Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007544.1 Kokia drynarioides strain JFW-HI SEQ_122172, 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: 18143
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34


Found at i:1365 original size:22 final size:21

Alignment explanation


    Indices: 1338--1389  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 21

       1328 CAATACACCA

                    * *          
       1338 GGTTGTGGTTTAACTACCAAT
          1 GGTTGTGGATAAACTACCAAT

                   *          *   
       1359 GGTTTGTAGATAAACTACTAAT
          1 GG-TTGTGGATAAACTACCAAT

                     
       1381 GGTTGTGGA
          1 GGTTGTGGA

       1390 CACGCAACAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 2
        0.78            0.16        0.06

Matches are distributed among these distances:
  21    8  0.32
  22   17  0.68

ACGTcount: A:0.27, C:0.10, G:0.27, T:0.37


Consensus pattern (21 bp):   
GGTTGTGGATAAACTACCAAT

Found at i:2747 original size:43 final size:42

Alignment explanation


    Indices: 2690--2923  Score: 253
    Period size: 41  Copynumber: 5.5  Consensus size: 42

       2680 GAGAAACTTG

                                         *                
       2690 ATATATAAATGGAAGACTCATGTCTCAGGTTGAGCAA-GAGAATTT
          1 ATAT-TAAA-GGAAGACTCATGTCTCAGGATGAG-AATGAG-ATTT

                 *                 **  *    *          
       2735 ATATTGAAGGAAGACTCATGTCTTGGGTTGAGCATGAGAATTT
          1 ATATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAG-ATTT

                    *           *                      
       2778 ATATTAAAAGAAGACTCATGACTC-GAGATGAGAATGAGATTT
          1 ATATTAAAGGAAGACTCATGTCTCAG-GATGAGAATGAGATTT

                                    *                 
       2820 -TATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGA-TT
          1 ATATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTT

                           * *       *             *  
       2860 ATATTAAAGGAAGACCCCTGTCTCAAGATGAGAATGAG-GTT
          1 ATATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTT

                    *              
       2901 ATATTAAAAGAAGACTCATGTCT
          1 ATATTAAAGGAAGACTCATGTCT

       2924 TGAAATGAGT


Statistics
Matches: 165,  Mismatches: 19, Indels: 14
        0.83            0.10        0.07

Matches are distributed among these distances:
  40    2  0.01
  41   89  0.54
  42    7  0.04
  43   60  0.36
  44    3  0.02
  45    4  0.02

ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28


Consensus pattern (42 bp):   
ATATTAAAGGAAGACTCATGTCTCAGGATGAGAATGAGATTT

Found at i:3577 original size:21 final size:21

Alignment explanation


    Indices: 3525--3577  Score: 79
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       3515 CTGTGCATAT

                    *           *
       3525 TTGTATCGGTAGTTAGGATGT
          1 TTGTATCGTTAGTTAGGATGC

                  *              
       3546 TTGTATTGTTAGTTAGGATGC
          1 TTGTATCGTTAGTTAGGATGC

                       
       3567 TTGTATCGTTA
          1 TTGTATCGTTA

       3578 CAAGTTGTAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.19, C:0.06, G:0.28, T:0.47


Consensus pattern (21 bp):   
TTGTATCGTTAGTTAGGATGC

Found at i:7091 original size:26 final size:25

Alignment explanation


    Indices: 7024--7101  Score: 70
    Period size: 26  Copynumber: 3.0  Consensus size: 25

       7014 ATTGATCGAC

                                 *    
       7024 TCGTTGACTTTGACTATTGACTTTGA
          1 TCGTTGACTTTGACT-TTGACGTTGA

                *        *              
       7050 --GTAGACATGTTAACTTTGACCGTTGA
          1 TCGTTGAC-T-TTGACTTTGA-CGTTGA

                                      
       7076 TCGTTGACTTTGACTTTGATCGTTGA
          1 TCGTTGACTTTGACTTTGA-CGTTGA

       7102 CTCTTTTTTA


Statistics
Matches: 41,  Mismatches: 6, Indels: 10
        0.72            0.11        0.18

Matches are distributed among these distances:
  24    5  0.12
  25    5  0.12
  26   25  0.61
  27    1  0.02
  28    5  0.12

ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42


Consensus pattern (25 bp):   
TCGTTGACTTTGACTTTGACGTTGA

Found at i:7096 original size:19 final size:20

Alignment explanation


    Indices: 7062--7103  Score: 68
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       7052 AGACATGTTA

                                
       7062 ACTTTGACCGTTGATCGTTG
          1 ACTTTGACCGTTGATCGTTG

                     *          
       7082 ACTTTGA-CTTTGATCGTTG
          1 ACTTTGACCGTTGATCGTTG

               
       7101 ACT
          1 ACT

       7104 CTTTTTTACC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  19   14  0.67
  20    7  0.33

ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43


Consensus pattern (20 bp):   
ACTTTGACCGTTGATCGTTG

Found at i:12984 original size:17 final size:17

Alignment explanation


    Indices: 12954--12986  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      12944 TAAAACCAAT

                             
      12954 TTGATATGACCGACCCA
          1 TTGATATGACCGACCCA

                             
      12971 TTGAT-TGACTCGACCC
          1 TTGATATGAC-CGACCC

      12987 GACCCGTTGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27


Consensus pattern (17 bp):   
TTGATATGACCGACCCA
Done.