AutoCloner

Multiple sequence alignment - TraesCS7D01G167300

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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	TraesCS7D01G167300	chr7D	100.000	3787	0	0	1	3787	117747893	117751679	0.000000e+00	6994.0
1	TraesCS7D01G167300	chr7B	89.483	1179	80	23	1784	2933	78227960	78229123	0.000000e+00	1450.0
2	TraesCS7D01G167300	chr7B	89.036	1058	63	16	731	1773	78226888	78227907	0.000000e+00	1262.0
3	TraesCS7D01G167300	chr7B	85.998	1207	106	35	1784	2950	78321777	78322960	0.000000e+00	1234.0
4	TraesCS7D01G167300	chr7B	89.605	885	50	17	900	1773	78320869	78321722	0.000000e+00	1086.0
5	TraesCS7D01G167300	chr7B	86.772	378	25	7	4	358	78267748	78268123	7.620000e-107	398.0
6	TraesCS7D01G167300	chr7B	82.143	308	50	4	3483	3787	609025329	609025634	3.750000e-65	259.0
7	TraesCS7D01G167300	chr7B	79.856	139	27	1	23	161	44480506	44480369	2.410000e-17	100.0
8	TraesCS7D01G167300	chr7A	88.545	1196	80	28	1784	2954	122164515	122165678	0.000000e+00	1397.0
9	TraesCS7D01G167300	chr7A	88.926	605	52	8	1176	1773	122163860	122164456	0.000000e+00	732.0
10	TraesCS7D01G167300	chr7A	94.301	193	11	0	931	1123	122163329	122163521	2.860000e-76	296.0
11	TraesCS7D01G167300	chr7A	95.513	156	6	1	505	660	122163124	122163278	8.120000e-62	248.0
12	TraesCS7D01G167300	chr1A	81.775	417	65	10	3372	3785	14164639	14165047	4.690000e-89	339.0
13	TraesCS7D01G167300	chr1A	82.979	235	38	2	3483	3717	572238514	572238282	1.070000e-50	211.0
14	TraesCS7D01G167300	chr1A	78.827	307	61	4	3483	3787	449926291	449925987	1.780000e-48	204.0
15	TraesCS7D01G167300	chr5D	86.275	306	40	2	3484	3787	426280595	426280290	7.840000e-87	331.0
16	TraesCS7D01G167300	chr5D	89.024	82	8	1	3371	3452	352845978	352845898	2.410000e-17	100.0
17	TraesCS7D01G167300	chr2B	83.601	311	43	7	3483	3787	663782710	663782402	6.190000e-73	285.0
18	TraesCS7D01G167300	chr2B	84.270	89	13	1	73	161	71879283	71879370	6.740000e-13	86.1
19	TraesCS7D01G167300	chr5B	83.388	307	46	5	3483	3787	706993563	706993260	2.880000e-71	279.0
20	TraesCS7D01G167300	chr5B	82.667	300	46	2	3489	3787	516059682	516059388	1.040000e-65	261.0
21	TraesCS7D01G167300	chr2D	81.908	304	50	4	3487	3787	20725886	20726187	6.280000e-63	252.0
22	TraesCS7D01G167300	chr4D	86.585	82	10	1	3372	3453	397513050	397512970	5.210000e-14	89.8
23	TraesCS7D01G167300	chr6D	81.250	112	18	2	3342	3450	361544961	361545072	1.870000e-13	87.9
24	TraesCS7D01G167300	chr6D	87.719	57	6	1	2961	3016	138401526	138401470	8.780000e-07	65.8
25	TraesCS7D01G167300	chr1B	95.918	49	1	1	2966	3013	664044027	664043979	1.130000e-10	78.7
26	TraesCS7D01G167300	chr1B	95.918	49	1	1	2966	3013	664052465	664052417	1.130000e-10	78.7
27	TraesCS7D01G167300	chr6B	95.745	47	1	1	2966	3011	22987315	22987269	1.460000e-09	75.0
28	TraesCS7D01G167300	chr6A	77.600	125	26	2	205	327	593926522	593926398	1.460000e-09	75.0
29	TraesCS7D01G167300	chrUn	93.878	49	2	1	2966	3013	92722824	92722776	5.250000e-09	73.1
30	TraesCS7D01G167300	chrUn	93.878	49	2	1	2966	3013	347977189	347977141	5.250000e-09	73.1
31	TraesCS7D01G167300	chrUn	93.878	49	2	1	2966	3013	378080389	378080341	5.250000e-09	73.1
32	TraesCS7D01G167300	chr4A	88.333	60	6	1	2955	3013	718869870	718869929	1.890000e-08	71.3
33	TraesCS7D01G167300	chr3B	85.938	64	5	3	2948	3010	173382367	173382427	8.780000e-07	65.8
34	TraesCS7D01G167300	chr4B	100.000	29	0	0	155	183	617868519	617868491	2.000000e-03	54.7

