Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014314.1 Corchorus olitorius cultivar O-4 contig14347, 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: 3699
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38


Found at i:682 original size:132 final size:132

Alignment explanation


    Indices: 445--708  Score: 528
    Period size: 132  Copynumber: 2.0  Consensus size: 132

        435 TCTAAACTTC

                                                                             
        445 AAAACCATTGACCTGAAATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAA
          1 AAAACCATTGACCTGAAATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAA

                                                                             
        510 GGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCAATATGTAATTTCATTTATCAATTAA
         66 GGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCAATATGTAATTTCATTTATCAATTAA

              
        575 AT
        131 AT

                                                                             
        577 AAAACCATTGACCTGAAATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAA
          1 AAAACCATTGACCTGAAATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAA

                                                                             
        642 GGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCAATATGTAATTTCATTTATCAATTAA
         66 GGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCAATATGTAATTTCATTTATCAATTAA

              
        707 AT
        131 AT

        709 TAAATATATT


Statistics
Matches: 132,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 132  132  1.00

ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40


Consensus pattern (132 bp):   
AAAACCATTGACCTGAAATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAA
GGGTAAACATGTATTTATCAAATTAAACTTTTAAGGTTCAATATGTAATTTCATTTATCAATTAA
AT

Found at i:836 original size:39 final size:39

Alignment explanation


    Indices: 780--899  Score: 204
    Period size: 39  Copynumber: 3.1  Consensus size: 39

        770 TTTAATTCCT

                     *          *                   
        780 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA

                                                   
        820 ATGTAATACTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAATACTATAATAACTGAAATACTTACATTAATTAA

                                         *         
        859 ATGTAATACTATAATAACTGAAATACTTATATTAATTAA
          1 ATGTAATACTATAATAACTGAAATACTTACATTAATTAA

              
        898 AT
          1 AT

        900 TTTTAGGTAT


Statistics
Matches: 77,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  39   69  0.90
  40    8  0.10

ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38


Consensus pattern (39 bp):   
ATGTAATACTATAATAACTGAAATACTTACATTAATTAA

Found at i:846 original size:17 final size:17

Alignment explanation


    Indices: 824--885  Score: 61
    Period size: 17  Copynumber: 3.4  Consensus size: 17

        814 AATTAAATGT

                             
        824 AATACTATAATAACTGA
          1 AATACTATAATAACTGA

                              *  *
        841 AATACTTACATTAATTAAATGT
          1 AATAC-T--A-TAA-TAACTGA

                             
        863 AATACTATAATAACTGA
          1 AATACTATAATAACTGA

                  
        880 AATACT
          1 AATACT

        886 TATATTAATT


Statistics
Matches: 36,  Mismatches: 4, Indels: 10
        0.72            0.08        0.20

Matches are distributed among these distances:
  17   16  0.44
  18    4  0.11
  19    1  0.03
  20    1  0.03
  21    4  0.11
  22   10  0.28

ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34


Consensus pattern (17 bp):   
AATACTATAATAACTGA

Found at i:931 original size:26 final size:25

Alignment explanation


    Indices: 890--939  Score: 82
    Period size: 26  Copynumber: 2.0  Consensus size: 25

        880 AATACTTATA

                       *             
        890 TTAATTAAATTTTTAGGTATTTGTT
          1 TTAATTAAATTCTTAGGTATTTGTT

                                     
        915 TTAATTCAAATTCTTAGGTATTTGT
          1 TTAATT-AAATTCTTAGGTATTTGT

        940 GTAAACGTAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  25    6  0.26
  26   17  0.74

ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56


Consensus pattern (25 bp):   
TTAATTAAATTCTTAGGTATTTGTT

Found at i:1984 original size:36 final size:36

Alignment explanation


    Indices: 1937--2006  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1927 GAGATTTTGG

                         *      *               
       1937 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1973 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       2007 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:3372 original size:58 final size:58

Alignment explanation


    Indices: 3269--3383  Score: 151
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       3259 ATAGCATCAT

                      *                                    *          
       3269 GCCTCGGTCCTAAAACGTCATTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACGTCATTTTTAGGCATCTAATAAAAAAACATGCCACTCGATAA

                *               *      *             *           *    
       3327 GCCTTGGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGCCACTTGATA
          1 GCCTCGGTCCGAAAACGTC-ATTTTTAGGCATCTAATAAAAAAACATGCCACTCGATA

       3384 TTTGATTAAT


Statistics
Matches: 49,  Mismatches: 7, Indels: 2
        0.84            0.12        0.03

Matches are distributed among these distances:
  58   34  0.69
  59   15  0.31

ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30


Consensus pattern (58 bp):   
GCCTCGGTCCGAAAACGTCATTTTTAGGCATCTAATAAAAAAACATGCCACTCGATAA
Done.