Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008824.1 Corchorus capsularis cultivar CVL-1 contig08845, 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: 4493
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35


Found at i:570 original size:14 final size:14

Alignment explanation


    Indices: 538--602  Score: 55
    Period size: 14  Copynumber: 4.6  Consensus size: 14

        528 ATTCAAAACC

                      *    
        538 TTTTTGAAAACTCA-
          1 TTTTTG-AAAGTCAT

                           
        552 TTTTTGAAAGTCATT
          1 TTTTTGAAAGTCA-T

                          
        567 TTTTTGAAAG-CAT
          1 TTTTTGAAAGTCAT

                      *    
        580 TTTCTTGAAAATC-T
          1 TTT-TTGAAAGTCAT

                *    
        594 TTTTCGAAA
          1 TTTTTGAAA

        603 ACATCTTTTG


Statistics
Matches: 44,  Mismatches: 3, Indels: 9
        0.79            0.05        0.16

Matches are distributed among these distances:
  13   15  0.34
  14   18  0.41
  15   11  0.25

ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48


Consensus pattern (14 bp):   
TTTTTGAAAGTCAT

Found at i:570 original size:15 final size:14

Alignment explanation


    Indices: 552--589  Score: 58
    Period size: 14  Copynumber: 2.6  Consensus size: 14

        542 TGAAAACTCA

                           
        552 TTTTTGAAAGTCATT
          1 TTTTTGAAAG-CATT

                          
        567 TTTTTGAAAGCATT
          1 TTTTTGAAAGCATT

              *      
        581 TTCTTGAAA
          1 TTTTTGAAA

        590 ATCTTTTTCG


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   12  0.55
  15   10  0.45

ACGTcount: A:0.29, C:0.08, G:0.13, T:0.50


Consensus pattern (14 bp):   
TTTTTGAAAGCATT

Found at i:672 original size:8 final size:8

Alignment explanation


    Indices: 659--689  Score: 53
    Period size: 8  Copynumber: 3.8  Consensus size: 8

        649 GTCACAATTC

                    
        659 TTTTTTCT
          1 TTTTTTCT

                    
        667 TTTTTTCT
          1 TTTTTTCT

                     
        675 TTTTTTACT
          1 TTTTTT-CT

                  
        684 TTTTTT
          1 TTTTTT

        690 TTTGGGCAAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   8   14  0.64
   9    8  0.36

ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87


Consensus pattern (8 bp):   
TTTTTTCT
Done.