Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010221.1 Corchorus olitorius cultivar O-4 contig10253, 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, 918

Length: 1530
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27


Found at i:159 original size:21 final size:21

Alignment explanation


    Indices: 120--168  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        110 TCAATGCTTT

                         **       
        120 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
        142 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
        163 A-GAAGC
          1 AGGAAGC

        169 TACAATTCTC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:1164 original size:18 final size:18

Alignment explanation


    Indices: 1133--1167  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1123 GGTCGAAAAT

                    **        
       1133 TTTTTTATTTTATTTTTA
          1 TTTTTTATGATATTTTTA

                             
       1151 TTTTTTATGATATTTTT
          1 TTTTTTATGATATTTTT

       1168 CGATTAAACT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80


Consensus pattern (18 bp):   
TTTTTTATGATATTTTTA

Found at i:1317 original size:25 final size:24

Alignment explanation


    Indices: 1280--1326  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       1270 CAAGAAAATT

                                      
       1280 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       1306 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       1327 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA
Done.