Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015023.1 Corchorus capsularis cultivar CVL-1 contig15044, 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: 3705
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35


Found at i:653 original size:65 final size:65

Alignment explanation


    Indices: 514--652  Score: 210
    Period size: 64  Copynumber: 2.2  Consensus size: 65

        504 ACGTAGTTCA

                        *      *           *        *                        
        514 TTTTTTTTTTGTTCTCTAAGTTTTGCCTAAGTCGCCATTTTCAGGATTTTCAACTTAGCGAGCCT
          1 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGCCATTTGCAGGATTTTCAACTTAGCGAGCCT

                                                                            *
        579 TTTTTTTTTTG-GCTCTAACTTTTGCCTAAGCCGTCC-TTTGCAGGATTTTCAACTTAGCGAGCT
          1 TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCG-CCATTTGCAGGATTTTCAACTTAGCGAGCC

             
        642 T
         65 T

                      
        643 TTTTTTTTTT
          1 TTTTTTTTTT

        653 TTTTTTGGGT


Statistics
Matches: 68,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  64   55  0.81
  65   13  0.19

ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50


Consensus pattern (65 bp):   
TTTTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGCCATTTGCAGGATTTTCAACTTAGCGAGCCT

Found at i:2892 original size:16 final size:16

Alignment explanation


    Indices: 2871--2905  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2861 ATCTGAAATA

                            
       2871 CTTCAGAACTTTTCTG
          1 CTTCAGAACTTTTCTG

                   *        
       2887 CTTCAGAGCTTTTCTG
          1 CTTCAGAACTTTTCTG

               
       2903 CTT
          1 CTT

       2906 TCTGAATTGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46


Consensus pattern (16 bp):   
CTTCAGAACTTTTCTG
Done.