The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

Yuan, Jie; Yi, Ji; Zhan, Meixiao; Xie, Qingqing; Zhen, Ting Ting; Zhou, Jian; Li, Zeqing; Li, Zhou

doi:10.1186/s12864-021-08149-1

Table 2 Delta G cut-off values for primer sets

From: The web-based multiplex PCR primer design software Ultiplex and the associated experimental workflow: up to 100- plex multiplicity

deltaG cut-off	Primer names	Primer_sequences	Chr^*	Length	Left_site deltaG^△	Right_site deltaG^■
<−13 k cal/mol	T13k_1	GGCCTGGCTCTCTATACCCC	6	325	− 13,223	−15,028
	T13k_2	ACGTTGCTCCCGCTCACC	16	945	−14,693	− 14,693
	T13k_3	AAGACCACGAGGCACAGC	20	1778	−13,580	− 13,372
	T13k_4	CCACAGCATCGTGACCCTG	2	1453	−15,972	−15,972
	T13k_5	AGCAAGGAAGTGGACAGGTC	8	572	−13,149	−13,149
	T13k_6	GTGTAGGAGCTGCGCCTC	5	503	−13,483	−13,420
	T13k_7	ATCTGCAGCAGTTTGGAGCC	6	742	−13,454	−13,454
	T13k_8	TCTCCACGATGCCGGCTG	9	1402	−13,003	−14,414
	T13k_9	GTTTCTTCTCCATCGCGGGG	17	1130	−13,847	−13,573
	T13k_10	CTCCATGGCTGATCTCCCCT	16	1736	−13,195	−13,195
−12 ~ − 13 k cal/mol	T12k_1	CAGATCACCTACAGCGCCA	11	1635	−12,176	−12,176
	T12k_2	TAACCCCCATAGCCCTCAAC	1	1645	−12,460	− 12,621
	T12k_3	CATATGGCCGTGTCTGGGG	2	239	−12,572	−12,021
	T12k_4	CCAGCCCAGCATTCTCCAG	19	1864	−14,841	−12,519
	T12k_5	GCAGCAGGGATTGGATGGC	15	1776	−12,218	−12,218
	T12k_6	GCAGGGATTGGATGGCCC	11	855	−12,436	−12,115
	T12k_7	CATCTTCGATTTGAGTGCCCC	12	1868	−12,150	−12,150
	T12k_8	TTCTTGAAGAGGACGGTGCC	2	1298	−12,580	−12,380
	T12k_9	TCTGAGCATTTGGGCTTGC	3	984	−12,562	−12,671
	T12k_10	CAAGATGTCGGGGAGTGGCC	17	1502	−12,976	−12,900
−11 ~ − 12 k cal/mol	T11k_1	GGCTAAGGGGGTACACTTCA	x	657	−11,112	−11,112
	T11k_2	CTTGGAAGTGGACGTAGGTGT	x	802	−11,333	−11,333
	T11k_3	GGTGTCTGTCCCGGCCAG	4	529	−13,905	− 11,348
	T11k_4	CATTTACAATCCAGCCAAATCACT	7	1475	−11,879	−11,879
	T11k_5	GCTCCTGGGGCATAGGGATG	3	335	−11,911	−11,911
	T11k_6	CAGGGATTGGATGGCCCC	11	516	−11,193	−11,193
	T11k_7	CTGGCTTGGCACTGGTCT	15	916	−11,926	−11,322
	T11k_8	AGCCCTGTGTGGTTCCAAG	6	916	−11,194	−11,175
	T11k_9	CTCACTCCATCCTGGACGT	2	452	−11,110	−11,110
	T11k_10	GCTCACTCCATCCTGGACGT	2	452	−11,868	−11,868
−10 ~ − 11 k cal/mol	T10k_1	CCTCCTTGTGCCCTAGAGTT	14	185	−10,271	−10,271
	T10k_2	cctttctgttgcctGTGGTAAG	5	161	−10,543	−10,224
	T10k_3	GCTTTTCCTCATGGGGCAAA	4	447	−10,575	−10,809
	T10k_4	CCAGGACAAGGCCTCATCC	4	325	− 10,242	− 10,853
	T10k_5	TTCCATGGCAGACTTGTAAGGA	14	401	−10,934	−10,934
	T10k_6	CAGTGTGGTAAAAACGTCAGGATG	2	464	−10,167	−10,167
	T10k_7	AGTTGCAGAACCTTGCCCT	14	375	−10,812	−10,350
	T10k_8	TCGAGACGGGGGTAAAGGAG	X	147	−10,799	−10,073
	T10k_9	AGGAATTCATGCCTTTGGGACA	6	191	−10,203	−10,678
	T10k_10	CTGCTCCATGGCTGATCTCC	4	316	−10,235	−10,809
−9 ~ − 10 k cal/mol	T9k_1	ATGGAGGCTGGATAGGAGGT	1	162	− 9516	− 9084
	T9k_2	GCCTCCTTGTGCCCTAGAGT	14	187	− 9598	−9598
	T9k_3	GGGTCTTGGCAAGTGGTACTG	6	394	− 9068	− 9307
	T9k_4	GCTCCTGGGGCATAGGGAT	3	337	− 9737	−9737
	T9k_5	GATTTCAGGGTGGTCACAGT	2	419	− 9299	− 9050
	T9k_6	ACGCTGCTATGGTTCTACAG	17	276	− 9320	− 9506
	T9k_7	GCAGCAGGGACTCACCATTG	2	409	− 9396	− 9861
	T9k_8	ATTCAGCGTGATGTGTAATGAGG	9	428	− 9135	− 9334
	T9k_9	AGAGGCTCCTGCAATTGACAG	9	302	− 9394	− 9330
	T9k_10	TCAGACCAGTGCTACCTGAGAG	9	202	− 9438	− 9577

*: Chromosome number, △: Delta G value (cal/mol) of Left aligned site of the primer on the possible false amplicon, ■: Delta G value (cal/mol) of right aligned site of the primer on the possible false amplicon

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ISSN: 1471-2164

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