Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008040.1 Corchorus capsularis cultivar CVL-1 contig08061, 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: 11482
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:1662 original size:38 final size:38

Alignment explanation


    Indices: 1611--1686  Score: 125
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       1601 GCGGGATTCG

                          *                       
       1611 AATCTATGCACTTATTATATAACTTCCTCAACCTCTTC
          1 AATCTATGCACTTAGTATATAACTTCCTCAACCTCTTC

                              *         *         
       1649 AATCTATGCACTTAGTATGTAACTTCCTTAACCTCTTC
          1 AATCTATGCACTTAGTATATAACTTCCTCAACCTCTTC

       1687 TTATCATATG


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  38   35  1.00

ACGTcount: A:0.28, C:0.28, G:0.05, T:0.39


Consensus pattern (38 bp):   
AATCTATGCACTTAGTATATAACTTCCTCAACCTCTTC

Found at i:2790 original size:53 final size:53

Alignment explanation


    Indices: 2727--2832  Score: 212
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       2717 GTACCTAACC

                                                                 
       2727 CGCCCCGGGGTCTCTCTTCTCTTTTAACTTGATATATATATTTGTTTCTCTTA
          1 CGCCCCGGGGTCTCTCTTCTCTTTTAACTTGATATATATATTTGTTTCTCTTA

                                                                 
       2780 CGCCCCGGGGTCTCTCTTCTCTTTTAACTTGATATATATATTTGTTTCTCTTA
          1 CGCCCCGGGGTCTCTCTTCTCTTTTAACTTGATATATATATTTGTTTCTCTTA

       2833 TTACAGTCTC


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47


Consensus pattern (53 bp):   
CGCCCCGGGGTCTCTCTTCTCTTTTAACTTGATATATATATTTGTTTCTCTTA

Found at i:5714 original size:31 final size:30

Alignment explanation


    Indices: 5672--5751  Score: 92
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       5662 TAAAAGTACA

                  *                  *      
       5672 AAATTGATCCCTCAAGTGGACCAAACATA-GT
          1 AAATTGGTCCCTCAAGTGGA--AAAAATATGT

                                          
       5703 AAATTGGTCCCTCAAGT-GAAAAAATATGT
          1 AAATTGGTCCCTCAAGTGGAAAAAATATGT

              *  *              
       5732 AATTTAGTCCCTCAAGTGGA
          1 AAATTGGTCCCTCAAGTGGA

       5752 GTTAACCGAG


Statistics
Matches: 43,  Mismatches: 4, Indels: 5
        0.83            0.08        0.10

Matches are distributed among these distances:
  28    6  0.14
  29   17  0.40
  30    4  0.09
  31   16  0.37

ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26


Consensus pattern (30 bp):   
AAATTGGTCCCTCAAGTGGAAAAAATATGT

Found at i:6850 original size:13 final size:13

Alignment explanation


    Indices: 6832--6856  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       6822 CTTTGGTTCG

                         
       6832 GATAGTTTGGTGC
          1 GATAGTTTGGTGC

                        
       6845 GATAGTTTGGTG
          1 GATAGTTTGGTG

       6857 GTAGAGAAGA


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:0.16, C:0.04, G:0.40, T:0.40


Consensus pattern (13 bp):   
GATAGTTTGGTGC

Found at i:10122 original size:18 final size:18

Alignment explanation


    Indices: 10095--10137  Score: 77
    Period size: 18  Copynumber: 2.4  Consensus size: 18

      10085 TAAAAGGGTG

                 *            
      10095 GGAAATTTGAATTTCCCA
          1 GGAAAGTTGAATTTCCCA

                              
      10113 GGAAAGTTGAATTTCCCA
          1 GGAAAGTTGAATTTCCCA

                   
      10131 GGAAAGT
          1 GGAAAGT

      10138 GTTACTCTTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  18   24  1.00

ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28


Consensus pattern (18 bp):   
GGAAAGTTGAATTTCCCA
Done.