Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011828.1 Corchorus olitorius cultivar O-4 contig11861, 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: 17508
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:2874 original size:20 final size:20

Alignment explanation


    Indices: 2851--2896  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       2841 TATGCATGTG

                            *   
       2851 GAAAATGAAAAATGCTCATT
          1 GAAAATGAAAAATGCTAATT

                   *            
       2871 GAAAATGTAAAATGCTAATT
          1 GAAAATGAAAAATGCTAATT

                   
       2891 -AAAATG
          1 GAAAATG

       2897 CCACATACTT


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

Matches are distributed among these distances:
  19    6  0.25
  20   18  0.75

ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26


Consensus pattern (20 bp):   
GAAAATGAAAAATGCTAATT

Found at i:5410 original size:14 final size:14

Alignment explanation


    Indices: 5391--5421  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       5381 TCCTAACATT

                          
       5391 TCACTGCTTATATG
          1 TCACTGCTTATATG

                          
       5405 TCACTGCTTATATG
          1 TCACTGCTTATATG

               
       5419 TCA
          1 TCA

       5422 AGAAGAAAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42


Consensus pattern (14 bp):   
TCACTGCTTATATG

Found at i:6499 original size:26 final size:23

Alignment explanation


    Indices: 6465--6515  Score: 66
    Period size: 26  Copynumber: 2.1  Consensus size: 23

       6455 TATATAGATA

                                      
       6465 ATTAAATATATATTATATATACTAAT
          1 ATTAAATATATA-TATATA-A-TAAT

                *                  
       6491 ATTAGATATATATATATAATAAT
          1 ATTAAATATATATATATAATAAT

              
       6514 AT
          1 AT

       6516 ATATAATTGT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  23    6  0.25
  24    1  0.04
  25    6  0.25
  26   11  0.46

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (23 bp):   
ATTAAATATATATATATAATAAT

Found at i:17229 original size:27 final size:29

Alignment explanation


    Indices: 17184--17238  Score: 71
    Period size: 27  Copynumber: 2.0  Consensus size: 29

      17174 TTAAACTATA

                                         
      17184 CACATTATTATTGCAAAAA-AA-AAAATG
          1 CACATTATTATTGCAAAAAGAATAAAATG

                           *             
      17211 CACATTATTGA-TGCCAAAAGAATAAAAT
          1 CACATTATT-ATTGCAAAAAGAATAAAAT

      17239 AAAATTGCAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  27   16  0.67
  28    3  0.12
  29    5  0.21

ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25


Consensus pattern (29 bp):   
CACATTATTATTGCAAAAAGAATAAAATG

Found at i:17375 original size:24 final size:24

Alignment explanation


    Indices: 17330--17377  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      17320 TTACTTTATT

                             *      
      17330 TTCTTCAAACTTCAAAATTTTCAA
          1 TTCTTCAAACTTCAAAACTTTCAA

                     *               
      17354 TTCTCTCAACCTTC-AAACTTTCAA
          1 TTCT-TCAAACTTCAAAACTTTCAA

      17378 AACTCAATCA


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

Matches are distributed among these distances:
  24   13  0.62
  25    8  0.38

ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40


Consensus pattern (24 bp):   
TTCTTCAAACTTCAAAACTTTCAA
Done.