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Full_sseq returns sequence with N or X
Hello, I need the sequence from part of my Blastp hits. The full_sseq option from custom outfmt 6 returns the sequence with variable amino acids. For example: MIRSRSRATRGVRMKTFKATMTTAMLALXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNPVGKRDPFRSPIDELGPVNANPVAACNEPLCSFDLDQLKLVAVVTGDASPVAMVEDPAGRGHIVRRNTRMGRQGGKVTQILRDSVTVTEVFSGNGEIIKNPVTLQLKPDAKQDPAYNMMTGRNYGE I'm using the precompiled windows release.
The repeat masking is included in the output, there is no way to prevent that at this time unfortunately. If you need the unmasked target sequence, you need to pull it out of the database file again in downstream processing.
You can turn off the masking completely using --masking 0, but this is usually not recommended.
I have also observed this "X" incorporation in the qseq and sseq output for sequences with 100% qcov and 100% pident. When --masking was set to 0, the masking & unmasking process was reported to still occur and erroneous sequences with Xs in them were still present.
It also appears that BLASTP itself has the same "-" masking error. This will need to be fixed if people are using this function because it is incorporating X or - where the sequence is known.
That should not happen, please let me know your diamond version and command line to reproduce the problem.
(base) kostrouchov@myip:~$ diamond --version
diamond version 2.0.14
(base) kostrouchov@myip:~$ diamond makedb --in UP000002254.fasta -d UP000002254
diamond v2.0.14.152 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
#CPU threads: 64
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: UP000002254.fasta
Opening the database file... [0s]
Loading sequences... [0.234s]
Masking sequences... [0.114s]
Writing sequences... [0.042s]
Hashing sequences... [0.013s]
Loading sequences... [0s]
Writing trailer... [0.005s]
Closing the input file... [0s]
Closing the database file... [0s]
Database sequences 59102
Database letters 38840110
Database hash a67870a3f2e0fe21d90986a00fde24f8
Total time 0.411000s
0
(base) kostrouchov@myip:~$ diamond blastp --db UP000002254.fasta --query UP000005640.fasta --threads 60 --masking 0 -o hc70_a1.txt -f 6 qseq sseq qcovhsp pident --id 70 --query-cover 100
diamond v2.0.14.152 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
#CPU threads: 60
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
#Target sequences to report alignments for: 25
Opening the database... Database file is not a DIAMOND or BLAST database, treating as FASTA.
Database input file: UP000002254.fasta
Opening the database file... [0s]
Loading sequences... [0.282s]
Masking sequences... [0.105s]
Writing sequences... [0.043s]
Hashing sequences... [0.013s]
Loading sequences... [0s]
Writing trailer... [0.005s]
Closing the input file... [0s]
Closing the database file... [0s]
Database sequences 59102
Database letters 38840110
Database hash a67870a3f2e0fe21d90986a00fde24f8
Total time 0.450000s
[0.481s]
Database: UP000002254.fasta (type: Diamond database, sequences: 59102, letters: 38840110)
Block size = 2000000000
Opening the input file... [0s]
Opening the output file... [0s]
Loading query sequences... [0.228s]
Algorithm: Double-indexed
Building query histograms... [0.045s]
Allocating buffers... [0s]
Loading reference sequences... [0.06s]
Initializing temporary storage... [0s]
Building reference histograms... [0.06s]
Allocating buffers... [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
Building reference seed array... [0.051s]
Building query seed array... [0.036s]
Computing hash join... [0.021s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.321s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.021s]
Computing hash join... [0.014s]
Masking low complexity seeds... [0.009s]
Searching alignments... [0.259s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
Building reference seed array... [0.027s]
Building query seed array... [0.023s]
Computing hash join... [0.014s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.409s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
Building reference seed array... [0.024s]
Building query seed array... [0.019s]
Computing hash join... [0.014s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.251s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
Building reference seed array... [0.024s]
Building query seed array... [0.02s]
Computing hash join... [0.013s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.792s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.021s]
Computing hash join... [0.014s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.248s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
Building reference seed array... [0.027s]
Building query seed array... [0.023s]
Computing hash join... [0.013s]
Masking low complexity seeds... [0.009s]
Searching alignments... [0.248s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
Building reference seed array... [0.024s]
Building query seed array... [0.019s]
Computing hash join... [0.013s]
Masking low complexity seeds... [0.008s]
Searching alignments... [0.635s]
Deallocating buffers... [0.006s]
Clearing query masking... [0.01s]
Computing alignments... [11.677s]
Deallocating reference... [0.002s]
Loading reference sequences... [0s]
Deallocating buffers... [0.005s]
Deallocating queries... [0.002s]
Loading query sequences... [0s]
Closing the input file... [0s]
Closing the output file... [0.004s]
Cleaning up... [0s]
Total time = 16.475s
Reported 101105 pairwise alignments, 101105 HSPs.
