Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009132.1 Corchorus capsularis cultivar CVL-1 contig09153, 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: 8525
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33


Found at i:720 original size:20 final size:21

Alignment explanation


    Indices: 683--725  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        673 AACCCGTTAA

                         *       
        683 TTAAAGCGTGTCACTCGTGTC
          1 TTAAAGCGTGTCAATCGTGTC

                       *         
        704 TTAAA-CGTGTTAATCGTGTC
          1 TTAAAGCGTGTCAATCGTGTC

              
        724 TT
          1 TT

        726 GACACGATTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40


Consensus pattern (21 bp):   
TTAAAGCGTGTCAATCGTGTC

Found at i:783 original size:42 final size:43

Alignment explanation


    Indices: 713--795  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

        703 CTTAAACGTG

                        *                              
        713 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
          1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC

                                            *         
        756 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
          1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA

        796 GCCAAACACG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  41    1  0.03
  42   25  0.68
  43   11  0.30

ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23


Consensus pattern (43 bp):   
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC

Found at i:1869 original size:22 final size:22

Alignment explanation


    Indices: 1837--1884  Score: 87
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       1827 ACCCCAGATT

                                  
       1837 TCTTTTCCTTTATCCTTTAAAA
          1 TCTTTTCCTTTATCCTTTAAAA

                  *               
       1859 TCTTTTTCTTTATCCTTTAAAA
          1 TCTTTTCCTTTATCCTTTAAAA

                
       1881 TCTT
          1 TCTT

       1885 CGACTTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58


Consensus pattern (22 bp):   
TCTTTTCCTTTATCCTTTAAAA
Done.