AutoCloner

Multiple sequence alignment - TraesCS7A01G306500

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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	TraesCS7A01G306500	chr7A	100.000	2739	0	0	1	2739	432695752	432693014	0.000000e+00	5059.0
1	TraesCS7A01G306500	chr7A	96.855	159	5	0	659	817	432695005	432694847	1.620000e-67	267.0
2	TraesCS7A01G306500	chr7A	96.855	159	5	0	748	906	432695094	432694936	1.620000e-67	267.0
3	TraesCS7A01G306500	chr7A	81.493	335	51	6	2223	2555	209155810	209155485	5.820000e-67	265.0
4	TraesCS7A01G306500	chr7A	97.143	70	2	0	659	728	432694916	432694847	4.790000e-23	119.0
5	TraesCS7A01G306500	chr7A	97.143	70	2	0	837	906	432695094	432695025	4.790000e-23	119.0
6	TraesCS7A01G306500	chr7D	94.672	2740	115	13	1	2739	383975671	383972962	0.000000e+00	4222.0
7	TraesCS7A01G306500	chr7D	80.631	444	80	6	5	445	376327109	376326669	3.380000e-89	339.0
8	TraesCS7A01G306500	chr7D	85.156	256	36	2	2218	2471	199355913	199355658	7.520000e-66	261.0
9	TraesCS7A01G306500	chr7D	95.597	159	7	0	659	817	383974926	383974768	3.500000e-64	255.0
10	TraesCS7A01G306500	chr7D	95.597	159	7	0	748	906	383975015	383974857	3.500000e-64	255.0
11	TraesCS7A01G306500	chr7D	97.143	70	2	0	659	728	383974837	383974768	4.790000e-23	119.0
12	TraesCS7A01G306500	chr7D	97.143	70	2	0	837	906	383975015	383974946	4.790000e-23	119.0
13	TraesCS7A01G306500	chr7D	73.829	363	65	18	1837	2190	424111527	424111868	1.720000e-22	117.0
14	TraesCS7A01G306500	chr7D	75.000	224	46	9	1954	2172	415952888	415952670	8.070000e-16	95.3
15	TraesCS7A01G306500	chr7B	91.701	2663	145	22	1	2659	378391573	378388983	0.000000e+00	3624.0
16	TraesCS7A01G306500	chr7B	80.387	362	56	10	2218	2575	163488637	163488287	7.520000e-66	261.0
17	TraesCS7A01G306500	chr7B	95.597	159	7	0	748	906	378390928	378390770	3.500000e-64	255.0
18	TraesCS7A01G306500	chr7B	94.340	159	9	0	659	817	378390839	378390681	7.580000e-61	244.0
19	TraesCS7A01G306500	chr7B	92.941	85	5	1	2655	2739	378383032	378382949	3.700000e-24	122.0
20	TraesCS7A01G306500	chr7B	94.805	77	4	0	837	913	378390928	378390852	1.330000e-23	121.0
21	TraesCS7A01G306500	chr7B	95.714	70	3	0	659	728	378390750	378390681	2.230000e-21	113.0
22	TraesCS7A01G306500	chr7B	80.180	111	9	9	326	429	316404968	316404864	1.360000e-08	71.3
23	TraesCS7A01G306500	chr5D	81.870	353	54	9	2217	2564	460939878	460939531	3.450000e-74	289.0
24	TraesCS7A01G306500	chr5D	81.250	144	18	7	215	352	219223102	219223242	1.040000e-19	108.0
25	TraesCS7A01G306500	chr6A	79.299	314	55	9	2217	2526	140547907	140548214	7.680000e-51	211.0
