Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004874.1 Kokia drynarioides strain JFW-HI SEQ_118548, 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: 23826
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34


Found at i:4888 original size:2 final size:2

Alignment explanation


    Indices: 4881--4922  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       4871 ACCCTAAAAC

                                                                          
       4881 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4923 CAAGATTACA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:5348 original size:19 final size:20

Alignment explanation


    Indices: 5314--5351  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       5304 GTAGAGGTAA

                     *          
       5314 TAAAGTGTGCATAATAATAT
          1 TAAAGTGTGAATAATAATAT

                               
       5334 TAAAGTGT-AATAATAATA
          1 TAAAGTGTGAATAATAATA

       5352 ATAATAATAA


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

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34


Consensus pattern (20 bp):   
TAAAGTGTGAATAATAATAT

Found at i:5567 original size:18 final size:18

Alignment explanation


    Indices: 5546--5580  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       5536 GAATTCCAGT

                              
       5546 GAAAAACATAATTTCAAC
          1 GAAAAACATAATTTCAAC

                             
       5564 GAAAAACATAATTTCAA
          1 GAAAAACATAATTTCAA

       5581 GTGCTTAATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.57, C:0.14, G:0.06, T:0.23


Consensus pattern (18 bp):   
GAAAAACATAATTTCAAC

Found at i:6164 original size:7 final size:7

Alignment explanation


    Indices: 6152--6190  Score: 78
    Period size: 7  Copynumber: 5.6  Consensus size: 7

       6142 AAATTATCCA

                   
       6152 TTTTCTT
          1 TTTTCTT

                   
       6159 TTTTCTT
          1 TTTTCTT

                   
       6166 TTTTCTT
          1 TTTTCTT

                   
       6173 TTTTCTT
          1 TTTTCTT

                   
       6180 TTTTCTT
          1 TTTTCTT

                
       6187 TTTT
          1 TTTT

       6191 TAAGTAATAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   32  1.00

ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87


Consensus pattern (7 bp):   
TTTTCTT

Found at i:6878 original size:16 final size:15

Alignment explanation


    Indices: 6842--6880  Score: 53
    Period size: 14  Copynumber: 2.6  Consensus size: 15

       6832 TGTCTCAAAC

                           
       6842 ATAATTTATATATTT
          1 ATAATTTATATATTT

                            
       6857 AT-ATTTATATATTTT
          1 ATAATTTATATA-TTT

            *        
       6872 TTAATTTAT
          1 ATAATTTAT

       6881 GTTTTACCAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  14    9  0.43
  15    6  0.29
  16    6  0.29

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


Consensus pattern (15 bp):   
ATAATTTATATATTT

Found at i:7151 original size:20 final size:20

Alignment explanation


    Indices: 7128--7177  Score: 100
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       7118 TAATAAGTAT

                                
       7128 TAAATTTTAATAAATATTTG
          1 TAAATTTTAATAAATATTTG

                                
       7148 TAAATTTTAATAAATATTTG
          1 TAAATTTTAATAAATATTTG

                      
       7168 TAAATTTTAA
          1 TAAATTTTAA

       7178 ATTTGTTTTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   30  1.00

ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50


Consensus pattern (20 bp):   
TAAATTTTAATAAATATTTG

Found at i:22259 original size:3 final size:3

Alignment explanation


    Indices: 22251--22275  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      22241 GATCTTTGCC

                                             
      22251 ATT ATT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT A

      22276 ATTAATTAAT


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

Done.