Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023008.1 Corchorus olitorius cultivar O-4 contig23041, 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: 9622
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--41  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

                                                                         
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         42 AACCTCAGGA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:966 original size:29 final size:29

Alignment explanation


    Indices: 934--1005  Score: 135
    Period size: 29  Copynumber: 2.5  Consensus size: 29

        924 CTCTGATTGC

                                         
        934 AGCCAAATAAGCCCCTAACTCTTAAAAAA
          1 AGCCAAATAAGCCCCTAACTCTTAAAAAA

                                         
        963 AGCCAAATAAGCCCCTAACTCTTAAAAAA
          1 AGCCAAATAAGCCCCTAACTCTTAAAAAA

             *            
        992 AACCAAATAAGCCC
          1 AGCCAAATAAGCCC

       1006 TTTTCTGACG


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  29   42  1.00

ACGTcount: A:0.49, C:0.29, G:0.07, T:0.15


Consensus pattern (29 bp):   
AGCCAAATAAGCCCCTAACTCTTAAAAAA

Found at i:8056 original size:31 final size:31

Alignment explanation


    Indices: 8021--8090  Score: 113
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       8011 TTAATTTCCT

                         *                *
       8021 AAATCATAAGCTATAGAGAATCGCATTAAAG
          1 AAATCATAAGCTACAGAGAATCGCATTAAAC

                                   *       
       8052 AAATCATAAGCTACAGAGAATCGTATTAAAC
          1 AAATCATAAGCTACAGAGAATCGCATTAAAC

                    
       8083 AAATCATA
          1 AAATCATA

       8091 TTACGATTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  31   36  1.00

ACGTcount: A:0.50, C:0.14, G:0.13, T:0.23


Consensus pattern (31 bp):   
AAATCATAAGCTACAGAGAATCGCATTAAAC

Found at i:8451 original size:18 final size:18

Alignment explanation


    Indices: 8411--8454  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       8401 AAAAATTAAT

                      **      
       8411 TTTTTTTATTTTAATATA
          1 TTTTTTTATTGAAATATA

            *              *  
       8429 ATTTTTTATTGAAATTTA
          1 TTTTTTTATTGAAATATA

                    
       8447 TTTTTTTA
          1 TTTTTTTA

       8455 ATAATAATAA


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70


Consensus pattern (18 bp):   
TTTTTTTATTGAAATATA
Done.