Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001893.1 Corchorus capsularis cultivar CVL-1 contig01895, 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: 1964
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:520 original size:26 final size:26

Alignment explanation


    Indices: 491--558  Score: 109
    Period size: 26  Copynumber: 2.6  Consensus size: 26

        481 TTCCTTCATT

                                      
        491 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *            *       
        517 TTAATAATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
        543 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

        559 AAACTAAGTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  26   38  1.00

ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA

Found at i:582 original size:52 final size:51

Alignment explanation


    Indices: 491--608  Score: 122
    Period size: 52  Copynumber: 2.4  Consensus size: 51

        481 TTCCTTCATT

                *                                         *     
        491 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
          1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA

                                    *      *    *                
        543 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
          1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA

                               
        594 -T---CATAAACTAATTAA
          1 TTAAACATAAACTAATTAA

        609 TATTAAAAAT


Statistics
Matches: 58,  Mismatches: 5, Indels: 10
        0.79            0.07        0.14

Matches are distributed among these distances:
  47   10  0.17
  48    3  0.05
  50    1  0.02
  51   10  0.17
  52   28  0.48
  53    6  0.10

ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34


Consensus pattern (51 bp):   
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA

Found at i:628 original size:12 final size:12

Alignment explanation


    Indices: 611--641  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

        601 CTAATTAATA

                        
        611 TTAAAAATATTT
          1 TTAAAAATATTT

                    *   
        623 TTAAAAATTTTT
          1 TTAAAAATATTT

                   
        635 TTAAAAA
          1 TTAAAAA

        642 ACAAAGAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

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


Consensus pattern (12 bp):   
TTAAAAATATTT

Found at i:1322 original size:31 final size:31

Alignment explanation


    Indices: 1287--1371  Score: 125
    Period size: 31  Copynumber: 2.7  Consensus size: 31

       1277 GCATGCCACG

                                           
       1287 TGTCACTTTTTAGTACACGTGGCGTGACACA
          1 TGTCACTTTTTAGTACACGTGGCGTGACACA

                       *                 **
       1318 TGTCACTTTTTGGTACACGTGGCGTGACATG
          1 TGTCACTTTTTAGTACACGTGGCGTGACACA

             *         *           
       1349 TATCACTTTTTTGTACACGTGGC
          1 TGTCACTTTTTAGTACACGTGGC

       1372 ATGCCACGTC


Statistics
Matches: 49,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   49  1.00

ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36


Consensus pattern (31 bp):   
TGTCACTTTTTAGTACACGTGGCGTGACACA
Done.