Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009156.1 Corchorus capsularis cultivar CVL-1 contig09177, 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: 5227
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:926 original size:14 final size:13

Alignment explanation


    Indices: 892--936  Score: 54
    Period size: 13  Copynumber: 3.3  Consensus size: 13

        882 CTCGCTTCTA

                   *    *
        892 TTTTCTTTTTTTT
          1 TTTTCTTCTTTTC

                           
        905 TTTCTCTTCTGTTTC
          1 TTT-TCTTCT-TTTC

                         
        920 TTTTCTTCTTTTC
          1 TTTTCTTCTTTTC

                
        933 TTTT
          1 TTTT

        937 TATTTTCTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  13   11  0.39
  14   11  0.39
  15    6  0.21

ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80


Consensus pattern (13 bp):   
TTTTCTTCTTTTC

Found at i:942 original size:19 final size:18

Alignment explanation


    Indices: 892--945  Score: 65
    Period size: 19  Copynumber: 2.9  Consensus size: 18

        882 CTCGCTTCTA

                              
        892 TTTTCTTTTTTTTT-TTC
          1 TTTTCTTTTTTTTTCTTC

             *        *        
        909 TCTTCTGTTTCTTTTCTTC
          1 TTTTCT-TTTTTTTTCTTC

                              
        928 TTTTCTTTTTATTTTCTT
          1 TTTTCTTTTT-TTTTCTT

        946 TTTCCTTCTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 4
        0.79            0.11        0.11

Matches are distributed among these distances:
  17    5  0.17
  18   10  0.33
  19   15  0.50

ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80


Consensus pattern (18 bp):   
TTTTCTTTTTTTTTCTTC

Found at i:943 original size:24 final size:24

Alignment explanation


    Indices: 886--948  Score: 76
    Period size: 24  Copynumber: 2.7  Consensus size: 24

        876 TTAAATCTCG

                             *      
        886 CTTCTATTTTCTTTTTTTTTTTCT
          1 CTTCTATTTTCTTTTTTCTTTTCT

                  *                  
        910 CTTCT-GTTTCTTTTCTTCTTTTCT
          1 CTTCTATTTTCTTTT-TTCTTTTCT

               *            
        934 -TTTTATTTTCTTTTT
          1 CTTCTATTTTCTTTTT

        949 CCTTCTCCTT


Statistics
Matches: 33,  Mismatches: 4, Indels: 5
        0.79            0.10        0.12

Matches are distributed among these distances:
  23   12  0.36
  24   21  0.64

ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78


Consensus pattern (24 bp):   
CTTCTATTTTCTTTTTTCTTTTCT

Found at i:3156 original size:18 final size:19

Alignment explanation


    Indices: 3129--3170  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       3119 AAGAAAATAG

                       *       
       3129 AAAG-AAAAGGGAAG-AAA
          1 AAAGAAAAAGGAAAGTAAA

                                
       3146 AAAGAAAAAGGAAAGTTAAA
          1 AAAGAAAAAGGAAAG-TAAA

                 
       3166 AAAGA
          1 AAAGA

       3171 TAGAACGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  17    4  0.19
  18    9  0.43
  20    8  0.38

ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05


Consensus pattern (19 bp):   
AAAGAAAAAGGAAAGTAAA

Found at i:4861 original size:28 final size:24

Alignment explanation


    Indices: 4844--4890  Score: 78
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       4834 CTCTTAATCC

                                     
       4844 ATTTTAATCTCAACCAAACTAC-TA
          1 ATTTTAATCTCAACCAAACT-CTTA

                                   
       4868 ATTTTAATCTCAACCAAACTCTT
          1 ATTTTAATCTCAACCAAACTCTT

       4891 CAAGATTACT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  23    1  0.05
  24   21  0.95

ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36


Consensus pattern (24 bp):   
ATTTTAATCTCAACCAAACTCTTA
Done.