Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004073.1 Kokia drynarioides strain JFW-HI SEQ_117239, 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: 8789
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31


Found at i:2362 original size:36 final size:36

Alignment explanation


    Indices: 2280--2362  Score: 98
    Period size: 36  Copynumber: 2.3  Consensus size: 36

       2270 CAAAATATAA

                 *                              
       2280 TCACTATCACATGGAATGAAAAACATACCCACATAT
          1 TCACTTTCACATGGAATGAAAAACATACCCACATAT

             *             *     *                
       2316 TTA-TTGTCACATGGCATGAATAACATA-CCATCATAT
          1 TCACTT-TCACATGGAATGAAAAACATACCCA-CATAT

                       
       2352 TCACTTTCACA
          1 TCACTTTCACA

       2363 ACAGTCATCA


Statistics
Matches: 39,  Mismatches: 5, Indels: 6
        0.78            0.10        0.12

Matches are distributed among these distances:
  35    4  0.10
  36   33  0.85
  37    2  0.05

ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29


Consensus pattern (36 bp):   
TCACTTTCACATGGAATGAAAAACATACCCACATAT

Found at i:7380 original size:40 final size:40

Alignment explanation


    Indices: 7254--7380  Score: 103
    Period size: 40  Copynumber: 3.1  Consensus size: 40

       7244 CTCGTAAAAA

                                                    
       7254 ATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGG
          1 ATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGG

                      *    *****   * *     *  *   ****
       7294 ATCTGAATAAACAAACCTCGGATAAAGAAACAG-CGTAAAAA
          1 ATCTG-AT-ATCAAAGAGAAGATCATGAAACTGTGGTACCGG

                                                    
       7335 ATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGG
          1 ATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGG

                  
       7375 ATCTGA
          1 ATCTGA

       7381 ATAAACAAAC


Statistics
Matches: 56,  Mismatches: 28, Indels: 6
        0.62            0.31        0.07

Matches are distributed among these distances:
  39   15  0.27
  40   16  0.29
  41   10  0.18
  42   15  0.27

ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20


Consensus pattern (40 bp):   
ATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGG

Found at i:7381 original size:81 final size:81

Alignment explanation


    Indices: 7246--7403  Score: 316
    Period size: 81  Copynumber: 2.0  Consensus size: 81

       7236 TTCAAAATCT

                                                                             
       7246 CGTAAAAAATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGGATCTGAATAAACAAACC
          1 CGTAAAAAATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGGATCTGAATAAACAAACC

                            
       7311 TCGGATAAAGAAACAG
         66 TCGGATAAAGAAACAG

                                                                             
       7327 CGTAAAAAATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGGATCTGAATAAACAAACC
          1 CGTAAAAAATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGGATCTGAATAAACAAACC

                        
       7392 TCGGATAAAGAA
         66 TCGGATAAAGAA

       7404 TCATAGAAGA


Statistics
Matches: 77,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  81   77  1.00

ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19


Consensus pattern (81 bp):   
CGTAAAAAATCTGATATCAAAGAGAAGATCATGAAACTGTGGTACCGGATCTGAATAAACAAACC
TCGGATAAAGAAACAG
Done.