Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009536.1 Corchorus olitorius cultivar O-4 contig09568, 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: 7212
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:955 original size:17 final size:18

Alignment explanation


    Indices: 933--966  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        923 TTCTCCTCCC

                              
        933 TGAATG-TTTTTCACATG
          1 TGAATGTTTTTTCACATG

                             
        950 TGAATGTTTTTTCACAT
          1 TGAATGTTTTTTCACAT

        967 TTATATTATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    6  0.38
  18   10  0.62

ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50


Consensus pattern (18 bp):   
TGAATGTTTTTTCACATG

Found at i:3597 original size:36 final size:36

Alignment explanation


    Indices: 3556--3629  Score: 148
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       3546 AATTAAATGA

                                                
       3556 ATGTATATATATACTCGTAGAAATGATATAATATTT
          1 ATGTATATATATACTCGTAGAAATGATATAATATTT

                                                
       3592 ATGTATATATATACTCGTAGAAATGATATAATATTT
          1 ATGTATATATATACTCGTAGAAATGATATAATATTT

              
       3628 AT
          1 AT

       3630 TTCGGTCAAT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   38  1.00

ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42


Consensus pattern (36 bp):   
ATGTATATATATACTCGTAGAAATGATATAATATTT

Found at i:3620 original size:19 final size:19

Alignment explanation


    Indices: 3562--3621  Score: 56
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       3552 ATGAATGTAT

                               
       3562 ATATATACTCGTAGAAATG
          1 ATATATACTCGTAGAAATG

                       *     *   
       3581 ATATAATA-T-TTATG-TAT-
          1 ATAT-ATACTCGTA-GAAATG

                               
       3598 ATATATACTCGTAGAAATG
          1 ATATATACTCGTAGAAATG

                 
       3617 ATATA
          1 ATATA

       3622 ATATTTATTT


Statistics
Matches: 31,  Mismatches: 4, Indels: 12
        0.66            0.09        0.26

Matches are distributed among these distances:
  16    3  0.10
  17    6  0.19
  18    8  0.26
  19   11  0.35
  20    3  0.10

ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38


Consensus pattern (19 bp):   
ATATATACTCGTAGAAATG
Done.