AutoCloner

Multiple sequence alignment - TraesCS5B01G172000

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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	TraesCS5B01G172000	chr5B	100.000	2647	0	0	1	2647	316530682	316533328	0.000000e+00	4889.0
1	TraesCS5B01G172000	chr5B	95.061	1640	59	14	455	2091	316561031	316562651	0.000000e+00	2560.0
2	TraesCS5B01G172000	chr5B	91.083	471	30	7	1	459	316558646	316559116	6.220000e-176	627.0
3	TraesCS5B01G172000	chr5B	87.253	557	45	9	2103	2643	316603784	316604330	1.740000e-171	612.0
4	TraesCS5B01G172000	chr5D	85.180	2328	189	70	285	2508	278440569	278442844	0.000000e+00	2244.0
5	TraesCS5B01G172000	chr5D	86.148	1978	176	59	575	2508	278357881	278359804	0.000000e+00	2045.0
6	TraesCS5B01G172000	chr5D	89.706	204	14	4	1	197	278440363	278440566	1.220000e-63	254.0
7	TraesCS5B01G172000	chr5D	84.286	280	21	11	305	577	278357479	278357742	4.370000e-63	252.0
8	TraesCS5B01G172000	chr5D	85.922	206	19	5	1	197	278351831	278352035	7.420000e-51	211.0
9	TraesCS5B01G172000	chr5D	100.000	29	0	0	285	313	278352038	278352066	1.000000e-03	54.7
10	TraesCS5B01G172000	chr5A	88.991	1735	111	32	288	1988	370107814	370106126	0.000000e+00	2073.0
11	TraesCS5B01G172000	chr5A	90.323	62	5	1	2552	2613	669594141	669594201	2.180000e-11	80.5
12	TraesCS5B01G172000	chr2A	85.816	141	14	3	1	135	30237513	30237653	7.640000e-31	145.0
13	TraesCS5B01G172000	chr2A	86.792	106	12	1	1	104	30248330	30248435	1.660000e-22	117.0
14	TraesCS5B01G172000	chr2A	92.063	63	5	0	193	255	435799686	435799748	3.630000e-14	89.8
15	TraesCS5B01G172000	chr2A	93.333	60	4	0	196	255	634609025	634608966	3.630000e-14	89.8
16	TraesCS5B01G172000	chr2A	82.353	102	11	3	1813	1911	23754983	23754886	6.070000e-12	82.4
17	TraesCS5B01G172000	chr2A	82.000	100	11	4	2552	2646	604868490	604868587	7.860000e-11	78.7
18	TraesCS5B01G172000	chr2A	87.755	49	6	0	256	304	447156309	447156261	1.020000e-04	58.4
19	TraesCS5B01G172000	chr2B	85.606	132	12	3	1	125	487238466	487238335	5.950000e-27	132.0
20	TraesCS5B01G172000	chr2B	93.548	62	4	0	194	255	148404593	148404532	2.810000e-15	93.5
21	TraesCS5B01G172000	chr2B	94.595	37	1	1	249	284	47613873	47613837	3.680000e-04	56.5
22	TraesCS5B01G172000	chr6B	84.962	133	13	4	1	126	64690399	64690267	7.690000e-26	128.0
23	TraesCS5B01G172000	chr6B	89.552	67	5	2	2552	2618	164137358	164137422	1.690000e-12	84.2
24	TraesCS5B01G172000	chr4A	93.651	63	4	0	194	256	583920250	583920312	7.800000e-16	95.3
25	TraesCS5B01G172000	chr4A	92.500	40	2	1	256	295	683427952	683427914	3.680000e-04	56.5
26	TraesCS5B01G172000	chr3A	92.188	64	5	0	192	255	521303640	521303577	1.010000e-14	91.6
27	TraesCS5B01G172000	chr3A	84.706	85	9	4	2552	2635	469050584	469050665	6.070000e-12	82.4
28	TraesCS5B01G172000	chr1B	92.188	64	5	0	192	255	654278679	654278616	1.010000e-14	91.6
