Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019809.1 Corchorus olitorius cultivar O-4 contig19842, 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: 2513
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32


Found at i:10 original size:1 final size:1

Alignment explanation


    Indices: 5--33  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

          1 ATTC

                                         
          5 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

         34 CTAAATGGGC


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

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:95 original size:34 final size:36

Alignment explanation


    Indices: 45--111  Score: 95
    Period size: 34  Copynumber: 1.9  Consensus size: 36

         35 TAAATGGGCA

                                                 
         45 GGCCAGGCGCAGGCCCAGCCTG-CTAGCCAGCACGCG
          1 GGCCAGGCGCAGGCCCAGCCTGTC-AGCCAGCACGCG

                               *             
         81 GGCCA-GCGC-GGCCCAGCGTGTCAGCCAGCAC
          1 GGCCAGGCGCAGGCCCAGCCTGTCAGCCAGCAC

        112 ATGGCCCAGC


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  34   19  0.66
  35    5  0.17
  36    5  0.17

ACGTcount: A:0.16, C:0.42, G:0.36, T:0.06


Consensus pattern (36 bp):   
GGCCAGGCGCAGGCCCAGCCTGTCAGCCAGCACGCG

Found at i:121 original size:34 final size:35

Alignment explanation


    Indices: 51--122  Score: 85
    Period size: 34  Copynumber: 2.1  Consensus size: 35

         41 GGCAGGCCAG

                                       *   *   
         51 GCGCAGGCCCAGCCTGCTAGCCAGCACGCGGGCCA
          1 GCGCAGGCCCAGCCTGCTAGCCAGCACACGGCCCA

                         *               *      
         86 GCGC-GGCCCAGCGTG-TCAGCCAGCACATGGCCCA
          1 GCGCAGGCCCAGCCTGCT-AGCCAGCACACGGCCCA

               
        120 GCG
          1 GCG

        123 TGCTAGGCTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  33    1  0.03
  34   27  0.84
  35    4  0.12

ACGTcount: A:0.17, C:0.42, G:0.35, T:0.07


Consensus pattern (35 bp):   
GCGCAGGCCCAGCCTGCTAGCCAGCACACGGCCCA

Found at i:211 original size:21 final size:20

Alignment explanation


    Indices: 164--215  Score: 59
    Period size: 21  Copynumber: 2.5  Consensus size: 20

        154 CCAAAGTTTT

                     *        * 
        164 AAAAAAAATTAAATAAAATA
          1 AAAAAAAATAAAATAAAAGA

                                 *
        184 AATAAAAAATAAAATAGAAAGG
          1 AA-AAAAAATAAAATA-AAAGA

                      
        206 AAAAAAAATA
          1 AAAAAAAATA

        216 TGAGGAAAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    2  0.07
  21   20  0.74
  22    5  0.19

ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15


Consensus pattern (20 bp):   
AAAAAAAATAAAATAAAAGA

Found at i:257 original size:25 final size:23

Alignment explanation


    Indices: 207--253  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        197 ATAGAAAGGA

                      *            
        207 AAAAAAATATGAGGAAAAAAAAG
          1 AAAAAAATATAAGGAAAAAAAAG

                              *    
        230 AAAAAAATATAAGGAAAATAAAG
          1 AAAAAAATATAAGGAAAAAAAAG

             
        253 A
          1 A

        254 GAAATTTGGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11


Consensus pattern (23 bp):   
AAAAAAATATAAGGAAAAAAAAG
Done.