Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021515.1 Corchorus olitorius cultivar O-4 contig21548, 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: 3768
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36


Found at i:920 original size:9 final size:9

Alignment explanation


    Indices: 880--920  Score: 50
    Period size: 10  Copynumber: 4.6  Consensus size: 9

        870 AAATGTTTTC

                      
        880 AAAAATCCAA
          1 AAAAAT-CAA

                      
        890 AAAAATTCAA
          1 AAAAA-TCAA

                     
        900 AAAAATC--
          1 AAAAATCAA

                     
        907 AAAAATCAA
          1 AAAAATCAA

                 
        916 AAAAA
          1 AAAAA

        921 GAATTTTATC


Statistics
Matches: 28,  Mismatches: 0, Indels: 7
        0.80            0.00        0.20

Matches are distributed among these distances:
   7    7  0.25
   9    7  0.25
  10   13  0.46
  11    1  0.04

ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12


Consensus pattern (9 bp):   
AAAAATCAA

Found at i:1078 original size:51 final size:52

Alignment explanation


    Indices: 939--1081  Score: 261
    Period size: 52  Copynumber: 2.8  Consensus size: 52

        929 TCAATTTAAG

                                    *                           
        939 TTTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTC
          1 TTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC

                      *                                         
        991 TTTTTCAAATCGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC
          1 TTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC

                                                    
       1043 TTTTT-AAATTGGGAAAGTTCCCACCAGTTTTCAAAGTAT
          1 TTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTAT

       1082 CTTTATCCTA


Statistics
Matches: 88,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  51   33  0.38
  52   55  0.62

ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38


Consensus pattern (52 bp):   
TTTTTCAAATTGGGAAAGTTCCCACCAGTTTTCAAAGTATTCAATTTAGCTC

Found at i:1713 original size:16 final size:16

Alignment explanation


    Indices: 1692--1732  Score: 73
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1682 TTGGAACTCC

                            
       1692 GGCGGAGGCCCGACGT
          1 GGCGGAGGCCCGACGT

                      *     
       1708 GGCGGAGGCCTGACGT
          1 GGCGGAGGCCCGACGT

                     
       1724 GGCGGAGGC
          1 GGCGGAGGC

       1733 GATTCCCAGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.12, C:0.27, G:0.54, T:0.07


Consensus pattern (16 bp):   
GGCGGAGGCCCGACGT
Done.