Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007237.1 Corchorus capsularis cultivar CVL-1 contig07258, 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: 29809
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:542 original size:166 final size:167

Alignment explanation


    Indices: 246--577  Score: 452
    Period size: 166  Copynumber: 2.0  Consensus size: 167

        236 AAATGTCCTA

                 *                  *           *           * **     *       
        246 AACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGACTTGCTTTTGGAGTTAGAGAA
          1 AACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGACTTGATGATGGAGCTAGAGAA

              * **            *       *                                      
        311 CTTATTTTTTTCGTCTTTTCCTACTTTGCAGATTACTTAAATGTCCTAACTTTTGATTATTGAGG
         66 CTAACATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTATTGAGG

             *         *   *                     
        376 GGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATG
        131 GAATTAAATAACTAAACTTTTTGGTCATTTCTCAATG

                                         *        *                        * 
        413 AACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGA-TTGATGAT-GAGCTAGATA
          1 AACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAA-GACTTGATGATGGAGCTAGAGA

                                                              *    *   *     
        476 ACTAACATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCTTGAG
         65 ACTAACATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTATTGAG

                                                 
        541 GGAATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
        130 GGAATTAAATAACTAAACTTTTTGGTCATTTCTCAAT

        578 TGACAAATGA


Statistics
Matches: 143,  Mismatches: 21, Indels: 3
        0.86            0.13        0.02

Matches are distributed among these distances:
 166   99  0.69
 167   42  0.29
 168    2  0.01

ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39


Consensus pattern (167 bp):   
AACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGACTTGATGATGGAGCTAGAGAA
CTAACATTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTATTGAGG
GAATTAAATAACTAAACTTTTTGGTCATTTCTCAATG

Found at i:5340 original size:33 final size:33

Alignment explanation


    Indices: 5285--5408  Score: 142
    Period size: 33  Copynumber: 3.7  Consensus size: 33

       5275 CCGCGCAACA

                             *                 
       5285 CCGGCCACAAGACCGGCTACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT

                                              
       5320 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT

                 *           **    **  *    *
       5353 CCGGCTACAACCGGCCAAACGACCCGGCCATGC
          1 CCGGCCACAACCGGCCACGCGACATGGACATGT

                                   
       5386 CCGGCCACAACCGGCCACGCGAC
          1 CCGGCCACAACCGGCCACGCGAC

       5409 CCTTTGTCTA


Statistics
Matches: 76,  Mismatches: 11, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  32    1  0.01
  33   67  0.88
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.42, G:0.27, T:0.08


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGT

Found at i:10734 original size:15 final size:15

Alignment explanation


    Indices: 10693--10741  Score: 62
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      10683 TTTGCTCAAC

                 *    *    
      10693 TTACATAACAAATAT
          1 TTACAAAACATATAT

                             
      10708 TTATCAAGAACATATAT
          1 TTA-CAA-AACATATAT

                           
      10725 TTACAAAACATATAT
          1 TTACAAAACATATAT

              
      10740 TT
          1 TT

      10742 CACTTCAAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  15   14  0.47
  16    5  0.17
  17   11  0.37

ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37


Consensus pattern (15 bp):   
TTACAAAACATATAT

Found at i:25467 original size:13 final size:13

Alignment explanation


    Indices: 25446--25475  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      25436 GGTGAGTACG

                *        
      25446 GCATGGCATGGGT
          1 GCATAGCATGGGT

                         
      25459 GCATAGCATGGGT
          1 GCATAGCATGGGT

                
      25472 GCAT
          1 GCAT

      25476 GGGTGTTGGT


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23


Consensus pattern (13 bp):   
GCATAGCATGGGT
Done.