AutoCloner

Multiple sequence alignment - TraesCS1A01G191000

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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	TraesCS1A01G191000	chr1A	100.000	2774	0	0	1	2774	345302681	345305454	0.000000e+00	5123.0
1	TraesCS1A01G191000	chr3A	95.896	1852	30	9	1	1846	621118252	621116441	0.000000e+00	2957.0
2	TraesCS1A01G191000	chr3B	93.662	1704	66	12	578	2252	636869696	636868006	0.000000e+00	2510.0
3	TraesCS1A01G191000	chr3B	93.194	382	16	5	205	576	636870236	636869855	1.120000e-153	553.0
4	TraesCS1A01G191000	chr3B	95.341	279	8	3	1	279	752378547	752378820	3.280000e-119	438.0
5	TraesCS1A01G191000	chr3B	95.610	205	5	2	1	205	636873458	636873258	2.660000e-85	326.0
6	TraesCS1A01G191000	chr3B	90.612	245	9	2	2297	2535	636867926	636867690	2.070000e-81	313.0
7	TraesCS1A01G191000	chr3B	92.627	217	7	4	120	334	638931767	638931976	1.250000e-78	303.0
8	TraesCS1A01G191000	chr3B	90.476	126	4	5	1	122	638931473	638931594	2.860000e-35	159.0
9	TraesCS1A01G191000	chr3B	89.908	109	4	4	1	109	718681905	718682006	1.730000e-27	134.0
10	TraesCS1A01G191000	chr3B	96.491	57	1	1	367	423	296065314	296065259	2.940000e-15	93.5
11	TraesCS1A01G191000	chr3B	100.000	29	0	0	1276	1304	708459453	708459425	1.000000e-03	54.7
12	TraesCS1A01G191000	chr3D	95.734	1336	46	5	921	2252	477630965	477629637	0.000000e+00	2141.0
13	TraesCS1A01G191000	chr3D	94.307	527	27	2	2251	2774	477629668	477629142	0.000000e+00	804.0
14	TraesCS1A01G191000	chr3D	93.432	472	21	4	410	878	477633217	477632753	0.000000e+00	691.0
15	TraesCS1A01G191000	chr3D	95.778	379	10	4	1	379	477633585	477633213	8.500000e-170	606.0
16	TraesCS1A01G191000	chr5A	91.800	1061	69	7	569	1614	607391586	607392643	0.000000e+00	1461.0
17	TraesCS1A01G191000	chr5A	88.788	330	28	8	186	509	607391235	607391561	2.000000e-106	396.0
18	TraesCS1A01G191000	chr5D	91.260	778	51	7	569	1339	486746799	486747566	0.000000e+00	1044.0
19	TraesCS1A01G191000	chr5D	89.300	486	38	10	1350	1828	486748497	486748975	5.110000e-167	597.0
20	TraesCS1A01G191000	chr5D	86.408	515	36	17	2	509	486746287	486746774	1.460000e-147	532.0
21	TraesCS1A01G191000	chr5B	90.845	284	15	5	1	279	599314032	599314309	1.210000e-98	370.0
22	TraesCS1A01G191000	chr5B	89.055	201	13	5	1591	1790	598297187	598296995	9.930000e-60	241.0
23	TraesCS1A01G191000	chr4A	84.472	161	9	9	2532	2690	722486272	722486418	8.010000e-31	145.0

