Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001413.1 Corchorus olitorius cultivar O-4 contig01413, 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: 7246
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30


Found at i:1437 original size:37 final size:37

Alignment explanation


    Indices: 1380--1450  Score: 106
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       1370 TCCTATACTG

                                                 
       1380 GGCCCAAAGTCAGTTCATAAATAAAGGCAAAGCCCAA
          1 GGCCCAAAGTCAGTTCATAAATAAAGGCAAAGCCCAA

                    * *    *             *    
       1417 GGCCCAAATTGAGTTGATAAATAAAGGCACAGCC
          1 GGCCCAAAGTCAGTTCATAAATAAAGGCAAAGCC

       1451 GTGTTGCAAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   30  1.00

ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15


Consensus pattern (37 bp):   
GGCCCAAAGTCAGTTCATAAATAAAGGCAAAGCCCAA

Found at i:7136 original size:24 final size:24

Alignment explanation


    Indices: 7104--7151  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       7094 GACAACTTAC

                                    
       7104 TTCCTTCCTCTTCCATAAAAATCT
          1 TTCCTTCCTCTTCCATAAAAATCT

                                    
       7128 TTCCTTCCTCTTCCATAAAAATCT
          1 TTCCTTCCTCTTCCATAAAAATCT

       7152 CTGCTTCTGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.25, C:0.33, G:0.00, T:0.42


Consensus pattern (24 bp):   
TTCCTTCCTCTTCCATAAAAATCT

Found at i:7158 original size:24 final size:24

Alignment explanation


    Indices: 7105--7158  Score: 90
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       7095 ACAACTTACT

                                   *
       7105 TCCTTCCTCTTCCATAAAAATCTT
          1 TCCTTCCTCTTCCATAAAAATCTC

                                    
       7129 TCCTTCCTCTTCCATAAAAATCTC
          1 TCCTTCCTCTTCCATAAAAATCTC

             *    
       7153 TGCTTC
          1 TCCTTC

       7159 TGCAATAAAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   28  1.00

ACGTcount: A:0.22, C:0.35, G:0.02, T:0.41


Consensus pattern (24 bp):   
TCCTTCCTCTTCCATAAAAATCTC
Done.