Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013020.1 Corchorus olitorius cultivar O-4 contig13053, 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: 7408
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:3810 original size:18 final size:19

Alignment explanation


    Indices: 3768--3808  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       3758 AATGGTTAAC

                               
       3768 AAAATTTACTTATAACAAA
          1 AAAATTTACTTATAACAAA

                               
       3787 AAAATTTACTTATAACAAA
          1 AAAATTTACTTATAACAAA

               
       3806 AAA
          1 AAA

       3809 TTGATGAGTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29


Consensus pattern (19 bp):   
AAAATTTACTTATAACAAA

Found at i:6104 original size:39 final size:40

Alignment explanation


    Indices: 6048--6123  Score: 118
    Period size: 39  Copynumber: 1.9  Consensus size: 40

       6038 ATTTAAAGGG

                                            *       
       6048 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACACTAATTAA

                     *          *                
       6088 ATGTAATA-CTATAATAACTGAAATACTTACACTAAT
          1 ATGTAATATATATAATAACTAAAATACTTACACTAAT

       6124 ACTTAGGTAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  39   25  0.76
  40    8  0.24

ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACACTAATTAA

Found at i:6123 original size:21 final size:20

Alignment explanation


    Indices: 6059--6124  Score: 57
    Period size: 17  Copynumber: 3.3  Consensus size: 20

       6049 TGTAATATAT

                     *          
       6059 ATAATAACTAAAATACTTAC
          1 ATAATAACTGAAATACTTAC

                     *  *         
       6079 ATTAATTAAATGTAATAC-T--
          1 A-TAA-TAACTGAAATACTTAC

                                
       6098 ATAATAACTGAAATACTTAC
          1 ATAATAACTGAAATACTTAC

                   
       6118 ACTAATA
          1 A-TAATA

       6125 CTTAGGTATT


Statistics
Matches: 35,  Mismatches: 5, Indels: 11
        0.69            0.10        0.22

Matches are distributed among these distances:
  17   10  0.29
  18    4  0.11
  19    1  0.03
  20    2  0.06
  21    9  0.26
  22    9  0.26

ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33


Consensus pattern (20 bp):   
ATAATAACTGAAATACTTAC

Found at i:7211 original size:36 final size:36

Alignment explanation


    Indices: 7164--7233  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       7154 GAGATTTTGG

                         *      *               
       7164 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       7200 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       7234 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.