Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018455.1 Corchorus olitorius cultivar O-4 contig18488, 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: 8711
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:1389 original size:19 final size:18

Alignment explanation


    Indices: 1352--1399  Score: 57
    Period size: 16  Copynumber: 2.8  Consensus size: 18

       1342 TGAAATTCAT

                              
       1352 TAATTATTTATTAAATAA
          1 TAATTATTTATTAAATAA

                         * *  
       1370 TAATTATTT-TT-CAGAA
          1 TAATTATTTATTAAATAA

                           
       1386 TAATTA-TTATTAAA
          1 TAATTATTTATTAAA

       1400 ATTTCCTTCT


Statistics
Matches: 25,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  15    2  0.08
  16   11  0.44
  17    3  0.12
  18    9  0.36

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50


Consensus pattern (18 bp):   
TAATTATTTATTAAATAA

Found at i:4104 original size:24 final size:24

Alignment explanation


    Indices: 4070--4119  Score: 82
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       4060 TAAAAACCAT

                  *                 
       4070 TTTTTTTTTTTCGTTTCATGACAG
          1 TTTTTTATTTTCGTTTCATGACAG

                       *            
       4094 TTTTTTATTTTGGTTTCATGACAG
          1 TTTTTTATTTTCGTTTCATGACAG

              
       4118 TT
          1 TT

       4120 GACACCAAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.14, C:0.10, G:0.14, T:0.62


Consensus pattern (24 bp):   
TTTTTTATTTTCGTTTCATGACAG

Found at i:4610 original size:75 final size:75

Alignment explanation


    Indices: 4493--4634  Score: 266
    Period size: 75  Copynumber: 1.9  Consensus size: 75

       4483 CACCCTTTAC

                                                                             
       4493 AAATTTTAATTTTTCTAACCCTTAAATTAAAATTAAAATTTTAACTTGGGCTAAACTTAGTGAAT
          1 AAATTTTAATTTTTCTAACCCTTAAATTAAAATTAAAATTTTAACTTGGGCTAAACTTAGTGAAT

                      
       4558 TATTAAATTA
         66 TATTAAATTA

                                              **                             
       4568 AAATTTTAATTTTTCTAACCCTTAAATTAAAATTTTAATTTTAACTTGGGCTAAACTTAGTGAAT
          1 AAATTTTAATTTTTCTAACCCTTAAATTAAAATTAAAATTTTAACTTGGGCTAAACTTAGTGAAT

              
       4633 TA
         66 TA

       4635 GTTATATATT


Statistics
Matches: 65,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  75   65  1.00

ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44


Consensus pattern (75 bp):   
AAATTTTAATTTTTCTAACCCTTAAATTAAAATTAAAATTTTAACTTGGGCTAAACTTAGTGAAT
TATTAAATTA

Found at i:7668 original size:28 final size:27

Alignment explanation


    Indices: 7620--7672  Score: 70
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       7610 ATTTTGACGT

                   *       **          
       7620 TTTGCCCTCTAAACTTTAATTTGGATG
          1 TTTGCCCCCTAAACTGCAATTTGGATG

                                      
       7647 TTTGCCCCCTAAACTCGCAATTTGGA
          1 TTTGCCCCCTAAACT-GCAATTTGGA

       7673 CTCAATTTAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  27   14  0.64
  28    8  0.36

ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38


Consensus pattern (27 bp):   
TTTGCCCCCTAAACTGCAATTTGGATG
Done.