Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007191.1 Corchorus olitorius cultivar O-4 contig07216, 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: 1839
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32


Found at i:682 original size:25 final size:25

Alignment explanation


    Indices: 654--778  Score: 77
    Period size: 25  Copynumber: 5.2  Consensus size: 25

        644 TCCATTACCT

                    *                
        654 AATTGGAAAAGGTGGTAATCATCCA
          1 AATTGGAAGAGGTGGTAATCATCCA

                     *    *      *    *
        679 AATT--AATTAGG-AGTCAA-AATCCT
          1 AATTGGAA-GAGGTGGT-AATCATCCA

                                     
        702 AATTGGAAGAGGTGGTAATCATCCA
          1 AATTGGAAGAGGTGGTAATCATCCA

                     *    *      *    *
        727 AATT--AATTAGG-AGTCAA-AATCCT
          1 AATTGGAA-GAGGTGGT-AATCATCCA

                                     
        750 AATTGGAAGAGGTGGTAATCATCCA
          1 AATTGGAAGAGGTGGTAATCATCCA

                
        775 AATT
          1 AATT

        779 AATTAGGAGT


Statistics
Matches: 72,  Mismatches: 16, Indels: 24
        0.64            0.14        0.21

Matches are distributed among these distances:
  23   24  0.33
  24   20  0.28
  25   28  0.39

ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27


Consensus pattern (25 bp):   
AATTGGAAGAGGTGGTAATCATCCA

Found at i:689 original size:48 final size:48

Alignment explanation


    Indices: 651--809  Score: 309
    Period size: 48  Copynumber: 3.3  Consensus size: 48

        641 GAGTCCATTA

                       *                                    
        651 CCTAATTGGAAAAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT
          1 CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT

                                                            
        699 CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT
          1 CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT

                                                            
        747 CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT
          1 CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT

                           
        795 CCTAATTGGAAGAGG
          1 CCTAATTGGAAGAGG

        810 AGTGCATGAG


Statistics
Matches: 110,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  48  110  1.00

ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26


Consensus pattern (48 bp):   
CCTAATTGGAAGAGGTGGTAATCATCCAAATTAATTAGGAGTCAAAAT

Found at i:700 original size:23 final size:23

Alignment explanation


    Indices: 674--801  Score: 75
    Period size: 23  Copynumber: 5.4  Consensus size: 23

        664 GGTGGTAATC

                                   
        674 ATCCAAATTAATTAGGAGTCAAA
          1 ATCCAAATTAATTAGGAGTCAAA

                *         *    *      *
        697 ATCCTAATTGGAA-GAGGTGGT-AATC
          1 ATCCAAATT--AATTAGG-AGTCAA-A

                                   
        722 ATCCAAATTAATTAGGAGTCAAA
          1 ATCCAAATTAATTAGGAGTCAAA

                *         *    *      *
        745 ATCCTAATTGGAA-GAGGTGGT-AATC
          1 ATCCAAATT--AATTAGG-AGTCAA-A

                                   
        770 ATCCAAATTAATTAGGAGTCAAA
          1 ATCCAAATTAATTAGGAGTCAAA

                *    
        793 ATCCTAATT
          1 ATCCAAATT

        802 GGAAGAGGAG


Statistics
Matches: 76,  Mismatches: 17, Indels: 24
        0.65            0.15        0.21

Matches are distributed among these distances:
  23   32  0.42
  24   20  0.26
  25   24  0.32

ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28


Consensus pattern (23 bp):   
ATCCAAATTAATTAGGAGTCAAA
Done.