Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020893.1 Corchorus olitorius cultivar O-4 contig20926, 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: 3376
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:580 original size:18 final size:17

Alignment explanation


    Indices: 557--594  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

        547 CCCAAATTAC

                              
        557 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
        575 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
        592 TTA
          1 TTA

        595 AATGAATTAA


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

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:592 original size:8 final size:9

Alignment explanation


    Indices: 561--594  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

        551 AATTACTTAT

                     
        561 GGAAATTAG
          1 GGAAATTAG

                    *
        570 GGAAATTAT
          1 GGAAATTAG

                     
        579 GGAAATTA-
          1 GGAAATTAG

                    
        587 GGAAATTA
          1 GGAAATTA

        595 AATGAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG

Found at i:2006 original size:48 final size:48

Alignment explanation


    Indices: 1870--2012  Score: 182
    Period size: 49  Copynumber: 3.0  Consensus size: 48

       1860 CAAGCAATCC

                *      *                                  *  
       1870 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACT-ACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TGACAAAATTGATCT

                     *                         *              
       1918 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTTATGACAAAATTGATCT

                                  *         *             
       1967 TTTAATTTTCATTGCACTTTTTATCAATTTTTTTGACAAAATTGAT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTATGACAAAATTGAT

       2013 TGGCACGCTC


Statistics
Matches: 82,  Mismatches: 9, Indels: 8
        0.83            0.09        0.08

Matches are distributed among these distances:
  47    5  0.06
  48   34  0.41
  49   37  0.45
  50    6  0.07

ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52


Consensus pattern (48 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATGACAAAATTGATCT
Done.