Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024646.1 Corchorus olitorius cultivar O-4 contig24679, 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: 21092
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:196 original size:15 final size:15

Alignment explanation


    Indices: 157--189  Score: 52
    Period size: 13  Copynumber: 2.3  Consensus size: 15

        147 GACCCAAAAG

                           
        157 AAAAGAAA-AA-GAA
          1 AAAAGAAAGAAGGAA

                           
        170 AAAAGAAAGAAGGAA
          1 AAAAGAAAGAAGGAA

                 
        185 AAAAG
          1 AAAAG

        190 GGAGAAGACC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  13    8  0.44
  14    2  0.11
  15    8  0.44

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (15 bp):   
AAAAGAAAGAAGGAA

Found at i:288 original size:46 final size:45

Alignment explanation


    Indices: 228--343  Score: 144
    Period size: 46  Copynumber: 2.5  Consensus size: 45

        218 ACATTTTGAG

                                                          
        228 AAACTAATAAGGAAATGGGTCTTTAAAAAAGAAATGGACTTTGAAT
          1 AAACTAATAAGGAAATGGG-CTTTAAAAAAGAAATGGACTTTGAAT

             *                    *     ** *              
        274 -TACTAAATAAGGAAATGGGCTCTAAAATGGTAATGGACTTTGAAT
          1 AAACT-AATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT

                     *               
        319 GAAACTAATGAGGAAATGGGCTTTA
          1 -AAACTAATAAGGAAATGGGCTTTA

        344 TTAAAATGGA


Statistics
Matches: 59,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  45   25  0.42
  46   31  0.53
  47    3  0.05

ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27


Consensus pattern (45 bp):   
AAACTAATAAGGAAATGGGCTTTAAAAAAGAAATGGACTTTGAAT

Found at i:7944 original size:16 final size:16

Alignment explanation


    Indices: 7914--7947  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       7904 GAGCTACTCG

                            
       7914 ATACAAATATATATAT
          1 ATACAAATATATATAT

                             
       7930 ATACATAATAT-TATAT
          1 ATACA-AATATATATAT

              
       7946 AT
          1 AT

       7948 TTAATTAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41


Consensus pattern (16 bp):   
ATACAAATATATATAT

Found at i:8882 original size:29 final size:30

Alignment explanation


    Indices: 8849--8913  Score: 80
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       8839 ATCATCATAT

                           **             
       8849 AATAAGCT-CTCGAATTTTAATTTCAATCA
          1 AATAAGCTCCTCGAACCTTAATTTCAATCA

                                *     *   
       8878 AATAAG-TCCTCGAACCTTATTTTCAGTCA
          1 AATAAGCTCCTCGAACCTTAATTTCAATCA

                   
       8907 AATAAGC
          1 AATAAGC

       8914 CATCTAATCT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  28    1  0.03
  29   29  0.97

ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34


Consensus pattern (30 bp):   
AATAAGCTCCTCGAACCTTAATTTCAATCA

Found at i:16558 original size:42 final size:42

Alignment explanation


    Indices: 16512--16614  Score: 190
    Period size: 42  Copynumber: 2.5  Consensus size: 42

      16502 GAATGAATAA

                                                      
      16512 AGTAGGCTCAATAGCCCCAACATGAGGTAAAAAGTTTCTTTC
          1 AGTAGGCTCAATAGCCCCAACATGAGGTAAAAAGTTTCTTTC

                                                      
      16554 AGTAGGCTCAATAGCCCCAACATGAGGTAAAAAGTTTCTTTC
          1 AGTAGGCTCAATAGCCCCAACATGAGGTAAAAAGTTTCTTTC

                     *          
      16596 AGTAGGCTCCATA-CCCCAA
          1 AGTAGGCTCAATAGCCCCAA

      16615 AACTAATACC


Statistics
Matches: 60,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  41    6  0.10
  42   54  0.90

ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24


Consensus pattern (42 bp):   
AGTAGGCTCAATAGCCCCAACATGAGGTAAAAAGTTTCTTTC

Found at i:17936 original size:2 final size:2

Alignment explanation


    Indices: 17931--17978  Score: 96
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      17921 AAAAAGAAGG

                                                                          
      17931 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                    
      17973 GA GA GA
          1 GA GA GA

      17979 AACAAACCTT


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   46  1.00

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


Consensus pattern (2 bp):   
GA

Found at i:19668 original size:24 final size:24

Alignment explanation


    Indices: 19637--19683  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      19627 ACCCCAAAAC

                                     
      19637 CAAAACCCTAGAAAG-AAATCCAAT
          1 CAAAACCC-AGAAAGAAAATCCAAT

                      *            
      19661 CAAAACCCAGGAAGAAAATCCAA
          1 CAAAACCCAGAAAGAAAATCCAA

      19684 AAACCCATCA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    5  0.24
  24   16  0.76

ACGTcount: A:0.55, C:0.26, G:0.11, T:0.09


Consensus pattern (24 bp):   
CAAAACCCAGAAAGAAAATCCAAT
Done.