Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021391.1 Corchorus olitorius cultivar O-4 contig21424, 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: 23268
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:608 original size:31 final size:30

Alignment explanation


    Indices: 573--673  Score: 109
    Period size: 31  Copynumber: 3.3  Consensus size: 30

        563 CCGTTTCACG

                                           
        573 GAGGGACTAAATTGATCGCTTTTCAATAGTA
          1 GAGGGACTAAATTGATCG-TTTTCAATAGTA

                               *           *
        604 GAGGGACTAAATTGA-CAGATTTC-AT-GATG
          1 GAGGGACTAAATTGATC-GTTTTCAATAG-TA

                              *            
        633 GAGGGACTAAATTGATCTTTTTTCAATAGTA
          1 GAGGGACTAAATTGATC-GTTTTCAATAGTA

            *         
        664 CAGGGACTAA
          1 GAGGGACTAA

        674 TTAAGTACTT


Statistics
Matches: 58,  Mismatches: 7, Indels: 10
        0.77            0.09        0.13

Matches are distributed among these distances:
  28    1  0.02
  29   18  0.31
  30   10  0.17
  31   28  0.48
  32    1  0.02

ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31


Consensus pattern (30 bp):   
GAGGGACTAAATTGATCGTTTTCAATAGTA

Found at i:21725 original size:20 final size:21

Alignment explanation


    Indices: 21679--21726  Score: 53
    Period size: 20  Copynumber: 2.3  Consensus size: 21

      21669 GAGCTGGCAT

                                *
      21679 ATATGCATTAGTATAGAATAT
          1 ATATGCATTAGTATAGAATAC

             *          * *      
      21700 AGATGCATT-GTGTGGAATAC
          1 ATATGCATTAGTATAGAATAC

                   
      21720 ATATGCA
          1 ATATGCA

      21727 GACTATATAT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  20   14  0.64
  21    8  0.36

ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33


Consensus pattern (21 bp):   
ATATGCATTAGTATAGAATAC
Done.