Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011833.1 Corchorus capsularis cultivar CVL-1 contig11854, 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: 13217
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35


Found at i:333 original size:18 final size:18

Alignment explanation


    Indices: 312--346  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        302 GTATTATATA

                               
        312 TAAATAA-TATAATATAAT
          1 TAAATAATTAT-ATATAAT

                             
        330 TAAATAATTATATATAA
          1 TAAATAATTATATATAA

        347 CCTTTACATC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   13  0.81
  19    3  0.19

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (18 bp):   
TAAATAATTATATATAAT

Found at i:3648 original size:45 final size:45

Alignment explanation


    Indices: 3566--3655  Score: 126
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       3556 TAATAGAGTA

                     *                *                  
       3566 GTGGAATTATTAAAAGATCCCTACCCTAAATTAATGATAAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG

                                       **   *     *      
       3611 GTGGAATTACTAAAAGATCCCTACCCCGGATTCATGATGAGCTGG
          1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG

       3656 AAAAGTAATC


Statistics
Matches: 39,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  45   39  1.00

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27


Consensus pattern (45 bp):   
GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG

Found at i:7236 original size:19 final size:17

Alignment explanation


    Indices: 7209--7255  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 17

       7199 CCAATAAGAG

                *              
       7209 ATATGTAGTAATAAATACT
          1 ATATATAGTAAT--ATACT

                      *      
       7228 ATATATAGTACTATACT
          1 ATATATAGTAATATACT

                        
       7245 ATATATA-TAAT
          1 ATATATAGTAAT

       7256 TTTTTCATCT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  16    3  0.12
  17   12  0.48
  19   10  0.40

ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40


Consensus pattern (17 bp):   
ATATATAGTAATATACT

Found at i:12358 original size:4 final size:4

Alignment explanation


    Indices: 12349--12382  Score: 50
    Period size: 4  Copynumber: 8.5  Consensus size: 4

      12339 ATGTAAAAAC

                                          *    *      
      12349 CATA CATA CATA CATA CATA CATA TATA TATA CA
          1 CATA CATA CATA CATA CATA CATA CATA CATA CA

      12383 CATATATATA


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   4   28  1.00

ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29


Consensus pattern (4 bp):   
CATA

Found at i:12498 original size:6 final size:6

Alignment explanation


    Indices: 12486--12516  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

      12476 ACTCACACAC

                     *                          
      12486 AAATAT AATTAT AAATAT AAATAT AAATAT A
          1 AAATAT AAATAT AAATAT AAATAT AAATAT A

      12517 CATCAAAGTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (6 bp):   
AAATAT

Done.