Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009981.1 Corchorus capsularis cultivar CVL-1 contig10002, 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: 17013
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28


Found at i:10757 original size:45 final size:45

Alignment explanation


    Indices: 10692--10787  Score: 151
    Period size: 45  Copynumber: 2.2  Consensus size: 45

      10682 GGGAAACTAA

                          *                              
      10692 AAAAAG-AAAAAAATAAAACTTGGCCTAAAATAGAAAGAGGT-CG
          1 AAAAAGAAAAAAAAAAAAACTTGGCCTAAAATAGAAAGAGGTCCG

                                                  *       
      10735 AAAAAGAAAAAAGAAAAAAACTTGGCCTAAAATAGAAATAGGTCCG
          1 AAAAAGAAAAAA-AAAAAAACTTGGCCTAAAATAGAAAGAGGTCCG

                   
      10781 AAAAAGA
          1 AAAAAGA

      10788 TAAGTAAATA


Statistics
Matches: 48,  Mismatches: 2, Indels: 3
        0.91            0.04        0.06

Matches are distributed among these distances:
  43    6  0.12
  44    5  0.10
  45   28  0.58
  46    9  0.19

ACGTcount: A:0.60, C:0.09, G:0.18, T:0.12


Consensus pattern (45 bp):   
AAAAAGAAAAAAAAAAAAACTTGGCCTAAAATAGAAAGAGGTCCG

Found at i:11393 original size:15 final size:16

Alignment explanation


    Indices: 11363--11393  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

      11353 AACAGGGGAT

                            
      11363 TAAAGAAAATCAATTA
          1 TAAAGAAAATCAATTA

                            
      11379 TAAAGAAAA-CAATTA
          1 TAAAGAAAATCAATTA

      11394 AACTAAAAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    6  0.40
  16    9  0.60

ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23


Consensus pattern (16 bp):   
TAAAGAAAATCAATTA

Found at i:15695 original size:17 final size:18

Alignment explanation


    Indices: 15651--15699  Score: 57
    Period size: 17  Copynumber: 2.8  Consensus size: 18

      15641 GAAATTTTGA

                    *         
      15651 GAAATTATCAAAACAAGT
          1 GAAATTATAAAAACAAGT

            *   *             
      15669 TAAAAT-TAAAAACAA-T
          1 GAAATTATAAAAACAAGT

                           
      15685 GAAATTATAAAAACA
          1 GAAATTATAAAAACA

      15700 GGGAATTAAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  16    5  0.20
  17   16  0.64
  18    4  0.16

ACGTcount: A:0.63, C:0.08, G:0.06, T:0.22


Consensus pattern (18 bp):   
GAAATTATAAAAACAAGT

Found at i:15696 original size:16 final size:17

Alignment explanation


    Indices: 15651--15696  Score: 51
    Period size: 15  Copynumber: 2.7  Consensus size: 17

      15641 GAAATTTTGA

                               
      15651 GAAATTATCAAAACAAGTT
          1 GAAATTAT-AAAACAAG-T

            *                
      15670 AAAATTA-AAAACAA-T
          1 GAAATTATAAAACAAGT

                        
      15685 GAAATTATAAAA
          1 GAAATTATAAAA

      15697 ACAGGGAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  15    7  0.29
  16    4  0.17
  17    7  0.29
  19    6  0.25

ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24


Consensus pattern (17 bp):   
GAAATTATAAAACAAGT
Done.