Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023438.1 Corchorus olitorius cultivar O-4 contig23471, 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: 4398
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35


Found at i:2574 original size:8 final size:9

Alignment explanation


    Indices: 2548--2576  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       2538 CCTAAATTAC

                     
       2548 TTATGGAAA
          1 TTATGGAAA

                     
       2557 TTATGGAAA
          1 TTATGGAAA

                     
       2566 TTA-GGAAA
          1 TTATGGAAA

               
       2574 TTA
          1 TTA

       2577 AAGAAATTAA


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

Matches are distributed among these distances:
   8    8  0.40
   9   12  0.60

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


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:2582 original size:17 final size:17

Alignment explanation


    Indices: 2552--2585  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2542 AATTACTTAT

                    **       
       2552 GGAAATTATGGAAATTA
          1 GGAAATTAAAGAAATTA

                             
       2569 GGAAATTAAAGAAATTA
          1 GGAAATTAAAGAAATTA

       2586 AATGTGTTTA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26


Consensus pattern (17 bp):   
GGAAATTAAAGAAATTA

Found at i:3927 original size:49 final size:48

Alignment explanation


    Indices: 3852--3992  Score: 162
    Period size: 49  Copynumber: 2.9  Consensus size: 48

       3842 CAAGCAATCC

                                              ** *           
       3852 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTATAAAATTGAACT
          1 TTTA-TTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT

                                         *                *  
       3900 TTTATTTTTACTTGCATCTTTTTCTCAATCTTTAAGACAAAATTGATCT
          1 TTTATTTTTACTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT

                *                  *          *           
       3949 TTTAATTTT-CATTGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTATTTTTAC-TTGCACTTTTTCTCAATTTTTAAGACAAAATTGA

       3993 TTGGCACGCT


Statistics
Matches: 81,  Mismatches: 9, Indels: 7
        0.84            0.09        0.07

Matches are distributed among these distances:
  47   18  0.22
  48   23  0.28
  49   40  0.49

ACGTcount: A:0.28, C:0.15, G:0.06, T:0.52


Consensus pattern (48 bp):   
TTTATTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Done.