Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017183.1 Corchorus olitorius cultivar O-4 contig17216, 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: 4706
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33


Found at i:37 original size:30 final size:30

Alignment explanation


    Indices: 1--181  Score: 335
    Period size: 30  Copynumber: 6.0  Consensus size: 30

                                          
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

                                         *
         31 TTGTAAGACCATGACAACTTCTGGTGTCAT
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

                                         *
         61 TTGTAAGACCATGACAACTTCTGGTGTCAT
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

                                  *       
         91 TTGTAAGACCATGACAACTTCTAGTGTCAA
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

                                          
        121 TTGTAAGACCATGACAACTTCTGGTGTCAA
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

                                          
        151 TTGTAAGACCATGACAACTTCTGGTGTCAA
          1 TTGTAAGACCATGACAACTTCTGGTGTCAA

             
        181 T
          1 T

        182 ATATATTAGC


Statistics
Matches: 147,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30  147  1.00

ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31


Consensus pattern (30 bp):   
TTGTAAGACCATGACAACTTCTGGTGTCAA

Found at i:963 original size:16 final size:15

Alignment explanation


    Indices: 938--971  Score: 50
    Period size: 16  Copynumber: 2.2  Consensus size: 15

        928 GTGTGGGAGG

                         * 
        938 TGAGAAAAAAAATTA
          1 TGAGAAAAAAAATGA

                            
        953 TGAGAAAAAAAAATGA
          1 TGAG-AAAAAAAATGA

               
        969 TGA
          1 TGA

        972 TGGAAAAGGG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    4  0.24
  16   13  0.76

ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18


Consensus pattern (15 bp):   
TGAGAAAAAAAATGA

Found at i:1273 original size:22 final size:24

Alignment explanation


    Indices: 1238--1296  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 24

       1228 ATAAATGTTG

                            *      *
       1238 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
       1260 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                          
       1283 CTTGATAATATCTT
          1 C-TGATAAT-TCTT

       1297 GCCAGATAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  22   10  0.33
  23   10  0.33
  24    7  0.23
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA
Done.