PRIMERS, plasmids, freezer stocks, etc.

	A	B	C	D	E	F	G	H	I	K	L	M	N
1	Number	Primer Name	Sequence	for sequencing?	Forward?	Tm (finnzyme)	Warning?	bp	Order Submitted	Comments	Order file name	Order file location	extra notes

2	2	FLS_reverse_8	GCCggaACCACCggtGCCGCCggaCTCCAGGGCGTGAA	FALSE	FALSE				10/21/2011	FLS was WRONG: Re-made & re-ordered it	2011_10_20_Primer_order_translation_fusion_Try1	Mac	wrong but I forget why
3	3	ADH_forward_8	tccGGCGGCaccGGTGGTtccGGCGGCCATCATCGGCA	FALSE	FALSE				10/21/2011		2011_10_20_Primer_order_translation_fusion_Try1	Mac	omitted 14 bp!!
4	4	ACS_reverse -- BEFORE ACS!!	CCTTCTTAATGTTATACAGTGTTA	TRUE	FALSE	54.3			10/21/2011		2011_10_20_Primer_order_translation_fusion_Try1	Mac
5	5	DHAK_forward	TAACACTGTATAACATTAAGAAGG	TRUE	TRUE	54.27			10/21/2011		2011_10_20_Primer_order_translation_fusion_Try1	Mac
6	6	FLS_reverse_8	GCCggaACCACCggtGCCGCCggaCTCCAGGGCG	FALSE	FALSE				?	Corrected FLS_reverse_8; gave Erick the broken tube.		Mac
7	7	VR	attaccgcctttgagtgagc	TRUE	FALSE	63.5	*			Works like VF2 does in pCM66		Mac
8	8	VF2	tgccacctgacgtctaagaa	TRUE	TRUE	63.9						Mac
9	9	VF_J1	GCTTTCGCTAAGGATGATTTCTGG	TRUE	TRUE	67.8				Tm=58; starts right before BioBrick prefix		Mac
10	10	FLS-verify-300-L	GCCGGTCAGAAACAGGACC	TRUE	FALSE	67.4			12/15/2011			Mac
11	11	FLS-verify-300-R	GGGCTGGACCCTGCACTT	TRUE	TRUE	68.1			12/15/2011			Mac
12	12	DHAK-verify-300-L	GTACGCCGCTCGCGTTTT	TRUE	FALSE	68.73			12/15/2011
13	13	DHAK-verify-300-R	CGAAAGAGATCGTTGCAAAGAGC	TRUE	TRUE	68.3			12/15/2011
14	14	ACS-verify-300-L	ACCTTCCCAGATAATCGCGG	TRUE	FALSE	67.39			12/15/2011
15	15	ACS-verify-300-R	AGGCCAAGCGATCTACGC	TRUE	TRUE	65.81			12/15/2011
16	16	ADH-verify-300-L	GATCAGACGGATGTCCGGTT	TRUE	FALSE	66.6			12/15/2011
17	17	ADH-verify-300-R	CAAGACGACATTGAGGCATCC	TRUE	TRUE	67.1			12/15/2011
18	18	FLS-610-F	CAGAACGCCCGGTCATTGT	TRUE	TRUE	68.7				numbering starts from ATG on gene, and counts to starting bp of primer	2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
19	19	ADH-220-F	TTGATGCCACTAGCGCAGG	TRUE	TRUE	68				F is for forward, R is for reverse. (This is different from L/R above)	2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
20	20	ADH-835-F	CGCATTATCTGCCGGCGT	TRUE	TRUE	70					2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
21	21	ACS-404-F	GGCGATCTACATGCCGATG	TRUE	TRUE	66.95					2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
22	22	ACS-1000-F	CTAATTGGCCGACCCCGG	TRUE	TRUE	69.9					2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
23	23	DHAK-273-F	AATGAAAACGCGAGCGGC	TRUE	TRUE	68.8					2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
24	24	DHAK-894-F	CCGGTTCAGACCATTGCG	TRUE	TRUE	68.1	*	18		WARNING - non-specific sequencing in 10-208678147 when the priming sequence was verified	2011_12_25_Primer_Order_verify_translation_fusion_product	Mac
25	25	GBD-end-F	CTCCGAAGGCAAGCACCA	TRUE	TRUE	68			1/8/2012	start primer to verify insert of Berkeley Scaffolds	2012_01_08-primers-to-verify-scaffolds	Mac
26	26	TrrnB-start-R	tgttcgggcccaagcttc	TRUE	FALSE	69			1/8/2012	reverse primer to verify insert of Berkeley Scaffolds (ordered with F letter; later changed to R because it goes backward!)	2012_01_08-primers-to-verify-scaffolds	Mac
27	27	ADH_F_8-v2	GCCggaACCACCggtGCCGCCggaAGCAAACGTAAAGTGGCCAT	FALSE	FALSE			44	1/17/2012	fixed version of primer3: primer3 was missing 14 bp!!
