Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012514.1 Corchorus olitorius cultivar O-4 contig12547, 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: 8022
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27


Found at i:437 original size:8 final size:9

Alignment explanation


    Indices: 401--438  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

        391 CTCAAATTAC

                     
        401 TTATGGAAA
          1 TTATGGAAA

               *     
        410 TTAAGGAAA
          1 TTATGGAAA

                     
        419 TTATGGAAA
          1 TTATGGAAA

                     
        428 TTAT-GAAA
          1 TTATGGAAA

               
        436 TTA
          1 TTA

        439 AATGAATTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    7  0.26
   9   20  0.74

ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:1791 original size:49 final size:47

Alignment explanation


    Indices: 1714--1854  Score: 160
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       1704 CAAGCAATCC

                *      *                                    
       1714 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                          *          *  
       1762 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                        *         *                      
       1811 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       1855 TTGGCACGCT


Statistics
Matches: 79,  Mismatches: 9, Indels: 11
        0.80            0.09        0.11

Matches are distributed among these distances:
  47   15  0.19
  48   22  0.28
  49   35  0.44
  50    7  0.09

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:2721 original size:15 final size:15

Alignment explanation


    Indices: 2680--2723  Score: 70
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       2670 TGCTAGGGTG

                    *      
       2680 AATGGTGCAAACAAC
          1 AATGGTGCGAACAAC

                           
       2695 AATGGTGCGAACAAC
          1 AATGGTGCGAACAAC

                   *      
       2710 AATGGTGTGAACAA
          1 AATGGTGCGAACAA

       2724 TAACGGAAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16


Consensus pattern (15 bp):   
AATGGTGCGAACAAC
Done.