Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19768

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, 940

Length: 1568
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22


Found at i:352 original size:15 final size:15

Alignment explanation


    Indices: 334--368  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        324 ACGGGGTCCA

                           
        334 TCTCCTAGGGTTGCC
          1 TCTCCTAGGGTTGCC

                          *
        349 TCTCCTAGGGTTGCT
          1 TCTCCTAGGGTTGCC

                 
        364 TCTCC
          1 TCTCC

        369 AAGAGCTGCT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.06, C:0.34, G:0.23, T:0.37


Consensus pattern (15 bp):   
TCTCCTAGGGTTGCC

Found at i:378 original size:15 final size:15

Alignment explanation


    Indices: 360--417  Score: 53
    Period size: 15  Copynumber: 3.7  Consensus size: 15

        350 CTCCTAGGGT

                           
        360 TGCTTCTCCAAGAGC
          1 TGCTTCTCCAAGAGC

                         *    
        375 TGCTTCCCCTCCACGAGC
          1 TGCTT---CTCCAAGAGC

               *  *  *     
        393 TGCATCCCCTAGAGC
          1 TGCTTCTCCAAGAGC

                      
        408 TGCTTCTCCA
          1 TGCTTCTCCA

        418 CCTCCACCTC


Statistics
Matches: 32,  Mismatches: 8, Indels: 6
        0.70            0.17        0.13

Matches are distributed among these distances:
  15   19  0.59
  18   13  0.41

ACGTcount: A:0.16, C:0.41, G:0.17, T:0.26


Consensus pattern (15 bp):   
TGCTTCTCCAAGAGC

Found at i:392 original size:18 final size:17

Alignment explanation


    Indices: 365--413  Score: 57
    Period size: 18  Copynumber: 2.9  Consensus size: 17

        355 AGGGTTGCTT

                              
        365 CTCCAAGAGCTGCTTCCC
          1 CTCC-AGAGCTGCTTCCC

                         *    
        383 CTCCACGAGCTGCATCCC
          1 CTCCA-GAGCTGCTTCCC

                           
        401 CT--AGAGCTGCTTC
          1 CTCCAGAGCTGCTTC

        414 TCCACCTCCA


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  15    9  0.32
  16    1  0.04
  17    1  0.04
  18   17  0.61

ACGTcount: A:0.16, C:0.43, G:0.18, T:0.22


Consensus pattern (17 bp):   
CTCCAGAGCTGCTTCCC

Found at i:458 original size:15 final size:15

Alignment explanation


    Indices: 438--484  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

        428 CACCCCACCC

                           
        438 CCTCGAGCTGCTTCT
          1 CCTCGAGCTGCTTCT

                   *       
        453 CCTCGAGTTGCTTCT
          1 CCTCGAGCTGCTTCT

              **   *       
        468 CCAAGAGGTGCTTCT
          1 CCTCGAGCTGCTTCT

              
        483 CC
          1 CC

        485 AAAACCTGCT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   28  1.00

ACGTcount: A:0.11, C:0.36, G:0.21, T:0.32


Consensus pattern (15 bp):   
CCTCGAGCTGCTTCT

Done.