Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020632.1 Corchorus olitorius cultivar O-4 contig20665, 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: 9050
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:1308 original size:26 final size:27

Alignment explanation


    Indices: 1279--1342  Score: 67
    Period size: 26  Copynumber: 2.4  Consensus size: 27

       1269 ATTATTATTA

                                       
       1279 TTTTCCTCCTAATTCTCTT-ATTTTCC
          1 TTTTCCTCCTAATTCTCTTCATTTTCC

                 *    **    *   *      
       1305 TTTTCTTCCTTTTTCTTTTCTTTTTCC
          1 TTTTCCTCCTAATTCTCTTCATTTTCC

                       
       1332 TTCTTCCTCCT
          1 TT-TTCCTCCT

       1343 TATATTATAA


Statistics
Matches: 30,  Mismatches: 6, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  26   15  0.50
  27    8  0.27
  28    7  0.23

ACGTcount: A:0.05, C:0.31, G:0.00, T:0.64


Consensus pattern (27 bp):   
TTTTCCTCCTAATTCTCTTCATTTTCC

Found at i:3415 original size:42 final size:42

Alignment explanation


    Indices: 3356--3438  Score: 141
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3346 GTTAAGTCTT

                                                       
       3356 GAAAATTCTCTGTAAATTTAA-AAATACTCAACTCAAATCATA
          1 GAAAATTCTCTGTAAA-TTAAGAAATACTCAACTCAAATCATA

                     *                               
       3398 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATCAT
          1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT

       3439 CATCCTTAAC


Statistics
Matches: 39,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  41    4  0.10
  42   35  0.90

ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31


Consensus pattern (42 bp):   
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA

Found at i:3572 original size:55 final size:56

Alignment explanation


    Indices: 3502--3613  Score: 199
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       3492 TTTATTTTGT

                                                                    
       3502 AGAATAATTAAGTAGAGATA-GAGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGAGGATAGGATTTATTATAACATTTATTGTGTGAA

                                  *  *                              
       3557 AGAATAATTAAGTAGAGATAGGGGGGTAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGAGGATAGGATTTATTATAACATTTATTGTGTGAA

             
       3613 A
          1 A

       3614 AGGAAACACA


Statistics
Matches: 54,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  55   20  0.37
  56   34  0.63

ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGGAGGATAGGATTTATTATAACATTTATTGTGTGAA

Found at i:3810 original size:2 final size:2

Alignment explanation


    Indices: 3803--3836  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3793 TAATATGTAG

                                                              
       3803 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       3837 GTTCAAGCAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.