT.DTX3L.G501R
+- MT.POM121C.G3107R|1|HH|1|MT.FAT3.R4848T
 101:
-- MT.PEX1.V356I|0|HH|1|MT.POM121C.G3107R
+- MT.POM121C.G3107R|1|HH|1|MT.SUMF2.G23A
 102:
-- MT.PEX1.V356I|0|HH|1|MT.NRCAM.P838H
+- MT.POM121C.G3107R|1|HH|1|MT.ACSL3.S345N
 103:
-- MT.PEX1.V356I|0|HH|1|MT.FAT3.R4848T
+- MT.POM121C.G3107R|1|HH|1|MT.TP53.R157H
 104:
-- MT.PEX1.V356I|0|HH|1|MT.SUMF2.G23A
+- MT.POM121C.G3107R|1|HH|0|MT.PRDM15.G654W
 105:
-- MT.PEX1.V356I|0|HH|1|MT.ACSL3.S345N
+- MT.POM121C.G3107R|1|HH|0|MT.FAT3.R4848T
 106:
-- MT.PEX1.V356I|0|HH|1|MT.TP53.R157H
+- MT.POM121C.G3107R|1|HH|1|MT.PRDM15.G654W
 107:
-- MT.PEX1.V356I|0|HH|1|MT.PRDM15.G654W
+- MT.POM121C.G3107R|1|HH|1|MT.PEX1.V356I
 108:
-- MT.PEX1.V356I|0|HH|1|MT.CASP10.S654R
+- MT.POM121C.G3107R|1|HH|1|MT.CASP10.S654R
 109:
 - MT.DTX3L.G501R|0|HH|1|MT.POM121C.G3107R
 110:
@@ -233,185 +233,185 @@
 117:
 - MT.DTX3L.G501R|0|HH|1|MT.CASP10.S654R
 118:
-- MT.DTX3L.G501R|1|HH|0|MT.NRCAM.P838H
+- MT.ACSL3.S345N|0|HH|1|MT.DTX3L.G501R
 119:
-- MT.DTX3L.G501R|1|HH|0|MT.POM121C.G3107R
+- MT.ACSL3.S345N|0|HH|1|MT.POM121C.G3107R
 120:
-- MT.DTX3L.G501R|1|HH|1|MT.POM121C.G3107R
+- MT.ACSL3.S345N|0|HH|1|MT.NRCAM.P838H
 121:
-- MT.DTX3L.G501R|1|HH|1|MT.NRCAM.P838H
+- MT.ACSL3.S345N|0|HH|1|MT.FAT3.R4848T
 122:
-- MT.DTX3L.G501R|1|HH|0|MT.CASP10.S654R
+- MT.ACSL3.S345N|0|HH|1|MT.SUMF2.G23A
 123:
-- MT.DTX3L.G501R|1|HH|0|MT.ACSL3.S345N
+- MT.ACSL3.S345N|0|HH|1|MT.TP53.R157H
 124:
-- MT.DTX3L.G501R|1|HH|0|MT.SUMF2.G23A
+- MT.ACSL3.S345N|0|HH|1|MT.PRDM15.G654W
 125:
-- MT.DTX3L.G501R|1|HH|0|MT.TP53.R157H
+- MT.ACSL3.S345N|0|HH|1|MT.PEX1.V356I
 126:
-- MT.DTX3L.G501R|1|HH|0|MT.PEX1.V356I
+- MT.ACSL3.S345N|0|HH|1|MT.CASP10.S654R
 127:
-- MT.DTX3L.G501R|1|HH|1|MT.FAT3.R4848T
+- MT.SUMF2.G23A|1|HH|1|MT.DTX3L.G501R
 128:
-- MT.DTX3L.G501R|1|HH|1|MT.SUMF2.G23A
+- MT.SUMF2.G23A|1|HH|0|MT.NRCAM.P838H
 129:
-- MT.DTX3L.G501R|1|HH|1|MT.ACSL3.S345N
+- MT.SUMF2.G23A|1|HH|0|MT.POM121C.G3107R
 130:
-- MT.DTX3L.G501R|1|HH|1|MT.TP53.R157H
+- MT.SUMF2.G23A|1|HH|1|MT.POM121C.G3107R
 131:
-- MT.DTX3L.G501R|1|HH|0|MT.PRDM15.G654W
+- MT.SUMF2.G23A|1|HH|1|MT.NRCAM.P838H
 132:
-- MT.DTX3L.G501R|1|HH|0|MT.FAT3.R4848T
+- MT.SUMF2.G23A|1|HH|0|MT.CASP10.S654R
 133:
-- MT.DTX3L.G501R|1|HH|1|MT.PRDM15.G654W
+- MT.SUMF2.G23A|1|HH|0|MT.ACSL3.S345N
 134:
-- MT.DTX3L.G501R|1|HH|1|MT.PEX1.V356I
+- MT.SUMF2.G23A|1|HH|0|MT.TP53.R157H
 135:
-- MT.DTX3L.G501R|1|HH|1|MT.CASP10.S654R
+- MT.SUMF2.G23A|1|HH|0|MT.PEX1.V356I
 136:
-- MT.ACSL3.S345N|1|HH|1|MT.DTX3L.G501R
+- MT.SUMF2.G23A|1|HH|0|MT.DTX3L.G501R
 137:
-- MT.ACSL3.S345N|1|HH|0|MT.NRCAM.P838H
+- MT.SUMF2.G23A|1|HH|1|MT.FAT3.R4848T
 138:
-- MT.ACSL3.S345N|1|HH|0|MT.POM121C.G3107R
+- MT.SUMF2.G23A|1|HH|1|MT.ACSL3.S345N
 139:
-- MT.ACSL3.S345N|1|HH|1|MT.POM121C.G3107R
+- MT.SUMF2.G23A|1|HH|1|MT.TP53.R157H
 140:
-- MT.ACSL3.S345N|1|HH|1|MT.NRCAM.P838H
+- MT.SUMF2.G23A|1|HH|0|MT.PRDM15.G654W
 141:
-- MT.ACSL3.S345N|1|HH|0|MT.CASP10.S654R
+- MT.SUMF2.G23A|1|HH|0|MT.FAT3.R4848T
 142:
-- MT.ACSL3.S345N|1|HH|0|MT.SUMF2.G23A
+- MT.SUMF2.G23A|1|HH|1|MT.PRDM15.G654W
 143:
-- MT.ACSL3.S345N|1|HH|0|MT.TP53.R157H
+- MT.SUMF2.G23A|1|HH|1|MT.PEX1.V356I
 144:
-- MT.ACSL3.S345N|1|HH|0|MT.PEX1.V356I
+- MT.SUMF2.G23A|1|HH|1|MT.CASP10.S654R
 145:
-- MT.ACSL3.S345N|1|HH|0|MT.DTX3L.G501R
+- MT.PRDM15.G654W|1|HH|1|MT.DTX3L.G501R
 146:
-- MT.ACSL3.S345N|1|HH|1|MT.FAT3.R4848T
+- MT.PRDM15.G654W|1|HH|0|MT.NRCAM.P838H
 147:
-- MT.ACSL3.S345N|1|HH|1|MT.SUMF2.G23A
+- MT.PRDM15.G654W|1|HH|0|MT.POM121C.G3107R
 148:
-- MT.ACSL3.S345N|1|HH|1|MT.TP53.R157H
+- MT.PRDM15.G654W|1|HH|1|MT.POM121C.G3107R
 149:
-- MT.ACSL3.S345N|1|HH|0|MT.PRDM15.G654W
+- MT.PRDM15.G654W|1|HH|1|MT.NRCAM.P838H
 150:
-- MT.ACSL3.S345N|1|HH|0|MT.FAT3.R4848T
+- MT.PRDM15.G654W|1|HH|0|MT.CASP10.S654R
 151:
-- MT.ACSL3.S345N|1|HH|1|MT.PRDM15.G654W
+- MT.PRDM15.G654W|1|HH|0|MT.ACSL3.S345N
 152:
-- MT.ACSL3.S345N|1|HH|1|MT.PEX1.V356I
+- MT.PRDM15.G654W|1|HH|0|MT.SUMF2.G23A
 153:
-- MT.ACSL3.S345N|1|HH|1|MT.CASP10.S654R
+- MT.PRDM15.G654W|1|HH|0|MT.TP53.R157H
 154:
-- MT.ACSL3.S345N|0|HH|1|MT.DTX3L.G501R
+- MT.PRDM15.G654W|1|HH|0|MT.PEX1.V356I
 155:
-- MT.ACSL3.S345N|0|HH|1|MT.POM121C.G3107R
