Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020222.1 Corchorus olitorius cultivar O-4 contig20255, 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: 13212
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:3902 original size:19 final size:18

Alignment explanation


    Indices: 3869--3904  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3859 TTGAAATAGT

                              
       3869 TCTTCAAAAATCTTCAAG
          1 TCTTCAAAAATCTTCAAG

                     *        
       3887 TCTTCAAATTATCTTCAA
          1 TCTTCAAA-AATCTTCAA

       3905 ATGGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39


Consensus pattern (18 bp):   
TCTTCAAAAATCTTCAAG

Found at i:9393 original size:11 final size:11

Alignment explanation


    Indices: 9377--9416  Score: 57
    Period size: 11  Copynumber: 3.8  Consensus size: 11

       9367 ATGTAAACAC

                       
       9377 AAATAAACATG
          1 AAATAAACATG

                       
       9388 AAAT-AACATG
          1 AAATAAACATG

                     * 
       9398 -AATAAACAAG
          1 AAATAAACATG

                     
       9408 AAATAAACA
          1 AAATAAACA

       9417 ACCAAATAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 4
        0.84            0.03        0.13

Matches are distributed among these distances:
   9    3  0.12
  10   11  0.42
  11   12  0.46

ACGTcount: A:0.68, C:0.10, G:0.07, T:0.15


Consensus pattern (11 bp):   
AAATAAACATG

Found at i:9417 original size:11 final size:11

Alignment explanation


    Indices: 9377--9433  Score: 55
    Period size: 11  Copynumber: 5.3  Consensus size: 11

       9367 ATGTAAACAC

                     * 
       9377 AAATAAACATG
          1 AAATAAACAAG

                     * 
       9388 AAAT-AACATG
          1 AAATAAACAAG

                       
       9398 -AATAAACAAG
          1 AAATAAACAAG

                       *
       9408 AAATAAACAACC
          1 AAATAAACAA-G

                   *   
       9420 AAATAAAAAAG
          1 AAATAAACAAG

               
       9431 AAA
          1 AAA

       9434 ACCCTAGTTA


Statistics
Matches: 39,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
   9    3  0.08
  10   11  0.28
  11   16  0.41
  12    9  0.23

ACGTcount: A:0.70, C:0.11, G:0.07, T:0.12


Consensus pattern (11 bp):   
AAATAAACAAG
Done.