AutoCloner

Multiple sequence alignment - TraesCS7B01G343200

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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	TraesCS7B01G343200	chr7B	100.000	3083	0	0	1	3083	598470538	598467456	0.000000e+00	5694.0
1	TraesCS7B01G343200	chr7B	94.454	2272	84	20	819	3083	644531045	644528809	0.000000e+00	3459.0
2	TraesCS7B01G343200	chr7B	94.603	667	26	4	162	820	644538085	644537421	0.000000e+00	1024.0
3	TraesCS7B01G343200	chr7B	84.982	546	73	8	1394	1936	105888519	105889058	2.090000e-151	545.0
4	TraesCS7B01G343200	chr7B	96.970	165	5	0	1	165	644540075	644539911	8.420000e-71	278.0
5	TraesCS7B01G343200	chr7A	89.940	3161	211	42	1	3083	638703995	638700864	0.000000e+00	3976.0
6	TraesCS7B01G343200	chr7A	83.333	126	16	4	1	123	362715073	362715196	9.040000e-21	111.0
7	TraesCS7B01G343200	chr7D	92.652	2368	109	13	1	2335	552957422	552955087	0.000000e+00	3349.0
8	TraesCS7B01G343200	chr7D	89.024	574	40	7	2395	2957	552955088	552954527	0.000000e+00	689.0
9	TraesCS7B01G343200	chr3A	85.923	547	69	8	1394	1936	7158481	7159023	7.410000e-161	577.0
10	TraesCS7B01G343200	chr3D	85.558	547	71	8	1394	1936	1873002	1872460	1.600000e-157	566.0
11	TraesCS7B01G343200	chr3D	75.089	562	112	20	1383	1926	4818804	4818253	1.430000e-58	237.0
12	TraesCS7B01G343200	chrUn	75.614	529	101	23	1433	1942	236970880	236971399	1.430000e-58	237.0
13	TraesCS7B01G343200	chrUn	79.932	294	52	6	1654	1942	35392178	35391887	3.120000e-50	209.0
14	TraesCS7B01G343200	chr5B	89.231	65	6	1	2334	2397	336799770	336799834	2.550000e-11	80.5
15	TraesCS7B01G343200	chr5B	82.353	85	9	3	2320	2400	397836420	397836338	5.520000e-08	69.4
16	TraesCS7B01G343200	chr1B	88.571	70	3	2	2333	2397	142039723	142039654	2.550000e-11	80.5
17	TraesCS7B01G343200	chr6B	88.060	67	6	2	2333	2397	703353374	703353308	9.170000e-11	78.7
18	TraesCS7B01G343200	chr4A	89.062	64	5	1	2334	2397	731341880	731341941	9.170000e-11	78.7
19	TraesCS7B01G343200	chr2B	86.301	73	5	4	2334	2402	766079470	766079399	1.190000e-09	75.0

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	TraesCS7B01G343200	chr7B	598467456	598470538	3082	True	5694	5694	100.0000	1	3083	1	chr7B.!!$R1	3082
1	TraesCS7B01G343200	chr7B	644528809	644531045	2236	True	3459	3459	94.4540	819	3083	1	chr7B.!!$R2	2264
2	TraesCS7B01G343200	chr7B	644537421	644540075	2654	True	651	1024	95.7865	1	820	2	chr7B.!!$R3	819
3	TraesCS7B01G343200	chr7B	105888519	105889058	539	False	545	545	84.9820	1394	1936	1	chr7B.!!$F1	542
