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Table 3 Barcode sequence space(s) defined by program parameters.

From: BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing

  Parameters Results
Run Len
-1
Min. Dist.
-m
GC Low
-c
GC High
-g
Homo-polymer
-p
Hair-pin
-a
Hetero-duplex
-b
Dels.
-d
Initial Barcode Pool Final Barcode Pool Exec. Time (sec.) 1
            System A 2 System B 3
1 4 3 0.3 0.7 3 5 5 1 256 7 0.0 (0.0) 0.0 (0.0)
2 5 3 0.3 0.7 3 5 5 1 1024 26 0.0 (0.0) 0.0 (0.0)
3 6 3 0.3 0.7 3 5 5 1 4096 82 0.4 (0.5) 0.2 (0.4)
4 7 3 0.3 0.7 3 5 5 1 16384 218 3.0 (0.0) 1.2 (0.4)
5 8 3 0.3 0.7 3 5 5 1 65536 760 54 (0.0) 24 (0.4)
6 4 9 3 0.3 0.7 3 5 5 1 262144 2774 978 (0.4) 419 (5.4)
7 9 3 0.3 0.7 3 5 5 0 262144 3113 12 (0.0) 6.0 (0.0)
8 9 4 0.3 0.7 3 5 5 1 262144 593 159 (0.4) 68 (0.8)
9 9 3 0.3 0.7 4 5 5 1 262144 3294 1536 (0.8) 655 (5.8)
10 9 3 0.3 0.7 3 4 4 1 262144 2774 979 (0.7) 416 (1.2)
11 9 3 0.3 0.7 3 6 6 1 262144 2774 977 (1.1) 419 (9.3)
12 9 3 0.4 0.6 3 5 5 1 262144 2155 493 (0.5) 211 (0.8)
13 9 3 0.3 0.7 2 5 5 1 262144 779 42 (0.4) 18 (0.4)
14 9 3 0.2 0.8 3 5 5 1 262144 2914 1153 (0.8) 491 (4.9)
15 9 3 0.1 0.9 3 5 5 1 262144 2910 1177 (0.0) 505 (5.5)
16 10 3 0.3 0.7 3 5 5 1 1.10E+06 9375 16507 (1857) 6650 (23)
  1. 1 Elapsed time of execution: Mean (St. Dev) seconds.
  2. 2 Executed on a 2 GHz Intel Core Duo MacBook Pro. 1 GB 667 MHz DDR2 SDRAM. Mac OSX version 10.5.4.
  3. 3 Executed on a workstation with 2 × 3 GHz Dual-Core Intel Xeon 5160 processors. 12 GB 800 MHz DDR2 FB-DIMM. Fedora Core 5 operating system.
  4. 4 Default parameters