Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015972.1 Corchorus olitorius cultivar O-4 contig16005, 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: 5617
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35


Found at i:1098 original size:49 final size:48

Alignment explanation


    Indices: 1033--1161  Score: 154
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       1023 TACTTTTCAC

                                 **                 *       
       1033 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTATTTTTACT
          1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

                                              *               
       1081 TGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTT-CAT
          1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTAC-T

            *  *      *          *           
       1130 CGCGCTTTTTATCAATTTTT-TGACAAAATTGA
          1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGA

       1162 TTGGCACGCT


Statistics
Matches: 71,  Mismatches: 8, Indels: 5
        0.85            0.10        0.06

Matches are distributed among these distances:
  47   11  0.15
  48   20  0.28
  49   40  0.56

ACGTcount: A:0.28, C:0.16, G:0.07, T:0.50


Consensus pattern (48 bp):   
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTACT

Found at i:2367 original size:30 final size:30

Alignment explanation


    Indices: 2306--2368  Score: 74
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       2296 GCTTATACAT

                  *     *         *       
       2306 AGATTTTACATTTATGAAAACATTTACAAG
          1 AGATTTCACATTCATGAAAACAATTACAAG

                                       *   
       2336 AGATTTCACATTCA-GAAGAACAATTATAAG
          1 AGATTTCACATTCATGAA-AACAATTACAAG

               
       2366 AGA
          1 AGA

       2369 AGAGTTTTTT


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  29    3  0.11
  30   25  0.89

ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30


Consensus pattern (30 bp):   
AGATTTCACATTCATGAAAACAATTACAAG
Done.