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	TraesCS1A01G191000	chr1A	345302681	345305454	2773	False	5123.000000	5123	100.000000	1	2774	1	chr1A.!!$F1	2773
1	TraesCS1A01G191000	chr3A	621116441	621118252	1811	True	2957.000000	2957	95.896000	1	1846	1	chr3A.!!$R1	1845
2	TraesCS1A01G191000	chr3B	636867690	636873458	5768	True	925.500000	2510	93.269500	1	2535	4	chr3B.!!$R3	2534
3	TraesCS1A01G191000	chr3B	638931473	638931976	503	False	231.000000	303	91.551500	1	334	2	chr3B.!!$F3	333
4	TraesCS1A01G191000	chr3D	477629142	477633585	4443	True	1060.500000	2141	94.812750	1	2774	4	chr3D.!!$R1	2773
5	TraesCS1A01G191000	chr5A	607391235	607392643	1408	False	928.500000	1461	90.294000	186	1614	2	chr5A.!!$F1	1428
6	TraesCS1A01G191000	chr5D	486746287	486748975	2688	False	724.333333	1044	88.989333	2	1828	3	chr5D.!!$F1	1826

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
362	3569	2.375174	AGTAGCCTTGGGTCATTGTTCA	59.625	45.455	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2226	8313	0.239347	ACGTCCTAACCGTGAAGTCG	59.761	55.0	0.0	0.0	37.12	4.18	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
35	39	7.359598	GCGTAGAGCCTTTTATAATCTCATGTG	60.360	40.741	0.00	0.00	40.81	3.21
36	40	7.653713	CGTAGAGCCTTTTATAATCTCATGTGT	59.346	37.037	0.00	0.00	0.00	3.72
362	3569	2.375174	AGTAGCCTTGGGTCATTGTTCA	59.625	45.455	0.00	0.00	0.00	3.18
454	3672	7.546316	GGTTAACACAAATTTACAACTGGTGTT	59.454	33.333	18.87	18.87	46.19	3.32
614	3994	7.724305	ATTTACTGTTCTTTCTCTTAACGCA	57.276	32.000	0.00	0.00	0.00	5.24
1047	6173	2.436646	AAATCAGTGCCCCTCGCG	60.437	61.111	0.00	0.00	42.08	5.87
1261	6387	1.081906	GCGTGCACTGTGGTCAATG	60.082	57.895	16.19	0.00	0.00	2.82
1419	7465	1.990160	TTGGTGTCTCGGCAAAGGGT	61.990	55.000	0.00	0.00	0.00	4.34
1599	7653	1.210931	CATGACAACAAGGCCGCAG	59.789	57.895	0.00	0.00	0.00	5.18
1701	7758	4.711949	CGCTGTGGCAGAGGGCTT	62.712	66.667	15.58	0.00	44.01	4.35
1702	7759	2.671070	GCTGTGGCAGAGGGCTTA	59.329	61.111	14.04	0.00	44.01	3.09
1703	7760	1.002134	GCTGTGGCAGAGGGCTTAA	60.002	57.895	14.04	0.00	44.01	1.85
1849	7912	6.891908	AGGGCTCTTCTTTTAGATGCAATAAA	59.108	34.615	0.00	0.00	0.00	1.40
1850	7913	7.562821	AGGGCTCTTCTTTTAGATGCAATAAAT	59.437	33.333	7.95	0.00	0.00	1.40
1851	7914	8.850156	GGGCTCTTCTTTTAGATGCAATAAATA	58.150	33.333	7.95	0.00	0.00	1.40
1964	8030	9.482627	CACTAGAAAAAGATACAAGAGAGTTGT	57.517	33.333	0.00	0.00	36.49	3.32
