Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009595.1 Corchorus capsularis cultivar CVL-1 contig09616, 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: 3735
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34


Found at i:49 original size:29 final size:29

Alignment explanation


    Indices: 7--93  Score: 86
    Period size: 29  Copynumber: 2.9  Consensus size: 29

          1 AACGTC

                *                        
          7 CCAAAATTGAAGTTCAGGGGGCAAAATGT
          1 CCAAGATTGAAGTTCAGGGGGCAAAATGT

                                       *  
         36 CCAAGATTGAAGTTC-GGGGGACAAAACGT
          1 CCAAGATTGAAGTTCAGGGGG-CAAAATGT

              *    * **                  
         65 CTAAACGCTACAAGTTCAGGGGGCAAAAT
          1 C-CAA-GATTGAAGTTCAGGGGGCAAAAT

         94 TGTTGTTTAA


Statistics
Matches: 47,  Mismatches: 7, Indels: 6
        0.78            0.12        0.10

Matches are distributed among these distances:
  28    5  0.11
  29   22  0.47
  30    2  0.04
  31   13  0.28
  32    5  0.11

ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18


Consensus pattern (29 bp):   
CCAAGATTGAAGTTCAGGGGGCAAAATGT

Found at i:1170 original size:46 final size:45

Alignment explanation


    Indices: 1027--1170  Score: 153
    Period size: 46  Copynumber: 3.1  Consensus size: 45

       1017 TAAAATATGT

                *                              *      *   
       1027 TATATTATATATGTTTTTATTATATATAAATAAAAAAAATTTTAAA
          1 TATAGTATATATGTTTTTATTATATATAAAT-AAATAAATTTAAAA

                *       *  * * *      *  *       *        
       1073 TATATTATATATATTATAAATATATTTTATATAAATATATTTAAAA
          1 TATAGTATATATGTTTTTATTATA-TATAAATAAATAAATTTAAAA

            *                                             
       1119 CATAGTATATATGTTTTTATTATATATAAATAAATAAACTTTAAAA
          1 TATAGTATATATGTTTTTATTATATATAAATAAATAAA-TTTAAAA

                  
       1165 TATAGT
          1 TATAGT

       1171 TTAAATATAT


Statistics
Matches: 77,  Mismatches: 19, Indels: 4
        0.77            0.19        0.04

Matches are distributed among these distances:
  45   11  0.14
  46   61  0.79
  47    5  0.06

ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47


Consensus pattern (45 bp):   
TATAGTATATATGTTTTTATTATATATAAATAAATAAATTTAAAA

Found at i:2501 original size:15 final size:16

Alignment explanation


    Indices: 2481--2510  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2471 ATAAATGATT

                            
       2481 TATAA-TATTTAAATA
          1 TATAATTATTTAAATA

                           
       2496 TATAATTATTTAAAT
          1 TATAATTATTTAAAT

       2511 TAGAAAATGG


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

Matches are distributed among these distances:
  15    5  0.36
  16    9  0.64

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (16 bp):   
TATAATTATTTAAATA

Done.