Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012660.1 Kokia drynarioides strain JFW-HI SEQ_127671, 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: 6714
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36


Found at i:1889 original size:50 final size:50

Alignment explanation


    Indices: 1814--1913  Score: 200
    Period size: 50  Copynumber: 2.0  Consensus size: 50

       1804 TTATGATAGA

                                                              
       1814 GCCAATTGTCAACGTGTCATAATATTCTATTGATTCTGAAGCTGAAGTTT
          1 GCCAATTGTCAACGTGTCATAATATTCTATTGATTCTGAAGCTGAAGTTT

                                                              
       1864 GCCAATTGTCAACGTGTCATAATATTCTATTGATTCTGAAGCTGAAGTTT
          1 GCCAATTGTCAACGTGTCATAATATTCTATTGATTCTGAAGCTGAAGTTT

       1914 TTGTTGTGTT


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  50   50  1.00

ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38


Consensus pattern (50 bp):   
GCCAATTGTCAACGTGTCATAATATTCTATTGATTCTGAAGCTGAAGTTT

Found at i:3405 original size:13 final size:13

Alignment explanation


    Indices: 3387--3416  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       3377 AAATCCCATA

                     *   
       3387 ACTTGGATGGCTC
          1 ACTTGGATGACTC

                         
       3400 ACTTGGATGACTC
          1 ACTTGGATGACTC

                
       3413 ACTT
          1 ACTT

       3417 TCCCCACCTC


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33


Consensus pattern (13 bp):   
ACTTGGATGACTC

Found at i:4859 original size:12 final size:12

Alignment explanation


    Indices: 4842--4867  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4832 ATGATGGGCT

                        
       4842 GATTAGAAATTA
          1 GATTAGAAATTA

                        
       4854 GATTAGAAATTA
          1 GATTAGAAATTA

              
       4866 GA
          1 GA

       4868 GCTAATGTGC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31


Consensus pattern (12 bp):   
GATTAGAAATTA

Found at i:5223 original size:3 final size:3

Alignment explanation


    Indices: 5185--5209  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

       5175 TATTAAATCC

                                             
       5185 ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT A

       5210 ATGAATTTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (3 bp):   
ATT

Found at i:5953 original size:17 final size:17

Alignment explanation


    Indices: 5923--5997  Score: 78
    Period size: 17  Copynumber: 4.4  Consensus size: 17

       5913 GTGAATTTTT

                            * 
       5923 AATTTGAAAATAAATTTA
          1 AATTT-AAAATAAATTCA

                    *        
       5941 AATTTAAAGTAAATTCA
          1 AATTTAAAATAAATTCA

              * *     *    * 
       5958 AACTCAAAATGAATTTA
          1 AATTTAAAATAAATTCA

                  *          
       5975 AATTTAGAATAAATTCA
          1 AATTTAAAATAAATTCA

                  
       5992 AATTTA
          1 AATTTA

       5998 TTAAAATTAA


Statistics
Matches: 45,  Mismatches: 12, Indels: 1
        0.78            0.21        0.02

Matches are distributed among these distances:
  17   40  0.89
  18    5  0.11

ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36


Consensus pattern (17 bp):   
AATTTAAAATAAATTCA

Found at i:5973 original size:34 final size:34

Alignment explanation


    Indices: 5929--5993  Score: 105
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       5919 TTTTAATTTG

                                               
       5929 AAAATAAATTTAAATTTA-AAGTAAATTCAAACTC
          1 AAAATAAATTTAAATTTAGAA-TAAATTCAAACTC

                 *                         
       5963 AAAATGAATTTAAATTTAGAATAAATTCAAA
          1 AAAATAAATTTAAATTTAGAATAAATTCAAA

       5994 TTTATTAAAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  34   27  0.93
  35    2  0.07

ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32


Consensus pattern (34 bp):   
AAAATAAATTTAAATTTAGAATAAATTCAAACTC
Done.