Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022980.1 Corchorus olitorius cultivar O-4 contig23013, 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: 3850
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Found at i:535 original size:21 final size:20

Alignment explanation


    Indices: 486--535  Score: 55
    Period size: 21  Copynumber: 2.4  Consensus size: 20

        476 TTTTTCTTCT

                      *          
        486 ACTACCTTTATTCACAAGTTC
          1 ACTA-CTTTAATCACAAGTTC

                              *   
        507 ACTCACTTTAATCAACAATTTC
          1 ACT-ACTTTAATC-ACAAGTTC

                   
        529 ACTACTT
          1 ACTACTT

        536 CGTCACTTTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  21   14  0.56
  22   11  0.44

ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38


Consensus pattern (20 bp):   
ACTACTTTAATCACAAGTTC

Found at i:1643 original size:26 final size:26

Alignment explanation


    Indices: 1607--1656  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       1597 GTCCCTTTGG

                       * *            
       1607 AAAAAAAAAAGTGTGTTAGTAACCTC
          1 AAAAAAAAAAGGGAGTTAGTAACCTC

                *                   
       1633 AAAAGAAAAAGGGAGTTAGTAACC
          1 AAAAAAAAAAGGGAGTTAGTAACC

       1657 CCTAAATCAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   21  1.00

ACGTcount: A:0.52, C:0.10, G:0.20, T:0.18


Consensus pattern (26 bp):   
AAAAAAAAAAGGGAGTTAGTAACCTC

Found at i:2678 original size:76 final size:75

Alignment explanation


    Indices: 2591--2735  Score: 175
    Period size: 76  Copynumber: 1.9  Consensus size: 75

       2581 CTATGACATA

                 *           *                   *                           
       2591 GCCCATCTGGGTGATCAGGCAAAACACAT-GTGTCTCCAGACAAACCATGTGGGCACCCAGCTGC
          1 GCCCACCTGGGTGATCAAGCAAAACACATGGTGT-TCAAGAC-AACCATGTGGGCACCCAGCTGC

                        
       2655 AGTCGTGACACT
         64 AGTCGTGACACT

                        *          *                *             *     *  * 
       2667 GCCCACCTGGGTTATCAAGCAAACCACATGGGTGTTCAAGGCAACCATGTGGGCGCCCAGGTGGA
          1 GCCCACCTGGGTGATCAAGCAAAACACAT-GGTGTTCAAGACAACCATGTGGGCACCCAGCTGCA

                
       2732 GTCG
         65 GTCG

       2736 GGGTTCTAGT


Statistics
Matches: 58,  Mismatches: 9, Indels: 4
        0.82            0.13        0.06

Matches are distributed among these distances:
  76   49  0.84
  77    5  0.09
  78    4  0.07

ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18


Consensus pattern (75 bp):   
GCCCACCTGGGTGATCAAGCAAAACACATGGTGTTCAAGACAACCATGTGGGCACCCAGCTGCAG
TCGTGACACT
Done.