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/home/cluster1/data/bu01/1121861/jlex/rdloci/alignments/j_seqs.aln
CLUSTAL W (1.83) multiple sequence alignment J178_Red_locus2_EQ ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC J230_Red_locus1_NK ATGGAATCAGTAAAAACAGAAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTGAC J282_Red_locus2_EQ ATGGAATCAGTAAAAACAGGAAAAGCAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J258_Red_locus1_SN ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J170_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTGAC J282_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC J99_Red_locus1_NK ATGGAATCAGTAAAAACAGTAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J254_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J166_Red_locus1_KD ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAAC J178_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J170_Green_locus2_SN ------------------------------------------------------------ J258_Green_locus2_SN ------------------------------------------------------------ J230_Green_locus2_SN ------------------------------------------------------------ J99_Green_locus2_SN ------------------------------------------------------------ J166_Green_locus2_KD ------------------------------------------------------------ J254_Green_locus2_SN ------------------------------------------------------------ J166_Green_locus1_SN ------------------------------------------------------------ J178_Red_locus2_EQ ACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGA J230_Red_locus1_NK ACAAAGGCAAATAAAGAGGCTCATTTAAAACAAGCGAGTGCCATTACAAATACGCTCAGA J282_Red_locus2_EQ ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGA J258_Red_locus1_SN ACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGA J170_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGA J282_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCACCATTACAAATATAATCAGA J99_Red_locus1_NK ACAGAGGCAAGTAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATACGCTCCGA J254_Red_locus1_NK GCAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAATGCCATTACAAATATAATCAGA J166_Red_locus1_KD GCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGA J178_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGA J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J170_Green_locus2_SN ----------------ATGCCTATTATAAGGGTTTTAGTAATGCTTGCAACAATGATGAT J258_Green_locus2_SN ----------------ATGCCTATTATAAGGGTTTTAGTAATGCTTGCAACAATGATGAT J230_Green_locus2_SN ----------------ATGCCTATTATAAGGGTTTTAGTAATGCTTGCAACAATGATGAT J99_Green_locus2_SN ----------------ATGCCTGTTATAAGAGTTTTAGTAATGCTTGCAACAATGATGAT J166_Green_locus2_KD ----------------ATGCCTGTTATAAGAGTTTTAGCAATGCTTGCAACAATGATGAT J254_Green_locus2_SN ------------------------------------------------------------ J166_Green_locus1_SN ------------------------------------------------------------ J178_Red_locus2_EQ TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACAC J230_Red_locus1_NK TCAATTGGTGGGTTTTTTACAAAAATTGTAAAGAGAGTTAGAGAACTTGTAAAAAAACAC J282_Red_locus2_EQ TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACAT J258_Red_locus1_SN TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACAC J170_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACAC J282_Red_locus1_NK TCAATTGGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACAC J99_Red_locus1_NK TCAATTGGTGGGATTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTGAAAAAACAT J254_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACAT J166_Red_locus1_KD TCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACAC J178_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACAC J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J170_Green_locus2_SN GAAGTTAGGAAAAACGGCAAAAGAA---AAGAAAGTTTTTAAGAATGTGGGAGTGTCTAT J258_Green_locus2_SN