Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000465.1 Corchorus capsularis cultivar CVL-1 contig00465, 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, 628

Length: 1047
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.45


Found at i:579 original size:13 final size:13

Alignment explanation


    Indices: 533--580  Score: 53
    Period size: 13  Copynumber: 3.6  Consensus size: 13

        523 TCATTTTTTT

                         
        533 TCTCTTTTCTTAC
          1 TCTCTTTTCTTAC

                       * *
        546 TCT-TTTTACTAAT
          1 TCTCTTTT-CTTAC

                          
        559 TACTCTTTTCTTAC
          1 T-CTCTTTTCTTAC

                    
        573 TCTCTTTT
          1 TCTCTTTT

        581 ATTTATTACC


Statistics
Matches: 28,  Mismatches: 4, Indels: 6
        0.74            0.11        0.16

Matches are distributed among these distances:
  12    4  0.14
  13   14  0.50
  14    6  0.21
  15    4  0.14

ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62


Consensus pattern (13 bp):   
TCTCTTTTCTTAC

Found at i:595 original size:29 final size:27

Alignment explanation


    Indices: 536--603  Score: 77
    Period size: 27  Copynumber: 2.5  Consensus size: 27

        526 TTTTTTTTCT

                                      *
        536 CTTTTCTTACTCTTTTTACTAATTACT
          1 CTTTTCTTACTCTTTTTACTAATTACA

                               * *       
        563 CTTTTCTTACTCTCTTTTATTTATTACCA
          1 CTTTTCTTACTCT-TTTTACTAATTA-CA

                          
        592 C-TTT-TTACTCTT
          1 CTTTTCTTACTCTT

        604 ACTGATTACC


Statistics
Matches: 36,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  26    1  0.03
  27   20  0.56
  28   13  0.36
  29    2  0.06

ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60


Consensus pattern (27 bp):   
CTTTTCTTACTCTTTTTACTAATTACA

Found at i:721 original size:16 final size:16

Alignment explanation


    Indices: 691--731  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        681 CTCTCATTGA

                            
        691 TTACC-TTTTTACTCT
          1 TTACCATTTTTACTCT

                       *    
        706 TTACCATTTTTGCTCT
          1 TTACCATTTTTACTCT

                      
        722 TTACCGATTT
          1 TTACC-ATTT

        732 ACTGATTACT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    5  0.22
  16   14  0.61
  17    4  0.17

ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56


Consensus pattern (16 bp):   
TTACCATTTTTACTCT

Found at i:798 original size:40 final size:39

Alignment explanation


    Indices: 723--833  Score: 123
    Period size: 40  Copynumber: 2.7  Consensus size: 39

        713 TTTTGCTCTT

                *                        *          
        723 TACCGATTTACTGATTACTTCTTTTACTCCTACTCTTAAA
          1 TACCAATTTACTGATTACTTCTTTTACT-TTACTCTTAAA

                 *                                 *
        763 TACCATTTTACTGATTACTTCTTTTACTTTGACTCTTAAT
          1 TACCAATTTACTGATTACTTCTTTTACTTT-ACTCTTAAA

              *   *          *             
        803 TATCAAATTACTGATTAATCTCTTTTTACTT
          1 TACCAATTTACTGATTACT-TC-TTTTACTT

        834 AATTACTGAT


Statistics
Matches: 60,  Mismatches: 8, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  39    1  0.02
  40   49  0.82
  41    2  0.03
  42    8  0.13

ACGTcount: A:0.25, C:0.21, G:0.05, T:0.50


Consensus pattern (39 bp):   
TACCAATTTACTGATTACTTCTTTTACTTTACTCTTAAA
Done.