Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015139.1 Corchorus olitorius cultivar O-4 contig15172, 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: 2042
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28


Found at i:596 original size:48 final size:47

Alignment explanation


    Indices: 521--655  Score: 175
    Period size: 49  Copynumber: 2.8  Consensus size: 47

        511 GAGCGTGCCA

                        *         *                 *      
        521 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAGTGAAAATTAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG

                                                              
        568 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGT-AAAAATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGC-AGTGAAAAATAAAAG

            *           *                           
        617 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAG-GAAA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAGTGAAA

        656 TGTAAAGGAT


Statistics
Matches: 78,  Mismatches: 5, Indels: 10
        0.84            0.05        0.11

Matches are distributed among these distances:
  47   17  0.22
  48   18  0.23
  49   40  0.51
  50    3  0.04

ACGTcount: A:0.50, C:0.06, G:0.16, T:0.27


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAGTGAAAAATAAAAG

Found at i:1973 original size:18 final size:17

Alignment explanation


    Indices: 1944--1981  Score: 58
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1934 TTAATTCATT

                             
       1944 TAATTTCCTAATTCCCA
          1 TAATTTCCTAATTCCCA

                          *   
       1961 TAATTTCCCTAATTTCCA
          1 TAATTT-CCTAATTCCCA

               
       1979 TAA
          1 TAA

       1982 GTAATTTGGG


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

Matches are distributed among these distances:
  17    6  0.32
  18   13  0.68

ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAATTTCCTAATTCCCA
Done.