Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008909.1 Kokia drynarioides strain JFW-HI SEQ_123598, 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: 13007
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31


Found at i:1179 original size:3 final size:3

Alignment explanation


    Indices: 1171--1196  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       1161 CAATAACAAG

                                              
       1171 AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AA

       1197 CAACAACAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:3782 original size:21 final size:22

Alignment explanation


    Indices: 3742--3782  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       3732 CTTTAATGTT

                   *              
       3742 CAATTTGGTAACTGAGTTTTAC
          1 CAATTTGATAACTGAGTTTTAC

                         *      
       3764 CAATTTGAT-ACTTAGTTTT
          1 CAATTTGATAACTGAGTTTT

       3783 TTTTTTTTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    9  0.53
  22    8  0.47

ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46


Consensus pattern (22 bp):   
CAATTTGATAACTGAGTTTTAC

Found at i:4672 original size:26 final size:26

Alignment explanation


    Indices: 4643--4696  Score: 90
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       4633 AGATCCACTC

                        *             
       4643 AAGTTAAACTGATACTGCAAAACCTT
          1 AAGTTAAACTGACACTGCAAAACCTT

                            *         
       4669 AAGTTAAACTGACACTTCAAAACCTT
          1 AAGTTAAACTGACACTGCAAAACCTT

              
       4695 AA
          1 AA

       4697 ACTTCATTGC


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.44, C:0.20, G:0.09, T:0.26


Consensus pattern (26 bp):   
AAGTTAAACTGACACTGCAAAACCTT

Found at i:11373 original size:23 final size:23

Alignment explanation


    Indices: 11314--11391  Score: 79
    Period size: 23  Copynumber: 3.4  Consensus size: 23

      11304 CTTTTTACAA

                        *       *   
      11314 AAAATCTTCACTCTT-ATTGCTAG
          1 AAAATCTTCACTGTTCATT-ATAG

                    * *            
      11337 -AAATCTTTATTGTTCATTATAG
          1 AAAATCTTCACTGTTCATTATAG

                 *                 
      11359 AAAATTTTCACTGTTCATTATAG
          1 AAAATCTTCACTGTTCATTATAG

             *        
      11382 AGAATCTTCA
          1 AAAATCTTCA

      11392 ATATTTGTCT


Statistics
Matches: 44,  Mismatches: 9, Indels: 4
        0.77            0.16        0.07

Matches are distributed among these distances:
  22   14  0.32
  23   30  0.68

ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42


Consensus pattern (23 bp):   
AAAATCTTCACTGTTCATTATAG

Found at i:11936 original size:16 final size:16

Alignment explanation


    Indices: 11917--11947  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      11907 TCTCAAAACC

                   *        
      11917 CCAATTTTTGAAATCT
          1 CCAATTTGTGAAATCT

                           
      11933 CCAATTTGTGAAATC
          1 CCAATTTGTGAAATC

      11948 CCTAAAATCT


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:0.32, C:0.19, G:0.10, T:0.39


Consensus pattern (16 bp):   
CCAATTTGTGAAATCT

Found at i:12043 original size:30 final size:30

Alignment explanation


    Indices: 12002--12071  Score: 113
    Period size: 30  Copynumber: 2.3  Consensus size: 30

      11992 ATTTTTGTAT

                *                    *    
      12002 ATCCTTAATCCCTTATTCCCAAATCGTGAA
          1 ATCCCTAATCCCTTATTCCCAAATCATGAA

                                          
      12032 ATCCCTAATCCCTTATTCCCAAATCATGAA
          1 ATCCCTAATCCCTTATTCCCAAATCATGAA

                      
      12062 ATCCCATAAT
          1 ATCCC-TAAT

      12072 TTTTGGAAAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  30   33  0.89
  31    4  0.11

ACGTcount: A:0.33, C:0.31, G:0.04, T:0.31


Consensus pattern (30 bp):   
ATCCCTAATCCCTTATTCCCAAATCATGAA
Done.