+- MT.PRDM15.G654W|1|HH|0|MT.DTX3L.G501R
 156:
-- MT.ACSL3.S345N|0|HH|1|MT.NRCAM.P838H
+- MT.PRDM15.G654W|1|HH|1|MT.FAT3.R4848T
 157:
-- MT.ACSL3.S345N|0|HH|1|MT.FAT3.R4848T
+- MT.PRDM15.G654W|1|HH|1|MT.SUMF2.G23A
 158:
-- MT.ACSL3.S345N|0|HH|1|MT.SUMF2.G23A
+- MT.PRDM15.G654W|1|HH|1|MT.ACSL3.S345N
 159:
-- MT.ACSL3.S345N|0|HH|1|MT.TP53.R157H
+- MT.PRDM15.G654W|1|HH|1|MT.TP53.R157H
 160:
-- MT.ACSL3.S345N|0|HH|1|MT.PRDM15.G654W
+- MT.PRDM15.G654W|1|HH|0|MT.FAT3.R4848T
 161:
-- MT.ACSL3.S345N|0|HH|1|MT.PEX1.V356I
+- MT.PRDM15.G654W|1|HH|1|MT.PEX1.V356I
 162:
-- MT.ACSL3.S345N|0|HH|1|MT.CASP10.S654R
+- MT.PRDM15.G654W|1|HH|1|MT.CASP10.S654R
 163:
-- MT.NRCAM.P838H|1|HH|1|MT.DTX3L.G501R
+- MT.NRCAM.P838H|0|HH|1|MT.DTX3L.G501R
 164:
-- MT.NRCAM.P838H|1|HH|0|MT.POM121C.G3107R
+- MT.NRCAM.P838H|0|HH|1|MT.POM121C.G3107R
 165:
-- MT.NRCAM.P838H|1|HH|1|MT.POM121C.G3107R
+- MT.NRCAM.P838H|0|HH|1|MT.FAT3.R4848T
 166:
-- MT.NRCAM.P838H|1|HH|0|MT.CASP10.S654R
+- MT.NRCAM.P838H|0|HH|1|MT.SUMF2.G23A
 167:
-- MT.NRCAM.P838H|1|HH|0|MT.ACSL3.S345N
+- MT.NRCAM.P838H|0|HH|1|MT.ACSL3.S345N
 168:
-- MT.NRCAM.P838H|1|HH|0|MT.SUMF2.G23A
+- MT.NRCAM.P838H|0|HH|1|MT.TP53.R157H
 169:
-- MT.NRCAM.P838H|1|HH|0|MT.TP53.R157H
+- MT.NRCAM.P838H|0|HH|1|MT.PRDM15.G654W
 170:
-- MT.NRCAM.P838H|1|HH|0|MT.PEX1.V356I
+- MT.NRCAM.P838H|0|HH|1|MT.PEX1.V356I
 171:
-- MT.NRCAM.P838H|1|HH|0|MT.DTX3L.G501R
+- MT.NRCAM.P838H|0|HH|1|MT.CASP10.S654R
 172:
-- MT.NRCAM.P838H|1|HH|1|MT.FAT3.R4848T
+- MT.FAT3.R4848T|1|HH|1|MT.DTX3L.G501R
 173:
-- MT.NRCAM.P838H|1|HH|1|MT.SUMF2.G23A
+- MT.FAT3.R4848T|1|HH|0|MT.NRCAM.P838H
 174:
-- MT.NRCAM.P838H|1|HH|1|MT.ACSL3.S345N
+- MT.FAT3.R4848T|1|HH|0|MT.POM121C.G3107R
 175:
-- MT.NRCAM.P838H|1|HH|1|MT.TP53.R157H
+- MT.FAT3.R4848T|1|HH|1|MT.POM121C.G3107R
 176:
-- MT.NRCAM.P838H|1|HH|0|MT.PRDM15.G654W
+- MT.FAT3.R4848T|1|HH|1|MT.NRCAM.P838H
 177:
-- MT.NRCAM.P838H|1|HH|0|MT.FAT3.R4848T
+- MT.FAT3.R4848T|1|HH|0|MT.CASP10.S654R
 178:
-- MT.NRCAM.P838H|1|HH|1|MT.PRDM15.G654W
+- MT.FAT3.R4848T|1|HH|0|MT.ACSL3.S345N
 179:
-- MT.NRCAM.P838H|1|HH|1|MT.PEX1.V356I
+- MT.FAT3.R4848T|1|HH|0|MT.SUMF2.G23A
 180:
-- MT.NRCAM.P838H|1|HH|1|MT.CASP10.S654R
+- MT.FAT3.R4848T|1|HH|0|MT.TP53.R157H
 181:
-- MT.NRCAM.P838H|0|HH|1|MT.DTX3L.G501R
+- MT.FAT3.R4848T|1|HH|0|MT.PEX1.V356I
 182:
-- MT.NRCAM.P838H|0|HH|1|MT.POM121C.G3107R
+- MT.FAT3.R4848T|1|HH|0|MT.DTX3L.G501R
 183:
-- MT.NRCAM.P838H|0|HH|1|MT.FAT3.R4848T
+- MT.FAT3.R4848T|1|HH|1|MT.SUMF2.G23A
 184:
-- MT.NRCAM.P838H|0|HH|1|MT.SUMF2.G23A
+- MT.FAT3.R4848T|1|HH|1|MT.ACSL3.S345N
 185:
-- MT.NRCAM.P838H|0|HH|1|MT.ACSL3.S345N
+- MT.FAT3.R4848T|1|HH|1|MT.TP53.R157H
 186:
-- MT.NRCAM.P838H|0|HH|1|MT.TP53.R157H
+- MT.FAT3.R4848T|1|HH|0|MT.PRDM15.G654W
 187:
-- MT.NRCAM.P838H|0|HH|1|MT.PRDM15.G654W
+- MT.FAT3.R4848T|1|HH|1|MT.PRDM15.G654W
 188:
-- MT.NRCAM.P838H|0|HH|1|MT.PEX1.V356I
+- MT.FAT3.R4848T|1|HH|1|MT.PEX1.V356I
 189:
-- MT.NRCAM.P838H|0|HH|1|MT.CASP10.S654R
+- MT.FAT3.R4848T|1|HH|1|MT.CASP10.S654R
 190:
-- MT.PRDM15.G654W|1|HH|1|MT.DTX3L.G501R
+- MT.TP53.R157H|1|HH|1|MT.DTX3L.G501R
 191:
-- MT.PRDM15.G654W|1|HH|0|MT.NRCAM.P838H
+- MT.TP53.R157H|1|HH|0|MT.NRCAM.P838H
 192:
-- MT.PRDM15.G654W|1|HH|0|MT.POM121C.G3107R
+- MT.TP53.R157H|1|HH|0|MT.POM121C.G3107R
 193:
-- MT.PRDM15.G654W|1|HH|1|MT.POM121C.G3107R
+- MT.TP53.R157H|1|HH|1|MT.POM121C.G3107R
 194:
-- MT.PRDM15.G654W|1|HH|1|MT.NRCAM.P838H
+- MT.TP53.R157H|1|HH|1|MT.NRCAM.P838H
 195:
-- MT.PRDM15.G654W|1|HH|0|MT.CASP10.S654R
+- MT.TP53.R157H|1|HH|0|MT.CASP10.S654R
 196:
-- MT.PRDM15.G654W|1|HH|0|MT.ACSL3.S345N
+- MT.TP53.R157H|1|HH|0|MT.ACSL3.S345N
 197:
-- MT.PRDM15.G654W|1|HH|0|MT.SUMF2.G23A
+- MT.TP53.R157H|1|HH|0|MT.SUMF2.G23A
 198:
-- MT.PRDM15.G654W|1|HH|0|MT.TP53.R157H
+- MT.TP53.R157H|1|HH|0|MT.PEX1.V356I
 199:
-- MT.PRDM15.G654W|1|HH|0|MT.PEX1.V356I
+- MT.TP53.R157H|1|HH|0|MT.DTX3L.G501R
 200:
-- MT.PRDM15.G654W|1|HH|0|MT.DTX3L.G501R
+- MT.TP53.R157H|1|HH|1|MT.FAT3.R4848T
 201:
-- MT.PRDM15.G654W|1|HH|1|MT.FAT3.R4848T
+- MT.TP53.R157H|1|HH|1|MT.SUMF2.G23A
 202:
-- MT.PRDM15.G654W|1|HH|1|MT.SUMF2.G23A
+- MT.TP53.R157H|1|HH|1|MT.ACSL3.S345N
 203:
-- MT.PRDM15.G654W|1|HH|1|MT.ACSL3.S345N
