Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013159.1 Corchorus capsularis cultivar CVL-1 contig13180, 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: 15041
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:983 original size:6 final size:6

Alignment explanation


    Indices: 967--1009  Score: 52
    Period size: 6  Copynumber: 7.3  Consensus size: 6

        957 CTAAGCAAAG

                        *      *    *                          
        967 TAAAT- TAAATA TAAATA TAATTC TAAATC TAAATC TAAATC TA
          1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA

       1010 TAGCAATTAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
   5    5  0.15
   6   29  0.85

ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37


Consensus pattern (6 bp):   
TAAATC

Found at i:10193 original size:30 final size:30

Alignment explanation


    Indices: 10159--10230  Score: 92
    Period size: 30  Copynumber: 2.4  Consensus size: 30

      10149 CCGGTTATGC

                            **        *    
      10159 CCGGTCTTGTGCAATTGGC-CCATGCCATGG
          1 CCGGTCTTGTGCAA-TCCCTCCATGCAATGG

                  *                       
      10189 CCGGTCATGTGCAATCCCTCCATGCAATGG
          1 CCGGTCTTGTGCAATCCCTCCATGCAATGG

                        
      10219 CCGGTCTTGTGC
          1 CCGGTCTTGTGC

      10231 GATGGCTTCC


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  29    2  0.06
  30   34  0.94

ACGTcount: A:0.14, C:0.32, G:0.28, T:0.26


Consensus pattern (30 bp):   
CCGGTCTTGTGCAATCCCTCCATGCAATGG

Found at i:12013 original size:31 final size:30

Alignment explanation


    Indices: 11972--12053  Score: 101
    Period size: 31  Copynumber: 2.7  Consensus size: 30

      11962 GCTAAATACC

                 *                         
      11972 CAAAAAAATCCCTTATGTTTTGCTTTTGGAA
          1 CAAAATAATCCCTTATGTTTT-CTTTTGGAA

                                  *      * 
      12003 CAAAATAATCCCTTATGTTGTTTTTTTGGGA
          1 CAAAATAATCCCTTATGTT-TTCTTTTGGAA

                *          *    
      12034 CAAATTAATCCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

      12054 CAAAAATGAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  30    1  0.02
  31   42  0.93
  32    2  0.04

ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTCTTTTGGAA

Found at i:15014 original size:30 final size:30

Alignment explanation


    Indices: 14978--15040  Score: 110
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      14968 CATCTTCAAG

                                           
      14978 TCCATGATAAGTCCTT-GGCGCATCATTCCC
          1 TCCATGATAAG-CCTTGGGCGCATCATTCCC

                                          
      15008 TCCATGATAAGCCTTGGGCGCATCATTCCC
          1 TCCATGATAAGCCTTGGGCGCATCATTCCC

               
      15038 TCC
          1 TCC

      15041 C


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  29    4  0.12
  30   28  0.88

ACGTcount: A:0.19, C:0.35, G:0.17, T:0.29


Consensus pattern (30 bp):   
TCCATGATAAGCCTTGGGCGCATCATTCCC
Done.