Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024717.1 Corchorus olitorius cultivar O-4 contig24750, 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: 25446
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:109 original size:4 final size:4

Alignment explanation


    Indices: 55--124  Score: 52
    Period size: 4  Copynumber: 17.0  Consensus size: 4

         45 TCTATATACC

                        *           *        *     *               *      
         55 TATT TATCT TTTT TATT TATC TATT ATTTT TACT TATT T-TT CTAAT TATT
          1 TATT TAT-T TATT TATT TATT TATT -TATT TATT TATT TATT -TATT TATT

                              *     
        105 TATT TATT TATT TATC TATT
          1 TATT TATT TATT TATT TATT

        125 ACTTTTTTTA


Statistics
Matches: 50,  Mismatches: 12, Indels: 8
        0.71            0.17        0.11

Matches are distributed among these distances:
   3    2  0.04
   4   41  0.82
   5    7  0.14

ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70


Consensus pattern (4 bp):   
TATT

Found at i:2537 original size:23 final size:23

Alignment explanation


    Indices: 2505--2556  Score: 72
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       2495 GACGCAGGGA

                 *                 
       2505 CAAAATTTTTTTTTTTAT-GACG
          1 CAAAACTTTTTTTTTTATCGACG

                                    
       2527 CAGAAAC-TTTTTTTTTATCGACG
          1 CA-AAACTTTTTTTTTTATCGACG

                   
       2550 CAAAACT
          1 CAAAACT

       2557 GAAAACAGAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  22   17  0.65
  23    9  0.35

ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44


Consensus pattern (23 bp):   
CAAAACTTTTTTTTTTATCGACG

Found at i:2540 original size:22 final size:22

Alignment explanation


    Indices: 2512--2556  Score: 74
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2502 GGACAAAATT

                                   
       2512 TTTTTTTTTAT-GACGCAGAAAC
          1 TTTTTTTTTATCGACGCA-AAAC

                                  
       2534 TTTTTTTTTATCGACGCAAAAC
          1 TTTTTTTTTATCGACGCAAAAC

             
       2556 T
          1 T

       2557 GAAAACAGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  22   16  0.73
  23    6  0.27

ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47


Consensus pattern (22 bp):   
TTTTTTTTTATCGACGCAAAAC

Found at i:12515 original size:91 final size:90

Alignment explanation


    Indices: 12360--12531  Score: 308
    Period size: 91  Copynumber: 1.9  Consensus size: 90

      12350 AAATAAAGAA

                                              *                   *          
      12360 AACCAAGCTAAACTTAATTTCTTAAGCGGCGATGTAGAGAATATTACAAACATATTGATTACAGC
          1 AACCAAGCTAAACTTAATTTCTTAAGCGGCGATGCAGAGAATATTACAAACATACTGATTACAGC

                                     
      12425 CCACATCCACTTAGCAGGAAAAAAT
         66 CCACATCCACTTAGCAGGAAAAAAT

                                         *                                   
      12450 AACCAAGCTAAACTTAATTTCTTAAGCGGTGATGACAGAGAATATTACAAACATACTGATTACAG
          1 AACCAAGCTAAACTTAATTTCTTAAGCGGCGATG-CAGAGAATATTACAAACATACTGATTACAG

                             
      12515 CCCACATCCACTTAGCA
         65 CCCACATCCACTTAGCA

      12532 TTAATTGCAT


Statistics
Matches: 78,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  90   33  0.42
  91   45  0.58

ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24


Consensus pattern (90 bp):   
AACCAAGCTAAACTTAATTTCTTAAGCGGCGATGCAGAGAATATTACAAACATACTGATTACAGC
CCACATCCACTTAGCAGGAAAAAAT
Done.