Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011325.1 Corchorus olitorius cultivar O-4 contig11358, 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: 6024
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32


Found at i:2111 original size:18 final size:18

Alignment explanation


    Indices: 2088--2127  Score: 80
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2078 GTTTAGAGTC

                              
       2088 ATTAAGTTAGAAATTAAA
          1 ATTAAGTTAGAAATTAAA

                              
       2106 ATTAAGTTAGAAATTAAA
          1 ATTAAGTTAGAAATTAAA

                
       2124 ATTA
          1 ATTA

       2128 TTGGGTTGCC


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

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35


Consensus pattern (18 bp):   
ATTAAGTTAGAAATTAAA

Found at i:2146 original size:75 final size:75

Alignment explanation


    Indices: 2028--2166  Score: 278
    Period size: 75  Copynumber: 1.9  Consensus size: 75

       2018 TGCAAAATAA

                                                                             
       2028 AAAATTAAGTTAGAAATTAAAATTATTGGGTTGCCTCCCAACAAGTGCTTGTTTAGAGTCATTAA
          1 AAAATTAAGTTAGAAATTAAAATTATTGGGTTGCCTCCCAACAAGTGCTTGTTTAGAGTCATTAA

                      
       2093 GTTAGAAATT
         66 GTTAGAAATT

                                                                            
       2103 AAAATTAAGTTAGAAATTAAAATTATTGGGTTGCCTCCCAACAAGTGCTTGTTTAGAGTCATTA
          1 AAAATTAAGTTAGAAATTAAAATTATTGGGTTGCCTCCCAACAAGTGCTTGTTTAGAGTCATTA

       2167 GCTCGACTAA


Statistics
Matches: 64,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  75   64  1.00

ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35


Consensus pattern (75 bp):   
AAAATTAAGTTAGAAATTAAAATTATTGGGTTGCCTCCCAACAAGTGCTTGTTTAGAGTCATTAA
GTTAGAAATT

Found at i:4656 original size:29 final size:29

Alignment explanation


    Indices: 4600--4657  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4590 CTTGAAATAA

                               * *       
       4600 ATCTTCAATGGTCTTCAAGTCTCCAATTT
          1 ATCTTCAATGGTCTTCAAGACACCAATTT

                                    *     
       4629 ATCTTCAAATGGTCTTCAA-ACACGAATTT
          1 ATCTTC-AATGGTCTTCAAGACACCAATTT

       4658 CGAATCTCCA


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29   13  0.52
  30   12  0.48

ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38


Consensus pattern (29 bp):   
ATCTTCAATGGTCTTCAAGACACCAATTT
Done.