Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017124.1 Corchorus olitorius cultivar O-4 contig17157, 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: 9209
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:3492 original size:29 final size:29

Alignment explanation


    Indices: 3428--3531  Score: 142
    Period size: 29  Copynumber: 3.7  Consensus size: 29

       3418 AAGTGAACCT

                           *     *     * 
       3428 AAAATGACCAAAAT-GCCCT-CA-GTGTA
          1 AAAATGACCAAAATACCCCTGAATGTGCA

               *                         
       3454 AAATTGACCAAAATACCCCTGAATGTGCA
          1 AAAATGACCAAAATACCCCTGAATGTGCA

                                         
       3483 AAAATGACCAAAATACCCCTGAATGTGCA
          1 AAAATGACCAAAATACCCCTGAATGTGCA

                          *     
       3512 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATACCCCT

       3532 AGGTGATTCT


Statistics
Matches: 69,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  26   13  0.19
  27    4  0.06
  28    1  0.01
  29   51  0.74

ACGTcount: A:0.43, C:0.25, G:0.13, T:0.18


Consensus pattern (29 bp):   
AAAATGACCAAAATACCCCTGAATGTGCA

Found at i:4173 original size:10 final size:10

Alignment explanation


    Indices: 4158--4187  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       4148 ATCCGAGCCT

                      
       4158 CATGCCCGGC
          1 CATGCCCGGC

                     *
       4168 CATGCCCGGG
          1 CATGCCCGGC

                      
       4178 CATGCCCGGC
          1 CATGCCCGGC

       4188 ACCACGAGCC


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

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.10, C:0.47, G:0.33, T:0.10


Consensus pattern (10 bp):   
CATGCCCGGC

Found at i:7042 original size:48 final size:46

Alignment explanation


    Indices: 6984--7091  Score: 126
    Period size: 48  Copynumber: 2.3  Consensus size: 46

       6974 AATGAACAAT

                                   ***                       
       6984 AAAAAGTAAAAGATCAATTTTATCTTAAAAATTGAAAAAAAGTGCAAGG
          1 AAAAA-TAAAAGATCAATTTTATAGCAAAAATTGAAAAAAAGTGC-A-G

                                *            **           
       7033 AAAAATAAAAGATCAATTTTGTAGCAAAAATTGCGAAAAAGTGCAG
          1 AAAAATAAAAGATCAATTTTATAGCAAAAATTGAAAAAAAGTGCAG

                *        
       7079 AAAAGTAAAAGAT
          1 AAAAATAAAAGAT

       7092 TGCTTAAGTG


Statistics
Matches: 52,  Mismatches: 7, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  46   13  0.25
  47    1  0.02
  48   33  0.63
  49    5  0.10

ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22


Consensus pattern (46 bp):   
AAAAATAAAAGATCAATTTTATAGCAAAAATTGAAAAAAAGTGCAG

Found at i:8384 original size:9 final size:8

Alignment explanation


    Indices: 8364--8397  Score: 50
    Period size: 8  Copynumber: 4.0  Consensus size: 8

       8354 TTAATTCATT

                    
       8364 TAATTTCC
          1 TAATTTCC

                    
       8372 TAATTTCC
          1 TAATTTCC

                      
       8380 ATAATTTTCC
          1 -TAA-TTTCC

                    
       8390 TAATTTCC
          1 TAATTTCC

       8398 ATAAGTAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   8   13  0.54
   9    6  0.25
  10    5  0.21

ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50


Consensus pattern (8 bp):   
TAATTTCC

Found at i:8390 original size:18 final size:18

Alignment explanation


    Indices: 8367--8401  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       8357 ATTCATTTAA

                              
       8367 TTTCCTAATTTCCATAAT
          1 TTTCCTAATTTCCATAAT

                             
       8385 TTTCCTAATTTCCATAA
          1 TTTCCTAATTTCCATAA

       8402 GTAATTTGGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.29, C:0.23, G:0.00, T:0.49


Consensus pattern (18 bp):   
TTTCCTAATTTCCATAAT
Done.