Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013021.1 Corchorus olitorius cultivar O-4 contig13054, 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: 9384
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Found at i:704 original size:57 final size:58

Alignment explanation


    Indices: 601--709  Score: 175
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        591 ATCATGCATC

                 *     *                                              
        601 GGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT
          1 GGTCCGAAAACATCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT

                                 *                         *    
        659 GGTCCGAAAACATCTTTTTTATGCATCTAAT-AAAAAACATGTCACTTGATA
          1 GGTCCGAAAACATCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

        710 TTTGATTATT


Statistics
Matches: 47,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  57   19  0.40
  58   28  0.60

ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32


Consensus pattern (58 bp):   
GGTCCGAAAACATCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAAGCCTT

Found at i:1841 original size:18 final size:20

Alignment explanation


    Indices: 1802--1841  Score: 57
    Period size: 18  Copynumber: 2.1  Consensus size: 20

       1792 ACTGAATTTA

                                
       1802 TTGATAACATTCAAAAAGCT
          1 TTGATAACATTCAAAAAGCT

                           *    
       1822 TTGATAAC-TT-AAATAGCT
          1 TTGATAACATTCAAAAAGCT

              
       1840 TT
          1 TT

       1842 TTAATGAACA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  18    9  0.47
  19    2  0.11
  20    8  0.42

ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38


Consensus pattern (20 bp):   
TTGATAACATTCAAAAAGCT

Found at i:4489 original size:22 final size:23

Alignment explanation


    Indices: 4461--4503  Score: 79
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       4451 TAGAAGGAGT

                                   
       4461 AGGTTTTACT-TTCCTACCAGAA
          1 AGGTTTTACTATTCCTACCAGAA

                                 
       4483 AGGTTTTACTATTCCTACCAG
          1 AGGTTTTACTATTCCTACCAG

       4504 GATTAGGATT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  22   10  0.50
  23   10  0.50

ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37


Consensus pattern (23 bp):   
AGGTTTTACTATTCCTACCAGAA

Done.