Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012039.1 Corchorus olitorius cultivar O-4 contig12072, 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: 38252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:9197 original size:26 final size:24

Alignment explanation


    Indices: 9133--9196  Score: 67
    Period size: 23  Copynumber: 2.7  Consensus size: 24

       9123 GAAATTTTCC

                   *  *   *         
       9133 TTTACTTCTTCGTTGTAATTTC-T
          1 TTTACTTTTTTGTTTTAATTTCTT

               *                     
       9156 TTTCCTTTTTTGTTTTAATTTCTTT
          1 TTTACTTTTTTGTTTTAATTTC-TT

                       *    
       9181 TTTACTTTTTTATTTT
          1 TTTACTTTTTTGTTTT

       9197 TTATTTCTGA


Statistics
Matches: 33,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  23   18  0.55
  25   15  0.45

ACGTcount: A:0.11, C:0.12, G:0.05, T:0.72


Consensus pattern (24 bp):   
TTTACTTTTTTGTTTTAATTTCTT

Found at i:15447 original size:17 final size:17

Alignment explanation


    Indices: 15427--15467  Score: 57
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      15417 TTGACCACCG

                              
      15427 GTGATCTT-GCATCACTA
          1 GTGATCTTAG-ATCACTA

                             
      15444 GTGATCTTAGATCACTA
          1 GTGATCTTAGATCACTA

              *    
      15461 GTAATCT
          1 GTGATCT

      15468 GAGGAGCCCC


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

Matches are distributed among these distances:
  17   21  0.95
  18    1  0.05

ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37


Consensus pattern (17 bp):   
GTGATCTTAGATCACTA

Found at i:21855 original size:2 final size:2

Alignment explanation


    Indices: 21848--21885  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      21838 TTCTTTTAAG

                                                                    
      21848 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

      21886 TTCCTTTACC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
CT

Found at i:32474 original size:12 final size:11

Alignment explanation


    Indices: 32417--32475  Score: 55
    Period size: 11  Copynumber: 5.1  Consensus size: 11

      32407 CAAAATCTAA

                  *    
      32417 AATTATCTTTT
          1 AATTATTTTTT

                       
      32428 AATTATTTTTT
          1 AATTATTTTTT

            *            
      32439 TATTGATTTTTAT
          1 AATT-ATTTTT-T

                  *    *
      32452 AATTTAATTTTC
          1 AA-TTATTTTTT

                       
      32464 AATTATTTTTT
          1 AATTATTTTTT

             
      32475 A
          1 A

      32476 TTTAAATATT


Statistics
Matches: 38,  Mismatches: 7, Indels: 6
        0.75            0.14        0.12

Matches are distributed among these distances:
  11   21  0.55
  12    8  0.21
  13    7  0.18
  14    2  0.05

ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66


Consensus pattern (11 bp):   
AATTATTTTTT

Found at i:35678 original size:42 final size:42

Alignment explanation


    Indices: 35619--35699  Score: 144
    Period size: 42  Copynumber: 1.9  Consensus size: 42

      35609 GCTAACTCTT

                                        *             
      35619 GAAAATTCTCTGTAAATTAAGAAATACTGAACTCAAATCATA
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

                     *                             
      35661 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC

      35700 CTGATTCTTG


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   37  1.00

ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:35840 original size:56 final size:56

Alignment explanation


    Indices: 35765--35877  Score: 181
    Period size: 56  Copynumber: 2.0  Consensus size: 56

      35755 TTTATTTTAT

                          *                         *               
      35765 AGAATAATTAAGTATAGATAGGGGGATAGGATTTATCATAGCATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATCATAACATTTATTGTGTGAA

                  *                     *       *                   
      35821 AGAATATTTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATCATAACATTTATTGTGTGAA

             
      35877 A
          1 A

      35878 AGAAACTAAT


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  56   52  1.00

ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGGGGGATAGGATTTATCATAACATTTATTGTGTGAA

Found at i:36573 original size:22 final size:23

Alignment explanation


    Indices: 36543--36589  Score: 69
    Period size: 22  Copynumber: 2.1  Consensus size: 23

      36533 TTTTAGTTTA

                     *             
      36543 TAATATTCTTGCGTCATTCGGGT
          1 TAATATTCTCGCGTCATTCGGGT

                       *           
      36566 TAAT-TTCTCGGGTCATTCGGGT
          1 TAATATTCTCGCGTCATTCGGGT

              
      36588 TA
          1 TA

      36590 CGAGTTTGTC


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

Matches are distributed among these distances:
  22   18  0.82
  23    4  0.18

ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43


Consensus pattern (23 bp):   
TAATATTCTCGCGTCATTCGGGT
Done.