Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015727.1 Corchorus olitorius cultivar O-4 contig15760, 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: 15820
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1462 original size:25 final size:24

Alignment explanation


    Indices: 1434--1490  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       1424 GTGGATTGTA

                        *            
       1434 AAATAAATTGAATAATTAAGACATT
          1 AAATAAATTGAAGAATTAA-ACATT

                     *              
       1459 AAATAAATTTAAGAATTAAACATT
          1 AAATAAATTGAAGAATTAAACATT

                     
       1483 AAA-AAATT
          1 AAATAAATT

       1491 CAAGGTTGAC


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    5  0.17
  24    8  0.27
  25   17  0.57

ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32


Consensus pattern (24 bp):   
AAATAAATTGAAGAATTAAACATT

Found at i:9051 original size:31 final size:30

Alignment explanation


    Indices: 8986--9051  Score: 96
    Period size: 31  Copynumber: 2.2  Consensus size: 30

       8976 AGTGACCTGC

                                     *   *
       8986 TATCCACTCTTTAATGTAGTTAGATTAGAC
          1 TATCCACTCTTTAATGTAGTTAGATAAGAA

                                        *  
       9016 TATCCACTCTTTATATGTAGTTAGATAATAA
          1 TATCCACTCTTTA-ATGTAGTTAGATAAGAA

                 
       9047 TATCC
          1 TATCC

       9052 CAATTTTATC


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  30   13  0.41
  31   19  0.59

ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41


Consensus pattern (30 bp):   
TATCCACTCTTTAATGTAGTTAGATAAGAA

Found at i:9060 original size:31 final size:31

Alignment explanation


    Indices: 8986--9060  Score: 82
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       8976 AGTGACCTGC

                  *                   *   *
       8986 TATCCACTCTTTA-ATGTAGTTAGATTAGAC
          1 TATCCAATCTTTATATGTAGTTAGATAAGAA

                  *                     *  
       9016 TATCCACTCTTTATATGTAGTTAGATAATAA
          1 TATCCAATCTTTATATGTAGTTAGATAAGAA

                           
       9047 TATCCCAAT-TTTAT
          1 TAT-CCAATCTTTAT

       9061 CAACCATTTT


Statistics
Matches: 39,  Mismatches: 4, Indels: 3
        0.85            0.09        0.07

Matches are distributed among these distances:
  30   13  0.33
  31   22  0.56
  32    4  0.10

ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43


Consensus pattern (31 bp):   
TATCCAATCTTTATATGTAGTTAGATAAGAA
Done.