Here is some example sequences that I tried aligning:
>LS_comp37_c0_seq1_len=2308_path=[1:0-2307] AAAAAAAAAAAAAAAAAAAAAAATGTTAAAAATCAAAAGACTCTTAACTTACAAGATATG ATAGTATCATATCATCCATAAATACTGTATGATATCATAATAAGATGCCACATATAACAA AAATATATAATGTTGCCAAAGACAGAAAGTCACACTCGATAAATTCAAATACATAGTTAA ATATGCAGAAGGCTCTTGAACTTGAACTTGAACTTGAACTTAATTATTACATGCATAAAA ATTGAATAGTTCATCCATAAACGACGACAGACTCTCCCTTGTGCTCACGTGGTGGCAAAT GCCACGTTGTTTGAGCCGATTCTCCTTATTTCATTTTGGTGCTTGAAGAATTACGTACGA ACTATGCCTTGGAAAAACTTTGGTAGAATTTAAGTAAGTAAACGATGGCTCATCATCATC TCTCATGCAAAGGGCTCGAATAAGGTTCTGGTCATTTGTTGATGTATTATAGGATGTTGT GTGCCGTGCCCATCTCCATTATGGTACATCAACTGCGCCATCCTTCCTAAATCAACTGCA CATCCTATAAAATCTTTGCCAAATGGAGAATCCTTCGACACCCTCTCCGCATTCATCTTC TTCCACACCTCCGCTATCAGCCATTTCACGTGCTTCCGCGCCTCCGCCTCCGATGCATTG TAGTCACTCATGTAGCACTGAAGTGATTTCGGCACATCCCCTCTGCTCACCTCTTCCACC GAGGTTCCCAAATCATCAGCAAGCCGCAGAACGAAGGATGACCAGCGAACTAAATCGTGG TATTTGTACAAACTGTCGACGGTCTCTTTTGTGAACGAATCTGTTACTCGGAAGAATATG TGCGTTAACATACAGGGCCCACTTATCGACTGCCATGAGTTCTCCAAATACTCTTCCAAA CTTGGTTTGTGTCCGCCGTAGAACCACCGTGCCTCTACCATATACTTATCCGCCAAATCC ACCCACGATTGCCGCAGGTAGGGTATAACGTTGACGCCTTTCTCCTTCATAACATCGTAC GATGTATCATCGACGAAGTTGTTGAGTGCAAGAAAGCACAGTTGCATGTAATCGGGAAGT TGGTCGATTGAGTCTATATCCCATCTCCGAATGAGTTCTGTGAATTGTTCGAGTTCTTCT AAGGTGCCGTAGACATCATAAATATCATCGATCACCGTAATCAGAGCGTTGACTTTGCCC ATCATTATCCTTGCACTTGCATGCTGACGTGGCTCGATGATCCCAGTATTCCAAAAGTAG CATTCCACCAGTCTATCCCTTGCGAAGGGCAGCTTCTCAACAAACCCAGTATTTCTCCAC CACCGGAAGGATTCTTTGAGTTCTTGTTGAAAATGAGCTTGAACAATATTTAAGTCGAGT ATGGCAAGCTCCAACACTACTGGATTCATGTCGGGCCTCTTCCTATACCATTCGATCCAC ACAGGTGCATTTGGCCTTTTAATCCTCCAATGAAGTGGGATTTCTAAAGAATATGCGATT CTTGTTAAAAGGTCGCCATCAACACCACCCTCGTTCACTCTTCCCTCCAAAAATTTGGTG GCGAATTCCCTCGCTGACTCGAGCGTGGTTTCGCCTTCCGTCAACAGAAAGGAAGCTTCA TACAGTTGCAACAATCCTCTGGTGTCGTCGCTAAGGCTTTCTTTGAACTCACCCTCCTCG TTCTTGAAACTGTCGAATACCTCTTGTGCGACTTGAAAACCATGTTCTCTGAGGAGCCTA