Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018110.1 Corchorus olitorius cultivar O-4 contig18143, 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: 7055
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29


Found at i:4501 original size:80 final size:80

Alignment explanation


    Indices: 4411--4569  Score: 264
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       4401 AATAATCGAG

                                                           *           *     
       4411 GGATGATGGTATGAGAAAAAAGTTGTCAACTTTTGGTGTATTGATACGGGTGAGCAAAATCGACC
          1 GGATGATGGTATGAGAAAAAAGTTGTCAACTTTTGGTGTATTGATACAGGTGAGCAAAACCGACC

                           
       4476 CGACCCAAATAACCT
         66 CGACCCAAATAACCT

                                 *       *                           *       
       4491 GGATGATGGTATGAGAAAAAATTTGTCAATTTTTGGTGTATTGATACAGGTGAGCAAGACCGACC
          1 GGATGATGGTATGAGAAAAAAGTTGTCAACTTTTGGTGTATTGATACAGGTGAGCAAAACCGACC

              *           
       4556 CGTCCCAAATAACC
         66 CGACCCAAATAACC

       4570 CGATCAGTTT


Statistics
Matches: 73,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  80   73  1.00

ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26


Consensus pattern (80 bp):   
GGATGATGGTATGAGAAAAAAGTTGTCAACTTTTGGTGTATTGATACAGGTGAGCAAAACCGACC
CGACCCAAATAACCT

Found at i:6249 original size:22 final size:21

Alignment explanation


    Indices: 6224--6278  Score: 62
    Period size: 19  Copynumber: 2.7  Consensus size: 21

       6214 CGAAGTTCAT

                                  
       6224 ATTTGAAGACTTATTGAAGATA
          1 ATTTGAAGA-TTATTGAAGATA

                                *
       6246 ATTTGAAGA-T-TTGAAGATC
          1 ATTTGAAGATTATTGAAGATA

                           
       6265 A-TTGAAGAATTATT
          1 ATTTGAAG-ATTATT

       6279 TCAACAAGCA


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.34
  20    2  0.07
  21    2  0.07
  22    9  0.31

ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38


Consensus pattern (21 bp):   
ATTTGAAGATTATTGAAGATA

Done.