4	TraesCS7B01G343200	chr7A	638700864	638703995	3131	True	3976	3976	89.9400	1	3083	1	chr7A.!!$R1	3082
5	TraesCS7B01G343200	chr7D	552954527	552957422	2895	True	2019	3349	90.8380	1	2957	2	chr7D.!!$R1	2956
6	TraesCS7B01G343200	chr3A	7158481	7159023	542	False	577	577	85.9230	1394	1936	1	chr3A.!!$F1	542
7	TraesCS7B01G343200	chr3D	1872460	1873002	542	True	566	566	85.5580	1394	1936	1	chr3D.!!$R1	542
8	TraesCS7B01G343200	chr3D	4818253	4818804	551	True	237	237	75.0890	1383	1926	1	chr3D.!!$R2	543
9	TraesCS7B01G343200	chrUn	236970880	236971399	519	False	237	237	75.6140	1433	1942	1	chrUn.!!$F1	509

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
74	75	0.179156	GCATGAAGCATGACCAACGG	60.179	55.000	11.31	0.0	43.81	4.44	F
534	2396	1.072505	GCGGAGGAAAGGGTTCACA	59.927	57.895	0.00	0.0	35.25	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1848	3766	1.079197	CTGGCGGTAGTGCATGACA	60.079	57.895	0.0	0.0	36.28	3.58	R
2379	4308	1.233369	CCTACTCCCTCCGTCCCAT	59.767	63.158	0.0	0.0	0.00	4.00	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
28	29	3.792401	TGACATAATCCTAGTTGCCACG	58.208	45.455	0.00	0.00	0.00	4.94
74	75	0.179156	GCATGAAGCATGACCAACGG	60.179	55.000	11.31	0.00	43.81	4.44
240	2094	3.092301	GGGAGCAAAATATATGGAGGCC	58.908	50.000	0.00	0.00	0.00	5.19
265	2119	3.319031	AGGAAGGAAATAGGGCAATGG	57.681	47.619	0.00	0.00	0.00	3.16
534	2396	1.072505	GCGGAGGAAAGGGTTCACA	59.927	57.895	0.00	0.00	35.25	3.58
660	2523	2.047179	GGACAGTCGGCCCAAGAC	60.047	66.667	0.00	0.00	38.81	3.01
762	2633	2.494870	GCGTGAGAGGACTAGGGTTTAA	59.505	50.000	0.00	0.00	0.00	1.52
985	2873	2.153645	CTACAAATGTCTGCCAGCACA	58.846	47.619	0.00	0.00	0.00	4.57
1009	2897	1.446792	CTTCTCGCCATGACGCTGT	60.447	57.895	0.00	0.00	0.00	4.40
1908	3829	2.048690	GCCATCGCGGAGATCCTC	60.049	66.667	6.13	0.00	37.52	3.71
1916	3837	3.849951	GGAGATCCTCGCCGCCAA	61.850	66.667	0.00	0.00	0.00	4.52
2031	3952	2.995872	GCTGAGCGAGAGTCCGGTT	61.996	63.158	0.00	0.00	40.59	4.44
2086	4007	4.142403	TGGCATCGTTGATCCTTTGATTTC	60.142	41.667	0.00	0.00	0.00	2.17
2144	4069	4.883083	TGAGCATTCCGAGAACCATATAC	58.117	43.478	0.00	0.00	0.00	1.47
2146	4071	4.887748	AGCATTCCGAGAACCATATACTG	58.112	43.478	0.00	0.00	0.00	2.74
2147	4072	4.345257	AGCATTCCGAGAACCATATACTGT	59.655	41.667	0.00	0.00	0.00	3.55
2148	4073	5.057149	GCATTCCGAGAACCATATACTGTT	58.943	41.667	0.00	0.00	0.00	3.16
2149	4074	6.041637	AGCATTCCGAGAACCATATACTGTTA	59.958	38.462	0.00	0.00	0.00	2.41
