Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017747.1 Corchorus olitorius cultivar O-4 contig17780, 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: 2994
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.27


Found at i:1752 original size:42 final size:42

Alignment explanation


    Indices: 1689--1775  Score: 104
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       1679 TATCACGCCA

                                        * *   *       
       1689 GGCCATGCCCAGCACCACAAGCCTCAGCTGCGCCTCATGCCC
          1 GGCCATGCCCAGCACCACAAGCCTCAGCCGAGCCACATGCCC

                           * *         *               
       1731 GGCCATGCCC-GCCATCTCAAGCCTCATCCGAGCCACATGCCC
          1 GGCCATGCCCAG-CACCACAAGCCTCAGCCGAGCCACATGCCC

               
       1773 GGC
          1 GGC

       1776 TAGGACCGGC


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  41    1  0.03
  42   37  0.97

ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13


Consensus pattern (42 bp):   
GGCCATGCCCAGCACCACAAGCCTCAGCCGAGCCACATGCCC

Found at i:1988 original size:21 final size:21

Alignment explanation


    Indices: 1962--2016  Score: 76
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1952 CGCCCATTCA

                                  
       1962 CCGTGCCACCACCGG-TCAAGC
          1 CCGTGCCACCACCGGCT-AAGC

                              *  
       1983 CCGTGCCACCACCGGCTATGC
          1 CCGTGCCACCACCGGCTAAGC

                    *    
       2004 CCGTGCCATCACC
          1 CCGTGCCACCACC

       2017 ATTCACTGCC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  21   30  0.97
  22    1  0.03

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCTAAGC

Found at i:2392 original size:15 final size:14

Alignment explanation


    Indices: 2372--2401  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       2362 ATCTTTTTAA

                           
       2372 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       2387 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       2401 T
          1 T

       2402 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:2639 original size:50 final size:50

Alignment explanation


    Indices: 2565--2665  Score: 184
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       2555 TGGGGGAGAG

                                                              
       2565 AGTTTAGTTAATAGAGAGTCTGCATGCATCATAATCTTAAAATATGCCAT
          1 AGTTTAGTTAATAGAGAGTCTGCATGCATCATAATCTTAAAATATGCCAT

                                                  *       *   
       2615 AGTTTAGTTAATAGAGAGTCTGCATGCATCATAATCTTCAAATATGGCAT
          1 AGTTTAGTTAATAGAGAGTCTGCATGCATCATAATCTTAAAATATGCCAT

             
       2665 A
          1 A

       2666 ATTTTTTCGA


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  50   49  1.00

ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34


Consensus pattern (50 bp):   
AGTTTAGTTAATAGAGAGTCTGCATGCATCATAATCTTAAAATATGCCAT
Done.