Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002496.1 Corchorus olitorius cultivar O-4 contig02496, 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: 2800
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35


Found at i:1262 original size:90 final size:91

Alignment explanation


    Indices: 1136--1314  Score: 270
    Period size: 90  Copynumber: 1.9  Consensus size: 91

       1126 TAATCCCCTT

                      *                 *           *                    *   
       1136 TAAACTGGAAGTGTGTAAGATTAAAGACTTGATCTTATTAGTAAATACACTTAT-GGGATCGAAC
          1 TAAACTGGAAATGTGTAAGATTAAAGACCTGATCTTATTAATAAATACACTTATGGGGATCCAAC

                                      
       1200 TTATAATCTCACTCTTGCCCAACCAA
         66 TTATAATCTCACTCTTGCCCAACCAA

                                           *                                 
       1226 TAAACTGGAAATGTGTAAGATTAAAGACCTGGTCTTATTAATAAATACACTTATGACGGGGATCC
          1 TAAACTGGAAATGTGTAAGATTAAAGACCTGATCTTATTAATAAATACACTTAT---GGGGATCC

                    *               
       1291 AACTTATAGTCTCACTCTTGCCCA
         63 AACTTATAATCTCACTCTTGCCCA

       1315 CCTCTTTTGG


Statistics
Matches: 79,  Mismatches: 6, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  90   50  0.63
  94   29  0.37

ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Consensus pattern (91 bp):   
TAAACTGGAAATGTGTAAGATTAAAGACCTGATCTTATTAATAAATACACTTATGGGGATCCAAC
TTATAATCTCACTCTTGCCCAACCAA

Found at i:2771 original size:2 final size:2

Alignment explanation


    Indices: 2764--2795  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       2754 AAAGCTACAC

                                                           
       2764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2796 CACTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.