Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009518.1 Corchorus capsularis cultivar CVL-1 contig09539, 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: 35317
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:11538 original size:2 final size:2

Alignment explanation


    Indices: 11531--11566  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      11521 AGAAATGAAG

                                                                 
      11531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      11567 CTAGTATCGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:25715 original size:2 final size:2

Alignment explanation


    Indices: 25708--25743  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      25698 AAAGAAGAAA

                                                                 
      25708 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

      25744 TAATATAATT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AG

Found at i:33390 original size:22 final size:22

Alignment explanation


    Indices: 33350--33424  Score: 73
    Period size: 22  Copynumber: 3.4  Consensus size: 22

      33340 GAGATTACCA

                           *       
      33350 AAATTTCATATG-TAAGTTACTG
          1 AAATTTCATATGAT-GGTTACTG

                                   
      33372 AAATTTCATATGATGGTTA-TCG
          1 AAATTTCATATGATGGTTACT-G

                    * *  *      * 
      33394 AAATTTCAAACGAAGGTTACGG
          1 AAATTTCATATGATGGTTACTG

                     
      33416 AAATTTCAT
          1 AAATTTCAT

      33425 GAGATAGTTA


Statistics
Matches: 44,  Mismatches: 6, Indels: 6
        0.79            0.11        0.11

Matches are distributed among these distances:
  21    1  0.02
  22   42  0.95
  23    1  0.02

ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36


Consensus pattern (22 bp):   
AAATTTCATATGATGGTTACTG

Found at i:34302 original size:22 final size:22

Alignment explanation


    Indices: 34272--34345  Score: 78
    Period size: 22  Copynumber: 3.4  Consensus size: 22

      34262 CATAGGTAGG

                       *   *      
      34272 TTTCATAGGGATATTGTCAAAA
          1 TTTCATAGGGAGATTATCAAAA

                *       *         
      34294 TTTCGTAGGGAGGTTATCAAAA
          1 TTTCATAGGGAGATTATCAAAA

                   *         *     
      34316 TTTCATATGGATG-TTACCAAAA
          1 TTTCATAGGGA-GATTATCAAAA

                    
      34338 TTTCATAG
          1 TTTCATAG

      34346 ATAAGTTACC


Statistics
Matches: 43,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  22   42  0.98
  23    1  0.02

ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36


Consensus pattern (22 bp):   
TTTCATAGGGAGATTATCAAAA

Found at i:34649 original size:13 final size:13

Alignment explanation


    Indices: 34631--34665  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      34621 AATCTAAATC

                   *     
      34631 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                         
      34644 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
      34657 TAAAGCAAA
          1 TAAAGCAAA

      34666 CAATAATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   21  1.00

ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20


Consensus pattern (13 bp):   
TAAAGCAAATTAA
Done.