Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009625.1 Kokia drynarioides strain JFW-HI SEQ_124341, 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: 3351
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:235 original size:18 final size:18

Alignment explanation


    Indices: 212--246  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        202 TAGATTAGTT

                              
        212 AGAGTTCTAGTTTAATTA
          1 AGAGTTCTAGTTTAATTA

                  *  *       
        230 AGAGTTTTATTTTAATT
          1 AGAGTTCTAGTTTAATT

        247 TATTTATCTT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.31, C:0.03, G:0.14, T:0.51


Consensus pattern (18 bp):   
AGAGTTCTAGTTTAATTA

Found at i:358 original size:25 final size:24

Alignment explanation


    Indices: 322--368  Score: 69
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        312 AGTTAATAAT

                                     
        322 AATTCTCTTTGAGTTTTTCTTTAAG
          1 AATTCTCTTTGAGTTTTT-TTTAAG

                                   
        347 AATTGCTC-TTGAGTTTTTTTTA
          1 AATT-CTCTTTGAGTTTTTTTTA

        369 GAAGTTGTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  24    4  0.19
  25   14  0.67
  26    3  0.14

ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57


Consensus pattern (24 bp):   
AATTCTCTTTGAGTTTTTTTTAAG

Found at i:2277 original size:19 final size:20

Alignment explanation


    Indices: 2244--2281  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2234 ATATTGTTTT

                   *            
       2244 TATTTTTTTTCTTTTTCTCG
          1 TATTTTTATTCTTTTTCTCG

                               
       2264 TATTTTTATT-TTTTTCTC
          1 TATTTTTATTCTTTTTCTC

       2282 TACTTTTTTA


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

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

ACGTcount: A:0.08, C:0.13, G:0.03, T:0.76


Consensus pattern (20 bp):   
TATTTTTATTCTTTTTCTCG

Found at i:2291 original size:20 final size:21

Alignment explanation


    Indices: 2244--2292  Score: 61
    Period size: 19  Copynumber: 2.5  Consensus size: 21

       2234 ATATTGTTTT

                                 
       2244 TATTTTTT-TTCTTTTTCTCG
          1 TATTTTTTATTCTTTTTCTCG

                                 
       2264 TA-TTTTTATT-TTTTTCTC-
          1 TATTTTTTATTCTTTTTCTCG

                       
       2282 TACTTTTTTAT
          1 TA-TTTTTTAT

       2293 CACTTTTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  18    2  0.08
  19   13  0.50
  20   11  0.42

ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76


Consensus pattern (21 bp):   
TATTTTTTATTCTTTTTCTCG
Done.