+- MT.TP53.R157H|1|HH|0|MT.PRDM15.G654W
 204:
-- MT.PRDM15.G654W|1|HH|1|MT.TP53.R157H
+- MT.TP53.R157H|1|HH|0|MT.FAT3.R4848T
 205:
-- MT.PRDM15.G654W|1|HH|0|MT.FAT3.R4848T
+- MT.TP53.R157H|1|HH|1|MT.PRDM15.G654W
 206:
-- MT.PRDM15.G654W|1|HH|1|MT.PEX1.V356I
+- MT.TP53.R157H|1|HH|1|MT.PEX1.V356I
 207:
-- MT.PRDM15.G654W|1|HH|1|MT.CASP10.S654R
+- MT.TP53.R157H|1|HH|1|MT.CASP10.S654R
 208:
 - MT.PRDM15.G654W|0|HH|1|MT.DTX3L.G501R
 209:
@@ -431,109 +431,110 @@
 216:
 - MT.PRDM15.G654W|0|HH|1|MT.CASP10.S654R
 217:
-- MT.POM121C.G3107R|1|HH|1|MT.DTX3L.G501R
+- MT.POM121C.G3107R|0|HH|1|MT.DTX3L.G501R
 218:
-- MT.POM121C.G3107R|1|HH|0|MT.NRCAM.P838H
+- MT.POM121C.G3107R|0|HH|1|MT.NRCAM.P838H
 219:
-- MT.POM121C.G3107R|1|HH|1|MT.NRCAM.P838H
+- MT.POM121C.G3107R|0|HH|1|MT.FAT3.R4848T
 220:
-- MT.POM121C.G3107R|1|HH|0|MT.CASP10.S654R
+- MT.POM121C.G3107R|0|HH|1|MT.SUMF2.G23A
 221:
-- MT.POM121C.G3107R|1|HH|0|MT.ACSL3.S345N
+- MT.POM121C.G3107R|0|HH|1|MT.ACSL3.S345N
 222:
-- MT.POM121C.G3107R|1|HH|0|MT.SUMF2.G23A
+- MT.POM121C.G3107R|0|HH|1|MT.TP53.R157H
 223:
-- MT.POM121C.G3107R|1|HH|0|MT.TP53.R157H
+- MT.POM121C.G3107R|0|HH|1|MT.PRDM15.G654W
 224:
-- MT.POM121C.G3107R|1|HH|0|MT.PEX1.V356I
+- MT.POM121C.G3107R|0|HH|1|MT.PEX1.V356I
 225:
-- MT.POM121C.G3107R|1|HH|0|MT.DTX3L.G501R
+- MT.POM121C.G3107R|0|HH|1|MT.CASP10.S654R
 226:
-- MT.POM121C.G3107R|1|HH|1|MT.FAT3.R4848T
+- MT.NRCAM.P838H|1|HH|1|MT.DTX3L.G501R
 227:
-- MT.POM121C.G3107R|1|HH|1|MT.SUMF2.G23A
+- MT.NRCAM.P838H|1|HH|0|MT.POM121C.G3107R
 228:
-- MT.POM121C.G3107R|1|HH|1|MT.ACSL3.S345N
+- MT.NRCAM.P838H|1|HH|1|MT.POM121C.G3107R
 229:
-- MT.POM121C.G3107R|1|HH|1|MT.TP53.R157H
+- MT.NRCAM.P838H|1|HH|0|MT.CASP10.S654R
 230:
-- MT.POM121C.G3107R|1|HH|0|MT.PRDM15.G654W
+- MT.NRCAM.P838H|1|HH|0|MT.ACSL3.S345N
 231:
-- MT.POM121C.G3107R|1|HH|0|MT.FAT3.R4848T
+- MT.NRCAM.P838H|1|HH|0|MT.SUMF2.G23A
 232:
-- MT.POM121C.G3107R|1|HH|1|MT.PRDM15.G654W
+- MT.NRCAM.P838H|1|HH|0|MT.TP53.R157H
 233:
-- MT.POM121C.G3107R|1|HH|1|MT.PEX1.V356I
+- MT.NRCAM.P838H|1|HH|0|MT.PEX1.V356I
 234:
-- MT.POM121C.G3107R|1|HH|1|MT.CASP10.S654R
+- MT.NRCAM.P838H|1|HH|0|MT.DTX3L.G501R
 235:
-- MT.POM121C.G3107R|0|HH|1|MT.DTX3L.G501R
+- MT.NRCAM.P838H|1|HH|1|MT.FAT3.R4848T
 236:
-- MT.POM121C.G3107R|0|HH|1|MT.NRCAM.P838H
+- MT.NRCAM.P838H|1|HH|1|MT.SUMF2.G23A
 237:
-- MT.POM121C.G3107R|0|HH|1|MT.FAT3.R4848T
+- MT.NRCAM.P838H|1|HH|1|MT.ACSL3.S345N
 238:
-- MT.POM121C.G3107R|0|HH|1|MT.SUMF2.G23A
+- MT.NRCAM.P838H|1|HH|1|MT.TP53.R157H
 239:
-- MT.POM121C.G3107R|0|HH|1|MT.ACSL3.S345N
+- MT.NRCAM.P838H|1|HH|0|MT.PRDM15.G654W
 240:
-- MT.POM121C.G3107R|0|HH|1|MT.TP53.R157H
+- MT.NRCAM.P838H|1|HH|0|MT.FAT3.R4848T
 241:
-- MT.POM121C.G3107R|0|HH|1|MT.PRDM15.G654W
+- MT.NRCAM.P838H|1|HH|1|MT.PRDM15.G654W
 242:
-- MT.POM121C.G3107R|0|HH|1|MT.PEX1.V356I
+- MT.NRCAM.P838H|1|HH|1|MT.PEX1.V356I
 243:
-- MT.POM121C.G3107R|0|HH|1|MT.CASP10.S654R
+- MT.NRCAM.P838H|1|HH|1|MT.CASP10.S654R
 244:
-- MT.FAT3.R4848T|1|HH|1|MT.DTX3L.G501R
+- MT.FAT3.R4848T|0|HH|1|MT.DTX3L.G501R
 245:
-- MT.FAT3.R4848T|1|HH|0|MT.NRCAM.P838H
+- MT.FAT3.R4848T|0|HH|1|MT.POM121C.G3107R
 246:
-- MT.FAT3.R4848T|1|HH|0|MT.POM121C.G3107R
+- MT.FAT3.R4848T|0|HH|1|MT.NRCAM.P838H
 247:
-- MT.FAT3.R4848T|1|HH|1|MT.POM121C.G3107R
+- MT.FAT3.R4848T|0|HH|1|MT.SUMF2.G23A
 248:
-- MT.FAT3.R4848T|1|HH|1|MT.NRCAM.P838H
+- MT.FAT3.R4848T|0|HH|1|MT.ACSL3.S345N
 249:
-- MT.FAT3.R4848T|1|HH|0|MT.CASP10.S654R
+- MT.FAT3.R4848T|0|HH|1|MT.TP53.R157H
 250:
-- MT.FAT3.R4848T|0|HH|1|MT.DTX3L.G501R
+- MT.FAT3.R4848T|0|HH|1|MT.PRDM15.G654W
 251:
-- MT.FAT3.R4848T|0|HH|1|MT.POM121C.G3107R
+- MT.FAT3.R4848T|0|HH|1|MT.PEX1.V356I
 252:
-- MT.FAT3.R4848T|0|HH|1|MT.NRCAM.P838H
+- MT.FAT3.R4848T|0|HH|1|MT.CASP10.S654R
 253:
-- MT.FAT3.R4848T|0|HH|1|MT.SUMF2.G23A
+- MT.ACSL3.S345N|1|HH|1|MT.DTX3L.G501R
 254:
-- MT.FAT3.R4848T|0|HH|1|MT.ACSL3.S345N
-- MT.FAT3.R4848T|1|HH|0|MT.ACSL3.S345N
+- MT.ACSL3.S345N|1|HH|0|MT.NRCAM.P838H
 255:
-- MT.FAT3.R4848T|0|HH|1|MT.TP53.R157H
+- MT.ACSL3.S345N|1|HH|0|MT.POM121C.G3107R
 256:
-- MT.FAT3.R4848T|0|HH|1|MT.PRDM15.G654W
+- MT.ACSL3.S345N|1|HH|1|MT.POM121C.G3107R
 257:
-- MT.FAT3.R4848T|0|HH|1|MT.PEX1.V356I