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	TraesCS7D01G167300	chr7D	117747893	117751679	3786	False	6994.00	6994	100.00000	1	3787	1	chr7D.!!$F1	3786
1	TraesCS7D01G167300	chr7B	78226888	78229123	2235	False	1356.00	1450	89.25950	731	2933	2	chr7B.!!$F3	2202
2	TraesCS7D01G167300	chr7B	78320869	78322960	2091	False	1160.00	1234	87.80150	900	2950	2	chr7B.!!$F4	2050
3	TraesCS7D01G167300	chr7A	122163124	122165678	2554	False	668.25	1397	91.82125	505	2954	4	chr7A.!!$F1	2449

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	Self end TH	Hairpin	End Stability	Orientation
709	710	0.034089	CTTCAACATCCACCCCTCCC	60.034	60.0	0.0	0.0	0.00	4.3	F
1404	1694	0.033504	CCATACCCGAGATGGTTCCG	59.966	60.0	0.0	0.0	39.29	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1515	1805	0.167470	CTGCAGGTGACATGCGAAAG	59.833	55.0	17.68	5.71	46.87	2.62	R
3318	3749	0.107165	ACCGGGCTTTAGCTGAATCC	60.107	55.0	6.32	2.58	41.70	3.01	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
19	20	2.218953	AGCGAACTTCGTTGTTCAGA	57.781	45.000	12.62	0.00	44.59	3.27
20	21	2.546778	AGCGAACTTCGTTGTTCAGAA	58.453	42.857	12.62	0.00	44.59	3.02
21	22	2.540101	AGCGAACTTCGTTGTTCAGAAG	59.460	45.455	12.62	3.93	44.59	2.85
22	23	2.538449	GCGAACTTCGTTGTTCAGAAGA	59.462	45.455	12.62	0.00	44.76	2.87
23	24	3.601812	GCGAACTTCGTTGTTCAGAAGAC	60.602	47.826	12.62	5.14	44.76	3.01
24	25	3.797256	CGAACTTCGTTGTTCAGAAGACT	59.203	43.478	17.93	0.00	44.76	3.24
25	26	4.267928	CGAACTTCGTTGTTCAGAAGACTT	59.732	41.667	17.93	0.00	44.76	3.01
26	27	5.554696	CGAACTTCGTTGTTCAGAAGACTTC	60.555	44.000	7.14	7.14	44.76	3.01
27	28	3.797256	ACTTCGTTGTTCAGAAGACTTCG	59.203	43.478	9.53	5.31	44.76	3.79
28	29	3.431922	TCGTTGTTCAGAAGACTTCGT	57.568	42.857	9.53	0.00	34.02	3.85
29	30	4.556942	TCGTTGTTCAGAAGACTTCGTA	57.443	40.909	9.53	0.00	34.02	3.43
30	31	4.923893	TCGTTGTTCAGAAGACTTCGTAA	58.076	39.130	9.53	5.51	34.02	3.18
31	32	4.736793	TCGTTGTTCAGAAGACTTCGTAAC	59.263	41.667	20.21	20.21	32.98	2.50
32	33	4.373717	CGTTGTTCAGAAGACTTCGTAACG	60.374	45.833	20.94	20.43	34.20	3.18
33	34	3.635331	TGTTCAGAAGACTTCGTAACGG	58.365	45.455	20.94	7.17	34.20	4.44
34	35	2.985139	GTTCAGAAGACTTCGTAACGGG	59.015	50.000	15.43	1.89	34.02	5.28
35	36	1.542915	TCAGAAGACTTCGTAACGGGG	59.457	52.381	9.53	0.00	34.02	5.73
36	37	1.542915	CAGAAGACTTCGTAACGGGGA	59.457	52.381	9.53	0.00	34.02	4.81
37	38	2.029649	CAGAAGACTTCGTAACGGGGAA	60.030	50.000	9.53	0.00	34.02	3.97
38	39	2.230750	AGAAGACTTCGTAACGGGGAAG	59.769	50.000	9.53	0.00	44.04	3.46
39	40	0.245813	AGACTTCGTAACGGGGAAGC	59.754	55.000	1.00	0.00	42.62	3.86
40	41	1.074872	GACTTCGTAACGGGGAAGCG	61.075	60.000	1.00	0.00	42.62	4.68
41	42	2.432972	TTCGTAACGGGGAAGCGC	60.433	61.111	0.00	0.00	0.00	5.92
42	43	3.938019	TTCGTAACGGGGAAGCGCC	62.938	63.158	2.29	0.00	0.00	6.53
52	53	4.135493	GAAGCGCCGTCGAGCAAC	62.135	66.667	2.29	4.97	37.25	4.17

