Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014697.1 Corchorus capsularis cultivar CVL-1 contig14718, 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: 18142
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:12473 original size:2 final size:2

Alignment explanation


    Indices: 12466--12501  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      12456 GGATGTTGAG

                                                                 
      12466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12502 TAATGCCTAG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:17995 original size:40 final size:40

Alignment explanation


    Indices: 17919--18023  Score: 122
    Period size: 40  Copynumber: 2.6  Consensus size: 40

      17909 ATCAGTAATT

                         *          **                 
      17919 AAGTAAAAAGAGATTAATCAGTAATTTGATAATTAAGAGTCA-
          1 AAGT-AAAAGA-AGTAATCAGTAAAATGATAATTAAGAGT-AG

                                      *  *          
      17961 AAGTAAAAGAAGTAATCAGTAAAATGGTATTTAAGAGTAG
          1 AAGTAAAAGAAGTAATCAGTAAAATGATAATTAAGAGTAG

            *                      
      18001 GAGTAAAAGAAGTAATCAGTAAA
          1 AAGTAAAAGAAGTAATCAGTAAA

      18024 TCGGTAAAGA


Statistics
Matches: 56,  Mismatches: 6, Indels: 4
        0.85            0.09        0.06

Matches are distributed among these distances:
  39    1  0.02
  40   45  0.80
  41    6  0.11
  42    4  0.07

ACGTcount: A:0.51, C:0.04, G:0.20, T:0.25


Consensus pattern (40 bp):   
AAGTAAAAGAAGTAATCAGTAAAATGATAATTAAGAGTAG

Found at i:18060 original size:15 final size:16

Alignment explanation


    Indices: 18021--18061  Score: 57
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      18011 AGTAATCAGT

                             
      18021 AAATCGGTAAAGAGCAA
          1 AAAT-GGTAAAGAGCAA

                         *  
      18038 AAATGGTAAAGAGTAA
          1 AAATGGTAAAGAGCAA

                     
      18054 AAA-GGTAA
          1 AAATGGTAA

      18062 TCAATGAGAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15    5  0.22
  16   14  0.61
  17    4  0.17

ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15


Consensus pattern (16 bp):   
AAATGGTAAAGAGCAA
Done.