Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017395.1 Corchorus olitorius cultivar O-4 contig17428, 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: 18940
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:1578 original size:19 final size:18

Alignment explanation


    Indices: 1545--1580  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1535 TTGAAATTAT

                              
       1545 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1563 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1581 TAAGCCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:9621 original size:23 final size:21

Alignment explanation


    Indices: 9579--9681  Score: 84
    Period size: 23  Copynumber: 4.7  Consensus size: 21

       9569 TCTACTAACA

                     *           
       9579 AAGATTATTTAAAAATCTTAT
          1 AAGATTATTAAAAAATCTTAT

                                   
       9600 AAGAGTTATTAAAGAAATCTTAT
          1 AAGA-TTATTAAA-AAATCTTAT

                   *           *   
       9623 AAG-TTACT-AAAAATGCACTAT
          1 AAGATTATTAAAAAAT-C-TTAT

               *     *             
       9644 AAGCTTAATAAAAAACATCTTAT
          1 AAGATT-ATTAAAAA-ATCTTAT

                           
       9667 AAGATTAATTAAAAA
          1 AAGATT-ATTAAAAA

       9682 GTTATTAAGT


Statistics
Matches: 66,  Mismatches: 8, Indels: 14
        0.75            0.09        0.16

Matches are distributed among these distances:
  19    4  0.06
  20    3  0.05
  21   14  0.21
  22    9  0.14
  23   29  0.44
  24    5  0.08
  25    2  0.03

ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33


Consensus pattern (21 bp):   
AAGATTATTAAAAAATCTTAT

Found at i:12231 original size:50 final size:52

Alignment explanation


    Indices: 12156--12264  Score: 195
    Period size: 50  Copynumber: 2.1  Consensus size: 52

      12146 CTATGGGATT

                                                                
      12156 TTCGAAATTTACAGATCGCCTACCAAATGAGAGAGACTGCAGGTTAAC-GG-
          1 TTCGAAATTTACAGATCGCCTACCAAATGAGAGAGACTGCAGGTTAACGGGA

                                                    *           
      12206 TTCGAAATTTACAGATCGCCTACCAAATGAGAGAGACTGCGGGTTAACGGGA
          1 TTCGAAATTTACAGATCGCCTACCAAATGAGAGAGACTGCAGGTTAACGGGA

                   
      12258 TTCGAAA
          1 TTCGAAA

      12265 CTAGAATTCT


Statistics
Matches: 56,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  50   47  0.84
  51    2  0.04
  52    7  0.12

ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22


Consensus pattern (52 bp):   
TTCGAAATTTACAGATCGCCTACCAAATGAGAGAGACTGCAGGTTAACGGGA
Done.