Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013932.1 Corchorus capsularis cultivar CVL-1 contig13953, 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: 3612
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38


Found at i:39 original size:19 final size:20

Alignment explanation


    Indices: 8--45  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

          1 TGATATT

                                
          8 TAAAAATTGAAATT-AAAAG
          1 TAAAAATTGAAATTCAAAAG

                                
         27 TAAAATATT-AAATTCAAAA
          1 TAAAA-ATTGAAATTCAAAA

         46 AATAATAGTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29


Consensus pattern (20 bp):   
TAAAAATTGAAATTCAAAAG

Found at i:380 original size:31 final size:31

Alignment explanation


    Indices: 344--409  Score: 107
    Period size: 31  Copynumber: 2.1  Consensus size: 31

        334 TGACAATTTA

                                          * 
        344 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
          1 GAAATATGTTTTAAA-AATAAGGGTACAATCG

                                           
        375 GAAATATGTTTTAAAAATAAGGGTACAATCG
          1 GAAATATGTTTTAAAAATAAGGGTACAATCG

                
        406 GAAA
          1 GAAA

        410 ACATAAAGTT


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  30    2  0.06
  31   31  0.94

ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27


Consensus pattern (31 bp):   
GAAATATGTTTTAAAAATAAGGGTACAATCG

Found at i:1000 original size:58 final size:58

Alignment explanation


    Indices: 910--1019  Score: 175
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        900 TTTTGGCCAT

                                                **                    
        910 AAGTTATCGGATTGATATTAACCTTGGAACGTAAAGGGAGGGGAGAAAAAAAAAGTTG
          1 AAGTTATCGGATTGATATTAACCTTGGAACGTAAAGAAAGGGGAGAAAAAAAAAGTTG

                   *             *   *                          
        968 AAGTTATTGGATTGATATTAATCTTTGAACGTAAAGAAAGGGGAGAAAAAAA
          1 AAGTTATCGGATTGATATTAACCTTGGAACGTAAAGAAAGGGGAGAAAAAAA

       1020 GTTTGACCTC


Statistics
Matches: 47,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  58   47  1.00

ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25


Consensus pattern (58 bp):   
AAGTTATCGGATTGATATTAACCTTGGAACGTAAAGAAAGGGGAGAAAAAAAAAGTTG

Found at i:2976 original size:29 final size:30

Alignment explanation


    Indices: 2929--2985  Score: 73
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       2919 GAACTTTGCC

                                           
       2929 AAAAGTGTCAAATAAGTGT-TCAAACTATGA
          1 AAAAGTGTCAAATAAGTGTCT-AAACTATGA

                         **             
       2959 AAAAG-GTCAAATTGGTGTCTAAACTAT
          1 AAAAGTGTCAAATAAGTGTCTAAACTAT

       2986 TAGATTTCGG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  29   18  0.75
  30    6  0.25

ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28


Consensus pattern (30 bp):   
AAAAGTGTCAAATAAGTGTCTAAACTATGA
Done.