Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012817.1 Corchorus olitorius cultivar O-4 contig12850, 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: 7129
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:951 original size:9 final size:9

Alignment explanation


    Indices: 937--962  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

        927 AAATGGTTGC

                     
        937 TTTGTTTTG
          1 TTTGTTTTG

                     
        946 TTTGTTTTG
          1 TTTGTTTTG

                    
        955 TTTGTTTT
          1 TTTGTTTT

        963 ATGCTTATTG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81


Consensus pattern (9 bp):   
TTTGTTTTG

Found at i:3402 original size:15 final size:16

Alignment explanation


    Indices: 3369--3408  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       3359 TTACTTTGCT

                            
       3369 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       3385 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
       3400 TTGCTTTCT
          1 TTGTTTTCT

       3409 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:4957 original size:21 final size:22

Alignment explanation


    Indices: 4933--4973  Score: 66
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       4923 TCGCCTCATC

                                  
       4933 CATTCATTCAT-CATACCATGG
          1 CATTCATTCATGCATACCATGG

                           *    
       4954 CATTCATTCATGCATCCCAT
          1 CATTCATTCATGCATACCAT

       4974 TAAACCTTAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34


Consensus pattern (22 bp):   
CATTCATTCATGCATACCATGG
Done.