Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010602.1 Corchorus olitorius cultivar O-4 contig10634, 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: 15895
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31


Found at i:9065 original size:127 final size:127

Alignment explanation


    Indices: 8924--9153  Score: 424
    Period size: 127  Copynumber: 1.8  Consensus size: 127

       8914 CATTGTTTAA

                              *                              *               
       8924 ACTTTTATAGTTTTACTCGACTAAAAACTCTATTTTTATTTAATTAAATTTAATATCCTTATAAC
          1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC

                                    *                                     
       8989 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAATATATATTAGATTTTTTTAAATAT
         66 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAATATATATTAGATTTTTTTAAATAT

                                                                           * 
       9051 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
          1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC

                                                  
       9116 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAA
         66 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAA

       9154 CTTAGATATA


Statistics
Matches: 99,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 127   99  1.00

ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50


Consensus pattern (127 bp):   
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAATATATATTAGATTTTTTTAAATAT

Found at i:11265 original size:7 final size:7

Alignment explanation


    Indices: 11253--11286  Score: 68
    Period size: 7  Copynumber: 4.9  Consensus size: 7

      11243 TTTGCCTTCT

                   
      11253 CTCTTTA
          1 CTCTTTA

                   
      11260 CTCTTTA
          1 CTCTTTA

                   
      11267 CTCTTTA
          1 CTCTTTA

                   
      11274 CTCTTTA
          1 CTCTTTA

                  
      11281 CTCTTT
          1 CTCTTT

      11287 CCCCTTTCTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   27  1.00

ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59


Consensus pattern (7 bp):   
CTCTTTA

Found at i:11293 original size:14 final size:14

Alignment explanation


    Indices: 11253--11293  Score: 55
    Period size: 14  Copynumber: 2.9  Consensus size: 14

      11243 TTTGCCTTCT

                    *     
      11253 CTCTTTACTCTTTA
          1 CTCTTTACCCTTTA

                    *     
      11267 CTCTTTACTCTTTA
          1 CTCTTTACCCTTTA

                  *      
      11281 CTCTTTCCCCTTT
          1 CTCTTTACCCTTT

      11294 CTCCTTCCTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  14   25  1.00

ACGTcount: A:0.10, C:0.34, G:0.00, T:0.56


Consensus pattern (14 bp):   
CTCTTTACCCTTTA

Found at i:11293 original size:21 final size:21

Alignment explanation


    Indices: 11253--11293  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11243 TTTGCCTTCT

                           *     
      11253 CTCTTTACTCTTTACTCTTTA
          1 CTCTTTACTCTTTACCCTTTA

                         *      
      11274 CTCTTTACTCTTTCCCCTTT
          1 CTCTTTACTCTTTACCCTTT

      11294 CTCCTTCCTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.10, C:0.34, G:0.00, T:0.56


Consensus pattern (21 bp):   
CTCTTTACTCTTTACCCTTTA

Found at i:15870 original size:2 final size:2

Alignment explanation


    Indices: 15863--15895  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      15853 GTAATTCTCA

                                                             
      15863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.