AutoCloner

Multiple sequence alignment - TraesCS3A01G269900

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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	TraesCS3A01G269900	chr3A	100.000	4117	0	0	1	4117	496701429	496705545	0.000000e+00	7603.0
1	TraesCS3A01G269900	chr3A	98.148	54	1	0	3968	4021	496705343	496705396	1.220000e-15	95.3
2	TraesCS3A01G269900	chr3A	98.148	54	1	0	3915	3968	496705396	496705449	1.220000e-15	95.3
3	TraesCS3A01G269900	chr3B	94.159	4143	184	27	1	4117	487905065	487909175	0.000000e+00	6257.0
4	TraesCS3A01G269900	chr3B	96.296	54	2	0	3968	4021	487908974	487909027	5.670000e-14	89.8
5	TraesCS3A01G269900	chr3B	96.296	54	1	1	3915	3968	487909027	487909079	2.040000e-13	87.9
6	TraesCS3A01G269900	chr3D	95.351	3893	123	21	268	4117	374205234	374209111	0.000000e+00	6133.0
7	TraesCS3A01G269900	chr3D	96.241	266	8	2	1	266	374204226	374204489	6.320000e-118	435.0
8	TraesCS3A01G269900	chr3D	75.472	265	51	13	1947	2207	339253212	339252958	2.600000e-22	117.0
9	TraesCS3A01G269900	chr3D	96.296	54	2	0	3968	4021	374208910	374208963	5.670000e-14	89.8
10	TraesCS3A01G269900	chr4A	82.133	750	107	20	3150	3884	658261515	658262252	5.850000e-173	617.0
11	TraesCS3A01G269900	chr7B	82.013	745	105	16	3150	3877	164158543	164157811	1.270000e-169	606.0
12	TraesCS3A01G269900	chr2B	81.004	737	111	19	3150	3878	785240117	785240832	3.590000e-155	558.0
13	TraesCS3A01G269900	chr2B	79.892	741	119	20	3150	3878	793487407	793488129	2.190000e-142	516.0
14	TraesCS3A01G269900	chr6B	80.641	749	119	20	3150	3891	351224964	351224235	1.290000e-154	556.0
15	TraesCS3A01G269900	chr4B	80.707	736	117	18	3150	3877	16558151	16557433	2.160000e-152	549.0
16	TraesCS3A01G269900	chr2A	82.629	639	94	11	3150	3776	778620349	778619716	2.160000e-152	549.0

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	TraesCS3A01G269900	chr3A	496701429	496705545	4116	False	2597.866667	7603	98.765333	1	4117	3	chr3A.!!$F1	4116
1	TraesCS3A01G269900	chr3B	487905065	487909175	4110	False	2144.900000	6257	95.583667	1	4117	3	chr3B.!!$F1	4116
2	TraesCS3A01G269900	chr3D	374204226	374209111	4885	False	2219.266667	6133	95.962667	1	4117	3	chr3D.!!$F1	4116
3	TraesCS3A01G269900	chr4A	658261515	658262252	737	False	617.000000	617	82.133000	3150	3884	1	chr4A.!!$F1	734
4	TraesCS3A01G269900	chr7B	164157811	164158543	732	True	606.000000	606	82.013000	3150	3877	1	chr7B.!!$R1	727
5	TraesCS3A01G269900	chr2B	785240117	785240832	715	False	558.000000	558	81.004000	3150	3878	1	chr2B.!!$F1	728
6	TraesCS3A01G269900	chr2B	793487407	793488129	722	False	516.000000	516	79.892000	3150	3878	1	chr2B.!!$F2	728
7	TraesCS3A01G269900	chr6B	351224235	351224964	729	True	556.000000	556	80.641000	3150	3891	1	chr6B.!!$R1	741
8	TraesCS3A01G269900	chr4B	16557433	16558151	718	True	549.000000	549	80.707000	3150	3877	1	chr4B.!!$R1	727
9	TraesCS3A01G269900	chr2A	778619716	778620349	633	True	549.000000	549	82.629000	3150	3776	1	chr2A.!!$R1	626

