Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016614.1 Corchorus olitorius cultivar O-4 contig16647, 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: 30033
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:20392 original size:14 final size:14

Alignment explanation


    Indices: 20373--20407  Score: 70
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      20363 AGGTCAAATT

                          
      20373 AAAGCCCTAATCAA
          1 AAAGCCCTAATCAA

                          
      20387 AAAGCCCTAATCAA
          1 AAAGCCCTAATCAA

                   
      20401 AAAGCCC
          1 AAAGCCC

      20408 CAATTAACCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   21  1.00

ACGTcount: A:0.49, C:0.31, G:0.09, T:0.11


Consensus pattern (14 bp):   
AAAGCCCTAATCAA

Found at i:23127 original size:21 final size:21

Alignment explanation


    Indices: 23103--23145  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      23093 CGCACAGAGA

                   *             
      23103 GGTTTCATGCTCATCGGAGTT
          1 GGTTTCAAGCTCATCGGAGTT

                          *      
      23124 GGTTTCAAGCTCATTGGAGTT
          1 GGTTTCAAGCTCATCGGAGTT

             
      23145 G
          1 G

      23146 TCTAAGATGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.16, C:0.16, G:0.30, T:0.37


Consensus pattern (21 bp):   
GGTTTCAAGCTCATCGGAGTT

Found at i:24032 original size:25 final size:24

Alignment explanation


    Indices: 23996--24042  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      23986 TCCTTCTATT

                                    
      23996 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
      24019 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

      24043 AATTTTTAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.