26	TraesCS7A01G306500	chr3D	77.473	364	68	14	2253	2607	434949471	434949113	3.580000e-49	206.0
27	TraesCS7A01G306500	chr2D	78.274	336	61	10	2223	2556	73591143	73590818	3.580000e-49	206.0
28	TraesCS7A01G306500	chr5A	80.220	273	41	10	180	446	292735582	292735847	2.780000e-45	193.0
29	TraesCS7A01G306500	chr5B	79.545	264	41	9	167	424	238563919	238563663	2.800000e-40	176.0
30	TraesCS7A01G306500	chr2B	89.873	79	3	4	375	452	373270097	373270171	2.250000e-16	97.1
31	TraesCS7A01G306500	chr2B	84.337	83	9	4	369	448	647590234	647590153	8.130000e-11	78.7
32	TraesCS7A01G306500	chr6D	86.585	82	3	8	368	446	112822493	112822569	1.750000e-12	84.2
33	TraesCS7A01G306500	chr4B	85.915	71	10	0	2137	2207	581065675	581065745	2.920000e-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	TraesCS7A01G306500	chr7A	432693014	432695752	2738	True	1166.2	5059	97.5992	1	2739	5	chr7A.!!$R2	2738
1	TraesCS7A01G306500	chr7D	383972962	383975671	2709	True	994.0	4222	96.0304	1	2739	5	chr7D.!!$R4	2738
2	TraesCS7A01G306500	chr7B	378388983	378391573	2590	True	871.4	3624	94.4314	1	2659	5	chr7B.!!$R4	2658

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
356	357	0.625849	ACTGCCATAGGTTGAAGGGG	59.374	55.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1943	1945	0.60864	CTGAGAGGTACAAAGGCGGT	59.391	55.0	0.0	0.0	0.0	5.68	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
29	30	2.014010	TCTGAAATTGCCCCTTTGCT	57.986	45.000	0.00	0.00	0.00	3.91
32	33	3.091545	CTGAAATTGCCCCTTTGCTCTA	58.908	45.455	0.00	0.00	0.00	2.43
42	43	2.435805	CCCTTTGCTCTATAGTGCTGGA	59.564	50.000	23.29	10.05	35.73	3.86
50	51	4.878397	GCTCTATAGTGCTGGAACAACATT	59.122	41.667	17.51	0.00	36.57	2.71
102	103	7.762615	CAGTATTTGATGAATTCCAGTTTGCAT	59.237	33.333	2.27	0.00	0.00	3.96
136	137	4.675510	CCACAAGATATTGCATTGGACAC	58.324	43.478	0.00	0.00	0.00	3.67
213	214	1.478837	CGGCTCCTCCTCACATACCTA	60.479	57.143	0.00	0.00	0.00	3.08
231	232	8.660435	ACATACCTAGTTGGATGCATTACTTAT	58.340	33.333	13.15	5.44	39.71	1.73
356	357	0.625849	ACTGCCATAGGTTGAAGGGG	59.374	55.000	0.00	0.00	0.00	4.79
462	464	1.260544	AAAGTCCTCTGGCCAAATGC	58.739	50.000	7.01	0.00	40.16	3.56
571	573	3.662247	ATAAGCCGGTTTCTAGGATCG	57.338	47.619	6.88	0.00	0.00	3.69
1019	1021	1.800586	CAGACACAAACACATCTCCCG	59.199	52.381	0.00	0.00	0.00	5.14
1125	1127	4.007644	TCACTGGCAGTGGAGGCG	62.008	66.667	38.88	19.05	45.94	5.52
1678	1680	4.666512	ACTTGTAAGGGCATCTTCAATGT	58.333	39.130	0.00	0.00	36.93	2.71
1688	1690	2.859165	TCTTCAATGTGGACCCTCAC	57.141	50.000	0.00	0.00	38.09	3.51
1762	1764	0.818296	AGTAGCTCATCGGTCCACAC	59.182	55.000	0.00	0.00	0.00	3.82
1818	1820	0.469892	CAAACTGGAAGGGGGCTTGT	60.470	55.000	0.00	0.00	39.30	3.16
