Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002729.1 Corchorus capsularis cultivar CVL-1 contig02737, 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, 775

Length: 1292
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35


Found at i:789 original size:30 final size:30

Alignment explanation


    Indices: 753--824  Score: 83
    Period size: 29  Copynumber: 2.4  Consensus size: 30

        743 CTTAGCAACA

                           ****           
        753 GGGCTTATTTGACTTTTTTTAAGAGTTCAG
          1 GGGCTTATTTGACTTGAAATAAGAGTTCAG

                        *         *       
        783 GGGCTTATTTG-GTTGAAATAATAGTTCAG
          1 GGGCTTATTTGACTTGAAATAAGAGTTCAG

                         
        812 GGGCTTATTTGAC
          1 GGGCTTATTTGAC

        825 GGTTCGGTGT


Statistics
Matches: 34,  Mismatches: 7, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  29   23  0.68
  30   11  0.32

ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42


Consensus pattern (30 bp):   
GGGCTTATTTGACTTGAAATAAGAGTTCAG

Found at i:1183 original size:3 final size:3

Alignment explanation


    Indices: 1175--1212  Score: 67
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       1165 ATTAAGAATT

                                                              
       1175 TAA TAA TAA TAA TAA TAA TAA TGAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T

       1213 TTTAATTTTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3   31  0.91
   4    3  0.09

ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:1186 original size:22 final size:22

Alignment explanation


    Indices: 1167--1212  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1157 ATCAATAAAT

                    *              
       1167 TAAGAATTTAATAATAATAATAA
          1 TAAGAA-TGAATAATAATAATAA

               *                  
       1190 TAATAATGAATAATAATAATAA
          1 TAAGAATGAATAATAATAATAA

             
       1212 T
          1 T

       1213 TTTAATTTTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22   16  0.76
  23    5  0.24

ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35


Consensus pattern (22 bp):   
TAAGAATGAATAATAATAATAA
Done.