AutoCloner

Multiple sequence alignment - TraesCS7A01G406000

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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	TraesCS7A01G406000	chr7A	100.000	2681	0	0	1	2681	589456297	589458977	0.000000e+00	4951.0
1	TraesCS7A01G406000	chr7D	90.806	2741	138	40	1	2681	515823869	515826555	0.000000e+00	3561.0
2	TraesCS7A01G406000	chr7B	92.256	1640	65	13	355	1955	548165238	548166854	0.000000e+00	2268.0
3	TraesCS7A01G406000	chr7B	90.152	264	22	4	1	263	548164799	548165059	9.190000e-90	340.0
4	TraesCS7A01G406000	chr2A	79.820	555	87	20	2143	2681	420141428	420141973	5.420000e-102	381.0
5	TraesCS7A01G406000	chr2B	78.424	533	93	17	2150	2666	488873724	488874250	7.160000e-86	327.0
6	TraesCS7A01G406000	chr4A	80.749	374	62	7	2316	2680	629466205	629465833	1.570000e-72	283.0
7	TraesCS7A01G406000	chr1B	77.281	537	87	24	2151	2671	575417537	575417020	1.570000e-72	283.0
8	TraesCS7A01G406000	chr3D	80.307	391	62	11	2294	2670	169739692	169740081	5.650000e-72	281.0
9	TraesCS7A01G406000	chr6B	80.702	342	52	10	2310	2641	604061421	604061084	1.230000e-63	254.0
10	TraesCS7A01G406000	chr5D	81.672	311	46	7	2340	2641	192319131	192318823	5.730000e-62	248.0
11	TraesCS7A01G406000	chr5B	78.989	376	63	11	2311	2674	680615314	680615685	2.670000e-60	243.0
12	TraesCS7A01G406000	chr3B	80.195	308	45	11	2382	2680	18728111	18727811	1.620000e-52	217.0
13	TraesCS7A01G406000	chr3B	75.147	511	94	23	2144	2639	734732550	734732058	2.700000e-50	209.0
14	TraesCS7A01G406000	chr3B	80.153	131	21	5	2146	2274	228737295	228737422	2.840000e-15	93.5
15	TraesCS7A01G406000	chr1D	79.612	309	42	16	2343	2638	463999626	463999926	4.530000e-48	202.0
16	TraesCS7A01G406000	chr4D	74.297	249	50	10	2142	2386	509124911	509124673	2.840000e-15	93.5
17	TraesCS7A01G406000	chr4D	81.818	88	14	2	2150	2236	98927179	98927265	3.700000e-09	73.1
18	TraesCS7A01G406000	chr2D	79.825	114	23	0	2144	2257	391819824	391819711	1.710000e-12	84.2

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	TraesCS7A01G406000	chr7A	589456297	589458977	2680	False	4951	4951	100.000	1	2681	1	chr7A.!!$F1	2680
1	TraesCS7A01G406000	chr7D	515823869	515826555	2686	False	3561	3561	90.806	1	2681	1	chr7D.!!$F1	2680
2	TraesCS7A01G406000	chr7B	548164799	548166854	2055	False	1304	2268	91.204	1	1955	2	chr7B.!!$F1	1954
3	TraesCS7A01G406000	chr2A	420141428	420141973	545	False	381	381	79.820	2143	2681	1	chr2A.!!$F1	538
