Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022151.1 Corchorus olitorius cultivar O-4 contig22184, 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: 4477
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Found at i:588 original size:3 final size:3

Alignment explanation


    Indices: 571--605  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

        561 TCACTGGAAA

                     *   *                                
        571 AAG AAG AGG AGG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

        606 AAAAAAAAAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   30  1.00

ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:680 original size:6 final size:6

Alignment explanation


    Indices: 669--733  Score: 69
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        659 AAAAGAGAGG

                                    *                     *          
        669 AAAGAA AAAGAA AAAGGAA AAGGAA AAAGAA AAAGGAA AAGGAA AAA-AA
          1 AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAGAA

                 *            
        718 AAGAGGA AAAGAA AAA
          1 AA-AGAA AAAGAA AAA

        734 AAATATATTA


Statistics
Matches: 49,  Mismatches: 6, Indels: 8
        0.78            0.10        0.13

Matches are distributed among these distances:
   5    4  0.08
   6   32  0.65
   7   13  0.27

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (6 bp):   
AAAGAA

Found at i:694 original size:13 final size:12

Alignment explanation


    Indices: 669--733  Score: 76
    Period size: 12  Copynumber: 5.2  Consensus size: 12

        659 AAAAGAGAGG

                *       
        669 AAAGAAAAAGAA
          1 AAAGGAAAAGAA

                         
        681 AAAGGAAAAGGAA
          1 AAAGGAAAA-GAA

                *     * 
        694 AAAGAAAAAGGA
          1 AAAGGAAAAGAA

                     *  
        706 AAAGGAAAAAAA
          1 AAAGGAAAAGAA

                         
        718 AAGAGGAAAAGAA
          1 AA-AGGAAAAGAA

               
        731 AAA
          1 AAA

        734 AAATATATTA


Statistics
Matches: 44,  Mismatches: 7, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  12   22  0.50
  13   22  0.50

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (12 bp):   
AAAGGAAAAGAA

Found at i:696 original size:19 final size:19

Alignment explanation


    Indices: 672--733  Score: 101
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        662 AGAGAGGAAA

                               
        672 GAAAAAGAAAAAGGAAAAG
          1 GAAAAAGAAAAAGGAAAAG

                               
        691 GAAAAAGAAAAAGGAAAAG
          1 GAAAAAGAAAAAGGAAAAG

                                
        710 GAAAAA-AAAAGAGGAAAA-
          1 GAAAAAGAAAA-AGGAAAAG

                  
        728 GAAAAA
          1 GAAAAA

        734 AAATATATTA


Statistics
Matches: 42,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  18   10  0.24
  19   32  0.76

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (19 bp):   
GAAAAAGAAAAAGGAAAAG

Found at i:1942 original size:13 final size:13

Alignment explanation


    Indices: 1912--1952  Score: 52
    Period size: 13  Copynumber: 3.4  Consensus size: 13

       1902 CCCGTTGAGG

                         
       1912 AAATG-TTT-TAT
          1 AAATGCTTTATAT

              *          
       1923 AACTGCTTTATAT
          1 AAATGCTTTATAT

                         
       1936 AAATGCTTTATA-
          1 AAATGCTTTATAT

                 
       1948 AAATG
          1 AAATG

       1953 TTTTGGGTGC


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  11    4  0.15
  12    8  0.31
  13   14  0.54

ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44


Consensus pattern (13 bp):   
AAATGCTTTATAT
Done.