Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014126.1 Corchorus capsularis cultivar CVL-1 contig14147, 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: 9124
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34


Found at i:2913 original size:27 final size:28

Alignment explanation


    Indices: 2869--2943  Score: 82
    Period size: 27  Copynumber: 2.8  Consensus size: 28

       2859 AAAGTGTGTT

                  *      *              
       2869 AAAAATTACCAAACTGCCCCTGAATGAG
          1 AAAAATGACCAAAATGCCCCTGAATGAG

             *                   * *  * 
       2897 -CAAATGACCAAAATG-CCCTTAGTGCG
          1 AAAAATGACCAAAATGCCCCTGAATGAG

                                 
       2923 AAAAATGACCAAAATGCCCCT
          1 AAAAATGACCAAAATGCCCCT

       2944 TAAGTGACAC


Statistics
Matches: 38,  Mismatches: 7, Indels: 4
        0.78            0.14        0.08

Matches are distributed among these distances:
  26    8  0.21
  27   26  0.68
  28    4  0.11

ACGTcount: A:0.41, C:0.27, G:0.15, T:0.17


Consensus pattern (28 bp):   
AAAAATGACCAAAATGCCCCTGAATGAG

Found at i:3660 original size:156 final size:155

Alignment explanation


    Indices: 3342--3662  Score: 448
    Period size: 156  Copynumber: 2.1  Consensus size: 155

       3332 TCTTATCAAA

                 *        **         *           *    *                 *    
       3342 TGCCCAGAGGACTTTTCAATGCAAATTCTGAATAGACGCCTTTGATCAAGAATTTTGAAACTATG
          1 TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGACACCTTCGATCAAGAATTTTGAAAATATG

                            *                                                
       3407 AAAAACTTGATGAAATGAAATGGTACCCAGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAAT
         66 AAAAACTTGATGAAATAAAATGGTACCCAGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAAT

             *         *          *  
       3472 TGATACCCGGAGGTTTCTGAATTTG
        131 TAATACCCGGAAGTTTCTGAATCTG

             **                                                *             
       3497 TATCCGGAGGACTTACCAATGCAAACTCTGAACT-GACACCTTCGATCAAGGATTTT-AAAATAT
          1 TGCCCGGAGGACTTACCAATGCAAACTCTGAA-TAGACACCTTCGATCAAGAATTTTGAAAATAT

                           *               *                                 
       3560 GATATAAACTTGATGGAATAAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCAG
         65 GA-A-AAACTTGATGAAATAAAATGGTACCCAGAGGTTTTACCAATTGCCCGGAGGACTTATCAG

                     *                  
       3625 AATTAATACTCGGAAGTTTCTGAATCTG
        128 AATTAATACCCGGAAGTTTCTGAATCTG

                      
       3653 TGCCCGGAGG
          1 TGCCCGGAGG

       3663 TTTCTGAATT


Statistics
Matches: 144,  Mismatches: 19, Indels: 5
        0.86            0.11        0.03

Matches are distributed among these distances:
 154    8  0.06
 155   46  0.32
 156   90  0.62

ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28


Consensus pattern (155 bp):   
TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGACACCTTCGATCAAGAATTTTGAAAATATG
AAAAACTTGATGAAATAAAATGGTACCCAGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAAT
TAATACCCGGAAGTTTCTGAATCTG

Found at i:3683 original size:22 final size:22

Alignment explanation


    Indices: 3635--3720  Score: 82
    Period size: 22  Copynumber: 3.8  Consensus size: 22

       3625 AATTAATACT

                *          *      
       3635 CGGAAGTTTCTGAATCTGTGCC
          1 CGGAGGTTTCTGAATTTGTGCC

                                  
       3657 CGGAGGTTTCTGAATTTGTGCC
          1 CGGAGGTTTCTGAATTTGTGCC

                         *     ****  
       3679 CGGAGGACTTATCAGAATTAACACC
          1 CGGAGG--TT-TCTGAATTTGTGCC

                             
       3704 CGGAGGTTTCTGAATTT
          1 CGGAGGTTTCTGAATTT

       3721 AAACCCGGAG


Statistics
Matches: 52,  Mismatches: 9, Indels: 6
        0.78            0.13        0.09

Matches are distributed among these distances:
  22   33  0.63
  23    2  0.04
  24    2  0.04
  25   15  0.29

ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31


Consensus pattern (22 bp):   
CGGAGGTTTCTGAATTTGTGCC

Found at i:3726 original size:22 final size:22

Alignment explanation


    Indices: 3655--3731  Score: 75
    Period size: 22  Copynumber: 3.4  Consensus size: 22

       3645 TGAATCTGTG

                               ***
       3655 CCCGGAGGTTTCTGAATTTGTG
          1 CCCGGAGGTTTCTGAATTTAAA

                           *          
       3677 CCCGGAGGACTTATCAGAA-TTAACA
          1 CCCGGAGG--TT-TCTGAATTTAA-A

                                  
       3702 CCCGGAGGTTTCTGAATTTAAA
          1 CCCGGAGGTTTCTGAATTTAAA

                    
       3724 CCCGGAGG
          1 CCCGGAGG

       3732 ACTTACCAAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 10
        0.75            0.08        0.17

Matches are distributed among these distances:
  22   22  0.49
  23    6  0.13
  24    4  0.09
  25   13  0.29

ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26


Consensus pattern (22 bp):   
CCCGGAGGTTTCTGAATTTAAA

Found at i:8381 original size:22 final size:22

Alignment explanation


    Indices: 8355--8449  Score: 84
    Period size: 22  Copynumber: 4.2  Consensus size: 22

       8345 ATTAATACCC

                                * 
       8355 GAGGTTTCTGAATTTCTGCCTG
          1 GAGGTTTCTGAATTTCTGCCCG

                           *      
       8377 GAGGTTTCTGAATTTGTGCCCG
          1 GAGGTTTCTGAATTTCTGCCCG

                       *      *  *    
       8399 GAGGACTTATCAGAATTAAC-ACCCG
          1 GAGG--TT-TCTGAATT-TCTGCCCG

                           * *    
       8424 GAGGTTTCTGAATTTGTACCCG
          1 GAGGTTTCTGAATTTCTGCCCG

                
       8446 GAGG
          1 GAGG

       8450 ACTTACCAAT


Statistics
Matches: 59,  Mismatches: 9, Indels: 10
        0.76            0.12        0.13

Matches are distributed among these distances:
  22   40  0.68
  23    2  0.03
  24    2  0.03
  25   15  0.25

ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32


Consensus pattern (22 bp):   
GAGGTTTCTGAATTTCTGCCCG
Done.