Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009495.1 Corchorus capsularis cultivar CVL-1 contig09516, 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: 24862
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:140 original size:2 final size:2

Alignment explanation


    Indices: 135--181  Score: 55
    Period size: 2  Copynumber: 25.0  Consensus size: 2

        125 AAAAAAAAAC

                                  *                             *         
        135 AT AT AT AT -T A- AT AA AT AT AT AT AT AT AT AT AT AC AT AT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                       
        174 AT AT AT AT
          1 AT AT AT AT

        182 TTTATGTATA


Statistics
Matches: 38,  Mismatches: 4, Indels: 6
        0.79            0.08        0.12

Matches are distributed among these distances:
   1    3  0.08
   2   35  0.92

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:4526 original size:21 final size:22

Alignment explanation


    Indices: 4497--4537  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4487 GTTTTATGCC

                                  
       4497 CTTCCTCCA-ACAAGACTTCCG
          1 CTTCCTCCACACAAGACTTCCG

                *               
       4518 CTTCTTCCACACAAGACTTC
          1 CTTCCTCCACACAAGACTTC

       4538 TGATTTGGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21    8  0.44
  22   10  0.56

ACGTcount: A:0.24, C:0.41, G:0.07, T:0.27


Consensus pattern (22 bp):   
CTTCCTCCACACAAGACTTCCG

Found at i:22576 original size:31 final size:31

Alignment explanation


    Indices: 22539--22598  Score: 111
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      22529 ATAATTATTA

                                           
      22539 TTATAAAATAATAAAAGAAAATAATTAAAGG
          1 TTATAAAATAATAAAAGAAAATAATTAAAGG

                        *                
      22570 TTATAAAATAATCAAAGAAAATAATTAAA
          1 TTATAAAATAATAAAAGAAAATAATTAAA

      22599 ACCTTTGTGA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.65, C:0.02, G:0.07, T:0.27


Consensus pattern (31 bp):   
TTATAAAATAATAAAAGAAAATAATTAAAGG

Found at i:24094 original size:5 final size:5

Alignment explanation


    Indices: 24084--24121  Score: 58
    Period size: 5  Copynumber: 7.6  Consensus size: 5

      24074 AGTAACAACA

                                           *    *        
      24084 AAAAC AAAAC AAAAC AAAAC AAAAC AGAAC CAAAC AAA
          1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA

      24122 GCCACTTCCT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   5   29  1.00

ACGTcount: A:0.76, C:0.21, G:0.03, T:0.00


Consensus pattern (5 bp):   
AAAAC

Done.