Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016303.1 Corchorus olitorius cultivar O-4 contig16336, 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: 1827
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39


Found at i:454 original size:29 final size:30

Alignment explanation


    Indices: 394--474  Score: 110
    Period size: 29  Copynumber: 2.7  Consensus size: 30

        384 GCTAAATACC

                 *                    *    
        394 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
          1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA

                                          
        425 CAAAATAATCCCTTATGTTTT-TTTCGGGA
          1 CAAAATAATCCCTTATGTTTTCTTTCGGGA

                *          *     
        454 CAAATTAATCCCTTACGTTTT
          1 CAAAATAATCCCTTATGTTTT

        475 AAAAATGAGC


Statistics
Matches: 46,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  29   26  0.57
  31   20  0.43

ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTCTTTCGGGA

Found at i:594 original size:31 final size:31

Alignment explanation


    Indices: 559--643  Score: 152
    Period size: 31  Copynumber: 2.7  Consensus size: 31

        549 AGGGACTGAT

                                           
        559 TTGTCCCAAAAGAAAAACATAAGGGATTTTA
          1 TTGTCCCAAAAGAAAAACATAAGGGATTTTA

                                          *
        590 TTGTCCCAAAAGAAAAACATAAGGGATTTTT
          1 TTGTCCCAAAAGAAAAACATAAGGGATTTTA

                             *     
        621 TTGTCCCAAAAGAAAAATATAAG
          1 TTGTCCCAAAAGAAAAACATAAG

        644 AGAATTTTTT


Statistics
Matches: 52,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  31   52  1.00

ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26


Consensus pattern (31 bp):   
TTGTCCCAAAAGAAAAACATAAGGGATTTTA

Found at i:652 original size:31 final size:30

Alignment explanation


    Indices: 558--653  Score: 138
    Period size: 31  Copynumber: 3.1  Consensus size: 30

        548 AAGGGACTGA

                                     *    
        558 TTTGTCCCAAAAGAAAAACATAAGGGATTT
          1 TTTGTCCCAAAAGAAAAACATAAGGAATTT

                                        *   
        588 TATTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 T-TTGTCCCAAAAGAAAAACATAA-GGAATTT

                              *            
        620 TTTGTCCCAAAAGAAAAATATAAGAGAATTT
          1 TTTGTCCCAAAAGAAAAACATAAG-GAATTT

               
        651 TTT
          1 TTT

        654 TTAGTAGTCT


Statistics
Matches: 59,  Mismatches: 4, Indels: 5
        0.87            0.06        0.07

Matches are distributed among these distances:
  30    2  0.03
  31   51  0.86
  32    6  0.10

ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30


Consensus pattern (30 bp):   
TTTGTCCCAAAAGAAAAACATAAGGAATTT

Found at i:1413 original size:50 final size:50

Alignment explanation


    Indices: 1355--1449  Score: 172
    Period size: 50  Copynumber: 1.9  Consensus size: 50

       1345 TTTATAACTA

                               *                    *         
       1355 TTTTATTTTTACCATTTTATTATTTTAATTAAATATATTTTTTAATATAC
          1 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAATATAC

                                                         
       1405 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAA
          1 TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAA

       1450 ATGACATTAT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   43  1.00

ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61


Consensus pattern (50 bp):   
TTTTATTTTTACCATTTTACTATTTTAATTAAATATATTTCTTAATATAC

Found at i:1797 original size:31 final size:31

Alignment explanation


    Indices: 1707--1799  Score: 150
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       1697 ATTAAATACT

                            *           *   
       1707 AAAAAAATTCTCTTATATTTTTCTTTTGAGAC
          1 AAAAAAA-TCTCTTATGTTTTTCTTTTGGGAC

                     *                     
       1739 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
          1 AAAAAAATCTCTTATGTTTTTCTTTTGGGAC

                                          
       1770 AAAAAAATCTCTTATGTTTTTCTTTTGGGA
          1 AAAAAAATCTCTTATGTTTTTCTTTTGGGA

       1800 TAAATCAGTC


Statistics
Matches: 57,  Mismatches: 4, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  31   50  0.88
  32    7  0.12

ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45


Consensus pattern (31 bp):   
AAAAAAATCTCTTATGTTTTTCTTTTGGGAC
Done.