Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016050.1 Corchorus capsularis cultivar CVL-1 contig16071, 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: 15268
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33


Found at i:6136 original size:2 final size:2

Alignment explanation


    Indices: 6129--6158  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       6119 ACTATTATTC

                                                        
       6129 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

       6159 ATACATATGT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:10484 original size:2 final size:2

Alignment explanation


    Indices: 10477--10513  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      10467 AAAGGAAATC

                                                                   
      10477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      10514 CTAGTTAGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:11756 original size:22 final size:22

Alignment explanation


    Indices: 11731--11794  Score: 128
    Period size: 22  Copynumber: 2.9  Consensus size: 22

      11721 AAGAAATAAA

                                  
      11731 TTAAATTCAGGTTTAGCCCCCC
          1 TTAAATTCAGGTTTAGCCCCCC

                                  
      11753 TTAAATTCAGGTTTAGCCCCCC
          1 TTAAATTCAGGTTTAGCCCCCC

                                
      11775 TTAAATTCAGGTTTAGCCCC
          1 TTAAATTCAGGTTTAGCCCC

      11795 TAGTTATAAA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   42  1.00

ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33


Consensus pattern (22 bp):   
TTAAATTCAGGTTTAGCCCCCC

Found at i:12696 original size:11 final size:11

Alignment explanation


    Indices: 12653--12690  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      12643 TTCCTATATA

                *      
      12653 AAATAAATTAT
          1 AAATTAATTAT

                        
      12664 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
      12675 AAATTAATTAT
          1 AAATTAATTAT

                 
      12686 AAATT
          1 AAATT

      12691 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:14492 original size:68 final size:68

Alignment explanation


    Indices: 14383--14509  Score: 227
    Period size: 68  Copynumber: 1.9  Consensus size: 68

      14373 ATTTTTATCA

                             *       *                                       
      14383 AAAAGATTAATAAAGGAGGAAATTGTGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
          1 AAAAGATTAATAAAGGAAGAAATTGCGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC

               
      14448 AAT
         66 AAT

                       *                                               
      14451 AAAAGATTAATTAAGGAAGAAATTGCGGATCTAACATATTGTAATTAGAATGTAATTAA
          1 AAAAGATTAATAAAGGAAGAAATTGCGGATCTAACATATTGTAATTAGAATGTAATTAA

      14510 GGAGGAAATC


Statistics
Matches: 56,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  68   56  1.00

ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31


Consensus pattern (68 bp):   
AAAAGATTAATAAAGGAAGAAATTGCGGATCTAACATATTGTAATTAGAATGTAATTAATCAATC
AAT

Found at i:14612 original size:22 final size:22

Alignment explanation


    Indices: 14584--14634  Score: 102
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      14574 ATGATATATA

                                  
      14584 TGATTAAATTTATCTAATTGAT
          1 TGATTAAATTTATCTAATTGAT

                                  
      14606 TGATTAAATTTATCTAATTGAT
          1 TGATTAAATTTATCTAATTGAT

                   
      14628 TGATTAA
          1 TGATTAA

      14635 TCAAATTTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   29  1.00

ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49


Consensus pattern (22 bp):   
TGATTAAATTTATCTAATTGAT

Found at i:14629 original size:26 final size:25

Alignment explanation


    Indices: 14584--14651  Score: 72
    Period size: 26  Copynumber: 2.8  Consensus size: 25

      14574 ATGATATATA

                                     
      14584 TGATTAAATTTATCT-A--ATTGAT
          1 TGATTAAATTTATCTAATTATTGAT

                                      
      14606 TGATTAAATTTATCTAATTGATTGAT
          1 TGATTAAATTTATCTAATT-ATTGAT

             *  *                
      14632 TAATCAAATTT-TACTAATTA
          1 TGATTAAATTTAT-CTAATTA

      14652 CAATATGCAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  22   15  0.38
  23    1  0.03
  25    2  0.05
  26   21  0.54

ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49


Consensus pattern (25 bp):   
TGATTAAATTTATCTAATTATTGAT
Done.