Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007071.1 Kokia drynarioides strain JFW-HI SEQ_121680, 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: 3671
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34


Found at i:1318 original size:15 final size:15

Alignment explanation


    Indices: 1287--1317  Score: 55
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       1277 AAATAATTCT

                           
       1287 AATCGTTTGAAAAAA
          1 AATCGTTTGAAAAAA

                           
       1302 AATCG-TTGAAAAAA
          1 AATCGTTTGAAAAAA

              
       1316 AA
          1 AA

       1318 AATAATAGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   11  0.69
  15    5  0.31

ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23


Consensus pattern (15 bp):   
AATCGTTTGAAAAAA

Found at i:1783 original size:105 final size:106

Alignment explanation


    Indices: 1647--1854  Score: 382
    Period size: 106  Copynumber: 2.0  Consensus size: 106

       1637 TCGTTCAACT

                        *                                                    
       1647 CTTGGATCATCAGACTATCAATTGAACTTGTAAAAGTATGAAATCAA-GTATATATATTATATAT
          1 CTTGGATCATCACACTATCAATTGAACTTGTAAAAGTATGAAATCAACGTATATATATTATATAT

                                            *        
       1711 GTACATATATTTGAGATATTACATTTTGAGGTTTTGGAACC
         66 GTACATATATTTGAGATATTACATTTTGAGGTGTTGGAACC

                                                                             
       1752 CTTGGATCATCACACTATCAATTGAACTTGTAAAAGTATGAAATCAACGTATATATATTATATAT
          1 CTTGGATCATCACACTATCAATTGAACTTGTAAAAGTATGAAATCAACGTATATATATTATATAT

               *                                  
       1817 GTATATATATTTGAGATATTACATTTTGAGGTGTTGGA
         66 GTACATATATTTGAGATATTACATTTTGAGGTGTTGGA

       1855 TTTTGGAGGT


Statistics
Matches: 99,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
 105   46  0.46
 106   53  0.54

ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38


Consensus pattern (106 bp):   
CTTGGATCATCACACTATCAATTGAACTTGTAAAAGTATGAAATCAACGTATATATATTATATAT
GTACATATATTTGAGATATTACATTTTGAGGTGTTGGAACC

Found at i:2310 original size:21 final size:19

Alignment explanation


    Indices: 2294--2331  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 19

       2284 ATACATGTCT

                                 
       2294 TTAAGGTATC-GAAACATAGC
          1 TTAAGGTATCAG-AACAT-GC

                              
       2314 TTAAGGTATCAGAACATG
          1 TTAAGGTATCAGAACATG

       2332 GGGGTTATGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    1  0.06
  20   15  0.88
  21    1  0.06

ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26


Consensus pattern (19 bp):   
TTAAGGTATCAGAACATGC

Found at i:2997 original size:32 final size:29

Alignment explanation


    Indices: 2932--2997  Score: 78
    Period size: 32  Copynumber: 2.2  Consensus size: 29

       2922 ATAGTTTAAA

                              *      *   
       2932 TATCACATGAAACATTTTCAAAGTATAAG
          1 TATCACATGAAACATTTTAAAAGTACAAG

                                           *
       2961 TATCACATGAAACATTTTATTAAAAGTACAAT
          1 TATCACATGAAACA--TT-TTAAAAGTACAAG

                 
       2993 TATCA
          1 TATCA

       2998 AATGTGATCT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  29   14  0.45
  31    2  0.06
  32   15  0.48

ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33


Consensus pattern (29 bp):   
TATCACATGAAACATTTTAAAAGTACAAG

Found at i:3109 original size:162 final size:162

Alignment explanation


    Indices: 2839--3166  Score: 602
    Period size: 162  Copynumber: 2.0  Consensus size: 162

       2829 CCTAATTCGA

                                          *                                  
       2839 GTGATCTGAATCTCTAACCCCTTAGAGTCTGGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT
          1 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT

                                                                             
       2904 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT
         66 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT

                                            
       2969 GAAACATTTTATTAAAAGTACAATTATCAAAT
        131 GAAACATTTTATTAAAAGTACAATTATCAAAT

                                                                    *        
       3001 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTTAAACATTT
          1 GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT

                    *                        *  *             *              
       3066 TATAAAAATACAAGTACCATAGTTTAAATATCATATTAAACATTTTCAAATTATAAGTATCACAT
         66 TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT

                                            
       3131 GAAACATTTTATTAAAAGTACAATTATCAAAT
        131 GAAACATTTTATTAAAAGTACAATTATCAAAT

                
       3163 GTGA
          1 GTGA

       3167 CGTTATCCAT


Statistics
Matches: 160,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 162  160  1.00

ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34


Consensus pattern (162 bp):   
GTGATCTGAATCTCTAACCCCTTAGAGTCTAGAGGTAAAGTAAAAGATGTTTTTTTAAAACATTT
TATAAAAACACAAGTACCATAGTTTAAATATCACATGAAACATTTTCAAAGTATAAGTATCACAT
GAAACATTTTATTAAAAGTACAATTATCAAAT
Done.