Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019294.1 Corchorus olitorius cultivar O-4 contig19327, 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: 8213
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:430 original size:2 final size:2

Alignment explanation


    Indices: 425--473  Score: 98
    Period size: 2  Copynumber: 24.5  Consensus size: 2

        415 TATATATATA

                                                                          
        425 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG

                      
        467 TG TG TG T
          1 TG TG TG T

        474 TGATGCATTC


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   47  1.00

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


Consensus pattern (2 bp):   
TG

Found at i:5406 original size:21 final size:20

Alignment explanation


    Indices: 5377--5419  Score: 68
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       5367 ATACTCATAA

                       *        
       5377 AGAAGTTTCAAGCTCATTGG
          1 AGAAGTTTCAAACTCATTGG

                                 
       5397 AGAAGGTTTCAAACTCATTGG
          1 AGAA-GTTTCAAACTCATTGG

              
       5418 AG
          1 AG

       5420 TTGCCTAAGG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  20    4  0.19
  21   17  0.81

ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28


Consensus pattern (20 bp):   
AGAAGTTTCAAACTCATTGG

Found at i:7817 original size:33 final size:33

Alignment explanation


    Indices: 7716--7820  Score: 99
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       7706 TTGCAAAGAG

                                      *      * 
       7716 TGTTTT-AGATGTTG-TTAGTGATGATACTAAACC
          1 TGTTTTAAG-TGTTGTTTA-TGATGAAACTAAATC

             **              *      *        
       7749 TAATTTAAGTGTTGTTTGTGATGACACTAAATC
          1 TGTTTTAAGTGTTGTTTATGATGAAACTAAATC

                   *                          
       7782 TGTTTTAGGTGTTGTTTATGATGAAAC-AAATTC
          1 TGTTTTAAGTGTTGTTTATGATGAAACTAAA-TC

                  
       7815 TGTTTT
          1 TGTTTT

       7821 GGATGCTAAT


Statistics
Matches: 59,  Mismatches: 10, Indels: 6
        0.79            0.13        0.08

Matches are distributed among these distances:
  32    3  0.05
  33   52  0.88
  34    4  0.07

ACGTcount: A:0.27, C:0.08, G:0.20, T:0.46


Consensus pattern (33 bp):   
TGTTTTAAGTGTTGTTTATGATGAAACTAAATC
Done.