AutoCloner

Multiple sequence alignment - TraesCS2D01G459600

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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	TraesCS2D01G459600	chr2D	100.000	3027	0	0	1	3027	566263863	566260837	0.000000e+00	5590.0
1	TraesCS2D01G459600	chr2D	84.068	885	86	24	1306	2163	566656395	566655539	0.000000e+00	802.0
2	TraesCS2D01G459600	chr2D	85.740	547	64	12	1540	2086	566302380	566301848	1.580000e-157	566.0
3	TraesCS2D01G459600	chr2D	88.312	462	25	12	558	1010	566303373	566302932	7.430000e-146	527.0
4	TraesCS2D01G459600	chr2D	87.119	427	40	11	789	1212	566656870	566656456	1.270000e-128	470.0
5	TraesCS2D01G459600	chr2D	82.162	370	46	11	1052	1415	566302929	566302574	1.760000e-77	300.0
6	TraesCS2D01G459600	chr2D	95.238	84	2	1	493	574	566303475	566303392	6.810000e-27	132.0
7	TraesCS2D01G459600	chr2D	96.774	62	2	0	106	167	566303718	566303657	1.480000e-18	104.0
8	TraesCS2D01G459600	chr2D	86.842	76	10	0	198	273	566657551	566657476	5.380000e-13	86.1
9	TraesCS2D01G459600	chr2B	90.547	2486	120	41	106	2573	679032201	679029813	0.000000e+00	3182.0
10	TraesCS2D01G459600	chr2B	83.901	851	95	22	1306	2138	679696794	679697620	0.000000e+00	774.0
11	TraesCS2D01G459600	chr2B	80.795	1057	139	37	1045	2086	679071596	679070589	0.000000e+00	769.0
12	TraesCS2D01G459600	chr2B	87.521	601	58	6	1538	2138	679743830	679744413	0.000000e+00	678.0
13	TraesCS2D01G459600	chr2B	87.446	462	28	13	558	1010	679072032	679071592	3.480000e-139	505.0
14	TraesCS2D01G459600	chr2B	87.872	437	36	13	787	1215	679729837	679730264	5.830000e-137	497.0
15	TraesCS2D01G459600	chr2B	87.443	438	36	15	787	1215	679696308	679696735	1.260000e-133	486.0
16	TraesCS2D01G459600	chr2B	89.547	287	24	3	291	574	679072334	679072051	2.870000e-95	359.0
17	TraesCS2D01G459600	chr2B	84.158	303	14	12	2603	2884	679029827	679029538	2.310000e-66	263.0
18	TraesCS2D01G459600	chr2B	95.161	62	2	1	106	166	679072321	679072260	2.480000e-16	97.1
19	TraesCS2D01G459600	chr2B	93.478	46	3	0	116	161	679729186	679729231	5.420000e-08	69.4
20	TraesCS2D01G459600	chr2A	92.081	2134	114	33	106	2217	706490271	706488171	0.000000e+00	2953.0
21	TraesCS2D01G459600	chr2A	81.499	1481	164	60	719	2163	706530805	706529399	0.000000e+00	1116.0
22	TraesCS2D01G459600	chr2A	90.847	732	36	15	2306	3027	706487960	706487250	0.000000e+00	952.0
23	TraesCS2D01G459600	chr2A	80.564	993	129	38	1052	2028	706510965	706510021	0.000000e+00	706.0
24	TraesCS2D01G459600	chr2A	85.398	452	35	17	197	624	706511733	706511289	9.960000e-120	440.0
