Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014363.1 Corchorus olitorius cultivar O-4 contig14396, 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: 22938
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:473 original size:13 final size:13

Alignment explanation


    Indices: 457--481  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        447 AAGTCTTTTC

                         
        457 TCTTCTTCTTCTT
          1 TCTTCTTCTTCTT

                        
        470 TCTTCTTCTTCT
          1 TCTTCTTCTTCT

        482 CTAGTTTCTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (13 bp):   
TCTTCTTCTTCTT

Found at i:497 original size:18 final size:18

Alignment explanation


    Indices: 453--499  Score: 51
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        443 CAGTAAGTCT

                         *     
        453 TTTCTCTTCTTCTTCTTTC
          1 TTTCTCTTC-TCTACTTTC

                          *    
        472 -TTCTTCTTCTCTAGTTTC
          1 TTTC-TCTTCTCTACTTTC

                      
        490 TTTCTCTTCT
          1 TTTCTCTTCT

        500 TCCTCGATAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  18   16  0.67
  19    8  0.33

ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66


Consensus pattern (18 bp):   
TTTCTCTTCTCTACTTTC

Found at i:10051 original size:31 final size:30

Alignment explanation


    Indices: 10016--10079  Score: 101
    Period size: 31  Copynumber: 2.1  Consensus size: 30

      10006 AAGTCCGTGA

                                *        * 
      10016 ACTATATGAAAATATTCAACTTAGTTCCTGT
          1 ACTATATGAAAATATTCAACATAG-TCCTCT

                                          
      10047 ACTATATGAAAATATTCAACATAGTCCTCT
          1 ACTATATGAAAATATTCAACATAGTCCTCT

               
      10077 ACT
          1 ACT

      10080 CCAATTTGGG


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  30    8  0.26
  31   23  0.74

ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36


Consensus pattern (30 bp):   
ACTATATGAAAATATTCAACATAGTCCTCT

Found at i:12872 original size:13 final size:13

Alignment explanation


    Indices: 12850--12889  Score: 53
    Period size: 13  Copynumber: 3.1  Consensus size: 13

      12840 CAGAGAATAT

                         
      12850 TATCAACAGAAGA
          1 TATCAACAGAAGA

                 *       
      12863 TATCATCAGAAGA
          1 TATCAACAGAAGA

             *     *     
      12876 TTTCAACTGAAGA
          1 TATCAACAGAAGA

             
      12889 T
          1 T

      12890 TATTTCAGCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  13   23  1.00

ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25


Consensus pattern (13 bp):   
TATCAACAGAAGA

Found at i:13117 original size:15 final size:16

Alignment explanation


    Indices: 13097--13126  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      13087 GATCTTCCAA

                            
      13097 TCTTAAGTT-TTTATT
          1 TCTTAAGTTGTTTATT

                           
      13112 TCTTAAGTTGTTTAT
          1 TCTTAAGTTGTTTAT

      13127 ATTGTTATCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63


Consensus pattern (16 bp):   
TCTTAAGTTGTTTATT

Found at i:13220 original size:41 final size:41

Alignment explanation


    Indices: 13163--13283  Score: 133
    Period size: 41  Copynumber: 3.0  Consensus size: 41

      13153 TATAATATTG

                                                     *
      13163 AAAATTACCAT-TGACACCAAAAGTTGTCACTTTGGTAAATT
          1 AAAATTACC-TCTGACACCAAAAGTTGTCACTTTGGTAAATA

                              * *                      
      13204 AAAATTA-CTGCTGACACTAGAAGTTGTCA-TCTTGGTAAATA
          1 AAAATTACCT-CTGACACCAAAAGTTGTCACT-TTGGTAAATA

                      *                       *     
      13245 AAAATTACCTTTGACACCAGAAA-TTGTCACTTTAGTAAA
          1 AAAATTACCTCTGACACCA-AAAGTTGTCACTTTGGTAAA

      13284 ATACTTTTGA


Statistics
Matches: 67,  Mismatches: 7, Indels: 12
        0.78            0.08        0.14

Matches are distributed among these distances:
  39    1  0.01
  40    2  0.03
  41   59  0.88
  42    5  0.07

ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31


Consensus pattern (41 bp):   
AAAATTACCTCTGACACCAAAAGTTGTCACTTTGGTAAATA

Found at i:13600 original size:28 final size:28

Alignment explanation


    Indices: 13560--13615  Score: 112
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      13550 TATTGATTAG

                                        
      13560 ACACCTGAAGTTGTCATACTAGACCCAT
          1 ACACCTGAAGTTGTCATACTAGACCCAT

                                        
      13588 ACACCTGAAGTTGTCATACTAGACCCAT
          1 ACACCTGAAGTTGTCATACTAGACCCAT

      13616 GTGCTATCAA


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

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25


Consensus pattern (28 bp):   
ACACCTGAAGTTGTCATACTAGACCCAT
Done.