+- MT.ACSL3.S345N|1|HH|1|MT.NRCAM.P838H
 258:
-- MT.FAT3.R4848T|0|HH|1|MT.CASP10.S654R
+- MT.ACSL3.S345N|1|HH|0|MT.CASP10.S654R
 259:
-- MT.FAT3.R4848T|1|HH|0|MT.SUMF2.G23A
+- MT.ACSL3.S345N|1|HH|0|MT.SUMF2.G23A
 260:
-- MT.FAT3.R4848T|1|HH|0|MT.TP53.R157H
+- MT.ACSL3.S345N|1|HH|0|MT.TP53.R157H
 261:
-- MT.FAT3.R4848T|1|HH|0|MT.PEX1.V356I
+- MT.ACSL3.S345N|1|HH|0|MT.PEX1.V356I
 262:
-- MT.FAT3.R4848T|1|HH|0|MT.DTX3L.G501R
+- MT.ACSL3.S345N|1|HH|0|MT.DTX3L.G501R
 263:
-- MT.FAT3.R4848T|1|HH|1|MT.SUMF2.G23A
+- MT.ACSL3.S345N|1|HH|1|MT.FAT3.R4848T
 264:
-- MT.FAT3.R4848T|1|HH|1|MT.ACSL3.S345N
+- MT.ACSL3.S345N|1|HH|1|MT.SUMF2.G23A
 265:
-- MT.FAT3.R4848T|1|HH|1|MT.TP53.R157H
+- MT.ACSL3.S345N|1|HH|1|MT.TP53.R157H
 266:
-- MT.FAT3.R4848T|1|HH|0|MT.PRDM15.G654W
+- MT.ACSL3.S345N|1|HH|0|MT.PRDM15.G654W
 267:
-- MT.FAT3.R4848T|1|HH|1|MT.PRDM15.G654W
+- MT.ACSL3.S345N|1|HH|0|MT.FAT3.R4848T
 268:
-- MT.FAT3.R4848T|1|HH|1|MT.PEX1.V356I
+- MT.ACSL3.S345N|1|HH|1|MT.PRDM15.G654W
 269:
-- MT.FAT3.R4848T|1|HH|1|MT.CASP10.S654R
+- MT.ACSL3.S345N|1|HH|1|MT.PEX1.V356I
+270:
+- MT.ACSL3.S345N|1|HH|1|MT.CASP10.S654R
diff --git a/tests/test_data/pvacvector/clipped.1.AAY.fa b/tests/test_data/pvacvector/clipped.1.AAY.fa
new file mode 100644
index 00000000..18e351bc
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.1.AAY.fa
@@ -0,0 +1,54 @@
+>1
+AKEWELKAAYALRAQTL
+>2
+AKEWELKAAYPALRAQT
+>3
+AKEWELKAAYPLGMRGE
+>4
+AKEWELKAAYTAWATAM
+>5
+ANVVWKVAAYALRAQTL
+>6
+ANVVWKVAAYPALRAQT
+>7
+ANVVWKVAAYTAWATAM
+>8
+AWTAARVAAYALRAQTL
+>9
+AWTAARVAAYPALRAQT
+>10
+AWTAARVAAYPLGMRGE
+>11
+KAKEWELAAYALRAQTL
+>12
+KAKEWELAAYLPALRAQ
+>13
+KAKEWELAAYNPLGMRG
+>14
+KAKEWELAAYPALRAQT
+>15
+KAKEWELAAYPLGMRGE
+>16
+KAKEWELAAYPTAWATA
+>17
+KAKEWELAAYTAWATAM
+>18
+QANVVWKAAYALRAQTL
+>19
+QANVVWKAAYLPALRAQ
+>20
+QANVVWKAAYPALRAQT
+>21
+QANVVWKAAYPTAWATA
+>22
+QANVVWKAAYTAWATAM
+>23
+VAWTAARAAYALRAQTL
+>24
+VAWTAARAAYLPALRAQ
+>25
+VAWTAARAAYNPLGMRG
+>26
+VAWTAARAAYPALRAQT
+>27
+VAWTAARAAYPLGMRGE
diff --git a/tests/test_data/pvacvector/clipped.1.AAY.fa.key b/tests/test_data/pvacvector/clipped.1.AAY.fa.key
new file mode 100644
index 00000000..151b2486
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.1.AAY.fa.key
@@ -0,0 +1,57 @@
+1:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+2:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+3:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|AAY|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+4:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|AAY|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+5:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+6:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+7:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|AAY|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+8:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+9:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+10:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|AAY|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+11:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+12:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+13:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+14:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+15:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+16:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+17:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|AAY|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+18:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+19:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+20:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+21:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+22:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|AAY|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+23:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+24:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+25:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+26:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+27:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|AAY|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
