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/home/cluster1/data/bu01/1121861/jlex/rdloci/alignments/red_allele_inc.aln
CLUSTAL W (1.83) multiple sequence alignment J254_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J99_Red_locus1_NK ATGGAATCAGTAAAAACAGTAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J170_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTGAC J178_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC J282_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC 26695_Red_locus2_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAS-TAAC J258_Red_locus1_SN ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J282_Red_locus2_EQ ATGGAATCAGTAAAAACAGGAAAAGCAAATAAAGTTGGCAAAAACACAGAGACAGCTAAC J178_Red_locus2_EQ ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAAC J238_Red_locus1_NK ATGGAATCAGTAAAAACAGAAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTGAC M-HP1_Red_Locus ------------------------------------------------------------ 26695_Red_locus1_SN ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAATACAGAGATGGCTAAT 26695_Red_locus2_SN ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAATACAGAGATGGCTAAT 26695_Red_locus1_NK ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAATACAGAGATGGCTAAT J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J166_Red_locus1_KD ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAAC J254_Red_locus1_NK GCAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAATGCCATTACAAATATAATCAGA J99_Red_locus1_NK ACAGAGGCAAGTAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATACGCTCCGA J170_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGA J178_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGA J282_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCACCATTACAAATATAATCAGA 26695_Red_locus2_NK GCAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAATGCCATTACAAATATAATCAGA J258_Red_locus1_SN ACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGA J282_Red_locus2_EQ ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGA J178_Red_locus2_EQ ACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGA J238_Red_locus1_NK ACAAAGGCAAATAAAGAGGCTCATTTAAAACAAGCGAGTGCCATTACAAATACGCTCAGA M-HP1_Red_Locus ------------------------------------------------------------ 26695_Red_locus1_SN ACAAAGGCAAATAAAGAGRCTCATTTTAAACAAGYGAGCACCATTACAAATATAATCAGA 26695_Red_locus2_SN ACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCACCATTACAAATATAATCAGA 26695_Red_locus1_NK ACAAAGGCAAATAAAGAGACTCATTTTAAACAAGTGAGCGCCATTACAAATATAATCAGA J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J166_Red_locus1_KD GCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGA J254_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACAT J99_Red_locus1_NK TCAATTGGTGGGATTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTGAAAAAACAT J170_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACAC J178_Red_locus1_NK TCAATTAGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACAC J282_Red_locus1_NK TCAATTGGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACAC 26695_Red_locus2_NK TCAGTTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACAT J258_Red_locus1_SN TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACAC J282_Red_locus2_EQ TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACAT J178_Red_locus2_EQ TCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACAC J238_Red_locus1_NK TCAATTGGTGGGTTTTTTACAAAAATTGTAAAGAGAGTTAGAGAACTTGTAAAAAAACAC M-HP1_Red_Locus ------------------------------------------------------------ 26695_Red_locus1_SN TCARTTSGTGGGATTTTTACAAAAATTGCAAAGAAAGTTAGAGGACTTGTAAAAAAACAC 26695_Red_locus2_SN TCAATTCGTGGGATTTTTACAAAAATTGCAAAGAAAGTTAGAGGACTTGTAAAAAAACAC 26695_Red_locus1_NK TCAGTTGGTGGGTTTTTTACAAAAATTGCAAAGAGAGTTAGAGGACTTGTAAAAAAACAC J166_Red_locus2_KD ------------------------------------------------------------ J254_Red_locus2_EQ ------------------------------------------------------------ J166_Red_locus1_KD TCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACAC J254_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTAACCCATGTTGCGTGCAAGAAAGCGAAA J99_Red_locus1_NK CCCAAGAAAAGCAGTGTGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAGGGCAAAA J170_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAA J178_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCGAAA J282_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAGGGCAAAA 26695_Red_locus2_NK CCCGAGAAAAGCAGTGTGGCATTAGTAGTATTAACCCATGCTGCATGCAAGAAAGCGAAA J258_Red_locus1_SN CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAA J282_Red_locus2_EQ CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAA J178_Red_locus2_EQ CCCAAGAAAAGCAGGGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAA J238_Red_locus1_NK CCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAAAGCGAAA M-HP1_Red_Locus -----------------------------------------------CGGCGAAGC--AA 26695_Red_locus1_SN CCCAAGAAAAGCAGTGCGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAAAGCGAAA 26695_Red_locus2_SN CCCAAGAAAAGCAGTGCGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAAAGCGAAA 26695_Red_locus1_NK CCCAAGAAAAGCAGTGCGGCATTAGTAGTATTGACCCATATTGCGTGCAAGAAAGCGAAA J166_Red_locus2_KD ------------------------------------------GCGGGCA-GAAAGCAAAG J254_Red_locus2_EQ -------------------------------------CCGGTGCGGGCA-GAAAGCGAAA J166_Red_locus1_KD CCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAA * ** * J254_Red_locus1_NK GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J99_Red_locus1_NK GAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J170_Red_locus1_NK GAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J178_Red_locus1_NK GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J282_Red_locus1_NK GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT 26695_Red_locus2_NK GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J258_Red_locus1_SN GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCGAATCAAT J282_Red_locus2_EQ GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCGAATCAAT J178_Red_locus2_EQ GAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J238_Red_locus1_NK GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT M-HP1_Red_Locus GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT 26695_Red_locus1_SN GAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT 26695_Red_locus2_SN GAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT 26695_Red_locus1_NK GAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J166_Red_locus2_KD AATTGGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT J254_Red_locus2_EQ GAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCATATCAAT J166_Red_locus1_KD GAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAAT * * ************** ******************************* ****** J254_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC J99_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC J170_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC J178_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGTGGCAAGTTTATTATTAGCCGCTTGTAGC J282_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGC 26695_Red_locus2_NK TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGT J258_Red_locus1_SN TGGTGGAAGTATTC---AGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGT J282_Red_locus2_EQ TGGTGGAAGTATTC---AGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGT J178_Red_locus2_EQ TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC J238_Red_locus1_NK TGGTGGAAATATTCTTCAGGATTAACAATAGCGGCAAGTTTATTACTAGCCGCTTGTAGC M-HP1_Red_Locus TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC 26695_Red_locus1_SN TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGC 26695_Red_locus2_SN TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGC 26695_Red_locus1_NK TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGC J166_Red_locus2_KD TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGT J254_Red_locus2_EQ TGGTGGAAATATTC---AGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGT J166_Red_locus1_KD TGGTGGAAATATTC---AGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGT ******** ***** **** * ******* * *********** ************* J254_Red_locus1_NK GCTGGTGATATTGATAAACAAATAGAACTA J99_Red_locus1_NK ACTGGTGATATTGATAAACAAATAGAACTA J170_Red_locus1_NK GTTGGTGATACTGATAAACAGATAGAGTTA J178_Red_locus1_NK GTTGGTGATACTGATAAATAGATAGAGTTA J282_Red_locus1_NK GTTGGTGATACTGATAAACAGATAGAGTTA 26695_Red_locus2_NK GTTGGTGATATTGATAAACAGATAGAGTTA J258_Red_locus1_SN GCTGGTGATATTGATAAACAGATAGAGTTA J282_Red_locus2_EQ GCTGGTGATATTGATAAACAGATAGAGTTA J178_Red_locus2_EQ GTTGGTGATATTGATAAACAAATAGAGTTA J238_Red_locus1_NK GCTGGTGATATTGATAAACAAATAGAGTTA M-HP1_Red_Locus GCTGGTGATACTGATAAACAAATAGAGTTA 26695_Red_locus1_SN ACTGGTGATGTTAGTGAACAAATAGAACTA 26695_Red_locus2_SN ACTGGTGATGTTAGTGAACAAATAGAACTA 26695_Red_locus1_NK GCTGGTGATACTGATAAACAGATAGAACTA J166_Red_locus2_KD GTTGGTGATATTGATAAACAAATAGAACTA J254_Red_locus2_EQ GTTGGTGATACTGATAAACAGATAGAGTTA J166_Red_locus1_KD GTTGGTGATATTGATAAACAAATAGAACTA ******* * * ** * ***** **