28	28	Pdz-FLS-F	GTTTCTTCGAATTCGCGGCCGCTTCTAGAGatgGGCGTGAAAGAATCGCTGGTGGGTAGCGGCGCGATGATCACGGGCG	FALSE	FALSE	82		79	1/17/2012	BioBrick prefix, start, Janet's PDZ design, GSG linker, FLS
29	29	SH3-FLS-F	TTTCTTCGAATTCGCGGCCGCTTCTAGAGatgCCGCCGCCGGCGCTGCCGCCGAAAAGAAGGAGAGGTAGCGGCGCGATGATCACGGGCG	FALSE	FALSE	85		90	1/17/2012	1st useless base missing: to make 90 bp to make order cheaper! BioBrick prefix, start, Janet's SH3 design, GSG linker, FLS
30	30	Pdz-ADH-F	GTTTCTTCGAATTCGCGGCCGCTTCTAGAGatgGGCGTGAAAGAATCGCTGGTGggtagcggcAGCAAACGTAAAGTGGCCAT	FALSE	FALSE	81		83	1/17/2012	BioBrick prefix, start, Janet's PDZ design, GSG linker, ADH
31	31	SH3-ADH-F	GTTTCTTCGAATTCGCGGCCGCTTCTAGAGatgCCGCCGCCGGCGCTGCCGCCGAAAAGAAGGAGAggtagcggcAGCAAACGTAAAGTGGCCAT	FALSE	FALSE	84		95	1/17/2012	BioBrick prefix, start, Janet's SH3 design, GSG linker, ADH
32	32	FLS-R-biobricks	GTTTCTTCctgcagcggccgctactagtaCTCGAGTCATTACTCCAGGGCG	FALSE	FALSE	75		57	1/17/2012	includes 2 stop codons, & NotI between stops and BioBrick suffix. Reverse complement!
33	33	ADH-R-biobricks	GTTTCTTCctgcagcggccgctactagtaTCATTAAGCTGCCTCACCAGC	FALSE	FALSE	75		50	1/17/2012	includes 2 stop codons, no NotI, yes biobricks. Reverse complement!
34	34	FLS_rev_8-v3	GCCggaACCACCggtGCCGCCggaCTCCAGGGCGCCAGATTG	FALSE	FALSE	82		42	2/7/2012	improved (20 bp of homology instead of 10) to reduce mispriming
35	35	ADH_F_8-v3	tccGGCGGCaccGGTGGTtccGGCAGCAAACGTAAAGTGGCCAT	FALSE	FALSE	80		44	2/7/2012	correct sequence for homologous region
36	36	GibBrP-J23100	GTTTCTTCGAATTCCTGCTGCGGAGATCTTTGACGGCTAGCTCAGTC	FALSE	FALSE	72		47	2/24/2012	extra bps + GibsonBrickPrefix + 18 bp of J23100
37	37	FLS-8AA-GibBrS	CAAAGAAGCTCGAGAACCCTGTTGGATCCaccaccggtgccgccggaCTCCAGGGCGCCAGATTGAA	FALSE	FALSE	82		67	2/24/2012	reverse: 18 bp FLS w/o stop codons +GibsonBrick suffix
38	38	GibBrP-ADH-noStrt	GTTTCTTCGAATTCCTGCTGCGGAGATCTAGCAAACGTAAAGTGGCC	FALSE	FALSE	72		47	2/24/2012	extra bps + Gibson Brick prefix+ 18 AA of ADH w/o start codon
39	39	ADH-GibBrS	CAAAGAAGCTCGAGAACCCTGTTGGATCCTCATTAAGCTGCCTCACC	FALSE	FALSE	72		47	2/24/2012	reverse of: 18 bp of ADH + 2 stop codons + GibsonBrick suffix + extra cutting bps
40	40	FLS-fusion-control-R	CAAAGAAGCTCGAGAACCCTGTTGGATCCTCATTACTCCAGGGCGCCAG	FALSE	FALSE	75		49	2/27/2012
41	41	ADH-fusion-control-f	GTTTCTTCGAATTCCTGCTGCGGAGATCTAGGAGGTAAAACATATGAGCAAACGTAAAGTGGCCA	FALSE	FALSE	74		65	2/27/2012
42	42	lacI-seq-insert	gattcattaatgcagctggcac	TRUE	TRUE	65.79		22	2/27/2012	actually primer 124 is better for this purpose: you usually miss a little bit of what comes after lacI