diff --git a/tests/test_data/pvacvector/clipped.1.AAY.junctions.tsv b/tests/test_data/pvacvector/clipped.1.AAY.junctions.tsv
new file mode 100644
index 00000000..c6c53f4e
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.1.AAY.junctions.tsv
@@ -0,0 +1,11 @@
+left_peptide	left_partner_clip	spacer	right_partner_clip	right_peptide	junction_score	percentile
+ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	41697.23	93.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	36656.57	77.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	42175.93	95.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	1	FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	37986.59	81.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	44120.52	99.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	37986.59	81.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	37663.69	80.0
+USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	34809.68	70.0
diff --git a/tests/test_data/pvacvector/clipped.1.None.fa b/tests/test_data/pvacvector/clipped.1.None.fa
index ca1d3bb7..65c55258 100644
--- a/tests/test_data/pvacvector/clipped.1.None.fa
+++ b/tests/test_data/pvacvector/clipped.1.None.fa
@@ -1,72 +1,66 @@
 >1
-AKEWELALRAQT
+AKEWELKALRAQTL
 >2
-AKEWELKALRAQT
+AKEWELKPALRAQT
 >3
-AKEWELKPALRAQ
+AKEWELKPLGMRGE
 >4
-AKEWELKPLGMRG
+AKEWELKTAWATAM
 >5
-AKEWELKTAWATA
+ANVVWKVALRAQTL
 >6
-AKEWELLPALRAQ
+ANVVWKVPALRAQT
 >7
-AKEWELNPLGMRG
+ANVVWKVTAWATAM
 >8
-AKEWELPALRAQ
+APGPGPSLPALRAQ
 >9
-AKEWELPALRAQT
+APGPGPSPALRAQT
 >10
-AKEWELPLGMRG
+APGPGPSPTAWATA
 >11
-AKEWELPTAWATA
+APGPGPSTAWATAM
 >12
-AKEWELTAWATA
+AWTAARVALRAQTL
 >13
-ANVVWKALRAQT
+AWTAARVPALRAQT
 >14
-ANVVWKLPALRAQ
+AWTAARVPLGMRGE
 >15
-ANVVWKPALRAQ
+KAKEWELALRAQTL
 >16
-ANVVWKPALRAQT
+KAKEWELLPALRAQ
 >17
-ANVVWKPTAWATA
+KAKEWELNPLGMRG
 >18
-ANVVWKTAWATA
+KAKEWELPALRAQT
 >19
-ANVVWKVALRAQT
+KAKEWELPLGMRGE
 >20
-ANVVWKVPALRAQ
+KAKEWELPTAWATA
 >21
-ANVVWKVTAWATA
+KAKEWELTAWATAM
 >22
-AWTAARALRAQT
+PGPGPSFPALRAQT
 >23
-AWTAARLPALRAQ
+PGPGPSFTAWATAM
 >24
-AWTAARNPLGMRG
+QANVVWKALRAQTL
 >25
-AWTAARPALRAQ
+QANVVWKLPALRAQ
 >26
-AWTAARPALRAQT
+QANVVWKPALRAQT
 >27
-AWTAARPLGMRG
+QANVVWKPTAWATA
 >28
-AWTAARVALRAQT
+QANVVWKTAWATAM
 >29
-AWTAARVPALRAQ
+VAWTAARALRAQTL
 >30
-AWTAARVPLGMRG
+VAWTAARLPALRAQ
 >31
-PGPGPSFPALRAQ
+VAWTAARNPLGMRG
 >32
-PGPGPSFTAWATA
+VAWTAARPALRAQT
 >33
-PGPGPSLPALRAQ
->34
-PGPGPSPALRAQ
->35
-PGPGPSPTAWATA
->36
-PGPGPSTAWATA
+VAWTAARPLGMRGE
diff --git a/tests/test_data/pvacvector/clipped.1.None.fa.key b/tests/test_data/pvacvector/clipped.1.None.fa.key
index 8b9cf079..c92b428a 100644
--- a/tests/test_data/pvacvector/clipped.1.None.fa.key
+++ b/tests/test_data/pvacvector/clipped.1.None.fa.key
@@ -1,72 +1,69 @@
 1:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
-2:
 - AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
-3:
+2:
 - AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
-4:
+3:
 - AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
-5:
+4:
 - AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+5:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
 6:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 7:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 8:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 9:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 10:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 11:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 12:
-- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
 13:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 14:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
 15:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
 16:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 17:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
 18:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 19:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
 20:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 21:
-- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 22:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 23:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|0|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 24:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
