Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018070.1 Corchorus olitorius cultivar O-4 contig18103, 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: 7665
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:3802 original size:16 final size:15

Alignment explanation


    Indices: 3774--3845  Score: 62
    Period size: 16  Copynumber: 4.9  Consensus size: 15

       3764 AAGGATATTT

                            
       3774 AAGATTATATTTTTTA
          1 AAGATT-TATTTTTTA

                          * 
       3790 AATGATTTATTTTTGA
          1 AA-GATTTATTTTTTA

                         * 
       3806 AAGA--TA--TTTAA
          1 AAGATTTATTTTTTA

              *            
       3817 AAAATTTATTTTTTA
          1 AAGATTTATTTTTTA

                          
       3832 AAGGATTTATTTTT
          1 AA-GATTTATTTTT

       3846 AAGGATATAT


Statistics
Matches: 45,  Mismatches: 5, Indels: 12
        0.73            0.08        0.19

Matches are distributed among these distances:
  11    7  0.16
  13    4  0.09
  15    8  0.18
  16   22  0.49
  17    4  0.09

ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54


Consensus pattern (15 bp):   
AAGATTTATTTTTTA

Found at i:3806 original size:41 final size:41

Alignment explanation


    Indices: 3761--3853  Score: 127
    Period size: 42  Copynumber: 2.3  Consensus size: 41

       3751 TCCTCCATTG

                            *               *         
       3761 TTGAAGGATATTT-AAGATTATATTTTTTAAATGATTTATTT
          1 TTGAAGGATATTTAAAAATT-TATTTTTTAAAGGATTTATTT

                 *                                    
       3802 TTGAAAGATATTTAAAAAATTTATTTTTTAAAGGATTTATTT
          1 TTGAAGGATATTT-AAAAATTTATTTTTTAAAGGATTTATTT

                       
       3844 TT-AAGGATAT
          1 TTGAAGGATAT

       3854 ATTATGATGA


Statistics
Matches: 46,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  41   19  0.41
  42   22  0.48
  43    5  0.11

ACGTcount: A:0.38, C:0.00, G:0.12, T:0.51


Consensus pattern (41 bp):   
TTGAAGGATATTTAAAAATTTATTTTTTAAAGGATTTATTT

Found at i:3849 original size:14 final size:15

Alignment explanation


    Indices: 3784--3856  Score: 50
    Period size: 16  Copynumber: 5.1  Consensus size: 15

       3774 AAGATTATAT

                    *      
       3784 TTTTTAAATGATTTA
          1 TTTTTAAAGGATTTA

                            
       3799 TTTTTGAAA-GA--TA
          1 TTTTT-AAAGGATTTA

                    **     
       3812 --TTTAAAAAATTTA
          1 TTTTTAAAGGATTTA

                            
       3825 TTTTTTAAAGGATTTA
          1 -TTTTTAAAGGATTTA

                        *  
       3841 TTTTT-AAGGATATA
          1 TTTTTAAAGGATTTA

              
       3855 TT
          1 TT

       3857 ATGATGATAT


Statistics
Matches: 47,  Mismatches: 4, Indels: 15
        0.71            0.06        0.23

Matches are distributed among these distances:
  10    3  0.06
  11    4  0.09
  13    4  0.09
  14   10  0.21
  15   12  0.26
  16   14  0.30

ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53


Consensus pattern (15 bp):   
TTTTTAAAGGATTTA

Found at i:5693 original size:24 final size:24

Alignment explanation


    Indices: 5658--5708  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       5648 TTAAACCCTA

                                *   
       5658 GGGACTGCATGGCTCCATGGTGAG
          1 GGGACTGCATGGCTCCATGGCGAG

                                     
       5682 GGGACT-CAATGGCTCCATGGCGAG
          1 GGGACTGC-ATGGCTCCATGGCGAG

               
       5706 GGG
          1 GGG

       5709 CACACCTGCG


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

Matches are distributed among these distances:
  23    1  0.04
  24   24  0.96

ACGTcount: A:0.18, C:0.22, G:0.43, T:0.18


Consensus pattern (24 bp):   
GGGACTGCATGGCTCCATGGCGAG

Found at i:7504 original size:13 final size:13

Alignment explanation


    Indices: 7486--7510  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7476 GAAGGGAATA

                         
       7486 AGCAAAGAGTTTG
          1 AGCAAAGAGTTTG

                        
       7499 AGCAAAGAGTTT
          1 AGCAAAGAGTTT

       7511 TCTAAATGAT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24


Consensus pattern (13 bp):   
AGCAAAGAGTTTG
Done.