Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014718.1 Corchorus capsularis cultivar CVL-1 contig14739, 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: 15207
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:5569 original size:19 final size:18

Alignment explanation


    Indices: 5537--5574  Score: 58
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       5527 TTGAAATAAT

                     *        
       5537 TCTTCAATTGTCTTCAAA
          1 TCTTCAATTATCTTCAAA

                               
       5555 TCTTCAAATTATCTTCAAA
          1 TCTTC-AATTATCTTCAAA

             
       5574 T
          1 T

       5575 AATCTTCAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    5  0.28
  19   13  0.72

ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45


Consensus pattern (18 bp):   
TCTTCAATTATCTTCAAA

Found at i:5570 original size:11 final size:11

Alignment explanation


    Indices: 5553--5584  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       5543 ATTGTCTTCA

                       
       5553 AATCTTCAAAT
          1 AATCTTCAAAT

            *          
       5564 TATCTTCAAAT
          1 AATCTTCAAAT

                      
       5575 AATCTTCAAA
          1 AATCTTCAAA

       5585 CACGAACTTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38


Consensus pattern (11 bp):   
AATCTTCAAAT

Found at i:5581 original size:22 final size:22

Alignment explanation


    Indices: 5525--5584  Score: 65
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       5515 AATTATTACT

                *                 *
       5525 TCTTGAAATAATTCTTC-AATTG
          1 TCTTCAAATAA-TCTTCAAATTA

                                  
       5547 TCTTC--A-AATCTTCAAATTA
          1 TCTTCAAATAATCTTCAAATTA

                               
       5566 TCTTCAAATAATCTTCAAA
          1 TCTTCAAATAATCTTCAAA

       5585 CACGAACTTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  18    5  0.16
  19   11  0.34
  20    1  0.03
  21    1  0.03
  22   14  0.44

ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42


Consensus pattern (22 bp):   
TCTTCAAATAATCTTCAAATTA
Done.