Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008353.1 Kokia drynarioides strain JFW-HI SEQ_123020, 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: 11630
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34


Found at i:477 original size:16 final size:16

Alignment explanation


    Indices: 458--488  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        448 CATGTTTACT

                  *         
        458 CATTTATTTTATAATC
          1 CATTTAATTTATAATC

                           
        474 CATTTAATTTATAAT
          1 CATTTAATTTATAAT

        489 ATTCATAACT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55


Consensus pattern (16 bp):   
CATTTAATTTATAATC

Found at i:1121 original size:108 final size:109

Alignment explanation


    Indices: 926--1137  Score: 336
    Period size: 108  Copynumber: 1.9  Consensus size: 109

        916 AAATCAAGGC

                  *               *                                          
        926 AATGTTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCTAACTCGTTGGGTATGGTTTTACTTT
          1 AATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAAC-CGTTGGGTATGGTTTTACTTT

                             *                           
        991 GAACCTAAATAATTGAATATCCTATTTAAAAATCGATAAATATTT
         65 GAACCTAAATAATTGAACATCCTATTTAAAAATCGATAAATATTT

                                                *                      *     
       1036 AATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGTCCTAA-CGTTGGGTATGGTTTTTCTTTG
          1 AATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACCGTTGGGTATGGTTTTACTTTG

                   *                  *     *     
       1100 AACCTAAGTAATTGAACATCCTATTTTAAAATTGATAA
         66 AACCTAAATAATTGAACATCCTATTTAAAAATCGATAA

       1138 CAGTTCTTTA


Statistics
Matches: 94,  Mismatches: 8, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
 108   55  0.59
 110   39  0.41

ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41


Consensus pattern (109 bp):   
AATGTTATTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACCGTTGGGTATGGTTTTACTTTG
AACCTAAATAATTGAACATCCTATTTAAAAATCGATAAATATTT

Found at i:4810 original size:20 final size:20

Alignment explanation


    Indices: 4785--4822  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4775 ATGTCAACTT

                      *         
       4785 CAAGATTTGGTTTCTTGGAC
          1 CAAGATTTGGATTCTTGGAC

                              
       4805 CAAGATTTGGATTCTTGG
          1 CAAGATTTGGATTCTTGG

       4823 TTTTCTTGAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.21, C:0.13, G:0.26, T:0.39


Consensus pattern (20 bp):   
CAAGATTTGGATTCTTGGAC

Found at i:8141 original size:17 final size:18

Alignment explanation


    Indices: 8119--8152  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       8109 AATAACATTT

                              
       8119 TATAAA-TAACTAAAATA
          1 TATAAACTAACTAAAATA

                    *        
       8136 TATAAACTTACTAAAAT
          1 TATAAACTAACTAAAAT

       8153 TACATCTAGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32


Consensus pattern (18 bp):   
TATAAACTAACTAAAATA
Done.