Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_25827

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, 500

Length: 834
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27


Found at i:514 original size:15 final size:15

Alignment explanation


    Indices: 494--548  Score: 56
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        484 CCCAACCAGC

                           
        494 TTCTTCCGCCGCCCA
          1 TTCTTCCGCCGCCCA

                   *    *    
        509 TTCTTCCTCCAAACCCA
          1 TTCTTCCGCC--GCCCA

                 *          
        526 CTTCTGCCGCCGCCCA
          1 -TTCTTCCGCCGCCCA

                   
        542 TTCTTCC
          1 TTCTTCC

        549 TCCAAACCCG


Statistics
Matches: 31,  Mismatches: 6, Indels: 6
        0.72            0.14        0.14

Matches are distributed among these distances:
  15   15  0.48
  16    4  0.13
  17    4  0.13
  18    8  0.26

ACGTcount: A:0.11, C:0.51, G:0.09, T:0.29


Consensus pattern (15 bp):   
TTCTTCCGCCGCCCA

Found at i:530 original size:18 final size:17

Alignment explanation


    Indices: 505--557  Score: 56
    Period size: 15  Copynumber: 3.2  Consensus size: 17

        495 TCTTCCGCCG

                             
        505 CCCATTCTTCCTCCAAA
          1 CCCATTCTTCCTCCAAA

                     *  *    *
        522 CCCACTTCTGCCGCC--G
          1 CCCA-TTCTTCCTCCAAA

                             
        538 CCCATTCTTCCTCCAAA
          1 CCCATTCTTCCTCCAAA

               
        555 CCC
          1 CCC

        558 GCTTCTGCCA


Statistics
Matches: 27,  Mismatches: 6, Indels: 6
        0.69            0.15        0.15

Matches are distributed among these distances:
  15    8  0.30
  16    4  0.15
  17    7  0.26
  18    8  0.30

ACGTcount: A:0.17, C:0.53, G:0.06, T:0.25


Consensus pattern (17 bp):   
CCCATTCTTCCTCCAAA

Found at i:536 original size:33 final size:33

Alignment explanation


    Indices: 493--602  Score: 132
    Period size: 33  Copynumber: 3.3  Consensus size: 33

        483 TCCCAACCAG

                 *                           
        493 CTTCTTCCGCCGCCCATTCTTCCTCCAAACCCA
          1 CTTCTGCCGCCGCCCATTCTTCCTCCAAACCCA

                                            *
        526 CTTCTGCCGCCGCCCATTCTTCCTCCAAACCCG
          1 CTTCTGCCGCCGCCCATTCTTCCTCCAAACCCA

                    *        **  *            
        559 CTTCTGCCACC-CCCAGCGCTCCCTCCAAACCCA
          1 CTTCTGCCGCCGCCCA-TTCTTCCTCCAAACCCA

            *   *      
        592 TTTCAGCCGCC
          1 CTTCTGCCGCC

        603 ACCAGCTCCA


Statistics
Matches: 66,  Mismatches: 10, Indels: 2
        0.85            0.13        0.03

Matches are distributed among these distances:
  32    4  0.06
  33   62  0.94

ACGTcount: A:0.15, C:0.53, G:0.10, T:0.23


Consensus pattern (33 bp):   
CTTCTGCCGCCGCCCATTCTTCCTCCAAACCCA

Found at i:622 original size:36 final size:36

Alignment explanation


    Indices: 582--680  Score: 162
    Period size: 36  Copynumber: 2.8  Consensus size: 36

        572 CAGCGCTCCC

                        *     *                 
        582 TCCAAACCCATTTCAGCCGCCACCAGCTCCACTAGT
          1 TCCAAACCCATTGCAGCCTCCACCAGCTCCACTAGT

                                                
        618 TCCAAACCCATTGCAGCCTCCACCAGCTCCACTAGT
          1 TCCAAACCCATTGCAGCCTCCACCAGCTCCACTAGT

                *                *     
        654 TCCAGACCCATTGCAGCCTCCTCCAGC
          1 TCCAAACCCATTGCAGCCTCCACCAGC

        681 ACCTGCAGCA


Statistics
Matches: 59,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  36   59  1.00

ACGTcount: A:0.23, C:0.45, G:0.12, T:0.19


Consensus pattern (36 bp):   
TCCAAACCCATTGCAGCCTCCACCAGCTCCACTAGT
Done.