Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006528.1 Kokia drynarioides strain JFW-HI SEQ_121112, 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: 13518
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35


Found at i:1146 original size:18 final size:18

Alignment explanation


    Indices: 1108--1146  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       1098 TTAACAATGC

                         *  * 
       1108 TTTTATCTCAAAAGTATT
          1 TTTTATCTCAAAAATACT

                              
       1126 TTTTATCTCAAAAATACT
          1 TTTTATCTCAAAAATACT

               
       1144 TTT
          1 TTT

       1147 GAGAAAGAAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51


Consensus pattern (18 bp):   
TTTTATCTCAAAAATACT

Found at i:5307 original size:26 final size:25

Alignment explanation


    Indices: 5278--5364  Score: 75
    Period size: 26  Copynumber: 3.2  Consensus size: 25

       5268 TAAGATGACT

                                      
       5278 ATATAAAAAATTTTAATAAATAAAAA
          1 ATATAAAAAATTTTAA-AAATAAAAA

                 *              *       
       5304 ATATATAAAATTATTAAATATTAAAATA
          1 ATATAAAAAATT-TTAAA-AATAAAA-A

                                  *      
       5332 ATATAATATAAATATTTAAAAAAATAAAA
          1 ATATAA-A-AAAT-TTTAAAAATA-AAAA

                
       5361 ATAT
          1 ATAT

       5365 GGGTGGGCCT


Statistics
Matches: 49,  Mismatches: 5, Indels: 11
        0.75            0.08        0.17

Matches are distributed among these distances:
  26   12  0.24
  27   10  0.20
  28    6  0.12
  29    8  0.16
  30   12  0.24
  31    1  0.02

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (25 bp):   
ATATAAAAAATTTTAAAAATAAAAA

Found at i:7504 original size:18 final size:17

Alignment explanation


    Indices: 7472--7505  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       7462 TATTGTGTTC

                    *        
       7472 AATTTATTTTTTATTTG
          1 AATTTATTATTTATTTG

                             
       7489 AATTTAGTTATTTATTT
          1 AATTTA-TTATTTATTT

       7506 TATATTAATT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68


Consensus pattern (17 bp):   
AATTTATTATTTATTTG

Found at i:7702 original size:2 final size:2

Alignment explanation


    Indices: 7695--7732  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       7685 TTTCAAATCA

                                                                    
       7695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7733 TTCATTAGAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9277 original size:6 final size:6

Alignment explanation


    Indices: 9266--9300  Score: 54
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       9256 TCGAGTTTTT

                                                     
       9266 AATTTG AATTTG AATTTG AATTTCG -ATTTG AATTT
          1 AATTTG AATTTG AATTTG AATTT-G AATTTG AATTT

       9301 TTTAATTTTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   5    1  0.04
   6   25  0.93
   7    1  0.04

ACGTcount: A:0.31, C:0.03, G:0.14, T:0.51


Consensus pattern (6 bp):   
AATTTG

Done.