Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10001521

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: 13903
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1379 original size:49 final size:49

Alignment explanation


    Indices: 1322--1416  Score: 172
    Period size: 49  Copynumber: 1.9  Consensus size: 49

       1312 AAAATCAAGT

                                                             
       1322 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGGC
          1 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGGC

                             *          *                 
       1371 CTGATTCAAAATGTAGCGAGAGCAGGCTTAGGTGGATCAACCAGGA
          1 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGA

       1417 AAACATCGAG


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  49   44  1.00

ACGTcount: A:0.33, C:0.19, G:0.31, T:0.18


Consensus pattern (49 bp):   
CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGGC

Found at i:2560 original size:32 final size:33

Alignment explanation


    Indices: 2504--2565  Score: 90
    Period size: 32  Copynumber: 1.9  Consensus size: 33

       2494 TTGGGGCTTC

                      *    *                 
       2504 TTAAAAGAGTTTAATTAAAATTTTCAAAAAAAA
          1 TTAAAAGAGTATAATGAAAATTTTCAAAAAAAA

                             *            
       2537 TTAAAAG-GTATAATGAGAATTTTCAAAAA
          1 TTAAAAGAGTATAATGAAAATTTTCAAAAA

       2566 TTTGGGACCT


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  32   19  0.73
  33    7  0.27

ACGTcount: A:0.55, C:0.03, G:0.10, T:0.32


Consensus pattern (33 bp):   
TTAAAAGAGTATAATGAAAATTTTCAAAAAAAA

Found at i:3127 original size:4 final size:4

Alignment explanation


    Indices: 3118--3166  Score: 98
    Period size: 4  Copynumber: 12.2  Consensus size: 4

       3108 TGCTTGCACG

                                                                       
       3118 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
          1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA

             
       3166 C
          1 C

       3167 TTGGATGATG


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   45  1.00

ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24


Consensus pattern (4 bp):   
CATA

Found at i:3838 original size:28 final size:31

Alignment explanation


    Indices: 3797--3854  Score: 86
    Period size: 28  Copynumber: 2.0  Consensus size: 31

       3787 ATCTTAAATA

                          *                
       3797 ATTATAAAAAATTATTAAA-C-AATATTTAT
          1 ATTATAAAAAATTAATAAAGCGAATATTTAT

                                          
       3826 ATTA-AAAAAATTAATAAAGCGAATATTTA
          1 ATTATAAAAAATTAATAAAGCGAATATTTA

       3855 AAAAATTGAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28   13  0.50
  29    5  0.19
  30    8  0.31

ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36


Consensus pattern (31 bp):   
ATTATAAAAAATTAATAAAGCGAATATTTAT

Found at i:3881 original size:15 final size:15

Alignment explanation


    Indices: 3861--3889  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       3851 TTTAAAAAAT

                           
       3861 TGAATTAAATAAAGG
          1 TGAATTAAATAAAGG

                          
       3876 TGAATTAAATAAAG
          1 TGAATTAAATAAAG

       3890 AATGAAAGCA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28


Consensus pattern (15 bp):   
TGAATTAAATAAAGG

Found at i:11591 original size:28 final size:31

Alignment explanation


    Indices: 11550--11607  Score: 86
    Period size: 28  Copynumber: 2.0  Consensus size: 31

      11540 ATCTTAAATA

                          *                
      11550 ATTATAAAAAATTATTAAA-C-AATATTTAT
          1 ATTATAAAAAATTAATAAAGCAAATATTTAT

                                          
      11579 ATTA-AAAAAATTAATAAAGCAAATATTTA
          1 ATTATAAAAAATTAATAAAGCAAATATTTA

      11608 AAAAAATTGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28   13  0.50
  29    5  0.19
  30    8  0.31

ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36


Consensus pattern (31 bp):   
ATTATAAAAAATTAATAAAGCAAATATTTAT

Found at i:11608 original size:25 final size:24

Alignment explanation


    Indices: 11545--11615  Score: 70
    Period size: 28  Copynumber: 2.7  Consensus size: 24

      11535 TAGTTATCTT

                 *             *     
      11545 AAATAATTATAAAAAATTATTAAAC
          1 AAATATTTA-AAAAAATTAATAAAC

                                         
      11570 AATATTTATATTAAAAAAATTAATAAAGC
          1 AA-A--TAT-TTAAAAAAATTAATAAA-C

                             
      11599 AAATATTTAAAAAAATT
          1 AAATATTTAAAAAAATT

      11616 GAATTAAATA


Statistics
Matches: 39,  Mismatches: 2, Indels: 10
        0.76            0.04        0.20

Matches are distributed among these distances:
  25   13  0.33
  26    4  0.10
  28   16  0.41
  29    6  0.15

ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34


Consensus pattern (24 bp):   
AAATATTTAAAAAAATTAATAAAC
Done.