Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014124.1 Corchorus capsularis cultivar CVL-1 contig14145, 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: 24565
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:8756 original size:21 final size:21

Alignment explanation


    Indices: 8701--8762  Score: 72
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       8691 TGTTTTGAGC

                              *  
       8701 AAGAATATTCCAATCGATCCA
          1 AAGAATATTCCAATCGATTCA

               **                *
       8722 AAGCTTCATT-CAATCGATTCT
          1 AAGAAT-ATTCCAATCGATTCA

                                
       8743 AAGAATATTCCAATCGATTC
          1 AAGAATATTCCAATCGATTC

       8763 CAAGTTATGC


Statistics
Matches: 33,  Mismatches: 6, Indels: 4
        0.77            0.14        0.09

Matches are distributed among these distances:
  20    3  0.09
  21   27  0.82
  22    3  0.09

ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31


Consensus pattern (21 bp):   
AAGAATATTCCAATCGATTCA

Found at i:9250 original size:12 final size:12

Alignment explanation


    Indices: 9233--9258  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       9223 TTAGGTGTTC

                        
       9233 AATTGGAGGTCT
          1 AATTGGAGGTCT

                        
       9245 AATTGGAGGTCT
          1 AATTGGAGGTCT

              
       9257 AA
          1 AA

       9259 GGCCGACGAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31


Consensus pattern (12 bp):   
AATTGGAGGTCT

Found at i:10017 original size:19 final size:18

Alignment explanation


    Indices: 9991--10032  Score: 50
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       9981 AATTAATTAT

                               
       9991 TTTAATATTGA-ATTTTTA
          1 TTTAATATT-ATATTTTTA

                               
      10009 TTTATATATTATATTTTTA
          1 TTTA-ATATTATATTTTTA

            *    
      10028 CTTAA
          1 TTTAA

      10033 GAATTACTCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  18    6  0.29
  19   15  0.71

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62


Consensus pattern (18 bp):   
TTTAATATTATATTTTTA

Found at i:15860 original size:2 final size:2

Alignment explanation


    Indices: 15853--15885  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      15843 TTTCCGCTAA

                                                             
      15853 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      15886 AGTCTTAAAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:20627 original size:13 final size:14

Alignment explanation


    Indices: 20603--20634  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

      20593 GAATTTTAAT

                          
      20603 TAAATCTAACTAAG
          1 TAAATCTAACTAAG

                          
      20617 TAAAT-TAACTAAG
          1 TAAATCTAACTAAG

                  
      20630 -AAATC
          1 TAAATC

      20635 AATCAAGAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  12    4  0.24
  13    8  0.47
  14    5  0.29

ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28


Consensus pattern (14 bp):   
TAAATCTAACTAAG

Found at i:23761 original size:24 final size:27

Alignment explanation


    Indices: 23711--23763  Score: 76
    Period size: 26  Copynumber: 2.1  Consensus size: 27

      23701 AGGATGAAAT

                                       
      23711 TCCTCCTTATTTTCCTTCTCTTGATTC
          1 TCCTCCTTATTTTCCTTCTCTTGATTC

                    *                  
      23738 TCCTCC-TCTTTTCCTTC-CTT-ATTC
          1 TCCTCCTTATTTTCCTTCTCTTGATTC

              
      23762 TC
          1 TC

      23764 ATCACTAGAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  24    6  0.24
  25    3  0.12
  26   10  0.40
  27    6  0.24

ACGTcount: A:0.06, C:0.38, G:0.02, T:0.55


Consensus pattern (27 bp):   
TCCTCCTTATTTTCCTTCTCTTGATTC
Done.