AATGCAAGAGATGTGGAGTAGAGATCCCTTTCTTCTTTTGGAAAAGGGTTCTTGTAATAG TGATGGTCGAGATATATAGAGGACAAGATTTCTTTGAACTCATTCTGGAAATGATCGGAC AGCCCCATCCTCTGCAAGTCATCAATCAATTCAAGCTGTCGAATTTGATCCGTTTCTTTC TCCAATTCCATCTTCACCAAAGTGACCAGCTCAGAAGCCCTAATCGCGTGTTTGTACTCC TTATAATCACTGTGGAGGGATTGGATGAATTCGACATCCCAACGAGAAGGGTTGTAGTTT CCGGATCGTCTTTCAGTAGTGAGTTGCGAGGAGGAGCAAGACACACGGAGGCGAGATCGA CTAGTACCCTTAGTGTTAGAGAGCAATTTAGGAGAAGAATTCAAGTGTGAGGGTTGAAGA TAGGTCGTTAGCTTGCTAGGAATTGGCATTTGCATTGCACCACTAAACACTGTGAGAGCC ATGATTAATTAATCTTTGCTTTCTCCTTTTCTTCCACTCTCTTTCTATGTTTTTCTAGGA CGTACTGGTTTCTAAAATTTGAGATGCA >LS_spe_comp37_c0_seq1 AAAAAAAAAAAAAAAAAAAAAAATGTTAAAAATCGACTCTTAACTTACAAGATATGATAG TATCATATCATCCATAAATACTGTATGATATCATAATAAGATGCCACATATACAAAAATA TATAATGTTGCCAAAGACAGAAAGTCACACTCGATAAATTCATACATAGTTATATGCAGA AGGCTCTTGAACTTGAACTTGAACTTGAACTTAATTATTACATGCAATAATTGAATAGTT CATCCATAAACGACGACAGACTCTCCCTTGTGCTCACGTGGTGGCAAATGCCACGTTGTT TGAGCCGATTCTCCTTATTTCATTTTGGTGCTTGAAGAATTACGTACGAACTATGCCTTG GAAAAACTTTGGTAGAATTTAAGTAAGTAAACGATGGCTCATCATCATCTCTCATGCAAA GGGCTCGAATAAGGTTCTGGTCATTTGTTGATGTATTATAGGATGTTGTGTGCCGTGCCC ATCTCCATTATGGTACATCAACTGCGCCATCCTTCCTAAATCAACTGCACATCCTATAAA ATCTTTGCCAAATGGAGAATCCTTCGACACCCTCTCCGCATTCATCTTCTTCCACACCTC CGCTATCAGCCATTTCACGTGCTTCCGCGCCTCCGCCTCCGATGCATTGTAGTCACTCAT GTAGCACTGAAGTGATTTCGGCACATCCTCTGCTCACCTCTTCCACCGAGGTTCCCATCA TCAGCAAGCCGCAGAACGAAGGATGACCAGCGAACTAAATCGTGGTATTTGTACAACTGT CGACGGTCTCCTTTGTGAACGAATCTGTTACTCGGAAGAATATGTGCGTTAACATACAGG GCCCACTTATCGACTGCCATGAGTTCTCCAAATACTCTTCCAAACTTGGCGTGTCCGCCG TAGAACCACCGTGCCTCTACCATATACTTATCCGCCAAATCCACCCACGATTGCCGCAGG TAGGGTATAACGTTGACGCCTTTCTCCTTCATAACATCGTACGATGTATCATCGACGAAG TTGTTGAGTGCAAGAAAGCACAGTTGCATGTAATCGGGAAGTTGGTCGATTGAGTCTATA TCCCATCTCCGAATGAGTTCTGTGAATTGTTCGAGTTCTTCTAAGGTGCCGTAGACATCA TAAATATCATCGATCACCGTAATCAGAGCGTTGACTTTGCCCATCATTATCCTTGCACTT GCATGCTGACGTGGCTCGATGATCCCAGTATTCCAAAAGTAGCATTCCACCAGTCTATCC