4	TraesCS7A01G406000	chr2B	488873724	488874250	526	False	327	327	78.424	2150	2666	1	chr2B.!!$F1	516
5	TraesCS7A01G406000	chr1B	575417020	575417537	517	True	283	283	77.281	2151	2671	1	chr1B.!!$R1	520

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
68	69	0.321653	ATTCGACCACTGGTTCTGGC	60.322	55.0	1.13	0.0	35.25	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1809	1955	1.145738	ACTGTGGGGTTGCAAAGAGAT	59.854	47.619	0.0	0.0	0.0	2.75	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
34	35	2.875087	TGAGTCGTTCTTCCGTTTCA	57.125	45.000	0.00	0.00	0.00	2.69
58	59	2.631418	TCTCGAGTCAATTCGACCAC	57.369	50.000	13.13	1.08	46.69	4.16
68	69	0.321653	ATTCGACCACTGGTTCTGGC	60.322	55.000	1.13	0.00	35.25	4.85
92	93	4.515028	TCATCTTTGATTCCAGCTCCAT	57.485	40.909	0.00	0.00	0.00	3.41
162	163	3.216800	TGCTGCAGACAAACAGAGAAAT	58.783	40.909	20.43	0.00	35.90	2.17
163	164	3.633525	TGCTGCAGACAAACAGAGAAATT	59.366	39.130	20.43	0.00	35.90	1.82
171	173	8.420189	GCAGACAAACAGAGAAATTTTATTTCG	58.580	33.333	6.52	0.00	33.86	3.46
173	175	9.665264	AGACAAACAGAGAAATTTTATTTCGAC	57.335	29.630	6.52	5.74	33.86	4.20
174	176	8.488979	ACAAACAGAGAAATTTTATTTCGACG	57.511	30.769	6.52	0.00	33.86	5.12
221	248	4.134563	ACGGCAATTCTCAACAAAGTAGT	58.865	39.130	0.00	0.00	0.00	2.73
227	254	7.965107	GGCAATTCTCAACAAAGTAGTATCTTG	59.035	37.037	0.00	0.00	0.00	3.02
337	390	3.308401	TCATATTAGCTGGGCACTGAGA	58.692	45.455	0.00	0.00	0.00	3.27
357	471	7.554118	ACTGAGAATAACCAACAGATACCAATG	59.446	37.037	0.00	0.00	33.53	2.82
572	688	1.223487	CCGTCCCCAAATCCATCGT	59.777	57.895	0.00	0.00	0.00	3.73
604	720	1.601171	CAAGCCCTGTCTGGAGAGG	59.399	63.158	6.79	6.79	41.23	3.69
605	721	0.906756	CAAGCCCTGTCTGGAGAGGA	60.907	60.000	14.32	0.00	44.04	3.71
812	928	2.998480	TGGGCTTCCGCTTCCGTA	60.998	61.111	0.00	0.00	36.09	4.02
816	932	1.949631	GCTTCCGCTTCCGTATCCG	60.950	63.158	0.00	0.00	0.00	4.18
886	1011	4.880537	CGAGCCCACGCCTAGCAG	62.881	72.222	0.00	0.00	34.57	4.24
891	1016	2.182842	CCCACGCCTAGCAGCATTC	61.183	63.158	0.00	0.00	0.00	2.67
1287	1417	4.218578	CGCCAGCTGCTCTCCGAT	62.219	66.667	8.66	0.00	38.05	4.18
1684	1814	2.813908	CCGGTGCGCAGTAGGAAC	60.814	66.667	12.22	0.00	0.00	3.62
1691	1821	3.741344	GGTGCGCAGTAGGAACTAATATG	59.259	47.826	12.22	0.00	45.48	1.78
1746	1882	1.570813	TATCACTTCATCGGCTTGCG	58.429	50.000	0.00	0.00	0.00	4.85
1757	1893	3.378911	TCGGCTTGCGATATCATGTAA	57.621	42.857	3.12	0.00	0.00	2.41
