Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008364.1 Corchorus capsularis cultivar CVL-1 contig08385, 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: 11208
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34


Found at i:367 original size:22 final size:22

Alignment explanation


    Indices: 326--367  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        316 GACAAACCTA

                           *      
        326 TAACCCGAATGACCCGAGAAGT
          1 TAACCCGAATGACCCAAGAAGT

                   *    *       
        348 TAACCCGGATGAGCCAAGAA
          1 TAACCCGAATGACCCAAGAA

        368 TATTATAAAC


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

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12


Consensus pattern (22 bp):   
TAACCCGAATGACCCAAGAAGT

Found at i:2656 original size:70 final size:70

Alignment explanation


    Indices: 2580--2734  Score: 222
    Period size: 70  Copynumber: 2.2  Consensus size: 70

       2570 TAATTAAAAT

                    *        *           *     *           *                 
       2580 AGTAAAATGGTAAAATATAATAGTAATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
          1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATCAGATTTAATTAAATAAAAATAGAGTTTTT

                 
       2645 AGTTG
         66 AGTTG

                                    *            *                   *       
       2650 AGTAAAATAGTAAAATAAAATAGTTATAAAGATATCATATTTAATTAAATAAAAATATAGTTTTT
          1 AGTAAAATAGTAAAATAAAATAGTAATAAAGATATCAGATTTAATTAAATAAAAATAGAGTTTTT

                 
       2715 AGTTG
         66 AGTTG

                            
       2720 AGTAAAACTA-TAAAA
          1 AGTAAAA-TAGTAAAA

       2735 ATCTAAACAA


Statistics
Matches: 76,  Mismatches: 8, Indels: 2
        0.88            0.09        0.02

Matches are distributed among these distances:
  70   74  0.97
  71    2  0.03

ACGTcount: A:0.51, C:0.01, G:0.12, T:0.35


Consensus pattern (70 bp):   
AGTAAAATAGTAAAATAAAATAGTAATAAAGATATCAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTG

Found at i:2945 original size:84 final size:84

Alignment explanation


    Indices: 2857--3031  Score: 207
    Period size: 84  Copynumber: 2.1  Consensus size: 84

       2847 TTTTTTTAAT

                             *                                               
       2857 TAAAATAGT-AAA-ATGGTA-ATATAATTGCA-ATAAGGATATTAGATT-TAATTATATAAAAAT
          1 TAAAATAGTAAAATATGATAGATATAA--GCATATAA-GAT-TTA-ATTATAATTATATAAAAAT

             *                      
       2917 ATAGTTCTTAGTTGAGTAAAATAG
         61 AGAGTTCTTAGTTGAGTAAAATAG

                  *              *      *    *                               
       2941 TAAAATGGTAAAATATGATAGTTATAAGGATATTAGATTTAATTATAATTATATAAAAATAGAGT
          1 TAAAATAGTAAAATATGATAGATATAAGCATATAAGATTTAATTATAATTATATAAAAATAGAGT

             *                 
       3006 TTTTAGTTGAGTAAAATAG
         66 TCTTAGTTGAGTAAAATAG

                   
       3025 TAAAATA
          1 TAAAATA

       3032 AAATAGTTAT


Statistics
Matches: 78,  Mismatches: 8, Indels: 10
        0.81            0.08        0.10

Matches are distributed among these distances:
  83    3  0.04
  84   54  0.69
  85    8  0.10
  86    8  0.10
  87    5  0.06

ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37


Consensus pattern (84 bp):   
TAAAATAGTAAAATATGATAGATATAAGCATATAAGATTTAATTATAATTATATAAAAATAGAGT
TCTTAGTTGAGTAAAATAG

Found at i:3582 original size:15 final size:16

Alignment explanation


    Indices: 3559--3588  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       3549 GAACCATATG

                            
       3559 ACCCAAAACCAAAAAC
          1 ACCCAAAACCAAAAAC

                           
       3575 ACCC-AAACCAAAAA
          1 ACCCAAAACCAAAAA

       3589 TGACCTAAAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00


Consensus pattern (16 bp):   
ACCCAAAACCAAAAAC

Found at i:4118 original size:109 final size:109

Alignment explanation


    Indices: 3962--4255  Score: 473
    Period size: 109  Copynumber: 2.7  Consensus size: 109

       3952 TAAATTAAAA

                         **          *                                       
       3962 TGGTAAAAATAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTA
          1 TGGTAAAAATAAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTA

                                                          
       4026 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
         64 GAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT

                                                                             
       4072 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
          1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA

                                        *               
       4137 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
         66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT

                                                       *                 *   
       4181 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAGTAGAGTTTCTAG
          1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TTAAATG-A-AAA-TAGAGTTTTTAG

                      
       4246 TAGAATAAAA
         62 TAGAATAAAA

       4256 CTATAATAGT


Statistics
Matches: 173,  Mismatches: 6, Indels: 7
        0.93            0.03        0.04

Matches are distributed among these distances:
 109  121  0.70
 110   27  0.16
 111    1  0.01
 112    3  0.02
 113   21  0.12

ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37


Consensus pattern (109 bp):   
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Done.