Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09210

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: 2049
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22


Found at i:1244 original size:45 final size:45

Alignment explanation


    Indices: 1177--1514  Score: 328
    Period size: 45  Copynumber: 7.6  Consensus size: 45

       1167 TAAAAATGGT

                    *                                  * 
       1177 TCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATC
          1 TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

                    *        *                  *      * 
       1222 TCAGCTGAAAAGATGAACAAAGAGACAGCCTTGACAATAAATAAC
          1 TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

                                     **   **      *      
       1267 TCAGCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGTGAATAGC
          1 TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

                         *                         *   *  
       1312 TCAGCTGAGAAGACG-AGACAAGAGACAG-C-T-ACAGTTAATGGC
          1 TCAGCTGAGAAGATGAAGA-AAGAGACAGCCTTGACAGTAAATAGC

              *                       *              *   
       1354 TCGGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAGAGC
          1 TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

                *        *          *                   * 
       1399 TCGAAC-GAGAAGGTGAAGAAAGAAACAGCCTTGACAGTAAATAAC
          1 TC-AGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

              *         * *  *       **     *      *   *  
       1444 TCGGCTGAGAAGGTTAATAAAGAGATTG-CTTCACAAGTGAATGGC
          1 TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGAC-AGTAAATAGC

                             *        
       1489 TCAGCTGAGAAGATGAAAAAAGAGAC
          1 TCAGCTGAGAAGATGAAGAAAGAGAC

       1515 CACTGTGGCA


Statistics
Matches: 238,  Mismatches: 47, Indels: 16
        0.79            0.16        0.05

Matches are distributed among these distances:
  42   31  0.13
  43    4  0.02
  44   11  0.05
  45  191  0.80
  46    1  0.00

ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16


Consensus pattern (45 bp):   
TCAGCTGAGAAGATGAAGAAAGAGACAGCCTTGACAGTAAATAGC

Found at i:1467 original size:132 final size:135

Alignment explanation


    Indices: 1177--1514  Score: 312
    Period size: 132  Copynumber: 2.5  Consensus size: 135

       1167 TAAAAATGGT

                    *    *                   *      *   **         *        *
       1177 TCAGCTGAAAAGATGA-AGAAAGAGACAGCCTTGAC-AGTAAATATCTCAGCTGAAAAGATGAAC
          1 TCAGCTGAGAAGACGAGA-AAAGAGACAG-CTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAA

                                   *      *                   * **           
       1240 AAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAGGACAGT
         64 AAAGAGACAGCCTTGACAATAAAGAACTCAACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGT

            *    * 
       1305 GAATAGC
        129 AAATAAC

                              *                   *        *              *  
       1312 TCAGCTGAGAAGACGAGACAAGAGACAGC-T-AC-AGTTAATGGCTCGGCTGAGAAGATGAAGAA
          1 TCAGCTGAGAAGACGAGAAAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAAA

                  *         *      *              *                 **       
       1374 AGAGACGGCCTTGACAGTAAAGAGCTCGAAC-GAGAAGGTGAAGAAAGAAACAGCCTTGACAGTA
         66 AGAGACAGCCTTGACAATAAAGAACTC-AACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGTA

                  
       1438 AATAAC
        130 AATAAC

              *         ***           **                                     
       1444 TCGGCTGAGAAGGTTA-ATAAAGAGATTGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAA
          1 TCAGCTGAGAAGACGAGA-AAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAA

                   
       1508 AAGAGAC
         65 AAGAGAC

       1515 CACTGTGGCA


Statistics
Matches: 165,  Mismatches: 32, Indels: 12
        0.79            0.15        0.06

Matches are distributed among these distances:
 131    1  0.01
 132  100  0.61
 133    4  0.02
 134    3  0.02
 135   56  0.34
 136    1  0.01

ACGTcount: A:0.42, C:0.15, G:0.27, T:0.16


Consensus pattern (135 bp):   
TCAGCTGAGAAGACGAGAAAAGAGACAGCTTCACAAGTGAATGGCTCAGCTGAGAAGATGAAAAA
AGAGACAGCCTTGACAATAAAGAACTCAACTGAGAAGATGAAGAAAGAAACAGCCAGGACAGTAA
ATAAC

Found at i:1485 original size:177 final size:177

Alignment explanation


    Indices: 1171--1501  Score: 443
    Period size: 177  Copynumber: 1.9  Consensus size: 177

       1161 TCTGAATAAA

                 *                                         * *    *          
       1171 AATGGTTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAATATCTCAGCTGAAAAGAT
          1 AATGGCTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAAGAGCTCAACTGAAAAGAT

                     *                                                     * 
       1236 GAACAAAGAGACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAGGA
         66 GAACAAAGAAACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAGCA

                                                           
       1301 CAGTGAATAGCTCAGCTGAGAAGACGAGACAAGAGACAGCTACAGTT
        131 CAGTGAATAGCTCAGCTGAGAAGACGAGACAAGAGACAGCTACAGTT

                    *     *                 *                           *   *
       1348 AATGGCTCGGCTGAGAAGATGAAGAAAGAGACGGCCTTGACAGTAAAGAGCTCGAAC-GAGAAGG
          1 AATGGCTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAAGAGCTC-AACTGAAAAGA

                *                  *          *         * *  *        *      
       1412 TGAAGAAAGAAACAGCCTTGACAGTAAATAACTCGGCTGAGAAGGTTAATAAAGAGATTGCTTCA
         65 TGAACAAAGAAACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGC--CA

                       *               
       1477 -CA-AGTGAATGGCTCAGCTGAGAAGA
        128 GCACAGTGAATAGCTCAGCTGAGAAGA

       1502 TGAAAAAAGA


Statistics
Matches: 132,  Mismatches: 19, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 177  127  0.96
 178    3  0.02
 179    2  0.02

ACGTcount: A:0.41, C:0.15, G:0.27, T:0.16


Consensus pattern (177 bp):   
AATGGCTCAGCTGAAAAGATGAAGAAAGAGACAGCCTTGACAGTAAAGAGCTCAACTGAAAAGAT
GAACAAAGAAACAGCCTTGACAATAAATAACTCAGCTGAGAAGATGAAGAAAGAGATGGCCAGCA
CAGTGAATAGCTCAGCTGAGAAGACGAGACAAGAGACAGCTACAGTT

Done.