Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009359.1 Kokia drynarioides strain JFW-HI SEQ_124066, 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: 3768
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33


Found at i:262 original size:18 final size:19

Alignment explanation


    Indices: 233--273  Score: 66
    Period size: 19  Copynumber: 2.2  Consensus size: 19

        223 AGAAGAAGAG

                    *          
        233 AGAAAAAGGAAAAGGAAAA
          1 AGAAAAAGAAAAAGGAAAA

                               
        252 AGAAAAAGAAAAA-GAAAA
          1 AGAAAAAGAAAAAGGAAAA

                
        270 AGAA
          1 AGAA

        274 GATTTACATA


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

Matches are distributed among these distances:
  18    9  0.43
  19   12  0.57

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (19 bp):   
AGAAAAAGAAAAAGGAAAA

Found at i:263 original size:5 final size:6

Alignment explanation


    Indices: 233--273  Score: 64
    Period size: 6  Copynumber: 6.7  Consensus size: 6

        223 AGAAGAAGAG

                           *                               
        233 AGAAAA AGGAAAA GGAAAA AGAAAA AGAAAA AGAAAA AGAA
          1 AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAA

        274 GATTTACATA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   6   27  0.84
   7    5  0.16

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:971 original size:110 final size:110

Alignment explanation


    Indices: 766--972  Score: 261
    Period size: 110  Copynumber: 1.9  Consensus size: 110

        756 ATAAACCGAT

                                     *       *               *       *       
        766 GATATAAAAGGTGAGCCCAACTCTAGTTGGATATACCAACAAATATTACGCCCAGCGTTAGTCGG
          1 GATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACACCCAGCGCTAGTCGG

                           *    *                        
        831 ATAAACTGACAAGTTGTGTGTCCAGCACTAGTAAGATAAATTGAC
         66 ATAAACTGACAAGTTATGTGCCCAGCACTAGTAAGATAAATTGAC

                           *   **                  ** * *  *                 
        876 GATATAAAAGGTGAGTCCAGTTCTAATTGGATAAACCAATGATTTTTGCACCCAGCGCTAGTCGG
          1 GATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACACCCAGCGCTAGTCGG

                      * *            *      
        941 ATAAACTGACGATTTATGTGCCCAGTACTAGT
         66 ATAAACTGACAAGTTATGTGCCCAGCACTAGT

        973 CAGGTTAACT


Statistics
Matches: 80,  Mismatches: 17, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
 110   80  1.00

ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27


Consensus pattern (110 bp):   
GATATAAAAGGTGAGCCCAACTCTAATTGGATAAACCAACAAATATTACACCCAGCGCTAGTCGG
ATAAACTGACAAGTTATGTGCCCAGCACTAGTAAGATAAATTGAC

Found at i:1874 original size:41 final size:41

Alignment explanation


    Indices: 1813--1892  Score: 117
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1803 ACACTTAAAA

                                 *                   
       1813 ATATTAAAACAAATATTAAAATAACAAACAAATTAAAAACG
          1 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG

                        *                      *    
       1854 ATATTAAAACAATTCA-TAAAACAACAAACAAATTGAAAA
          1 ATATTAAAACAAAT-ATTAAAACAACAAACAAATTAAAAA

       1893 TACAATAAGC


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
  41   34  0.97
  42    1  0.03

ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21


Consensus pattern (41 bp):   
ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG

Found at i:2985 original size:4 final size:4

Alignment explanation


    Indices: 2976--3002  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

       2966 TACCATTTTC

                                             
       2976 AAAG AAAG AAAG AAAG AAAG AAAG AAA
          1 AAAG AAAG AAAG AAAG AAAG AAAG AAA

       3003 AGAATCAAGA


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

Matches are distributed among these distances:
   4   23  1.00

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (4 bp):   
AAAG

Done.