Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012354.1 Corchorus olitorius cultivar O-4 contig12387, 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: 14392
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:61 original size:19 final size:19

Alignment explanation


    Indices: 39--87  Score: 80
    Period size: 19  Copynumber: 2.5  Consensus size: 19

         29 TATTAATTAT

                        *      
         39 AATTAATAATAACAATTTA
          1 AATTAATAATAAAAATTTA

                               
         58 AATTAATAATAAAAATTTA
          1 AATTAATAATAAAAATTTA

                       
         77 AATTAAATAAT
          1 AATT-AATAAT

         88 TAATAATAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  19   22  0.79
  20    6  0.21

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (19 bp):   
AATTAATAATAAAAATTTA

Found at i:94 original size:7 final size:7

Alignment explanation


    Indices: 18--94  Score: 56
    Period size: 7  Copynumber: 11.6  Consensus size: 7

          8 TTTTGTTTTT

                  *
         18 TAATTAT
          1 TAATTAA

                  *
         25 TAATTAT
          1 TAATTAA

                   
         32 TAATT-A
          1 TAATTAA

                   
         38 TAATTAA
          1 TAATTAA

                   
         45 TAA-TAA
          1 TAATTAA

            *    * 
         51 CAATTTA
          1 TAATTAA

                   
         58 -AATTAA
          1 TAATTAA

                   
         64 TAA-TAA
          1 TAATTAA

            *    * 
         70 AAATTTA
          1 TAATTAA

                    
         77 -AATTAAA
          1 TAATT-AA

                   
         84 TAATTAA
          1 TAATTAA

                
         91 TAAT
          1 TAAT

         95 AATTAAAAAA


Statistics
Matches: 57,  Mismatches: 7, Indels: 12
        0.75            0.09        0.16

Matches are distributed among these distances:
   6   24  0.42
   7   29  0.51
   8    4  0.07

ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43


Consensus pattern (7 bp):   
TAATTAA

Found at i:220 original size:12 final size:12

Alignment explanation


    Indices: 203--227  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        193 CTACAAAATC

                        
        203 CGACATGATTTT
          1 CGACATGATTTT

                        
        215 CGACATGATTTT
          1 CGACATGATTTT

             
        227 C
          1 C

        228 TTTAAGATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40


Consensus pattern (12 bp):   
CGACATGATTTT

Found at i:5489 original size:30 final size:31

Alignment explanation


    Indices: 5426--5500  Score: 116
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       5416 CGTTTCTATT

                  *         *     *        
       5426 TTTAGGTTCAAATTGATCAACTTTTGAAAGG
          1 TTTAGGCTCAAATTGAGCAACTGTTGAAAGG

                                           
       5457 TTTAGGCTCAAATTGAGCAACTGTTG-AAGG
          1 TTTAGGCTCAAATTGAGCAACTGTTGAAAGG

                          
       5487 TTTAGGCTCAAATT
          1 TTTAGGCTCAAATT

       5501 AGTGGCTAAA


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  30   18  0.44
  31   23  0.56

ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36


Consensus pattern (31 bp):   
TTTAGGCTCAAATTGAGCAACTGTTGAAAGG

Found at i:10827 original size:19 final size:18

Alignment explanation


    Indices: 10803--10845  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 18

      10793 AGGAAATATT

                               
      10803 AATAATAATTATTCTAAAA
          1 AATAATAATTATT-TAAAA

                  *         * 
      10822 AATAATTATTATTTAATA
          1 AATAATAATTATTTAAAA

                  
      10840 AATAAT
          1 AATAAT

      10846 TAATAAATTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   10  0.45
  19   12  0.55

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (18 bp):   
AATAATAATTATTTAAAA

Found at i:10844 original size:18 final size:19

Alignment explanation


    Indices: 10803--10847  Score: 65
    Period size: 18  Copynumber: 2.4  Consensus size: 19

      10793 AGGAAATATT

                  *            
      10803 AATAATAATTATTCTAAAA
          1 AATAATTATTATTCTAAAA

                             * 
      10822 AATAATTATTATT-TAATA
          1 AATAATTATTATTCTAAAA

                    
      10840 AATAATTA
          1 AATAATTA

      10848 ATAAATTTCA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  18   12  0.50
  19   12  0.50

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (19 bp):   
AATAATTATTATTCTAAAA
Done.