Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023174.1 Corchorus olitorius cultivar O-4 contig23207, 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: 2036
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29


Found at i:1421 original size:33 final size:33

Alignment explanation


    Indices: 1399--1513  Score: 115
    Period size: 33  Copynumber: 3.5  Consensus size: 33

       1389 AGAATTTTTT

                                             
       1399 TCATCACAAACAACACCTAAAACAAATTTAGTG
          1 TCATCACAAACAACACCTAAAACAAATTTAGTG

                            *    ** **      *
       1432 TCATCACAAACAACACTTAAATTAGGTTTAGTA
          1 TCATCACAAACAACACCTAAAACAAATTTAGTG

                   *       *        *         
       1465 TCATCACTAACAACATCTAAAACAGATTTCA-TG
          1 TCATCACAAACAACACCTAAAACAAATTT-AGTG

                **          
       1498 TCATTGCAAACAACAC
          1 TCATCACAAACAACAC

       1514 TCAAATCAGG


Statistics
Matches: 64,  Mismatches: 17, Indels: 2
        0.77            0.20        0.02

Matches are distributed among these distances:
  33   63  0.98
  34    1  0.02

ACGTcount: A:0.44, C:0.23, G:0.07, T:0.25


Consensus pattern (33 bp):   
TCATCACAAACAACACCTAAAACAAATTTAGTG

Found at i:1477 original size:66 final size:66

Alignment explanation


    Indices: 1399--1525  Score: 175
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1389 AGAATTTTTT

                                                               *    *        
       1399 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
          1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG

              
       1463 TA
         65 TA

                   *       *        *            **                      
       1465 TCATCACTAACAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
          1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT

       1526 CAGAATTACT


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  66   52  0.98
  67    1  0.02

ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGT
A
Done.