Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011147.1 Corchorus capsularis cultivar CVL-1 contig11168, 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: 55190
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:9611 original size:29 final size:29

Alignment explanation


    Indices: 9579--9673  Score: 77
    Period size: 29  Copynumber: 3.2  Consensus size: 29

       9569 GGATTTTGAT

                  *                      
       9579 AGTTCAGGGGGTGAAAGTTCCAAATTAAA
          1 AGTTCAAGGGGTGAAAGTTCCAAATTAAA

                    *           *     *    *
       9608 AGTTCAAGAGG-GAAATTGTCCCAAGTTTAAT
          1 AGTTCAAGGGGTGAAA--GTTCCAA-ATTAAA

                      **                  
       9639 AGTAT-AAGGACTGAAAGTTCCAAATTAAA
          1 AGT-TCAAGGGGTGAAAGTTCCAAATTAAA

                  
       9668 AGTTCA
          1 AGTTCA

       9674 GGGAGGAAAA


Statistics
Matches: 49,  Mismatches: 11, Indels: 12
        0.68            0.15        0.17

Matches are distributed among these distances:
  28    5  0.10
  29   17  0.35
  30   12  0.24
  31   10  0.20
  32    5  0.10

ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26


Consensus pattern (29 bp):   
AGTTCAAGGGGTGAAAGTTCCAAATTAAA

Found at i:24435 original size:7 final size:7

Alignment explanation


    Indices: 24423--24456  Score: 68
    Period size: 7  Copynumber: 4.9  Consensus size: 7

      24413 AACAAACTCC

                   
      24423 CCACTAG
          1 CCACTAG

                   
      24430 CCACTAG
          1 CCACTAG

                   
      24437 CCACTAG
          1 CCACTAG

                   
      24444 CCACTAG
          1 CCACTAG

                  
      24451 CCACTA
          1 CCACTA

      24457 CCCTGCAAAT


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

Matches are distributed among these distances:
   7   27  1.00

ACGTcount: A:0.29, C:0.44, G:0.12, T:0.15


Consensus pattern (7 bp):   
CCACTAG

Found at i:26004 original size:12 final size:12

Alignment explanation


    Indices: 25982--26015  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

      25972 CAAAAGTTTA

                        
      25982 TAATA-ATATAG
          1 TAATATATATAG

                        
      25993 TAATATATATAG
          1 TAATATATATAG

              *        
      26005 TACTATATATA
          1 TAATATATATA

      26016 CAAAGATATG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11    5  0.24
  12   16  0.76

ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41


Consensus pattern (12 bp):   
TAATATATATAG
Done.