GAAGTTAGGAAAAACGGCAAAAGAA---AAGAAAGTTTTTAAGAATGTGGGAATGTCTAT J230_Green_locus2_SN GAAATTAGTAAAAACGGCAAAAGAA---AAGAAAGTTTTTAAGAATGTGGGAGTGTCTAT J99_Green_locus2_SN GAAATTAGTAAAAACGGCAAAAGAA---AAGAAAGTTTTTAAGAATGTGGGAATATCTAT J166_Green_locus2_KD GAAATTAGTGAAAACGGCAAAAGAA---AAGAAAGTTTTTAAGAATGTGGGAGTGTCTGT J254_Green_locus2_SN ------------------------------------------------------------ J166_Green_locus1_SN ------------------------------------------------------------ J178_Red_locus2_EQ CCCAAGAAAAGCAGGGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAA J230_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAAAGCGAAA J282_Red_locus2_EQ CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAA J258_Red_locus1_SN CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAA J170_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAA J282_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAGGGCAAAA J99_Red_locus1_NK CCCAAGAAAAGCAGTGTGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAGGGCAAAA J254_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTAACCCATGTTGCGTGCAAGAAAGCGAAA J166_Red_locus1_KD CCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAA J178_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCGAAA J166_Red_locus2_KD ------------------------------------------GCGGGCA-GAAAGCAAAG J254_Red_locus2_EQ -------------------------------------CCGGTGCGGGCA-GAAAGCGAAA J170_Green_locus2_SN AATGGGGATTGCTTTTTGGGAAGCGATAAAAGACTCGATAAAAAAACAAATTAAAAAAAG J258_Green_locus2_SN AATGGGGATTGCTTTTTGGGAAGCGATAAAAGACTCGATAAAAAAACAAATTAAAAAAAG J230_Green_locus2_SN AATGGGGATTGCTTTTTGGGAGGCGATAAAAGACTCGATAAAAAAGCAAATTAAAAAAAG J99_Green_locus2_SN AATGGGGATTGCTTTTTGGGAAGCGATAAAAGACTCGATAAAAAAACAAATTAAAAAAAG J166_Green_locus2_KD AATGGGGATTACTTTTTGGGAAGCGATAAAAGACTCAATAAAAAAACAAATTAAAAAAAG J254_Green_locus2_SN ------------------------------------------------------------ J166_Green_locus1_SN ------------------------------------------------------------ J178_Red_locus2_EQ GAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J230_Red_locus1_NK GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J282_Red_locus2_EQ GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCGAATCAA J258_Red_locus1_SN GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCGAATCAA J170_Red_locus1_NK GAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J282_Red_locus1_NK GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J99_Red_locus1_NK GAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J254_Red_locus1_NK GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J166_Red_locus1_KD GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J178_Red_locus1_NK GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J166_Red_locus2_KD AATTGGGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCAAATCAA J254_Red_locus2_EQ GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGC-TGAAAAAGAAAATCATATCAA J170_Green_locus2_SN CAATTGGATATGCGGGAATGTTAAGACTGCGGATGATTATTTAAAAACGCATCCTAACTC J258_Green_locus2_SN CAATTGGATATGCGGGAATGTTAAGACTGCGGATGATTATTTAAAAACGCACCCTAACTC J230_Green_locus2_SN CAATTGGATATGCGGGAATGTTAAGACTGCGGATGATTATTTAAAAACGCATCCTAACTC J99_Green_locus2_SN CGATTGGATATGCGGGAATGTTAAGACTGCGGATGATTATTTAAAAACGCATCCTAACTC J166_Green_locus2_KD CGATTGGATATGTGGGAATGTTAAGACTGCGGATGATTATTTAAAAACGCATCCTAACTC J254_Green_locus2_SN ---------------------------------------------------------CTC J166_Green_locus1_SN ------------------------------------------------------------ J178_Red_locus2_EQ TTGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTG-TA J230_Red_locus1_NK TTGGTGGAAATATTCTTCAGGATTAACAATAGCGGCAAGTTTATTACTAGCCGCTTG-TA J282_Red_locus2_EQ TTGGTGGAAGTATTC---AGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTG-TA J258_Red_locus1_SN TTGGTGGAAGTATTC---AGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTG-TA J170_Red_locus1_NK TTGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTG-TA J282_Red_locus1_NK TTGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTG-TA J99_Red_locus1_NK TTGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTG-TA J254_Red_locus1_NK TTGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTG-TA J166_Red_locus1_KD TTGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTG-TA J178_Red_locus1_NK TTGGTGGAAATATTC---AGGATTAACAATAGTGGCAAGTTTATTATTAGCCGCTTG-TA J166_Red_locus2_KD TTGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTG-TA J254_Red_locus2_EQ TTGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTG-TA J170_Green_locus2_SN ATGGTTTAATTCAGCAATAGGTGTAACAGCTTTAACAGCCATGCTTATGAATGTGTG-TT J258_Green_locus2_SN ATGGTTTAATTCAGCAATAGGTGTAACAGCTTTAACAGCCATGCTTATGAATGTGTG-TT J230_Green_locus2_SN ATGGTTTAATTCAGCAATAGGTGTAATAACGATAACAGCCATGCTTATGAATGTGTG-TT J99_Green_locus2_SN ATGGTTTAATTCAGCAATAGGTGTAACAGCGATAACAGCCATGCTTATGAATGTGTG-TT J166_Green_locus2_KD ATGGCTTAATTCAACAATAGGTGTAGTAACGATAACAACCATGCTTATGAATGTGTG-TT J254_Green_locus2_SN -TGGCTTA-TTCAGCAATAGGTGTAGCAACGATAACAACCATGCTTATGAATGTGTG-TT J166_Green_locus1_SN -------------GCAATAGGTGTAGCAACGATAACAACCATGCTTATGAATGTGTGCTT * *** * * ** * * * * ** * J178_Red_locus2_EQ GCGTTGGTGATATTGATAAACAAATAGAGTTA---------------------------- J230_Red_locus1_NK GCGCTGGTGATATTGATAAACAAATAGAGTTA---------------------------- J282_Red_locus2_EQ GTGCTGGTGATATTGATAAACAGATAGAGTTA---------------------------- J258_Red_locus1_SN GTGCTGGTGATATTGATAAACAGATAGAGTTA---------------------------- J170_Red_locus1_NK GCGTTGGTGATACTGATAAACAGATAGAGTTA---------------------------- J282_Red_locus1_NK GCGTTGGTGATACTGATAAACAGATAGAGTTA---------------------------- J99_Red_locus1_NK GCACTGGTGATATTGATAAACAAATAGAACTA---------------------------- J254_Red_locus1_NK GCGCTGGTGATATTGATAAACAAATAGAACTA---------------------------- J166_Red_locus1_KD GTGTTGGTGATATTGATAAACAAATAGAACTA---------------------------- J178_Red_locus1_NK GCGTTGGTGATACTGATAAATAGATAGAGTTA---------------------------- J166_Red_locus2_KD GTGTTGGTGATATTGATAAACAAATAGAACTA---------------------------- J254_Red_locus2_EQ GTGTTGGTGATACTGATAAACAGATAGAGTTAGAACAAGAAAAAAAGGAAGCTGAAAACG J170_Green_locus2_SN TTGCTGATGA--CCAATCCA-AAAAGGAAGTG---------------------------- J258_Green_locus2_SN TTGCTGATGA--CCAATCCA-AAAAGGAAGTG---------------------------- J230_Green_locus2_SN TTGCTGATGA--CCAATCCA-AAAAGGAAGTG---------------------------- J99_Green_locus2_SN TTGCTGATGA--CCAATCCA-AAAAAGAAGTG---------------------------- J166_Green_locus2_KD TTGCTGATGA--TCAATCCA-AAAAAGAAGTGGCTCAGCTCAAAAGGAAGCT--GAAACN J254_Green_locus2_SN TTGCTGATGA--CCAATCCA-AAAAGGAAGTG---------------------------- J166_Green_locus1_SN TTGCTGATGA--CCAATCCA-AAAAAGAAGTGGCTGAAACTCACAAGGAAGCTGAAAACG ** *** ** * * * ** * J178_Red_locus2_EQ ----------------------------------- J230_Red_locus1_NK ----------------------------------- J282_Red_locus2_EQ ----------------------------------- J258_Red_locus1_SN ----------------------------------- J170_Red_locus1_NK ----------------------------------- J282_Red_locus1_NK ----------------------------------- J99_Red_locus1_NK ----------------------------------- J254_Red_locus1_NK ----------------------------------- J166_Red_locus1_KD ----------------------------------- J178_Red_locus1_NK ----------------------------------- J166_Red_locus2_KD ----------------------------------- J254_Red_locus2_EQ CTAGGGATAGAGCAAACAAGAGTGGGATAGAACTA J170_Green_locus2_SN ----------------------------------- J258_Green_locus2_SN ----------------------------------- J230_Green_locus2_SN ----------------------------------- J99_Green_locus2_SN ----------------------------------- J166_Green_locus2_KD CTAGGGATAGAGCGAACAAGAGTGGGATAGAACTA J254_Green_locus2_SN ----------------------------------- J166_Green_locus1_SN CTAGGGATAGAGCAAACAAGAGTGGGATAGAACTG