Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014784.1 Corchorus olitorius cultivar O-4 contig14817, 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: 14755
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34


Found at i:2287 original size:27 final size:27

Alignment explanation


    Indices: 2257--2352  Score: 95
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       2247 TCTAAATTGC

                                       
       2257 CATTACTAAATAATATTTTAATTATTT
          1 CATTACTAAATAATATTTTAATTATTT

                 *             *          * 
       2284 CATTATTAAAATAATGGAAATTTAGATT-TGT
          1 CATTACT-AAATAAT---ATTTTA-ATTATTT

                                       
       2315 CATTACTAAATAATATTTTAATTATTT
          1 CATTACTAAATAATATTTTAATTATTT

            *    *     
       2342 TATTATTAAAT
          1 CATTACTAAAT

       2353 TAATGGAAAT


Statistics
Matches: 55,  Mismatches: 8, Indels: 12
        0.73            0.11        0.16

Matches are distributed among these distances:
  26    3  0.05
  27   22  0.40
  28    7  0.13
  30    7  0.13
  31   13  0.24
  32    3  0.05

ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49


Consensus pattern (27 bp):   
CATTACTAAATAATATTTTAATTATTT

Found at i:2321 original size:58 final size:58

Alignment explanation


    Indices: 2257--2369  Score: 208
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       2247 TCTAAATTGC

                                                                      
       2257 CATTACTAAATAATATTTTAATTATTTCATTATTAAAATAATGGAAATTTAGATTTGT
          1 CATTACTAAATAATATTTTAATTATTTCATTATTAAAATAATGGAAATTTAGATTTGT

                                       *         *                 
       2315 CATTACTAAATAATATTTTAATTATTTTATTATTAAATTAATGGAAATTTAGATT
          1 CATTACTAAATAATATTTTAATTATTTCATTATTAAAATAATGGAAATTTAGATT

       2370 ATCCTCATTA


Statistics
Matches: 53,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  58   53  1.00

ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48


Consensus pattern (58 bp):   
CATTACTAAATAATATTTTAATTATTTCATTATTAAAATAATGGAAATTTAGATTTGT

Found at i:4043 original size:14 final size:12

Alignment explanation


    Indices: 4010--4042  Score: 52
    Period size: 11  Copynumber: 2.9  Consensus size: 12

       4000 TAGACATTTT

                        
       4010 TATATT-TTATA
          1 TATATTATTATA

                        
       4021 TATATTATTATA
          1 TATATTATTATA

                       
       4033 T-TATTATTAT
          1 TATATTATTAT

       4043 TGGCCACTCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  11   15  0.71
  12    6  0.29

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (12 bp):   
TATATTATTATA

Found at i:6134 original size:21 final size:21

Alignment explanation


    Indices: 6099--6259  Score: 104
    Period size: 22  Copynumber: 7.8  Consensus size: 21

       6089 CACAAAGAGA

                      *           
       6099 TTATCAAAA-ATCATAGGAAGG
          1 TTATCAAAATTTCATAGG-AGG

                                  *
       6120 TTA-CAAAATTTCATAGGAAAGT
          1 TTATCAAAATTTCATAGG--AGG

                *             *   
       6142 TTATTAAAATTTCATAGTTAGG
          1 TTATCAAAATTTCATAG-GAGG

                    *    *       *
       6164 TTATCAAAGTTTCTTATGGAGT
          1 TTATCAAAATTTCATA-GGAGG

                  *     *        *
       6186 TTATCACAATTTTATAGGTA-A
          1 TTATCAAAATTTCATAGG-AGG

                              *  
       6207 TTATCAAAATTTCAT-GGTGG
          1 TTATCAAAATTTCATAGGAGG

                        *        
       6227 TTATCAAAATTTAATA-G-GG
          1 TTATCAAAATTTCATAGGAGG

                            
       6246 -T-TCAAAATTTCATA
          1 TTATCAAAATTTCATA

       6260 AAAATATTCA


Statistics
Matches: 111,  Mismatches: 21, Indels: 20
        0.73            0.14        0.13

Matches are distributed among these distances:
  17   12  0.11
  18    1  0.01
  19    2  0.02
  20   22  0.20
  21   25  0.23
  22   36  0.32
  23   13  0.12

ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39


Consensus pattern (21 bp):   
TTATCAAAATTTCATAGGAGG

Done.