Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012733.1 Corchorus capsularis cultivar CVL-1 contig12754, 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: 14985
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:1152 original size:12 final size:13

Alignment explanation


    Indices: 1137--1170  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       1127 AATCTAAAAC

                   *     
       1137 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       1149 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       1162 TAAAGCAAA
          1 TAAAGCAAA

       1171 CAATAATTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:7018 original size:21 final size:21

Alignment explanation


    Indices: 6994--7066  Score: 62
    Period size: 21  Copynumber: 3.6  Consensus size: 21

       6984 TCTATCTATC

                                 
       6994 TTGCATATTTAAATTTCTTGT
          1 TTGCATATTTAAATTTCTTGT

                        *   * *   
       7015 TTGCATA-TTAGGATTGCATGT
          1 TTGCATATTTA-AATTTCTTGT

                 *      *        
       7036 TT--AGATTTAATTTTCTTGT
          1 TTGCATATTTAAATTTCTTGT

                  *     
       7055 TTGCATGTTTAA
          1 TTGCATATTTAA

       7067 TTTTGTGTCT


Statistics
Matches: 38,  Mismatches: 10, Indels: 8
        0.68            0.18        0.14

Matches are distributed among these distances:
  19   10  0.26
  20    6  0.16
  21   22  0.58

ACGTcount: A:0.23, C:0.08, G:0.15, T:0.53


Consensus pattern (21 bp):   
TTGCATATTTAAATTTCTTGT

Found at i:12524 original size:21 final size:19

Alignment explanation


    Indices: 12485--12524  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      12475 ATTTTGATGA

                       *       
      12485 TTTTTCAAACTCTTTGAAT
          1 TTTTTCAAACTATTTGAAT

                                 
      12504 TTTTTCAAACATATATTGAAT
          1 TTTTTCAAAC-TAT-TTGAAT

      12525 GATTGATTTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19   10  0.56
  20    2  0.11
  21    6  0.33

ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50


Consensus pattern (19 bp):   
TTTTTCAAACTATTTGAAT

Found at i:13625 original size:8 final size:8

Alignment explanation


    Indices: 13612--13637  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

      13602 CTTGAAGATA

                    
      13612 ATTTGAAG
          1 ATTTGAAG

                    
      13620 ATTTGAAG
          1 ATTTGAAG

                    
      13628 ATTTGAAG
          1 ATTTGAAG

              
      13636 AT
          1 AT

      13638 CATTGAAGAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38


Consensus pattern (8 bp):   
ATTTGAAG
Done.