Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023658.1 Corchorus olitorius cultivar O-4 contig23691, 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: 4042
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31


Found at i:2431 original size:25 final size:25

Alignment explanation


    Indices: 2403--2490  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       2393 ACTTTCCCAA

                                     
       2403 TTTAAAAACTGGCTAAATTGGATAC
          1 TTTAAAAACTGGCTAAATTGGATAC

                          **  *  **** *
       2428 TTTAAAAACTGATGGGAACTTTCCCAA
          1 TTTAAAAACTG--GCTAAATTGGATAC

             *                       
       2455 TGTAAAAACTGGCTAAATTGGATAC
          1 TTTAAAAACTGGCTAAATTGGATAC

                       
       2480 TTTAAAAACTG
          1 TTTAAAAACTG

       2491 ATGGGAACTT


Statistics
Matches: 43,  Mismatches: 18, Indels: 4
        0.66            0.28        0.06

Matches are distributed among these distances:
  25   27  0.63
  27   16  0.37

ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31


Consensus pattern (25 bp):   
TTTAAAAACTGGCTAAATTGGATAC

Found at i:2451 original size:52 final size:53

Alignment explanation


    Indices: 2381--2568  Score: 296
    Period size: 52  Copynumber: 3.6  Consensus size: 53

       2371 ACTTAAACTG

                    *                                            
       2381 AAAA-TGACGGGAACTTTCCCAATTT-AAAAACTGGCTAAATTGGATACTTTA
          1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTGGCTAAATTGGATACTTTA

                                    *                            
       2432 AAAACTGATGGGAACTTTCCCAATGT-AAAAACTGGCTAAATTGGATACTTTA
          1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTGGCTAAATTGGATACTTTA

                                                                 *
       2484 AAAACTGATGGGAACTTTCCCAATTTGAAAAA--GAGCTAAATTGGATACTTTG
          1 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTG-GCTAAATTGGATACTTTA

                                             
       2536 AAAACTTGATGGGAACTTTCCCAATTTGAAAAA
          1 AAAAC-TGATGGGAACTTTCCCAATTTGAAAAA

       2569 AGAGCTAAAT


Statistics
Matches: 129,  Mismatches: 4, Indels: 6
        0.93            0.03        0.04

Matches are distributed among these distances:
  51    5  0.04
  52   92  0.71
  53   32  0.25

ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29


Consensus pattern (53 bp):   
AAAACTGATGGGAACTTTCCCAATTTGAAAAACTGGCTAAATTGGATACTTTA

Done.