Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011910.1 Corchorus olitorius cultivar O-4 contig11943, 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: 10685
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28


Found at i:852 original size:35 final size:35

Alignment explanation


    Indices: 787--853  Score: 89
    Period size: 35  Copynumber: 1.9  Consensus size: 35

        777 GATCCTCTTT

                   *                 *         
        787 GATATTGGAGTTAGTAGGATATTAATGTGTTTGGA
          1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA

                           *  * *           
        822 GATATTGAAGTTAGTGGGGTTTTAAGGTGTTT
          1 GATATTGAAGTTAGTAGGATATTAAGGTGTTT

        854 AAAGAGCTTA


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  35   27  1.00

ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42


Consensus pattern (35 bp):   
GATATTGAAGTTAGTAGGATATTAAGGTGTTTGGA

Found at i:1857 original size:21 final size:22

Alignment explanation


    Indices: 1831--1885  Score: 85
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       1821 CTTATTGAGT

                  *     *         
       1831 TTATCACAATTTTATA-GGTAA
          1 TTATCAAAATTTAATAGGGTAA

                                  
       1852 TTATCAAAATTTAATAGGGTAA
          1 TTATCAAAATTTAATAGGGTAA

                        
       1874 TTATCAAAATTT
          1 TTATCAAAATTT

       1886 CATAAAAATA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  21   14  0.45
  22   17  0.55

ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42


Consensus pattern (22 bp):   
TTATCAAAATTTAATAGGGTAA

Found at i:8354 original size:20 final size:21

Alignment explanation


    Indices: 8315--8360  Score: 58
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       8305 CAAAGAAAAC

                                 
       8315 GAAAAAAGAGAAACAAAGGA-
          1 GAAAAAAGAGAAACAAAGGAG

                       **  *     
       8335 GAAAAAAGAGACGCAGAGGAG
          1 GAAAAAAGAGAAACAAAGGAG

                 
       8356 GAAAA
          1 GAAAA

       8361 TGAAAGGACA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  20   17  0.77
  21    5  0.23

ACGTcount: A:0.63, C:0.07, G:0.30, T:0.00


Consensus pattern (21 bp):   
GAAAAAAGAGAAACAAAGGAG

Found at i:10186 original size:20 final size:20

Alignment explanation


    Indices: 10150--10189  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      10140 AGGAGAGTAA

                      *         
      10150 GAGTGACACGTTGCTAAAAG
          1 GAGTGACACGATGCTAAAAG

                                 
      10170 GAGTGACAC-ATGACTAAAAG
          1 GAGTGACACGATG-CTAAAAG

      10190 ACCAAATGAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    2  0.11
  20   16  0.89

ACGTcount: A:0.40, C:0.15, G:0.28, T:0.17


Consensus pattern (20 bp):   
GAGTGACACGATGCTAAAAG
Done.