Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006097.1 Corchorus capsularis cultivar CVL-1 contig06115, 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: 15696
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:4497 original size:2 final size:2

Alignment explanation


    Indices: 4492--4519  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4482 TGTGTGTGTG

                                                     
       4492 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

       4520 ACAATGTAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:9733 original size:17 final size:17

Alignment explanation


    Indices: 9711--9746  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       9701 AGTTGCCTCA

                             
       9711 TCACCCAACATCACACT
          1 TCACCCAACATCACACT

                             
       9728 TCACCCAACATCACACT
          1 TCACCCAACATCACACT

              
       9745 TC
          1 TC

       9747 TGTTCCACTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.33, C:0.47, G:0.00, T:0.19


Consensus pattern (17 bp):   
TCACCCAACATCACACT

Found at i:15518 original size:25 final size:24

Alignment explanation


    Indices: 15483--15541  Score: 75
    Period size: 25  Copynumber: 2.5  Consensus size: 24

      15473 TTCAAACCCT

                  *            *     
      15483 AAACTTAATTTCTAACAACTTCTTC
          1 AAACTTCATTTCTAACAA-ATCTTC

                       *            
      15508 AAACTTCATTTTTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                       
      15532 AAA-TTCATTT
          1 AAACTTCATTT

      15542 TCCTTCATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  23    7  0.23
  24    8  0.26
  25   16  0.52

ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:15575 original size:11 final size:11

Alignment explanation


    Indices: 15561--15609  Score: 53
    Period size: 11  Copynumber: 4.1  Consensus size: 11

      15551 TTAATCATAA

                       
      15561 ACTAATTAAAT
          1 ACTAATTAAAT

                         
      15572 ACTAATTAATAAT
          1 ACTAATT-A-AAT

                      *  
      15585 AAACTAATTAGAT
          1 --ACTAATTAAAT

                       
      15598 ACTAATTAAAT
          1 ACTAATTAAAT

             
      15609 A
          1 A

      15610 TAAACTAATA


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  11   18  0.56
  12    1  0.03
  13    5  0.16
  14    1  0.03
  15    7  0.22

ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35


Consensus pattern (11 bp):   
ACTAATTAAAT

Found at i:15580 original size:26 final size:25

Alignment explanation


    Indices: 15551--15618  Score: 100
    Period size: 26  Copynumber: 2.6  Consensus size: 25

      15541 TTCCTTCATT

                                      
      15551 TTAATCATAAACTAATTAAATACTAA
          1 TTAAT-ATAAACTAATTAAATACTAA

                              *       
      15577 TTAATAATAAACTAATTAGATACTAA
          1 TTAAT-ATAAACTAATTAAATACTAA

                            
      15603 TTAAATATAAACTAAT
          1 TT-AATATAAACTAAT

      15619 AAACTAAGTA


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  26   36  0.92
  27    3  0.08

ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35


Consensus pattern (25 bp):   
TTAATATAAACTAATTAAATACTAA

Found at i:15618 original size:15 final size:14

Alignment explanation


    Indices: 15551--15618  Score: 58
    Period size: 15  Copynumber: 5.1  Consensus size: 14

      15541 TTCCTTCATT

                           
      15551 TTAATCATAAACTAA
          1 TTAAT-ATAAACTAA

                          
      15566 TTAA-AT--ACTAA
          1 TTAATATAAACTAA

                           
      15577 TTAATAATAAACTAA
          1 TTAAT-ATAAACTAA

                *         
      15592 TT-AGAT--ACTAA
          1 TTAATATAAACTAA

                           
      15603 TTAAATATAAACTAA
          1 TT-AATATAAACTAA

             
      15618 T
          1 T

      15619 AAACTAAGTA


Statistics
Matches: 43,  Mismatches: 2, Indels: 16
        0.70            0.03        0.26

Matches are distributed among these distances:
  11   16  0.37
  13    9  0.21
  14    1  0.02
  15   17  0.40

ACGTcount: A:0.54, C:0.09, G:0.01, T:0.35


Consensus pattern (14 bp):   
TTAATATAAACTAA
Done.