Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000261.1 Corchorus olitorius cultivar O-4 contig00261, 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, 600

Length: 1001
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33


Found at i:285 original size:19 final size:20

Alignment explanation


    Indices: 261--299  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        251 AAAATTCTTA

                                 
        261 TTTTCTT-TATTTCTT-TTTT
          1 TTTTCTTCT-TTTCTTCTTTT

                                
        280 TTTTCTTCTTTTCTTCTTTT
          1 TTTTCTTCTTTTCTTCTTTT

        300 GGACCAGGCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19   13  0.72
  20    5  0.28

ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82


Consensus pattern (20 bp):   
TTTTCTTCTTTTCTTCTTTT

Found at i:482 original size:39 final size:39

Alignment explanation


    Indices: 379--487  Score: 159
    Period size: 38  Copynumber: 2.8  Consensus size: 39

        369 GCCAGGCCGT

                                 *       *    *    
        379 TGGGCCTGCGCTA-GCCCGCGCGCCTGGCTTGGCGCGCC
          1 TGGGCCTGCGCTAGGCCCGCGTGCCTGGCCTGGCACGCC

                                                   
        417 TGGGCCTGCGCT-GGCCCGCGTGCCTGGCCTGGCACGCC
          1 TGGGCCTGCGCTAGGCCCGCGTGCCTGGCCTGGCACGCC

                      *                      
        455 TGGGCCTGCGATAGGCCCGCGTGCCTGGGCCTG
          1 TGGGCCTGCGCTAGGCCCGCGTGCCT-GGCCTG

        488 CACAAGCAGG


Statistics
Matches: 64,  Mismatches: 4, Indels: 4
        0.89            0.06        0.06

Matches are distributed among these distances:
  38   45  0.70
  39   13  0.20
  40    6  0.09

ACGTcount: A:0.04, C:0.39, G:0.40, T:0.17


Consensus pattern (39 bp):   
TGGGCCTGCGCTAGGCCCGCGTGCCTGGCCTGGCACGCC
Done.