1872	1874	3.204827	CTCCGGCCCGCTCAAATG	61.205	66.667	0.00	0.00	0.00	2.32
1879	1881	1.028868	GCCCGCTCAAATGCTCTTCT	61.029	55.000	0.00	0.00	0.00	2.85
1925	1927	2.345760	CCCGCCTGCTTTGCATTCT	61.346	57.895	0.00	0.00	38.13	2.40
1943	1945	1.133167	TCTCACCCTCCTTGTCTGACA	60.133	52.381	6.36	6.36	0.00	3.58
1961	1963	0.320374	CACCGCCTTTGTACCTCTCA	59.680	55.000	0.00	0.00	0.00	3.27
1973	1975	2.071262	CCTCTCAGCTGCCTCCCAT	61.071	63.158	9.47	0.00	0.00	4.00
1993	1995	1.900351	CATCCTCGGACCTCTGCAA	59.100	57.895	0.00	0.00	0.00	4.08
2014	2016	3.941188	CCACCCACGTGCCTGTCT	61.941	66.667	10.91	0.00	38.79	3.41
2031	2033	1.805945	CTGCCTTGGACTACGACGC	60.806	63.158	0.00	0.00	0.00	5.19
2057	2059	0.249073	CCCAGGATTCGTCTACAGCG	60.249	60.000	0.00	0.00	0.00	5.18
2059	2061	1.268794	CCAGGATTCGTCTACAGCGAG	60.269	57.143	0.00	0.00	39.61	5.03
2163	2166	8.641499	TTATTGTTGACCATCTTGTTGTTTTC	57.359	30.769	0.00	0.00	0.00	2.29
2211	2214	2.159128	ACTGATGGAGAATGAGTGCGAG	60.159	50.000	0.00	0.00	30.71	5.03
2215	2218	0.737715	GGAGAATGAGTGCGAGCGTT	60.738	55.000	0.00	0.00	0.00	4.84
2220	2223	0.235665	ATGAGTGCGAGCGTTTTGTG	59.764	50.000	0.00	0.00	0.00	3.33
2314	2317	5.932883	GGAGGACTTGTTTCGATTCTAACTT	59.067	40.000	0.00	0.00	0.00	2.66
2337	2340	7.330946	ACTTGAGTATCGTTGAATTTCGAATCA	59.669	33.333	0.00	0.00	38.61	2.57
2487	2492	3.564225	AGTGTTGCGACTTAAAAGAAGGG	59.436	43.478	5.50	0.00	0.00	3.95
2502	2507	2.434336	AGAAGGGAAAACAAGGGCAAAC	59.566	45.455	0.00	0.00	0.00	2.93
2526	2531	0.772124	AGGTGACAGGGTTGGATGGT	60.772	55.000	0.00	0.00	0.00	3.55
2557	2562	2.880879	CGTGTCCGCGGATCAGTG	60.881	66.667	33.58	20.00	0.00	3.66
2565	2570	4.498520	CGGATCAGTGCGCGGACT	62.499	66.667	28.56	28.56	30.86	3.85
2578	2583	2.717530	CGCGGACTAATAGTGTGTCTC	58.282	52.381	0.00	0.00	0.00	3.36
2613	2618	5.255710	ACGTTGGAGATGTCTTCATAGAG	57.744	43.478	0.00	0.00	34.06	2.43
2723	2728	6.752351	GCCATTATTATCGATCACTGATACGT	59.248	38.462	0.00	0.00	0.00	3.57
2727	2732	9.776158	ATTATTATCGATCACTGATACGTCTTC	57.224	33.333	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	4.646492	CACTATAGAGCAAAGGGGCAATTT	59.354	41.667	6.78	0.00	35.83	1.82
29	30	7.715249	GGAATAATGTTGTTCCAGCACTATAGA	59.285	37.037	14.17	0.00	44.84	1.98
32	33	6.699575	GGAATAATGTTGTTCCAGCACTAT	57.300	37.500	14.17	0.00	44.84	2.12
102	103	1.761449	TCTTGTGGCAAGTGCAGAAA	58.239	45.000	5.52	0.00	44.36	2.52
136	137	2.419574	CCCCAACATCCCGTAGTTACAG	60.420	54.545	0.00	0.00	0.00	2.74
213	214	7.072454	TCCTTCCTATAAGTAATGCATCCAACT	59.928	37.037	0.00	1.24	0.00	3.16
231	232	1.062121	AGCAGCCCATAGTCCTTCCTA	60.062	52.381	0.00	0.00	0.00	2.94
