Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009855.1 Corchorus capsularis cultivar CVL-1 contig09876, 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: 7793
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31


Found at i:4959 original size:21 final size:22

Alignment explanation


    Indices: 4915--4960  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4905 AGCTAGCTAA

                                  
       4915 TTAGAATCCAAACATAGTTTTT
          1 TTAGAATCCAAACATAGTTTTT

                                  
       4937 TTAGAATCCAAACATAGTTTTT
          1 TTAGAATCCAAACATAGTTTTT

              
       4959 TT
          1 TT

       4961 TTCCTCTGTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43


Consensus pattern (22 bp):   
TTAGAATCCAAACATAGTTTTT

Found at i:6959 original size:20 final size:20

Alignment explanation


    Indices: 6930--6969  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6920 TTTTAACTTA

                 *              
       6930 GCGCTCAAGCTAATATCAAT
          1 GCGCTAAAGCTAATATCAAT

                                
       6950 GCGCTAAAGCTAATATCAAT
          1 GCGCTAAAGCTAATATCAAT

       6970 CTAATATCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25


Consensus pattern (20 bp):   
GCGCTAAAGCTAATATCAAT

Found at i:7695 original size:17 final size:17

Alignment explanation


    Indices: 7669--7708  Score: 64
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       7659 TTAGTATACC

                             
       7669 TTATAT-AAATATATAT
          1 TTATATAAAATATATAT

                             
       7685 TTATATAAAATATATAT
          1 TTATATAAAATATATAT

            *      
       7702 ATATATA
          1 TTATATA

       7709 TATATATCAT


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

Matches are distributed among these distances:
  16    6  0.27
  17   16  0.73

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (17 bp):   
TTATATAAAATATATAT

Found at i:7726 original size:2 final size:2

Alignment explanation


    Indices: 7670--7715  Score: 58
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       7660 TAGTATACCT

                     *            *             *                         
       7670 TA TA TA AA TA TA TA TT TA TA TA -A AA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       7711 TA TA T
          1 TA TA T

       7716 CATGCATATA


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
   1    1  0.03
   2   37  0.97

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA
Done.