Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016826.1 Corchorus olitorius cultivar O-4 contig16859, 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: 5707
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:306 original size:15 final size:15

Alignment explanation


    Indices: 276--317  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        266 TTACTTTGCT

                            
        276 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        292 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        307 TTGCTTTCTGT
          1 TTGTTTTCTGT

        318 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:563 original size:29 final size:29

Alignment explanation


    Indices: 493--561  Score: 120
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        483 GGCGCCGTTC

                                         
        493 CCGGGGAAGGGAACTTTTTCTGGTATTTG
          1 CCGGGGAAGGGAACTTTTTCTGGTATTTG

                                    *    
        522 CCGGGGAAGGGAACTTTTTCTGGTTTTTG
          1 CCGGGGAAGGGAACTTTTTCTGGTATTTG

                       
        551 CCAGGGGAAGG
          1 CC-GGGGAAGG

        562 AAAAATAGAC


Statistics
Matches: 38,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  29   30  0.79
  30    8  0.21

ACGTcount: A:0.17, C:0.14, G:0.38, T:0.30


Consensus pattern (29 bp):   
CCGGGGAAGGGAACTTTTTCTGGTATTTG

Found at i:851 original size:29 final size:28

Alignment explanation


    Indices: 815--901  Score: 84
    Period size: 29  Copynumber: 2.9  Consensus size: 28

        805 TAATTTATTA

                         *               
        815 GTTTTGCGATTTTGAAAAAAAAAAATTTT
          1 GTTTTGCG-TTTTAAAAAAAAAAAATTTT

                                            
        844 GTTTTGCGTTTTCTAAAAAAAAAAAAATTTTT
          1 GTTTTGCG-TTT-T-AAAAAAAAAAAA-TTTT

                *        * *          
        876 GTGTCTGCGTTTTTATAAAAAAAAAT
          1 GT-TTTGCGTTTTAAAAAAAAAAAAT

        902 ATATATTTTT


Statistics
Matches: 49,  Mismatches: 5, Indels: 8
        0.79            0.08        0.13

Matches are distributed among these distances:
  29   12  0.24
  30   11  0.22
  31   12  0.24
  32    9  0.18
  33    5  0.10

ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41


Consensus pattern (28 bp):   
GTTTTGCGTTTTAAAAAAAAAAAATTTT

Found at i:885 original size:33 final size:30

Alignment explanation


    Indices: 829--900  Score: 99
    Period size: 32  Copynumber: 2.3  Consensus size: 30

        819 TGCGATTTTG

                              *            
        829 AAAAAAAAAAATTTTGTTTTGCGTTTTCTAA
          1 AAAAAAAAAAATTTTGTTCTGCGTTTT-TAA

                                           *
        860 AAAAAAAAAAATTTTTGTGTCTGCGTTTTTAT
          1 AAAAAAAAAAA-TTTTGT-TCTGCGTTTTTAA

                     
        892 AAAAAAAAA
          1 AAAAAAAAA

        901 TATATATTTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  31   11  0.30
  32   17  0.46
  33    9  0.24

ACGTcount: A:0.47, C:0.06, G:0.10, T:0.38


Consensus pattern (30 bp):   
AAAAAAAAAAATTTTGTTCTGCGTTTTTAA

Found at i:3780 original size:15 final size:14

Alignment explanation


    Indices: 3760--3789  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3750 ATCTTTTTAA

                           
       3760 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       3775 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3789 T
          1 T

       3790 GTTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT
Done.