Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006801.1 Kokia drynarioides strain JFW-HI SEQ_121400, 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: 5684
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32


Found at i:384 original size:3 final size:3

Alignment explanation


    Indices: 376--428  Score: 97
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        366 TACATATATA

                                                                         * 
        376 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                  
        424 TAT TA
          1 TAT TA

        429 ACTTTTCTTT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   48  1.00

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:1299 original size:3 final size:3

Alignment explanation


    Indices: 1291--1341  Score: 65
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1281 GAGGCAACGC

                                                                        
       1291 CTT CTT CTT CTT CTT CCTT C-T CTT CTT CTT CTT -TT C-T CTT C-T
          1 CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

                       
       1333 CTT CTT CTT
          1 CTT CTT CTT

       1342 TTGCTTCAAT


Statistics
Matches: 43,  Mismatches: 0, Indels: 10
        0.81            0.00        0.19

Matches are distributed among these distances:
   2    8  0.19
   3   32  0.74
   4    3  0.07

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


Consensus pattern (3 bp):   
CTT

Found at i:1316 original size:18 final size:17

Alignment explanation


    Indices: 1293--1341  Score: 75
    Period size: 18  Copynumber: 2.9  Consensus size: 17

       1283 GGCAACGCCT

                              
       1293 TCTTCTTCTTCTTCCTTC
          1 TCTTCTTCTTCTT-CTTC

                             
       1311 TCTTCTTCTTCTT-TTC
          1 TCTTCTTCTTCTTCTTC

                            
       1327 TCTTC-TCTTCTTCTT
          1 TCTTCTTCTTCTTCTT

       1342 TTGCTTCAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    7  0.23
  16   10  0.33
  18   13  0.43

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


Consensus pattern (17 bp):   
TCTTCTTCTTCTTCTTC

Found at i:1317 original size:21 final size:21

Alignment explanation


    Indices: 1291--1341  Score: 86
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1281 GAGGCAACGC

                                  
       1291 CTTCTTCTTCTTCTTC-CTTCT
          1 CTTCTTCTTCTT-TTCTCTTCT

                                 
       1312 CTTCTTCTTCTTTTCTCTTCT
          1 CTTCTTCTTCTTTTCTCTTCT

                     
       1333 CTTCTTCTT
          1 CTTCTTCTT

       1342 TTGCTTCAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  20    3  0.10
  21   26  0.90

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


Consensus pattern (21 bp):   
CTTCTTCTTCTTTTCTCTTCT

Done.