CTTGCGAAGGGCAGCTTCTCAACAAACCCAGTATTTCTCCACCACCGGAAGGATTCTTTG AGTTCTTGTTGAAAATGAGCTTGAACAATATTTAAGTCGAGTATGGCAAGCTCCAACACT ACTGGATTCATGTCGGCCTCTTCCTATACCATTCGATCCACACAGGTGCATTTGGCCTTT TAATCCTCCAATGAAGTGGGATTTCTAAAGAATATGCGATTCTTGTTAAAAGGTCGCCAT CAACACCACCCTCGTTCACTCTTCCCTCCAAAAATTTGGTGGCGAATTCCCTCGCTGACT CGAGCGTGGTTTCGCCTTCTGTCAACAGAAAGGAAGCTTCATACAGTTGCAACAATCCTC TGGTGTCGTCGCTAAGGCTCTTTGAACTCACTCCTCGTTCTTGAAACTGTCGAATACCTC TTGTGCGACTTGAACCATGTTCTCTGAGGAGCCTAAATGCAAGAGATGTGGAGTAGAGAT CCCTCTTCTTTTCAAAGGGTTCTTGTAATAGTGATGGTCGAGATATATAGAGGACAAGAT TTCTTTGAACTCATTCTGATGATCGGACAGCCCCATCCTCTGCAAGTCATCGATCAATCA AGCTGTCGAATTTGATCCGTTTCTTTCTCCAATTCCATCACACCAAAGTGACTAGCTCAG AAGCCCTAATCGCGTGTTTGTACTCCTTATAATCACTGTGGAGGGATTGGATGAATTCGA CATCCCAACGAGAAATGTAGTTTCCGGATCGTCTTTCAGTAGTGAGTTGCGAGGAGGAGC AAGACACACGGAGGCGAGATCGACTAGTACCCTTAGTGTTAGAGAGCAATTTAGGAGAAG AATTCAAGTGTGAGGGTTGAAGATATGTCGTTAGCTTGCCGTACTGGTTTCTAAAATTTG AGATGCA >LS_wat_comp37_c0_seq1 AAAAAAAAAAAAAAAAAAAAAAATGTTAAAAATCGACTCTTAACTTACAAGATATGATAG TATCATATCATCCATAAATACTGTATGATATCATAATAAGATGCCACATATAACAAAAAT ATATAATGTTGCCAAAGACAGAAAGTCACACTCGATAAATTCAAATACATAGTTAAATAT GCAGAAGGCTCTTGAACTTGAACTTGAACTTGAACTTAATTATTACATGCATAAAAATTG AATAGTTCATCCATAAACGACGACAGACTCTCCCTTGTGCTCACGTGGTGGCAAATGCCA CGTTGTTTGAGCCGATTCTCCTTATTTCATTTTGGTGCTTGAAGAATTACGTACGAACTA TGCCTTGGAAAAACTTTGGTAGAATTAAGTAAGTAAACGATGGCTCATCATCATCTCTCA TGCAAAGGGCTCGAATAAGGCTGGTCATTTGTTGATGTATTATAGGATGTTGTGTGCCAT GCCCATCTCCATTATGGTACATCAACTGCGCCATCCTTCCCATATCAACTGCACATCCTA TAAAATCTTTGCCAAATGGAGAATCCTTCGACACCCTCTCTGCATTCATCTTCTTCCACA CCTCTGCTATCAGCCATTTCACGTGCTTTCGCGCCTCCGCCTCCGATGCATTGTAGTCAC TCATGTAGCACTGAAGTGATTTCGGCACGTCTCTGCTCACCTCTTCCACCGAGGTTCCCA AATCATCAGCAAGCCGCAGAACGAAGGATGACCAGCGAACTAAATCGTGGTATTTGTACA AACTGTCGACCGTCTCCTTTGTGAACGAATCTGTTACTCGGAAGAATATGTGCGTTAACA TACAGGGCCCACTTATCGACTGCCATGAGTTCTCCAAATACTCTTCCAAACTTGGTTTGT