Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016292.1 Corchorus capsularis cultivar CVL-1 contig16313, 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: 11881
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:255 original size:32 final size:32

Alignment explanation


    Indices: 218--297  Score: 101
    Period size: 32  Copynumber: 2.5  Consensus size: 32

        208 GGATATAACG

                                  *           
        218 TTATATAGCGGCGTCTGAAGAACA-AAACGCCGC
          1 TTATATAGCGGCGTCTGAA-AAAATAAACGCC-C

                   *     *                  
        251 -TATATAACGGCGCCTGAAAAAATAAACGCCC
          1 TTATATAGCGGCGTCTGAAAAAATAAACGCCC

                            
        282 TTATATAGCGGCGTCT
          1 TTATATAGCGGCGTCT

        298 AAATAATCAG


Statistics
Matches: 40,  Mismatches: 5, Indels: 5
        0.80            0.10        0.10

Matches are distributed among these distances:
  31    4  0.10
  32   36  0.90

ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21


Consensus pattern (32 bp):   
TTATATAGCGGCGTCTGAAAAAATAAACGCCC

Found at i:4322 original size:12 final size:13

Alignment explanation


    Indices: 4307--4339  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       4297 AAAAGAAAAA

                         
       4307 AAAT-TAAAATCT
          1 AAATCTAAAATCT

                         
       4319 AAATCT-AAATCT
          1 AAATCTAAAATCT

                     
       4331 AAATCTAAA
          1 AAATCTAAA

       4340 GCAGATTATA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  12   16  0.84
  13    3  0.16

ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30


Consensus pattern (13 bp):   
AAATCTAAAATCT

Found at i:10975 original size:2 final size:2

Alignment explanation


    Indices: 10964--10992  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      10954 AGAAATAAAA

                                                        
      10964 AT AT -T 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

      10993 TTAAAAGGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

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


Consensus pattern (2 bp):   
AT

Done.