2150	4075	6.145696	GCATTCCGAGAACCATATACTGTTAC	59.854	42.308	0.00	0.00	0.00	2.50
2151	4076	5.428496	TCCGAGAACCATATACTGTTACG	57.572	43.478	0.00	0.00	0.00	3.18
2152	4077	4.276678	TCCGAGAACCATATACTGTTACGG	59.723	45.833	17.97	17.97	41.46	4.02
2221	4147	4.446311	GCATGTCATACACCCCCTATCTTT	60.446	45.833	0.00	0.00	0.00	2.52
2245	4171	3.118992	TCTCCTCTGTGAACATTCCATCG	60.119	47.826	0.00	0.00	0.00	3.84
2306	4232	4.396478	GGAGAAAGGATAGCCAAAGTGTTC	59.604	45.833	0.00	0.00	36.29	3.18
2342	4268	6.461110	TTAAGAAATACACCTACTCCCTCG	57.539	41.667	0.00	0.00	0.00	4.63
2364	4290	3.869246	GGTCCCATAATGTAAGACGTGTG	59.131	47.826	0.00	0.00	0.00	3.82
2366	4292	4.565564	GTCCCATAATGTAAGACGTGTGAC	59.434	45.833	0.00	0.00	0.00	3.67
2368	4294	5.105106	TCCCATAATGTAAGACGTGTGACAT	60.105	40.000	9.87	9.87	34.00	3.06
2567	4566	1.763655	TCATCCCATCTCAGCGCCT	60.764	57.895	2.29	0.00	0.00	5.52
2645	4644	1.153086	GAGGCCTCATGATGCGGTT	60.153	57.895	28.43	5.18	0.00	4.44
2679	4678	1.542030	AGAATGACTCGCTCGTTCAGT	59.458	47.619	13.99	0.00	44.57	3.41
2680	4679	2.747989	AGAATGACTCGCTCGTTCAGTA	59.252	45.455	13.99	0.00	44.57	2.74
2681	4680	3.378742	AGAATGACTCGCTCGTTCAGTAT	59.621	43.478	13.99	0.00	44.57	2.12
2682	4681	4.575236	AGAATGACTCGCTCGTTCAGTATA	59.425	41.667	13.99	0.00	44.57	1.47
2683	4682	5.239744	AGAATGACTCGCTCGTTCAGTATAT	59.760	40.000	13.99	0.00	44.57	0.86
2684	4683	6.427242	AGAATGACTCGCTCGTTCAGTATATA	59.573	38.462	13.99	0.00	44.57	0.86
2685	4684	6.745159	ATGACTCGCTCGTTCAGTATATAT	57.255	37.500	0.00	0.00	0.00	0.86
2739	4756	8.851541	AAATAAATCAAGCAATGGTCAATTGT	57.148	26.923	5.13	0.00	46.37	2.71
2740	4757	9.941325	AAATAAATCAAGCAATGGTCAATTGTA	57.059	25.926	5.13	0.00	46.37	2.41
2741	4758	9.590451	AATAAATCAAGCAATGGTCAATTGTAG	57.410	29.630	5.13	0.00	46.37	2.74
2742	4759	5.587388	ATCAAGCAATGGTCAATTGTAGG	57.413	39.130	5.13	0.00	46.37	3.18
2743	4760	4.661222	TCAAGCAATGGTCAATTGTAGGA	58.339	39.130	5.13	0.00	46.37	2.94
2751	4768	7.282224	GCAATGGTCAATTGTAGGAGTATGTAA	59.718	37.037	5.13	0.00	46.37	2.41
2765	4784	7.641249	AGGAGTATGTAACAGTAGTAGGAAGT	58.359	38.462	0.00	0.00	0.00	3.01
2832	4851	1.259609	TTACCACGAACCCGAGACAT	58.740	50.000	0.00	0.00	39.50	3.06
2879	4899	0.330604	AGGCTCTGGCATGAATGTGT	59.669	50.000	0.00	0.00	40.87	3.72
2896	4916	9.685276	ATGAATGTGTATCAAGAATGGAAACTA	57.315	29.630	0.00	0.00	0.00	2.24
2948	4973	2.865343	GGCATCTGGCTTTTCATCTG	57.135	50.000	0.00	0.00	44.01	2.90
2950	4975	1.749634	GCATCTGGCTTTTCATCTGCT	59.250	47.619	0.00	0.00	40.25	4.24
