Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022007.1 Corchorus olitorius cultivar O-4 contig22040, 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: 5871
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32


Found at i:1302 original size:23 final size:23

Alignment explanation


    Indices: 1254--1327  Score: 118
    Period size: 23  Copynumber: 3.3  Consensus size: 23

       1244 CTTTGGCTTC

                    *              
       1254 TAGTCGACGACTTTGC-TC-CCT
          1 TAGTCGACAACTTTGCTTCTCCT

                                   
       1275 TAGTCGACAACTTTGCTTCTCCT
          1 TAGTCGACAACTTTGCTTCTCCT

                                   
       1298 TAGTCGACAACTTTGCTTCTCCT
          1 TAGTCGACAACTTTGCTTCTCCT

                    
       1321 T-GTCGAC
          1 TAGTCGAC

       1328 TTTGCCTCTT


Statistics
Matches: 50,  Mismatches: 1, Indels: 3
        0.93            0.02        0.06

Matches are distributed among these distances:
  21   15  0.30
  22    8  0.16
  23   27  0.54

ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36


Consensus pattern (23 bp):   
TAGTCGACAACTTTGCTTCTCCT

Found at i:2015 original size:6 final size:6

Alignment explanation


    Indices: 1989--2027  Score: 53
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       1979 AATTAGTGTA

                            *                             
       1989 AAAATT AAAAATT ATAA-T AAAATT AAAATT AAAATT AAA
          1 AAAATT -AAAATT AAAATT AAAATT AAAATT AAAATT AAA

       2028 TATGCAAATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
   5    4  0.14
   6   19  0.66
   7    6  0.21

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (6 bp):   
AAAATT

Found at i:2028 original size:17 final size:18

Alignment explanation


    Indices: 1989--2028  Score: 55
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       1979 AATTAGTGTA

                          *   
       1989 AAAATTAAAAATTATAAT
          1 AAAATTAAAAATTAAAAT

                              
       2007 AAAATT-AAAATTAAAAT
          1 AAAATTAAAAATTAAAAT

            *    
       2024 TAAAT
          1 AAAAT

       2029 ATGCAAATAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17   14  0.70
  18    6  0.30

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33


Consensus pattern (18 bp):   
AAAATTAAAAATTAAAAT

Found at i:4974 original size:8 final size:8

Alignment explanation


    Indices: 4961--4986  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       4951 TTCTTCGATG

                    
       4961 ATCTTCAA
          1 ATCTTCAA

                    
       4969 ATCTTCAA
          1 ATCTTCAA

                    
       4977 ATCTTCAA
          1 ATCTTCAA

              
       4985 AT
          1 AT

       4987 TATTTTCAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38


Consensus pattern (8 bp):   
ATCTTCAA
Done.