25	TraesCS2D01G459600	chr2A	93.676	253	11	3	659	911	706511289	706511042	1.020000e-99	374.0
26	TraesCS2D01G459600	chr2A	86.822	258	29	3	106	361	706511908	706511654	1.780000e-72	283.0
27	TraesCS2D01G459600	chr2A	94.444	108	6	0	3	110	706490415	706490308	1.870000e-37	167.0
28	TraesCS2D01G459600	chr2A	89.474	76	8	0	198	273	706531401	706531326	2.480000e-16	97.1
29	TraesCS2D01G459600	chr2A	92.424	66	5	0	106	171	706511797	706511732	8.930000e-16	95.3
30	TraesCS2D01G459600	chr7A	83.607	61	9	1	3	63	89911672	89911613	4.220000e-04	56.5

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	TraesCS2D01G459600	chr2D	566260837	566263863	3026	True	5590.000000	5590	100.000000	1	3027	1	chr2D.!!$R1	3026
1	TraesCS2D01G459600	chr2D	566655539	566657551	2012	True	452.700000	802	86.009667	198	2163	3	chr2D.!!$R3	1965
2	TraesCS2D01G459600	chr2D	566301848	566303718	1870	True	325.800000	566	89.645200	106	2086	5	chr2D.!!$R2	1980
3	TraesCS2D01G459600	chr2B	679029538	679032201	2663	True	1722.500000	3182	87.352500	106	2884	2	chr2B.!!$R1	2778
4	TraesCS2D01G459600	chr2B	679743830	679744413	583	False	678.000000	678	87.521000	1538	2138	1	chr2B.!!$F1	600
5	TraesCS2D01G459600	chr2B	679696308	679697620	1312	False	630.000000	774	85.672000	787	2138	2	chr2B.!!$F2	1351
6	TraesCS2D01G459600	chr2B	679070589	679072334	1745	True	432.525000	769	88.237250	106	2086	4	chr2B.!!$R2	1980
7	TraesCS2D01G459600	chr2B	679729186	679730264	1078	False	283.200000	497	90.675000	116	1215	2	chr2B.!!$F3	1099
8	TraesCS2D01G459600	chr2A	706487250	706490415	3165	True	1357.333333	2953	92.457333	3	3027	3	chr2A.!!$R1	3024
9	TraesCS2D01G459600	chr2A	706529399	706531401	2002	True	606.550000	1116	85.486500	198	2163	2	chr2A.!!$R3	1965
10	TraesCS2D01G459600	chr2A	706510021	706511908	1887	True	379.660000	706	87.776800	106	2028	5	chr2A.!!$R2	1922

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
188	341	0.179116	CTCCAGATGCAGTGTCCTCG	60.179	60.0	0.0	0.0	0.00	4.63	F
947	1487	0.508641	CTCGGCAGAACGACAAACAG	59.491	55.0	0.0	0.0	38.06	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1208	1752	1.072505	GGGCGAAACAACAGGAGGA	59.927	57.895	0.0	0.0	0.0	3.71	R
2576	3397	0.036306	CCGGGCAAACTACACTTCCT	59.964	55.000	0.0	0.0	0.0	3.36	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	1.809869	CTAGCAGCGCCTGTCTACA	59.190	57.895	2.29	0.00	33.43	2.74
34	35	1.153745	CAGCGCCTGTCTACACCTC	60.154	63.158	2.29	0.00	0.00	3.85
90	91	6.376581	CCTTGGCTCTCATTTCTCTTAAATGT	59.623	38.462	9.56	0.00	38.44	2.71
188	341	0.179116	CTCCAGATGCAGTGTCCTCG	60.179	60.000	0.00	0.00	0.00	4.63
