Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016599.1 Corchorus olitorius cultivar O-4 contig16632, 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: 30905
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:15366 original size:30 final size:30

Alignment explanation


    Indices: 15328--15408  Score: 101
    Period size: 36  Copynumber: 2.5  Consensus size: 30

      15318 TTCTTCCTAA

                                          
      15328 CTCT-TATCATAATTTTCATTTCCTATTGT
          1 CTCTGTATCATAATTTTCATTTCCTATTGT

                                                
      15357 CTCTGTATCATAATTTAATTTTTCATTTCCTATTGT
          1 CTCTGTATC---A--TAA-TTTTCATTTCCTATTGT

                            
      15393 CTCTGTATCATAATTT
          1 CTCTGTATCATAATTT

      15409 AATTTGTTCT


Statistics
Matches: 45,  Mismatches: 0, Indels: 13
        0.78            0.00        0.22

Matches are distributed among these distances:
  29    4  0.09
  30    7  0.16
  31    3  0.07
  33    2  0.04
  35    3  0.07
  36   26  0.58

ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54


Consensus pattern (30 bp):   
CTCTGTATCATAATTTTCATTTCCTATTGT

Found at i:15383 original size:36 final size:36

Alignment explanation


    Indices: 15340--15413  Score: 148
    Period size: 36  Copynumber: 2.1  Consensus size: 36

      15330 CTTATCATAA

                                                
      15340 TTTTCATTTCCTATTGTCTCTGTATCATAATTTAAT
          1 TTTTCATTTCCTATTGTCTCTGTATCATAATTTAAT

                                                
      15376 TTTTCATTTCCTATTGTCTCTGTATCATAATTTAAT
          1 TTTTCATTTCCTATTGTCTCTGTATCATAATTTAAT

              
      15412 TT
          1 TT

      15414 GTTCTATAGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   38  1.00

ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57


Consensus pattern (36 bp):   
TTTTCATTTCCTATTGTCTCTGTATCATAATTTAAT

Found at i:17588 original size:19 final size:19

Alignment explanation


    Indices: 17564--17600  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      17554 AAATCAGGTA

                               
      17564 TTCTTAATTTCAATATTCC
          1 TTCTTAATTTCAATATTCC

                              
      17583 TTCTTAATTTCAATATTC
          1 TTCTTAATTTCAATATTC

      17601 TTTTCATTCG


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

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.27, C:0.19, G:0.00, T:0.54


Consensus pattern (19 bp):   
TTCTTAATTTCAATATTCC

Found at i:17853 original size:53 final size:53

Alignment explanation


    Indices: 17791--17896  Score: 194
    Period size: 53  Copynumber: 2.0  Consensus size: 53

      17781 GGCAGAGGAT

                        *                                        
      17791 CCTAATATCATTTTCATTTTTCTTGACTTTTATTAATATTTATTATAAAAAAA
          1 CCTAATATCATTCTCATTTTTCTTGACTTTTATTAATATTTATTATAAAAAAA

                                      *                          
      17844 CCTAATATCATTCTCATTTTTCTTGATTTTTATTAATATTTATTATAAAAAAA
          1 CCTAATATCATTCTCATTTTTCTTGACTTTTATTAATATTTATTATAAAAAAA

      17897 ATTTATTAAT


Statistics
Matches: 51,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  53   51  1.00

ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51


Consensus pattern (53 bp):   
CCTAATATCATTCTCATTTTTCTTGACTTTTATTAATATTTATTATAAAAAAA

Found at i:24273 original size:43 final size:43

Alignment explanation


    Indices: 24226--24311  Score: 163
    Period size: 43  Copynumber: 2.0  Consensus size: 43

      24216 GTTTAGTCCC

                                                       
      24226 GGCTGCAAAGTAGATATTTATGACTCATTTTACAATTTTGTGT
          1 GGCTGCAAAGTAGATATTTATGACTCATTTTACAATTTTGTGT

                           *                           
      24269 GGCTGCAAAGTAGATGTTTATGACTCATTTTACAATTTTGTGT
          1 GGCTGCAAAGTAGATATTTATGACTCATTTTACAATTTTGTGT

      24312 TGTCATGCAG


Statistics
Matches: 42,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  43   42  1.00

ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42


Consensus pattern (43 bp):   
GGCTGCAAAGTAGATATTTATGACTCATTTTACAATTTTGTGT
Done.