Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022363.1 Corchorus olitorius cultivar O-4 contig22396, 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: 7548
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3412 original size:18 final size:18

Alignment explanation


    Indices: 3389--3454  Score: 51
    Period size: 18  Copynumber: 3.4  Consensus size: 18

       3379 TTTTTTCATA

                              
       3389 TAATAATTAGTTAATATT
          1 TAATAATTAGTTAATATT

                         *  **    *
       3407 TAATAATCTTTATATTTTTCATA
          1 TAATAA---TTA-GTTAAT-ATT

                              
       3430 TAATAATTAGTTAATATT
          1 TAATAATTAGTTAATATT

                   
       3448 TAATAAT
          1 TAATAAT

       3455 CTTTATAAGA


Statistics
Matches: 35,  Mismatches: 8, Indels: 10
        0.66            0.15        0.19

Matches are distributed among these distances:
  18   15  0.43
  19    3  0.09
  20    3  0.09
  21    3  0.09
  22    3  0.09
  23    8  0.23

ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52


Consensus pattern (18 bp):   
TAATAATTAGTTAATATT

Found at i:3437 original size:41 final size:41

Alignment explanation


    Indices: 3380--3461  Score: 164
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       3370 AACCATTTTT

                                                     
       3380 TTTTTCATATAATAATTAGTTAATATTTAATAATCTTTATA
          1 TTTTTCATATAATAATTAGTTAATATTTAATAATCTTTATA

                                                     
       3421 TTTTTCATATAATAATTAGTTAATATTTAATAATCTTTATA
          1 TTTTTCATATAATAATTAGTTAATATTTAATAATCTTTATA

       3462 AGATATATAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   41  1.00

ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54


Consensus pattern (41 bp):   
TTTTTCATATAATAATTAGTTAATATTTAATAATCTTTATA

Found at i:5739 original size:15 final size:15

Alignment explanation


    Indices: 5719--5753  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       5709 TAGGATAGAA

                           
       5719 AATTGTTTGTTTTTG
          1 AATTGTTTGTTTTTG

                           
       5734 AATTGTTTGTTTTTG
          1 AATTGTTTGTTTTTG

            *    
       5749 GATTG
          1 AATTG

       5754 ATTATTCCCC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63


Consensus pattern (15 bp):   
AATTGTTTGTTTTTG
Done.