Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018283.1 Corchorus olitorius cultivar O-4 contig18316, 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: 2201
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31


Found at i:931 original size:14 final size:13

Alignment explanation


    Indices: 885--949  Score: 78
    Period size: 14  Copynumber: 4.8  Consensus size: 13

        875 TAAAGGATTT

                         
        885 TTTTCAAAAATGA
          1 TTTTCAAAAATGA

                           
        898 TTTTCAAGAAACTG-
          1 TTTTCAA-AAA-TGA

             *            
        912 TCTTCAAGAAATGA
          1 TTTTCAA-AAATGA

                         
        926 TTTTCAAAAATGA
          1 TTTTCAAAAATGA

                       
        939 GTTTTCAAAAA
          1 -TTTTCAAAAA

        950 GGTTTTGAGT


Statistics
Matches: 46,  Mismatches: 2, Indels: 7
        0.84            0.04        0.13

Matches are distributed among these distances:
  13   15  0.33
  14   29  0.63
  15    2  0.04

ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35


Consensus pattern (13 bp):   
TTTTCAAAAATGA

Found at i:1622 original size:19 final size:19

Alignment explanation


    Indices: 1593--1640  Score: 62
    Period size: 20  Copynumber: 2.5  Consensus size: 19

       1583 TCTAAAGAAA

                           *    
       1593 AAAGAAAAAAATG-AGAAAG
          1 AAAGAAAAAAA-GAAAAAAG

                                
       1612 CAAAGAAAAAAAGAAAAAAG
          1 -AAAGAAAAAAAGAAAAAAG

                     
       1632 AAAGAAAAA
          1 AAAGAAAAA

       1641 TCAAAAGGTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  19   10  0.38
  20   16  0.62

ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02


Consensus pattern (19 bp):   
AAAGAAAAAAAGAAAAAAG

Found at i:1637 original size:11 final size:11

Alignment explanation


    Indices: 1586--1640  Score: 58
    Period size: 11  Copynumber: 4.8  Consensus size: 11

       1576 GCAGCAATCT

                       
       1586 AAAGAAAAAAG
          1 AAAGAAAAAAG

                     *  
       1597 AAA-AAAATGAG
          1 AAAGAAAA-AAG

                        *
       1608 AAAGCAAAGAAAA
          1 AAAG-AAA-AAAG

                       
       1621 AAAGAAAAAAG
          1 AAAGAAAAAAG

                     
       1632 AAAGAAAAA
          1 AAAGAAAAA

       1641 TCAAAAGGTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 8
        0.75            0.08        0.17

Matches are distributed among these distances:
  10    4  0.11
  11   20  0.56
  12    3  0.08
  13    8  0.22
  14    1  0.03

ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02


Consensus pattern (11 bp):   
AAAGAAAAAAG

Found at i:1637 original size:28 final size:27

Alignment explanation


    Indices: 1586--1638  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 27

       1576 GCAGCAATCT

                               *       
       1586 AAAGAAAAAAGAAAAAAATGAGAAAGC
          1 AAAGAAAAAAGAAAAAAATAAGAAAGC

                                       
       1613 AAAGAAAAAAAGAAAAAAGA-AAGAAA
          1 AAAG-AAAAAAGAAAAAA-ATAAGAAA

       1639 AATCAAAAGG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27    4  0.17
  28   18  0.78
  29    1  0.04

ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02


Consensus pattern (27 bp):   
AAAGAAAAAAGAAAAAAATAAGAAAGC
Done.