Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010141.1 Corchorus capsularis cultivar CVL-1 contig10162, 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: 7840
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:104 original size:15 final size:14

Alignment explanation


    Indices: 53--145  Score: 58
    Period size: 11  Copynumber: 7.1  Consensus size: 14

         43 TTATGATTAG

                        * 
         53 TTTTAATTAGTTAA
          1 TTTTAATTAGTTTA

              **      *   
         67 TTAAAATTA-CTTA
          1 TTTTAATTAGTTTA

            *             
         80 GTTT-ATTAGTTTA
          1 TTTTAATTAGTTTA

                           
         93 TGTTTAATTAG--TA
          1 T-TTTAATTAGTTTA

              *           
        106 -TCTAATTAGTTTA
          1 TTTTAATTAGTTTA

                           
        119 TTATTAATTAG--TA
          1 TT-TTAATTAGTTTA

                          
        132 -TTTAATTAGTTTA
          1 TTTTAATTAGTTTA

             
        145 T
          1 T

        146 GATTAAAATG


Statistics
Matches: 58,  Mismatches: 11, Indels: 20
        0.65            0.12        0.22

Matches are distributed among these distances:
  11   16  0.28
  12    5  0.09
  13   14  0.24
  14   11  0.19
  15   12  0.21

ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56


Consensus pattern (14 bp):   
TTTTAATTAGTTTA

Found at i:113 original size:26 final size:26

Alignment explanation


    Indices: 84--151  Score: 102
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         74 TACTTAGTTT

                                      
         84 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGTTTAATTAGTATCTA

                                    *  
        110 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAGTATCTA

                       *    
        136 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

        152 AATGAAGGAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   37  0.97

ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAGTATCTA

Found at i:199 original size:24 final size:25

Alignment explanation


    Indices: 160--219  Score: 79
    Period size: 25  Copynumber: 2.5  Consensus size: 25

        150 AAAATGAAGG

                              *      
        160 AAAATGAA-TTTGAAG-ATTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

                                     
        183 AAAATGAAGTTTGAAGAAGTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

            *    *      
        208 GAAATTAAGTTT
          1 AAAATGAAGTTT

        220 AGGGTTTGAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  23    8  0.25
  24    7  0.22
  25   17  0.53

ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37


Consensus pattern (25 bp):   
AAAATGAAGTTTGAAGAAGTTGTTA

Found at i:551 original size:2 final size:2

Alignment explanation


    Indices: 546--582  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        536 TTTTATTATC

                                                                   
        546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        583 GATAGGATGG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6149 original size:12 final size:12

Alignment explanation


    Indices: 6132--6165  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       6122 AAAGTGTATT

                        
       6132 ATGAAGATGATC
          1 ATGAAGATGATC

                   *   *
       6144 ATGAAGAAGATG
          1 ATGAAGATGATC

                      
       6156 ATGAAGATGA
          1 ATGAAGATGA

       6166 AGAAGGTGAG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.47, C:0.03, G:0.29, T:0.21


Consensus pattern (12 bp):   
ATGAAGATGATC

Found at i:7425 original size:31 final size:31

Alignment explanation


    Indices: 7376--7437  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7366 AGTTTTGTAA

                       * *     *           
       7376 AACTTTTAAAATGCCTATTGTACCCTTATTT
          1 AACTTTTAAAACGACTATTATACCCTTATTT

                   *              *        
       7407 AACTTTTGAAACGACTATTATATCCTTATTT
          1 AACTTTTAAAACGACTATTATACCCTTATTT

       7438 GTCTAATATA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45


Consensus pattern (31 bp):   
AACTTTTAAAACGACTATTATACCCTTATTT
Done.