Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010404.1 Corchorus capsularis cultivar CVL-1 contig10425, 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: 21911
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:9616 original size:11 final size:11

Alignment explanation


    Indices: 9600--9631  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       9590 GAAGTTCGTG

                       
       9600 TTTGAAGATTA
          1 TTTGAAGATTA

                     * 
       9611 TTTGAAGATAA
          1 TTTGAAGATTA

                      
       9622 TTTGAAGATT
          1 TTTGAAGATT

       9632 TGAAAATTAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44


Consensus pattern (11 bp):   
TTTGAAGATTA

Found at i:9641 original size:30 final size:30

Alignment explanation


    Indices: 9600--9659  Score: 86
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       9590 GAAGTTCGTG

                  *                   *    
       9600 TTTGAAGATTATTTGAAG-ATAATTTGAAGA
          1 TTTGAAAATTA-TTGAAGAATAATTTCAAGA

                                          
       9630 TTTGAAAATTATTGAAGAATAATTTCAAGA
          1 TTTGAAAATTATTGAAGAATAATTTCAAGA

       9660 AGCAAGAATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29    6  0.22
  30   21  0.78

ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38


Consensus pattern (30 bp):   
TTTGAAAATTATTGAAGAATAATTTCAAGA

Found at i:11007 original size:6 final size:6

Alignment explanation


    Indices: 10996--11026  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      10986 ATAATTGCCA

                                                 
      10996 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
          1 TAGATT TAGATT TAGATT TAGATT TAGATT TA

      11027 CTTTGCTTAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.20
   6   20  0.80

ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52


Consensus pattern (6 bp):   
TAGATT

Found at i:15796 original size:19 final size:19

Alignment explanation


    Indices: 15760--15806  Score: 51
    Period size: 19  Copynumber: 2.5  Consensus size: 19

      15750 TTTTTGAAAG

                         **    
      15760 ATTAAAT-TTATTTGTATT
          1 ATTAAATATTATTACTATT

            *                  
      15778 TTTAAATATTATTACTATT
          1 ATTAAATATTATTACTATT

                      
      15797 ATTAATATAT
          1 ATTAA-ATAT

      15807 AAGTCAATAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  18    6  0.26
  19   13  0.57
  20    4  0.17

ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57


Consensus pattern (19 bp):   
ATTAAATATTATTACTATT

Found at i:18948 original size:11 final size:11

Alignment explanation


    Indices: 18919--18963  Score: 56
    Period size: 11  Copynumber: 4.2  Consensus size: 11

      18909 CAAAACGATT

                      *
      18919 CATTAA-AAAC
          1 CATTAATAAAA

                *      
      18929 CATTTATAAAA
          1 CATTAATAAAA

                       
      18940 CATTAATAAAA
          1 CATTAATAAAA

              *        
      18951 CAGTAATAAAA
          1 CATTAATAAAA

              
      18962 CA
          1 CA

      18964 GTTCCTCAAC


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  10    5  0.17
  11   25  0.83

ACGTcount: A:0.60, C:0.13, G:0.02, T:0.24


Consensus pattern (11 bp):   
CATTAATAAAA

Found at i:20340 original size:18 final size:18

Alignment explanation


    Indices: 20283--20342  Score: 54
    Period size: 18  Copynumber: 3.3  Consensus size: 18

      20273 CTTGGCCCGC

                    *         
      20283 GCCTGGCCCGCGCGCCAG
          1 GCCTGGCCTGCGCGCCAG

              *                 
      20301 GCTTGGCACTTG-G-GCC-G
          1 GCCTGGC-C-TGCGCGCCAG

                               
      20318 CGCCTGGCCTGCGCGCCAG
          1 -GCCTGGCCTGCGCGCCAG

                  
      20337 GCCTGG
          1 GCCTGG

      20343 GCGTTTGGGC


Statistics
Matches: 33,  Mismatches: 3, Indels: 12
        0.69            0.06        0.25

Matches are distributed among these distances:
  16    2  0.06
  17    3  0.09
  18   24  0.73
  19    3  0.09
  20    1  0.03

ACGTcount: A:0.05, C:0.42, G:0.40, T:0.13


Consensus pattern (18 bp):   
GCCTGGCCTGCGCGCCAG

Found at i:21571 original size:59 final size:60

Alignment explanation


    Indices: 21475--21604  Score: 147
    Period size: 59  Copynumber: 2.2  Consensus size: 60

      21465 TTCTTGGGGA

                      *                  ** *             * *  *        
      21475 GAAATTGTCCTAATTTTGATAGTTTAGAGGGTGAAAGTTTC-AAATTAGAAGTTTAAGGG
          1 GAAATTGTCCCAATTTTGATAGTTTAGAGACTAAAAGTTTCAAAATAAAAAATTTAAGGG

                       *                                             *   
      21534 GAAATTGTCCCGATTTTGATAGTTTA-ATGACTAAAAGTTTCAAAATAAAAAATTTAGGGG
          1 GAAATTGTCCCAATTTTGATAGTTTAGA-GACTAAAAGTTTCAAAATAAAAAATTTAAGGG

                *      
      21594 GAAAATGTCCC
          1 GAAATTGTCCC

      21605 TTTTGTAAGA


Statistics
Matches: 59,  Mismatches: 10, Indels: 3
        0.82            0.14        0.04

Matches are distributed among these distances:
  58    1  0.02
  59   34  0.58
  60   24  0.41

ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33


Consensus pattern (60 bp):   
GAAATTGTCCCAATTTTGATAGTTTAGAGACTAAAAGTTTCAAAATAAAAAATTTAAGGG
Done.