29	TraesCS5B01G172000	chr1B	91.935	62	4	1	2552	2613	263553060	263553120	4.690000e-13	86.1
30	TraesCS5B01G172000	chr1B	100.000	32	0	0	256	287	563052942	563052911	2.850000e-05	60.2
31	TraesCS5B01G172000	chr6A	93.333	60	4	0	196	255	479391171	479391230	3.630000e-14	89.8
32	TraesCS5B01G172000	chr4D	82.727	110	10	7	1791	1898	463708151	463708253	3.630000e-14	89.8
33	TraesCS5B01G172000	chr4D	80.672	119	13	5	1796	1911	437288276	437288387	1.690000e-12	84.2
34	TraesCS5B01G172000	chr3B	93.333	60	4	0	196	255	173371591	173371532	3.630000e-14	89.8
35	TraesCS5B01G172000	chr3B	90.323	62	4	2	2552	2613	240535054	240535113	2.180000e-11	80.5
36	TraesCS5B01G172000	chr7D	83.721	86	8	6	2552	2635	606010302	606010221	2.830000e-10	76.8
37	TraesCS5B01G172000	chr3D	87.879	66	4	4	2543	2606	519675221	519675284	1.020000e-09	75.0
38	TraesCS5B01G172000	chr3D	94.737	38	1	1	248	284	191460603	191460640	1.020000e-04	58.4
39	TraesCS5B01G172000	chr1A	94.444	36	2	0	249	284	587847791	587847756	3.680000e-04	56.5
40	TraesCS5B01G172000	chr1D	94.444	36	1	1	256	290	395556899	395556864	1.000000e-03	54.7
41	TraesCS5B01G172000	chr2D	100.000	28	0	0	256	283	398691357	398691384	5.000000e-03	52.8

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	TraesCS5B01G172000	chr5B	316530682	316533328	2646	False	4889.0	4889	100.000	1	2647	1	chr5B.!!$F1	2646
1	TraesCS5B01G172000	chr5B	316558646	316562651	4005	False	1593.5	2560	93.072	1	2091	2	chr5B.!!$F3	2090
2	TraesCS5B01G172000	chr5B	316603784	316604330	546	False	612.0	612	87.253	2103	2643	1	chr5B.!!$F2	540
3	TraesCS5B01G172000	chr5D	278440363	278442844	2481	False	1249.0	2244	87.443	1	2508	2	chr5D.!!$F3	2507
4	TraesCS5B01G172000	chr5D	278357479	278359804	2325	False	1148.5	2045	85.217	305	2508	2	chr5D.!!$F2	2203
5	TraesCS5B01G172000	chr5A	370106126	370107814	1688	True	2073.0	2073	88.991	288	1988	1	chr5A.!!$R1	1700

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
714	2810	0.394216	ATCTACGGCCAGCAATGCAA	60.394	50.0	8.35	0.0	0.0	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2329	4504	0.035458	AGGAAACAGTTCGCCAGGAG	59.965	55.0	7.65	0.0	34.28	3.69	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
93	96	2.180769	CCAACGACGATGGCGAGA	59.819	61.111	11.47	0.00	41.64	4.04
99	102	4.458829	ACGATGGCGAGAGGGGGA	62.459	66.667	0.00	0.00	41.64	4.81
167	180	0.887247	CCATGGCCACAATTTCGTCA	59.113	50.000	8.16	0.00	0.00	4.35
206	219	4.623932	TGAAGCACAAGTACTTCATCCT	57.376	40.909	4.77	0.00	45.48	3.24
239	252	9.747898	AATACTTGTCCTCAAAATGGTTGTATA	57.252	29.630	0.00	0.00	32.87	1.47
276	289	1.479323	CAAGTATTTCCGGACGGAGGA	59.521	52.381	13.64	7.39	46.06	3.71
334	348	3.118261	TCACTGGTCTTGCTCTCTGTTTT	60.118	43.478	0.00	0.00	0.00	2.43
511	2447	8.950210	CACCAGACAAATTACTGAACAGATTAT	58.050	33.333	8.87	0.00	36.38	1.28
