Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023736.1 Corchorus olitorius cultivar O-4 contig23769, 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: 18964
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Found at i:3232 original size:21 final size:21

Alignment explanation


    Indices: 3199--3247  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3189 AAGAATTGTA

                          **     
       3199 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       3219 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       3240 GCATTCCT
          1 GC-TTCCT

       3248 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:4307 original size:27 final size:27

Alignment explanation


    Indices: 4262--4352  Score: 146
    Period size: 27  Copynumber: 3.4  Consensus size: 27

       4252 TTTACTTCCT

                                       
       4262 ATTTTGGTCATTTGCATGTCCAGGGGC
          1 ATTTTGGTCATTTGCATGTCCAGGGGC

                      *   *            
       4289 ATTTTGGTCAATTGTATGTCCAGGGGC
          1 ATTTTGGTCATTTGCATGTCCAGGGGC

                            **         
       4316 ATTTTGGTCATTTGCACATCCAGGGGC
          1 ATTTTGGTCATTTGCATGTCCAGGGGC

                      
       4343 ATTTTGGTCA
          1 ATTTTGGTCA

       4353 CTTCAAGTAC


Statistics
Matches: 58,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   58  1.00

ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37


Consensus pattern (27 bp):   
ATTTTGGTCATTTGCATGTCCAGGGGC

Found at i:7664 original size:16 final size:17

Alignment explanation


    Indices: 7633--7665  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       7623 GGGGATTAAG

                       *     
       7633 AGCTAGTTTTCTTTGAA
          1 AGCTAGTTTTCATTGAA

                             
       7650 AGCTA-TTTTCATTGAA
          1 AGCTAGTTTTCATTGAA

       7666 CTTCAGTGGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45


Consensus pattern (17 bp):   
AGCTAGTTTTCATTGAA

Found at i:12926 original size:24 final size:22

Alignment explanation


    Indices: 12845--12932  Score: 77
    Period size: 24  Copynumber: 3.7  Consensus size: 22

      12835 ACGGAGGAAG

                            *      
      12845 AAAGAAAGAAAAAAAAAGAAAAA
          1 AAAG-AAGAAAAAAAAGGAAAAA

                       *       *   
      12868 CAAAGAAGAAAGAAAAGGAGAAA
          1 -AAAGAAGAAAAAAAAGGAAAAA

              *    *                 
      12891 AATGAATAAAGAAAAAAGGATAAAA
          1 AAAGAA-GAA-AAAAAAGGA-AAAA

                             
      12916 AAAGAAGAAGAAAAAAG
          1 AAAGAAGAA-AAAAAAG

      12933 ACACGTTACT


Statistics
Matches: 52,  Mismatches: 9, Indels: 6
        0.78            0.13        0.09

Matches are distributed among these distances:
  22    5  0.10
  23   17  0.33
  24   22  0.42
  25    8  0.15

ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03


Consensus pattern (22 bp):   
AAAGAAGAAAAAAAAGGAAAAA
Done.