Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009542.1 Corchorus capsularis cultivar CVL-1 contig09563, 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: 39356
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30


Found at i:1374 original size:34 final size:34

Alignment explanation


    Indices: 1331--1399  Score: 129
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1321 TACAATATAC

                                              
       1331 CTAATCTATGACCACAAAGAATAACTTATCACAT
          1 CTAATCTATGACCACAAAGAATAACTTATCACAT

                            *                 
       1365 CTAATCTATGACCACAGAGAATAACTTATCACAT
          1 CTAATCTATGACCACAAAGAATAACTTATCACAT

             
       1399 C
          1 C

       1400 ACTATTTATG


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26


Consensus pattern (34 bp):   
CTAATCTATGACCACAAAGAATAACTTATCACAT

Found at i:7516 original size:2 final size:2

Alignment explanation


    Indices: 7509--7543  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       7499 TGAAGGAACG

                                                                
       7509 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 A

       7544 AGTTTATTTA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9818 original size:22 final size:22

Alignment explanation


    Indices: 9770--9818  Score: 55
    Period size: 23  Copynumber: 2.2  Consensus size: 22

       9760 TATTAATTTT

                                  
       9770 TAAATTTAAAAAAAAAAAAACA
          1 TAAATTTAAAAAAAAAAAAACA

            *       *         *    
       9792 AAAATTATTAAAAAAAAATAA-A
          1 TAAATT-TAAAAAAAAAAAAACA

                 
       9814 TAAAT
          1 TAAAT

       9819 AAAGTAAAGG


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  22   10  0.45
  23   12  0.55

ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22


Consensus pattern (22 bp):   
TAAATTTAAAAAAAAAAAAACA

Found at i:26328 original size:55 final size:53

Alignment explanation


    Indices: 26234--26351  Score: 200
    Period size: 55  Copynumber: 2.2  Consensus size: 53

      26224 CAGTCAAATG

                *                        *                       
      26234 CAATGAACCATCATATTCTTTTTTTTCTTTTTTTTTATTAACCACCTCCATAT
          1 CAATTAACCATCATATTCTTTTTTTTCTTATTTTTTATTAACCACCTCCATAT

                                                                   
      26287 CAATTAACCATCATATTCTTTTTTTTTTCTTATTTTTTATTAACCACCTCCATAT
          1 CAATTAACCATCATATTC--TTTTTTTTCTTATTTTTTATTAACCACCTCCATAT

                      
      26342 CAATTAACCA
          1 CAATTAACCA

      26352 CAGGTGACTG


Statistics
Matches: 61,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  53   17  0.28
  55   44  0.72

ACGTcount: A:0.27, C:0.23, G:0.01, T:0.49


Consensus pattern (53 bp):   
CAATTAACCATCATATTCTTTTTTTTCTTATTTTTTATTAACCACCTCCATAT

Found at i:28816 original size:2 final size:2

Alignment explanation


    Indices: 28809--28847  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      28799 GCCAATGGAC

                                                                      
      28809 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
          1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G

      28848 AGAGAGAGAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
GT

Found at i:36340 original size:29 final size:30

Alignment explanation


    Indices: 36280--36361  Score: 87
    Period size: 29  Copynumber: 2.7  Consensus size: 30

      36270 GCACATAGCA

                 *         *            * 
      36280 TTTTTGACATGTGGCGTGCCACGTGTC-CT
          1 TTTTTTACATGTGGCATGCCACGTGTCATT

                                           
      36309 TTTTTTACATGTGGCATGCCACGTGGT-ATT
          1 TTTTTTACATGTGGCATGCCACGT-GTCATT

                       *           
      36339 TTTTTGGTACACGTGGCATGCCA
          1 TTTTT--TACATGTGGCATGCCA

      36362 TGTTGGATGC


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  29   22  0.49
  30    8  0.18
  32   15  0.33

ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39


Consensus pattern (30 bp):   
TTTTTTACATGTGGCATGCCACGTGTCATT

Found at i:39324 original size:2 final size:2

Alignment explanation


    Indices: 39319--39356  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      39309 TGTGTGTGTG

                                                                    
      39319 TA TA TA TA 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 TA TA TA TA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Done.