2964	4989	5.408204	TCATCTGCTTGCAATTGTATACG	57.592	39.130	7.40	0.00	0.00	3.06
2965	4990	4.875536	TCATCTGCTTGCAATTGTATACGT	59.124	37.500	7.40	0.00	0.00	3.57
2966	4991	6.045955	TCATCTGCTTGCAATTGTATACGTA	58.954	36.000	7.40	0.00	0.00	3.57
2967	4992	5.712217	TCTGCTTGCAATTGTATACGTAC	57.288	39.130	7.40	0.00	0.00	3.67
2969	4994	6.566141	TCTGCTTGCAATTGTATACGTACTA	58.434	36.000	7.40	0.00	0.00	1.82
3058	5086	3.068024	TGGTTTTCATCAAGACTTGCCAC	59.932	43.478	10.50	1.05	0.00	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	4.442332	CCTGTGTATATTCCGTGGCAACTA	60.442	45.833	0.00	0.00	37.61	2.24
74	75	1.745087	ACATGGGTGATTGATTGTCGC	59.255	47.619	0.00	0.00	0.00	5.19
135	159	5.261216	TCTTAAACCATTTGGGAGTGATCC	58.739	41.667	0.96	0.00	41.15	3.36
240	2094	5.482163	TTGCCCTATTTCCTTCCTTTTTG	57.518	39.130	0.00	0.00	0.00	2.44
265	2119	2.027751	GCGGTCGAGGAGGTATGC	59.972	66.667	0.00	0.00	0.00	3.14
295	2149	2.593134	GCTCATCCGTCTGCGATGC	61.593	63.158	0.00	0.00	41.33	3.91
429	2283	0.242825	CAGTCCGCTGTCGAAAGGTA	59.757	55.000	4.40	0.00	37.92	3.08
455	2317	8.349983	GGTTAGAGAGAAAGAGAGATATGTGAC	58.650	40.741	0.00	0.00	0.00	3.67
460	2322	9.753674	CCATAGGTTAGAGAGAAAGAGAGATAT	57.246	37.037	0.00	0.00	0.00	1.63
462	2324	7.505585	CACCATAGGTTAGAGAGAAAGAGAGAT	59.494	40.741	0.00	0.00	31.02	2.75
520	2382	1.068121	CCCTCTGTGAACCCTTTCCT	58.932	55.000	0.00	0.00	0.00	3.36
524	2386	0.104409	ACTCCCCTCTGTGAACCCTT	60.104	55.000	0.00	0.00	0.00	3.95
534	2396	0.757188	CGCTGTATCCACTCCCCTCT	60.757	60.000	0.00	0.00	0.00	3.69
552	2414	1.651987	AGAACGGTGGTGATTATGCG	58.348	50.000	0.00	0.00	0.00	4.73
577	2439	2.163412	TGCTACGGGTTAACGTCGTATT	59.837	45.455	23.41	8.95	45.08	1.89
660	2523	2.067932	TTTCCTCCTGTGTGGGCTGG	62.068	60.000	0.00	0.00	36.20	4.85
817	2689	3.535561	TGCTAGCAGGAAACTTATCAGC	58.464	45.455	14.93	0.00	40.21	4.26
1009	2897	3.691342	CACGCTCCCGACCTCCAA	61.691	66.667	0.00	0.00	38.29	3.53
1848	3766	1.079197	CTGGCGGTAGTGCATGACA	60.079	57.895	0.00	0.00	36.28	3.58
2031	3952	4.923871	GTGTTCTCTCTACAAGCGAAATCA	59.076	41.667	0.00	0.00	30.77	2.57
2086	4007	3.323979	ACAGGACAGTAACACTACAAGGG	59.676	47.826	0.00	0.00	0.00	3.95
2144	4069	2.029290	AGGACAGTAACAGCCGTAACAG	60.029	50.000	0.00	0.00	0.00	3.16
2146	4071	2.738013	AGGACAGTAACAGCCGTAAC	57.262	50.000	0.00	0.00	0.00	2.50
2147	4072	4.018490	TCATAGGACAGTAACAGCCGTAA	58.982	43.478	0.00	0.00	0.00	3.18
2148	4073	3.623703	TCATAGGACAGTAACAGCCGTA	58.376	45.455	0.00	0.00	0.00	4.02
2149	4074	2.453521	TCATAGGACAGTAACAGCCGT	58.546	47.619	0.00	0.00	0.00	5.68
