Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013875.1 Corchorus olitorius cultivar O-4 contig13908, 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: 13033
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:4156 original size:16 final size:16

Alignment explanation


    Indices: 4135--4177  Score: 86
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       4125 TCTTGATAGG

                            
       4135 AAGGAAGAAAAATGGT
          1 AAGGAAGAAAAATGGT

                            
       4151 AAGGAAGAAAAATGGT
          1 AAGGAAGAAAAATGGT

                       
       4167 AAGGAAGAAAA
          1 AAGGAAGAAAA

       4178 TTTCCTCAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   27  1.00

ACGTcount: A:0.60, C:0.00, G:0.30, T:0.09


Consensus pattern (16 bp):   
AAGGAAGAAAAATGGT

Found at i:8417 original size:12 final size:12

Alignment explanation


    Indices: 8400--8426  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       8390 AAGATGCTAT

                        
       8400 AACCCCAAACAA
          1 AACCCCAAACAA

                        
       8412 AACCCCAAACAA
          1 AACCCCAAACAA

               
       8424 AAC
          1 AAC

       8427 AGTTCCACTA


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00


Consensus pattern (12 bp):   
AACCCCAAACAA

Found at i:11420 original size:10 final size:10

Alignment explanation


    Indices: 11405--11447  Score: 50
    Period size: 11  Copynumber: 4.1  Consensus size: 10

      11395 TCTTTTTAAC

                      
      11405 TTTCCTTTTT
          1 TTTCCTTTTT

                       
      11415 TTTCCTCTTTT
          1 TTTCCT-TTTT

            *   *      
      11426 CTTCTTTTTCT
          1 TTTCCTTTT-T

                      
      11437 TTTCCTTTTT
          1 TTTCCTTTTT

             
      11447 T
          1 T

      11448 CTTTTTTTTC


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  10   11  0.41
  11   16  0.59

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (10 bp):   
TTTCCTTTTT

Found at i:11432 original size:20 final size:19

Alignment explanation


    Indices: 11409--11471  Score: 76
    Period size: 20  Copynumber: 3.2  Consensus size: 19

      11399 TTTAACTTTC

                                
      11409 CTTTTTTTTCCTCTTTTCTT
          1 CTTTTTTTT-CTCTTTTCTT

                                 
      11429 CTTTTTCTTT-TCCTTTT-TT
          1 CTTTTT-TTTCT-CTTTTCTT

                                
      11448 CTTTTTTTTCTCTTATTCTT
          1 CTTTTTTTTCTCTT-TTCTT

                
      11468 CTTT
          1 CTTT

      11472 CTCAACCCGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 10
        0.79            0.00        0.21

Matches are distributed among these distances:
  18    6  0.16
  19   12  0.32
  20   17  0.45
  21    3  0.08

ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76


Consensus pattern (19 bp):   
CTTTTTTTTCTCTTTTCTT

Found at i:11439 original size:22 final size:22

Alignment explanation


    Indices: 11410--11458  Score: 73
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      11400 TTAACTTTCC

                                  
      11410 TTTT-TTTTCCTCTTTTCTTCT
          1 TTTTCTTTTCCTCTTTTCTTCT

                        *       * 
      11431 TTTTCTTTTCCTTTTTTCTTTT
          1 TTTTCTTTTCCTCTTTTCTTCT

                  
      11453 TTTTCT
          1 TTTTCT

      11459 CTTATTCTTC


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  21    4  0.16
  22   21  0.84

ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80


Consensus pattern (22 bp):   
TTTTCTTTTCCTCTTTTCTTCT
Done.