1990	8056	7.882791	TCTGGTTAATTTCTAGAAACATGAGCA	59.117	33.333	19.94	19.63	32.51	4.26
2010	8076	5.056480	AGCAAAAACTGTTAAAAGATGCCC	58.944	37.500	0.00	0.00	31.91	5.36
2043	8109	2.753043	TCGACCGACCTGGCTACC	60.753	66.667	0.00	0.00	43.94	3.18
2046	8112	2.040606	ACCGACCTGGCTACCCAT	59.959	61.111	0.00	0.00	43.94	4.00
2050	8116	1.410004	CGACCTGGCTACCCATAAGA	58.590	55.000	0.00	0.00	41.21	2.10
2053	8119	1.838077	ACCTGGCTACCCATAAGACAC	59.162	52.381	0.00	0.00	41.21	3.67
2079	8164	4.644685	ACACTGTCAAGGTTGCTTACAATT	59.355	37.500	0.00	0.00	38.27	2.32
2138	8224	5.593909	TCAAATGAACAACACATGAGAACCT	59.406	36.000	0.00	0.00	0.00	3.50
2219	8306	3.188786	GTCGGCCTGCAACGCTAG	61.189	66.667	0.00	0.00	0.00	3.42
2222	8309	2.032634	CGGCCTGCAACGCTAGAAA	61.033	57.895	0.00	0.00	0.00	2.52
2223	8310	1.502190	GGCCTGCAACGCTAGAAAC	59.498	57.895	0.00	0.00	0.00	2.78
2224	8311	0.955919	GGCCTGCAACGCTAGAAACT	60.956	55.000	0.00	0.00	0.00	2.66
2225	8312	0.444260	GCCTGCAACGCTAGAAACTC	59.556	55.000	0.00	0.00	0.00	3.01
2226	8313	1.079503	CCTGCAACGCTAGAAACTCC	58.920	55.000	0.00	0.00	0.00	3.85
2227	8314	0.716108	CTGCAACGCTAGAAACTCCG	59.284	55.000	0.00	0.00	0.00	4.63
2228	8315	0.315886	TGCAACGCTAGAAACTCCGA	59.684	50.000	0.00	0.00	0.00	4.55
2229	8316	0.714439	GCAACGCTAGAAACTCCGAC	59.286	55.000	0.00	0.00	0.00	4.79
2230	8317	1.669211	GCAACGCTAGAAACTCCGACT	60.669	52.381	0.00	0.00	0.00	4.18
2231	8318	2.673833	CAACGCTAGAAACTCCGACTT	58.326	47.619	0.00	0.00	0.00	3.01
2232	8319	2.633199	ACGCTAGAAACTCCGACTTC	57.367	50.000	0.00	0.00	0.00	3.01
2233	8320	1.884579	ACGCTAGAAACTCCGACTTCA	59.115	47.619	0.00	0.00	0.00	3.02
2234	8321	2.251893	CGCTAGAAACTCCGACTTCAC	58.748	52.381	0.00	0.00	0.00	3.18
2235	8322	2.251893	GCTAGAAACTCCGACTTCACG	58.748	52.381	0.00	0.00	0.00	4.35
2243	8330	3.413522	CCGACTTCACGGTTAGGAC	57.586	57.895	0.00	0.00	46.70	3.85
2244	8331	0.455633	CCGACTTCACGGTTAGGACG	60.456	60.000	0.00	0.00	46.70	4.79
2245	8332	0.239347	CGACTTCACGGTTAGGACGT	59.761	55.000	0.00	0.00	46.82	4.34
2256	8343	2.288886	GGTTAGGACGTGTCAAAGCTCT	60.289	50.000	0.00	0.00	0.00	4.09
2266	8353	2.100749	TGTCAAAGCTCTGACTTCACGA	59.899	45.455	20.44	0.00	45.03	4.35
2273	8360	3.957497	AGCTCTGACTTCACGATTAGGAT	59.043	43.478	0.00	0.00	0.00	3.24
2297	8384	1.148310	CGAACAGAAGAACATGCCGT	58.852	50.000	0.00	0.00	0.00	5.68
2348	8500	3.636043	ACACGAGTTGCAACGCCG	61.636	61.111	31.13	31.13	36.47	6.46
