Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020332.1 Corchorus olitorius cultivar O-4 contig20365, 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: 40488
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:3756 original size:38 final size:38

Alignment explanation


    Indices: 3714--3787  Score: 121
    Period size: 38  Copynumber: 1.9  Consensus size: 38

       3704 TAAATTGTTT

                    *                             
       3714 AATTTCATGGATTTTTGTTTCAAGTGTTTTACTTTTCC
          1 AATTTCATAGATTTTTGTTTCAAGTGTTTTACTTTTCC

                                *          *    
       3752 AATTTCATAGATTTTTGTTTTAAGTGTTTTAGTTTT
          1 AATTTCATAGATTTTTGTTTCAAGTGTTTTACTTTT

       3788 TCATGTAAAG


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  38   33  1.00

ACGTcount: A:0.20, C:0.08, G:0.14, T:0.58


Consensus pattern (38 bp):   
AATTTCATAGATTTTTGTTTCAAGTGTTTTACTTTTCC

Found at i:6040 original size:22 final size:22

Alignment explanation


    Indices: 6015--6079  Score: 54
    Period size: 22  Copynumber: 3.2  Consensus size: 22

       6005 CACAGAGTTG

                                  
       6015 GTCAATACTTCGAACTGAATGA
          1 GTCAATACTTCGAACTGAATGA

                      *            
       6037 GTCAA-A-TTTG---TG-ATCG-
          1 GTCAATACTTCGAACTGAAT-GA

                                  
       6053 GTCAATACTTCGAACTGAATGA
          1 GTCAATACTTCGAACTGAATGA

            *    
       6075 ATCAA
          1 GTCAA

       6080 ATCTGTGATC


Statistics
Matches: 32,  Mismatches: 3, Indels: 16
        0.63            0.06        0.31

Matches are distributed among these distances:
  16    7  0.22
  17    4  0.12
  18    3  0.09
  20    3  0.09
  21    4  0.12
  22   11  0.34

ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29


Consensus pattern (22 bp):   
GTCAATACTTCGAACTGAATGA

Found at i:6065 original size:38 final size:38

Alignment explanation


    Indices: 6014--6089  Score: 134
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       6004 ACACAGAGTT

                                   *      *       
       6014 GGTCAATACTTCGAACTGAATGAGTCAAATTTGTGATC
          1 GGTCAATACTTCGAACTGAATGAATCAAATCTGTGATC

                                                  
       6052 GGTCAATACTTCGAACTGAATGAATCAAATCTGTGATC
          1 GGTCAATACTTCGAACTGAATGAATCAAATCTGTGATC

       6090 TGTGATCCAC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   36  1.00

ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Consensus pattern (38 bp):   
GGTCAATACTTCGAACTGAATGAATCAAATCTGTGATC

Found at i:22567 original size:20 final size:20

Alignment explanation


    Indices: 22542--22581  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      22532 AACTCTCACG

                                
      22542 GAATATGAGTTTGTTTGTAA
          1 GAATATGAGTTTGTTTGTAA

                                
      22562 GAATATGAGTTTGTTTGTAA
          1 GAATATGAGTTTGTTTGTAA

      22582 TTTGTTTGTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45


Consensus pattern (20 bp):   
GAATATGAGTTTGTTTGTAA

Found at i:26949 original size:14 final size:14

Alignment explanation


    Indices: 26930--26960  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      26920 CTCCAAAAGG

                       *  
      26930 AAATATATATACAT
          1 AAATATATATAAAT

                          
      26944 AAATATATATAAAT
          1 AAATATATATAAAT

               
      26958 AAA
          1 AAA

      26961 AAAAAAAACA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32


Consensus pattern (14 bp):   
AAATATATATAAAT

Found at i:30688 original size:12 final size:11

Alignment explanation


    Indices: 30671--30700  Score: 51
    Period size: 12  Copynumber: 2.6  Consensus size: 11

      30661 ACTTTTAGCT

                       
      30671 TTTTTTTTTTA
          1 TTTTTTTTTTA

                        
      30682 TTATTTTTTTTA
          1 TT-TTTTTTTTA

                   
      30694 TTTTTTT
          1 TTTTTTT

      30701 AATTAAAATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  11    7  0.39
  12   11  0.61

ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90


Consensus pattern (11 bp):   
TTTTTTTTTTA

Found at i:32375 original size:22 final size:22

Alignment explanation


    Indices: 32336--32380  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      32326 GAAACTCAGG

                        **         
      32336 AGAAAGGAGAGATTGAAAGGAAA
          1 AGAAAGGAGAGAAAGAAA-GAAA

                                  
      32359 AGAAA-GAGAGAAAGAAAGAAA
          1 AGAAAGGAGAGAAAGAAAGAAA

             
      32380 A
          1 A

      32381 TGTGTCGAGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21    5  0.25
  22   10  0.50
  23    5  0.25

ACGTcount: A:0.64, C:0.00, G:0.31, T:0.04


Consensus pattern (22 bp):   
AGAAAGGAGAGAAAGAAAGAAA
Done.