Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012408.1 Corchorus capsularis cultivar CVL-1 contig12429, 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: 27185
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--37  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 AT

                                                                   
          3 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         38 GCATATGCAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:43 original size:21 final size:21

Alignment explanation


    Indices: 3--43  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

          1 AT

                   *       *     
          3 TATATATTATATATATATATA
          1 TATATATAATATATACATATA

                          *     
         24 TATATATAATATATGCATAT
          1 TATATATAATATATACATAT

         44 GCAAAAGCAT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49


Consensus pattern (21 bp):   
TATATATAATATATACATATA

Found at i:4636 original size:18 final size:17

Alignment explanation


    Indices: 4594--4636  Score: 50
    Period size: 18  Copynumber: 2.4  Consensus size: 17

       4584 TAAATAAATA

                             
       4594 AATATAAATATAAATGT
          1 AATATAAATATAAATGT

                    *          
       4611 AATAATAATTATAAATAGT
          1 AAT-ATAAATATAAAT-GT

             *     
       4630 ACTATAA
          1 AATATAA

       4637 GAAAATAAGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  17    3  0.14
  18   15  0.68
  19    4  0.18

ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35


Consensus pattern (17 bp):   
AATATAAATATAAATGT

Found at i:21858 original size:11 final size:11

Alignment explanation


    Indices: 21844--21890  Score: 62
    Period size: 11  Copynumber: 4.5  Consensus size: 11

      21834 ATATAAATAA

                       
      21844 TATATCTATAC
          1 TATATCTATAC

                       
      21855 TATATCTATAC
          1 TATATCTATAC

                  *   *
      21866 TATA--AATAA
          1 TATATCTATAC

                       
      21875 TATATCTATAC
          1 TATATCTATAC

                 
      21886 TATAT
          1 TATAT

      21891 ATAAAAGTAC


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
   9    7  0.23
  11   23  0.77

ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45


Consensus pattern (11 bp):   
TATATCTATAC

Found at i:21880 original size:20 final size:20

Alignment explanation


    Indices: 21855--21894  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      21845 ATATCTATAC

                                
      21855 TATATCTATACTATAAATAA
          1 TATATCTATACTATAAATAA

                           *    
      21875 TATATCTATACTATATATAA
          1 TATATCTATACTATAAATAA

      21895 AAGTACGAGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.47, C:0.10, G:0.00, T:0.42


Consensus pattern (20 bp):   
TATATCTATACTATAAATAA

Found at i:22212 original size:109 final size:108

Alignment explanation


    Indices: 21986--22258  Score: 417
    Period size: 109  Copynumber: 2.5  Consensus size: 108

      21976 CTATTATAGT

                        *                     *                              
      21986 TTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTTT
          1 TTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTTT

                                                           *
      22051 ATTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAAT
         61 ATTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAAC

                                                                             
      22099 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTTATTT
          1 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTAC-TTTA-TT

                                       *                 
      22164 TTACCAAAAAATTTGGATATA-TAAAATTTTTTCTAATATACAAC
         64 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAAC

                                                                 
      22208 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
          1 TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA

      22259 TAATTTTTTT


Statistics
Matches: 153,  Mismatches: 4, Indels: 11
        0.91            0.02        0.07

Matches are distributed among these distances:
 108   37  0.24
 109   71  0.46
 110   25  0.16
 113   20  0.13

ACGTcount: A:0.39, C:0.12, G:0.02, T:0.48


Consensus pattern (108 bp):   
TTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTTT
ACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAAC
Done.