Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004169.1 Corchorus capsularis cultivar CVL-1 contig04177, 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: 5308
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:3505 original size:2 final size:2

Alignment explanation


    Indices: 3500--3547  Score: 52
    Period size: 2  Copynumber: 26.0  Consensus size: 2

       3490 TTTTTATTAT

                                                                           
       3500 TA TA TA TA TA TA TA GTA TA -A TA TA -A TA TA -A TA TA -A TA TA
          1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                          
       3539 -A TA TA TA TA
          1 TA TA TA TA TA

       3548 ATTAGTAGCA


Statistics
Matches: 40,  Mismatches: 0, Indels: 12
        0.77            0.00        0.23

Matches are distributed among these distances:
   1    5  0.12
   2   33  0.82
   3    2  0.05

ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:3523 original size:5 final size:5

Alignment explanation


    Indices: 3503--3549  Score: 69
    Period size: 5  Copynumber: 9.4  Consensus size: 5

       3493 TTATTATTAT

                         *                                           
       3503 ATATA TATATA GTATA ATATA ATATA ATATA ATATA ATAT- ATATA AT
          1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT

       3550 TAGTAGCATA


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
   4    4  0.11
   5   29  0.76
   6    5  0.13

ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43


Consensus pattern (5 bp):   
ATATA

Found at i:5138 original size:2 final size:2

Alignment explanation


    Indices: 5131--5162  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       5121 ATTATTATTC

                                                           
       5131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       5163 CTAGATCTAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
TA

Done.