1809	1955	2.094390	GCAGTGTTCATAGTACCACGGA	60.094	50.000	0.00	0.00	33.14	4.69
1842	1989	2.232452	CCCCACAGTTAGTCACTCTCTG	59.768	54.545	7.39	7.39	30.92	3.35
1946	2103	4.392940	CCAGTGAACCTGAATCTGAAAGT	58.607	43.478	0.00	0.00	44.49	2.66
1960	2117	8.087750	TGAATCTGAAAGTTGAAACAAACAGTT	58.912	29.630	0.00	0.00	37.34	3.16
1961	2118	7.816945	ATCTGAAAGTTGAAACAAACAGTTG	57.183	32.000	0.00	0.00	36.27	3.16
2005	2162	5.947443	AGTGAAGCTGAATTTGTTAGCATC	58.053	37.500	0.00	0.00	39.84	3.91
2008	2165	4.978083	AGCTGAATTTGTTAGCATCCAG	57.022	40.909	0.00	0.00	39.84	3.86
2021	2178	2.091166	AGCATCCAGGCCATTTCCAATA	60.091	45.455	5.01	0.00	0.00	1.90
2033	2190	6.756542	GGCCATTTCCAATACAATTGTCTAAC	59.243	38.462	15.85	0.00	0.00	2.34
2040	2197	8.492673	TCCAATACAATTGTCTAACACATCTC	57.507	34.615	15.85	0.00	33.90	2.75
2066	2223	2.101750	TGTACTTCAAGCGAGTCCACAA	59.898	45.455	0.00	0.00	0.00	3.33
2071	2228	5.003804	ACTTCAAGCGAGTCCACAAATAAT	58.996	37.500	0.00	0.00	0.00	1.28
2074	2233	7.174253	ACTTCAAGCGAGTCCACAAATAATAAA	59.826	33.333	0.00	0.00	0.00	1.40
2098	2257	5.524646	ACCAATCAAAGCTGAAACAAACATG	59.475	36.000	0.00	0.00	34.49	3.21
2104	2263	2.031682	AGCTGAAACAAACATGACTCGC	60.032	45.455	0.00	0.00	0.00	5.03
2139	2298	4.946784	ACATAACGGAAGAATCTGCAAC	57.053	40.909	0.00	0.00	35.16	4.17
2148	2307	2.363683	AGAATCTGCAACTGCTTAGGC	58.636	47.619	2.95	0.00	42.66	3.93
2155	2314	1.407989	GCAACTGCTTAGGCCATCTCT	60.408	52.381	5.01	0.00	38.21	3.10
2175	2334	4.675029	CGGCGACCCTCAAACCGT	62.675	66.667	0.00	0.00	39.05	4.83
2189	2348	0.810031	AACCGTCCGCATATGTCTGC	60.810	55.000	4.29	0.00	38.81	4.26
2214	2373	2.203523	TGTCCGGACCGTGGAAGA	60.204	61.111	31.19	7.57	37.23	2.87
2239	2398	0.606604	AACGCGGTCCTGTATCAGTT	59.393	50.000	12.47	0.00	0.00	3.16
2308	2476	4.097361	GAGGGGGTGCGGGAGTTC	62.097	72.222	0.00	0.00	0.00	3.01
2314	2482	2.342648	GTGCGGGAGTTCGGAGTT	59.657	61.111	0.00	0.00	0.00	3.01
2339	2507	1.581912	CGCTAAACGTCGCGCTCTA	60.582	57.895	5.56	0.00	43.01	2.43
2341	2509	0.522915	GCTAAACGTCGCGCTCTACT	60.523	55.000	5.56	0.00	0.00	2.57
2364	2534	0.762461	CTGGCCCACCCAAAAGGAAA	60.762	55.000	0.00	0.00	44.81	3.13
2413	2583	1.065109	ACTGTTTCCGCGCCAAAAC	59.935	52.632	19.85	19.85	36.21	2.43
2415	2585	2.070654	CTGTTTCCGCGCCAAAACCT	62.071	55.000	22.33	0.00	35.07	3.50
2460	2631	1.134788	CGCTCTTCACCTAATTCCCGT	60.135	52.381	0.00	0.00	0.00	5.28
2476	2649	0.178973	CCGTCCTTTTTCCCACCCTT	60.179	55.000	0.00	0.00	0.00	3.95
