Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011882.1 Corchorus capsularis cultivar CVL-1 contig11903, 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: 4821
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:1391 original size:22 final size:24

Alignment explanation


    Indices: 1339--1400  Score: 65
    Period size: 22  Copynumber: 2.6  Consensus size: 24

       1329 AATTAAATCT

                 *                   
       1339 AACAAACAAGTAAAATTACTAAGAA
          1 AACAATCAAGTAAAATTAC-AAGAA

             *                      
       1364 AGCAATCAAG-AAAATTA-AAGAA
          1 AACAATCAAGTAAAATTACAAGAA

                  *  *     
       1386 AACAATTAATTAAAA
          1 AACAATCAAGTAAAA

       1401 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:2704 original size:19 final size:18

Alignment explanation


    Indices: 2671--2706  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2661 TTGAAATAAT

                              
       2671 TCTTCAATGATCTTCAAG
          1 TCTTCAATGATCTTCAAG

                     *        
       2689 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       2707 AAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAG

Found at i:3073 original size:18 final size:19

Alignment explanation


    Indices: 3045--3081  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       3035 TCACATACAC

                       *       
       3045 AAAAAGAGGCCTAACACAT
          1 AAAAAGAGGCCCAACACAT

                               
       3064 AAAAAG-GGCCCAACACAT
          1 AAAAAGAGGCCCAACACAT

       3082 CTCTTTTCCT


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

Matches are distributed among these distances:
  18   11  0.65
  19    6  0.35

ACGTcount: A:0.51, C:0.24, G:0.16, T:0.08


Consensus pattern (19 bp):   
AAAAAGAGGCCCAACACAT
Done.