Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011880.1 Corchorus capsularis cultivar CVL-1 contig11901, 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: 6220
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30


Found at i:413 original size:13 final size:13

Alignment explanation


    Indices: 395--419  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        385 ATAGAAGTGG

                         
        395 TTCAAACCGCCTC
          1 TTCAAACCGCCTC

                        
        408 TTCAAACCGCCT
          1 TTCAAACCGCCT

        420 GCAAAACCTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.44, G:0.08, T:0.24


Consensus pattern (13 bp):   
TTCAAACCGCCTC

Found at i:4798 original size:22 final size:24

Alignment explanation


    Indices: 4746--4807  Score: 65
    Period size: 22  Copynumber: 2.6  Consensus size: 24

       4736 AATTAAATCT

                 *                   
       4746 AACAAACAAGTAAAATTACTAAGAA
          1 AACAATCAAGTAAAATTAC-AAGAA

             *                      
       4771 AGCAATCAAG-AAAATTA-AAGAA
          1 AACAATCAAGTAAAATTACAAGAA

                  *  *     
       4793 AACAATTAATTAAAA
          1 AACAATCAAGTAAAA

       4808 AGCAGTGAAT


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  22   12  0.39
  23    4  0.13
  24    7  0.23
  25    8  0.26

ACGTcount: A:0.65, C:0.10, G:0.08, T:0.18


Consensus pattern (24 bp):   
AACAATCAAGTAAAATTACAAGAA

Found at i:6113 original size:19 final size:18

Alignment explanation


    Indices: 6080--6116  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       6070 CTTGAATAAT

                              
       6080 TCTTCAATGATCTTCAAG
          1 TCTTCAATGATCTTCAAG

                     *         
       6098 TCTTCAAATTATCTTCAAG
          1 TCTTC-AATGATCTTCAAG

       6117 AAATCTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAG
Done.