Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013107.1 Corchorus capsularis cultivar CVL-1 contig13128, 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: 5161
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36


Found at i:1814 original size:166 final size:164

Alignment explanation


    Indices: 1547--1854  Score: 458
    Period size: 166  Copynumber: 1.9  Consensus size: 164

       1537 ATGTGGAATC

                         *                        *                   *      
       1547 ACTAAAAGATCCCTACCCCAGATTAATGAGCAGCGAGATAACTAATTTTTTCATCTTTTCCCACT
          1 ACTAAAAGATCCCAACCCCAGATTAATGAGCAGCGAGAGAACTAATTTTTTCATCTTTACCCACT

                                    *                             *          
       1612 TGACAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAGACTTTTTGGT
         66 TGACAGATTACTTAAATGTCCTAAATTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGT

                                              
       1677 CATTTCTCAATTAACTTTAATAGAGTATGAAATT
        131 CATTTCTCAATTAACTTTAATAGAGTATGAAATT

                  *            *                                    *        
       1711 ACTAAATGATCCCAACCCCGGATTAATGATG-AGCTG-GAGAACTAATTTTTTTCCGTCTTTACC
          1 ACTAAAAGATCCCAACCCCAGATTAATGA-GCAGC-GAGAGAACTAA-TTTTTT-CATCTTTACC

            *     **                         *                               
       1774 TACTTGGTAGATTACTTAAATGTCCTAAATTTTTATTCTTGAGGGGATTAAATAACTAAACTTTT
         62 CACTTGACAGATTACTTAAATGTCCTAAATTTTGATTCTTGAGGGGATTAAATAACTAAACTTTT

                            
       1839 TGGTCATTTCTCAATT
        127 TGGTCATTTCTCAATT

       1855 GACAAATGAC


Statistics
Matches: 128,  Mismatches: 12, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 164   37  0.29
 165    8  0.06
 166   83  0.65

ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38


Consensus pattern (164 bp):   
ACTAAAAGATCCCAACCCCAGATTAATGAGCAGCGAGAGAACTAATTTTTTCATCTTTACCCACT
TGACAGATTACTTAAATGTCCTAAATTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGT
CATTTCTCAATTAACTTTAATAGAGTATGAAATT

Found at i:3774 original size:5 final size:5

Alignment explanation


    Indices: 3764--3789  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       3754 TGAGATTTAC

                                           
       3764 TTCTT TTCTT TTCTT TTCTT TTCTT T
          1 TTCTT TTCTT TTCTT TTCTT TTCTT T

       3790 CCATTCTCAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (5 bp):   
TTCTT

Done.