Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002611.1 Corchorus olitorius cultivar O-4 contig02613, 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: 2324
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Found at i:235 original size:13 final size:13

Alignment explanation


    Indices: 217--249  Score: 66
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        207 AAGCATGATA

                         
        217 TATCTTATCTTAC
          1 TATCTTATCTTAC

                         
        230 TATCTTATCTTAC
          1 TATCTTATCTTAC

                   
        243 TATCTTA
          1 TATCTTA

        250 CTATTATATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55


Consensus pattern (13 bp):   
TATCTTATCTTAC

Found at i:683 original size:15 final size:15

Alignment explanation


    Indices: 653--701  Score: 64
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        643 TGGTAGAGAG

                  *        
        653 GAAATGAGAAGGAAA
          1 GAAATGGGAAGGAAA

                      *     
        668 GAAGA-GGGATGGAAA
          1 GAA-ATGGGAAGGAAA

                           
        683 GAAATGGGAAGGAAA
          1 GAAATGGGAAGGAAA

                
        698 GAAA
          1 GAAA

        702 AGCTTCTCTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  14    1  0.03
  15   27  0.93
  16    1  0.03

ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06


Consensus pattern (15 bp):   
GAAATGGGAAGGAAA

Found at i:1395 original size:2 final size:2

Alignment explanation


    Indices: 1388--1413  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1378 TGATTTCTTA

                                                  
       1388 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1414 TGTCCAATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.