Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006191.1 Corchorus capsularis cultivar CVL-1 contig06209, 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: 12322
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29


Found at i:5994 original size:32 final size:33

Alignment explanation


    Indices: 5943--6009  Score: 100
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       5933 GCGCCTTCTT

                      *                       
       5943 TTTTTTTTTTTCCGAATCAAATTAATTATTGGTC
          1 TTTTTTTTTTGCC-AATCAAATTAATTATTGGTC

                                  *          
       5977 TTTTTTTTTTGCC-ATCAAATTTATTATTGGTC
          1 TTTTTTTTTTGCCAATCAAATTAATTATTGGTC

             
       6009 T
          1 T

       6010 AAAAATTAAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  32   19  0.61
  34   12  0.39

ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58


Consensus pattern (33 bp):   
TTTTTTTTTTGCCAATCAAATTAATTATTGGTC

Found at i:7212 original size:2 final size:2

Alignment explanation


    Indices: 7205--7238  Score: 59
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       7195 AGCAGACTAC

                                                              
       7205 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T

       7239 CATGTTAAGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   29  0.94
   3    2  0.06

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:10243 original size:15 final size:15

Alignment explanation


    Indices: 10225--10256  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      10215 GCAAAAGGAC

                           
      10225 ATAATTGCCTATTCT
          1 ATAATTGCCTATTCT

                           
      10240 ATAATTGCCTATTCT
          1 ATAATTGCCTATTCT

              
      10255 AT
          1 AT

      10257 CCTGCCAAAG


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

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47


Consensus pattern (15 bp):   
ATAATTGCCTATTCT
Done.