Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_03867

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: 2379
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27


Found at i:1341 original size:54 final size:54

Alignment explanation


    Indices: 1283--1449  Score: 153
    Period size: 54  Copynumber: 3.1  Consensus size: 54

       1273 TTTCAGATTT

                                                       *          
       1283 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGCGATCAACTTC
          1 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC

                         *       *   *   *  *         *    * *        
       1337 CTAG-AGCGGAATTAACGT-CAACTCCTGATAAGG-TCATTATTGGAAACCAAACTT-
          1 CTAGAAG-GGAATCAAC-TCCCACTTCTGGT-GGGCTCATTACTGGAGATC-AACTTC

                                     *        **       *          
       1391 CTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTTGTTACTGGGGATCAACTTC
          1 CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC

                 
       1445 CTAGA
          1 CTAGA

       1450 GCGGAATTAA


Statistics
Matches: 84,  Mismatches: 21, Indels: 16
        0.69            0.17        0.13

Matches are distributed among these distances:
  53   10  0.12
  54   64  0.76
  55   10  0.12

ACGTcount: A:0.28, C:0.25, G:0.22, T:0.26


Consensus pattern (54 bp):   
CTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGAGATCAACTTC

Found at i:1421 original size:108 final size:108

Alignment explanation


    Indices: 1281--1514  Score: 380
    Period size: 108  Copynumber: 2.2  Consensus size: 108

       1271 GATTTCAGAT

                                       *                                     
       1281 TTCTAGAAGGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
          1 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG

                             *             *            
       1346 AATTAACGT-CAACTCCTGATAAGGTCATTATTGGAAACCAAAC
         66 AATTAACGTCCAA-TCCAGATAAGGTCATTACTGGAAACCAAAC

                                                **       *                   
       1389 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTTGTTACTGGGGATCAACTTCCTAGAGCGG
          1 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG

                  *                                    
       1454 AATTAATGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC
         66 AATTAACGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC

                    *         
       1497 TTCTAGAAAGGAATCAAC
          1 TTCTAGAAGGGAATCAAC

       1515 CATAACCCCT


Statistics
Matches: 117,  Mismatches: 8, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
 108  114  0.97
 109    3  0.03

ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25


Consensus pattern (108 bp):   
TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGCGATCAACTTCCTAGAGCGG
AATTAACGTCCAATCCAGATAAGGTCATTACTGGAAACCAAAC

Found at i:1503 original size:54 final size:54

Alignment explanation


    Indices: 1331--1503  Score: 126
    Period size: 54  Copynumber: 3.2  Consensus size: 54

       1321 ACTGGCGATC

                                 *                        *         
       1331 AACTTCCTAGAGCGGAATTAACGT-CAACTCCTGATAAGGTCATTATTGGAAACCA
          1 AACTTCCTAGAGCGGAATTAATGTCCAA-TCC-GATAAGGTCATTACTGGAAACCA

                               *     *    *    *  *    **       ** *  
       1386 AACTT-CTAGAAG-GGAATCAACT-CCCACTTCCGGT-GGGCTTGTTACTGGGGATC-
          1 AACTTCCTAG-AGCGGAATTAA-TGTCCA-ATCCGATAAGG-TCATTACTGGAAACCA

                                                                   
       1439 AACTTCCTAGAGCGGAATTAATGTCCAATCCAGATAAGGTCATTACTGGAAACCA
          1 AACTTCCTAGAGCGGAATTAATGTCCAATCC-GATAAGGTCATTACTGGAAACCA

                       
       1494 AACTT-CTAGA
          1 AACTTCCTAGA

       1504 AAGGAATCAA


Statistics
Matches: 85,  Mismatches: 22, Indels: 23
        0.65            0.17        0.18

Matches are distributed among these distances:
  53   13  0.15
  54   53  0.62
  55   19  0.22

ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25


Consensus pattern (54 bp):   
AACTTCCTAGAGCGGAATTAATGTCCAATCCGATAAGGTCATTACTGGAAACCA
Done.