Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017557.1 Corchorus olitorius cultivar O-4 contig17590, 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: 5853
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25


Found at i:577 original size:62 final size:62

Alignment explanation


    Indices: 480--692  Score: 376
    Period size: 62  Copynumber: 3.5  Consensus size: 62

        470 ACACGACAGA

                                                                          
        480 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                  *                                                       
        542 CACGAATGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                         *                                           *    
        604 CACGAAGGTACACAAGAAG--AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAACAGG
          1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

                *                        
        664 CACGGAGGTACACGAGAAGACAGAGGAAG
          1 CACGAAGGTACACGAGAAGACAGAGGAAG

        693 ACAGACACGA


Statistics
Matches: 143,  Mismatches: 6, Indels: 4
        0.93            0.04        0.03

Matches are distributed among these distances:
  60   57  0.40
  62   86  0.60

ACGTcount: A:0.36, C:0.22, G:0.39, T:0.04


Consensus pattern (62 bp):   
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG

Found at i:712 original size:34 final size:34

Alignment explanation


    Indices: 659--753  Score: 172
    Period size: 34  Copynumber: 2.8  Consensus size: 34

        649 GGCGAGGCCA

                *    *                        
        659 ACAGGCACGGAGGTACACGAGAAGACAGAGGAAG
          1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG

                                              
        693 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG
          1 ACAGACACGAAGGTACACGAGAAGACAGAGGAAG

                                       
        727 ACAGACACGAAGGTACACGAGAAGACA
          1 ACAGACACGAAGGTACACGAGAAGACA

        754 CAGTGGTGCT


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   59  1.00

ACGTcount: A:0.45, C:0.19, G:0.33, T:0.03


Consensus pattern (34 bp):   
ACAGACACGAAGGTACACGAGAAGACAGAGGAAG

Found at i:1623 original size:44 final size:45

Alignment explanation


    Indices: 1573--1680  Score: 128
    Period size: 45  Copynumber: 2.4  Consensus size: 45

       1563 GAAAACGTGC

                      *            *                     
       1573 AGGAGATCAAGGAAAG-TTAGAATCCATGACTGCCAAATGCTTCA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTCA

                         *     * **       *            * 
       1617 AGGAGATCAAAGAGAGCTTTGGCCCCATGATTGCCAAATGCTTTA
          1 AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTCA

                         *     
       1662 AGGAGATCAAAGAGAGCTT
          1 AGGAGATCAAAGAAAGCTT

       1681 TGGCTCCATG


Statistics
Matches: 55,  Mismatches: 8, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  44   14  0.25
  45   41  0.75

ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21


Consensus pattern (45 bp):   
AGGAGATCAAAGAAAGCTTAGAACCCATGACTGCCAAATGCTTCA

Found at i:1652 original size:45 final size:45

Alignment explanation


    Indices: 1596--1696  Score: 175
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       1586 AAGTTAGAAT

                  *                                      
       1596 CCATGACTGCCAAATGCTTCAAGGAGATCAAAGAGAGCTTTGGCC
          1 CCATGATTGCCAAATGCTTCAAGGAGATCAAAGAGAGCTTTGGCC

                               *                        *
       1641 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
          1 CCATGATTGCCAAATGCTTCAAGGAGATCAAAGAGAGCTTTGGCC

                       
       1686 CCATGATTGCC
          1 CCATGATTGCC

       1697 GAGTGCACAA


Statistics
Matches: 53,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   53  1.00

ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24


Consensus pattern (45 bp):   
CCATGATTGCCAAATGCTTCAAGGAGATCAAAGAGAGCTTTGGCC
Done.