AutoCloner

Multiple sequence alignment - TraesCS1B01G173500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G173500	chr1B	100.000	3607	0	0	936	4542	310190354	310186748	0.000000e+00	6661.0
1	TraesCS1B01G173500	chr1B	100.000	610	0	0	1	610	310191289	310190680	0.000000e+00	1127.0
2	TraesCS1B01G173500	chr6B	84.748	1567	229	10	945	2507	209240932	209239372	0.000000e+00	1561.0
3	TraesCS1B01G173500	chr2B	80.822	511	93	3	936	1445	781198083	781198589	3.290000e-106	396.0
4	TraesCS1B01G173500	chr1A	92.672	232	17	0	4307	4538	532401290	532401059	7.280000e-88	335.0
5	TraesCS1B01G173500	chr7B	75.676	185	39	6	4341	4522	514044834	514045015	2.250000e-13	87.9
6	TraesCS1B01G173500	chr3B	85.882	85	9	2	2528	2609	728222811	728222727	2.250000e-13	87.9
7	TraesCS1B01G173500	chr3B	84.706	85	10	2	2528	2609	728252187	728252103	1.050000e-11	82.4
8	TraesCS1B01G173500	chr3B	86.301	73	9	1	2538	2609	728232887	728232815	1.350000e-10	78.7
9	TraesCS1B01G173500	chr3B	83.529	85	11	2	2528	2609	728242755	728242671	4.870000e-10	76.8
10	TraesCS1B01G173500	chr5B	79.464	112	20	3	4416	4525	549774182	549774292	4.870000e-10	76.8

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G173500	chr1B	310186748	310191289	4541	True	3894	6661	100.000	1	4542	2	chr1B.!!$R1	4541
1	TraesCS1B01G173500	chr6B	209239372	209240932	1560	True	1561	1561	84.748	945	2507	1	chr6B.!!$R1	1562
2	TraesCS1B01G173500	chr2B	781198083	781198589	506	False	396	396	80.822	936	1445	1	chr2B.!!$F1	509

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
209	210	0.034059	GACCTCTACATCATGCCGGG	59.966	60.0	2.18	0.00	5.73	F
598	599	0.034616	CTGCCCCGATCTCTGGATTC	59.965	60.0	0.00	31.46	2.52	F
1683	1684	0.037303	AAGACATCCCACTGCCTGTG	59.963	55.0	0.00	45.80	3.66	F
1952	1953	0.106708	GACTGGCAACCTGACTGTGA	59.893	55.0	0.00	37.70	3.58	F
3050	3052	0.107410	ACACCAGAAACCACGCTCAA	60.107	50.0	0.00	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1641	1642	0.034059	AAACTGGTCGCTCACTGAGG	59.966	55.0	8.17	0.00	3.86	R
2232	2233	0.036671	TGCAGATCTCACTGGTGCAG	60.037	55.0	0.00	39.17	4.41	R
3031	3033	0.107410	TTGAGCGTGGTTTCTGGTGT	60.107	50.0	0.00	0.00	4.16	R
3373	3375	0.107993	GCTCTACTGATGTGCCTGCA	60.108	55.0	0.00	0.00	4.41	R
4022	4024	0.032130	GATGCAAGATACGCCGGAGA	59.968	55.0	13.83	0.00	3.71	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	4.400109	GCGTCGACGTGCTCCTGA	62.400	66.667	35.48	0.00	42.22	3.86
35	36	2.485582	CGTCGACGTGCTCCTGAT	59.514	61.111	29.08	0.00	34.11	2.90
36	37	1.583967	CGTCGACGTGCTCCTGATC	60.584	63.158	29.08	0.00	34.11	2.92
37	38	1.506718	GTCGACGTGCTCCTGATCA	59.493	57.895	0.00	0.00	0.00	2.92
38	39	0.524392	GTCGACGTGCTCCTGATCAG	60.524	60.000	16.24	16.24	0.00	2.90
47	48	3.221222	CCTGATCAGGGTCCCGAC	58.779	66.667	31.14	0.00	44.87	4.79
48	49	1.685765	CCTGATCAGGGTCCCGACA	60.686	63.158	31.14	0.98	44.87	4.35
49	50	1.517832	CTGATCAGGGTCCCGACAC	59.482	63.158	15.38	0.00	34.18	3.67
50	51	1.229051	TGATCAGGGTCCCGACACA	60.229	57.895	0.99	5.10	37.14	3.72
51	52	0.617535	TGATCAGGGTCCCGACACAT	60.618	55.000	0.99	0.00	37.14	3.21
52	53	0.105039	GATCAGGGTCCCGACACATC	59.895	60.000	0.99	0.00	37.14	3.06
53	54	0.325671	ATCAGGGTCCCGACACATCT	60.326	55.000	0.99	0.00	37.14	2.90
54	55	0.544357	TCAGGGTCCCGACACATCTT	60.544	55.000	0.99	0.00	37.14	2.40
55	56	0.391661	CAGGGTCCCGACACATCTTG	60.392	60.000	0.99	0.00	37.14	3.02
56	57	1.078426	GGGTCCCGACACATCTTGG	60.078	63.158	0.00	0.00	34.14	3.61
57	58	1.677552	GGTCCCGACACATCTTGGT	59.322	57.895	0.00	0.00	0.00	3.67
58	59	0.673644	GGTCCCGACACATCTTGGTG	60.674	60.000	0.00	0.00	44.35	4.17
64	65	3.266964	CACATCTTGGTGTGCGGG	58.733	61.111	0.81	0.00	42.51	6.13
65	66	1.302431	CACATCTTGGTGTGCGGGA	60.302	57.895	0.81	0.00	42.51	5.14
66	67	0.888736	CACATCTTGGTGTGCGGGAA	60.889	55.000	0.81	0.00	42.51	3.97
67	68	0.179004	ACATCTTGGTGTGCGGGAAA	60.179	50.000	0.00	0.00	0.00	3.13
68	69	0.958091	CATCTTGGTGTGCGGGAAAA	59.042	50.000	0.00	0.00	0.00	2.29
69	70	1.339610	CATCTTGGTGTGCGGGAAAAA	59.660	47.619	0.00	0.00	0.00	1.94
70	71	1.698506	TCTTGGTGTGCGGGAAAAAT	58.301	45.000	0.00	0.00	0.00	1.82
71	72	1.339610	TCTTGGTGTGCGGGAAAAATG	59.660	47.619	0.00	0.00	0.00	2.32

