Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020759.1 Corchorus olitorius cultivar O-4 contig20792, 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: 3090
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Found at i:52 original size:2 final size:2

Alignment explanation


    Indices: 45--70  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

         35 TATTATAGTG

                                                  
         45 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

         71 AAATAGAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:341 original size:31 final size:31

Alignment explanation


    Indices: 303--364  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        293 GGTTTTGTAA

                               *           
        303 AATTTTTGAAACGCCTATTGTACCCTTATTT
          1 AATTTTTGAAACGCCTATTATACCCTTATTT

                         *        *        
        334 AATTTTTGAAACGTCTATTATATCCTTATTT
          1 AATTTTTGAAACGCCTATTATACCCTTATTT

        365 GTCTAACATA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.27, C:0.16, G:0.08, T:0.48


Consensus pattern (31 bp):   
AATTTTTGAAACGCCTATTATACCCTTATTT

Found at i:1012 original size:2 final size:2

Alignment explanation


    Indices: 1005--1032  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        995 AACATGCAAT

                                                     
       1005 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

       1033 ATAATAATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:1632 original size:109 final size:109

Alignment explanation


    Indices: 1441--1654  Score: 392
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       1431 TAGTCAATTT

                                                                             
       1441 GGTGCTTGTATTTTTCATTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
          1 GGTGCTTGTATTTTTCATTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT

                                                        
       1506 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATTATA
         66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATTATA

                            *                      *               *         
       1550 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTTTGTGTGCTT
          1 GGTGCTTGTATTTTTCATTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT

                                     *              
       1615 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAAT
         66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAAT

       1655 AACAAGTGGA


Statistics
Matches: 101,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 109  101  1.00

ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44


Consensus pattern (109 bp):   
GGTGCTTGTATTTTTCATTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATTATA

Found at i:2442 original size:42 final size:42

Alignment explanation


    Indices: 2383--2463  Score: 135
    Period size: 42  Copynumber: 1.9  Consensus size: 42

       2373 GATTAGTCTT

                                     *                
       2383 GAAAATTCTCTGCAAATTAAGAAATTCTCAACTCAAATCATA
          1 GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATCATA

                     *  *                          
       2425 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
          1 GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATC

       2464 CTGATCCTTA


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  42   36  1.00

ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30


Consensus pattern (42 bp):   
GAAAATTCTCTGCAAATTAAGAAATACTCAACTCAAATCATA

Found at i:2601 original size:56 final size:57

Alignment explanation


    Indices: 2529--2643  Score: 187
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       2519 TTTATTTTGT

                                   *                                 
       2529 AGAATAATTAAGTAGAGATAGG-TGAATAGAAATTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGAGGAATAGAAATTATTATAACATTTATTGTGTGAA

                                     *   *  *                        
       2585 AGAATAATTAAGTAGAGATAGGAGGGATATAATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATAGGAGGAATAGAAATTATTATAACATTTATTGTGTGAA

              
       2642 AG
          1 AG

       2644 GAAACAGATA


Statistics
Matches: 54,  Mismatches: 4, Indels: 1
        0.92            0.07        0.02

Matches are distributed among these distances:
  56   22  0.41
  57   32  0.59

ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34


Consensus pattern (57 bp):   
AGAATAATTAAGTAGAGATAGGAGGAATAGAAATTATTATAACATTTATTGTGTGAA

Done.