Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013434.1 Corchorus olitorius cultivar O-4 contig13467, 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: 8733
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:1012 original size:17 final size:17

Alignment explanation


    Indices: 992--1024  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        982 ATGAAAGAGG

                             
        992 AATGAAAGAGGAAGATC
          1 AATGAAAGAGGAAGATC

                            
       1009 AATGAAAGAGGAAGAT
          1 AATGAAAGAGGAAGAT

       1025 TAAGTTCGAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.55, C:0.03, G:0.30, T:0.12


Consensus pattern (17 bp):   
AATGAAAGAGGAAGATC

Found at i:4849 original size:16 final size:16

Alignment explanation


    Indices: 4824--4870  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       4814 AGAAAGGAAG

                 *     * *  
       4824 AAGAAGGAAAATAGAA
          1 AAGAAAGAAAAGAAAA

                            
       4840 AAGAAAGAAAAGAAAA
          1 AAGAAAGAAAAGAAAA

                            
       4856 AAGAAA-AAGAAGAAA
          1 AAGAAAGAA-AAGAAA

       4871 TAAGTGGAGT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  15    2  0.07
  16   25  0.93

ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02


Consensus pattern (16 bp):   
AAGAAAGAAAAGAAAA

Found at i:4860 original size:21 final size:22

Alignment explanation


    Indices: 4816--4870  Score: 60
    Period size: 21  Copynumber: 2.5  Consensus size: 22

       4806 GGGGAGAGAG

                *              *   
       4816 AAAGGAAGAAGAAGGAAAATAGA
          1 AAAGAAAGAA-AAGGAAAAAAGA

                                  
       4839 AAAGAAAGAAAA-GAAAAAAGA
          1 AAAGAAAGAAAAGGAAAAAAGA

                        
       4860 AAA-AGAAGAAA
          1 AAAGA-AAGAAA

       4871 TAAGTGGAGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  20    1  0.03
  21   17  0.59
  22    2  0.07
  23    9  0.31

ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02


Consensus pattern (22 bp):   
AAAGAAAGAAAAGGAAAAAAGA

Found at i:5794 original size:2 final size:2

Alignment explanation


    Indices: 5787--5816  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       5777 CAAAGGTTGC

                                                        
       5787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5817 GTTTATACCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6022 original size:8 final size:9

Alignment explanation


    Indices: 5986--6023  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       5976 CCCAAATTAC

                     
       5986 TTATGGAAA
          1 TTATGGAAA

               *     
       5995 TTAAGGAAA
          1 TTATGGAAA

                     
       6004 TTATGGAAA
          1 TTATGGAAA

                     
       6013 TTAT-GAAA
          1 TTATGGAAA

               
       6021 TTA
          1 TTA

       6024 AATGAATTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    7  0.26
   9   20  0.74

ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:7439 original size:48 final size:48

Alignment explanation


    Indices: 7313--7443  Score: 149
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       7303 TACTTTACGC

                 *                            *          *   
       7313 CGCACGTTTTCTCAATTTTTACT-ACAAAATTGAACTTTTATTTTTACT
          1 CGCACTTTTTCTCAATTTTTA-TGACAAAATTGATCTTTTATTTTCACT

            *               *     *                           
       7361 TGCATCTTTTTCTCAAATTTTAAGACAAAATTGATCTTTTAATTTTCA-T
          1 CGCA-CTTTTTCTCAATTTTTATGACAAAATTGATCTTTT-ATTTTCACT

                      *         *             
       7410 CGCACTTTTTATCAATTTTTTTGACAAAATTGAT
          1 CGCACTTTTTCTCAATTTTTATGACAAAATTGAT

       7444 TGGCACGCTC


Statistics
Matches: 69,  Mismatches: 11, Indels: 6
        0.80            0.13        0.07

Matches are distributed among these distances:
  48   29  0.42
  49   34  0.49
  50    6  0.09

ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48


Consensus pattern (48 bp):   
CGCACTTTTTCTCAATTTTTATGACAAAATTGATCTTTTATTTTCACT

Found at i:8288 original size:15 final size:15

Alignment explanation


    Indices: 8268--8304  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       8258 TGCTAGGGTG

                           
       8268 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                    *  *   
       8283 AATGGTGCGAATAAC
          1 AATGGTGCAAACAAC

                   
       8298 AATGGTG
          1 AATGGTG

       8305 TGAACAATAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.41, C:0.14, G:0.27, T:0.19


Consensus pattern (15 bp):   
AATGGTGCAAACAAC
Done.