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//home/cluster1/data/bu01/1121861/jlex/rdloci/alignments/Founder_Red_and_Monkey_L1_Red.txt

>J166_Red_locus1_KD
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAACTA

>J170_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTGACACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGATCAATTAGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAAGAATTAGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGCGTTGGTGATACTGATAAACAGATAGAGTTA

>J178_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAACACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCGCCATTACAAATATAATCAGATCAATTAGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCGAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGTGGCAAGTTTATTATTAGCCGCTTGTAGCGTTGGTGATACTGATAAATAGATAGAGTTA

>J178_Red_locus2_EQ
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAACACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGATCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAGGGCGGCATTAGTAGTATTGACCCATGTTGCATGCAGGAAAGCGAAAGAATTGGACGATAAAGTCCAAGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGCGTTGGTGATATTGATAAACAAATAGAGTTA

>J238_Red_locus1_NK
ATGGAATCAGTAAAAACAGAAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTGACACAAAGGCAAATAAAGAGGCTCATTTAAAACAAGCGAGTGCCATTACAAATACGCTCAGATCAATTGGTGGGTTTTTTACAAAAATTGTAAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAAAGCGAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCTTCAGGATTAACAATAGCGGCAAGTTTATTACTAGCCGCTTGTAGCGCTGGTGATATTGATAAACAAATAGAGTTA

>J254_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAACGCAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAATGCCATTACAAATATAATCAGATCAATTAGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACATCCCAAGAAAAGCAATGCGGCATTAGTAGTATTAACCCATGTTGCGTGCAAGAAAGCGAAAGAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGCGCTGGTGATATTGATAAACAAATAGAACTA

>J258_Red_locus1_SN
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACACAGAGACAGCTAACACAAAGGCAAATAAAGAGGCTCATTTTAAACAAGCGAGCGCCATTACAAATACGCTCAGATCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACACCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCGAATCAATTGGTGGAAGTATTCAGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGCTGGTGATATTGATAAACAGATAGAGTTA

>J282_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAAGTTGGCAAAAACGCAGAGACAGCTAACACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGCACCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAAATTGCAAAGAAAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGCATGCAAGAGGGCAAAAGAATTAGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGCGTTGGTGATACTGATAAACAGATAGAGTTA

>J282_Red_locus2_EQ
ATGGAATCAGTAAAAACAGGAAAAGCAAATAAAGTTGGCAAAAACACAGAGACAGCTAACACAAAGGCAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATCGCAAAGAGAGTTAGAGAACTTGTAAAAAGACATCCCAAGAAAAGCAATGCGGCATTAGTAGTATTGACCCATGTTGTGTGCAGGAAAGCGAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCGAATCAATTGGTGGAAGTATTCAGGACTCACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGCTGGTGATATTGATAAACAGATAGAGTTA

>98-147_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-149_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAACCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-150_red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAACCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-151_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAACCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-152_Red_locus1_NK
ATGGATCNGTAAAAACGGGAAAACAAATAAGGTTGGCANGACACAGAGATGGCTAACGCAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAACCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGACAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-169_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-170_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-171_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-180_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACGGAGATGGCTAACGCGAAGACAAATGCCGAGACTCATTTTAAACAAGCGAGGGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-182_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-208_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-210_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG

>98-212_Red_locus1_NK
ATGGAATCAGTAAAAACAGGAAAAACAAATAAGGTTGGCAAGAACACAGAGATGGCTAACGCAAAGACAAATAAAGAGACTCATTTTAAACAAGCGAGTGCCATTACAAATATAATCAGATCAATTGGTGGGTTTTTTACAAAGATTATGAAGAGAGTTAGAGAACTTGTAAAAAAACACCCCAAGAAAAGCAAGGCGGCATTAGTAGTATTGACCCATGTTGCGTGCAAGAAAGCAAAAGAATTGGACGATAAAGTCCAGGATAAATCCAAACAAGCTGAAAAAGAAAATCAAATCAATTGGTGGAAATATTCAGGATTAACAATAGCGGCAAGTTTATTATTAGCCGCTTGTAGTGTTGGTGATATTGATAAACAAATAGAGTTG