Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006850.1 Corchorus capsularis cultivar CVL-1 contig06871, 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: 19185
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31


Found at i:173 original size:6 final size:6

Alignment explanation


    Indices: 157--188  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

        147 AAATCAAAGC

                                                  
        157 AAATC- AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

        189 GTAGAATTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.19
   6   21  0.81

ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28


Consensus pattern (6 bp):   
AAATCT

Found at i:16261 original size:17 final size:17

Alignment explanation


    Indices: 16235--16271  Score: 65
    Period size: 17  Copynumber: 2.2  Consensus size: 17

      16225 TCCCCCTCAT

                             
      16235 GGTACCAGGTAGCATGA
          1 GGTACCAGGTAGCATGA

                 *           
      16252 GGTACTAGGTAGCATGA
          1 GGTACCAGGTAGCATGA

               
      16269 GGT
          1 GGT

      16272 GCTGGATAAC


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

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.27, C:0.14, G:0.38, T:0.22


Consensus pattern (17 bp):   
GGTACCAGGTAGCATGA

Found at i:17629 original size:2 final size:2

Alignment explanation


    Indices: 17622--17654  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      17612 AGAAATACTA

                                                              
      17622 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      17655 TGTTGGGGAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.97

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Done.