Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_34824

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, 460

Length: 768
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22


Found at i:418 original size:30 final size:30

Alignment explanation


    Indices: 384--478  Score: 86
    Period size: 30  Copynumber: 3.2  Consensus size: 30

        374 AGAAAAACAA

                            *             
        384 CTACAATTACAACAACAACAACAACAATGG
          1 CTACAATTACAACAACTACAACAACAATGG

                  **     *  *              
        414 CTAC-ACCACAAGTAAGTACAACAACAATGG
          1 CTACAATTACAA-CAACTACAACAACAATGG

                 *      *  *               
        444 CTACACTCT-CAGCAGCTACAACAACAATGG
          1 CTACAAT-TACAACAACTACAACAACAATGG

                 
        474 CTACA
          1 CTACA

        479 GCGGGAACTA


Statistics
Matches: 50,  Mismatches: 12, Indels: 6
        0.74            0.18        0.09

Matches are distributed among these distances:
  29    5  0.10
  30   43  0.86
  31    2  0.04

ACGTcount: A:0.45, C:0.29, G:0.11, T:0.15


Consensus pattern (30 bp):   
CTACAATTACAACAACTACAACAACAATGG

Found at i:489 original size:27 final size:27

Alignment explanation


    Indices: 395--527  Score: 95
    Period size: 30  Copynumber: 4.7  Consensus size: 27

        385 TACAATTACA

                 *                      *
        395 ACAACAACAACAACAATGGCTACACCACA
          1 ACAACTACAACAACAATGGCTACA--ACG

              *  *                    *  *
        424 AGTAAGTACAACAACAATGGCTACACTCTC
          1 A-CAACTACAACAACAATGGCTACA-AC-G

                *                    *  
        454 AGCAGCTACAACAACAATGGCTACAGCG
          1 A-CAACTACAACAACAATGGCTACAACG

            **          *      *     * 
        482 GGAACTACAACACCAATGGGTACAATG
          1 ACAACTACAACAACAATGGCTACAACG

                               
        509 ACAACTACAACAACAATGG
          1 ACAACTACAACAACAATGG

        528 GTATGAGACA


Statistics
Matches: 82,  Mismatches: 20, Indels: 6
        0.76            0.19        0.06

Matches are distributed among these distances:
  27   36  0.44
  29    4  0.05
  30   42  0.51

ACGTcount: A:0.44, C:0.28, G:0.15, T:0.13


Consensus pattern (27 bp):   
ACAACTACAACAACAATGGCTACAACG

Found at i:528 original size:27 final size:27

Alignment explanation


    Indices: 459--530  Score: 90
    Period size: 27  Copynumber: 2.7  Consensus size: 27

        449 CTCTCAGCAG

                           *    *  **  
        459 CTACAACAACAATGGCTACAGCGGGAA
          1 CTACAACAACAATGGGTACAACGACAA

                    *            *     
        486 CTACAACACCAATGGGTACAATGACAA
          1 CTACAACAACAATGGGTACAACGACAA

                              
        513 CTACAACAACAATGGGTA
          1 CTACAACAACAATGGGTA

        531 TGAGACAGAG


Statistics
Matches: 38,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14


Consensus pattern (27 bp):   
CTACAACAACAATGGGTACAACGACAA
Done.