Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016117.1 Corchorus capsularis cultivar CVL-1 contig16138, 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: 12387
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:3665 original size:13 final size:12

Alignment explanation


    Indices: 3647--3689  Score: 54
    Period size: 10  Copynumber: 3.7  Consensus size: 12

       3637 TGAAACTTGA

                         
       3647 AAAATAAAGACAT
          1 AAAATAAAG-CAT

                        
       3660 AAAATAAAG-A-
          1 AAAATAAAGCAT

                        
       3670 AAAATAAAGCAT
          1 AAAATAAAGCAT

               *    
       3682 AAACTAAA
          1 AAAATAAA

       3690 TAACGAAACT


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  10    9  0.33
  11    2  0.07
  12    7  0.26
  13    9  0.33

ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14


Consensus pattern (12 bp):   
AAAATAAAGCAT

Found at i:3672 original size:22 final size:22

Alignment explanation


    Indices: 3645--3689  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 22

       3635 AATGAAACTT

                                   
       3645 GAAAAATAAAGACATAAAATAAA
          1 GAAAAATAAAG-CATAAAATAAA

                             *    
       3668 GAAAAATAAAGCATAAACTAAA
          1 GAAAAATAAAGCATAAAATAAA

       3690 TAACGAAACT


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

Matches are distributed among these distances:
  22   10  0.48
  23   11  0.52

ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13


Consensus pattern (22 bp):   
GAAAAATAAAGCATAAAATAAA

Found at i:11938 original size:19 final size:18

Alignment explanation


    Indices: 11905--11940  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      11895 TTGAAATAAT

                              
      11905 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
      11923 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

      11941 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.