43	43	FLS-BamHI-F	GCACGCCCGGACCCAGCTGATTTAG	FALSE	FALSE	81		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
44	44	FLS-BamHI-R	CTAAATCAGCTGGGTCCGGGCGTGC	FALSE	FALSE	81		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
45	45	DHAK-BglII-F	CCCAAGCACCGAAGACCTCATTAGC	FALSE	FALSE	77		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
46	46	DHAK-BglII-R	GCTAATGAGGTCTTCGGTGCTTGGG	FALSE	FALSE	77		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
47	47	DHAK-BamHI-F	GAAAGTCCTGGACCCTATCCCAAGC	FALSE	FALSE	77		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
48	48	DHAK-BamHI-R	GCTTGGGATAGGGTCCAGGACTTTC	FALSE	FALSE	77		25	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
49	49	ACS-BamHI-F	CCTTGGCGGACCCGGGTGTCG	FALSE	FALSE	81		21	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
50	50	ACS-BamHI-R	CGACACCCGGGTCCGCCAAGG	FALSE	FALSE	81		21	2/2/2012	for site-directed mutagenesis to make them BglBrick-firendly
51	51	FLS_rev_6	accactagtactaccgccctccagggcgcc	FALSE	FALSE	80.4		30	3/7/2012	Tm for homology region = 58.8 (12 bp); Tm for linker = 54.7 (21 bp) via Finnzyme calculator. Whole sequence Tm = 80.4
52	52	ADH_F_6	ggcggtagtactagtggtagcaaacgtaaagtggc	FALSE	FALSE	75.2		35	3/7/2012	Tm for linker = 54.7 (21 bp) via Finnzyme calculator. Tm for homology region = 56.9 (17 bp); Whole sequence Tm = 75.2
53	53	FLS_rev_6-control	accactagtactaccgccttatcactccagggcg	FALSE	FALSE	73.4		34	3/7/2012	Tm for homology region = 58.7 (16 bp); Tm for linker = 54.7 (21 bp) via Finnzyme calculator. Whole sequence Tm = 73.4
54	54	ADH_F_6-control	ggcggtagtactagtggtaggaggtaaaacatatgagcaaacgtaaagtg	FALSE	FALSE	78.4		50	3/7/2012	Tm for linker = 54.7 (21 bp) via Finnzyme calculator. Tm for homology region = 58.3 (18 bp); Whole sequence Tm = 78.4
55	55	SH3-ADH-add-EloRBS	GTTTCTTCtctagagTAACACTGTATAACATTAAGAaaagaggagaaataCTAGAGatgCCGCCGC	FALSE	FALSE			66	3/20/2012	Add Elowitz RBS (BBa_B0034) in front since cloning didn't work well. 10 bp homology with PDZ-FLS; use with VR to make part. These include a spacer that I don't need (I found out after the fact)
56	56	PDZ-ADH-add-EloRBS	GTTTCTTCtctagagTAACACTGTATAACATTAAGAaaagaggagaaataCTAGAGatgGGCGTGAAAGAA	FALSE	FALSE			71	3/20/2012
57	57	J23110-ACS-promoter-F	TTCTTCGAATTCGCGGCCGCTTCTAGAGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCAGGAGGTAAAAAAAATGAGC	FALSE	FALSE				4/12/2012	For changing the pLac promoter to J23110. Tm for homologour region on ACS-DHAK is 57oC by Finnzymes.
