Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005176.1 Kokia drynarioides strain JFW-HI SEQ_119032, 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: 4207
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37


Found at i:93 original size:16 final size:15

Alignment explanation


    Indices: 66--112  Score: 51
    Period size: 16  Copynumber: 3.0  Consensus size: 15

         56 CTTTATGCTA

                           
         66 TTTTTT-AATTTTTT
          1 TTTTTTGAATTTTTT

                            *
         80 TTTTTATGAATTTTGTC
          1 TTTTT-TGAATTTT-TT

                            
         97 TTTTTTGAATATTTTT
          1 TTTTTTGAAT-TTTTT

        113 ATAATTTGTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  14    5  0.19
  15    1  0.04
  16   12  0.44
  17    9  0.33

ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74


Consensus pattern (15 bp):   
TTTTTTGAATTTTTT

Found at i:1342 original size:34 final size:34

Alignment explanation


    Indices: 1294--1360  Score: 116
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1284 AACATCTGGG

                *          *                  
       1294 TAAGGTAAAAGGTAATAAATTAAAAATATTTGGA
          1 TAAGATAAAAGGTAAAAAATTAAAAATATTTGGA

                                             
       1328 TAAGATAAAAGGTAAAAAATTAAAAATATTTGG
          1 TAAGATAAAAGGTAAAAAATTAAAAATATTTGG

       1361 GTTTAGTTTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.55, C:0.00, G:0.16, T:0.28


Consensus pattern (34 bp):   
TAAGATAAAAGGTAAAAAATTAAAAATATTTGGA

Found at i:2792 original size:14 final size:16

Alignment explanation


    Indices: 2757--2796  Score: 52
    Period size: 14  Copynumber: 2.8  Consensus size: 16

       2747 TTTGAAATAT

                            
       2757 TTAAAATCTAAATTAA
          1 TTAAAATCTAAATTAA

                            
       2773 TT-AAATCT-AATT-A
          1 TTAAAATCTAAATTAA

                        
       2786 TTAAAAT-TAAA
          1 TTAAAATCTAAA

       2797 AGTTGATACC


Statistics
Matches: 22,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  13    4  0.18
  14   10  0.45
  15    6  0.27
  16    2  0.09

ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40


Consensus pattern (16 bp):   
TTAAAATCTAAATTAA

Found at i:3142 original size:22 final size:20

Alignment explanation


    Indices: 3107--3151  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       3097 AATTTTTTAA

                              *  
       3107 TTTTTAATTTTTTATAGATTT
          1 TTTTTAATTTTTTAT-GAATT

                 *               
       3128 TTTTTTATATTTTTATGAATT
          1 TTTTTAAT-TTTTTATGAATT

               
       3149 TTT
          1 TTT

       3152 AATTAATTAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   14  0.67
  22    7  0.33

ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73


Consensus pattern (20 bp):   
TTTTTAATTTTTTATGAATT

Found at i:4067 original size:4 final size:4

Alignment explanation


    Indices: 4054--4092  Score: 53
    Period size: 4  Copynumber: 9.8  Consensus size: 4

       4044 AAAATTGAAG

                                 *                           
       4054 GAAA -AAA GAAA GAAAA AAAA GAAA GAAA GAAA GAAA GAA
          1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAA

       4093 GGAAGAAGGA


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   3    3  0.10
   4   25  0.81
   5    3  0.10

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (4 bp):   
GAAA

Done.