Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015965.1 Corchorus olitorius cultivar O-4 contig15998, 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: 6106
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:2803 original size:17 final size:18

Alignment explanation


    Indices: 2768--2805  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2758 CCCAAATTAC

                              
       2768 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTAGGGAAA

                 *            
       2786 TTATGTAAATTA-GGAAA
          1 TTATGGAAATTAGGGAAA

               
       2803 TTA
          1 TTA

       2806 AATGAATTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    8  0.42
  18   11  0.58

ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34


Consensus pattern (18 bp):   
TTATGGAAATTAGGGAAA

Found at i:4152 original size:49 final size:47

Alignment explanation


    Indices: 4077--4216  Score: 169
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       4067 TCCACAATCC

                *                                           
       4077 TTTACTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                *                              *          *  
       4124 TTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                                   *                      
       4173 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       4217 TTGGCACGCT


Statistics
Matches: 82,  Mismatches: 6, Indels: 10
        0.84            0.06        0.10

Matches are distributed among these distances:
  47   20  0.24
  48   20  0.24
  49   41  0.50
  50    1  0.01

ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51


Consensus pattern (47 bp):   
TTTAATTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Done.