Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016212.1 Corchorus capsularis cultivar CVL-1 contig16233, 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: 13182
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32


Found at i:1008 original size:7 final size:6

Alignment explanation


    Indices: 952--1008  Score: 55
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        942 GCCCAAAAAA

                         *                           *               
        952 AAAAGGG AAAAGT AAAAGG AAAA-G AAAA-G AAAAGA AAAAGG AAAAGGG
          1 AAAA-GG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAA-GG

                      
       1000 AAATAGG AA
          1 AAA-AGG AA

       1009 GAATAATAAT


Statistics
Matches: 43,  Mismatches: 4, Indels: 6
        0.81            0.08        0.11

Matches are distributed among these distances:
   5   10  0.23
   6   19  0.44
   7   13  0.30
   8    1  0.02

ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04


Consensus pattern (6 bp):   
AAAAGG

Found at i:7449 original size:31 final size:31

Alignment explanation


    Indices: 7411--7473  Score: 126
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7401 GTGCAGCGAC

                                           
       7411 GGCGACGGTTTCCGGCTAAGCCTATGACCGG
          1 GGCGACGGTTTCCGGCTAAGCCTATGACCGG

                                           
       7442 GGCGACGGTTTCCGGCTAAGCCTATGACCGG
          1 GGCGACGGTTTCCGGCTAAGCCTATGACCGG

             
       7473 G
          1 G

       7474 AAAAATAATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.16, C:0.29, G:0.37, T:0.19


Consensus pattern (31 bp):   
GGCGACGGTTTCCGGCTAAGCCTATGACCGG

Found at i:13053 original size:2 final size:2

Alignment explanation


    Indices: 13046--13093  Score: 78
    Period size: 2  Copynumber: 23.5  Consensus size: 2

      13036 CATATAGTTC

                                                               *           
      13046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT ACT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T

                   
      13089 AT AT A
          1 AT AT A

      13094 AGTCTAAACT


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   2   41  0.95
   3    2  0.05

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.