Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023188.1 Corchorus olitorius cultivar O-4 contig23221, 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: 19357
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:231 original size:20 final size:21

Alignment explanation


    Indices: 202--244  Score: 63
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        192 TTTAAAAAAT

                                  
        202 TTCATTTTTCTTCTTTTCT-TT
          1 TTCATTTTTCTT-TTTTCTATT

                                 
        223 TTC-TTTTTCTTTTTTCTATT
          1 TTCATTTTTCTTTTTTCTATT

              
        243 TT
          1 TT

        245 TTAAATATCA


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

Matches are distributed among these distances:
  19    6  0.29
  20   12  0.57
  21    3  0.14

ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79


Consensus pattern (21 bp):   
TTCATTTTTCTTTTTTCTATT

Found at i:842 original size:61 final size:61

Alignment explanation


    Indices: 716--830  Score: 176
    Period size: 61  Copynumber: 1.9  Consensus size: 61

        706 TTGTACCACA

                                      *     *         *                  
        716 AAATTTCTAAACTATGTCTCATCTTTCTATTTTCTAACCACGTACTAAAGATGAAAGGTAC
          1 AAATTTCTAAACTATGTCTCATCTTTATATTTCCTAACCACGCACTAAAGATGAAAGGTAC

                                  *     *      *                  
        777 AAATTTCTAAACTATGTCTCATGTTTATGTTTCCTTACCACGCACTAAAGATGA
          1 AAATTTCTAAACTATGTCTCATCTTTATATTTCCTAACCACGCACTAAAGATGA

        831 TAGTACTAAA


Statistics
Matches: 48,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  61   48  1.00

ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37


Consensus pattern (61 bp):   
AAATTTCTAAACTATGTCTCATCTTTATATTTCCTAACCACGCACTAAAGATGAAAGGTAC

Found at i:1266 original size:2 final size:2

Alignment explanation


    Indices: 1261--1339  Score: 73
    Period size: 2  Copynumber: 42.0  Consensus size: 2

       1251 GTAGTGTGTG

                                                                           
       1261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA GT-
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA

              *                                      *                     
       1301 TCC T- TA -A TA TA TA TA TA T- TA T- TA TG TA TA TA TA TA TA TA
          1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1340 ATTATTATTA


Statistics
Matches: 66,  Mismatches: 2, Indels: 18
        0.77            0.02        0.21

Matches are distributed among these distances:
   1    7  0.11
   2   57  0.86
   3    2  0.03

ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:10653 original size:93 final size:93

Alignment explanation


    Indices: 10551--10735  Score: 325
    Period size: 93  Copynumber: 2.0  Consensus size: 93

      10541 TTGTTTAAAT

                         *                                                   
      10551 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                           *      *     
      10616 TTTTATTTTTACCATTTTACTATTTTAC
         66 TTTTATTTTTACCATATTACTAATTTAC

                                                                         *   
      10644 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA

                        *              
      10709 TTTTATTTTTACGATATTACTAATTTA
         66 TTTTATTTTTACCATATTACTAATTTA

      10736 ATTAAAAAAC


Statistics
Matches: 87,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  93   87  1.00

ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52


Consensus pattern (93 bp):   
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATATTACTAATTTAC

Found at i:11044 original size:25 final size:24

Alignment explanation


    Indices: 11016--11074  Score: 68
    Period size: 25  Copynumber: 2.5  Consensus size: 24

      11006 TTACCCAATC

                           *        
      11016 ATTAATTATTAATTTTTTAAAAAT
          1 ATTAATTATTAATTTATTAAAAAT

                       *              
      11040 AATTAAGTTA-AAATTTATTAAAAAT
          1 -ATTAA-TTATTAATTTATTAAAAAT

                       
      11065 -TTAATTATTA
          1 ATTAATTATTA

      11075 TGATTGATCT


Statistics
Matches: 29,  Mismatches: 3, Indels: 6
        0.76            0.08        0.16

Matches are distributed among these distances:
  22    3  0.10
  23    5  0.17
  25   18  0.62
  26    3  0.10

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (24 bp):   
ATTAATTATTAATTTATTAAAAAT
Done.