2528	2708	2.111384	GGCTGTTAGAGATGGAGGTGA	58.889	52.381	0.00	0.00	0.00	4.02
2542	2722	4.760047	GTGACTGCGGTGCCGGAT	62.760	66.667	5.05	0.15	39.39	4.18
2599	2779	0.662374	CTACGTGGCAAACTCGTCGT	60.662	55.000	4.05	3.33	45.12	4.34
2601	2781	2.248431	GTGGCAAACTCGTCGTGC	59.752	61.111	0.00	0.00	37.55	5.34
2641	2821	2.428890	GGAGGAGAATCTCAAGAAGCGA	59.571	50.000	12.79	0.00	35.58	4.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	2.656002	TCGAATTGACTCGAGATCCCT	58.344	47.619	21.68	0.00	42.69	4.20
58	59	3.822735	TCAAAGATGAAAGCCAGAACCAG	59.177	43.478	0.00	0.00	30.99	4.00
68	69	4.703575	TGGAGCTGGAATCAAAGATGAAAG	59.296	41.667	0.00	0.00	39.49	2.62
92	93	1.374947	CGTGCCAGGGAGAAGGAAA	59.625	57.895	0.00	0.00	0.00	3.13
162	163	6.847956	TGGAACTTTCTCGTCGAAATAAAA	57.152	33.333	0.00	0.00	40.62	1.52
163	164	6.847956	TTGGAACTTTCTCGTCGAAATAAA	57.152	33.333	0.00	0.00	40.62	1.40
171	173	3.463944	TCCAGTTTGGAACTTTCTCGTC	58.536	45.455	0.00	0.00	45.00	4.20
199	225	4.134563	ACTACTTTGTTGAGAATTGCCGT	58.865	39.130	0.00	0.00	0.00	5.68
337	390	8.821686	TGATTCATTGGTATCTGTTGGTTATT	57.178	30.769	0.00	0.00	0.00	1.40
357	471	9.502145	TGCTTTTGTTCGATGTTAATATGATTC	57.498	29.630	0.00	0.00	0.00	2.52
368	482	3.476552	TCTCCTTGCTTTTGTTCGATGT	58.523	40.909	0.00	0.00	0.00	3.06
459	575	2.866762	CGCCTATCTGCAGAAACCTAAC	59.133	50.000	22.50	5.97	0.00	2.34
589	705	1.000993	TCTCCTCTCCAGACAGGGC	59.999	63.158	0.00	0.00	38.24	5.19
591	707	0.628522	TCCTCTCCTCTCCAGACAGG	59.371	60.000	0.00	0.00	39.47	4.00
886	1011	1.894282	GCTCGGGCTTAGGGAATGC	60.894	63.158	0.00	0.00	35.22	3.56
887	1012	1.595382	CGCTCGGGCTTAGGGAATG	60.595	63.158	5.36	0.00	36.09	2.67
888	1013	2.822399	CGCTCGGGCTTAGGGAAT	59.178	61.111	5.36	0.00	36.09	3.01
1684	1814	8.615211	ACACAACATGATAACAGCACATATTAG	58.385	33.333	0.00	0.00	0.00	1.73
1691	1821	4.681025	CCAAACACAACATGATAACAGCAC	59.319	41.667	0.00	0.00	0.00	4.40
1757	1893	3.871594	GCGCAAGAAACATACTGGAGTAT	59.128	43.478	0.30	0.00	40.13	2.12
1809	1955	1.145738	ACTGTGGGGTTGCAAAGAGAT	59.854	47.619	0.00	0.00	0.00	2.75
1960	2117	8.210265	TCACTGGTAATGCTGATTTGATATACA	58.790	33.333	0.00	0.00	0.00	2.29
1961	2118	8.607441	TCACTGGTAATGCTGATTTGATATAC	57.393	34.615	0.00	0.00	0.00	1.47
2005	2162	4.080975	ACAATTGTATTGGAAATGGCCTGG	60.081	41.667	9.97	0.00	0.00	4.45
2008	2165	5.343307	AGACAATTGTATTGGAAATGGCC	57.657	39.130	11.95	0.00	0.00	5.36
