Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012434.1 Corchorus olitorius cultivar O-4 contig12467, 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: 7779
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         40 TGAATGATTT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:2338 original size:20 final size:19

Alignment explanation


    Indices: 2302--2352  Score: 59
    Period size: 20  Copynumber: 2.7  Consensus size: 19

       2292 CAATATAAGA

                         *     
       2302 TTTT-TTTTTGTTGTTTTG
          1 TTTTGTTTTTGTTATTTTG

                               *
       2320 TTTTGTTTTTGTATATTTTT
          1 TTTTGTTTTTGT-TATTTTG

                   *     
       2340 TTTTGTTGTTGTT
          1 TTTTGTTTTTGTT

       2353 TTTGCATCAG


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  18    4  0.14
  19    8  0.29
  20   16  0.57

ACGTcount: A:0.04, C:0.00, G:0.16, T:0.80


Consensus pattern (19 bp):   
TTTTGTTTTTGTTATTTTG

Found at i:4839 original size:6 final size:6

Alignment explanation


    Indices: 4814--4859  Score: 67
    Period size: 6  Copynumber: 7.8  Consensus size: 6

       4804 CTTTTTGTCG

                          *   *                                   
       4814 TTTGGT TTTGG- GTTGCT TTTGGT TTTGGT TTTGGT TTTGGT TTTGG
          1 TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGGT TTTGG

       4860 GTTTCATTTG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   5    3  0.09
   6   32  0.91

ACGTcount: A:0.00, C:0.02, G:0.35, T:0.63


Consensus pattern (6 bp):   
TTTGGT

Done.