Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005467.1 Corchorus capsularis cultivar CVL-1 contig05485, 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: 12040
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:760 original size:19 final size:21

Alignment explanation


    Indices: 714--761  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        704 TGTGACACGC

                                 *
        714 CACATGTACCAAAAAGTCGTGC
          1 CACATGTACCAAAAAGTCG-GA

                                 
        736 CACATGTACCAAAAAG-C-GA
          1 CACATGTACCAAAAAGTCGGA

                   
        755 CACATGT
          1 CACATGT

        762 CACGTGGCAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19    8  0.32
  21    1  0.04
  22   16  0.64

ACGTcount: A:0.40, C:0.27, G:0.17, T:0.17


Consensus pattern (21 bp):   
CACATGTACCAAAAAGTCGGA

Found at i:8243 original size:28 final size:28

Alignment explanation


    Indices: 8211--8264  Score: 90
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       8201 ATTATATATA

                      *       *         
       8211 AATTTCTAAGTAGTCGTATTGCCAAATC
          1 AATTTCTAAGCAGTCGTACTGCCAAATC

                                      
       8239 AATTTCTAAGCAGTCGTACTGCCAAA
          1 AATTTCTAAGCAGTCGTACTGCCAAA

       8265 ATTGAAGCAC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31


Consensus pattern (28 bp):   
AATTTCTAAGCAGTCGTACTGCCAAATC

Found at i:10411 original size:2 final size:2

Alignment explanation


    Indices: 10360--10392  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      10350 GCATATAAAG

                                                              
      10360 AT AT A- 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

      10393 TCTTCCTGGA


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


Consensus pattern (2 bp):   
AT
Done.