2396	8548	2.517959	CCTCTGACCAAATTGGAGCAA	58.482	47.619	20.25	6.67	40.96	3.91
2400	8552	2.827322	CTGACCAAATTGGAGCAATGGA	59.173	45.455	20.25	0.00	40.96	3.41
2459	8617	7.277098	TCGCACGCTTAATTAGAAATTAAGACT	59.723	33.333	25.48	12.75	41.63	3.24
2485	8643	7.107542	AGATAAACTAAATTAGCACCAACGGA	58.892	34.615	0.00	0.00	0.00	4.69
2610	8769	1.570979	GGATTTGGTGATCCCCTTCCT	59.429	52.381	0.00	0.00	39.79	3.36
2619	8778	1.357761	GATCCCCTTCCTTTCACCCAA	59.642	52.381	0.00	0.00	0.00	4.12
2663	8824	1.288932	CTCCAATCCCACCCCTCAAAT	59.711	52.381	0.00	0.00	0.00	2.32
2727	8888	7.157347	TGCACATAAAAATATTGTTTGGCAGA	58.843	30.769	0.00	0.00	0.00	4.26
2729	8890	8.667463	GCACATAAAAATATTGTTTGGCAGATT	58.333	29.630	0.00	0.00	0.00	2.40
2756	8917	6.260271	GGACTGCCTTTGTACTATTGGATAAC	59.740	42.308	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
362	3569	4.712337	AGTTACTATACTGGCTGCTTCACT	59.288	41.667	0.00	0.00	0.00	3.41
1261	6387	3.501445	GTGGATATCAAGATGCTTGAGCC	59.499	47.826	14.32	14.37	41.18	4.70
1599	7653	1.812922	CATCTGGCAGCACGTCTCC	60.813	63.158	10.34	0.00	0.00	3.71
1701	7758	5.985530	CGATCTGTGCTTGATCACCTTATTA	59.014	40.000	0.00	0.00	40.03	0.98
1702	7759	4.813161	CGATCTGTGCTTGATCACCTTATT	59.187	41.667	0.00	0.00	40.03	1.40
1703	7760	4.141846	ACGATCTGTGCTTGATCACCTTAT	60.142	41.667	0.00	0.00	40.03	1.73
1850	7913	9.372189	GGTTATTCCTGTACTAGAACCCTATTA	57.628	37.037	0.00	0.00	30.75	0.98
1851	7914	7.015001	CGGTTATTCCTGTACTAGAACCCTATT	59.985	40.741	0.00	0.00	32.89	1.73
1852	7915	6.492772	CGGTTATTCCTGTACTAGAACCCTAT	59.507	42.308	0.00	0.00	32.89	2.57
1926	7992	2.961526	TTCTAGTGAATCGGAGCACC	57.038	50.000	9.37	0.00	35.67	5.01
1928	7994	5.147330	TCTTTTTCTAGTGAATCGGAGCA	57.853	39.130	0.00	0.00	31.56	4.26
1964	8030	7.882791	TGCTCATGTTTCTAGAAATTAACCAGA	59.117	33.333	20.41	10.81	32.36	3.86
1990	8056	5.815222	GTGTGGGCATCTTTTAACAGTTTTT	59.185	36.000	0.00	0.00	0.00	1.94
1996	8062	6.007076	TCTATTGTGTGGGCATCTTTTAACA	58.993	36.000	0.00	0.00	0.00	2.41
2010	8076	3.119291	GGTCGAGATGCTCTATTGTGTG	58.881	50.000	0.00	0.00	0.00	3.82
2043	8109	3.727726	TGACAGTGTGTGTGTCTTATGG	58.272	45.455	0.00	0.00	44.02	2.74
2046	8112	3.196901	ACCTTGACAGTGTGTGTGTCTTA	59.803	43.478	0.00	0.00	44.02	2.10
2050	8116	2.083774	CAACCTTGACAGTGTGTGTGT	58.916	47.619	0.00	0.00	40.56	3.72
2053	8119	1.382522	AGCAACCTTGACAGTGTGTG	58.617	50.000	0.00	0.00	0.00	3.82
