Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007235.1 Corchorus capsularis cultivar CVL-1 contig07256, 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: 22115
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:19 original size:2 final size:2

Alignment explanation


    Indices: 13--53  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

          3 GGCCTAATCG

                                           *                             
         13 AT AT AT AT AT AT AT AT AT AT AC 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 AT AT A

         54 CTTACTAGTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:619 original size:13 final size:13

Alignment explanation


    Indices: 598--636  Score: 62
    Period size: 13  Copynumber: 3.0  Consensus size: 13

        588 AAAGAAATCT

                          
        598 AAAGTAAAGATTTA
          1 AAAG-AAAGATTTA

                         
        612 AAAGAAAGATTTA
          1 AAAGAAAGATTTA

                         
        625 AAAGAAAG-TTTA
          1 AAAGAAAGATTTA

        637 GTAAAAACAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  12    4  0.16
  13   17  0.68
  14    4  0.16

ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26


Consensus pattern (13 bp):   
AAAGAAAGATTTA

Found at i:10006 original size:17 final size:18

Alignment explanation


    Indices: 9984--10017  Score: 61
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       9974 AATGCAATGC

                              
       9984 AAACTATATG-AAAACTT
          1 AAACTATATGCAAAACTT

                             
      10001 AAACTATATGCAAAACT
          1 AAACTATATGCAAAACT

      10018 ATGAACAAAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26


Consensus pattern (18 bp):   
AAACTATATGCAAAACTT

Found at i:11703 original size:88 final size:88

Alignment explanation


    Indices: 11560--11732  Score: 267
    Period size: 88  Copynumber: 2.0  Consensus size: 88

      11550 GTTAATTTCA

                           *                                                 
      11560 AAAATCTCCTAAGTTGACCTGAAAAGGGTTGAGTTCACCCTTTTTAGGGTCAGCTCA-GAAGATT
          1 AAAATCTCCTAAGTTAACCTGAAAAGGGTTGAGTTCACCCTTTTTAGGGTCAGCTCAGGAA-ATT

                         *          
      11624 TGGGCCAAACGTACATAAATTTTT
         65 TGGGCCAAACGTAAATAAATTTTT

                 *    *                                       *          *   
      11648 AAAATTTCCTGAGTTAACCTGAAAAGGGTTGAGTTCACCCTTTTTAGGGTTAGCTCAGGAACTTT
          1 AAAATCTCCTAAGTTAACCTGAAAAGGGTTGAGTTCACCCTTTTTAGGGTCAGCTCAGGAAATTT

            *                   
      11713 TGGCCAAACGTAAATAAATT
         66 GGGCCAAACGTAAATAAATT

      11733 CCTGTGTCGA


Statistics
Matches: 77,  Mismatches: 7, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  88   74  0.96
  89    3  0.04

ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31


Consensus pattern (88 bp):   
AAAATCTCCTAAGTTAACCTGAAAAGGGTTGAGTTCACCCTTTTTAGGGTCAGCTCAGGAAATTT
GGGCCAAACGTAAATAAATTTTT

Found at i:17348 original size:19 final size:18

Alignment explanation


    Indices: 17324--17359  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      17314 TGAAGATTTC

                               
      17324 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      17343 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      17360 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.