Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009601.1 Corchorus olitorius cultivar O-4 contig09633, 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: 2479
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39


Found at i:740 original size:58 final size:58

Alignment explanation


    Indices: 645--754  Score: 152
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        635 ATTAATCAAA

                                                          *           
        645 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT

                *           *                       *             
        703 TATCGAGTGACATGTTTTTTAATTAGATGTC-T-AAAAAATACGTTTTAGGACC
          1 TATCAAGTGACATGTTCTTT-ATTAGATG-CATAAAAAAAGACGTTTTAGGACC

        755 GAGGCATGAT


Statistics
Matches: 46,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  58   36  0.78
  59    9  0.20
  60    1  0.02

ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35


Consensus pattern (58 bp):   
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT

Found at i:1589 original size:36 final size:36

Alignment explanation


    Indices: 1542--1611  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1532 TTCAATAACC

                         *      *               
       1542 TTACATCTTTTGTGATTTTGGTTATCAAATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCAAATTTCTTA

                  *                    *      
       1578 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCAAATTTCT

       1612 CCAAAATCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCAAATTTCTTA
Done.