Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014151.1 Corchorus olitorius cultivar O-4 contig14184, 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: 22681
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:1005 original size:13 final size:13

Alignment explanation


    Indices: 984--1013  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

        974 GTACAAAATT

                         
        984 ATTAATGGAGGAA
          1 ATTAATGGAGGAA

                *        
        997 ATTATTGGAGGAA
          1 ATTAATGGAGGAA

                
       1010 ATTA
          1 ATTA

       1014 GTTGAATTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30


Consensus pattern (13 bp):   
ATTAATGGAGGAA

Found at i:3805 original size:24 final size:24

Alignment explanation


    Indices: 3753--3837  Score: 89
    Period size: 24  Copynumber: 3.5  Consensus size: 24

       3743 GCAACTAACG

                     *     * *  *   
       3753 ATTTGAAGTATCAGTAGATGGAGC
          1 ATTTGAAGTCTCAGTTGCTGAAGC

            *          *            
       3777 CTTTGAAGTCTGAGTTGCTGAAGC
          1 ATTTGAAGTCTCAGTTGCTGAAGC

                     *          *   
       3801 ATTTGAAGTATCAGTTGCTGGAGC
          1 ATTTGAAGTCTCAGTTGCTGAAGC

                 *       
       3825 ATTTGTAGTCTCA
          1 ATTTGAAGTCTCA

       3838 TCAGATCCAT


Statistics
Matches: 49,  Mismatches: 12, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  24   49  1.00

ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34


Consensus pattern (24 bp):   
ATTTGAAGTCTCAGTTGCTGAAGC

Found at i:12157 original size:19 final size:19

Alignment explanation


    Indices: 12133--12169  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      12123 TCTATGATTT

                                
      12133 ATTTCATTGTT-ATTAACTA
          1 ATTTCA-TGTTAATTAACTA

                              
      12152 ATTTCATGTTAATTAACT
          1 ATTTCATGTTAATTAACT

      12170 TCACTCGATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.32, C:0.11, G:0.05, T:0.51


Consensus pattern (19 bp):   
ATTTCATGTTAATTAACTA

Found at i:22365 original size:15 final size:16

Alignment explanation


    Indices: 22332--22371  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      22322 TTACTTTGCT

                            
      22332 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      22348 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      22363 TTGCTTTCT
          1 TTGTTTTCT

      22372 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA
Done.