Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001148.1 Corchorus capsularis cultivar CVL-1 contig01148, 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, 702

Length: 1170
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40


Found at i:653 original size:12 final size:13

Alignment explanation


    Indices: 612--656  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        602 AATTATTGTT

                         
        612 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
        625 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
        638 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
        650 TGCTTTA
          1 TGCTTTA

        657 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:664 original size:6 final size:6

Alignment explanation


    Indices: 653--685  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        643 TATAATCTGC

                                                  
        653 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT

        686 GCTTTGCTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (6 bp):   
TTTAGA

Found at i:1118 original size:61 final size:60

Alignment explanation


    Indices: 970--1120  Score: 234
    Period size: 61  Copynumber: 2.5  Consensus size: 60

        960 ATTTGTTTTG

                    *                                                     
        970 TTTTCCGTTTTTTTCTAAAAAAAAAAGA-TTTTTGCGTCGATAAAAAAAAAGTTTTTTGCGT
          1 TTTTCCG-ATTTTTCTAAAAAAAAAA-ATTTTTTGCGTCGATAAAAAAAAAGTTTTTTGCGT

                                                            *             
       1031 TTTTCCGATTTTTCTAAAAAAAAAAATTTTTTGCGTTCGAT-AAAAAACAGTTTTTTTGCGT
          1 TTTTCCGATTTTTCTAAAAAAAAAAATTTTTTGCG-TCGATAAAAAAAAAG-TTTTTTGCGT

                                         
       1092 TTTTCCGATTTTTCTAAAAAAAAAAATTT
          1 TTTTCCGATTTTTCTAAAAAAAAAAATTT

       1121 CCGTTTTTAA


Statistics
Matches: 85,  Mismatches: 2, Indels: 6
        0.91            0.02        0.06

Matches are distributed among these distances:
  59    1  0.01
  60   33  0.39
  61   51  0.60

ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44


Consensus pattern (60 bp):   
TTTTCCGATTTTTCTAAAAAAAAAAATTTTTTGCGTCGATAAAAAAAAAGTTTTTTGCGT
Done.