620	2705	5.581874	CCCATTTTGTTGGAGATTAACATGC	59.418	40.000	0.00	0.00	39.25	4.06
690	2786	1.510480	GACAGCTCACCCAACTGCAC	61.510	60.000	0.00	0.00	34.72	4.57
714	2810	0.394216	ATCTACGGCCAGCAATGCAA	60.394	50.000	8.35	0.00	0.00	4.08
735	2831	4.735132	CACCGACGCATCCACCGT	62.735	66.667	0.00	0.00	42.31	4.83
770	2872	6.307031	TGCAATGTACATACAAACGTTCTT	57.693	33.333	9.21	0.00	39.99	2.52
965	3071	6.215845	ACCACAAATGCAAATCTACTGTTTC	58.784	36.000	0.00	0.00	0.00	2.78
1036	3143	1.205064	CAAGCGCTGTTGTCTTCCG	59.795	57.895	12.58	0.00	0.00	4.30
1063	3173	1.902556	GGCCATGGCTTGCTTCAAT	59.097	52.632	34.70	0.00	41.60	2.57
1382	3492	4.682334	TCACGTCGGGGGCCTACA	62.682	66.667	0.84	0.00	0.00	2.74
1533	3643	0.175302	CTGCTGGAGCTCGACATCTT	59.825	55.000	7.83	0.00	42.66	2.40
1701	3813	7.650504	GCTACGTGGATGTTTGTGATAGTATTA	59.349	37.037	1.81	0.00	0.00	0.98
1794	3936	3.853671	GTGGATGCTGCTCGTTTAAATTG	59.146	43.478	0.00	0.00	0.00	2.32
1920	4066	4.735369	TCAGTTCTCATTGCCCCTAAAAA	58.265	39.130	0.00	0.00	0.00	1.94
1945	4092	2.260434	GAGTACACGCCGCCTTGA	59.740	61.111	0.00	0.00	0.00	3.02
1974	4123	2.583593	GCGAGAGTGCCATCCGAC	60.584	66.667	0.00	0.00	0.00	4.79
1980	4129	1.072331	AGAGTGCCATCCGACTTGTTT	59.928	47.619	0.00	0.00	0.00	2.83
1991	4140	1.063469	CGACTTGTTTGTTTCACGCCT	59.937	47.619	0.00	0.00	0.00	5.52
2031	4181	2.029828	CGATATCTCCCTAGCACGCTTT	60.030	50.000	0.00	0.00	0.00	3.51
2054	4204	2.549134	CGCCATCCGATATTGGTGGTTA	60.549	50.000	22.01	2.22	39.36	2.85
2091	4241	3.372458	GCTTTTCCTCTGGGATCCTCAAT	60.372	47.826	12.58	0.00	41.87	2.57
2092	4242	3.939740	TTTCCTCTGGGATCCTCAATG	57.060	47.619	12.58	3.91	41.87	2.82
2095	4245	1.424302	CCTCTGGGATCCTCAATGCAT	59.576	52.381	12.58	0.00	33.58	3.96
2100	4250	2.176148	TGGGATCCTCAATGCATGTGAT	59.824	45.455	12.58	0.00	0.00	3.06
2115	4265	4.872124	GCATGTGATATGATTGCGGATCTA	59.128	41.667	0.00	0.00	35.69	1.98
2127	4277	1.146637	CGGATCTACGAGGAGGTACG	58.853	60.000	0.00	0.00	35.47	3.67
2136	4286	0.179000	GAGGAGGTACGTCCGTCCTA	59.821	60.000	24.89	0.00	40.97	2.94
2137	4287	0.842635	AGGAGGTACGTCCGTCCTAT	59.157	55.000	24.89	7.36	42.05	2.57
2138	4288	1.213926	AGGAGGTACGTCCGTCCTATT	59.786	52.381	24.89	6.69	42.05	1.73
2139	4289	2.027385	GGAGGTACGTCCGTCCTATTT	58.973	52.381	18.27	0.00	41.99	1.40
2140	4290	2.033927	GGAGGTACGTCCGTCCTATTTC	59.966	54.545	18.27	0.00	41.99	2.17
2141	4291	2.684881	GAGGTACGTCCGTCCTATTTCA	59.315	50.000	4.15	0.00	41.99	2.69
2142	4292	3.091545	AGGTACGTCCGTCCTATTTCAA	58.908	45.455	0.00	0.00	41.99	2.69
2159	4309	1.376812	AATTCTTCGGGTGGGTCGC	60.377	57.895	0.00	0.00	0.00	5.19
2198	4349	1.553248	CTTCCTGTGGGGTTATCGTCA	59.447	52.381	0.00	0.00	36.25	4.35
2207	4378	2.947621	TTATCGTCACGCTCGCGC	60.948	61.111	11.65	0.00	44.19	6.86
2310	4485	3.932580	CTCGCGTTAGCCAGGCACA	62.933	63.158	15.80	0.00	41.18	4.57
2330	4505	4.619227	CGTGCACCCGGTTCACCT	62.619	66.667	13.88	0.00	0.00	4.00