Showing 1 to 25 of 1,009 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	7.867136	ACGAAGTCTTCTGAACAACGAAGTTC	61.867	42.308	10.81	14.71	45.63	3.01
7	8	3.777478	ACGAAGTCTTCTGAACAACGAA	58.223	40.909	10.81	0.00	29.74	3.85
8	9	3.431922	ACGAAGTCTTCTGAACAACGA	57.568	42.857	10.81	0.00	29.74	3.85
9	10	4.373717	CGTTACGAAGTCTTCTGAACAACG	60.374	45.833	18.87	16.44	43.93	4.10
10	11	4.085210	CCGTTACGAAGTCTTCTGAACAAC	60.085	45.833	6.24	11.35	43.93	3.32
11	12	4.046462	CCGTTACGAAGTCTTCTGAACAA	58.954	43.478	6.24	3.60	43.93	2.83
12	13	3.551454	CCCGTTACGAAGTCTTCTGAACA	60.551	47.826	6.24	0.00	43.93	3.18
13	14	2.985139	CCCGTTACGAAGTCTTCTGAAC	59.015	50.000	6.24	12.08	43.93	3.18
14	15	2.029649	CCCCGTTACGAAGTCTTCTGAA	60.030	50.000	6.24	2.03	43.93	3.02
15	16	1.542915	CCCCGTTACGAAGTCTTCTGA	59.457	52.381	6.24	0.00	43.93	3.27
16	17	1.542915	TCCCCGTTACGAAGTCTTCTG	59.457	52.381	6.24	6.90	43.93	3.02
17	18	1.915141	TCCCCGTTACGAAGTCTTCT	58.085	50.000	6.24	1.16	43.93	2.85
18	19	2.603953	CTTCCCCGTTACGAAGTCTTC	58.396	52.381	6.24	2.18	43.93	2.87
19	20	1.337541	GCTTCCCCGTTACGAAGTCTT	60.338	52.381	6.24	0.00	43.93	3.01
20	21	0.245813	GCTTCCCCGTTACGAAGTCT	59.754	55.000	6.24	0.00	43.93	3.24
21	22	1.074872	CGCTTCCCCGTTACGAAGTC	61.075	60.000	6.24	0.00	43.93	3.01
23	24	2.450345	GCGCTTCCCCGTTACGAAG	61.450	63.158	6.24	3.18	38.81	3.79
24	25	2.432972	GCGCTTCCCCGTTACGAA	60.433	61.111	6.24	0.00	0.00	3.85
25	26	4.440127	GGCGCTTCCCCGTTACGA	62.440	66.667	7.64	0.00	0.00	3.43
35	36	4.135493	GTTGCTCGACGGCGCTTC	62.135	66.667	5.31	3.08	37.46	3.86
40	41	3.712881	GTGTGGTTGCTCGACGGC	61.713	66.667	0.00	0.00	0.00	5.68
41	42	3.041940	GGTGTGGTTGCTCGACGG	61.042	66.667	0.00	0.00	0.00	4.79
42	43	3.403057	CGGTGTGGTTGCTCGACG	61.403	66.667	0.00	0.00	0.00	5.12
43	44	2.279918	ACGGTGTGGTTGCTCGAC	60.280	61.111	0.00	0.00	0.00	4.20
44	45	2.028484	GACGGTGTGGTTGCTCGA	59.972	61.111	0.00	0.00	0.00	4.04

Showing 1 to 25 of 1,011 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.