Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002216.1 Kokia drynarioides strain JFW-HI SEQ_114207, 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: 1753
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:1365 original size:23 final size:23

Alignment explanation


    Indices: 1332--1434  Score: 111
    Period size: 23  Copynumber: 4.5  Consensus size: 23

       1322 GCTGGGGAAA

                 *          *      
       1332 CAGTAAGCACACACAGTGC-AAT
          1 CAGTAGGCACACACAGCGCAAAT

                   *    *    *      
       1354 CCAGTAGACACAAACAGTGC-AAT
          1 -CAGTAGGCACACACAGCGCAAAT

                    *    *         
       1377 CAGTAGGCGCACATAGCGCAAAT
          1 CAGTAGGCACACACAGCGCAAAT

                         *         
       1400 CAGTAGGCACACATAGCGCAAAT
          1 CAGTAGGCACACACAGCGCAAAT

                        
       1423 CAGTAGGCACAC
          1 CAGTAGGCACAC

       1435 GAAGTGCGAA


Statistics
Matches: 70,  Mismatches: 9, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
  22   14  0.20
  23   56  0.80

ACGTcount: A:0.39, C:0.27, G:0.21, T:0.13


Consensus pattern (23 bp):   
CAGTAGGCACACACAGCGCAAAT

Found at i:1449 original size:23 final size:23

Alignment explanation


    Indices: 1400--1473  Score: 98
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       1390 TAGCGCAAAT

                             *      
       1400 CAGTAGGCACAC-ATAGCGC-AAA
          1 CAGTAGGCACACGA-AGTGCGAAA

                                    
       1422 TCAGTAGGCACACGAAGTGCGAAA
          1 -CAGTAGGCACACGAAGTGCGAAA

                 *                 
       1446 CAGTAAGCACACGAAGTGCGAAA
          1 CAGTAGGCACACGAAGTGCGAAA

                 
       1469 CAGTA
          1 CAGTA

       1474 AGCGTGCTAG


Statistics
Matches: 47,  Mismatches: 2, Indels: 4
        0.89            0.04        0.08

Matches are distributed among these distances:
  23   43  0.91
  24    4  0.09

ACGTcount: A:0.41, C:0.23, G:0.26, T:0.11


Consensus pattern (23 bp):   
CAGTAGGCACACGAAGTGCGAAA

Found at i:1474 original size:23 final size:23

Alignment explanation


    Indices: 1423--1476  Score: 99
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1413 TAGCGCAAAT

                 *                 
       1423 CAGTAGGCACACGAAGTGCGAAA
          1 CAGTAAGCACACGAAGTGCGAAA

                                   
       1446 CAGTAAGCACACGAAGTGCGAAA
          1 CAGTAAGCACACGAAGTGCGAAA

                    
       1469 CAGTAAGC
          1 CAGTAAGC

       1477 GTGCTAGCAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   30  1.00

ACGTcount: A:0.41, C:0.22, G:0.28, T:0.09


Consensus pattern (23 bp):   
CAGTAAGCACACGAAGTGCGAAA
Done.