 25:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 26:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 27:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 28:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
 29:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
 30:
-- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 31:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|0|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
 32:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|0|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
 33:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
-34:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
-35:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
-36:
-- FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10|1|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
diff --git a/tests/test_data/pvacvector/clipped.1.None.junctions.tsv b/tests/test_data/pvacvector/clipped.1.None.junctions.tsv
index 2f7fcbeb..c6c53f4e 100644
--- a/tests/test_data/pvacvector/clipped.1.None.junctions.tsv
+++ b/tests/test_data/pvacvector/clipped.1.None.junctions.tsv
@@ -1,12 +1,11 @@
 left_peptide	left_partner_clip	spacer	right_partner_clip	right_peptide	junction_score	percentile
 ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	41697.23	93.0
-ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	1	None	1	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	32358.39	62.0
 FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	36656.57	77.0
 FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	42175.93	95.0
-FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	1	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	39486.0	87.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
 FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	1	FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	37986.59	81.0
-FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
-FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	37986.59	81.0
 FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	44120.52	99.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	37986.59	81.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
 FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	37663.69	80.0
 USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	34809.68	70.0
diff --git a/tests/test_data/pvacvector/clipped.2.None.fa b/tests/test_data/pvacvector/clipped.2.None.fa
new file mode 100644
index 00000000..bc3d706a
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.2.None.fa
@@ -0,0 +1,88 @@
+>1
+AKEWELKALRAQTL
+>2
+AKEWELKAWATAMN
+>3
+AKEWELKLGMRGEI
+>4
+AKEWELKLRAQTLP
+>5
+ANVVWKVALRAQTL
+>6
+ANVVWKVAWATAMN
+>7
+ANVVWKVLRAQTLP
+>8
+AWTAARVALRAQTL
+>9
+AWTAARVLGMRGEI
+>10
+AWTAARVLRAQTLP
+>11
+KAKEWELALRAQTL
+>12
+KAKEWELAWATAMN
+>13
+KAKEWELLGMRGEI
+>14
+KAKEWELLRAQTLP
+>15
+QANVVWKALRAQTL
+>16
+QANVVWKAWATAMN
+>17
+QANVVWKLRAQTLP
+>18
+RKAKEWEALRAQTL
+>19
+RKAKEWEAWATAMN
+>20
+RKAKEWELGMRGEI
+>21
+RKAKEWELPALRAQ
+>22
+RKAKEWELRAQTLP
+>23
+RKAKEWENPLGMRG
+>24
+RKAKEWEPALRAQT
+>25
+RKAKEWEPLGMRGE
+>26
+RKAKEWEPTAWATA
+>27
+RKAKEWETAWATAM
+>28
+RVAWTAAALRAQTL
+>29
+RVAWTAALGMRGEI
+>30
+RVAWTAALPALRAQ
+>31
+RVAWTAALRAQTLP
+>32
+RVAWTAANPLGMRG
+>33
+RVAWTAAPALRAQT
+>34
+RVAWTAAPLGMRGE
+>35
+VAWTAARALRAQTL
+>36
+VAWTAARLGMRGEI
+>37
+VAWTAARLRAQTLP
+>38
+YQANVVWALRAQTL
+>39
+YQANVVWAWATAMN
+>40
+YQANVVWLPALRAQ
+>41
+YQANVVWLRAQTLP
+>42
+YQANVVWPALRAQT
+>43
+YQANVVWPTAWATA
+>44
+YQANVVWTAWATAM
diff --git a/tests/test_data/pvacvector/clipped.2.None.fa.key b/tests/test_data/pvacvector/clipped.2.None.fa.key
new file mode 100644
index 00000000..e6968096
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.2.None.fa.key
@@ -0,0 +1,94 @@
