Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006759.1 Corchorus capsularis cultivar CVL-1 contig06780, 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: 15294
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31


Found at i:4931 original size:17 final size:17

Alignment explanation


    Indices: 4906--4947  Score: 59
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       4896 GTCAAGATTT

                             
       4906 GAAGAAAAAGAAAAAAA
          1 GAAGAAAAAGAAAAAAA

                *           *
       4923 GAAGGAAAAGAAAAAAT
          1 GAAGAAAAAGAAAAAAA

                     
       4940 GAA-AAAAA
          1 GAAGAAAAA

       4948 TGGAAAAATT


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  16    4  0.18
  17   18  0.82

ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02


Consensus pattern (17 bp):   
GAAGAAAAAGAAAAAAA

Found at i:5206 original size:39 final size:41

Alignment explanation


    Indices: 5108--5222  Score: 162
    Period size: 41  Copynumber: 2.9  Consensus size: 41

       5098 TTTCTATTTA

                 *               *             *     
       5108 AGCAATTCCAAGAGAAGACTTCTGGAAAATAAATATTTTTT
          1 AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATAGTTTTT

                       *                             
       5149 AGCAAATCCAAAAGAAGACTTTTGGAAAATAAAT-GTTTTT
          1 AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATAGTTTTT

                                     *    *    
       5189 AG-AAATCCAAGAGAAGACTTTTGGGAAATTAATA
          1 AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATA

       5223 AAATTGATCA


Statistics
Matches: 66,  Mismatches: 7, Indels: 3
        0.87            0.09        0.04

Matches are distributed among these distances:
  39   28  0.42
  40    7  0.11
  41   31  0.47

ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29


Consensus pattern (41 bp):   
AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATAGTTTTT

Found at i:9102 original size:2 final size:2

Alignment explanation


    Indices: 9095--9126  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       9085 TTTTATTACA

                                                 *         
       9095 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9127 GTAGAAATTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Done.