Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005519.1 Corchorus olitorius cultivar O-4 contig05543, 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, 619

Length: 1032
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38


Found at i:192 original size:21 final size:22

Alignment explanation


    Indices: 159--206  Score: 80
    Period size: 21  Copynumber: 2.2  Consensus size: 22

        149 TATTATTATT

                                  
        159 TAAATATATATAAACGGAATAA
          1 TAAATATATATAAACGGAATAA

                          *       
        181 TAAATA-ATATAAATGGAATAA
          1 TAAATATATATAAACGGAATAA

                 
        202 TAAAT
          1 TAAAT

        207 TTAAATATAT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  21   19  0.76
  22    6  0.24

ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29


Consensus pattern (22 bp):   
TAAATATATATAAACGGAATAA

Found at i:255 original size:29 final size:28

Alignment explanation


    Indices: 213--269  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        203 AAATTTAAAT

                     *                   
        213 ATATATGTACTAATTGTAATAGTAATTAA
          1 ATATATGTAATAATTGTAATAGT-ATTAA

                                        
        242 ATATATGTAATAATTGTAATAGTATTAA
          1 ATATATGTAATAATTGTAATAGTATTAA

        270 TAATAATAGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  28    5  0.19
  29   22  0.81

ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42


Consensus pattern (28 bp):   
ATATATGTAATAATTGTAATAGTATTAA

Found at i:310 original size:18 final size:18

Alignment explanation


    Indices: 284--321  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

        274 AATAGAGTAT

                              
        284 TATTCATATAAATGAATA
          1 TATTCATATAAATGAATA

                *        *    
        302 TATTTATATAAATTAATA
          1 TATTCATATAAATGAATA

              
        320 TA
          1 TA

        322 ATAATATAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45


Consensus pattern (18 bp):   
TATTCATATAAATGAATA

Found at i:328 original size:18 final size:18

Alignment explanation


    Indices: 289--350  Score: 56
    Period size: 18  Copynumber: 3.4  Consensus size: 18

        279 AGTATTATTC

                    *      * *
        289 ATATAAATGAATATATTT
          1 ATATAAATTAATATAATA

                              
        307 ATATAAATTAATATAATA
          1 ATATAAATTAATATAATA

                                 
        325 ATATAGAATATTAATAT-ATA
          1 ATAT--AA-ATTAATATAATA

                   
        345 A-ATAAA
          1 ATATAAA

        351 ATATGCATTA


Statistics
Matches: 38,  Mismatches: 3, Indels: 8
        0.78            0.06        0.16

Matches are distributed among these distances:
  16    1  0.03
  17    2  0.05
  18   19  0.50
  19    2  0.05
  20    6  0.16
  21    8  0.21

ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39


Consensus pattern (18 bp):   
ATATAAATTAATATAATA

Found at i:339 original size:21 final size:19

Alignment explanation


    Indices: 313--354  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        303 ATTTATATAA

                             *   
        313 ATTAATATAATAATATAGAAT
          1 ATTAATAT-ATAA-ATAAAAT

                               
        334 ATTAATATATAAATAAAAT
          1 ATTAATATATAAATAAAAT

              
        353 AT
          1 AT

        355 GCATTATATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  19    8  0.40
  20    4  0.20
  21    8  0.40

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (19 bp):   
ATTAATATATAAATAAAAT
Done.