+1:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+2:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+3:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+4:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+5:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+6:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+7:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+8:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+9:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+10:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|0|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+11:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+12:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+13:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+14:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+15:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+16:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+17:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+18:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+19:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+20:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+21:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+22:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+23:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+24:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+25:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+26:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+27:
+- AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|2|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+28:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+29:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+30:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+31:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+32:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|0|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+33:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+34:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|2|1|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+35:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+36:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|2|USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9
+37:
+- ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9|1|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+38:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+39:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|2|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+40:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+41:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|2|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+42:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|0|FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|1|FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9
+43:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|0|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
+44:
+- USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|2|1|ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9
diff --git a/tests/test_data/pvacvector/clipped.2.None.junctions.tsv b/tests/test_data/pvacvector/clipped.2.None.junctions.tsv
new file mode 100644
index 00000000..099a498c
--- /dev/null
+++ b/tests/test_data/pvacvector/clipped.2.None.junctions.tsv
@@ -0,0 +1,15 @@
+left_peptide	left_partner_clip	spacer	right_partner_clip	right_peptide	junction_score	percentile
+AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	2	None	1	FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	34542.94	69.0
+AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	2	None	2	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	32431.99	62.0
+AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	2	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	34657.5	70.0
+AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	2	None	0	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	34542.94	69.0
+ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	41697.23	93.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	36656.57	77.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	42175.93	95.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	1	None	1	FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	37986.59	81.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	44120.52	99.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10	37986.59	81.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9	37203.58	78.0
+FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9	0	None	0	USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	37663.69	80.0
+USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9	0	None	0	AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8	34809.68	70.0
diff --git a/tests/test_data/pvacvector/clipped.result.fa b/tests/test_data/pvacvector/clipped.result.fa
index 0e36c254..697cc2b6 100644
--- a/tests/test_data/pvacvector/clipped.result.fa
+++ b/tests/test_data/pvacvector/clipped.result.fa
@@ -1,6 +1,6 @@
->ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9,FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10,FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9,USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9,AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8|Median_Junction_Score:35704.5875|Lowest_Junction_Score:32358.39|All_Junction_Scores:32358.39,37986.59,37663.69,34809.68
-PTAWATAMNNLGHGSRRVAWTAAR
-ALRAQTLPGLRGQAAPAPGPGPS
+>ENOX1.ENST00000261488.10.FS.55C/CA_pos17_len9,AFAP1.ENST00000420658.5.missense.798R/L_pos8_len8,FAM129C.ENST00000335393.8.FS.291CG/C_pos15_len10,FAM129C.ENST00000335393.8.FS.291CG/C_pos7_len9,USP15.ENST00000280377.9.FS.345-346G/GT_pos11_len9|Median_Junction_Score:37972.6125|Lowest_Junction_Score:34542.94|All_Junction_Scores:41697.23,34542.94,37986.59,37663.69
+PTAWATAMNNLGHGSRRVAWTAARV
+KSQAAPGSSPCLGHVLRKAKEWE
+PALRAQTLPGLRGQAAPAPGPGPS
 PALRAQTLPGLRGQAAPAPGPGPS
 NPLGMRGEIAKSYAELYQANVVWKV
-KSQAAPGSSPCLGHVLRKAKEWELK
diff --git a/tests/test_pvacvector.py b/tests/test_pvacvector.py
index ae9b40d7..2b599828 100644
--- a/tests/test_pvacvector.py
+++ b/tests/test_pvacvector.py
@@ -290,7 +290,7 @@ def test_pvacvector_clipping(self):
             '-n', self.input_n_mer,
             '-k',
             '-b', '32000',
-            '--max-clip-length', '1',
+            '--max-clip-length', '2',
             '--allow-n-peptide-exclusion', '0',
             '--spacers', 'None,AAY',
         ])
@@ -307,6 +307,14 @@ def test_pvacvector_clipping(self):
             os.path.join(output_dir.name, "1", "None", "junctions.tsv"),
             os.path.join(self.test_data_dir, "clipped.1.None.junctions.tsv")
         ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "1", "AAY", "junctions.tsv"),
+            os.path.join(self.test_data_dir, "clipped.1.AAY.junctions.tsv")
+        ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "2", "None", "junctions.tsv"),
+            os.path.join(self.test_data_dir, "clipped.2.None.junctions.tsv")
+        ))
 
         self.assertTrue(compare(
             os.path.join(output_dir.name, "0", "None", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv"),
@@ -332,6 +340,22 @@ def test_pvacvector_clipping(self):
             os.path.join(output_dir.name, "1", "None", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv.key"),
             os.path.join(self.test_data_dir, "clipped.1.None.fa.key")
         ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "1", "AAY", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv"),
+            os.path.join(self.test_data_dir, "clipped.1.AAY.fa")
+        ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "1", "AAY", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv.key"),
+            os.path.join(self.test_data_dir, "clipped.1.AAY.fa.key")
+        ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "2", "None", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv"),
+            os.path.join(self.test_data_dir, "clipped.2.None.fa")
+        ))
+        self.assertTrue(compare(
+            os.path.join(output_dir.name, "2", "None", "MHC_Class_I", "tmp", "test_pvacvector_produces_expected_output.fa.split_1-2.8.tsv.key"),
+            os.path.join(self.test_data_dir, "clipped.2.None.fa.key")
+        ))
 
         self.assertTrue(compare(
             os.path.join(output_dir.name, "test_pvacvector_produces_expected_output_results.fa"),