Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006263.1 Corchorus olitorius cultivar O-4 contig06288, 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: 2035
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39


Found at i:1166 original size:23 final size:23

Alignment explanation


    Indices: 1117--1166  Score: 64
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1107 GAACTTACTT

                           *   ** *
       1117 AAATACCTATGATGTGTAAGGTT
          1 AAATACCTATGATGTCTAAAATC

                                   
       1140 AAATACCTATGATGTCTAAAATC
          1 AAATACCTATGATGTCTAAAATC

                
       1163 AAAT
          1 AAAT

       1167 TAAAAGAACA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32


Consensus pattern (23 bp):   
AAATACCTATGATGTCTAAAATC

Found at i:1296 original size:25 final size:26

Alignment explanation


    Indices: 1246--1301  Score: 80
    Period size: 25  Copynumber: 2.2  Consensus size: 26

       1236 TTTGGATTTT

                                      
       1246 TTATTATATTGATTTATAAAAATTAA
          1 TTATTATATTGATTTATAAAAATTAA

                                  *    
       1272 TTATTAT-TTG-TTATATAAAAGTTAA
          1 TTATTATATTGATT-TATAAAAATTAA

                 
       1297 TTATT
          1 TTATT

       1302 CATCTTATAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  24    2  0.07
  25   19  0.68
  26    7  0.25

ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54


Consensus pattern (26 bp):   
TTATTATATTGATTTATAAAAATTAA

Found at i:1309 original size:24 final size:24

Alignment explanation


    Indices: 1260--1312  Score: 63
    Period size: 25  Copynumber: 2.2  Consensus size: 24

       1250 TATATTGATT

                                 *   
       1260 TATAAAAATTAATTATTATTTGTTA
          1 TATAAAAATTAATTATTA-TTCTTA

                   *                 
       1285 TATAAAAGTTAATTATTCA-TCTTA
          1 TATAAAAATTAATTATT-ATTCTTA

                
       1309 TATA
          1 TATA

       1313 TATTACAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  24    8  0.32
  25   16  0.64
  26    1  0.04

ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49


Consensus pattern (24 bp):   
TATAAAAATTAATTATTATTCTTA
Done.