Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004673.1 Kokia drynarioides strain JFW-HI SEQ_118223, 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: 2528
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:214 original size:16 final size:15

Alignment explanation


    Indices: 188--231  Score: 53
    Period size: 15  Copynumber: 3.3  Consensus size: 15

        178 AAAATTAATT

                           
        188 ATTTTTTAAAATATA
          1 ATTTTTTAAAATATA

                           
        203 ATTTTTTAAAA-AT-
          1 ATTTTTTAAAATATA

                           
        216 A--TTTTAAAA-ATA
          1 ATTTTTTAAAATATA

                
        228 ATTT
          1 ATTT

        232 AAAATTATTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 7
        0.79            0.00        0.21

Matches are distributed among these distances:
  11   10  0.38
  12    1  0.04
  13    1  0.04
  14    3  0.12
  15   11  0.42

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (15 bp):   
ATTTTTTAAAATATA

Found at i:222 original size:11 final size:11

Alignment explanation


    Indices: 206--246  Score: 55
    Period size: 11  Copynumber: 3.6  Consensus size: 11

        196 AAATATAATT

                       
        206 TTTTAAAAATA
          1 TTTTAAAAATA

                       
        217 TTTTAAAAATA
          1 TTTTAAAAATA

            *       *  
        228 ATTTAAAATTA
          1 TTTTAAAAATA

                    
        239 TTTCTAAA
          1 TTT-TAAA

        247 TATAAAATTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  11   22  0.85
  12    4  0.15

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46


Consensus pattern (11 bp):   
TTTTAAAAATA

Found at i:235 original size:22 final size:23

Alignment explanation


    Indices: 207--251  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        197 AATATAATTT

                                   
        207 TTTAAAAATATTT-TAAAAATAA
          1 TTTAAAAATATTTCTAAAAATAA

                   *          *    
        229 TTTAAAATTATTTCTAAATATAA
          1 TTTAAAAATATTTCTAAAAATAA

        252 AATTATTAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  22   12  0.60
  23    8  0.40

ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44


Consensus pattern (23 bp):   
TTTAAAAATATTTCTAAAAATAA

Found at i:1120 original size:7 final size:6

Alignment explanation


    Indices: 1087--1117  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       1077 AAACCCTATT

                       *                        
       1087 GAAGGG GAAGAG GAAGGG GAAGGG GAAGGG G
          1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G

       1118 GAATGGGAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00


Consensus pattern (6 bp):   
GAAGGG

Found at i:1236 original size:11 final size:11

Alignment explanation


    Indices: 1195--1235  Score: 57
    Period size: 11  Copynumber: 3.8  Consensus size: 11

       1185 ATAATTTTAT

                *      
       1195 ATTTAAAAATA
          1 ATTTTAAAATA

                    *  
       1206 ATTTTAAATTA
          1 ATTTTAAAATA

                       
       1217 ATTTTAAAAT-
          1 ATTTTAAAATA

                     
       1227 ATTTTAAAA
          1 ATTTTAAAA

       1236 AATAATTAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  10    9  0.33
  11   18  0.67

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (11 bp):   
ATTTTAAAATA
Done.