Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007224.1 Kokia drynarioides strain JFW-HI SEQ_121839, 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: 3414
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:1451 original size:17 final size:18

Alignment explanation


    Indices: 1413--1451  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1403 TGCATTCTTA

                          **  
       1413 TTGTCACTACATTTTGTT
          1 TTGTCACTACATTTCCTT

                              
       1431 TTGTCACTACA-TTCCTT
          1 TTGTCACTACATTTCCTT

                
       1448 TTGT
          1 TTGT

       1452 TAACTTAGTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17    8  0.42
  18   11  0.58

ACGTcount: A:0.15, C:0.21, G:0.10, T:0.54


Consensus pattern (18 bp):   
TTGTCACTACATTTCCTT

Found at i:2068 original size:16 final size:16

Alignment explanation


    Indices: 2047--2077  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2037 AAAAAAAATG

                            
       2047 AGAAAAAGAAAGAAAA
          1 AGAAAAAGAAAGAAAA

                           
       2063 AGAAAAAGAAAGAAA
          1 AGAAAAAGAAAGAAA

       2078 TTTTTTGATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (16 bp):   
AGAAAAAGAAAGAAAA

Found at i:2456 original size:54 final size:54

Alignment explanation


    Indices: 2380--2489  Score: 211
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       2370 AGTTTTTTAA

                                                                  
       2380 TTGTCTCTTTTGTATCTCATTTAGCATGCATCATGAGCATTTCATACCTAGTTT
          1 TTGTCTCTTTTGTATCTCATTTAGCATGCATCATGAGCATTTCATACCTAGTTT

                                                           *      
       2434 TTGTCTCTTTTGTATCTCATTTAGCATGCATCATGAGCATTTCATACTTAGTTT
          1 TTGTCTCTTTTGTATCTCATTTAGCATGCATCATGAGCATTTCATACCTAGTTT

              
       2488 TT
          1 TT

       2490 ATATTTTTCA


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   55  1.00

ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48


Consensus pattern (54 bp):   
TTGTCTCTTTTGTATCTCATTTAGCATGCATCATGAGCATTTCATACCTAGTTT
Done.