Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012295.1 Corchorus olitorius cultivar O-4 contig12328, 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: 7495
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:163 original size:29 final size:29

Alignment explanation


    Indices: 125--193  Score: 111
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        115 CTATTTTCCT

                                          
        125 TCCCCTGGCAAAAACCAGAAAAAGTTCCCC
          1 TCCCC-GGCAAAAACCAGAAAAAGTTCCCC

                       *                *
        155 TCCCCGGCAAATACCAGAAAAAGTTCCCT
          1 TCCCCGGCAAAAACCAGAAAAAGTTCCCC

                      
        184 TCCCCGGCAA
          1 TCCCCGGCAA

        194 CGGCGCCAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  29   32  0.86
  30    5  0.14

ACGTcount: A:0.33, C:0.38, G:0.14, T:0.14


Consensus pattern (29 bp):   
TCCCCGGCAAAAACCAGAAAAAGTTCCCC

Found at i:393 original size:15 final size:16

Alignment explanation


    Indices: 375--408  Score: 61
    Period size: 15  Copynumber: 2.2  Consensus size: 16

        365 TGACAGAGAG

                            
        375 CAATTAAAC-AGAAAA
          1 CAATTAAACTAGAAAA

                            
        390 CAATTAAACTAGAAAA
          1 CAATTAAACTAGAAAA

               
        406 CAA
          1 CAA

        409 AGCAGAGTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15    9  0.50
  16    9  0.50

ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15


Consensus pattern (16 bp):   
CAATTAAACTAGAAAA

Found at i:1184 original size:11 final size:11

Alignment explanation


    Indices: 1168--1193  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       1158 CCTTTGCCTA

                       
       1168 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       1179 AAAACTAGAAG
          1 AAAACTAGAAG

                
       1190 AAAA
          1 AAAA

       1194 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:3438 original size:6 final size:6

Alignment explanation


    Indices: 3427--3454  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       3417 TCAAATTTTT

                                            
       3427 AAGATG AAGATG AAGATG AAGATG AAGA
          1 AAGATG AAGATG AAGATG AAGATG AAGA

       3455 GATATTATAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.54, C:0.00, G:0.32, T:0.14


Consensus pattern (6 bp):   
AAGATG

Done.