Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012028.1 Kokia drynarioides strain JFW-HI SEQ_127026, 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: 1694
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42


Found at i:1275 original size:14 final size:14

Alignment explanation


    Indices: 1254--1307  Score: 58
    Period size: 14  Copynumber: 3.9  Consensus size: 14

       1244 TATATTTTGC

                           
       1254 TATTATTTTATCTAT
          1 TATTATTTTAT-TAT

                          
       1269 T-TTATTTTATTAT
          1 TATTATTTTATTAT

                         * 
       1282 TATTATTATT-TTTT
          1 TATTATT-TTATTAT

                   *    
       1296 TATTATTATATT
          1 TATTATTTTATT

       1308 TTTAGTATGT


Statistics
Matches: 34,  Mismatches: 2, Indels: 7
        0.79            0.05        0.16

Matches are distributed among these distances:
  13    5  0.15
  14   26  0.76
  15    3  0.09

ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72


Consensus pattern (14 bp):   
TATTATTTTATTAT

Found at i:1275 original size:25 final size:25

Alignment explanation


    Indices: 1246--1307  Score: 65
    Period size: 25  Copynumber: 2.5  Consensus size: 25

       1236 CTTCATTCTA

                  *                   
       1246 TATTTTGCTATTATT-TTATCTATTT
          1 TATTTTACTATTATTATTAT-TATTT

                   *             *   
       1271 TATTTTATTATTATTATTATTTTTT
          1 TATTTTACTATTATTATTATTATTT

                         
       1296 TATTATTA-TATT
          1 TATT-TTACTATT

       1308 TTTAGTATGT


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  25   25  0.78
  26    7  0.22

ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71


Consensus pattern (25 bp):   
TATTTTACTATTATTATTATTATTT

Found at i:1281 original size:17 final size:16

Alignment explanation


    Indices: 1261--1309  Score: 62
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       1251 TGCTATTATT

                             
       1261 TTATCTATTTTATTTTA
          1 TTAT-TATTTTATTTTA

                            *
       1278 TTATTATTATTATTTTT
          1 TTATTATT-TTATTTTA

                    *      
       1295 TTATTATTATATTTT
          1 TTATTATTTTATTTT

       1310 TAGTATGTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  16   10  0.34
  17   19  0.66

ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73


Consensus pattern (16 bp):   
TTATTATTTTATTTTA

Found at i:1283 original size:3 final size:3

Alignment explanation


    Indices: 1254--1304  Score: 56
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1244 TATATTTTGC

                                                                      * 
       1254 TAT TAT T-T TAT CTAT T-T TAT T-T TAT TAT TAT TAT TAT T-T TTT
          1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                       
       1296 TAT TAT TAT
          1 TAT TAT TAT

       1305 ATTTTTAGTA


Statistics
Matches: 42,  Mismatches: 1, Indels: 10
        0.79            0.02        0.19

Matches are distributed among these distances:
   2    8  0.19
   3   31  0.74
   4    3  0.07

ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73


Consensus pattern (3 bp):   
TAT

Found at i:1310 original size:17 final size:18

Alignment explanation


    Indices: 1256--1310  Score: 60
    Period size: 17  Copynumber: 3.0  Consensus size: 18

       1246 TATTTTGCTA

                                
       1256 TTATT-TTATCTATTTTATT
          1 TTATTATTAT-TATTTT-TT

                          *   
       1275 TTATTATTATTATTATTT
          1 TTATTATTATTATTTTTT

                               
       1293 TT-TTATTATTATATTTTT
          1 TTATTATTATTAT-TTTTT

       1311 AGTATGTTTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  17   10  0.31
  18    8  0.25
  19   10  0.31
  20    4  0.12

ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75


Consensus pattern (18 bp):   
TTATTATTATTATTTTTT
Done.