Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003876.1 Kokia drynarioides strain JFW-HI SEQ_116910, 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: 12099
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33


Found at i:4192 original size:6 final size:6

Alignment explanation


    Indices: 4181--4207  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       4171 AGGGACAACC

                                           
       4181 ATAGCA ATAGCA ATAGCA ATAGCA ATA
          1 ATAGCA ATAGCA ATAGCA ATAGCA ATA

       4208 TCAAAATATT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19


Consensus pattern (6 bp):   
ATAGCA

Found at i:5403 original size:5 final size:5

Alignment explanation


    Indices: 5384--5417  Score: 52
    Period size: 5  Copynumber: 7.0  Consensus size: 5

       5374 GTTAAAAAAG

                  *                                  
       5384 GTTTT TTTTT G-TTT GTTTT GTTTT GTTTT GTTTT
          1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT

       5418 AGAGTCCGGT


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
   4    4  0.15
   5   22  0.85

ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82


Consensus pattern (5 bp):   
GTTTT

Found at i:8582 original size:18 final size:16

Alignment explanation


    Indices: 8551--8594  Score: 56
    Period size: 14  Copynumber: 2.8  Consensus size: 16

       8541 AGTTTACGGT

                        *    
       8551 TTAAAAATTTTAATTAA
          1 TTAAAAA-TTTATTTAA

                            
       8568 TT--AAATTTATTTAA
          1 TTAAAAATTTATTTAA

                         
       8582 TTAAAAATTTATT
          1 TTAAAAATTTATT

       8595 CTCATTTCAT


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

Matches are distributed among these distances:
  14   10  0.42
  15    3  0.12
  16    9  0.38
  17    2  0.08

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (16 bp):   
TTAAAAATTTATTTAA

Found at i:10076 original size:21 final size:19

Alignment explanation


    Indices: 10052--10090  Score: 60
    Period size: 21  Copynumber: 1.9  Consensus size: 19

      10042 AATTGCCTCC

                                 
      10052 CTATCTAAGACCATGTTTCCT
          1 CTATCTAAG-CCAT-TTTCCT

                              
      10073 CTATCTAAGCCATTTTCC
          1 CTATCTAAGCCATTTTCC

      10091 GGAGGATTAT


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

Matches are distributed among these distances:
  19    5  0.28
  20    4  0.22
  21    9  0.50

ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38


Consensus pattern (19 bp):   
CTATCTAAGCCATTTTCCT
Done.