Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009162.1 Corchorus capsularis cultivar CVL-1 contig09183, 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: 19828
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:3129 original size:27 final size:26

Alignment explanation


    Indices: 3089--3139  Score: 66
    Period size: 27  Copynumber: 1.9  Consensus size: 26

       3079 ATTACCCCCA

                           *          
       3089 AAAGTGACCAAAATATCCCTGAAACG
          1 AAAGTGACCAAAATACCCCTGAAACG

                      *    *         
       3115 AAAGATGACCGAAATGCCCCTGAAA
          1 AAAG-TGACCAAAATACCCCTGAAA

       3140 TGACCAAAGT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  26    4  0.19
  27   17  0.81

ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14


Consensus pattern (26 bp):   
AAAGTGACCAAAATACCCCTGAAACG

Found at i:7591 original size:21 final size:21

Alignment explanation


    Indices: 7566--7648  Score: 73
    Period size: 21  Copynumber: 3.8  Consensus size: 21

       7556 TATCTTAGAT

                                  
       7566 ATAAT-ATATATTATTAAATAA
          1 ATAATAATATATT-TTAAATAA

                                  
       7587 ATAATGAATATATTTTAAAT-A
          1 ATAAT-AATATATTTTAAATAA

                        *   *      
       7608 ATAAATAATGA-GTTTAAAATAA
          1 AT-AATAAT-ATATTTTAAATAA

                               
       7630 ATTAATAATATATATTTAA
          1 A-TAATAATATAT-TTTAA

       7649 TTACTAAACG


Statistics
Matches: 50,  Mismatches: 4, Indels: 14
        0.74            0.06        0.21

Matches are distributed among these distances:
  21   19  0.38
  22   19  0.38
  23   12  0.24

ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41


Consensus pattern (21 bp):   
ATAATAATATATTTTAAATAA

Found at i:11831 original size:33 final size:33

Alignment explanation


    Indices: 11787--11878  Score: 123
    Period size: 33  Copynumber: 2.8  Consensus size: 33

      11777 TTTGGATTCT

                *             *              
      11787 ATTGTTCCCACTAATATTATGCCTCAGAATGAG
          1 ATTGCTCCCACTAATATTGTGCCTCAGAATGAG

                         *  *         *       
      11820 ATTG-TCGCCACTGATGTTGTGCCTCGGAATGAG
          1 ATTGCTC-CCACTAATATTGTGCCTCAGAATGAG

                                      
      11853 ATTGCTCCCACTAATATTGTGCCTCA
          1 ATTGCTCCCACTAATATTGTGCCTCA

      11879 ACGAACACAC


Statistics
Matches: 50,  Mismatches: 7, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  32    2  0.04
  33   46  0.92
  34    2  0.04

ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33


Consensus pattern (33 bp):   
ATTGCTCCCACTAATATTGTGCCTCAGAATGAG

Found at i:12562 original size:6 final size:6

Alignment explanation


    Indices: 12553--12579  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      12543 ATATATATAA

                                           
      12553 TATATT TATATT TATATT TATATT TAT
          1 TATATT TATATT TATATT TATATT TAT

      12580 TTATTTCATC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (6 bp):   
TATATT

Found at i:13980 original size:2 final size:2

Alignment explanation


    Indices: 13968--14008  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      13958 AGAAAACAAT

                  *                                                      
      13968 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      14009 TGATACTAGA


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:15817 original size:23 final size:23

Alignment explanation


    Indices: 15783--15835  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      15773 GCGCGAGTGA

                   *      **       
      15783 CCGGCCATGCGACTTGGAGAAGC
          1 CCGGCCACGCGACTCAGAGAAGC

                                *  
      15806 CCGGCCACGCGACTCAGAGATGC
          1 CCGGCCACGCGACTCAGAGAAGC

                   
      15829 CCGGCCA
          1 CCGGCCA

      15836 TCACCGGCCA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  23   26  1.00

ACGTcount: A:0.21, C:0.38, G:0.32, T:0.09


Consensus pattern (23 bp):   
CCGGCCACGCGACTCAGAGAAGC

Found at i:15866 original size:33 final size:33

Alignment explanation


    Indices: 15806--15878  Score: 87
    Period size: 33  Copynumber: 2.2  Consensus size: 33

      15796 TTGGAGAAGC

                              *               
      15806 CCGGCCACGCGACTCAGAGATGCCCGGCCATC-A
          1 CCGGCCACGCGACTCAGACATGCCCGGCCA-CAA

                            *      *          
      15839 CCGGCCACGCGACAT-GGACATGTCCGGCCACAA
          1 CCGGCCACGCGAC-TCAGACATGCCCGGCCACAA

                   
      15872 CCGGCCA
          1 CCGGCCA

      15879 TCGCCTGGCG


Statistics
Matches: 35,  Mismatches: 3, Indels: 4
        0.83            0.07        0.10

Matches are distributed among these distances:
  32    1  0.03
  33   33  0.94
  34    1  0.03

ACGTcount: A:0.22, C:0.42, G:0.27, T:0.08


Consensus pattern (33 bp):   
CCGGCCACGCGACTCAGACATGCCCGGCCACAA
Done.