2021	2178	7.283127	ACACTTTGAGATGTGTTAGACAATTGT	59.717	33.333	11.78	11.78	43.88	2.71
2033	2190	5.613360	CGCTTGAAGTACACTTTGAGATGTG	60.613	44.000	0.00	0.00	36.11	3.21
2040	2197	3.184581	GGACTCGCTTGAAGTACACTTTG	59.815	47.826	0.00	0.00	36.11	2.77
2066	2223	9.995003	TGTTTCAGCTTTGATTGGTTTATTATT	57.005	25.926	0.00	0.00	0.00	1.40
2071	2228	7.099764	TGTTTGTTTCAGCTTTGATTGGTTTA	58.900	30.769	0.00	0.00	0.00	2.01
2074	2233	5.083533	TGTTTGTTTCAGCTTTGATTGGT	57.916	34.783	0.00	0.00	0.00	3.67
2098	2257	0.750182	AGGAGTAGGCAGAGCGAGTC	60.750	60.000	0.00	0.00	0.00	3.36
2104	2263	3.253677	CCGTTATGTAGGAGTAGGCAGAG	59.746	52.174	0.00	0.00	0.00	3.35
2139	2298	2.546795	CCGTTAGAGATGGCCTAAGCAG	60.547	54.545	3.32	0.00	42.56	4.24
2148	2307	1.067582	GGGTCGCCGTTAGAGATGG	59.932	63.158	0.00	0.00	37.49	3.51
2155	2314	1.004679	GGTTTGAGGGTCGCCGTTA	60.005	57.895	0.00	0.00	0.00	3.18
2189	2348	2.105128	GGTCCGGACAGCTCGATG	59.895	66.667	34.40	0.00	0.00	3.84
2214	2373	1.537814	TACAGGACCGCGTTGGATGT	61.538	55.000	4.92	5.91	42.00	3.06
2299	2467	2.506438	CGAACTCCGAACTCCCGC	60.506	66.667	0.00	0.00	41.76	6.13
2300	2468	2.181021	CCGAACTCCGAACTCCCG	59.819	66.667	0.00	0.00	41.76	5.14
2301	2469	1.214853	GTCCGAACTCCGAACTCCC	59.785	63.158	0.00	0.00	41.76	4.30
2303	2471	0.728466	CGTGTCCGAACTCCGAACTC	60.728	60.000	0.00	0.00	41.76	3.01
2304	2472	1.285023	CGTGTCCGAACTCCGAACT	59.715	57.895	0.00	0.00	41.76	3.01
2305	2473	2.370393	GCGTGTCCGAACTCCGAAC	61.370	63.158	0.00	0.00	41.76	3.95
2306	2474	1.236616	TAGCGTGTCCGAACTCCGAA	61.237	55.000	0.00	0.00	41.76	4.30
2307	2475	1.236616	TTAGCGTGTCCGAACTCCGA	61.237	55.000	0.00	0.00	41.76	4.55
2308	2476	0.387622	TTTAGCGTGTCCGAACTCCG	60.388	55.000	0.00	0.00	35.63	4.63
2451	2622	3.423749	GTGGGAAAAAGGACGGGAATTA	58.576	45.455	0.00	0.00	0.00	1.40
2460	2631	3.699025	AGAAAAGGGTGGGAAAAAGGA	57.301	42.857	0.00	0.00	0.00	3.36
2476	2649	4.687464	GGCGACGGAAGGAAGAAA	57.313	55.556	0.00	0.00	0.00	2.52
2507	2680	2.114616	CACCTCCATCTCTAACAGCCT	58.885	52.381	0.00	0.00	0.00	4.58
2515	2695	1.326213	CCGCAGTCACCTCCATCTCT	61.326	60.000	0.00	0.00	0.00	3.10
2528	2708	3.740128	GATCATCCGGCACCGCAGT	62.740	63.158	2.83	0.00	38.24	4.40
2530	2710	4.545706	GGATCATCCGGCACCGCA	62.546	66.667	2.83	0.00	38.24	5.69
2564	2744	0.747255	GTAGCCGAGCTGATCTTCCA	59.253	55.000	8.44	0.00	40.10	3.53
2641	2821	2.034066	CACCCACTGGCGACCATT	59.966	61.111	0.00	0.00	30.82	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.