Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021727.1 Corchorus olitorius cultivar O-4 contig21760, 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: 10613
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:1901 original size:31 final size:29

Alignment explanation


    Indices: 1863--1956  Score: 109
    Period size: 31  Copynumber: 3.1  Consensus size: 29

       1853 GAAAATATAT

                                  *        
       1863 ATTTTTTTTTCTAAAAACGCAGGAACAAGAA
          1 ATTTTTTTTTCTAAAAACGCA-AAACAA-AA

                      *                   
       1894 ATTTTTTTTTTTAGAAAACGCAAAACAAAA
          1 ATTTTTTTTTCTA-AAAACGCAAAACAAAA

            *                              
       1924 TTTTTTTTTTC-AAAAACGCAAAACTAATAA
          1 ATTTTTTTTTCTAAAAACGCAAAAC-AA-AA

               
       1954 ATT
          1 ATT

       1957 AAAAACGCAA


Statistics
Matches: 55,  Mismatches: 5, Indels: 7
        0.82            0.07        0.10

Matches are distributed among these distances:
  28   12  0.22
  29    3  0.05
  30   15  0.27
  31   17  0.31
  32    8  0.15

ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37


Consensus pattern (29 bp):   
ATTTTTTTTTCTAAAAACGCAAAACAAAA

Found at i:1927 original size:28 final size:29

Alignment explanation


    Indices: 1863--1956  Score: 102
    Period size: 28  Copynumber: 3.1  Consensus size: 29

       1853 GAAAATATAT

                                  *        
       1863 ATTTTTTTTTCTAAAAACGCAGGAACAAGAA
          1 ATTTTTTTTT-TAAAAACGCA-AAACAAGAA

                                           
       1894 ATTTTTTTTTTTAGAAAACGCAAAAC-A-AA
          1 A-TTTTTTTTTTA-AAAACGCAAAACAAGAA

                                        *  
       1923 ATTTTTTTTTTCAAAAACGCAAAACTAATAA
          1 ATTTTTTTTTT-AAAAACGCAAAAC-AAGAA

               
       1954 ATT
          1 ATT

       1957 AAAAACGCAA


Statistics
Matches: 56,  Mismatches: 1, Indels: 12
        0.81            0.01        0.17

Matches are distributed among these distances:
  28   22  0.39
  29    4  0.07
  30    2  0.04
  31   11  0.20
  32   17  0.30

ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37


Consensus pattern (29 bp):   
ATTTTTTTTTTAAAAACGCAAAACAAGAA

Found at i:2119 original size:29 final size:30

Alignment explanation


    Indices: 2078--2150  Score: 112
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       2068 GTCTATTTTT

                                           
       2078 CCTTCCCCTGGCAAAAACCAGAAAAAGTT-C
          1 CCTTCCCC-GGCAAAAACCAGAAAAAGTTAC

                          *               
       2108 CCTTCCCCGGCAAATACCAGAAAAAGTTAC
          1 CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

             *           
       2138 CTTTCCCCGGCAA
          1 CCTTCCCCGGCAA

       2151 CGGCGACAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  29   19  0.47
  30   21  0.52

ACGTcount: A:0.33, C:0.36, G:0.14, T:0.18


Consensus pattern (30 bp):   
CCTTCCCCGGCAAAAACCAGAAAAAGTTAC

Found at i:3127 original size:11 final size:11

Alignment explanation


    Indices: 3111--3136  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       3101 CCTTTGCCTA

                       
       3111 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       3122 AAAACTAGAAG
          1 AAAACTAGAAG

                
       3133 AAAA
          1 AAAA

       3137 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.