Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023958.1 Corchorus olitorius cultivar O-4 contig23991, 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: 7267
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:1035 original size:19 final size:18

Alignment explanation


    Indices: 1002--1037  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

        992 TTGAGATAAT

                              
       1002 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1020 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1038 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:2597 original size:30 final size:29

Alignment explanation


    Indices: 2557--2613  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       2547 GTTCATTAAT

                                           
       2557 GAAACTTGAAAATTAAAGACATAAGATAAAG
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG

                                       
       2588 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

       2614 CTAATCCTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAG

Found at i:3119 original size:25 final size:25

Alignment explanation


    Indices: 3091--3154  Score: 94
    Period size: 25  Copynumber: 2.6  Consensus size: 25

       3081 GCGGCTACCA

                                   *  
       3091 CGCAGCAG-CAGCAGCAGGCTTGCTC
          1 CGCAG-AGACAGCAGCAGGCTTGATC

                      *              
       3116 CGCAGAGACAACAGCAGGCTTGATC
          1 CGCAGAGACAGCAGCAGGCTTGATC

                          
       3141 CGCAGAGACAGCAG
          1 CGCAGAGACAGCAG

       3155 GTACTTGCTG


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
  24    2  0.06
  25   33  0.94

ACGTcount: A:0.28, C:0.31, G:0.31, T:0.09


Consensus pattern (25 bp):   
CGCAGAGACAGCAGCAGGCTTGATC

Done.