GTCCGCCGTAGAACCACCGTGCCTCTACCATATACTTATCCGCCAAATCCACCCACGATT GCCGCAGGTAGGGTATAACGTTGACGCCTTTCTCCTTCATAACATCGTACGATGTATCAT CGACGAAGTTGTTGAGTGCGAGAAAGCACAGTTGCATGTAATCGGGAAGTTGGTCGATTG AGTCTATATCCCATCTCCGAATGAGGTCTGTGAAGTGTTCGAGTTCTTCTAAGGTGCCGT AGACATCATAAATATCATCGATCACCGTAATCAGAGCGTTGACTTTGCCCATCATTATCC TTGCACTTGCATGCTGACGTGGCTCGATGATCCCAGTATTCCAAAAGTAGCATTCCACCA GTCTATCCCTTGCGAAGGGCAGCTTCTCAACAAACCCAGTATTTCTCCACCACCGGAAGG ATTCTTTGAGTTCTTGTTGAAAATGAGCTTGAACAATATTTAAGTCGAGTATGGCAAGGT CCAACACTACTGGATTCATGTCGGGCCTCTTCCTATACGAATCGATCCACACAGGTGCAT TTGGCCTTTTAATCCTCCAATGAAGTGGGATTTCTAAAGAATATGCGATTCTTGTTAAAA GGTCGCCATCAACACCACCCTCGTTCACTCTTCCCTCCAAAAATTTGGTGGCGAATCTCG CTGACTCGAGCGTCGTTTCGCCTTCCGTCAACAGAAAGAAGCTTCATACAGTTGCAACAA TCCTCTGGTGTCGTCGCTAAGGCTTTCTTTGAACTCACCCTCCTCGTTCTTGAAACTGTC GAATACCTCTTGTGCGACTTGAAAACCATGTTCTCTGAAGGAGCCTAAATGCAAGAGATG TGGAGTAGAGATCTTTCTTCTTTTGGAAAAGGGTTCTTGTAATAGTGATGGTCGAGATAT ATAGAGGACAAGATTTCTTTGAACTCATTCTGGAAATGATCGGACAGCCCCATCCTCTGC AAGTCATCAATCAATTCAAGCTGTCGAATTGATCCGTTTCTTTCTCCAATTCCATCTTCA CCAAAGTGACCAGCTCAGAAGCCCTAATCGCGTGCTTGTACTCCTTATAATCACTGTGGA GGGATTGGATGAATTCGACATCCCAACGAGAAGGGTTGTAGTTTCCGGATCGTCTTTCCG GTAGTGAGTTGCGAGGAGGAGCAAGACACACGGAGGCGAGATCGACTAGTACCGTTAGTG TTAGAGAGCAATTTAGGAGAAGAATTCAAGTGTGAGGGTTGAAGATAGGTCGTTAGCTTG CTAGGAATTGGCATTTGCATTGCACCACTAAACACTGTGAGAGCCATGATTAATTAATCT CTGCTTTCT >LS_pep_comp37_c0_seq1 AAAAAAAAAAAAAAAAAAAAAAATGTTAAAAATCAAAAGACTCTTAACTTACAAGATATG AAGTATCATATCATCCATAAATACTGTATGATATCATAATAAGATGCCACATATAACAAA AATATATAATGTTGCCAAAGACAGAAAGTCACACTCGATAAATTCAAGTACATAGTTAAA TATGCAGAAGGCTCTTGAACTTGAACTTGAACTTGAACTTAATTATTACATGCATAAAAA TTGAATAGTTCATCCATAAACGACGACAGACTCTCCCTTGTGCTCACGTGGTGGCAAATG CCACGTTGTTTGAGCCGATTCTCCTTATTTCATTTTGGTGCTTGAAGAATTACGTACGAA CTATGCCTTGGAAAAACTTTGGTAGAATTTAAGTAAGTAAACGATGGCTCATCATCATCA CCTCTCATGCAAAGGGCTCGAATAAGGTTCTGGTCATTTGTTGATGTATTATAGGATGTT