Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012502.1 Corchorus olitorius cultivar O-4 contig12535, 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: 5063
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26


Found at i:455 original size:44 final size:45

Alignment explanation


    Indices: 405--512  Score: 137
    Period size: 45  Copynumber: 2.4  Consensus size: 45

        395 GAAAACGTGC

                      *            *                     
        405 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTTA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

                         *     * **       *              
        449 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

                         *     
        494 AGGAGATCAAAGAGAGCTT
          1 AGGAGATCAAAGAAAGCTT

        513 TGGCCTACCA


Statistics
Matches: 56,  Mismatches: 7, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  44   14  0.25
  45   42  0.75

ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22


Consensus pattern (45 bp):   
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTTA

Found at i:484 original size:45 final size:46

Alignment explanation


    Indices: 428--530  Score: 181
    Period size: 45  Copynumber: 2.2  Consensus size: 46

        418 AAGTTAGAAT

                  *                                       
        428 CCATGACTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC-
          1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCA

                                                           
        473 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCTA
          1 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCC-A

                       
        520 CCATGATTGCC
          1 CCATGATTGCC

        531 GAGTGCACAA


Statistics
Matches: 55,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  45   44  0.80
  47   11  0.20

ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24


Consensus pattern (46 bp):   
CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCCA

Found at i:4673 original size:24 final size:25

Alignment explanation


    Indices: 4629--4675  Score: 62
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       4619 AGAGAGAAAA

                            *        
       4629 AGGAAGAGAGAGAAAGTGAAAAAGG
          1 AGGAAGAGAGAGAAAGAGAAAAAGG

                                    
       4654 AGGAATGAGA-AGAAA-AGAAAAA
          1 AGGAA-GAGAGAGAAAGAGAAAAA

       4676 ATAGGGTTTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  24    6  0.30
  25   10  0.50
  26    4  0.20

ACGTcount: A:0.62, C:0.00, G:0.34, T:0.04


Consensus pattern (25 bp):   
AGGAAGAGAGAGAAAGAGAAAAAGG
Done.