2079	8164	1.271379	GCTTGCTTGGGTAGAGGTGAA	60.271	52.381	0.00	0.00	0.00	3.18
2138	8224	1.378531	GTGCATCACATAGGCCGAAA	58.621	50.000	0.00	0.00	32.61	3.46
2206	8293	0.444260	GAGTTTCTAGCGTTGCAGGC	59.556	55.000	3.81	3.81	0.00	4.85
2226	8313	0.239347	ACGTCCTAACCGTGAAGTCG	59.761	55.000	0.00	0.00	37.12	4.18
2233	8320	1.870993	GCTTTGACACGTCCTAACCGT	60.871	52.381	0.00	0.00	39.52	4.83
2234	8321	0.788391	GCTTTGACACGTCCTAACCG	59.212	55.000	0.00	0.00	0.00	4.44
2235	8322	2.067013	GAGCTTTGACACGTCCTAACC	58.933	52.381	0.00	0.00	0.00	2.85
2236	8323	2.731976	CAGAGCTTTGACACGTCCTAAC	59.268	50.000	0.00	0.00	0.00	2.34
2237	8324	2.626266	TCAGAGCTTTGACACGTCCTAA	59.374	45.455	2.15	0.00	0.00	2.69
2238	8325	2.030185	GTCAGAGCTTTGACACGTCCTA	60.030	50.000	27.55	0.00	45.32	2.94
2239	8326	1.040646	TCAGAGCTTTGACACGTCCT	58.959	50.000	2.15	0.00	0.00	3.85
2240	8327	1.140816	GTCAGAGCTTTGACACGTCC	58.859	55.000	27.55	3.78	45.32	4.79
2246	8333	2.743938	TCGTGAAGTCAGAGCTTTGAC	58.256	47.619	25.79	25.79	46.14	3.18
2247	8334	3.667497	ATCGTGAAGTCAGAGCTTTGA	57.333	42.857	2.15	2.15	0.00	2.69
2248	8335	4.328440	CCTAATCGTGAAGTCAGAGCTTTG	59.672	45.833	0.00	0.00	0.00	2.77
2249	8336	4.220821	TCCTAATCGTGAAGTCAGAGCTTT	59.779	41.667	0.00	0.00	0.00	3.51
2250	8337	3.764434	TCCTAATCGTGAAGTCAGAGCTT	59.236	43.478	0.00	0.00	0.00	3.74
2251	8338	3.357203	TCCTAATCGTGAAGTCAGAGCT	58.643	45.455	0.00	0.00	0.00	4.09
2256	8343	4.674362	CGACACATCCTAATCGTGAAGTCA	60.674	45.833	0.00	0.00	34.69	3.41
2266	8353	5.661056	TCTTCTGTTCGACACATCCTAAT	57.339	39.130	0.00	0.00	33.76	1.73
2273	8360	2.543848	GCATGTTCTTCTGTTCGACACA	59.456	45.455	0.00	0.00	0.00	3.72
2297	8384	0.843309	TGGCAAGAAGAACAGGGTCA	59.157	50.000	0.00	0.00	0.00	4.02
2348	8500	3.509137	TTGTCTGTGGTCGTCCGGC	62.509	63.158	0.00	0.00	36.30	6.13
2396	8548	6.959606	AATAGGGTATACATGCTCTTCCAT	57.040	37.500	5.01	0.00	0.00	3.41
2434	8592	7.399523	AGTCTTAATTTCTAATTAAGCGTGCG	58.600	34.615	19.71	4.60	39.92	5.34
2459	8617	8.259411	TCCGTTGGTGCTAATTTAGTTTATCTA	58.741	33.333	5.38	0.00	0.00	1.98
2610	8769	0.637195	TTTGAGGGGGTTGGGTGAAA	59.363	50.000	0.00	0.00	0.00	2.69
2619	8778	2.215758	TGGGGGATTTGAGGGGGT	59.784	61.111	0.00	0.00	0.00	4.95
2727	8888	4.862641	ATAGTACAAAGGCAGTCCCAAT	57.137	40.909	0.00	0.00	35.39	3.16
2729	8890	3.308117	CCAATAGTACAAAGGCAGTCCCA	60.308	47.826	0.00	0.00	35.39	4.37

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.