Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007893.1 Kokia drynarioides strain JFW-HI SEQ_122534, 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: 4936
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37


Found at i:120 original size:6 final size:6

Alignment explanation


    Indices: 76--116  Score: 73
    Period size: 6  Copynumber: 6.8  Consensus size: 6

         66 ACAAAAGAAT

                                                    *      
         76 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGA GAGAG
          1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAG

        117 AGAGGATACT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00


Consensus pattern (6 bp):   
GAGAGG

Found at i:891 original size:22 final size:22

Alignment explanation


    Indices: 840--892  Score: 65
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        830 TTGTTTAAAA

                 *                
        840 AATTAATAAAAATATATATAAT
          1 AATTAGTAAAAATATATATAAT

              *                    
        862 AAGT-GTAAAAGATATATAT-AT
          1 AATTAGTAAAA-ATATATATAAT

                      
        883 AATTAGTAAA
          1 AATTAGTAAA

        893 TATTAAATGA


Statistics
Matches: 26,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  21   10  0.38
  22   16  0.62

ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34


Consensus pattern (22 bp):   
AATTAGTAAAAATATATATAAT

Found at i:1364 original size:19 final size:18

Alignment explanation


    Indices: 1337--1373  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       1327 GCTTTTAAAC

                *              
       1337 AATATGAAATTATTAAAAA
          1 AATAGGAAATTA-TAAAAA

                              
       1356 AATAGGAAATTATAAAAA
          1 AATAGGAAATTATAAAAA

       1374 TTATATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    6  0.35
  19   11  0.65

ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27


Consensus pattern (18 bp):   
AATAGGAAATTATAAAAA

Found at i:1453 original size:10 final size:10

Alignment explanation


    Indices: 1432--1468  Score: 51
    Period size: 9  Copynumber: 3.9  Consensus size: 10

       1422 CTTCAATAGA

                      
       1432 TTTTAT-TAT
          1 TTTTATATAT

                      
       1441 TTTTATATAT
          1 TTTTATATAT

                 *    
       1451 TTTTAGAT-T
          1 TTTTATATAT

                     
       1460 TTTTATATA
          1 TTTTATATA

       1469 ATTCCTAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
   9   14  0.58
  10   10  0.42

ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70


Consensus pattern (10 bp):   
TTTTATATAT

Found at i:2897 original size:18 final size:18

Alignment explanation


    Indices: 2874--2916  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2864 TTTTCAATTG

                               
       2874 TAATTAATTTAAAATT-TT
          1 TAATTAA-TTAAAATTATT

                        *     
       2892 TAATTAATTAAACTTATT
          1 TAATTAATTAAAATTATT

                   
       2910 TAATTAA
          1 TAATTAA

       2917 AAATTTATTC


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    7  0.30
  18   16  0.70

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51


Consensus pattern (18 bp):   
TAATTAATTAAAATTATT
Done.