34719 queries aligned.
(base) kostrouchov@myip:~$ grep "XXXX" hc70_a1.txt | head -n 10
MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLVSEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPCTTRPHKEGEVPGVDYIFITVEDFMELEKSGALLESGTYEDNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGEMPSQPYPAPVYSQPEELKEQMDDTKPTKPEDNEEPDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTELGTKPLQAPGFREKPLFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPTDGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPALHRSSFPDSTEAFDPRKPDPYELYEKSRAIYESRQQVPPRTSFRMDSSGPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYTNSNHAAPSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPTSAPSSEKQSPMAQQSPLAQQSPLAQPSPATPNSPIAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLSDYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYDEPAPWSSPAAAAPGLPEVGVSLDDGLAPFSPSHPAPPSDPSHQISPGPTWDIKREHDVRKPKELSACGQKKQRLGEQRERSASPQRAARPRLEEAPGGQGRPEAGRPASEARAPGLAAADAADAARAGGKEAPRAAAGSELCRREGPGAAPAFAGPGGGGSGALEAEGRAGARAGPRPGPRPPGGAPARKAAVAPGPWKVPGSDKLPSVLKPGASAASR MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLASEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGETPSQPYPAPVYSQPEELKEQMDDAKPTKPEENEESDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTDLGTKPLQAPGFREKPLFTRDASQLKGTFLSITLKKSSMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPADGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPTLHRTSFPDSTEAFDPRKPDPYELYEKSRAIYESRQQVPPRTSFRMDSSGPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYANSNHAATSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPASAPSSEKQSPMAQQSPLAQPSPATPNSPVAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLADYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYDDPGSRSAAAAAAPGLQEVGAPPEDGPPPLAPSHPAPPSEPSRHTGPDPPWDSKREHDVRKPKELAAGGQKKQRLGEQAERPASPRRAARPGLEGAPGGLPEAGAPGPAADAAGRGGGGGQGAPRGAAGAELGRRGGPGAAPALAGRGGGGAGARAPGGAPPRRAAVAPGPWKVPGSDRLPGARRPGAPTAGR 100 89.8
MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLVSEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPCTTRPHKEGEVPGVDYIFITVEDFMELEKSGALLESGTYEDNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGEMPSQPYPAPVYSQPEELKEQMDDTKPTKPEDNEEPDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTELGTKPLQAPGFREKPLFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPTDGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPALHRSSFPDSTEAFDPRKPDPYELYEKSRAIYESRQQVPPRTSFRMDSSGPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYTNSNHAAPSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPTSAPSSEKQSPMAQQSPLAQQSPLAQPSPATPNSPIAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLSDYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYDEPAPWSSPAAAAPGLPEVGVSLDDGLAPFSPSHPAPPSDPSHQISPGPTWDIKREHDVRKPKELSACGQKKQRLGEQRERSASPQRAARPRLEEAPGGQGRPEAGRPASEARAPGLAAADAADAARAGGKEAPRAAAGSELCRREGPGAAPAFAGPGGGGSGALEAEGRAGARAGPRPGPRPPGGAPARKAAVAPGPWKVPGSDKLPSVLKPGASAASR MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLASEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGETPSQPYPAPVYSQPEELKEQMDDAKPTKPEENEESDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTDLGTKPLQAPGFREKPLFTRDASQLKGTFLSITLKKSSMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPADGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPTLHRTSFPDSTEAFDPRKPDPYELYEKSRAIYESRRPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYANSNHAATSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPASAPSSEKQSPMAQQSPLAQPSPATPNSPVAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLADYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYDDPGSRSAAAAAAPGLQEVGAPPEDGPPPLAPSHPAPPSEPSRHTGPDPPWDSKREHDVRKPKELAAGGQKKQRLGEQAERPASPRRAARPGLEGAPGGLPEAGAPGPAADAAGRGGGGGQGAPRGAAGAELGRRGGPGAAPALAGRGGGGAGARAPGGAPPRRAAVAPGPWKVPGSDRLPGARRPGAPTAGR 100 88.7
MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLVSEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPCTTRPHKEGEVPGVDYIFITVEDFMELEKSGALLESGTYEDNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGEMPSQPYPAPVYSQPEELKEQMDDTKPTKPEDNEEPDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTELGTKPLQAPGFREKPLFTRDASQLKGTFLSTTLKKSNMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPTDGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPALHRSSFPDSTEAFDPRKPDPYELYEKSRAIYESRQQVPPRTSFRMDSSGPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYTNSNHAAPSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPTSAPSSEKQSPMAQQSPLAQQSPLAQPSPATPNSPIAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLSDYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYGMVPSSLSMCMKSDKHGSPYFYLLGHPKDTTNPPPGVLPLPPPQVCRK MSKSLKKKSHWTSKVHESVIGRNPEGQLGFELKGGAENGQFPYLGEVKPGKVAYESGSKLASEELLLEVNETPVAGLTIRDVLAVIKHCKDPLRLKCVKQGGIVDKDLRHYLNLRFQKGSVDHELQQIIRDNLYLRTVPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXNYYGTPKPPAEPAPLLLNVTDQILPGATPSAEGKRKRNKSVSNMEKASIEPPEEEEEERPVVNGNGVVVTPESSEHEDKSAGASGETPSQPYPAPVYSQPEELKEQMDDAKPTKPEENEESDPLPDNWEMAYTEKGEVYFIDHNTKTTSWLDPRLAKKAKPPEECKENELPYGWEKIDDPIYGTYYVDHINRRTQFENPVLEAKRKLQQHNMPHTDLGTKPLQAPGFREKPLFTRDASQLKGTFLSITLKKSSMGFGFTIIGGDEPDEFLQVKSVIPDGPAAQDGKMETGDVIVYINEVCVLGHTHADVVKLFQSVPIGQSVNLVLCRGYPLPFDPEDPANSMVPPLAIMERPPPVMVNGRHNYETYLEYISRTSQSVPDITDRPPHSLHSMPADGQLDGTYPPPVHDDNVSMASSGATQAELMTLTIVKGAQGFGFTIADSPTGQRVKQILDIQGCPGLCEGDLIVEINQQNVQNLSHTEVVDILKDCPIGSETSLIIHRGGFFSPWKTPKPIMDRWENQGSPQTSLSAPAIPQNLPFPPTLHRTSFPDSTEAFDPRKPDPYELYEKSRAIYESRQQVPPRTSFRMDSSGPDYKELDVHLRRMESGFGFRILGGDEPGQPILIGAVIAMGSADRDGRLHPGDELVYVDGIPVAGKTHRYVIDLMHHAARNGQVNLTVRRKVLCGGEPCPENGRSPGSVSTHHSSPRSDYATYANSNHAATSSNASPPEGFASHSLQTSDVVIHRKENEGFGFVIISSLNRPESGSTITVPHKIGRIIDGSPADRCAKLKVGDRILAVNGQSIINMPHADIVKLIKDAGLSVTLRIIPQEELNSPASAPSSEKQSPMAQQSPLAQPSPATPNSPVAQPAPPQPLQLQGHENSYRSEVKARQDVKPDIRQPPFTDYRQPPLDYRQPPGGDYQQPPPLDYRQPPLLDYRQHSPDTRQYPLADYRQPQDFDYFTVDMEKGAKGFGFSIRGGREYKMDLYVLRLAEDGPAIRNGRMRVGDQIIEINGESTRDMTHARAIELIKSGGRRVRLLLKRGTGQVPEYGMVPSSLSMCMKSDKHGSPYFYLLGHPKDTTTPAPAALPPPPPQGCRK 100 94.6
I have tried but can't reproduce the problem, would it be possible to send me your fasta input files?