200	353	1.947456	GTGTCCTCGACTTTGCCTTTT	59.053	47.619	0.00	0.00	33.15	2.27
227	382	5.771165	TCGCACCACATAATATAGTACTCCA	59.229	40.000	0.00	0.00	0.00	3.86
233	388	9.601810	ACCACATAATATAGTACTCCAGAATCA	57.398	33.333	0.00	0.00	0.00	2.57
249	404	9.265901	CTCCAGAATCAATTAGACATTAATCGT	57.734	33.333	0.00	0.00	0.00	3.73
327	482	6.380095	AGTACTCCAGAATCGATTAGACAC	57.620	41.667	11.38	8.40	0.00	3.67
346	501	9.687210	TTAGACACTAATCGTTGCGATATAATT	57.313	29.630	4.41	0.00	46.30	1.40
474	730	3.877508	GGGCGGATACTATTGAATATGGC	59.122	47.826	0.00	0.00	0.00	4.40
740	1222	6.347321	CCAAATTTGTTTCGGGCAGTTAATTC	60.347	38.462	16.73	0.00	0.00	2.17
947	1487	0.508641	CTCGGCAGAACGACAAACAG	59.491	55.000	0.00	0.00	38.06	3.16
959	1499	4.000988	ACGACAAACAGACACAGAAAAGT	58.999	39.130	0.00	0.00	0.00	2.66
994	1535	2.125106	CCGCCGAGAAAGGGAAGG	60.125	66.667	0.00	0.00	0.00	3.46
1208	1752	1.272928	TGATCTGCTGGTGAGTCCTCT	60.273	52.381	0.00	0.00	37.07	3.69
1209	1753	1.408702	GATCTGCTGGTGAGTCCTCTC	59.591	57.143	0.00	0.00	40.79	3.20
1252	1799	2.106684	GTTTCTCCTCCCCTGTTCTTGT	59.893	50.000	0.00	0.00	0.00	3.16
1278	1825	4.098055	TCAAGATGCTCTGTTCGTCTAC	57.902	45.455	0.00	0.00	0.00	2.59
1291	1839	5.149273	TGTTCGTCTACGTATGAACAAGAC	58.851	41.667	24.16	15.43	46.93	3.01
1299	1847	3.983344	ACGTATGAACAAGACGGTTACAC	59.017	43.478	13.93	0.00	40.84	2.90
1300	1848	3.058520	CGTATGAACAAGACGGTTACACG	59.941	47.826	0.00	0.00	40.31	4.49
1411	1967	3.807209	GCCTGGTTAGATTATGTCCGCAT	60.807	47.826	0.00	0.00	39.03	4.73
1506	2148	5.607477	TCTTCGTGTTCATACCAGTCTTTT	58.393	37.500	0.00	0.00	0.00	2.27
1834	2487	4.680237	CCCTCAAGCACGGCGTCA	62.680	66.667	10.85	0.00	0.00	4.35
2017	2670	3.173390	GAATGCTGCCGCCGATGAC	62.173	63.158	0.00	0.00	34.43	3.06
2197	2861	9.748708	TCAGAAATTCAAATTGGACTTTGTTAG	57.251	29.630	3.06	0.00	37.39	2.34
2263	2928	7.992754	AATTCTTAGCTGTTCTGTTCATTCT	57.007	32.000	0.00	0.00	0.00	2.40
2267	2932	4.613925	AGCTGTTCTGTTCATTCTCTCA	57.386	40.909	0.00	0.00	0.00	3.27
2269	2934	4.060900	GCTGTTCTGTTCATTCTCTCACA	58.939	43.478	0.00	0.00	0.00	3.58
2279	2944	7.362662	TGTTCATTCTCTCACAAATTAGCAAC	58.637	34.615	0.00	0.00	0.00	4.17
2282	2947	3.334691	TCTCTCACAAATTAGCAACGGG	58.665	45.455	0.00	0.00	0.00	5.28
2377	3197	2.677337	GCAACTGAGCTGGATCTTCTTC	59.323	50.000	0.00	0.00	0.00	2.87
2449	3269	7.113704	ACGTTCCTTTAGTATTTTCTCAACG	57.886	36.000	0.00	0.00	38.97	4.10
2592	3413	6.327279	ACAAAATAGGAAGTGTAGTTTGCC	57.673	37.500	3.64	0.00	38.44	4.52
2595	3416	0.036306	AGGAAGTGTAGTTTGCCCGG	59.964	55.000	0.00	0.00	0.00	5.73
2614	3435	5.675323	GCCCGGTGTAGAAAAATCACAATAC	60.675	44.000	0.00	0.00	34.27	1.89
