Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015088.1 Corchorus olitorius cultivar O-4 contig15121, 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: 3540
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38


Found at i:695 original size:36 final size:36

Alignment explanation


    Indices: 648--717  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        638 GAGATTTTGG

                         *      *               
        648 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        684 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        718 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:2073 original size:59 final size:58

Alignment explanation


    Indices: 1976--2086  Score: 168
    Period size: 59  Copynumber: 1.9  Consensus size: 58

       1966 ATAGCATCAT

                 *    *                                    *          
       1976 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCCATAA
          1 GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGCCACTCCATAA

                                       *             *           
       2034 GCCTCAGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAAGAACATGCCACT
          1 GCCTCAGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGCCACT

       2087 TGATGTTTGA


Statistics
Matches: 47,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  58   17  0.36
  59   30  0.64

ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30


Consensus pattern (58 bp):   
GCCTCAGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGCCACTCCATAA

Found at i:3076 original size:19 final size:21

Alignment explanation


    Indices: 3054--3093  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3044 CCTTATACTA

                                 
       3054 TATAA-ATTTTT-ATAACCTT
          1 TATAACATTTTTAATAACCTT

                  *              
       3073 TATAACTTTTTTAATAACCTT
          1 TATAACATTTTTAATAACCTT

       3094 AAAGAAGAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    5  0.28
  20    5  0.28
  21    8  0.44

ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53


Consensus pattern (21 bp):   
TATAACATTTTTAATAACCTT
Done.