Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002988.1 Kokia drynarioides strain JFW-HI SEQ_115475, 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, 785

Length: 1309
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35


Found at i:359 original size:23 final size:23

Alignment explanation


    Indices: 333--459  Score: 127
    Period size: 23  Copynumber: 5.5  Consensus size: 23

        323 TAACGCAAAT

                 *        *        
        333 CAGTAGGCACACGATGTGCGAAA
          1 CAGTAAGCACACGAAGTGCGAAA

                                   
        356 CAGTAAGCACACGAAGTGCGAAA
          1 CAGTAAGCACACGAAGTGCGAAA

                               *   
        379 CAGTAAGCACACGAAGTGCTAAA
          1 CAGTAAGCACACGAAGTGCGAAA

                      *          *  *
        402 CAG-AGAGCATAC-ACAGTGCTAAT
          1 CAGTA-AGCACACGA-AGTGCGAAA

                                *   
        425 CAG-AGAGCACACGAAGTGCTAAA
          1 CAGTA-AGCACACGAAGTGCGAAA

                         
        448 CAG-AGAGCACAC
          1 CAGTA-AGCACAC

        460 ACAATGCTAA


Statistics
Matches: 94,  Mismatches: 7, Indels: 6
        0.88            0.07        0.06

Matches are distributed among these distances:
  22    2  0.02
  23   91  0.97
  24    1  0.01

ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11


Consensus pattern (23 bp):   
CAGTAAGCACACGAAGTGCGAAA

Found at i:389 original size:46 final size:46

Alignment explanation


    Indices: 333--462  Score: 158
    Period size: 46  Copynumber: 2.8  Consensus size: 46

        323 TAACGCAAAT

                 *        *    *                            
        333 CAGTAGGCACACGATGTGCGAAACAGTA-AGCACACGA-AGTGCGAAA
          1 CAGTAAGCACACGAAGTGCTAAACAG-AGAGCACAC-ACAGTGCGAAA

                                            *         *  *
        379 CAGTAAGCACACGAAGTGCTAAACAGAGAGCATACACAGTGCTAAT
          1 CAGTAAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCGAAA

                                                   
        425 CAG-AGAGCACACGAAGTGCTAAACAGAGAGCACACACA
          1 CAGTA-AGCACACGAAGTGCTAAACAGAGAGCACACACA

        463 ATGCTAATCA


Statistics
Matches: 74,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  45    3  0.04
  46   71  0.96

ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11


Consensus pattern (46 bp):   
CAGTAAGCACACGAAGTGCTAAACAGAGAGCACACACAGTGCGAAA

Found at i:467 original size:23 final size:23

Alignment explanation


    Indices: 386--478  Score: 107
    Period size: 23  Copynumber: 4.0  Consensus size: 23

        376 AAACAGTAAG

                                     
        386 CACACGAAGTGCTAAACAGAGAGCA
          1 CACAC-AA-TGCTAAACAGAGAGCA

            *     *      *         
        411 TACACAGTGCTAATCAGAGAGCA
          1 CACACAATGCTAAACAGAGAGCA

                   *                
        434 CACGA-AGTGCTAAACAGAGAGCA
          1 CAC-ACAATGCTAAACAGAGAGCA

                         *        
        457 CACACAATGCTAATCAGAGAGC
          1 CACACAATGCTAAACAGAGAGC

        479 GCGCTAGTGT


Statistics
Matches: 59,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  22    1  0.02
  23   52  0.88
  24    2  0.03
  25    4  0.07

ACGTcount: A:0.42, C:0.24, G:0.23, T:0.12


Consensus pattern (23 bp):   
CACACAATGCTAAACAGAGAGCA

Found at i:468 original size:46 final size:46

Alignment explanation


    Indices: 384--478  Score: 172
    Period size: 46  Copynumber: 2.1  Consensus size: 46

        374 CGAAACAGTA

                                       *     *            
        384 AGCACACGAAGTGCTAAACAGAGAGCATACACAGTGCTAATCAGAG
          1 AGCACACGAAGTGCTAAACAGAGAGCACACACAATGCTAATCAGAG

                                                          
        430 AGCACACGAAGTGCTAAACAGAGAGCACACACAATGCTAATCAGAG
          1 AGCACACGAAGTGCTAAACAGAGAGCACACACAATGCTAATCAGAG

               
        476 AGC
          1 AGC

        479 GCGCTAGTGT


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  46   47  1.00

ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12


Consensus pattern (46 bp):   
AGCACACGAAGTGCTAAACAGAGAGCACACACAATGCTAATCAGAG
Done.