Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Cotton_D_gene_10023079 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 3438 ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33 Found at i:1682 original size:720 final size:720 Alignment explanation
Indices: 82--2198 Score: 3095 Period size: 720 Copynumber: 2.9 Consensus size: 720 72 TGTAGCTAAG * * * * ** * * * * 82 TGCTCAAGGTGTCGCGACAAGGTGTCAACTCCATGTTTTGGCTGTGCCGAGGATTGTGGGTTTTA 1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA * * * * * 147 CCTTCACAAGGTATGCGCTGAGGCACCTTTGGAGCTTCATCACCCTTTTCATCCTGATCATCC-T 66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCAT-C---TCATCCAT * * 211 CTTCTTCTTATGCAAAATGCACTTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATC 127 CCTCTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATC * 276 TGGTCGCAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGT 192 TGGTCACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGT * 341 TTACATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGTTGAAGA- 257 TTACATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAA-AC * 405 ACTTGAAGATGATAGTAAGTGCTTCGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTC 321 ACTTGAAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTC * * * 470 CTAACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCCTTCAAACTGAATCTTGTGTGC 386 CTGACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGC * * * 535 CATCGCGAACATCCTCTTGTTCTACAATTTAATAGCCAACGGCTCTCTTGCAAGATATGCAG--A 451 CATCGCGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCA * * * 598 -GAAATCAATGTAGAAGCTATAGGATTTGTTTATGGTTGTTCTCCTTGTACGTTTGTTGTTCACA 516 GGAAA-CAA-G--G-CG-AATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACA * * 662 TTGAATGTGCATCGCAATCACCATTGCAAGTTATTAAGAGTACAAATCATGAACATCCATTTACC 575 TTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACC * 727 TTGTTTAACGGTCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCA 640 TTGTTTAACGGGCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCA 792 AAGGGGTGTAACTGAT 705 AAGGGGTGTAACTGAT * 808 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCGGAGCACTGTGGGTTTTA 1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA * 873 TCTTCATAAGGTATGTGCCAAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC 66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC 938 TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT 131 TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT * 1003 CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGATTTGTTTAC 196 CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTAC 1068 ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG 261 ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG * * 1133 AAGATGATAGTAAGTGCTTTGGGTGTTGGGAACCATTAGCAAAGTATACACACTTTTCTCCGGAC 326 AAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGAC * * * 1198 TGTGGATTTAATTTACATGACAAATGCGCCGAGCTTTCTTTCAAACTGAATCTTGAGTGCCATCG 391 TGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGCCATCG ** 1263 CGAACATCCTCTTGTTCTACAATTTTATAGCGAACAACTCTCTTGCAAGATATGCTGCCAGGAAA 456 CGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCAGGAAA * * * 1328 CAAGGCGAATAGGATTTTTTTATGGTTGTTCTCCCTGTAAGTCTGTTGTTCACATTGAATGTGCA 521 CAAGGCGAATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACATTGAATGTGCA 1393 TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG 586 TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG * * 1458 GCACCAACATCCCCTGTTTCTTATGTTGAATCAAGAGCAGCTGATGGATAATCAAAGGGGTGTAA 651 GCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCAAAGGGGTGTAA 1523 CTGAT 716 CTGAT * 1528 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTTCTGTGCAGAGCACTGTGGGTTTTA 1 TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA * 1593 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCATCCC-TTTCATCTCAACCATCCT 66 TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCA-CCCTTTTCATCTCATCCATCCT * 1657 CTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTCTGCAATAAATCTGG 130 CTTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGG * * 1722 TCACAAGTCTGTTTATCGCTGCTCTTCTTGTGAATTGAACTTTCATATTAAATGTGCTTTGTTTA 195 TCACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTA * * 1787 CATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGAGCATGTTGCCCTTCAACATCCATTGATT 260 CATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTC-A-A--GA-TGA-- ** * 1852 CCCAC-TGAAAATAGTGATGAAAAACTAAAAGATGTTTCTAAGTGCTTTGGGTGCCGGGAACCAT 318 AACACTTG---A-A--GATG----A-T-----A-G----TAAGTGCTTTGGGTGTCGGGAACCAT * * * * * * * 1916 TACCAAATTATACACACTTTTCTCCTTG-CCGTGGATTTAACTTACACGAGAAATGCACTGAGAT 362 TAGCAAAGTATACACACTTTTCTCC-TGACTGTGGATTTAATTTACATGAGAAATGCGCTGAGCT * * * * 1980 TCCTTTCAAATTGAATCAT-ATGTGGCATCGC-AAGCATCCTCTTGTCCTACAA-TTTAGTAGCG 426 TCCTTTCAAACTGAATCTTGA-GTGCCATCGCGAA-CATCCTCTTGTTCTACAATTTTA-TAGCG * * * * 2042 AACGGCTCTCTTGCAAGATATGCTGCCAGGTAACAAAGCGAAGAGGATTTGGTTATGGTTGTTCT 488 AACGGCTCTCTTGCAAGATATGCTGCCAGGAAACAAGGCGAATAGGATTTGTTTATGGTTGTTCT 2107 CCTTGTAAGTTTGTTGTTCACATTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTAC 553 CCTTGTAAGTTTGTTGTTCACATTGAATGTGCATCACAATCACCATTACAAGTTATTAAGAGTAC * * 2172 AAATCATGAACATTCATTCACCTTGTT 618 AAATCATGAACATCCATTTACCTTGTT 2199 GTTGAGACAA Statistics Matches: 1267, Mismatches: 86, Indels: 55 0.90 0.06 0.04 Matches are distributed among these distances: 720 480 0.38 721 5 0.00 722 9 0.01 723 366 0.29 724 2 0.00 725 8 0.01 726 107 0.08 727 3 0.00 729 1 0.00 730 1 0.00 732 4 0.00 736 1 0.00 737 1 0.00 742 1 0.00 743 1 0.00 746 7 0.01 747 269 0.21 748 1 0.00 ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34 Consensus pattern (720 bp): TGCTCGAGGTGTGGGGAGAAGGTGTCTGCTCCATGTTTTTGCTGTGCAGAGCACTGTGGGTTTTA TCTTCATAAGGTATGTGCCGAGGCACCTTTGGAGCTTAATCACCCTTTTCATCTCATCCATCCTC TTCTTATGCAAAATGCACCTTATTCATCTGGAATGTACATTTGCAATTTTTGCAATAAATCTGGT CACAAGTCTGTTTATCGCTGCTCTACTTGTGAATTGGACTTTCATATTAAATGTGCTTTGTTTAC ATTTAATATTGCTGAGAATAATTTGAAAGAGCTTGACCATGTTGCCCTTCAAGATGAAACACTTG AAGATGATAGTAAGTGCTTTGGGTGTCGGGAACCATTAGCAAAGTATACACACTTTTCTCCTGAC TGTGGATTTAATTTACATGAGAAATGCGCTGAGCTTCCTTTCAAACTGAATCTTGAGTGCCATCG CGAACATCCTCTTGTTCTACAATTTTATAGCGAACGGCTCTCTTGCAAGATATGCTGCCAGGAAA CAAGGCGAATAGGATTTGTTTATGGTTGTTCTCCTTGTAAGTTTGTTGTTCACATTGAATGTGCA TCACAATCACCATTACAAGTTATTAAGAGTACAAATCATGAACATCCATTTACCTTGTTTAACGG GCACCAACATCCCCTGTTTCTTATGTTAAATCAAGAGCAGCTGATGGACAATCAAAGGGGTGTAA CTGAT Done.