GTGTGCCGTGCCCATCTCCATTATGGTACATCAACTGCGCCATCCTTCCCATATCAACTG CACATCCTATAAAATCTTTGCCAAATGGAGAATCCTTCGACACCCTCTCTGCATTCATCT TCTTCCACACCTCTGCTATCAGCCATTTCACGTGCTTTCGCGCCTCCGCCTCCGACGCAT TGTAGTCACTCATGTAGCACTGAAGTGATTTCGGCACATCGCCTCTGCTCACCTCTTCCA CCGAGGTTCCCATCATCAGCAAGCCGCAGAACGAAGGATGACCAGCGAACTATCGTGGTA TTTGTACAAACTGTCGACGGTCTCCTTTGTGAACGAATCTGTTACTCGGAAGAATATGTG CGTTAACATACAGGGCCCACTTATCGACTGCCATGAGTTCTCCAAATACTCTTCCAAACT TGGTTTGTGTCCGCCGTAGAACCACCGTGCCTCTACCATATACTTATCCGCCAAATCCAC CCACGATTGCCGCAGGTAGGGTATAACGTTGACGCCTTTCTCCTTCATAACATCGTACGA TGTATCATCGACGAAGTTGTTGAGTGCAAGAAAGCACAGTTGCATGTAATCGGGAAGTTG GTCGATTGAGTCTATATCCCATCTCCGAATGAGGTCTGTGAATGTTCGAGTTCTTCTAAG GTGCCGTAGACATCATAAATATCATCGATCACCGTAATCAGAGCGTTGACTTTGCCCATC ATTATCCTTGCACTTGCATGCTGACGTGGCTCGATGATCCCAGTATTCCAAAAGTAGCAT TCCACCAGTCTATCCCTTGCGAAGGGCAGCTTCTCAACAAACCCAGTATTTCTCCACCAC CGGAAGGATTCTTTGAGTTCTTGTTGAAAATGAGCTTGAACATATTTAAGTCGAGTATGG CAAGCTCCAACACTACTGGATTCATGTCGGGCCTCTTCCTATACGAATCGATCCACACAG GTGCATTTGGCCTTTTAATCCTCCAATGAAGTGGGATTTCTAAAGAATATGCGATTCTTG TTAAAAGGTCGCCATCAACACCACCCTCGTTCACTCTTCCCTCCAAAAATTTGGTGGCGA ATCTCGCTGACTCGAGCGTCGTTTCGCCTTCCGTCAACAGAAAGAAGCTTCATACAGTTG CAACAATCCTCTGGTGTCGTCGCTAAGGCTTTCTATGAACTCACCCTCCTCGTTCTTGAA ACTGTCGAATAGCTCTTGTGCGACTTGAAAACCATGTTCTCTGAGGAGCCTAAATGCAAG AGATGTGGAGTAGAGATCACTTCTTTTGGAAAAGGGTTCTTGTAATAGTGATGGTCGAGA TATATAGAGGACAAGATTTCTTTGAACTCATTCTGGAAATGATCGGACAGCCCCATCCTC TGCAAGTCATCAATCAATTCAAGCTGTCGAATTTGATCCGTTTCTTTCTCCAATTCCATC TTCACCAAAGTGACTAGCTCAGAAGCCCTAATCGCGTGTTTGTACTCCTTATAATCACTG TGGAGGGATTGGATGAATTCGACATCCCAACGAGAAGGGTTGTAGTTTCCGGATCGTCTT TCAGGTAGTGAGTTGCGAGGAGGAGCAAGACACACGGAGGCGAGATCGACTAGTACCCTT AGTGTTAGAGAGCAATTTAGGAGGAAGAATTCAAGTGTGAGGGTTGAAGATAGGTCGTTA GCTTGCTAGGAATTGGCATTTGCATTGCACCACTAAACACTGTGAGAGCCATGATTAATT AATCTGCTTT
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