Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000405.1 Corchorus capsularis cultivar CVL-1 contig00405, 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: 12006
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:949 original size:17 final size:17

Alignment explanation


    Indices: 927--959  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        917 ACGACGGGTT

                             
        927 GGGTTTTGTTAAGGATA
          1 GGGTTTTGTTAAGGATA

                   *        
        944 GGGTTTTTTTAAGGAT
          1 GGGTTTTGTTAAGGAT

        960 TGGAGAAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.21, C:0.00, G:0.33, T:0.45


Consensus pattern (17 bp):   
GGGTTTTGTTAAGGATA

Found at i:4776 original size:23 final size:23

Alignment explanation


    Indices: 4746--4791  Score: 83
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4736 CAAACAATCT

                        *          
       4746 TGAGCACTCTCGTTCGGTCTCTA
          1 TGAGCACTCTCGCTCGGTCTCTA

                                   
       4769 TGAGCACTCTCGCTCGGTCTCTA
          1 TGAGCACTCTCGCTCGGTCTCTA

       4792 CAAACTAACA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.13, C:0.33, G:0.22, T:0.33


Consensus pattern (23 bp):   
TGAGCACTCTCGCTCGGTCTCTA

Found at i:5624 original size:18 final size:18

Alignment explanation


    Indices: 5603--5638  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       5593 TAGCATTTTC

                              
       5603 CTTTTTGACAATTTTCTT
          1 CTTTTTGACAATTTTCTT

                   *          
       5621 CTTTTTGGCAATTTTCTT
          1 CTTTTTGACAATTTTCTT

       5639 TCCCAATTAA


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

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.14, C:0.17, G:0.08, T:0.61


Consensus pattern (18 bp):   
CTTTTTGACAATTTTCTT

Found at i:7623 original size:14 final size:14

Alignment explanation


    Indices: 7604--7643  Score: 64
    Period size: 13  Copynumber: 2.9  Consensus size: 14

       7594 CTCACCCAAT

                          
       7604 TTTTTTAAAAAATA
          1 TTTTTTAAAAAATA

                          
       7618 TTTTTT-AAAAATA
          1 TTTTTTAAAAAATA

                         
       7631 TTTTTTAATAAAA
          1 TTTTTTAA-AAAA

       7644 AATATAATGT


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  13   13  0.54
  14    7  0.29
  15    4  0.17

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (14 bp):   
TTTTTTAAAAAATA

Done.