Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011433.1 Corchorus capsularis cultivar CVL-1 contig11454, 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: 16933
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:576 original size:15 final size:15

Alignment explanation


    Indices: 556--588  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

        546 AGTAAACAGT

                         * 
        556 TTCGGTGCCATCATC
          1 TTCGGTGCCATCACC

                           
        571 TTCGGTGCCATCACC
          1 TTCGGTGCCATCACC

               
        586 TTC
          1 TTC

        589 CTCCATGGCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.12, C:0.36, G:0.18, T:0.33


Consensus pattern (15 bp):   
TTCGGTGCCATCACC

Found at i:6172 original size:31 final size:31

Alignment explanation


    Indices: 6135--6206  Score: 144
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       6125 GGTTCTGTTT

                                           
       6135 AAAGGTTTAGACTCAAATTGAGTAAGTTTGG
          1 AAAGGTTTAGACTCAAATTGAGTAAGTTTGG

                                           
       6166 AAAGGTTTAGACTCAAATTGAGTAAGTTTGG
          1 AAAGGTTTAGACTCAAATTGAGTAAGTTTGG

                      
       6197 AAAGGTTTAG
          1 AAAGGTTTAG

       6207 GCCCAATTTG


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   41  1.00

ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32


Consensus pattern (31 bp):   
AAAGGTTTAGACTCAAATTGAGTAAGTTTGG

Found at i:11742 original size:26 final size:27

Alignment explanation


    Indices: 11686--11755  Score: 124
    Period size: 26  Copynumber: 2.6  Consensus size: 27

      11676 ATTAGGGTCG

                                       
      11686 CCCAGGGGCATTTTGGTCATTTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

                                       
      11713 CCCAGGGGCATTTTGGTCA-TTTTGCA
          1 CCCAGGGGCATTTTGGTCATTTTTGCA

                *            
      11739 CCCAAGGGCATTTTGGT
          1 CCCAGGGGCATTTTGGT

      11756 AAATTGGTGG


Statistics
Matches: 42,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  26   23  0.55
  27   19  0.45

ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34


Consensus pattern (27 bp):   
CCCAGGGGCATTTTGGTCATTTTTGCA
Done.