58	58	GBD-ACS-Gibson1-R	TTCGTCAGAAGAGTGGATAGCACGAGAACGTTTCTGCATAACGTGCATCAGAGCACCAACCAGCATTTTTTTTACCTCCTTCCACAC	FALSE	FALSE			87	5/21/2012	Adding GBD to pLac-ACS: start of GBD sequence
59	59	GBD-ACS-Gibson2-F	CTCGTGCTATCCACTCTTCTGACGAAGGTGAAGACCAGGCTGGTGACGAAGACGAAGACGGTAGCGGCAGCCAGATCCACAAGCATAC	FALSE	FALSE			88	5/21/2012	Adding GBD to pLac-ACS: end of GBD sequence
60	60	VR-RC	gctcactcaaaggcggtaat	TRUE	FALSE	63.5	*			reverse complement of VR. Works backward in pCM66
61	61	GBD-ACS-Gibson3-VR-RC-alternate	GCTAATCTAACTAACTAACCCTTAGTGACTCg	FALSE	FALSE					?? On 7/20/2012 I tried to figure out what this primer is and have no idea. Doesn't match anything
62	62	inside_GBD_F	GTGCTCTGATGCACGTTAT	TRUE	TRUE	59				Tm by finnzymes. One of two primers to verify gibson cloning
63	63	ACS_38_R	GATTGATAAGGCAACGGTCC	TRUE	FALSE	63.6				used with primer 62 on potential Gibson assembly, this --> 156 bp & shouldn't prime on un-modified template. **Use in conjuction with primer 59 and/or VF2 (as a positive control)
64	64	Eut-440-F	ttaaactttaccctgtgtga	TRUE	TRUE	55.35		20	5/22/2012 ish	ordered by Amanda
65	65	Eut-1213-F	agtgtgccgtcgcta	TRUE	TRUE	57.88		15	5/22/2012 ish
66	66	Eut-1944-F	cagtgggcgaacgat	TRUE	TRUE	59		15	5/22/2012 ish	use VF2 & VR to complete sequencing coverage
67	67	GA-1-p1-2012_06	atttctcctcttttgtgctcagtatcttgttatccgctcacaatgtcaattgttatccgctcacaattAGATCTCCGCAGCAGGAATTC	FALSE	FALSE			90		sew new FLS & ADH ec_ADH_sol with PDZ & SH3 into a new pSB3K3 vector: see red notebook for planning
68	68	GA-1-p2-2012_06	gataacaagatactgagcacaaaagaggagaaatactagaATGGCGATGATCACGGGCGG	FALSE	FALSE
69	69	GA-1-p3-2012_06	ctctttTCTTAATGTTATACAGTGTTATCTAGATCATTACACCAGCGATTCTTTCACGCCGCCGCTACCCTCCAGGGCGCCAGATTGAA	FALSE	FALSE	71.95		89
70	70	GA-1-p4-2012_06	AACACTGTATAACATTAAGAaaagaggagaaaTACTAGCATATGAGCAAGCGTAAAGTGG	FALSE	FALSE
71	71	GA-1-p5-2012_06	TCTCCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTAGAACCGCCGGCCGCTTC	FALSE	FALSE
72	72	GA-1-p6-2012_06	CCGCCGCCGGCGCTGCCGCCGAAAAGAAGGAGATAATGAGGATCCAACAGGGTTCTCGAG	FALSE	FALSE
73	73	DHAK_107-F	CCGTAAAACCGATTCTGA	TRUE	TRUE	59.19		18	5/26/2012
74	74	ACS-144-F	AAACCGTATCAAAAGGTAAAG	TRUE	TRUE	56.99		21	5/26/2012
75	75	EutS-186-R	accgatgtgtacatccgc	TRUE	FALSE	71.2		18
76	76	pGA3K3-pre-prefix-F	aatccttagctttcgctaaggat	TRUE	TRUE	62.52				works on pGA1C3, too!
