Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003343.1 Kokia drynarioides strain JFW-HI SEQ_116052, 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: 2311
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33


Found at i:838 original size:15 final size:15

Alignment explanation


    Indices: 818--857  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        808 ACCAAATATA

                           
        818 AAGATAAAATATTAT
          1 AAGATAAAATATTAT

                           
        833 AAGATAAAATATTAT
          1 AAGATAAAATATTAT

                       
        848 AAGA-AAAATA
          1 AAGATAAAATA

        858 ATAAAATAAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  14    6  0.24
  15   19  0.76

ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28


Consensus pattern (15 bp):   
AAGATAAAATATTAT

Found at i:914 original size:19 final size:19

Alignment explanation


    Indices: 870--918  Score: 55
    Period size: 19  Copynumber: 2.5  Consensus size: 19

        860 AAAATAAGAA

                             *  
        870 AAAAATCAAATCAAATGTAT
          1 AAAAAT-AAATCAAATGAAT

                                 
        890 ACAAAATAAAT-AAATGAATT
          1 A-AAAATAAATCAAATGAA-T

                     
        910 AAAAATAAA
          1 AAAAATAAA

        919 ATCTCCTCAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  19   14  0.54
  20    7  0.27
  21    5  0.19

ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22


Consensus pattern (19 bp):   
AAAAATAAATCAAATGAAT

Found at i:1214 original size:17 final size:17

Alignment explanation


    Indices: 1189--1259  Score: 79
    Period size: 17  Copynumber: 4.2  Consensus size: 17

       1179 AATAAGTTTG

                           * 
       1189 AATTTATTTTAAATTCA
          1 AATTTATTTTAAATTTA

                *     * *   *
       1206 AATTCATTTTGAGTTTG
          1 AATTTATTTTAAATTTA

                  *          
       1223 AATTTACTTTAAATTTA
          1 AATTTATTTTAAATTTA

                           * 
       1240 AATTTATTTTAAATTAA
          1 AATTTATTTTAAATTTA

               
       1257 AAT
          1 AAT

       1260 AAAATTAAAA


Statistics
Matches: 42,  Mismatches: 12, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  17   42  1.00

ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:1222 original size:34 final size:34

Alignment explanation


    Indices: 1183--1249  Score: 107
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1173 TTTTTAAATA

                        *                     
       1183 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
          1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG

                                 *     *     
       1217 AGTTTGAATTTACTTTAAATTTAAATTTATTTT
          1 AGTTTGAATTTACTTTAAATTCAAATTCATTTT

       1250 AAATTAAAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   30  1.00

ACGTcount: A:0.33, C:0.04, G:0.07, T:0.55


Consensus pattern (34 bp):   
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG

Found at i:1977 original size:19 final size:20

Alignment explanation


    Indices: 1955--1992  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1945 TTAACATTAA

                                
       1955 TAATAATAATAAAT-TTTTT
          1 TAATAATAATAAATATTTTT

                               
       1974 TAATAATAATAAATATTTT
          1 TAATAATAATAAATATTTT

       1993 GGTAATATTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (20 bp):   
TAATAATAATAAATATTTTT

Done.