Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016084.1 Corchorus capsularis cultivar CVL-1 contig16105, 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: 7911
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33


Found at i:1644 original size:19 final size:18

Alignment explanation


    Indices: 1611--1646  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1601 ATGAAATAAT

                              
       1611 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       1629 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       1647 GAAATCTTCA


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:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:3871 original size:25 final size:24

Alignment explanation


    Indices: 3836--3894  Score: 75
    Period size: 25  Copynumber: 2.5  Consensus size: 24

       3826 TTCAAACCCT

                  *            *     
       3836 AAACTTAATTTCTAACAACTTCTTC
          1 AAACTTCATTTCTAACAA-ATCTTC

                       *            
       3861 AAACTTCATTTTTAACAAATCTTC
          1 AAACTTCATTTCTAACAAATCTTC

                       
       3885 AAA-TTCATTT
          1 AAACTTCATTT

       3895 TCCTTCATTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  23    7  0.23
  24    8  0.26
  25   16  0.52

ACGTcount: A:0.37, C:0.20, G:0.00, T:0.42


Consensus pattern (24 bp):   
AAACTTCATTTCTAACAAATCTTC

Found at i:3933 original size:26 final size:26

Alignment explanation


    Indices: 3904--4021  Score: 102
    Period size: 26  Copynumber: 4.7  Consensus size: 26

       3894 TTCCTTCATT

                                      
       3904 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                 *     *      *       
       3930 TTAATAATAAAGTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *                     
       3956 TTAAACATAAACTAA-T-AA-ACTAA
          1 TTAATCATAAACTAATTAAATACTAA

            *     * *  *       *   *  
       3979 GTAAT-TTTAATTAATTAATTA-AAA
          1 TTAATCATAAACTAATTAAATACTAA

            *                  
       4003 CTAATCATAAACTAATTAA
          1 TTAATCATAAACTAATTAA

       4022 TATTAAAAAA


Statistics
Matches: 70,  Mismatches: 18, Indels: 9
        0.72            0.19        0.09

Matches are distributed among these distances:
  22    6  0.09
  23    9  0.13
  24    8  0.11
  25   12  0.17
  26   35  0.50

ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA
Done.