Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008979.1 Corchorus capsularis cultivar CVL-1 contig09000, 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: 27864
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:6723 original size:73 final size:73

Alignment explanation


    Indices: 6638--6775  Score: 197
    Period size: 73  Copynumber: 1.9  Consensus size: 73

       6628 ACTGGACCAT

                         **                          *                       
       6638 CACTTTTTTCTTCTTTTTTGGTTTGATTCTTTCCTTAATTATATGTAATT-CTTTTAGGATAACA
          1 CACTTTTTTCTTCAGTTTTGG-TTGATTCTTTCCTTAATTACATGTAATTCCTTTTAGGATAACA

                     
       6702 AATACCCAC
         65 AATACCCAC

                                       *   *   *         *                   
       6711 CACTTTTTTCTTCAGTTTTGGTTGATTTTTTGCTTGATTACATGTCATTCCTTTTAGGATAACAA
          1 CACTTTTTTCTTCAGTTTTGGTTGATTCTTTCCTTAATTACATGTAATTCCTTTTAGGATAACAA

       6776 GTACACTTCC


Statistics
Matches: 57,  Mismatches: 7, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  72   23  0.40
  73   34  0.60

ACGTcount: A:0.22, C:0.17, G:0.11, T:0.51


Consensus pattern (73 bp):   
CACTTTTTTCTTCAGTTTTGGTTGATTCTTTCCTTAATTACATGTAATTCCTTTTAGGATAACAA
ATACCCAC

Found at i:23904 original size:23 final size:23

Alignment explanation


    Indices: 23878--23924  Score: 94
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      23868 AAGGTAATCC

                                   
      23878 TCTCCTTCCCTTAATCCCACCCG
          1 TCTCCTTCCCTTAATCCCACCCG

                                   
      23901 TCTCCTTCCCTTAATCCCACCCG
          1 TCTCCTTCCCTTAATCCCACCCG

             
      23924 T
          1 T

      23925 GTATCCTATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.13, C:0.51, G:0.04, T:0.32


Consensus pattern (23 bp):   
TCTCCTTCCCTTAATCCCACCCG

Found at i:24833 original size:21 final size:21

Alignment explanation


    Indices: 24789--24839  Score: 63
    Period size: 18  Copynumber: 2.6  Consensus size: 21

      24779 TTACAATCTT

                  *              
      24789 ATAATATATAATATTAAATAA
          1 ATAATAAATAATATTAAATAA

                             *   
      24810 ATAATAAAT-ATATT--TTAA
          1 ATAATAAATAATATTAAATAA

                        
      24828 ATAATAAATAAT
          1 ATAATAAATAAT

      24840 GAGTTCAAAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  18   12  0.44
  19    2  0.07
  20    5  0.19
  21    8  0.30

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (21 bp):   
ATAATAAATAATATTAAATAA

Found at i:25892 original size:107 final size:107

Alignment explanation


    Indices: 25714--25977  Score: 415
    Period size: 107  Copynumber: 2.5  Consensus size: 107

      25704 AATTTTTCTA

                           * **            *                                 
      25714 ACCCTTAAAATAAAATTTTAATTTTAATTT-TGGCTAAACTTAGTG-AATTAGTTATATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                     *                                
      25777 TTTCTAAAATCCTATAACAATAAATTATTAATTATGAAATTT
         66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT

                                 *         *                       *         
      25819 ACCCTTAAAATAAAAATAAAAATTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA

                                             * *      
      25884 TTTCTAAAACCCTATAACAATAAATTATTAATTTTTAAATTT
         66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT

                                             *                  
      25926 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGACTAAACTTAGTGAAATTA
          1 ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTA

      25978 AGGCTAAACT


Statistics
Matches: 145,  Mismatches: 12, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 105   26  0.18
 106   14  0.10
 107  105  0.72

ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41


Consensus pattern (107 bp):   
ACCCTTAAAATAAAAATAAAATTTTAATTTGAGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Done.