Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019650.1 Corchorus olitorius cultivar O-4 contig19683, 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: 14848
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:2375 original size:7 final size:7

Alignment explanation


    Indices: 2344--2378  Score: 52
    Period size: 7  Copynumber: 4.9  Consensus size: 7

       2334 TAGGGTACGT

                   
       2344 AAGTCTC
          1 AAGTCTC

                    
       2351 AAAGTCTC
          1 -AAGTCTC

              *    
       2359 AACTCTC
          1 AAGTCTC

                   
       2366 AAGTCTC
          1 AAGTCTC

                  
       2373 AAGTCT
          1 AAGTCT

       2379 ATTTATGGCA


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

Matches are distributed among these distances:
   7   18  0.72
   8    7  0.28

ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29


Consensus pattern (7 bp):   
AAGTCTC

Found at i:2586 original size:24 final size:24

Alignment explanation


    Indices: 2554--2599  Score: 92
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       2544 GCCCAAGACT

                                    
       2554 GGCTTTAGATGGGTAAGAACTTGA
          1 GGCTTTAGATGGGTAAGAACTTGA

                                  
       2578 GGCTTTAGATGGGTAAGAACTT
          1 GGCTTTAGATGGGTAAGAACTT

       2600 TAAAGGTAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.28, C:0.09, G:0.33, T:0.30


Consensus pattern (24 bp):   
GGCTTTAGATGGGTAAGAACTTGA

Found at i:7952 original size:13 final size:13

Alignment explanation


    Indices: 7903--7957  Score: 56
    Period size: 13  Copynumber: 3.8  Consensus size: 13

       7893 CCTTGGTCTG

                   *     
       7903 ACGTGGCCTTGCC
          1 ACGTGGCATTGCC

                             
       7916 ACGTGGCATTTTGGTCC
          1 ACGTGGCA--TT-G-CC

                          
       7933 AACGTGGCATTGCC
          1 -ACGTGGCATTGCC

                       
       7947 ACGTGGCATTG
          1 ACGTGGCATTG

       7958 TCACATAAGC


Statistics
Matches: 36,  Mismatches: 1, Indels: 10
        0.77            0.02        0.21

Matches are distributed among these distances:
  13   18  0.50
  14    2  0.06
  15    3  0.08
  16    3  0.08
  17    2  0.06
  18    8  0.22

ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27


Consensus pattern (13 bp):   
ACGTGGCATTGCC

Found at i:9279 original size:42 final size:42

Alignment explanation


    Indices: 9231--9311  Score: 162
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       9221 AAATGGAAAA

                                                      
       9231 AAAATCCTTTCATTTACTGTAACACTTAACTGAAAATCAAAG
          1 AAAATCCTTTCATTTACTGTAACACTTAACTGAAAATCAAAG

                                                   
       9273 AAAATCCTTTCATTTACTGTAACACTTAACTGAAAATCA
          1 AAAATCCTTTCATTTACTGTAACACTTAACTGAAAATCA

       9312 GAATCCCTTC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   39  1.00

ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32


Consensus pattern (42 bp):   
AAAATCCTTTCATTTACTGTAACACTTAACTGAAAATCAAAG
Done.