Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019212.1 Corchorus olitorius cultivar O-4 contig19245, 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: 53211
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:12461 original size:16 final size:16

Alignment explanation


    Indices: 12440--12488  Score: 73
    Period size: 16  Copynumber: 3.1  Consensus size: 16

      12430 TGTGAGATTC

                            
      12440 AACTATTCGAGTCTAA
          1 AACTATTCGAGTCTAA

                             
      12456 AACTATTC-AGGTCTAA
          1 AACTATTCGA-GTCTAA

                       *    
      12472 AACTATTCGAGCCTAA
          1 AACTATTCGAGTCTAA

             
      12488 A
          1 A

      12489 TTGGATTAAA


Statistics
Matches: 30,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  15    1  0.03
  16   28  0.93
  17    1  0.03

ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29


Consensus pattern (16 bp):   
AACTATTCGAGTCTAA

Found at i:42602 original size:21 final size:19

Alignment explanation


    Indices: 42576--42633  Score: 62
    Period size: 19  Copynumber: 2.9  Consensus size: 19

      42566 GTTGATCTAA

                          *     *
      42576 TAATCTCATCTATATAGTACT
          1 TAATCTCATCTATACAGT--G

                  *    *       
      42597 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTATACAGTG

                              
      42616 TAATCTCATCTATACAGT
          1 TAATCTCATCTATACAGT

      42634 TACTAAATAG


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  19   16  0.52
  21   15  0.48

ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40


Consensus pattern (19 bp):   
TAATCTCATCTATACAGTG

Found at i:42722 original size:74 final size:74

Alignment explanation


    Indices: 42601--42748  Score: 287
    Period size: 74  Copynumber: 2.0  Consensus size: 74

      42591 AGTACTTAAT

                                                                             
      42601 CTAATCTGTACAGTGTAATCTCATCTATACAGTTACTAAATAGTGTCAATCGCACCATTACCGCA
          1 CTAATCTGTACAGTGTAATCTCATCTATACAGTTACTAAATAGTGTCAATCGCACCATTACCGCA

                     
      42666 CCGTTTTAC
         66 CCGTTTTAC

                               *                                             
      42675 CTAATCTGTACAGTGTAATTTCATCTATACAGTTACTAAATAGTGTCAATCGCACCATTACCGCA
          1 CTAATCTGTACAGTGTAATCTCATCTATACAGTTACTAAATAGTGTCAATCGCACCATTACCGCA

                     
      42740 CCGTTTTAC
         66 CCGTTTTAC

      42749 TAAACGCAGC


Statistics
Matches: 73,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  74   73  1.00

ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33


Consensus pattern (74 bp):   
CTAATCTGTACAGTGTAATCTCATCTATACAGTTACTAAATAGTGTCAATCGCACCATTACCGCA
CCGTTTTAC

Found at i:52936 original size:30 final size:28

Alignment explanation


    Indices: 52878--52939  Score: 79
    Period size: 30  Copynumber: 2.1  Consensus size: 28

      52868 CTTTGATATA

                                 *      
      52878 TATTATATTATATAATAATAATAATAAT
          1 TATTATATTATATAATAATAAGAATAAT

                                    **    
      52906 TATTATTATTACTATAATAATAAGGGTAAT
          1 TATTA-TATTA-TATAATAATAAGAATAAT

                
      52936 TATT
          1 TATT

      52940 TGATATACCA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  28    5  0.17
  29    5  0.17
  30   19  0.66

ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47


Consensus pattern (28 bp):   
TATTATATTATATAATAATAAGAATAAT
Done.