Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014833.1 Corchorus olitorius cultivar O-4 contig14866, 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: 36081
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:5308 original size:15 final size:15

Alignment explanation


    Indices: 5288--5319  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       5278 TTTTAACCTT

                        *  
       5288 TATCTATACTATCTA
          1 TATCTATACTATATA

                           
       5303 TATCTATACTATATA
          1 TATCTATACTATATA

              
       5318 TA
          1 TA

       5320 AAAGTACGAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47


Consensus pattern (15 bp):   
TATCTATACTATATA

Found at i:5387 original size:32 final size:32

Alignment explanation


    Indices: 5351--5411  Score: 104
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       5341 TTTTGAATCA

                     *            *         
       5351 TCTATTATATCCTTATTTTTCGTATATATCTG
          1 TCTATTATACCCTTATTTTTCGAATATATCTG

                                         
       5383 TCTATTATACCCTTATTTTTCGAATATAT
          1 TCTATTATACCCTTATTTTTCGAATATAT

       5412 TTCTTAAATG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.25, C:0.16, G:0.05, T:0.54


Consensus pattern (32 bp):   
TCTATTATACCCTTATTTTTCGAATATATCTG

Found at i:7870 original size:71 final size:71

Alignment explanation


    Indices: 7732--7870  Score: 208
    Period size: 71  Copynumber: 2.0  Consensus size: 71

       7722 TCCCAAATCT

                                  *                          *           **  
       7732 GAAATGACCCGAATTAGATATACACCCTAAACCCAAATCCAAAAGGATCCTACCAAACACATTCT
          1 GAAATGACCCGAATTAGATATAAACCCTAAACCCAAATCCAAAAGGATCATACCAAACACACCCT

                  
       7797 TTGTTG
         66 TTGTTG

                    *                                                    *   
       7803 GAAATGACGCGAATTCA-ATATAAACCCTAAACCCAAATCCAAAAGGATCATACCAAACACGCCC
          1 GAAATGACCCGAATT-AGATATAAACCCTAAACCCAAATCCAAAAGGATCATACCAAACACACCC

                
       7867 TTTG
         65 TTTG

       7871 CCGCCCAGTT


Statistics
Matches: 61,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  71   60  0.98
  72    1  0.02

ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20


Consensus pattern (71 bp):   
GAAATGACCCGAATTAGATATAAACCCTAAACCCAAATCCAAAAGGATCATACCAAACACACCCT
TTGTTG

Found at i:30681 original size:27 final size:27

Alignment explanation


    Indices: 30651--30702  Score: 95
    Period size: 27  Copynumber: 1.9  Consensus size: 27

      30641 TGGCCCGAAA

                                       
      30651 TCCAACCTCTTGCCCAACTTCCTGAAT
          1 TCCAACCTCTTGCCCAACTTCCTGAAT

                          *          
      30678 TCCAACCTCTTGCCGAACTTCCTGA
          1 TCCAACCTCTTGCCCAACTTCCTGA

      30703 TGTCGAAACT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.21, C:0.40, G:0.10, T:0.29


Consensus pattern (27 bp):   
TCCAACCTCTTGCCCAACTTCCTGAAT

Found at i:35891 original size:21 final size:21

Alignment explanation


    Indices: 35866--35948  Score: 73
    Period size: 22  Copynumber: 3.8  Consensus size: 21

      35856 TATCTTGGAT

                                  
      35866 ATAAT-ATATATTATTAAATAA
          1 ATAATAATATATT-TTAAATAA

                                  
      35887 ATAATAAATATATTTTAAAT-A
          1 ATAAT-AATATATTTTAAATAA

                        *   *      
      35908 ATAAATAATGA-GTTTAAAATAA
          1 AT-AATAAT-ATATTTTAAATAA

                               
      35930 ATAAATAATATATATTTAA
          1 AT-AATAATATAT-TTTAA

      35949 TTACTAAACG


Statistics
Matches: 51,  Mismatches: 4, Indels: 12
        0.76            0.06        0.18

Matches are distributed among these distances:
  21   19  0.37
  22   21  0.41
  23   11  0.22

ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40


Consensus pattern (21 bp):   
ATAATAATATATTTTAAATAA

Found at i:35899 original size:25 final size:25

Alignment explanation


    Indices: 35868--35916  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      35858 TCTTGGATAT

                        *             
      35868 AATATATATT-ATTAAATAAATAATA
          1 AATATATATTAAAT-AATAAATAATA

                   *                
      35893 AATATATTTTAAATAATAAATAAT
          1 AATATATATTAAATAATAAATAAT

      35917 GAGTTTAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   19  0.90
  26    2  0.10

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (25 bp):   
AATATATATTAAATAATAAATAATA
Done.