2150	4075	3.520290	TTCATAGGACAGTAACAGCCG	57.480	47.619	0.00	0.00	0.00	5.52
2151	4076	5.525378	CAGAATTCATAGGACAGTAACAGCC	59.475	44.000	8.44	0.00	0.00	4.85
2152	4077	5.007136	GCAGAATTCATAGGACAGTAACAGC	59.993	44.000	8.44	0.00	0.00	4.40
2221	4147	5.221322	CGATGGAATGTTCACAGAGGAGATA	60.221	44.000	0.00	0.00	0.00	1.98
2245	4171	5.982516	TGTAATGGAATGTTTTTGTGTCTGC	59.017	36.000	0.00	0.00	0.00	4.26
2334	4260	1.344087	ACATTATGGGACCGAGGGAGT	60.344	52.381	0.00	0.00	0.00	3.85
2342	4268	3.869246	CACACGTCTTACATTATGGGACC	59.131	47.826	0.00	0.00	0.00	4.46
2364	4290	4.750098	CCGTCCCATAATGTAAGACATGTC	59.250	45.833	18.47	18.47	37.97	3.06
2366	4292	4.956085	TCCGTCCCATAATGTAAGACATG	58.044	43.478	0.00	0.00	37.97	3.21
2368	4294	3.386726	CCTCCGTCCCATAATGTAAGACA	59.613	47.826	0.00	0.00	0.00	3.41
2373	4302	2.090943	ACTCCCTCCGTCCCATAATGTA	60.091	50.000	0.00	0.00	0.00	2.29
2379	4308	1.233369	CCTACTCCCTCCGTCCCAT	59.767	63.158	0.00	0.00	0.00	4.00
2567	4566	4.065088	GACCACATCAAGAAGCTTGTACA	58.935	43.478	2.10	0.00	0.00	2.90
2645	4644	2.093288	GTCATTCTGCTGGTCCAGATGA	60.093	50.000	23.77	18.17	41.18	2.92
2738	4755	8.970859	TTCCTACTACTGTTACATACTCCTAC	57.029	38.462	0.00	0.00	0.00	3.18
2739	4756	8.776119	ACTTCCTACTACTGTTACATACTCCTA	58.224	37.037	0.00	0.00	0.00	2.94
2740	4757	7.641249	ACTTCCTACTACTGTTACATACTCCT	58.359	38.462	0.00	0.00	0.00	3.69
2741	4758	7.878547	ACTTCCTACTACTGTTACATACTCC	57.121	40.000	0.00	0.00	0.00	3.85
2743	4760	9.571816	GGATACTTCCTACTACTGTTACATACT	57.428	37.037	0.00	0.00	39.14	2.12
2751	4768	7.005296	CCATACTGGATACTTCCTACTACTGT	58.995	42.308	0.00	0.00	40.96	3.55
2781	4800	1.693606	TCTGCATTGGTCTGTCTGTGA	59.306	47.619	0.00	0.00	0.00	3.58
2832	4851	6.320418	TCTTGGACTAGTACGATAATGCTTGA	59.680	38.462	0.00	0.00	0.00	3.02
2879	4899	5.045213	TGCCCAGTAGTTTCCATTCTTGATA	60.045	40.000	0.00	0.00	0.00	2.15
2896	4916	4.335647	CGCCCTGTCTTGCCCAGT	62.336	66.667	0.00	0.00	0.00	4.00
2938	4963	7.044510	CGTATACAATTGCAAGCAGATGAAAAG	60.045	37.037	4.94	1.53	0.00	2.27
2942	4967	4.875536	ACGTATACAATTGCAAGCAGATGA	59.124	37.500	4.94	0.00	0.00	2.92
2966	4991	8.705594	GGGTGCAGGATACATTGTATATATAGT	58.294	37.037	9.27	0.00	41.41	2.12
2967	4992	8.704668	TGGGTGCAGGATACATTGTATATATAG	58.295	37.037	9.27	0.85	41.41	1.31
2969	4994	7.509236	TGGGTGCAGGATACATTGTATATAT	57.491	36.000	9.27	0.00	41.41	0.86
3058	5086	6.017400	AGTTGCAGAAATAGGTCAACAATG	57.983	37.500	0.00	0.00	39.39	2.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.