Showing 1 to 25 of 1,782 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.685214	ATCAGGAGCACGTCGACGC	62.685	63.158	35.92	21.60	44.43	5.19
18	19	1.583967	GATCAGGAGCACGTCGACG	60.584	63.158	34.58	34.58	46.33	5.12
19	20	0.524392	CTGATCAGGAGCACGTCGAC	60.524	60.000	15.38	5.18	0.00	4.20
20	21	1.803289	CTGATCAGGAGCACGTCGA	59.197	57.895	15.38	0.00	0.00	4.20
21	22	4.391539	CTGATCAGGAGCACGTCG	57.608	61.111	15.38	0.00	0.00	5.12
31	32	1.257750	TGTGTCGGGACCCTGATCAG	61.258	60.000	16.24	16.24	33.49	2.90
32	33	0.617535	ATGTGTCGGGACCCTGATCA	60.618	55.000	9.41	11.08	33.49	2.92
33	34	0.105039	GATGTGTCGGGACCCTGATC	59.895	60.000	9.41	6.33	33.49	2.92
34	35	0.325671	AGATGTGTCGGGACCCTGAT	60.326	55.000	9.41	0.00	33.49	2.90
35	36	0.544357	AAGATGTGTCGGGACCCTGA	60.544	55.000	9.41	4.91	0.00	3.86
36	37	0.391661	CAAGATGTGTCGGGACCCTG	60.392	60.000	9.41	2.25	0.00	4.45
37	38	1.553690	CCAAGATGTGTCGGGACCCT	61.554	60.000	9.41	0.00	0.00	4.34
38	39	1.078426	CCAAGATGTGTCGGGACCC	60.078	63.158	0.00	0.00	0.00	4.46
39	40	0.673644	CACCAAGATGTGTCGGGACC	60.674	60.000	0.00	0.00	0.00	4.46
40	41	0.034896	ACACCAAGATGTGTCGGGAC	59.965	55.000	0.00	0.00	46.15	4.46
41	42	0.034756	CACACCAAGATGTGTCGGGA	59.965	55.000	0.00	0.00	46.15	5.14
42	43	2.543578	CACACCAAGATGTGTCGGG	58.456	57.895	0.00	0.00	46.15	5.14
48	49	0.179004	TTTCCCGCACACCAAGATGT	60.179	50.000	0.00	0.00	0.00	3.06
49	50	0.958091	TTTTCCCGCACACCAAGATG	59.042	50.000	0.00	0.00	0.00	2.90
50	51	1.698506	TTTTTCCCGCACACCAAGAT	58.301	45.000	0.00	0.00	0.00	2.40
51	52	1.339610	CATTTTTCCCGCACACCAAGA	59.660	47.619	0.00	0.00	0.00	3.02
52	53	1.782044	CATTTTTCCCGCACACCAAG	58.218	50.000	0.00	0.00	0.00	3.61
53	54	0.249657	GCATTTTTCCCGCACACCAA	60.250	50.000	0.00	0.00	0.00	3.67
54	55	1.365633	GCATTTTTCCCGCACACCA	59.634	52.632	0.00	0.00	0.00	4.17
55	56	1.374125	GGCATTTTTCCCGCACACC	60.374	57.895	0.00	0.00	0.00	4.16

Showing 1 to 25 of 1,819 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.