266	267	1.036707	TCCTTTCGGCTTTGGTTTGG	58.963	50.000	0.00	0.00	0.00	3.28
322	323	4.439305	TGGCAGTTCTATGAAACATTGC	57.561	40.909	0.00	0.00	32.49	3.56
461	463	6.857964	CCAATGGTTAATATGACTCGATTTGC	59.142	38.462	0.00	0.00	0.00	3.68
462	464	8.153479	TCCAATGGTTAATATGACTCGATTTG	57.847	34.615	0.00	0.00	0.00	2.32
558	560	1.066757	GACCCGACGATCCTAGAAACC	59.933	57.143	0.00	0.00	0.00	3.27
1019	1021	4.819630	TGGTCTTCATGGTCTTTGTGTTAC	59.180	41.667	0.00	0.00	0.00	2.50
1423	1425	4.824515	CTCCTCCCCGAGCCTCGT	62.825	72.222	13.83	0.00	38.40	4.18
1426	1428	2.279408	GTACTCCTCCCCGAGCCT	59.721	66.667	0.00	0.00	32.79	4.58
1678	1680	2.763215	GGGCATTGTGAGGGTCCA	59.237	61.111	0.00	0.00	0.00	4.02
1688	1690	1.422269	CGAACGGTTACGGGCATTG	59.578	57.895	0.00	0.00	46.48	2.82
1711	1713	1.750778	CAAATTATGCCCCGACTGCTT	59.249	47.619	0.00	0.00	0.00	3.91
1818	1820	2.052690	GCAGCGGTCCAGACTCCTA	61.053	63.158	0.00	0.00	0.00	2.94
1872	1874	3.133141	AGAAAAGTGGACCAGAAGAGC	57.867	47.619	0.00	0.00	0.00	4.09
1874	1876	3.458118	TGGAAGAAAAGTGGACCAGAAGA	59.542	43.478	0.00	0.00	0.00	2.87
1879	1881	2.777692	AGAGTGGAAGAAAAGTGGACCA	59.222	45.455	0.00	0.00	0.00	4.02
1925	1927	1.048601	GTGTCAGACAAGGAGGGTGA	58.951	55.000	4.32	0.00	0.00	4.02
1943	1945	0.608640	CTGAGAGGTACAAAGGCGGT	59.391	55.000	0.00	0.00	0.00	5.68
1961	1963	2.195139	GATGCATGGGAGGCAGCT	59.805	61.111	2.46	0.00	45.68	4.24
1973	1975	2.725312	GCAGAGGTCCGAGGATGCA	61.725	63.158	9.76	0.00	33.92	3.96
2014	2016	2.260434	GCGTCGTAGTCCAAGGCA	59.740	61.111	0.00	0.00	0.00	4.75
2059	2061	1.034292	GCAGGAAGGTTGAGGATGCC	61.034	60.000	0.00	0.00	0.00	4.40
2109	2112	0.893727	GGCATTTGACCGAACACCCT	60.894	55.000	0.00	0.00	0.00	4.34
2163	2166	2.470821	CCCGCCATCGTTTTACTCTAG	58.529	52.381	0.00	0.00	0.00	2.43
2211	2214	1.299089	GTCCTGTGGCACAAAACGC	60.299	57.895	22.31	6.67	44.16	4.84
2215	2218	1.227823	CTCGGTCCTGTGGCACAAA	60.228	57.895	22.31	10.01	44.16	2.83
2220	2223	2.680352	TCTCCTCGGTCCTGTGGC	60.680	66.667	0.00	0.00	0.00	5.01
2314	2317	7.589574	TTGATTCGAAATTCAACGATACTCA	57.410	32.000	9.57	0.00	38.30	3.41
2487	2492	3.799963	CCTAAACGTTTGCCCTTGTTTTC	59.200	43.478	23.46	0.00	36.14	2.29
2502	2507	1.071071	TCCAACCCTGTCACCTAAACG	59.929	52.381	0.00	0.00	0.00	3.60
2526	2531	1.376543	GACACGGATACTGGAGTCGA	58.623	55.000	0.00	0.00	0.00	4.20
2557	2562	1.197910	GACACACTATTAGTCCGCGC	58.802	55.000	0.00	0.00	0.00	6.86
2578	2583	8.370493	ACATCTCCAACGTATATCATCAAAAG	57.630	34.615	0.00	0.00	0.00	2.27
2592	2597	5.298026	TCTCTCTATGAAGACATCTCCAACG	59.702	44.000	0.00	0.00	37.87	4.10
2671	2676	8.100164	TCTTGATGACATGACAATAACCTACAA	58.900	33.333	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.