Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23085

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: 2172
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29


Found at i:530 original size:105 final size:102

Alignment explanation


    Indices: 421--875  Score: 389
    Period size: 105  Copynumber: 4.3  Consensus size: 102

        411 CTTTAATGCG

                             **                                              
        421 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCAT--TGCAA

                   *           *  * *   *           
        486 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACA
         64 GGAGAGGAT-ATTTCTGAAGCTGTAGATATAGTTCACACA

                                               *    *  *   *                 
        526 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACGTATAGTACATTAGTTGATGCGCATTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGAT--GCATTGCAA

                *    **          * *      *   *     
        591 GGAGGGGAGGGTTTCTGAAGCCGAAGATATTGTTGACACA
         64 GGAGAGGA-TATTTCTGAAGCTGTAGATATAGTTCACACA

                     *             *        *  *                             
        631 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGC--ATTGCAA

                            *                         
        696 GGAGAGGAGTATTTCTAAAGCTGTAGATACTA-TTGC-CACA
         64 GGAGAGGA-TATTTCTGAAGCTGTAGATA-TAGTT-CACACA

                          ** *                             ** *              
        736 ATGAGAAAGCAAGGTGTGGAGCCTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCA--TTGCAA

             *         *                 *  *          
        801 GAATG-GGATGGTTTCTGAAGCTG-A-ATGTATTGTCGACACA
         64 GGA-GAGGAT-ATTTCTGAAGCTGTAGATATAGT-TC-ACACA

                    *   *           *  *       
        841 ATGAGAAAACAATGCATTGAGCCTAATTTTGTCAC
          1 ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCAC

        876 ATACAGAACT


Statistics
Matches: 282,  Mismatches: 53, Indels: 30
        0.77            0.15        0.08

Matches are distributed among these distances:
 102    2  0.01
 103    7  0.02
 104    3  0.01
 105  264  0.94
 106    2  0.01
 107    4  0.01

ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29


Consensus pattern (102 bp):   
ATGAGAAAGCAAGGCATTGAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATTGCAAGG
AGAGGATATTTCTGAAGCTGTAGATATAGTTCACACA

Found at i:738 original size:210 final size:210

Alignment explanation


    Indices: 421--863  Score: 527
    Period size: 210  Copynumber: 2.1  Consensus size: 210

        411 CTTTAATGCG

                             **    *                                  *      
        421 ATGAGAAAGCAAGGCATCAAGCCTGATGTTGTCACCTATAATATATTGGTTGATGCATGGTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA

                            *  *  * *   *                            *       
        486 GGAGAGGCTAATTTCTGAATCTTTGGATGTAGTTCACACAATGAGAAAGCAAGGCATTGAGCCTG
         66 GGAGAGGCTAATTTCTAAAGCTGTAGATCTAGTTCACACAATGAGAAAGCAAGGCATGGAGCCTG

                      *    *          *     *         *                      
        551 ATGTTGTCACGTATAGTACA-TTAGTTGATGCGCATTGCAAGGAGGGGAGGGTTTCTGAAGCCGA
        131 ATGTTGTCACCTATAATACATTTA-TCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCCGA

                      *      
        615 A-GATATTGTTGACACA
        195 ATG-TATTGTCGACACA

                     *                      *  *                    *  *     
        631 ATGAGAAAGGAAGGCATTGAGCCCGATGTTGTGACGTATAATATATTGGTTGATGCGTATTGCAA
          1 ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA

                    *                                                **      
        696 GGAGAGGAGT-ATTTCTAAAGCTGTAGATACTA-TTGC-CACAATGAGAAAGCAAGGTGTGGAGC
         66 GGAGAGG-CTAATTTCTAAAGCTGTAGAT-CTAGTT-CACACAATGAGAAAGCAAGGCATGGAGC

                                 *              *         *    *            *
        758 CTGATGTTGTCACCTATAATATATTTATCGATGCACTTTGCAAGAATGGGATGGTTTCTGAAGCT
        128 CTGATGTTGTCACCTATAATACATTTATCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCC

                              
        823 GAATGTATTGTCGACACA
        193 GAATGTATTGTCGACACA

                    *   *          
        841 ATGAGAAAACAATGCATTGAGCC
          1 ATGAGAAAGCAAGGCATTGAGCC

        864 TAATTTTGTC


Statistics
Matches: 196,  Mismatches: 32, Indels: 10
        0.82            0.13        0.04

Matches are distributed among these distances:
 210  188  0.96
 211    8  0.04

ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28


Consensus pattern (210 bp):   
ATGAGAAAGCAAGGCATTGAGCCCGATGTTGTCACCTATAATATATTGGTTGATGCATAGTGCAA
GGAGAGGCTAATTTCTAAAGCTGTAGATCTAGTTCACACAATGAGAAAGCAAGGCATGGAGCCTG
ATGTTGTCACCTATAATACATTTATCGATGCACATTGCAAGAAGGGGAGGGTTTCTGAAGCCGAA
TGTATTGTCGACACA
Done.