2687	3509	2.358195	GGGTGCCCTATTGGACAAGAAT	60.358	50.000	0.00	0.00	35.39	2.40
2698	3520	8.473899	CCTATTGGACAAGAATCGATAGACTGC	61.474	44.444	0.00	0.00	42.30	4.40
2959	3800	8.940768	ATTGCGGCAAATACTTTGTATAAAAT	57.059	26.923	20.48	0.00	42.56	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.057547	CTGCTAGCCACTCGAGCGT	62.058	63.158	13.61	0.00	45.00	5.07
67	68	6.092670	CGACATTTAAGAGAAATGAGAGCCAA	59.907	38.462	15.08	0.00	39.36	4.52
80	81	1.927174	CCCGCAGTCGACATTTAAGAG	59.073	52.381	19.50	2.03	38.10	2.85
90	91	0.464916	TACTAGCATCCCGCAGTCGA	60.465	55.000	0.00	0.00	46.13	4.20
173	326	1.261480	AAGTCGAGGACACTGCATCT	58.739	50.000	0.00	0.00	34.60	2.90
200	353	7.654520	GGAGTACTATATTATGTGGTGCGAAAA	59.345	37.037	0.00	0.00	0.00	2.29
204	357	6.020971	TGGAGTACTATATTATGTGGTGCG	57.979	41.667	0.00	0.00	0.00	5.34
268	423	9.350951	GGTGCCAAAAGGAGTACTATATTATTT	57.649	33.333	0.00	0.00	0.00	1.40
273	428	4.407945	ACGGTGCCAAAAGGAGTACTATAT	59.592	41.667	0.00	0.00	0.00	0.86
274	429	3.770933	ACGGTGCCAAAAGGAGTACTATA	59.229	43.478	0.00	0.00	0.00	1.31
275	430	2.570302	ACGGTGCCAAAAGGAGTACTAT	59.430	45.455	0.00	0.00	0.00	2.12
277	432	0.763035	ACGGTGCCAAAAGGAGTACT	59.237	50.000	0.00	0.00	0.00	2.73
278	433	0.872388	CACGGTGCCAAAAGGAGTAC	59.128	55.000	0.00	0.00	0.00	2.73
279	434	0.470766	ACACGGTGCCAAAAGGAGTA	59.529	50.000	8.30	0.00	0.00	2.59
280	435	0.470766	TACACGGTGCCAAAAGGAGT	59.529	50.000	8.30	0.00	0.00	3.85
281	436	1.600023	TTACACGGTGCCAAAAGGAG	58.400	50.000	8.30	0.00	0.00	3.69
282	437	2.279935	ATTACACGGTGCCAAAAGGA	57.720	45.000	8.30	0.00	0.00	3.36
283	438	4.879545	ACTATATTACACGGTGCCAAAAGG	59.120	41.667	8.30	0.00	0.00	3.11
284	439	6.759827	AGTACTATATTACACGGTGCCAAAAG	59.240	38.462	8.30	2.07	0.00	2.27
474	730	4.880759	TGCAACCACTAAATTCATTGGTG	58.119	39.130	5.76	0.00	46.74	4.17
740	1222	7.382218	GGAAATGGTTGGAAGATTATTAATGCG	59.618	37.037	0.00	0.00	0.00	4.73
947	1487	3.206150	TCTGCTTCCACTTTTCTGTGTC	58.794	45.455	0.00	0.00	36.30	3.67
959	1499	1.548357	GGTCCTCTGCTCTGCTTCCA	61.548	60.000	0.00	0.00	0.00	3.53
994	1535	4.918201	CTCCGCCGCCATTCTCCC	62.918	72.222	0.00	0.00	0.00	4.30
1075	1619	3.458163	GGTCACCATCTCCGGCGA	61.458	66.667	9.30	0.00	0.00	5.54
1208	1752	1.072505	GGGCGAAACAACAGGAGGA	59.927	57.895	0.00	0.00	0.00	3.71
1209	1753	2.325082	CGGGCGAAACAACAGGAGG	61.325	63.158	0.00	0.00	0.00	4.30
1265	1812	4.966249	TGTTCATACGTAGACGAACAGAG	58.034	43.478	23.46	0.00	41.97	3.35
1278	1825	3.058520	CGTGTAACCGTCTTGTTCATACG	59.941	47.826	0.00	0.00	36.42	3.06
