Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006341.1 Kokia drynarioides strain JFW-HI SEQ_120916, 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: 4966
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:2521 original size:36 final size:36

Alignment explanation


    Indices: 2407--2511  Score: 149
    Period size: 36  Copynumber: 2.9  Consensus size: 36

       2397 TTTATAAAAG

                      *      *                   
       2407 TAAATATGTGGGTATGTAATTCATGT-CATGTGACAA
          1 TAAATATGTGAGTATGTTATTCAT-TCCATGTGACAA

                           *        *     *     
       2443 TAAATATGTGAGTATATTATTCATGCCATGAGACAA
          1 TAAATATGTGAGTATGTTATTCATTCCATGTGACAA

                                             
       2479 TAAATATGTGAGTATGTTATTCATTCCATGTGA
          1 TAAATATGTGAGTATGTTATTCATTCCATGTGA

       2512 TAGTGAATAT


Statistics
Matches: 60,  Mismatches: 8, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  36   60  1.00

ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37


Consensus pattern (36 bp):   
TAAATATGTGAGTATGTTATTCATTCCATGTGACAA

Found at i:3305 original size:46 final size:46

Alignment explanation


    Indices: 3244--3332  Score: 144
    Period size: 46  Copynumber: 1.9  Consensus size: 46

       3234 GCAAGCTCAT

                                     *           *         
       3244 AAAAAGGAGACTTAATTGAAGCAAAGA-GCTCATAACTTAGGCAAGC
          1 AAAAAGGAGACTTAATTGAAGCAAAAAGGCT-ATAACATAGGCAAGC

                                                       
       3290 AAAAAGGAGACTTAATTGAAGCAAAAAGGCTATAACATAGGCA
          1 AAAAAGGAGACTTAATTGAAGCAAAAAGGCTATAACATAGGCA

       3333 CATTTCACTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  46   37  0.93
  47    3  0.08

ACGTcount: A:0.48, C:0.13, G:0.21, T:0.17


Consensus pattern (46 bp):   
AAAAAGGAGACTTAATTGAAGCAAAAAGGCTATAACATAGGCAAGC

Found at i:3314 original size:22 final size:22

Alignment explanation


    Indices: 3244--3318  Score: 68
    Period size: 22  Copynumber: 3.3  Consensus size: 22

       3234 GCAAGCTCAT

                                  
       3244 AAAAAGGAGACTTAATTGAAGC
          1 AAAAAGGAGACTTAATTGAAGC

                                        
       3266 --AAA-GAG-CTCATAACTTAGGCAAGC
          1 AAAAAGGAGACT--TAA-TT--G-AAGC

                                  
       3290 AAAAAGGAGACTTAATTGAAGC
          1 AAAAAGGAGACTTAATTGAAGC

                   
       3312 AAAAAGG
          1 AAAAAGG

       3319 CTATAACATA


Statistics
Matches: 43,  Mismatches: 0, Indels: 20
        0.68            0.00        0.32

Matches are distributed among these distances:
  18    2  0.05
  19    3  0.07
  20    6  0.14
  21    2  0.05
  22   11  0.26
  23    2  0.05
  24    4  0.09
  25    2  0.05
  26    6  0.14
  27    3  0.07
  28    2  0.05

ACGTcount: A:0.49, C:0.12, G:0.23, T:0.16


Consensus pattern (22 bp):   
AAAAAGGAGACTTAATTGAAGC

Found at i:3315 original size:21 final size:21

Alignment explanation


    Indices: 3245--3315  Score: 58
    Period size: 20  Copynumber: 3.2  Consensus size: 21

       3235 CAAGCTCATA

                                 
       3245 AAAAGGAGACTTAATTGAAGC
          1 AAAAGGAGACTTAATTGAAGC

                                       
       3266 -AAA-GAG-CTCATAACTTAGGCAAGC
          1 AAAAGGAGACT--TAA-TT--G-AAGC

                                  
       3290 AAAAAGGAGACTTAATTGAAGC
          1 -AAAAGGAGACTTAATTGAAGC

                
       3312 AAAA
          1 AAAA

       3316 AGGCTATAAC


Statistics
Matches: 40,  Mismatches: 0, Indels: 20
        0.67            0.00        0.33

Matches are distributed among these distances:
  18    2  0.05
  19    3  0.08
  20    6  0.15
  21    6  0.15
  22    4  0.10
  23    2  0.05
  24    4  0.10
  25    2  0.05
  26    6  0.15
  27    3  0.08
  28    2  0.05

ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17


Consensus pattern (21 bp):   
AAAAGGAGACTTAATTGAAGC
Done.