Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015833.1 Corchorus capsularis cultivar CVL-1 contig15854, 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: 2892
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37


Found at i:402 original size:22 final size:21

Alignment explanation


    Indices: 369--418  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        359 CTTGTGAAGA

                  *              
        369 TTTTTAGTAACCTTATTAATC
          1 TTTTTAATAACCTTATTAATC

                               * *
        390 TTTTTAATAAACCTTATTATTT
          1 TTTTTAAT-AACCTTATTAATC

                   
        412 TTTTTAA
          1 TTTTTAA

        419 AAAAAATTCT


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  21    7  0.28
  22   18  0.72

ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58


Consensus pattern (21 bp):   
TTTTTAATAACCTTATTAATC

Found at i:537 original size:22 final size:21

Alignment explanation


    Indices: 503--546  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 21

        493 GCTATGTTTA

                    *        *    
        503 TTAGCAACGTTACTAAATTTTT
          1 TTAGCAACCTTAC-AAACTTTT

                *                
        525 TTAGTAACCTTACAAACTTTT
          1 TTAGCAACCTTACAAACTTTT

             
        546 T
          1 T

        547 ATTAACTTGT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  21    8  0.42
  22   11  0.58

ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45


Consensus pattern (21 bp):   
TTAGCAACCTTACAAACTTTT

Found at i:1668 original size:23 final size:23

Alignment explanation


    Indices: 1625--1668  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1615 ATTTGGGGCG

                     *             
       1625 ATTAATTGATTTGTTTAGTTGGA
          1 ATTAATTGAATTGTTTAGTTGGA

                             *    
       1648 ATTAATT-AATTGATTTGGTTG
          1 ATTAATTGAATTG-TTTAGTTG

       1669 AAAATATTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    4  0.22
  23   14  0.78

ACGTcount: A:0.27, C:0.00, G:0.20, T:0.52


Consensus pattern (23 bp):   
ATTAATTGAATTGTTTAGTTGGA

Found at i:2673 original size:28 final size:29

Alignment explanation


    Indices: 2623--2687  Score: 114
    Period size: 28  Copynumber: 2.3  Consensus size: 29

       2613 ACACTTATTC

                                         
       2623 TACTCAATATTTTTTAGGAAAAAATTATG
          1 TACTCAATATTTTTTAGGAAAAAATTATG

                             *           
       2652 TACTCAATATTTTTTA-TAAAAAATTATG
          1 TACTCAATATTTTTTAGGAAAAAATTATG

                    
       2680 TACTCAAT
          1 TACTCAAT

       2688 TTGACATTTG


Statistics
Matches: 35,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  28   19  0.54
  29   16  0.46

ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43


Consensus pattern (29 bp):   
TACTCAATATTTTTTAGGAAAAAATTATG
Done.