Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012258.1 Kokia drynarioides strain JFW-HI SEQ_127259, 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: 14068
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36

Warning! 25 characters in sequence are not A, C, G, or T


Found at i:1608 original size:18 final size:18

Alignment explanation


    Indices: 1569--1608  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1559 TTTAGCAATG

                             *
       1569 TTTTTATCTCAAAAGTAT
          1 TTTTTATCTCAAAAGTAC

                   *        * 
       1587 TTTTTATGTCAAAAGTGC
          1 TTTTTATCTCAAAAGTAC

                
       1605 TTTT
          1 TTTT

       1609 CAGAAGTAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53


Consensus pattern (18 bp):   
TTTTTATCTCAAAAGTAC

Found at i:4442 original size:13 final size:13

Alignment explanation


    Indices: 4410--4444  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       4400 CTAATTGCTC

                  *    * 
       4410 AAGGTAGGAAATT
          1 AAGGTATGAAAAT

                         
       4423 AAGGTATGAAAAT
          1 AAGGTATGAAAAT

                     
       4436 AAGGTATGA
          1 AAGGTATGA

       4445 GATTTTCTAC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.49, C:0.00, G:0.29, T:0.23


Consensus pattern (13 bp):   
AAGGTATGAAAAT

Found at i:12029 original size:20 final size:20

Alignment explanation


    Indices: 12004--12050  Score: 60
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      11994 AATAAAAAAT

                                 
      12004 AAATTAATACATTTA-TTTCA
          1 AAATTAATACATTTACTTT-A

                     **         
      12024 AAATTAATATGTTTACTTTA
          1 AAATTAATACATTTACTTTA

                   
      12044 AAATTAA
          1 AAATTAA

      12051 ATTAAAATAT


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

Matches are distributed among these distances:
  20   21  0.88
  21    3  0.12

ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45


Consensus pattern (20 bp):   
AAATTAATACATTTACTTTA

Found at i:12441 original size:16 final size:18

Alignment explanation


    Indices: 12404--12441  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      12394 TTAAGATATT

                              
      12404 TTTTTAGTTAAATAATAA
          1 TTTTTAGTTAAATAATAA

                      *       
      12422 TTTTT-GTTATATAA-AA
          1 TTTTTAGTTAAATAATAA

                
      12438 TTTT
          1 TTTT

      12442 ATTTATATGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    6  0.32
  17    8  0.42
  18    5  0.26

ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58


Consensus pattern (18 bp):   
TTTTTAGTTAAATAATAA

Found at i:13880 original size:4 final size:4

Alignment explanation


    Indices: 13850--13902  Score: 56
    Period size: 4  Copynumber: 13.2  Consensus size: 4

      13840 AACACATTAC

                 *     *                                                 
      13850 CTTT TTTT CCTT C-TT CTTT -TCTT CTTT CTTT CTTT CTTT CATTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT C-TTT CTTT

                  
      13898 CTTT C
          1 CTTT C

      13903 CCGTTTATTT


Statistics
Matches: 42,  Mismatches: 3, Indels: 8
        0.79            0.06        0.15

Matches are distributed among these distances:
   3    4  0.10
   4   33  0.79
   5    5  0.12

ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72


Consensus pattern (4 bp):   
CTTT

Done.