Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015766.1 Corchorus capsularis cultivar CVL-1 contig15787, 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: 3983
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29


Found at i:3303 original size:20 final size:21

Alignment explanation


    Indices: 3273--3318  Score: 85
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       3263 TCAAAAAAAA

                                 
       3273 AAAGTAAAAATAATGGTCTGC
          1 AAAGTAAAAATAATGGTCTGC

                                 
       3294 AAAG-AAAAATAATGGTCTGC
          1 AAAGTAAAAATAATGGTCTGC

                 
       3314 AAAGT
          1 AAAGT

       3319 CTGCAAAGAA


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

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.50, C:0.09, G:0.20, T:0.22


Consensus pattern (21 bp):   
AAAGTAAAAATAATGGTCTGC

Found at i:3320 original size:29 final size:30

Alignment explanation


    Indices: 3288--3348  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       3278 AAAAATAATG

                                          
       3288 GTCTGCAAAG-AAAAATAATGGTCTGCAAA
          1 GTCTGCAAAGAAAAAATAATGGTCTGCAAA

                                          
       3317 GTCTGCAAAGAAAAAATAATGGTCTGCAAA
          1 GTCTGCAAAGAAAAAATAATGGTCTGCAAA

              
       3347 GT
          1 GT

       3349 TATCATGAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  29   10  0.32
  30   21  0.68

ACGTcount: A:0.44, C:0.13, G:0.21, T:0.21


Consensus pattern (30 bp):   
GTCTGCAAAGAAAAAATAATGGTCTGCAAA

Found at i:3494 original size:92 final size:92

Alignment explanation


    Indices: 3337--3516  Score: 351
    Period size: 92  Copynumber: 2.0  Consensus size: 92

       3327 AAAAAATAAT

                                              *                              
       3337 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGATATTGTCTCCAATAATGCAAAGCTGACTCAT
          1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT

                                       
       3402 TGGATGAAGAGAAAGCCAAATTATGAA
         66 TGGATGAAGAGAAAGCCAAATTATGAA

                                                                             
       3429 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
          1 GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT

                                   
       3494 TGGATGAAGAGAAAGCCAAATTA
         66 TGGATGAAGAGAAAGCCAAATTA

       3517 AAGCCAAATT


Statistics
Matches: 87,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  92   87  1.00

ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26


Consensus pattern (92 bp):   
GGTCTGCAAAGTTATCATGAAGAATCTCTGCAGAAATTGTCTCCAATAATGCAAAGCTGACTCAT
TGGATGAAGAGAAAGCCAAATTATGAA
Done.