77	77	ec_ADH_sol-43-R	TCTTAATCATCAGGTCCGTGC	TRUE	FALSE	64.3
78	78	replace-p68	ttgtgagcggataacaattgacattgtgagcggataacaagatactgagcacaaaagaggagaaatactagATGGCGATGATCACGGGCG	FALSE	FALSE	73.96		90		had "scar" before prefix wrong
79	79	replace-p70	AACACTGTATAACATTAAGAaaagaggagaaaTACTAGATGAGCAAGCGTAAAGTGGCGA	FALSE	FALSE			60		needed to remove 3 bp before ADH start so RBS is stronger
80	80	replace-p78	agcggataacaagatactgagcacaaaagaggagaaatactagATGGCGATGATCACGGG	FALSE	FALSE	63.4		60
81	81	Gibson-FLS_F	attgtgagcggataacaattgacattgtgagcggataacaagatactgagcacaCGAGGAGGTAATATATGGCTATGATTACTGGTGGTG	FALSE	FALSE			90
82	82	Gibson-FLS_R	GTTATCTAGATCATTACACCAGCGATTCTTTCACGCCGCCGCTACCCGCGCCGGATTGGA	FALSE	FALSE			60
83	83	Gibson-ec_ADH_sol_F	CGGCGGCGTGAAAGAATCGCTGGTGTAATGATCTAGATAACACTGTATAACATTAAGAGAGACAAACGATATGAGCAAGCGTAAAGTGGC	FALSE	FALSE			90
84	84	Gibson-ec_ADH_sol_R	CCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTAGAACCGCCGGCCGCTTCACC	FALSE	FALSE			60
85	85	Gibson-pGA3K3_R	ttatccgctcacaatgtcaattgttatccgctcacaattAGATCTCCGCAGCAGGAATTC	FALSE	FALSE			60
86	86	Gibson-ADH_3K9D_F	GTGAAAGAATCGCTGGTGTAATGATCTAGATAACACTGTATAACATTAAGAGGAAGTCTAGGGatgCATATGAGCCTGGAAGATAAGGAC	FALSE	FALSE	68.8		90
87	87	Gibson-ADH_3K9D_R	AACCCTGTTGGATCCTCATTATCTCCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTCTCGAGGCTACCGCCTTCGCGAATGTC	FALSE	FALSE	79		60		oops... Tm seems to be 79+oC. Doesn't anneal. Alternate with Tm = 65: CCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTCTCGAGGCTACCGCCTTCGCG
88	88	Gbsn-ec_ADH_sol-higher exp_F	TAGATAACACTGTATAACATTAAGAGGGGGTAGCATAGTTATGAGCAAGCGTAAAG	FALSE	FALSE	65		56		the Tm that can bind to the reverse direction has Tm = 52.5 (shortened so this is the case).
89	89	Gbsn-ec_ADH_sol-higher exp_R	TTGCTCATAACTATGCTACCCCCTCTTAATGTTATACAGTGTTATCTAGATCATTACACC	FALSE	FALSE	65				Tm of misanneal = 55oC
90	90	Gbsn-ec_ADH_3K9D-higher_exp_F	ACTGTATAACATTAAGAATATCAAAAGGGAGGACCGGatgCATATGAGCCTGGAAGATAA	FALSE	FALSE	64		60		5' end of the primer mis-anneals but Tm = 48.
91	91	Gbsn-ec_ADH_3K9D-higher_exp_R	GcatCCGGTCCTCCCTTTTGATATTCTTAATGTTATACAGTGTTATCTAGATCATTACAC	FALSE	FALSE	63		60
92	92	ADH_3K9D-f	AGAATCGCTGGTGTAATGATCTAGATAACACTGTATAACATTAAGAATATCAAAAGGGAGGACCGGatgCATATGAGCCTGGAAGATAAG	FALSE	FALSE	65		90
93	93	ADH_3K9D-r	TCTCCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTCTCGAGGCTACCGCCTTC	FALSE	FALSE	69		60
94	94	ec_ADH_sol-f	CGGCGTGAAAGAATCGCTGGTGTAATGATCTAGATAACACTGTATAACATTAAGAGGGGGTAGCATAGTTATGAGCAAGCGTAAAGTGGC	FALSE	FALSE	69		90
95	95	ec_ADH_sol-r	ATTATCTCCTTCTTTTCGGCGGCAGCGCCGGCGGCGGGCCACCGCTAGAACCGCCGGCCG	FALSE	FALSE	65.5		90
96	96	FLS_LT09-163-R	CATAACCTTCCGCAGCGT	TRUE	FALSE	64.3		18		Primer 77 is 43-R, but I'll order this one anyway
97	97	FLS_LT09-400-F	CAACTGAACACATCCCGC	TRUE	TRUE	63.4		18
98	98	FLS_LT09-1070-F	CTTCCATCGCGGCTAAATC	TRUE	TRUE	65		19
99	99	FLS_LT09-1620-F	AACGTTGCTGTGGCCCTGG	TRUE	TRUE	64		19
100	100	ec_ADH_sol-100-R	TTCGGATCAATGCCGAC	TRUE	FALSE	63		17