Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020639.1 Corchorus olitorius cultivar O-4 contig20672, 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: 11477
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:4520 original size:14 final size:14

Alignment explanation


    Indices: 4498--4532  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       4488 ATATGGATTG

                *         
       4498 TTTTAAAATATGGA
          1 TTTTGAAATATGGA

                          
       4512 TTTTGAAATATGGA
          1 TTTTGAAATATGGA

              *    
       4526 TTCTGAA
          1 TTTTGAA

       4533 TTCTGAATTC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.37, C:0.03, G:0.17, T:0.43


Consensus pattern (14 bp):   
TTTTGAAATATGGA

Found at i:4929 original size:15 final size:15

Alignment explanation


    Indices: 4909--4938  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4899 AAGAGCTAGG

                     *     
       4909 ACTACTACTTCTACA
          1 ACTACTACTCCTACA

                           
       4924 ACTACTACTCCTACA
          1 ACTACTACTCCTACA

       4939 CCTAGTTCTA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30


Consensus pattern (15 bp):   
ACTACTACTCCTACA

Found at i:5205 original size:6 final size:6

Alignment explanation


    Indices: 5189--5221  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       5179 GTTGAAGAAG

                   *                              
       5189 GTGGGA ATGGGA GTGGGA GTGGGA GTGGGA GTG
          1 GTGGGA GTGGGA GTGGGA GTGGGA GTGGGA GTG

       5222 TGGGAACATG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.18, C:0.00, G:0.64, T:0.18


Consensus pattern (6 bp):   
GTGGGA

Found at i:10872 original size:12 final size:13

Alignment explanation


    Indices: 10847--10874  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      10837 CAACCCTCTC

                         
      10847 TTCTGAATTTTTT
          1 TTCTGAATTTTTT

                         
      10860 TTCTGAATTTTTT
          1 TTCTGAATTTTTT

              
      10873 TT
          1 TT

      10875 GCCTATTTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71


Consensus pattern (13 bp):   
TTCTGAATTTTTT
Done.