Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007834.1 Corchorus capsularis cultivar CVL-1 contig07855, 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: 34341
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:6008 original size:20 final size:21

Alignment explanation


    Indices: 5972--6010  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 21

       5962 CGTGAGGCAA

                        *        
       5972 ACCACATGGGGCGCCAAGCAT
          1 ACCACATGGGGCCCCAAGCAT

                               
       5993 ACCACAT-GGGCCCCAAGC
          1 ACCACATGGGGCCCCAAGC

       6011 TAGAGCCGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20   10  0.59
  21    7  0.41

ACGTcount: A:0.28, C:0.38, G:0.26, T:0.08


Consensus pattern (21 bp):   
ACCACATGGGGCCCCAAGCAT

Found at i:12722 original size:33 final size:33

Alignment explanation


    Indices: 12629--12731  Score: 109
    Period size: 33  Copynumber: 3.1  Consensus size: 33

      12619 GCAAAGAGTG

                  *               *      *   
      12629 TTTTAGATGTTGTTTGCGATGATACTAAACCTA
          1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA

            *                 *    *         *
      12662 ATTT-GAGTGTTGTTTGCAATGACACTAAATCTG
          1 TTTTAG-GTGTTGTTTGCGATGAAACTAAATCTA

                           **                
      12695 TTTTAGGTGTTGTTTATGATGAAACTAAATCTA
          1 TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA

                
      12728 TTTT
          1 TTTT

      12732 GGATGCTAAT


Statistics
Matches: 56,  Mismatches: 12, Indels: 4
        0.78            0.17        0.06

Matches are distributed among these distances:
  32    1  0.02
  33   54  0.96
  34    1  0.02

ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45


Consensus pattern (33 bp):   
TTTTAGGTGTTGTTTGCGATGAAACTAAATCTA

Found at i:13232 original size:30 final size:30

Alignment explanation


    Indices: 13174--13236  Score: 83
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      13164 TCTTCAAGGG

                                 ***      
      13174 GGAGGGAATGATGCGCCCAAGGTTTATCAT
          1 GGAGGGAATGATGCGCCCAAGACATATCAT

                                           
      13204 GGAGGGAATGATGCG-CCAAGAACATATCAT
          1 GGAGGGAATGATGCGCCCAAG-ACATATCAT

               
      13234 GGA
          1 GGA

      13237 CTTGAATATG


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  29    5  0.17
  30   24  0.83

ACGTcount: A:0.32, C:0.16, G:0.33, T:0.19


Consensus pattern (30 bp):   
GGAGGGAATGATGCGCCCAAGACATATCAT

Found at i:21260 original size:6 final size:6

Alignment explanation


    Indices: 21251--21275  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      21241 GGGCGACCAT

                                         
      21251 CGGTGA CGGTGA CGGTGA CGGTGA C
          1 CGGTGA CGGTGA CGGTGA CGGTGA C

      21276 AGTGTCAGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.16, C:0.20, G:0.48, T:0.16


Consensus pattern (6 bp):   
CGGTGA

Found at i:21830 original size:19 final size:19

Alignment explanation


    Indices: 21808--21846  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      21798 TTAAATAATT

                               
      21808 AAAAATAAATTAAATATAG
          1 AAAAATAAATTAAATATAG

                * *        *   
      21827 AAAATTTAATTAAATTTAG
          1 AAAAATAAATTAAATATAG

             
      21846 A
          1 A

      21847 CATAATTTAG


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

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33


Consensus pattern (19 bp):   
AAAAATAAATTAAATATAG

Found at i:23439 original size:37 final size:37

Alignment explanation


    Indices: 23387--23462  Score: 116
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      23377 TCCTTTGCCG

                      *                  *       
      23387 TTGTAAATTAGTTTTACCAGTCCTTTTATGTACTTTT
          1 TTGTAAATTAATTTTACCAGTCCTTTTATATACTTTT

                 *               *               
      23424 TTGTAGATTAATTTTACCAGTTCTTTTATATACTTTT
          1 TTGTAAATTAATTTTACCAGTCCTTTTATATACTTTT

              
      23461 TT
          1 TT

      23463 TCTCCCAATA


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  37   35  1.00

ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57


Consensus pattern (37 bp):   
TTGTAAATTAATTTTACCAGTCCTTTTATATACTTTT

Found at i:24845 original size:10 final size:10

Alignment explanation


    Indices: 24821--24849  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

      24811 GCTTATCGAT

                      
      24821 ATCTCCATG-
          1 ATCTCCATGC

                      
      24830 ATCTCCATGC
          1 ATCTCCATGC

                      
      24840 ATCTCCATGC
          1 ATCTCCATGC

      24850 TTCCTTGCAG


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

Matches are distributed among these distances:
   9    9  0.47
  10   10  0.53

ACGTcount: A:0.21, C:0.38, G:0.10, T:0.31


Consensus pattern (10 bp):   
ATCTCCATGC
Done.