Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013734.1 Kokia drynarioides strain JFW-HI SEQ_128762, 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, 850

Length: 1418
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.18

Warning! 314 characters in sequence are not A, C, G, or T


Found at i:1345 original size:17 final size:17

Alignment explanation


    Indices: 1317--1389  Score: 94
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       1307 TTGGAAATTG

                            *
       1317 AATTTA-TTTAAATTTT
          1 AATTTATTTTAAATTTA

             *               
       1333 ATTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

                     *       
       1350 AATTTATTTGAAATTTA
          1 AATTTATTTTAAATTTA

                    *    *   
       1367 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
       1384 AATTTA
          1 AATTTA

       1390 AAAAGTCCAA


Statistics
Matches: 49,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  16    5  0.10
  17   44  0.90

ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:1348 original size:23 final size:23

Alignment explanation


    Indices: 1323--1372  Score: 66
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1313 ATTGAATTTA

                           * *      
       1323 TTTAAATTTTATTT-TATTTTAAA
          1 TTTAAA-TTTATTTGAAATTTAAA

                                   
       1346 TTTAAATTTATTTGAAATTTAAA
          1 TTTAAATTTATTTGAAATTTAAA

                
       1369 TTTA
          1 TTTA

       1373 TTATAAAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  22    7  0.29
  23   17  0.71

ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60


Consensus pattern (23 bp):   
TTTAAATTTATTTGAAATTTAAA

Found at i:1365 original size:7 final size:6

Alignment explanation


    Indices: 1322--1391  Score: 51
    Period size: 6  Copynumber: 12.2  Consensus size: 6

       1312 AATTGAATTT

                        *     *  *                                  
       1322 ATTTAA ATTT-T ATTTTA TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA

                            *             
       1368 ATTT-- ATTATAA AATTAA ATTTAA A
          1 ATTTAA ATT-TAA ATTTAA ATTTAA A

       1392 AAGTCCAAAA


Statistics
Matches: 50,  Mismatches: 7, Indels: 14
        0.70            0.10        0.20

Matches are distributed among these distances:
   4    7  0.14
   5    5  0.10
   6   32  0.64
   7    6  0.12

ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54


Consensus pattern (6 bp):   
ATTTAA

Found at i:1373 original size:34 final size:33

Alignment explanation


    Indices: 1311--1389  Score: 104
    Period size: 34  Copynumber: 2.4  Consensus size: 33

       1301 GACTTATTGG

                 *               * *      *  
       1311 AAATTGAATTTATTTAAATTTTATTTTATTTTA
          1 AAATTAAATTTATTTAAATTTAAATTTATTATA

              *                               
       1344 AATTTAAATTTATTTGAAATTTAAATTTATTATA
          1 AAATTAAATTTATTT-AAATTTAAATTTATTATA

                        
       1378 AAATTAAATTTA
          1 AAATTAAATTTA

       1390 AAAAGTCCAA


Statistics
Matches: 39,  Mismatches: 6, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  33   13  0.33
  34   26  0.67

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54


Consensus pattern (33 bp):   
AAATTAAATTTATTTAAATTTAAATTTATTATA
Done.