Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007184.1 Corchorus capsularis cultivar CVL-1 contig07205, 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: 18562
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2379 original size:2 final size:2

Alignment explanation


    Indices: 2372--2399  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       2362 AACAATTTTC

                                                     
       2372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2400 GCTACTTTGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2678 original size:32 final size:32

Alignment explanation


    Indices: 2584--2678  Score: 127
    Period size: 32  Copynumber: 3.0  Consensus size: 32

       2574 GGGTATATTT

                    *                 *** * 
       2584 TTATATAGTGGCGTCTAAAGAACAAAGTGCAC
          1 TTATATAGCGGCGTCTAAAGAACAAAACACCC

                     *  *                   
       2616 TTATATAGCAGCATCTAAAGAACAAAACACCC
          1 TTATATAGCGGCGTCTAAAGAACAAAACACCC

                                           
       2648 TTATATAGCGGCGTCTAAAGAACAAAACACC
          1 TTATATAGCGGCGTCTAAAGAACAAAACACC

       2679 GCTATATTTA


Statistics
Matches: 54,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  32   54  1.00

ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21


Consensus pattern (32 bp):   
TTATATAGCGGCGTCTAAAGAACAAAACACCC

Found at i:4915 original size:21 final size:21

Alignment explanation


    Indices: 4889--4935  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       4879 TAATATTCAT

                                 
       4889 GTAATAAATAAATTTACATAA
          1 GTAATAAATAAATTTACATAA

                            *    
       4910 GTAATAAATAAATTTATATAA
          1 GTAATAAATAAATTTACATAA

                 
       4931 GTAAT
          1 GTAAT

       4936 TTCTTATATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36


Consensus pattern (21 bp):   
GTAATAAATAAATTTACATAA

Found at i:18219 original size:20 final size:19

Alignment explanation


    Indices: 18179--18216  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      18169 TTGTGACAAA

                       *   *   
      18179 AAAATAGCCACGTGGCATT
          1 AAAATAGCCACATGGAATT

                               
      18198 AAAATAGCCACATGGAATT
          1 AAAATAGCCACATGGAATT

      18217 TAATGAATTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21


Consensus pattern (19 bp):   
AAAATAGCCACATGGAATT

Found at i:18352 original size:21 final size:22

Alignment explanation


    Indices: 18326--18371  Score: 58
    Period size: 21  Copynumber: 2.1  Consensus size: 22

      18316 AAAAAAGGGG

                   **        *    
      18326 TTTGCTATTTACCG-CCTCCCT
          1 TTTGCTAAATACCGCCCCCCCT

                                  
      18347 TTTGCTAAATACCGCCCCCCCT
          1 TTTGCTAAATACCGCCCCCCCT

               
      18369 TTT
          1 TTT

      18372 TATAATTTTT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.13, C:0.39, G:0.09, T:0.39


Consensus pattern (22 bp):   
TTTGCTAAATACCGCCCCCCCT

Found at i:18546 original size:10 final size:9

Alignment explanation


    Indices: 18510--18545  Score: 56
    Period size: 10  Copynumber: 4.0  Consensus size: 9

      18500 AAAAAATCTT

                     
      18510 TTAAAAAAA
          1 TTAAAAAAA

                      
      18519 TTTAAAAAAA
          1 -TTAAAAAAA

                     
      18529 TT-AAAAAA
          1 TTAAAAAAA

                     
      18537 TTAAAAAAA
          1 TTAAAAAAA

      18546 AAAGAAAATG


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   8    8  0.32
   9    8  0.32
  10    9  0.36

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (9 bp):   
TTAAAAAAA

Found at i:18553 original size:17 final size:17

Alignment explanation


    Indices: 18511--18554  Score: 54
    Period size: 17  Copynumber: 2.5  Consensus size: 17

      18501 AAAAATCTTT

                              
      18511 TAAAAAAATTTAAAAAAA
          1 TAAAAAAA-TTAAAAAAA

             *               
      18529 TTAAAAAATTAAAAAAA
          1 TAAAAAAATTAAAAAAA

                      
      18546 -AAAGAAAAT
          1 TAAA-AAAAT

      18555 GGCGGAGC


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  16    2  0.09
  17   14  0.61
  18    7  0.30

ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20


Consensus pattern (17 bp):   
TAAAAAAATTAAAAAAA

Done.