Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017368.1 Corchorus olitorius cultivar O-4 contig17401, 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: 8969
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32


Found at i:15 original size:2 final size:2

Alignment explanation


    Indices: 9--46  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

          1 GAAGTACT

                                                                    
          9 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         47 ACCTGCAGCA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1185 original size:12 final size:12

Alignment explanation


    Indices: 1168--1238  Score: 58
    Period size: 12  Copynumber: 6.2  Consensus size: 12

       1158 TGCAAGTTGC

                     *  
       1168 TGAAAATGTGGT
          1 TGAAAATGTAGT

                        
       1180 TGAAAATGTAGT
          1 TGAAAATGTAGT

                        
       1192 TGAAAA--TA-T
          1 TGAAAATGTAGT

            *  *     * *
       1201 GGATAATGTTGA
          1 TGAAAATGTAGT

              *      *  
       1213 TGTAAATGTGGT
          1 TGAAAATGTAGT

                        
       1225 TGAAAATGTAGT
          1 TGAAAATGTAGT

              
       1237 TG
          1 TG

       1239 TCGAAGCTGC


Statistics
Matches: 44,  Mismatches: 12, Indels: 6
        0.71            0.19        0.10

Matches are distributed among these distances:
   9    5  0.11
  10    2  0.05
  11    1  0.02
  12   36  0.82

ACGTcount: A:0.37, C:0.00, G:0.28, T:0.35


Consensus pattern (12 bp):   
TGAAAATGTAGT

Found at i:2242 original size:65 final size:65

Alignment explanation


    Indices: 2161--2292  Score: 264
    Period size: 65  Copynumber: 2.0  Consensus size: 65

       2151 TTTTGTAAAG

                                                                             
       2161 CTTGGAGAGCCAAGGCTATTGTCGTGAAGCAAATGCACATGCAATATACAGAAGAGTTCAAGAGA
          1 CTTGGAGAGCCAAGGCTATTGTCGTGAAGCAAATGCACATGCAATATACAGAAGAGTTCAAGAGA

                                                                             
       2226 CTTGGAGAGCCAAGGCTATTGTCGTGAAGCAAATGCACATGCAATATACAGAAGAGTTCAAGAGA
          1 CTTGGAGAGCCAAGGCTATTGTCGTGAAGCAAATGCACATGCAATATACAGAAGAGTTCAAGAGA

              
       2291 CT
          1 CT

       2293 GAGGCATTAT


Statistics
Matches: 67,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  65   67  1.00

ACGTcount: A:0.36, C:0.17, G:0.26, T:0.20


Consensus pattern (65 bp):   
CTTGGAGAGCCAAGGCTATTGTCGTGAAGCAAATGCACATGCAATATACAGAAGAGTTCAAGAGA

Found at i:4831 original size:11 final size:11

Alignment explanation


    Indices: 4817--4863  Score: 58
    Period size: 11  Copynumber: 4.2  Consensus size: 11

       4807 TTTAATATTT

                   *   
       4817 ATTGCCATGTC
          1 ATTGCCACGTC

                 *     
       4828 ATTGCTACGTC
          1 ATTGCCACGTC

                       
       4839 ATTGCCACGTC
          1 ATTGCCACGTC

              *         
       4850 ATGGCCCACGTC
          1 ATTG-CCACGTC

              
       4862 AT
          1 AT

       4864 AGCTTAACAG


Statistics
Matches: 31,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  11   22  0.71
  12    9  0.29

ACGTcount: A:0.19, C:0.32, G:0.19, T:0.30


Consensus pattern (11 bp):   
ATTGCCACGTC

Found at i:5715 original size:7 final size:7

Alignment explanation


    Indices: 5703--5727  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       5693 ACACATAACG

                   
       5703 AAAACTC
          1 AAAACTC

                   
       5710 AAAACTC
          1 AAAACTC

                   
       5717 AAAACTC
          1 AAAACTC

                
       5724 AAAA
          1 AAAA

       5728 GAGAAACAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12


Consensus pattern (7 bp):   
AAAACTC

Found at i:6424 original size:8 final size:8

Alignment explanation


    Indices: 6411--6438  Score: 56
    Period size: 8  Copynumber: 3.5  Consensus size: 8

       6401 AAATATAATA

                    
       6411 AAAGGAAT
          1 AAAGGAAT

                    
       6419 AAAGGAAT
          1 AAAGGAAT

                    
       6427 AAAGGAAT
          1 AAAGGAAT

                
       6435 AAAG
          1 AAAG

       6439 TTTATCTTCG


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

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11


Consensus pattern (8 bp):   
AAAGGAAT

Found at i:7689 original size:18 final size:19

Alignment explanation


    Indices: 7654--7690  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       7644 GAAGTTCGTG

                               
       7654 TTTGAAGACAAGTTGAAGA
          1 TTTGAAGACAAGTTGAAGA

                     *         
       7673 TTTGAAGACCA-TTGAAGA
          1 TTTGAAGACAAGTTGAAGA

       7691 ATTATTTCCA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27


Consensus pattern (19 bp):   
TTTGAAGACAAGTTGAAGA
Done.