Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017231.1 Corchorus olitorius cultivar O-4 contig17264, 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: 7039
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31


Found at i:2177 original size:17 final size:17

Alignment explanation


    Indices: 2155--2190  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2145 TGATTTGTAA

                             
       2155 AGTTTGTTACACCAGAT
          1 AGTTTGTTACACCAGAT

                     *  *    
       2172 AGTTTGTTATACTAGAT
          1 AGTTTGTTACACCAGAT

              
       2189 AG
          1 AG

       2191 CTCTTTGTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39


Consensus pattern (17 bp):   
AGTTTGTTACACCAGAT

Found at i:3009 original size:22 final size:22

Alignment explanation


    Indices: 2978--3019  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2968 GACAAAGCTG

                 *    *    *      
       2978 TAACCTGAATTACCCGAGAAGT
          1 TAACCCGAATGACCCAAGAAGT

                                
       3000 TAACCCGAATGACCCAAGAA
          1 TAACCCGAATGACCCAAGAA

       3020 TATTATAAAC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17


Consensus pattern (22 bp):   
TAACCCGAATGACCCAAGAAGT

Found at i:4690 original size:13 final size:13

Alignment explanation


    Indices: 4651--4696  Score: 60
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       4641 TCATGCACCC

                          
       4651 AAAACAATTTAATT
          1 AAAACAATTTAA-T

                         
       4665 AAAAC-ATTT-AT
          1 AAAACAATTTAAT

                *        
       4676 AAAATAATTTAAT
          1 AAAACAATTTAAT

                    
       4689 AAAACAAT
          1 AAAACAAT

       4697 AATAAAATAG


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  11    5  0.18
  12    5  0.18
  13   13  0.46
  14    5  0.18

ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33


Consensus pattern (13 bp):   
AAAACAATTTAAT

Found at i:4701 original size:24 final size:25

Alignment explanation


    Indices: 4651--4705  Score: 76
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       4641 TCATGCACCC

                *               * *  
       4651 AAAACAATTTAATTAAAACATTTAT
          1 AAAATAATTTAATTAAAACAATAAT

                                     
       4676 AAAATAATTTAA-TAAAACAATAAT
          1 AAAATAATTTAATTAAAACAATAAT

                  
       4700 AAAATA
          1 AAAATA

       4706 GTTCCTCAAC


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  24   16  0.59
  25   11  0.41

ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31


Consensus pattern (25 bp):   
AAAATAATTTAATTAAAACAATAAT
Done.