Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007883.1 Corchorus olitorius cultivar O-4 contig07910, 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: 6985
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33


Found at i:1934 original size:2 final size:2

Alignment explanation


    Indices: 1927--1953  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1917 TCAAAATTAC

                                                    
       1927 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1954 GACTCTGATG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3080 original size:68 final size:70

Alignment explanation


    Indices: 2960--3090  Score: 221
    Period size: 68  Copynumber: 1.9  Consensus size: 70

       2950 ATTTTTTTCC

                                                                 *           
       2960 TAAAGGTTGCTCTCAAACACTAAATTCTTATAGATGTGTATCCTTCTTTTCTTGACAATGCAAAA
          1 TAAAGGTTGCTCTCAAACACT--ATTCTTATAGATGTGTATCCTTCTTTTCTTAACAATGCAAAA

                   
       3025 TTTTTTG
         64 TTTTTTG

                                                                         
       3032 TAAAGGTTGCTCTCAAACACT-TT-TTATAGATGTGTATCCTTCTTTTCTTAACAATGCAA
          1 TAAAGGTTGCTCTCAAACACTATTCTTATAGATGTGTATCCTTCTTTTCTTAACAATGCAA

       3091 TTTTAGTTCC


Statistics
Matches: 58,  Mismatches: 1, Indels: 4
        0.92            0.02        0.06

Matches are distributed among these distances:
  68   35  0.60
  69    2  0.03
  72   21  0.36

ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41


Consensus pattern (70 bp):   
TAAAGGTTGCTCTCAAACACTATTCTTATAGATGTGTATCCTTCTTTTCTTAACAATGCAAAATT
TTTTG

Found at i:6110 original size:24 final size:24

Alignment explanation


    Indices: 6078--6132  Score: 110
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       6068 ATAAGTTGAG

                                    
       6078 CAGCAGCAGGCAGAAGCCATTTTC
          1 CAGCAGCAGGCAGAAGCCATTTTC

                                    
       6102 CAGCAGCAGGCAGAAGCCATTTTC
          1 CAGCAGCAGGCAGAAGCCATTTTC

                   
       6126 CAGCAGC
          1 CAGCAGC

       6133 TCAACTTTCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   31  1.00

ACGTcount: A:0.29, C:0.31, G:0.25, T:0.15


Consensus pattern (24 bp):   
CAGCAGCAGGCAGAAGCCATTTTC

Found at i:6536 original size:29 final size:29

Alignment explanation


    Indices: 6494--6561  Score: 127
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       6484 TTTGCATATG

                                         
       6494 AAATTGAAAAATTGAAAAATGTAAGGACC
          1 AAATTGAAAAATTGAAAAATGTAAGGACC

                                  *      
       6523 AAATTGAAAAATTGAAAAATGTTAGGACC
          1 AAATTGAAAAATTGAAAAATGTAAGGACC

                      
       6552 AAATTGAAAA
          1 AAATTGAAAA

       6562 GATTATTTGC


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   38  1.00

ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22


Consensus pattern (29 bp):   
AAATTGAAAAATTGAAAAATGTAAGGACC
Done.