Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009560.1 Corchorus olitorius cultivar O-4 contig09592, 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: 1954
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37


Found at i:1767 original size:31 final size:30

Alignment explanation


    Indices: 1732--1844  Score: 151
    Period size: 28  Copynumber: 3.7  Consensus size: 30

       1722 TAAAATTTAA

                                           
       1732 TTGACACCAGAAGTTGTCATATTAAATTATC
          1 TTGACACCAGAAGTTGTCATA-TAAATTATC

                                           
       1763 TTGACACCAGAAGTTGTCATGA-AAATTA--
          1 TTGACACCAGAAGTTGTCAT-ATAAATTATC

                                              
       1791 TTGACACCAGAAGTTGTCATATCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATAT--AA--ATTATC

                                
       1825 TTGACACCAGAAGTTGTCAT
          1 TTGACACCAGAAGTTGTCAT

       1845 GCTGAGGAAA


Statistics
Matches: 74,  Mismatches: 0, Indels: 13
        0.85            0.00        0.15

Matches are distributed among these distances:
  27    1  0.01
  28   20  0.27
  30    8  0.11
  31   20  0.27
  32    5  0.07
  34   20  0.27

ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Consensus pattern (30 bp):   
TTGACACCAGAAGTTGTCATATAAATTATC

Found at i:1818 original size:59 final size:63

Alignment explanation


    Indices: 1731--1877  Score: 221
    Period size: 67  Copynumber: 2.3  Consensus size: 63

       1721 TTAAAATTTA

                                    *                                      
       1731 ATTGACACCAGAAGTTGTCATAT-TAA-ATTATCTTGACACCAGAAGTTGTCA-TGA-AAATT
          1 ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT

                                                                             
       1790 ATTGACACCAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGCTGAGGAAA
          1 ATTGACACCAGAAGTTGTCATATCAAA-TATTATCTTGACACCAGAAGTTGTCA--CTGA-GAAA

              
       1855 TT
         62 TT

                                 
       1857 ATTGACACCAGAAGTTGTCAT
          1 ATTGACACCAGAAGTTGTCAT

       1878 CCCAAGATTG


Statistics
Matches: 79,  Mismatches: 1, Indels: 8
        0.90            0.01        0.09

Matches are distributed among these distances:
  59   23  0.29
  60    2  0.03
  62   25  0.32
  65    3  0.04
  67   26  0.33

ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31


Consensus pattern (63 bp):   
ATTGACACCAGAAGTTGTCATATCAAATATTATCTTGACACCAGAAGTTGTCACTGAGAAATT

Done.