Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019391.1 Corchorus olitorius cultivar O-4 contig19424, 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: 39731
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:1135 original size:22 final size:20

Alignment explanation


    Indices: 1105--1144  Score: 53
    Period size: 22  Copynumber: 1.9  Consensus size: 20

       1095 TTCCTATATA

                                  
       1105 AAATAAATTATCAAATAATTAT
          1 AAATAAATTAT-AAA-AATTAT

                *             
       1127 AAATTAATTATAAAAATT
          1 AAATAAATTATAAAAATT

       1145 TGTTATGAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    3  0.18
  22   10  0.59

ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38


Consensus pattern (20 bp):   
AAATAAATTATAAAAATTAT

Found at i:5701 original size:12 final size:11

Alignment explanation


    Indices: 5684--5719  Score: 56
    Period size: 11  Copynumber: 3.4  Consensus size: 11

       5674 GAATTATGGC

                       
       5684 AAAAAAAAACT
          1 AAAAAAAAACT

                       
       5695 AAAAAAAAACT
          1 AAAAAAAAACT

                 *     
       5706 -AAAAGAAACT
          1 AAAAAAAAACT

                
       5716 AAAA
          1 AAAA

       5720 GGAAAAGAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  10    9  0.39
  11   14  0.61

ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08


Consensus pattern (11 bp):   
AAAAAAAAACT

Found at i:5720 original size:10 final size:10

Alignment explanation


    Indices: 5685--5719  Score: 52
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       5675 AATTATGGCA

                      
       5685 AAAAAAAACT
          1 AAAAAAAACT

                       
       5695 AAAAAAAAACT
          1 -AAAAAAAACT

                *     
       5706 AAAAGAAACT
          1 AAAAAAAACT

                
       5716 AAAA
          1 AAAA

       5720 GGAAAAGAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  10   13  0.57
  11   10  0.43

ACGTcount: A:0.80, C:0.09, G:0.03, T:0.09


Consensus pattern (10 bp):   
AAAAAAAACT
Done.