Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014702.1 Corchorus olitorius cultivar O-4 contig14735, 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: 75630
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:12396 original size:23 final size:23

Alignment explanation


    Indices: 12366--12419  Score: 108
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      12356 AATACTGTAT

                                   
      12366 CAAAAACTCAGAGAGTTGAGCCA
          1 CAAAAACTCAGAGAGTTGAGCCA

                                   
      12389 CAAAAACTCAGAGAGTTGAGCCA
          1 CAAAAACTCAGAGAGTTGAGCCA

                    
      12412 CAAAAACT
          1 CAAAAACT

      12420 TGATTAAACT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   31  1.00

ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13


Consensus pattern (23 bp):   
CAAAAACTCAGAGAGTTGAGCCA

Found at i:20829 original size:204 final size:203

Alignment explanation


    Indices: 20425--20842  Score: 694
    Period size: 204  Copynumber: 2.1  Consensus size: 203

      20415 TTAAATACAT

                                                           *                 
      20425 ATATAATTTTTTGGGTAATTATTTGATACACCGGCAGTGTAAATTTTGGACTCCACAAGCGGGTT
          1 ATAT-ATTTTTTGGGTAATTATTTGATACACCGGCAGTGTAAATTTTAGACTCCACAAGCGGGTT

                                                                    *  *     
      20490 GTGGAGTTGACACATGTCCATTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCTCTAAA
         65 GTGGAGTTGACACATGTCCATTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAA

                 *                                              *  *         
      20555 GGACACATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGTCGGTATATTGTA
        130 GGACAAATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGATATATTGTA

                     
      20620 TAATTTGCC
        195 TAATTTGCC

                                              *                   *          
      20629 ATATATTTTTTGGGTAATTATTTGATACACCGGCGGTGTAAATTTTAGACTCCATAAGCGGGTTG
          1 ATATATTTTTTGGGTAATTATTTGATACACCGGCAGTGTAAATTTTAGACTCCACAAGCGGGTTG

                                                                           * 
      20694 TGGAGTTGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAGA
         66 TGGAGTTGACACATGTCCATTTTTT-AATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAA

                             *    *                                  *       
      20759 GGACAAATGTCACCCTTTAGGATCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGATGTATTGTA
        130 GGACAAATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGATATATTGTA

                    *
      20824 TAATTTGCT
        195 TAATTTGCC

                       
      20833 ATAT-TTTTTT
          1 ATATATTTTTT

      20843 ATCATGAGAA


Statistics
Matches: 200,  Mismatches: 13, Indels: 3
        0.93            0.06        0.01

Matches are distributed among these distances:
 203   89  0.44
 204  111  0.56

ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38


Consensus pattern (203 bp):   
ATATATTTTTTGGGTAATTATTTGATACACCGGCAGTGTAAATTTTAGACTCCACAAGCGGGTTG
TGGAGTTGACACATGTCCATTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATCCCTAAAG
GACAAATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGATATATTGTAT
AATTTGCC

Found at i:41064 original size:1 final size:1

Alignment explanation


    Indices: 41058--41086  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

      41048 ATTTGGAGAG

                                         
      41058 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      41087 ATAACAATTT


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:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:52281 original size:16 final size:16

Alignment explanation


    Indices: 52257--52290  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      52247 AATTCGGTGA

                         *  
      52257 AATTAAGGGGGAATTG
          1 AATTAAGGGGGAACTG

                *           
      52273 AATTGAGGGGGAACTG
          1 AATTAAGGGGGAACTG

              
      52289 AA
          1 AA

      52291 AATAGTAGGA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.38, C:0.03, G:0.38, T:0.21


Consensus pattern (16 bp):   
AATTAAGGGGGAACTG

Found at i:52557 original size:19 final size:19

Alignment explanation


    Indices: 52533--52572  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      52523 TAACCACCAT

                               
      52533 CTTCCTTTGCTCATTGAAA
          1 CTTCCTTTGCTCATTGAAA

                               
      52552 CTTCCTTTGCTCATTGAAA
          1 CTTCCTTTGCTCATTGAAA

              
      52571 CT
          1 CT

      52573 GATCTACGAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42


Consensus pattern (19 bp):   
CTTCCTTTGCTCATTGAAA

Found at i:71176 original size:7 final size:7

Alignment explanation


    Indices: 71164--71191  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      71154 AGATTGAATC

                   
      71164 AAGTGGT
          1 AAGTGGT

                   
      71171 AAGTGGT
          1 AAGTGGT

                   
      71178 AAGTGGT
          1 AAGTGGT

                   
      71185 AAGTGGT
          1 AAGTGGT

      71192 TTGTTTCAGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29


Consensus pattern (7 bp):   
AAGTGGT

Done.