Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012511.1 Corchorus olitorius cultivar O-4 contig12544, 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: 34221
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31


Found at i:10782 original size:17 final size:18

Alignment explanation


    Indices: 10762--10798  Score: 51
    Period size: 17  Copynumber: 2.1  Consensus size: 18

      10752 TAATACCAAG

                               
      10762 CACCCCT-TCCTAC-CCCT
          1 CACCCCTCTCC-ACTCCCT

                              
      10779 CACCCCTCTCCACTCCCT
          1 CACCCCTCTCCACTCCCT

              
      10797 CA
          1 CA

      10799 ACCAAACTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  17    9  0.50
  18    9  0.50

ACGTcount: A:0.14, C:0.65, G:0.00, T:0.22


Consensus pattern (18 bp):   
CACCCCTCTCCACTCCCT

Found at i:16558 original size:18 final size:18

Alignment explanation


    Indices: 16525--16559  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      16515 TTTAGGTCGA

                    *  *      
      16525 ATTTTTTTTATTTTTTTT
          1 ATTTTTTTGATATTTTTT

                             
      16543 ATTTTTTTGATATTTTT
          1 ATTTTTTTGATATTTTT

      16560 CGATTAAACC


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83


Consensus pattern (18 bp):   
ATTTTTTTGATATTTTTT

Found at i:16559 original size:11 final size:9

Alignment explanation


    Indices: 16525--16550  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      16515 TTTAGGTCGA

                     
      16525 ATTTTTTTT
          1 ATTTTTTTT

                     
      16534 ATTTTTTTT
          1 ATTTTTTTT

                    
      16543 ATTTTTTT
          1 ATTTTTTT

      16551 GATATTTTTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (9 bp):   
ATTTTTTTT

Found at i:29023 original size:18 final size:18

Alignment explanation


    Indices: 28996--29030  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      28986 TCGACCAACT

                              
      28996 AGGAAAAAATAAATAAGA
          1 AGGAAAAAATAAATAAGA

                 *           
      29014 AGGAATAAATAAATAAG
          1 AGGAAAAAATAAATAAG

      29031 GATTGCACTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14


Consensus pattern (18 bp):   
AGGAAAAAATAAATAAGA

Found at i:34059 original size:2 final size:2

Alignment explanation


    Indices: 34054--34087  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      34044 ATACACACAC

                                                              
      34054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      34088 GATGATAATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.