Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016171.1 Corchorus capsularis cultivar CVL-1 contig16192, 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: 10956
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:1866 original size:2 final size:2

Alignment explanation


    Indices: 1861--1894  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1851 CCGGCCGTAA

                                                              
       1861 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

       1895 GTCATAAAAA


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

Found at i:7375 original size:19 final size:18

Alignment explanation


    Indices: 7351--7387  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       7341 TATGAGTAAG

                               
       7351 TAAAAATATAATATATAAA
          1 TAAAAATATAATAT-TAAA

                   *          
       7370 TAAAAATTTAATATTAAA
          1 TAAAAATATAATATTAAA

       7388 ACAATTAATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    4  0.24
  19   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (18 bp):   
TAAAAATATAATATTAAA

Found at i:7941 original size:11 final size:11

Alignment explanation


    Indices: 7925--7957  Score: 66
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       7915 ATTATTTTAC

                       
       7925 GGTAGTTTGTT
          1 GGTAGTTTGTT

                       
       7936 GGTAGTTTGTT
          1 GGTAGTTTGTT

                       
       7947 GGTAGTTTGTT
          1 GGTAGTTTGTT

       7958 CGAATATGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.09, C:0.00, G:0.36, T:0.55


Consensus pattern (11 bp):   
GGTAGTTTGTT
Done.