Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017007.1 Corchorus olitorius cultivar O-4 contig17040, 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: 6803
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:1808 original size:27 final size:28

Alignment explanation


    Indices: 1740--1814  Score: 75
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       1730 TTAAGATGTC

                    * *                 
       1740 AAAATTACTGCTTTACCCTTGGTCAGCT
          1 AAAATTACAGTTTTACCCTTGGTCAGCT

                                     *    
       1768 AAAATTACCA-TTTTACCCTTGGT-TGACT
          1 AAAATTA-CAGTTTTACCCTTGGTCAG-CT

                          *     
       1796 -AAATTACAGTTTTGCCCTT
          1 AAAATTACAGTTTTACCCTT

       1815 AAATGCCGGA


Statistics
Matches: 40,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  26    2  0.05
  27   16  0.40
  28   21  0.52
  29    1  0.03

ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39


Consensus pattern (28 bp):   
AAAATTACAGTTTTACCCTTGGTCAGCT

Found at i:5620 original size:60 final size:60

Alignment explanation


    Indices: 5527--5649  Score: 246
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       5517 ATATTCTAAA

                                                                        
       5527 ATCGATATGGATTAATATTTGATGCACTAACAGTATACAATTTCTATACACTGTCGGGCC
          1 ATCGATATGGATTAATATTTGATGCACTAACAGTATACAATTTCTATACACTGTCGGGCC

                                                                        
       5587 ATCGATATGGATTAATATTTGATGCACTAACAGTATACAATTTCTATACACTGTCGGGCC
          1 ATCGATATGGATTAATATTTGATGCACTAACAGTATACAATTTCTATACACTGTCGGGCC

               
       5647 ATC
          1 ATC

       5650 AAATGTTGAC


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  60   63  1.00

ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Consensus pattern (60 bp):   
ATCGATATGGATTAATATTTGATGCACTAACAGTATACAATTTCTATACACTGTCGGGCC

Found at i:6623 original size:14 final size:15

Alignment explanation


    Indices: 6599--6628  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       6589 GCGTCATATT

                           
       6599 TTTTATTAAAAAATA
          1 TTTTATTAAAAAATA

                           
       6614 TTTT-TTAAAAAATA
          1 TTTTATTAAAAAATA

             
       6628 T
          1 T

       6629 ATACTTTTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   11  0.73
  15    4  0.27

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (15 bp):   
TTTTATTAAAAAATA

Found at i:6691 original size:31 final size:29

Alignment explanation


    Indices: 6656--6723  Score: 82
    Period size: 30  Copynumber: 2.2  Consensus size: 29

       6646 AAACTGAGTT

                              *            
       6656 AGGGACCGAATTGCTCAATTAACTCCACTTC
          1 AGGGACC-AATTGCTC-ACTAACTCCACTTC

                                 * *      
       6687 AGGGACTCAATTGCTCACTAAGTTCACTTC
          1 AGGGAC-CAATTGCTCACTAACTCCACTTC

                   
       6717 AGGGACC
          1 AGGGACC

       6724 CATTTGCACA


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  29    1  0.03
  30   17  0.52
  31   14  0.42
  32    1  0.03

ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25


Consensus pattern (29 bp):   
AGGGACCAATTGCTCACTAACTCCACTTC
Done.