2498	4692	2.730094	GGTGCTTGGCTTGTGTGG	59.270	61.111	0.00	0.00	0.00	4.17
2501	4695	2.126596	TGCTTGGCTTGTGTGGGTG	61.127	57.895	0.00	0.00	0.00	4.61
2514	4708	4.016706	GGGTGGGGGTGTGTCGAG	62.017	72.222	0.00	0.00	0.00	4.04
2526	4720	2.338015	TGTCGAGTCGGGGTGCTAC	61.338	63.158	13.54	1.84	0.00	3.58
2527	4721	2.753043	TCGAGTCGGGGTGCTACC	60.753	66.667	13.54	0.00	37.60	3.18
2528	4722	2.754658	CGAGTCGGGGTGCTACCT	60.755	66.667	4.10	0.00	38.64	3.08
2529	4723	2.893398	GAGTCGGGGTGCTACCTG	59.107	66.667	5.48	2.96	38.64	4.00
2547	4741	6.152831	GCTACCTGGGTGTTTCAATCTTTTAT	59.847	38.462	2.07	0.00	0.00	1.40
2550	4744	6.209391	ACCTGGGTGTTTCAATCTTTTATCAG	59.791	38.462	0.00	0.00	0.00	2.90
2608	4802	1.654220	CGGGCACAAGGTTCAACAG	59.346	57.895	0.00	0.00	0.00	3.16
2613	4807	2.514803	GCACAAGGTTCAACAGGGTAT	58.485	47.619	0.00	0.00	0.00	2.73
2620	4814	4.798882	AGGTTCAACAGGGTATCAACAAA	58.201	39.130	0.00	0.00	0.00	2.83
2643	4837	2.390306	ATACACACACAGCCACCGCA	62.390	55.000	0.00	0.00	37.52	5.69
2644	4838	2.390306	TACACACACAGCCACCGCAT	62.390	55.000	0.00	0.00	37.52	4.73
2645	4839	2.979676	ACACACAGCCACCGCATG	60.980	61.111	0.00	0.00	37.52	4.06
2646	4840	2.669229	CACACAGCCACCGCATGA	60.669	61.111	0.00	0.00	37.52	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	81	2.490217	CCTCTCGCCATCGTCGTT	59.510	61.111	0.00	0.00	36.96	3.85
83	86	3.610669	CTCCCCCTCTCGCCATCG	61.611	72.222	0.00	0.00	0.00	3.84
167	180	4.157289	GCTTCATTCTGAACATGTCCACAT	59.843	41.667	0.00	0.00	32.82	3.21
206	219	4.627284	TTGAGGACAAGTATTTCCGGAA	57.373	40.909	14.35	14.35	36.95	4.30
334	348	2.139917	CCGTCGTTGTTTTCTGGATCA	58.860	47.619	0.00	0.00	0.00	2.92
511	2447	1.893137	ACTGATGGCGAGTACAGTTGA	59.107	47.619	0.00	0.00	40.03	3.18
620	2705	4.921470	ACGAACGACCATATTTCACTTG	57.079	40.909	0.14	0.00	0.00	3.16
735	2831	3.251972	TGTACATTGCATGCACGAAAGAA	59.748	39.130	22.58	3.73	28.94	2.52
770	2872	2.613026	TGCCTCTCAAGAAACAACGA	57.387	45.000	0.00	0.00	0.00	3.85
843	2946	2.534019	CGCTGTGCACGTCAGGTTT	61.534	57.895	13.13	0.00	33.98	3.27
965	3071	8.077386	ACGTTTGGGTTTGTTGTTTATATACAG	58.923	33.333	0.00	0.00	0.00	2.74
1003	3110	3.818387	GCGCTTGCTAGTACGTATCATA	58.182	45.455	0.00	0.00	35.07	2.15
1004	3111	2.662700	GCGCTTGCTAGTACGTATCAT	58.337	47.619	0.00	0.00	35.07	2.45
1063	3173	1.812686	CGAAGGACGTGGGGTTGAGA	61.813	60.000	0.00	0.00	37.22	3.27
1533	3643	1.003839	GTGGCTCATGGGTTGACGA	60.004	57.895	0.00	0.00	0.00	4.20
1616	3726	2.736682	GACCGCGCGCAACACTTAT	61.737	57.895	32.61	5.98	0.00	1.73
1630	3740	6.140110	ACACTCATTTTATTTTGAACGACCG	58.860	36.000	0.00	0.00	0.00	4.79
1945	4092	4.357947	TCTCGCGCGACAAAGCCT	62.358	61.111	31.40	0.00	0.00	4.58
1974	4123	1.199624	GCAGGCGTGAAACAAACAAG	58.800	50.000	11.29	0.00	35.74	3.16
1980	4129	2.844451	GCAAGGCAGGCGTGAAACA	61.844	57.895	14.27	0.00	35.74	2.83
