Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_32641

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, 651

Length: 1086
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27


Found at i:1010 original size:321 final size:315

Alignment explanation


    Indices: 423--1059  Score: 889
    Period size: 321  Copynumber: 2.0  Consensus size: 315

        413 GTTTCTTTAA

                  *                             *          * *            *  
        423 AGTTCTCACAAAAATCGACATCGAAAGAACACTATCGTTACCAGACAGCTACTTACAAGCTTTGC
          1 AGTTCTAACAAAAATCGACATCGAAAGAACACTATCATTACCAGACAACCACTTACAAGCTTCGC

                                        *  *           *               *     
        488 AACAATCACAACGGAGCCATGGAGGAAAGAAGTTGAAGGTTAAGGATGATATAGGAATCTTATGG
         66 AACAATCACAACGGAGCCATGGAGGAAAAAACTTGAAGGTTAAAGATGATATAGGAATCCTATGG

                   *        *   *  *             *                           
        553 AACTTTCGTTGCACAATACGGTCTGGGGCTGTTCGTAGACTCCACATAGTTTCCGGTTGGATCCA
        131 AACTTTCATTGCACAACACGATCCGGGGCTGTTCGTAAACTCCACATAGTTTCCGGTTGGATCCA

                             *      *                     *       *         *
        618 ATTTGTCCGGTTCAAACGGTTAAATACCGGTGATGCTATTGTTCTTTACAAAGATGATGATACAG
        196 ATTTGTCCGGTTCAAACAGTTAAACACCGGTGATGCTATTGTTCTTAACAAAGACGATGATACAC

                            *                                      
        683 TTACAGGTCCACATTATAAAATTGAAGTTGTCAAGGGCCATGGTGATAATTATTC
        261 TTACAGGTCCACATTACAAAATTGAAGTTGTCAAGGGCCATGGTGATAATTATTC

                     *                     *                  **             
        738 AGTTCTAACGAAAATCGACATCGAAAGAACATTATCATTACCAGACAACCGTTTACAAGCTTCGC
          1 AGTTCTAACAAAAATCGACATCGAAAGAACACTATCATTACCAGACAACCACTTACAAGCTTCGC

            *                                        *              * *      
        803 CACAATCACAACGGAGCCATGGAGATGGAGGAGAAAACTTGCAGGTTAAAGATGATGTCGGAATC
         66 AACAATCACAACGGAGCCAT-G-GA-GGA--A-AAAACTTGAAGGTTAAAGATGATATAGGAATC

                                *             *              *    *          
        868 CTATGGAACTTTCATTGCACTACACGATCCGGGGTTGTTCCG-AAACTCGACATGGTTTCCGGTT
        125 CTATGGAACTTTCATTGCACAACACGATCCGGGGCTGTT-CGTAAACTCCACATAGTTTCCGGTT

                                                      *                      
        932 GGATCCAATTTGTCCGGTTCAAACAGTTAAACACCGGTGATGTTATTGTTCTTAACAAAGACGAT
        189 GGATCCAATTTGTCCGGTTCAAACAGTTAAACACCGGTGATGCTATTGTTCTTAACAAAGACGAT

                                                *                 *       
        997 GATACACTTACAGGTCCACATTACAAAATTGAAGTTTTCAAGGGCCATGGTGATGATTATTC
        254 GATACACTTACAGGTCCACATTACAAAATTGAAGTTGTCAAGGGCCATGGTGATAATTATTC

             
       1059 A
          1 A

       1060 AGTTTTGTTC


Statistics
Matches: 280,  Mismatches: 35, Indels: 8
        0.87            0.11        0.02

Matches are distributed among these distances:
 315   75  0.27
 316    1  0.00
 317    2  0.01
 318    3  0.01
 320    1  0.00
 321  196  0.70
 322    2  0.01

ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27


Consensus pattern (315 bp):   
AGTTCTAACAAAAATCGACATCGAAAGAACACTATCATTACCAGACAACCACTTACAAGCTTCGC
AACAATCACAACGGAGCCATGGAGGAAAAAACTTGAAGGTTAAAGATGATATAGGAATCCTATGG
AACTTTCATTGCACAACACGATCCGGGGCTGTTCGTAAACTCCACATAGTTTCCGGTTGGATCCA
ATTTGTCCGGTTCAAACAGTTAAACACCGGTGATGCTATTGTTCTTAACAAAGACGATGATACAC
TTACAGGTCCACATTACAAAATTGAAGTTGTCAAGGGCCATGGTGATAATTATTC
Done.