Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016348.1 Corchorus olitorius cultivar O-4 contig16381, 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: 7427
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:3458 original size:16 final size:16

Alignment explanation


    Indices: 3437--3475  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       3427 TAGAAAGGGT

                       *    
       3437 AGAAATGGGAATGAAA
          1 AGAAATGGGAAGGAAA

                     *      
       3453 AGAAATGGGTAGGAAA
          1 AGAAATGGGAAGGAAA

                   
       3469 AGGAAAT
          1 A-GAAAT

       3476 AAGGAGTAGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  16   15  0.75
  17    5  0.25

ACGTcount: A:0.54, C:0.00, G:0.33, T:0.13


Consensus pattern (16 bp):   
AGAAATGGGAAGGAAA

Found at i:3671 original size:14 final size:13

Alignment explanation


    Indices: 3645--3683  Score: 51
    Period size: 13  Copynumber: 2.9  Consensus size: 13

       3635 CCCAAATTTT

                         
       3645 ATTTAAAAATAAA
          1 ATTTAAAAATAAA

                          
       3658 ATTTAAAAATTAAA
          1 ATTTAAAAA-TAAA

              **        
       3672 ATACAAAAATAA
          1 ATTTAAAAATAA

       3684 TTTAACTATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  13   12  0.52
  14   11  0.48

ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28


Consensus pattern (13 bp):   
ATTTAAAAATAAA

Found at i:3737 original size:26 final size:27

Alignment explanation


    Indices: 3707--3759  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       3697 TGAATATATA

                           *           
       3707 TAAATA-AGTTTTGATAAATTTAAATT
          1 TAAATAGAGTTTTGACAAATTTAAATT

                         **            
       3733 TAAATAGAGTTTTTCCAAATTTAAATT
          1 TAAATAGAGTTTTGACAAATTTAAATT

       3760 AAGATCCATA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  26    6  0.26
  27   17  0.74

ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45


Consensus pattern (27 bp):   
TAAATAGAGTTTTGACAAATTTAAATT

Found at i:6231 original size:79 final size:79

Alignment explanation


    Indices: 6100--6269  Score: 234
    Period size: 79  Copynumber: 2.2  Consensus size: 79

       6090 TTTTTGGAGG

                                    *  *                * *                  
       6100 CTTAATGCTATGTTTGGTAGGAAGTATTGAAATAGGAATGAAATTTGAGCTTAATGCTATATTTG
          1 CTTAATGCTATGTTTGGTAGGAAGGATGGAAATAGGAATGAAATCTAAGCTTAATGCTATATTTG

              **     *    
       6165 GTCTTGCCTTTGAA
         66 GTAGTGCCTCTGAA

                   *                                                     *   
       6179 CTTAATGATATGTTTGGTAGGAAGGATGGAAAT-GGAAATGAAATCTAAGCTTAATGCTATGTTT
          1 CTTAATGCTATGTTTGGTAGGAAGGATGGAAATAGG-AATGAAATCTAAGCTTAATGCTATATTT

                          *
       6243 GGTAGTGCCTCTGAG
         65 GGTAGTGCCTCTGAA

                        
       6258 CTTAATGCTATG
          1 CTTAATGCTATG

       6270 AGAGCAATCT


Statistics
Matches: 79,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  78    2  0.03
  79   77  0.97

ACGTcount: A:0.29, C:0.09, G:0.25, T:0.36


Consensus pattern (79 bp):   
CTTAATGCTATGTTTGGTAGGAAGGATGGAAATAGGAATGAAATCTAAGCTTAATGCTATATTTG
GTAGTGCCTCTGAA

Found at i:7390 original size:2 final size:2

Alignment explanation


    Indices: 7385--7423  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       7375 CGTGGAAAAT

                                                                      
       7385 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       7424 GTGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.