Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015040.1 Corchorus capsularis cultivar CVL-1 contig15061, 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: 8740
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:784 original size:156 final size:157

Alignment explanation


    Indices: 494--806  Score: 504
    Period size: 156  Copynumber: 2.0  Consensus size: 157

        484 CATTTCTCTC

                               *                  *                          
        494 CATTTTTTTATTATTGGATTTATAATATCCCATCATTATTTAATTTAGTTTAAACAATTCTCCTA
          1 CATTTTTTTATTATTGGATATATAATATCCCATCATTAATTAATTTAGTTTAAACAATTCTCCTA

                                                 *     *                     
        559 TTTGGAGTGTGAAACAGGATTGATTTTGTATTAATCAGAACCTGATGTGTTTAATAGAGAGACTA
         66 TTTGGAGTGTGAAACAGGATTGATTTTGTATTAATCAAAACCTAATGTGTTTAATAGAGAGACTA

                                       
        624 CGAGGGACTTGTATCGAAAA-GAAAAA
        131 CGAGGGACTTGTATCGAAAAGGAAAAA

                                           *                     *           
        650 CATTTTTTTATTATTGGATATATAATATCCCGTCATTAATTAATTTAGTTTAAGCAATTCTCCTA
          1 CATTTTTTTATTATTGGATATATAATATCCCATCATTAATTAATTTAGTTTAAACAATTCTCCTA

                    *                   *     *                         *    
        715 TTTGGAGTTTGAAACACGG-TTGATTTTTTATTAGTCAAAACCTAATGTGTTTAATAGAGGGACT
         66 TTTGGAGTGTGAAACA-GGATTGATTTTGTATTAATCAAAACCTAATGTGTTTAATAGAGAGACT

            *                           
        779 GCGAGGGACTTGTATCGAAAAGGAAAAA
        130 ACGAGGGACTTGTATCGAAAAGGAAAAA

        807 TGCATTCACG


Statistics
Matches: 144,  Mismatches: 11, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
 156  136  0.94
 157    8  0.06

ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38


Consensus pattern (157 bp):   
CATTTTTTTATTATTGGATATATAATATCCCATCATTAATTAATTTAGTTTAAACAATTCTCCTA
TTTGGAGTGTGAAACAGGATTGATTTTGTATTAATCAAAACCTAATGTGTTTAATAGAGAGACTA
CGAGGGACTTGTATCGAAAAGGAAAAA

Found at i:4635 original size:14 final size:15

Alignment explanation


    Indices: 4612--4640  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

       4602 TGGTGTCTCC

                           
       4612 ATCCTCCATTTAAAT
          1 ATCCTCCATTTAAAT

                           
       4627 ATCCT-CATTTAAAT
          1 ATCCTCCATTTAAAT

       4641 TTATGTTATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    9  0.64
  15    5  0.36

ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41


Consensus pattern (15 bp):   
ATCCTCCATTTAAAT

Found at i:7668 original size:31 final size:31

Alignment explanation


    Indices: 7630--7691  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7620 AAACCTTTTT

                       *                   
       7630 CTCTATTTCCGTGTCAACTAGGACCAAAACA
          1 CTCTATTTCCGCGTCAACTAGGACCAAAACA

                     *       *             
       7661 CTCTATTTCTGCGTCAATTAGGACCAAAACA
          1 CTCTATTTCCGCGTCAACTAGGACCAAAACA

       7692 GGTGGGAAGC


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.32, C:0.27, G:0.13, T:0.27


Consensus pattern (31 bp):   
CTCTATTTCCGCGTCAACTAGGACCAAAACA
Done.