2014	4164	3.768633	CAAAGCGTGCTAGGGAGAT	57.231	52.632	0.00	0.00	0.00	2.75
2031	4181	0.884259	CACCAATATCGGATGGCGCA	60.884	55.000	10.83	0.00	40.51	6.09
2091	4241	2.848691	TCCGCAATCATATCACATGCA	58.151	42.857	0.00	0.00	36.84	3.96
2092	4242	3.688185	AGATCCGCAATCATATCACATGC	59.312	43.478	0.00	0.00	36.79	4.06
2095	4245	4.217550	TCGTAGATCCGCAATCATATCACA	59.782	41.667	0.00	0.00	36.79	3.58
2100	4250	3.418047	TCCTCGTAGATCCGCAATCATA	58.582	45.455	0.00	0.00	36.79	2.15
2115	4265	1.743252	GACGGACGTACCTCCTCGT	60.743	63.158	8.95	3.27	43.00	4.18
2127	4277	4.270325	CCGAAGAATTGAAATAGGACGGAC	59.730	45.833	0.00	0.00	39.11	4.79
2136	4286	3.089284	GACCCACCCGAAGAATTGAAAT	58.911	45.455	0.00	0.00	0.00	2.17
2137	4287	2.510613	GACCCACCCGAAGAATTGAAA	58.489	47.619	0.00	0.00	0.00	2.69
2138	4288	1.609580	CGACCCACCCGAAGAATTGAA	60.610	52.381	0.00	0.00	0.00	2.69
2139	4289	0.036765	CGACCCACCCGAAGAATTGA	60.037	55.000	0.00	0.00	0.00	2.57
2140	4290	1.644786	GCGACCCACCCGAAGAATTG	61.645	60.000	0.00	0.00	0.00	2.32
2141	4291	1.376812	GCGACCCACCCGAAGAATT	60.377	57.895	0.00	0.00	0.00	2.17
2142	4292	2.267961	GCGACCCACCCGAAGAAT	59.732	61.111	0.00	0.00	0.00	2.40
2296	4471	3.788766	GCGTGTGCCTGGCTAACG	61.789	66.667	29.71	29.71	39.59	3.18
2318	4493	2.928396	CCAGGAGGTGAACCGGGT	60.928	66.667	6.32	0.00	42.08	5.28
2327	4502	0.250338	GAAACAGTTCGCCAGGAGGT	60.250	55.000	0.00	0.00	37.19	3.85
2328	4503	0.955919	GGAAACAGTTCGCCAGGAGG	60.956	60.000	0.00	0.00	34.28	4.30
2329	4504	0.035458	AGGAAACAGTTCGCCAGGAG	59.965	55.000	7.65	0.00	34.28	3.69
2330	4505	0.472471	AAGGAAACAGTTCGCCAGGA	59.528	50.000	7.65	0.00	34.28	3.86
2378	4572	1.134936	ACCAAGCGGGAAACAAACAAC	60.135	47.619	4.35	0.00	41.15	3.32
2498	4692	3.236003	GACTCGACACACCCCCACC	62.236	68.421	0.00	0.00	0.00	4.61
2501	4695	4.065281	CCGACTCGACACACCCCC	62.065	72.222	0.00	0.00	0.00	5.40
2514	4708	3.782443	CCCAGGTAGCACCCCGAC	61.782	72.222	0.00	0.00	39.75	4.79
2526	4720	6.434028	TCTGATAAAAGATTGAAACACCCAGG	59.566	38.462	0.00	0.00	0.00	4.45
2527	4721	7.452880	TCTGATAAAAGATTGAAACACCCAG	57.547	36.000	0.00	0.00	0.00	4.45
2528	4722	7.831691	TTCTGATAAAAGATTGAAACACCCA	57.168	32.000	0.00	0.00	0.00	4.51
2529	4723	9.196552	CTTTTCTGATAAAAGATTGAAACACCC	57.803	33.333	4.58	0.00	39.04	4.61
2566	4760	7.700656	CCGGAGGTTTGCTTTATTTATAAAGTG	59.299	37.037	18.51	2.11	45.68	3.16
2567	4761	7.768240	CCGGAGGTTTGCTTTATTTATAAAGT	58.232	34.615	18.51	3.42	45.68	2.66
2588	4782	1.527380	GTTGAACCTTGTGCCCGGA	60.527	57.895	0.73	0.00	0.00	5.14
2592	4786	0.755327	ACCCTGTTGAACCTTGTGCC	60.755	55.000	0.00	0.00	0.00	5.01
2608	4802	4.093850	GTGTGTATCCGTTTGTTGATACCC	59.906	45.833	7.08	0.00	41.60	3.69
2613	4807	3.532542	TGTGTGTGTATCCGTTTGTTGA	58.467	40.909	0.00	0.00	0.00	3.18
2620	4814	0.320421	GTGGCTGTGTGTGTATCCGT	60.320	55.000	0.00	0.00	0.00	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.