Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013889.1 Corchorus olitorius cultivar O-4 contig13922, 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: 16708
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:2554 original size:80 final size:80

Alignment explanation


    Indices: 2462--2621  Score: 257
    Period size: 80  Copynumber: 2.0  Consensus size: 80

       2452 TATCCTTTTT

                               *    * *                            *         
       2462 AATGTGGTATATATACGACGCTCATGTGTGAACTGTAATTAAACCCTTGAACAGAGATAATAGAA
          1 AATGTGGTATATATACGACACTCACGAGTGAACTGTAATTAAACCCTTGAACAGAAATAATAGAA

                           
       2527 TTGGGTTGGATCGAA
         66 TTGGGTTGGATCGAA

                                                      *     *            *   
       2542 AATGTGGTATATATACGACACTCACGAGTGAACTGTAATTAAGCCCTTTAACAGAAATAATGGAA
          1 AATGTGGTATATATACGACACTCACGAGTGAACTGTAATTAAACCCTTGAACAGAAATAATAGAA

                           
       2607 TTGGGTTGGATCGAA
         66 TTGGGTTGGATCGAA

       2622 GCTGGTGGTG


Statistics
Matches: 73,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  80   73  1.00

ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28


Consensus pattern (80 bp):   
AATGTGGTATATATACGACACTCACGAGTGAACTGTAATTAAACCCTTGAACAGAAATAATAGAA
TTGGGTTGGATCGAA

Found at i:3696 original size:30 final size:30

Alignment explanation


    Indices: 3662--3726  Score: 130
    Period size: 30  Copynumber: 2.2  Consensus size: 30

       3652 TCTGCTCCAA

                                          
       3662 ATATCGAATTTGCTAACCATCTACTCACAT
          1 ATATCGAATTTGCTAACCATCTACTCACAT

                                          
       3692 ATATCGAATTTGCTAACCATCTACTCACAT
          1 ATATCGAATTTGCTAACCATCTACTCACAT

                 
       3722 ATATC
          1 ATATC

       3727 ATAAGAACCG


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   35  1.00

ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34


Consensus pattern (30 bp):   
ATATCGAATTTGCTAACCATCTACTCACAT

Found at i:4772 original size:117 final size:116

Alignment explanation


    Indices: 4566--4798  Score: 439
    Period size: 117  Copynumber: 2.0  Consensus size: 116

       4556 TTGAAGGAGC

                                     *                                       
       4566 TTGAACTTTTTTCAACAAAAGTCTTTACTTCCCATTTTCTAAAAAGTTAGGCACAAATTTAAATG
          1 TTGAACTTTTTTCAACAAAAGTCTTCACTTCCCATTTTCTAAAAAGTTAGGCACAAATTTAAATG

                                     *                         
       4631 TTTATTTTTTTCTACTGATCATGAATATGATATTGAAATGGGCTACACAAT
         66 TTTATTTTTTTCTACTGATCATGAACATGATATTGAAATGGGCTACACAAT

                                                                             
       4682 TTGAACTTTTTTCAACAAAAGTCTTCACTTCCCATTTTCTAAAAAAGTTAGGCACAAATTTAAAT
          1 TTGAACTTTTTTCAACAAAAGTCTTCACTTCCCATTTTCT-AAAAAGTTAGGCACAAATTTAAAT

                                                                
       4747 GTTTATTTTTTTCTACTGATCATGAACATGATATTGAAATGGGCTACACAAT
         65 GTTTATTTTTTTCTACTGATCATGAACATGATATTGAAATGGGCTACACAAT

       4799 AGGAGATAGC


Statistics
Matches: 114,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 116   39  0.34
 117   75  0.66

ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39


Consensus pattern (116 bp):   
TTGAACTTTTTTCAACAAAAGTCTTCACTTCCCATTTTCTAAAAAGTTAGGCACAAATTTAAATG
TTTATTTTTTTCTACTGATCATGAACATGATATTGAAATGGGCTACACAAT

Found at i:5162 original size:13 final size:13

Alignment explanation


    Indices: 5144--5168  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5134 TCTATAACCT

                         
       5144 CATAAATCATATA
          1 CATAAATCATATA

                        
       5157 CATAAATCATAT
          1 CATAAATCATAT

       5169 TTATTATATT


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:0.52, C:0.16, G:0.00, T:0.32


Consensus pattern (13 bp):   
CATAAATCATATA

Found at i:5931 original size:3 final size:3

Alignment explanation


    Indices: 5923--5948  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       5913 TGAGATTGCT

                                              
       5923 ATG ATG ATG ATG ATG ATG ATG ATG AT
          1 ATG ATG ATG ATG ATG ATG ATG ATG AT

       5949 AATTCAACTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35


Consensus pattern (3 bp):   
ATG

Found at i:8631 original size:6 final size:7

Alignment explanation


    Indices: 8616--8640  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       8606 ATTTTGCAGG

                   
       8616 AAAAGAA
          1 AAAAGAA

                   
       8623 AAAAGAA
          1 AAAAGAA

                   
       8630 AAAAGAA
          1 AAAAGAA

                
       8637 AAAA
          1 AAAA

       8641 AAGAGAGCAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (7 bp):   
AAAAGAA
Done.