Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003681.1 Kokia drynarioides strain JFW-HI SEQ_116607, 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: 11707
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:475 original size:25 final size:23

Alignment explanation


    Indices: 447--492  Score: 65
    Period size: 23  Copynumber: 1.9  Consensus size: 23

        437 GTTTGATCCA

                                     
        447 AATTAAATTCTAAAAAAATAATTAG
          1 AATTAAA-TCT-AAAAAATAATTAG

                         *       
        472 AATTAAATCTAAACAATAATT
          1 AATTAAATCTAAAAAATAATT

        493 CCCTAATTGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23   10  0.50
  24    3  0.15
  25    7  0.35

ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33


Consensus pattern (23 bp):   
AATTAAATCTAAAAAATAATTAG

Found at i:3190 original size:10 final size:11

Alignment explanation


    Indices: 3171--3199  Score: 51
    Period size: 10  Copynumber: 2.7  Consensus size: 11

       3161 CATCAGGCTG

                       
       3171 TCTCTTTTCTT
          1 TCTCTTTTCTT

                       
       3182 TCT-TTTTCTT
          1 TCTCTTTTCTT

                    
       3192 TCTCTTTT
          1 TCTCTTTT

       3200 AGGTGTGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  10   10  0.59
  11    7  0.41

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (11 bp):   
TCTCTTTTCTT

Found at i:4341 original size:23 final size:22

Alignment explanation


    Indices: 4311--4359  Score: 57
    Period size: 23  Copynumber: 2.2  Consensus size: 22

       4301 AGAAATTTAG

                             *     
       4311 TAAT-CACTTAAT-TAACATGCA
          1 TAATGCACTT-ATCTAAAATGCA

                                   
       4332 TGAATGCACTTATCTAAAATGCA
          1 T-AATGCACTTATCTAAAATGCA

                 
       4355 TAATG
          1 TAATG

       4360 TAATAGATCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  21    1  0.04
  22    9  0.38
  23   14  0.58

ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33


Consensus pattern (22 bp):   
TAATGCACTTATCTAAAATGCA

Found at i:6280 original size:19 final size:18

Alignment explanation


    Indices: 6228--6281  Score: 63
    Period size: 19  Copynumber: 2.9  Consensus size: 18

       6218 ATTATAAACG

                     *    *   
       6228 AAATTAAAATATAACATA
          1 AAATTAAAAAATAAAATA

               *               
       6246 AAAATAATAAAATAAAATA
          1 AAATTAA-AAAATAAAATA

                             
       6265 AAATTAAAAAACTAAAA
          1 AAATTAAAAAA-TAAAA

       6282 AACGAAACAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  18   10  0.33
  19   20  0.67

ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22


Consensus pattern (18 bp):   
AAATTAAAAAATAAAATA

Found at i:9481 original size:30 final size:33

Alignment explanation


    Indices: 9413--9485  Score: 100
    Period size: 32  Copynumber: 2.3  Consensus size: 33

       9403 AAAATGTTAA

                                             
       9413 TGAGTGACTGATTTGTCATTTTTTTGATAACAT
          1 TGAGTGACTGATTTGTCATTTTTTTGATAACAT

                            *              * 
       9446 T-AGTGACTGATTTGTTA-TTTTTTGA-AA-GT
          1 TGAGTGACTGATTTGTCATTTTTTTGATAACAT

                       
       9475 TGAGTGACTGA
          1 TGAGTGACTGA

       9486 ATTGAAACTT


Statistics
Matches: 37,  Mismatches: 2, Indels: 5
        0.84            0.05        0.11

Matches are distributed among these distances:
  29    2  0.05
  30   11  0.30
  31    8  0.22
  32   15  0.41
  33    1  0.03

ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47


Consensus pattern (33 bp):   
TGAGTGACTGATTTGTCATTTTTTTGATAACAT

Found at i:11046 original size:14 final size:16

Alignment explanation


    Indices: 11015--11048  Score: 54
    Period size: 14  Copynumber: 2.2  Consensus size: 16

      11005 ATAATTTTTT

                            
      11015 TTATAAAAGTTATATA
          1 TTATAAAAGTTATATA

                            
      11031 TTATAAAA-TT-TATA
          1 TTATAAAAGTTATATA

                
      11045 TTAT
          1 TTAT

      11049 TTTTATTTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    8  0.44
  15    2  0.11
  16    8  0.44

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (16 bp):   
TTATAAAAGTTATATA
Done.