1291	1839	4.403706	CGCACGCACGTGTAACCG	62.404	66.667	22.66	14.27	46.90	4.44
1292	1840	3.332409	ACGCACGCACGTGTAACC	61.332	61.111	22.66	6.73	46.28	2.85
1386	1934	4.196193	CGGACATAATCTAACCAGGCAAA	58.804	43.478	0.00	0.00	0.00	3.68
1389	1937	2.143925	GCGGACATAATCTAACCAGGC	58.856	52.381	0.00	0.00	0.00	4.85
1411	1967	5.509716	TGCTCTTAAACCGATCGAAGATA	57.490	39.130	18.66	6.93	45.12	1.98
1465	2033	6.570058	CACGAAGAACGAAAACTCTGTAATTG	59.430	38.462	0.00	0.00	45.77	2.32
1603	2253	2.061220	CAGGTTGAGGTCCTGCTGA	58.939	57.895	0.00	0.00	44.46	4.26
1652	2305	2.990967	GCATGTGGTGGTGGTGGG	60.991	66.667	0.00	0.00	0.00	4.61
1819	2472	3.414700	GGTGACGCCGTGCTTGAG	61.415	66.667	0.00	0.00	0.00	3.02
1867	2520	4.329545	GTGAGGCAGGACGGGCAA	62.330	66.667	0.00	0.00	35.46	4.52
2017	2670	2.778299	TCTTTTCCCATTCACTCGGTG	58.222	47.619	0.00	0.00	34.45	4.94
2091	2745	9.132521	TCTAAGAAGTAACAAACTACGTAATGC	57.867	33.333	0.00	0.00	37.50	3.56
2165	2828	9.835389	AAGTCCAATTTGAATTTCTGATTTGAA	57.165	25.926	0.00	0.00	0.00	2.69
2238	2903	9.155975	GAGAATGAACAGAACAGCTAAGAATTA	57.844	33.333	0.00	0.00	0.00	1.40
2263	2928	3.410631	TCCCGTTGCTAATTTGTGAGA	57.589	42.857	0.00	0.00	0.00	3.27
2267	2932	5.497474	AGACTATTCCCGTTGCTAATTTGT	58.503	37.500	0.00	0.00	0.00	2.83
2269	2934	7.462571	AAAAGACTATTCCCGTTGCTAATTT	57.537	32.000	0.00	0.00	0.00	1.82
2377	3197	3.543494	CCGAGAACTGCATTAATTTTGCG	59.457	43.478	8.11	6.17	43.10	4.85
2449	3269	3.598330	GTCGTACGTACCGAGTATTGTC	58.402	50.000	19.67	3.90	34.56	3.18
2471	3291	7.523873	GGTATAAAATACCAGGGTACTCGTACC	60.524	44.444	16.15	16.15	43.93	3.34
2472	3292	7.371159	GGTATAAAATACCAGGGTACTCGTAC	58.629	42.308	10.56	0.00	37.53	3.67
2473	3293	6.206634	CGGTATAAAATACCAGGGTACTCGTA	59.793	42.308	14.73	0.00	37.44	3.43
2474	3294	5.010012	CGGTATAAAATACCAGGGTACTCGT	59.990	44.000	14.73	0.00	37.44	4.18
2475	3295	5.010012	ACGGTATAAAATACCAGGGTACTCG	59.990	44.000	14.73	0.00	37.44	4.18
2476	3296	6.218746	CACGGTATAAAATACCAGGGTACTC	58.781	44.000	14.73	0.00	37.44	2.59
2477	3297	5.070847	CCACGGTATAAAATACCAGGGTACT	59.929	44.000	14.73	0.00	37.44	2.73
2576	3397	0.036306	CCGGGCAAACTACACTTCCT	59.964	55.000	0.00	0.00	0.00	3.36
2578	3399	0.872388	CACCGGGCAAACTACACTTC	59.128	55.000	6.32	0.00	0.00	3.01
2592	3413	5.121142	ACGTATTGTGATTTTTCTACACCGG	59.879	40.000	0.00	0.00	34.18	5.28
2595	3416	7.723270	ACGTACGTATTGTGATTTTTCTACAC	58.277	34.615	21.41	0.00	35.45	2.90
2687	3509	1.452953	ATTCGGCGGCAGTCTATCGA	61.453	55.000	10.53	0.00	0.00	3.59
2698	3520	0.311790	CATGGATTTGGATTCGGCGG	59.688	55.000	7.21	0.00	0.00	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.