Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018142.1 Corchorus olitorius cultivar O-4 contig18175, 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: 1676
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35


Found at i:634 original size:6 final size:6

Alignment explanation


    Indices: 616--645  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

        606 AGATAGACTT

                                              
        616 ATATAG TATATAG ATATAG ATATAG ATATA
          1 ATATAG -ATATAG ATATAG ATATAG ATATA

        646 TAAAAGATAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37


Consensus pattern (6 bp):   
ATATAG

Found at i:635 original size:23 final size:21

Alignment explanation


    Indices: 588--631  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        578 TTTTGAAGTT

                                 
        588 TAGACTTATATAGTATATAGA
          1 TAGACTTATATAGTATATAGA

                                 
        609 TAGACTTATATAGTATATAGA
          1 TAGACTTATATAGTATATAGA

              
        630 TA
          1 TA

        632 TAGATATAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.43, C:0.05, G:0.14, T:0.39


Consensus pattern (21 bp):   
TAGACTTATATAGTATATAGA

Found at i:640 original size:12 final size:13

Alignment explanation


    Indices: 595--647  Score: 54
    Period size: 14  Copynumber: 3.9  Consensus size: 13

        585 GTTTAGACTT

                         
        595 ATATAGTATATAG
          1 ATATAGTATATAG

               *  *       
        608 ATAGACTTATATAG
          1 ATATA-GTATATAG

                          
        622 TATATAG-ATATAG
          1 -ATATAGTATATAG

                         
        635 ATATAGATATATA
          1 ATATAG-TATATA

        648 AAAGATAACT


Statistics
Matches: 32,  Mismatches: 4, Indels: 7
        0.74            0.09        0.16

Matches are distributed among these distances:
  12    6  0.19
  13   10  0.31
  14   12  0.38
  15    4  0.12

ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38


Consensus pattern (13 bp):   
ATATAGTATATAG
Done.