Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008813.1 Corchorus capsularis cultivar CVL-1 contig08834, whole genome shotgun sequence

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: 5262
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27


Found at i:652 original size:33 final size:32

Alignment explanation


    Indices: 615--722  Score: 110
    Period size: 33  Copynumber: 3.3  Consensus size: 32

        605 GCTGAGTCAA

                                   **         
        615 GTGGCCGGGTG-TGACCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGATG-CCGGGCATCTCCATGTCGC

                               *             
        648 GTGGCCGGTGATGGCCGGGAATCTCCATGTCGC
          1 GTGGCCGGTGAT-GCCGGGCATCTCCATGTCGC

            * *       *                *     
        681 ATTGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGATGC-CGGGCATCTCCATGTCGC

                     
        714 GTGGCCGGT
          1 GTGGCCGGT

        723 CACTCGCGCC


Statistics
Matches: 62,  Mismatches: 10, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  32    6  0.10
  33   55  0.89
  34    1  0.02

ACGTcount: A:0.10, C:0.28, G:0.41, T:0.21


Consensus pattern (32 bp):   
GTGGCCGGTGATGCCGGGCATCTCCATGTCGC

Found at i:2567 original size:17 final size:16

Alignment explanation


    Indices: 2547--2603  Score: 52
    Period size: 15  Copynumber: 3.7  Consensus size: 16

       2537 AAGAAAAGGG

                             
       2547 GTTTTTCTCAAAAAAAA
          1 GTTTTT-TCAAAAAAAA

                             
       2564 G-TTTTT-AAAGAAAAA
          1 GTTTTTTCAAA-AAAAA

                             
       2579 -TTGTTTTC-AAAAAAA
          1 GTT-TTTTCAAAAAAAA

                       
       2594 G-TTTTTCAAA
          1 GTTTTTTCAAA

       2604 TGCAAGTGCA


Statistics
Matches: 34,  Mismatches: 0, Indels: 14
        0.71            0.00        0.29

Matches are distributed among these distances:
  14    8  0.24
  15   15  0.44
  16   10  0.29
  17    1  0.03

ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39


Consensus pattern (16 bp):   
GTTTTTTCAAAAAAAA

Found at i:2599 original size:14 final size:14

Alignment explanation


    Indices: 2557--2603  Score: 58
    Period size: 15  Copynumber: 3.2  Consensus size: 14

       2547 GTTTTTCTCA

                         *
       2557 AAAAAAAGTTTTTA
          1 AAAAAAAGTTTTTC

                    *       
       2571 AAGAAAAATTGTTTTC
          1 AA-AAAAAGT-TTTTC

                          
       2587 AAAAAAAGTTTTTC
          1 AAAAAAAGTTTTTC

               
       2601 AAA
          1 AAA

       2604 TGCAAGTGCA


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  14   10  0.36
  15   12  0.43
  16    6  0.21

ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34


Consensus pattern (14 bp):   
AAAAAAAGTTTTTC

Found at i:4124 original size:45 final size:44

Alignment explanation


    Indices: 4074--4177  Score: 136
    Period size: 45  Copynumber: 2.3  Consensus size: 44

       4064 TTCAATAAGA

                                 *                       
       4074 TTATCAAAGTCGACCCCAAAATAGGTCTCGCTCAGTTTTCAGCAG
          1 TTATCAAAGTCGACCCCAAAACAGGTCTCGCTCAG-TTTCAGCAG

                      *    *  *         ***             
       4119 TTATCAAAGTTGACCTCAGAACAGGTCTTTTTCAGTTTCAGCAG
          1 TTATCAAAGTCGACCCCAAAACAGGTCTCGCTCAGTTTCAGCAG

                           
       4163 TTATCAAAGTCGACC
          1 TTATCAAAGTCGACC

       4178 ACAGACTACT


Statistics
Matches: 51,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  44   23  0.45
  45   28  0.55

ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30


Consensus pattern (44 bp):   
TTATCAAAGTCGACCCCAAAACAGGTCTCGCTCAGTTTCAGCAG

Found at i:4619 original size:33 final size:33

Alignment explanation


    Indices: 4574--4642  Score: 120
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       4564 TGATGTGTAC

                                       *     
       4574 TTTTGGCATTTTTTGCATCTCAATATTTTTGCA
          1 TTTTGGCATTTTTTGCATCTCAATATTCTTGCA

                   *                         
       4607 TTTTGGCGTTTTTTGCATCTCAATATTCTTGCA
          1 TTTTGGCATTTTTTGCATCTCAATATTCTTGCA

               
       4640 TTT
          1 TTT

       4643 CAGTCACATA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.16, C:0.16, G:0.13, T:0.55


Consensus pattern (33 bp):   
TTTTGGCATTTTTTGCATCTCAATATTCTTGCA
Done.