INVERTED REPEATS FOUND IN CONTROL REGION 1 (CR1) using einverted program of EMBOSS SUITE 6.6.0.0 USING DEFAULT PARAMETERS CR1_ARC2804: Score 52: 24/29 ( 82%) matches, 0 gaps 468 tgagctatctccccagagataccccaacc 496 || | ||||||||| |||||| | ||||| 911 accccatagaggggcctctatcgagttgg 883 CR1_ARC2804: Score 56: 24/28 ( 85%) matches, 0 gaps 1523 aatttatcattatttcaattaatgttta 1550 ||||||| ||| ||| || ||||||||| 1829 ttaaatattaacaaatttgattacaaat 1802 -------------------------------------------------------- CR1_MZB0099: Score 85: 31/33 ( 93%) matches, 0 gaps 277 tgaaaatacactaccataaatatagttacctat 309 |||||||||||||||||||||||| ||| |||| 2275 acttttatgtgatggtatttatattaatagata 2243 CR1_MZB0099: Score 54: 22/25 ( 88%) matches, 0 gaps 2614 aaaaaaagtcatgaatttcaaattc 2638 ||||||||| ||| |||||||||| 2711 tttttttcaatacaaaaagtttaag 2687 --------------------------------------------------------- CR1_ARC3221: Score 53: 19/20 ( 95%) matches, 0 gaps 909 atgtgggaaatctcattaaa 928 ||||||||||| |||||||| 1123 tacaccctttaaagtaattt 1104 --------------------------------------------------------- CR1_MZB0029: Score 55: 33/44 ( 75%) matches, 0 gaps 519 tttcttttagatatttcagctattttgaaaattttgccaatttt 562 ||| ||||| || ||| | |||||| | ||||| ||||||| 1315 aaaaaaaatttaaaaacgctttaaaacggtaaaaaccgttaaaa 1272 --------------------------------------------------------- CR1_ARC2888: Score 56: 40/41 ( 97%) matches, 5 gaps 2508 ttagta-ttattttttctctctata-aataattta-tagt-tatat 2549 |||||| || ||||||||| ||||| ||||||||| |||| ||||| 2830 aatcataaaaaaaaaagag-gatatattattaaatgatcagatata 2786 --------------------------------------------------------- CR1_MZB0028: Score 77: 43/56 ( 76%) matches, 0 gaps 857 tttgtcaagaaaaattattaatgatctaacattaaatatatatatacctctttttt 912 |||||| | ||||||||||||| |||||||| ||| | | || || | ||||| 1661 aaacagattcttttaataattacgagattgtattttttttttaaataccggaaaaa 1606 --------------------------------------------------------- CR1_ARC2547: Score 167: 61/65 ( 93%) matches, 0 gaps 974 ttatgctaacataagaccgattttcctaggctacattttcgggaatagcagaaaatccggccatg 1038 || |||||||||||||| |||||||||||||||||||||||||||||||||| |||| ||||||| 1776 aacacgattgtattctgcctaaaaggatccgatgtaaaagcccttatcgtctcttagaccggtac 1712 --------------------------------------------------------- CR1_MZB0110: Score 55: 57/80 ( 71%) matches, 2 gaps 651 tatttaataaatcggtaatcaattataatttactagaaaattatatttatagtaaggcaatttatatataaaatataaatta 732 ||||| ||||| |||| |||| || ||| | ||| || || || ||| | | || |||||| || ||||||||| 854 ataaaatattttaaaattaaataatttttaatta-atttcaaattatttaatattacataaattatata-ttgatatttaat 775 --------------------------------------------------------- CR1_MZB0052: Score 58: 46/60 ( 76%) matches, 2 gaps 1032 tatatattaa-ataatattataattagaacttttaaaatttatttatatataattaaaatat 1092 |||||| ||| || || | ||| ||| | ||||| | || | ||| |||||| ||| |||| 1290 atatattattaaatgatcagatttatcataaaaatataaacttaatttatatt-attatata 1230 --------------------------------------------------------- CR1_MZB0053: Score 61: 27/32 ( 84%) matches, 0 gaps 826 attataatttatttttatataattttaattta 857 |||||| ||||||||| |||||| |||||| 890 taatatataataaaaatgtattaattttaaat 859 CR1_MZB0053: Score 56: 48/70 ( 68%) matches, 0 gaps 1644 tcaagcaaggatcacctagcgtgagaattgtcaagcaaggatcacctagcgtgagaattgtcaagcaagg 1713 ||| || ||| ||| || ||| |||| ||| || ||| ||| || ||| |||| ||| || ||| 1787 agtgcgatccactaggaacgaactgttaagagtgcgatccactaggaacgaactgttaagagtgcgatcc 1718 --------------------------------------------------------- >CR1_MZB0023 NO INVERTED REPEATS --------------------------------------------------------- >CR1_MZB0043_partial NO INVERTED REPEATS --------------------------------------------------------- --------------------------------------------------------- --------------------------------------------------------- --------------------------------------------------------- ALIGNMENT OF CONTROL REGION 1 (CR1) USING BLASTALIGN #NEXUS [Aligned to seq CR1ARC2888 by BlastAlign. We have excluded sequences with more than 99% gaps] BEGIN DATA; dimensions ntax=10 nchar=600; format gap=- datatype=DNA; matrix CR1_ARC2888 