Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016084.1 Corchorus olitorius cultivar O-4 contig16117, 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: 11211
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35


Found at i:6165 original size:159 final size:163

Alignment explanation


    Indices: 5962--6279  Score: 455
    Period size: 170  Copynumber: 1.9  Consensus size: 163

       5952 CAAGAGTCAA

                                       *                               *     
       5962 TGATTCACATGGAGACCTGCGCAATAAGATTTTATTCTC-A-TTTTTA-TTTTTTATTTGCAGAG
          1 TGATTCACATGGAGACCTGCGCAATAAAATTTTATTCTCTATTTTTTATTTTTTTATTTACAGAG

                                        *         *                          
       6024 ATT-CAATCTTTATTCCATGGCTAGACTGACTGGATCTTTGAACATCAATAAATGCATGTTAATT
         66 ATTCCAATCTTTATTCCATGGCTAGACTAACTGGATCTATGAACATCAATAAATGCATGTTAATT

                                             
       6088 AGAATTATTCCTTAATTTATAAATCAATCACGG
        131 AGAATTATTCCTTAATTTATAAATCAATCACGG

                                   *                                         
       6121 TGATTCACATGGAGACCTGCGCAGTAAAATTTTATTCTCATTTTTTATTTTTTTATTTTTTTATT
          1 TGATTCACATGGAGACCTGCGCAATAAAATTTTATTCTC------TA-TTTTTTATTTTTTTATT

                   *    *                                            **      
       6186 TACAGAGGTTCCGATCTTTATTCCATGGCTAGACTAACTGGATCTATGAACATCAATTTATGCAT
         59 TACAGAGATTCCAATCTTTATTCCATGGCTAGACTAACTGGATCTATGAACATCAATAAATGCAT

                      *                  
       6251 GTTAATTAGATTTATTCCTTAATTTATAA
        124 GTTAATTAGAATTATTCCTTAATTTATAA

       6280 TTCAGTTTTT


Statistics
Matches: 138,  Mismatches: 10, Indels: 11
        0.87            0.06        0.07

Matches are distributed among these distances:
 159   37  0.27
 166    1  0.01
 168    6  0.04
 169   17  0.12
 170   77  0.56

ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42


Consensus pattern (163 bp):   
TGATTCACATGGAGACCTGCGCAATAAAATTTTATTCTCTATTTTTTATTTTTTTATTTACAGAG
ATTCCAATCTTTATTCCATGGCTAGACTAACTGGATCTATGAACATCAATAAATGCATGTTAATT
AGAATTATTCCTTAATTTATAAATCAATCACGG

Found at i:6174 original size:8 final size:8

Alignment explanation


    Indices: 6161--6186  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       6151 TTTATTCTCA

                    
       6161 TTTTTTAT
          1 TTTTTTAT

                    
       6169 TTTTTTAT
          1 TTTTTTAT

                    
       6177 TTTTTTAT
          1 TTTTTTAT

              
       6185 TT
          1 TT

       6187 ACAGAGGTTC


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

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88


Consensus pattern (8 bp):   
TTTTTTAT

Found at i:6384 original size:4 final size:4

Alignment explanation


    Indices: 6377--6401  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

       6367 ATATATATAT

                                           
       6377 ATAG ATAG ATAG ATAG ATAG ATAG A
          1 ATAG ATAG ATAG ATAG ATAG ATAG A

       6402 GAGAGAGAGA


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

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24


Consensus pattern (4 bp):   
ATAG

Found at i:6406 original size:2 final size:2

Alignment explanation


    Indices: 6399--6437  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       6389 ATAGATAGAT

                                                    *                 
       6399 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

       6438 TAGGGAAATT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:9090 original size:39 final size:39

Alignment explanation


    Indices: 9037--9114  Score: 147
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       9027 CAGATCAATA

                                                   
       9037 AATAATTTCTAATCCTTTTAACTAGTTTGTGACCCGTGC
          1 AATAATTTCTAATCCTTTTAACTAGTTTGTGACCCGTGC

                                 *                 
       9076 AATAATTTCTAATCCTTTTAATTAGTTTGTGACCCGTGC
          1 AATAATTTCTAATCCTTTTAACTAGTTTGTGACCCGTGC

       9115 GATTGCATGG


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42


Consensus pattern (39 bp):   
AATAATTTCTAATCCTTTTAACTAGTTTGTGACCCGTGC

Found at i:11186 original size:2 final size:2

Alignment explanation


    Indices: 11179--11211  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      11169 CTCTTATAGA

                                                             
      11179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


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

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.