Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004858.1 Corchorus capsularis cultivar CVL-1 contig04876, 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: 15906
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32


Found at i:1483 original size:2 final size:2

Alignment explanation


    Indices: 1476--1505  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1466 CTTGTCACGC

                                                *       
       1476 TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1506 GTGAGTTAAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:1559 original size:6 final size:6

Alignment explanation


    Indices: 1542--1572  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       1532 GTGCCGCTTA

                    *                           
       1542 GAGTTG GGGTTG GAGTTG GAGTTG GAGTTG G
          1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG G

       1573 TGGATGAGAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.13, C:0.00, G:0.55, T:0.32


Consensus pattern (6 bp):   
GAGTTG

Found at i:7080 original size:17 final size:17

Alignment explanation


    Indices: 7058--7092  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7048 GGGTGATGAC

                      *      
       7058 CACCCCTTCCTACCCCT
          1 CACCCCTTCCAACCCCT

                    *        
       7075 CACCCCTTGCAACCCCT
          1 CACCCCTTCCAACCCCT

             
       7092 C
          1 C

       7093 TAACCAAACA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.14, C:0.63, G:0.03, T:0.20


Consensus pattern (17 bp):   
CACCCCTTCCAACCCCT

Found at i:15333 original size:167 final size:165

Alignment explanation


    Indices: 15001--15481  Score: 569
    Period size: 167  Copynumber: 2.9  Consensus size: 165

      14991 GAATAAACAT

                                      ** *   *    *    *   *                 
      15001 GTGGAATT-ACTAAAAGATC-CCACCCCGGATTAATGAGGAGTGAGATAACTAAT-TTTTTCGTC
          1 GTGGAATTAAC-AAAAGATCTCCACCAAGCATTGATGATGAGTTAGAGAACTAATCTTTTTCGTC

                  *        *                              *                  
      15063 TTTTCCCACTTGGCATATTACTTAAATGTCCTAACTTTTGATTCTTTAGGGGATTAAATAACTAG
         65 TTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-

                                 *     *         
      15128 ACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
        129 ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA

                     *                    *  ** **               ** *      * 
      15165 GTGGAATTACCAAAAGATC-CCTACCAAGCCTTTCTTTTGGAGTTAGAGAACTTTTTTTTTTGGG
          1 GTGGAATTAACAAAAGATCTCC-ACCAAGCATTGATGAT-GAGTTAGAGAACTAATCTTTTT-CG

                             *                                              *
      15229 TCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAA-TTTCTGATTCTTGA-GGGATTAAATAAG
         63 TCTTTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTT-TGATTCTTGAGGGGATTAAATAAC

                                                    
      15292 TAATCTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA
        127 TAA-CTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA

                      *            *    *                                    
      15332 GTGGAATTAATAAAAGATCTCCATCAAGGATTGATGATGAGTTAGAGAACTAATCTTTTTCGTCT
          1 GTGGAATTAACAAAAGATCTCCACCAAGCATTGATGATGAGTTAGAGAACTAATCTTTTTCGTCT

              *        *                                          *          
      15397 TTACCTACTTGACAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTGAATAACTAAA
         66 TTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AA

                     *          
      15462 CTTTTTGGTTATTTCTCAAT
        130 CTTTTTGGTCATTTCTCAAT

      15482 TGACAAATGA


Statistics
Matches: 266,  Mismatches: 40, Indels: 20
        0.82            0.12        0.06

Matches are distributed among these distances:
 164   18  0.07
 165   52  0.20
 166   66  0.25
 167   84  0.32
 168   46  0.17

ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39


Consensus pattern (165 bp):   
GTGGAATTAACAAAAGATCTCCACCAAGCATTGATGATGAGTTAGAGAACTAATCTTTTTCGTCT
TTTCCTACTTGGCAAATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAC
TTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA

Found at i:15670 original size:17 final size:17

Alignment explanation


    Indices: 15650--15683  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      15640 TTCTCTCGTC

                 *           
      15650 GATTATTTTTTGAAAAA
          1 GATTACTTTTTGAAAAA

                             
      15667 GATTACTTTTTGAAAAA
          1 GATTACTTTTTGAAAAA

      15684 TATGTACCTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44


Consensus pattern (17 bp):   
GATTACTTTTTGAAAAA

Found at i:15883 original size:2 final size:2

Alignment explanation


    Indices: 15871--15906  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      15861 ACAATCTTAG

                                                                   
      15871 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.