tttcttataattttaaataaatctatatattttcacaaatttattttaaattatatttatagaagcataatatcatattaatacatagattaaatttttttttttttttagta-t-tattttttctctctataaataatttatagtt-atatctat-aaataatatagtaattagaattattaaaatttatttattattttattaaattaattataaattttttaatttataaataaatactattttcggagaaatattttataatttttctttttttctaagaaccgataattcaaatc-ataaacattagtttaaaca-ttagtatttatagattctgacaaatatagttatatatatatattatatttaattcatatgtaaaagtactatatagactagtaaattattatataggagaaaaaaaaaatactaacttttttcacccccatttatcgttactaaggc-ttttcatctaaacaccctaaaaataacccctatttttaccaaatttcatttttaaaaaaatccaaaataacaaaaaaaaag-gccattttttaaaaacttattaaatcttgctaccaagcactaaaattta CR1_MZB0052 --------------------------------------------------ttatatttattgagggataatatcatattaatgtatagggaaatttttttttttttttnagta-a-aaattttttcctctataaataatttatagtt-atatatattaaataatattataattagaacttttaaaatttatttat-atataattaaaata-ttacattatttttgatttatagataaatattatttttgtataaatattt-ataatatttctctctctttaac--ccgataattcaaatc-ataaacattagtttaaaca-ttagtatttatagattctgaccattatattcctatatat-tattatatttaattcaaatataaaaatactatttagactagtaaattattatataggagaaaaaaaaaa-actaattttttt------------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_MZB0053 -----------------------------------------------aaattatatttatagtaacctattttcatattaaaatataggt-aaatttttttttttttttaata-t-tattttgttactctataaataatttatagtt-atat-------------------------------------------------------------------tttttgatttataaataaata---------------------------------------------ccgataattctgctc-ataaacattagtttaaaca-attataaatttatattctgacaattgtattcttatatattt-ttatatttaattcatatataaaagaactatatagactagtaaattattatatagggg-------------------------------------gttcctaaggcattttcatctaaacaccc------------------------------------------------------------------------------------------------------------------ CR1_ARC2547 -----------------------------------------------------------------------------------------------ttttttttttttttagca-t-tatctttt-tctctataaataatttatagttaatatatat-aaata-----------------------------------------------------------------------------------------------------------------------agaaccgataattcaaatc-ataaaaattcgtttaaacaattattattc-taaattctgacaattatatgcttatttattt-ttatatttaattcatatataaaagtactatatagactagtaaattattat-tatgggaaaaaaaaaaaaccaaattttttcac---------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_MZB0099 -----------------------------------------------------------------------------------------------ttttttttttttttagta-aatatctatt-tctttataaataatttatagt-------------------------------------------------------------------------------------------------------------------------------------------ccgataattcaaatcaacaaaaattagtttaaact-ttgagagatatagattctgacaattata---------------------------------aaaagtactatatggactagtaaattattattaaagcgaaaaaaaaaa-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_ARC2804 --------------------------------------------------ttatatttatagagacatattttcatcttactatatagataaatttttttttttttttnagtact-tatttattc-ctctataaataatttatagtt-ttatctat-aaataatat-----------------------------------------------------------------------------------------------------------------------ccgataattcaaata-ataaacattagtttaaaca---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_MZB0028 ------------------------------------------------------------------------------------------------------------------------------ctctataaataatttatagat-atatatat-aaataat-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttatatttaattcatatataaaa------------------------------------------------------------------------------------------------------------------------------------------------------------aaaaaaagtgccattttttaaaaactt------------------------------- CR1_MZB0110 ----------------------------------------------------------------------------------------attaagttttttttttttttnagta-aatattttcgtcctttataaataatttatagtt-atat-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atatagattagtaaattattat------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_ARC3221 ------------------------------------------------------------------------------------------taaatttttttttttttt---------------------tataaataatttatagtt-atatatat-aaata-----------------------------------------------------------------------------------------------------------------------------gataattcaaatc-ataa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CR1_MZB0029 ------------------------------------------------------------------------------------------------------------------------------ctctataaataatttata------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ ; end;