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	Hairpin	End Stability	Orientation
388	1133	0.486879	AGAATTGGGTTGGGCTTGGA	59.513	50.0	0.00	3.53	F
1054	1801	0.106469	GCCATTCTTTCCTCCCTCCC	60.106	60.0	0.00	4.30	F
2081	2834	0.613853	CACCAGGAAGTACTCCCCGA	60.614	60.0	46.81	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2239	2992	0.108615	AGAAGAACTGTCGCCATCCG	60.109	55.000	0.00	38.61	4.18	R
2737	3499	0.028242	CGTCAAGATCCGTCTCCGAG	59.972	60.000	0.00	35.63	4.63	R
3264	4028	1.614903	CCTGAATGCAAGCTTTCCACA	59.385	47.619	15.34	31.57	4.17	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
173	174	8.410673	TTTCCCATCTATATCAGTAGACTCAC	57.589	38.462	0.00	0.00	33.78	3.51
235	236	4.558860	GTGCGAATTTCCATAAAGCACTTC	59.441	41.667	13.96	0.00	46.69	3.01
258	259	2.036958	TTGTGATGGTCATAAGCCGG	57.963	50.000	0.00	0.00	0.00	6.13
261	262	0.692756	TGATGGTCATAAGCCGGGGA	60.693	55.000	2.18	0.00	0.00	4.81
292	1036	1.369091	CGCTTGGGTGTAGGTGCATC	61.369	60.000	0.00	0.00	0.00	3.91
294	1038	1.742761	CTTGGGTGTAGGTGCATCTG	58.257	55.000	10.55	0.00	0.00	2.90
300	1044	1.734465	GTGTAGGTGCATCTGAACAGC	59.266	52.381	10.55	0.00	34.54	4.40
336	1081	0.692419	ATGAGGCAGTGACTAGGGGG	60.692	60.000	0.00	0.00	0.00	5.40
388	1133	0.486879	AGAATTGGGTTGGGCTTGGA	59.513	50.000	0.00	0.00	0.00	3.53
432	1177	5.049474	GCTTTACCTTTTTCAAATTGGCTGG	60.049	40.000	0.00	0.00	0.00	4.85
578	1323	2.566913	TCCGCTTTTTGCTGAACTACA	58.433	42.857	0.00	0.00	40.11	2.74
645	1390	8.787852	CCTATATTTTTAGAGTTTGCTCATCCC	58.212	37.037	0.00	0.00	44.00	3.85
655	1400	5.583932	AGTTTGCTCATCCCTATCCTTTTT	58.416	37.500	0.00	0.00	0.00	1.94
679	1424	5.824624	TCTTTTGAAGAACACTTGCTCATCT	59.175	36.000	0.00	0.00	33.83	2.90
682	1427	4.965814	TGAAGAACACTTGCTCATCTCTT	58.034	39.130	0.00	0.00	0.00	2.85
683	1428	4.993584	TGAAGAACACTTGCTCATCTCTTC	59.006	41.667	0.00	0.00	38.40	2.87
690	1435	7.750229	ACACTTGCTCATCTCTTCAATTTTA	57.250	32.000	0.00	0.00	0.00	1.52
782	1529	0.744771	GGATCGTTTGACTGGGCCTC	60.745	60.000	4.53	0.00	0.00	4.70
957	1704	1.298413	CGTACGTCTGGATGCCGAG	60.298	63.158	7.22	0.00	0.00	4.63
959	1706	2.782222	TACGTCTGGATGCCGAGGC	61.782	63.158	7.26	7.26	42.35	4.70
1048	1795	0.625849	TCCCCAGCCATTCTTTCCTC	59.374	55.000	0.00	0.00	0.00	3.71
1053	1800	0.922626	AGCCATTCTTTCCTCCCTCC	59.077	55.000	0.00	0.00	0.00	4.30
1054	1801	0.106469	GCCATTCTTTCCTCCCTCCC	60.106	60.000	0.00	0.00	0.00	4.30
1055	1802	1.601248	CCATTCTTTCCTCCCTCCCT	58.399	55.000	0.00	0.00	0.00	4.20
1059	1806	2.743131	TCTTTCCTCCCTCCCTTCTT	57.257	50.000	0.00	0.00	0.00	2.52
1316	2063	2.229302	GAGAGCTGGTACTTCTTCACGT	59.771	50.000	0.00	0.00	0.00	4.49
1318	2065	1.272769	AGCTGGTACTTCTTCACGTCC	59.727	52.381	0.00	0.00	0.00	4.79
2029	2782	2.030412	TGCCAGTTCACGCACGAT	59.970	55.556	0.00	0.00	0.00	3.73
2031	2784	2.317609	GCCAGTTCACGCACGATGT	61.318	57.895	0.00	0.00	0.00	3.06
2053	2806	4.814294	GTCTACACCGCCAGCCCG	62.814	72.222	0.00	0.00	0.00	6.13
2081	2834	0.613853	CACCAGGAAGTACTCCCCGA	60.614	60.000	0.00	0.00	46.81	5.14
2350	3103	2.426522	CTCGACCATGGCAAAGAAGAA	58.573	47.619	13.04	0.00	0.00	2.52
2465	3218	1.448013	GGCGACAACTACTCTGGCC	60.448	63.158	0.00	0.00	0.00	5.36
2528	3281	4.564116	ATTCTACGGCGGCGTCGG	62.564	66.667	40.80	30.93	33.75	4.79
2576	3329	1.768684	GACCCACAGCAGGAACTCCA	61.769	60.000	0.00	0.00	34.60	3.86
2591	3344	2.997315	CCAGTCCCGTGCTGAGGA	60.997	66.667	0.00	0.00	36.12	3.71
2641	3394	3.712881	GTGACGTCTGGGCGCAAC	61.713	66.667	17.92	1.07	34.88	4.17
2659	3412	2.665185	AAGAACACCAGCGCGGAC	60.665	61.111	22.10	11.36	38.63	4.79
2767	3529	0.611062	ATCTTGACGAGGACGACCCA	60.611	55.000	0.00	0.00	42.66	4.51
2822	3584	2.777832	AGCAGGTGAATCTTCAGGAC	57.222	50.000	0.00	0.00	37.98	3.85
3029	3793	7.888546	GGATTAGGTACATATAGGCATTTTGGT	59.111	37.037	0.00	0.00	0.00	3.67
3059	3823	6.205853	TCAAATTGTTGTACTTCTTGGCGTAT	59.794	34.615	0.00	0.00	36.07	3.06
3086	3850	4.675190	AATCGTTCAGCAACTTGATCAG	57.325	40.909	0.00	0.00	0.00	2.90
3126	3890	9.260002	AGTTTTCTCAATCGCAAATAAATTGTT	57.740	25.926	0.00	0.00	41.32	2.83
3293	4061	3.731716	TGCATTCAGGAAGTGCAGT	57.268	47.368	12.09	0.00	43.30	4.40
3309	4077	2.038952	TGCAGTGCTTCCTCACATAAGT	59.961	45.455	17.60	0.00	39.35	2.24
3329	4097	3.058501	AGTTTCCAAGTGAAAATACGGCG	60.059	43.478	4.80	4.80	44.30	6.46
3349	4119	2.223021	CGACCACAATTGCAATACCTCG	60.223	50.000	13.39	10.73	0.00	4.63
3355	4125	3.684788	ACAATTGCAATACCTCGACAGAC	59.315	43.478	13.39	0.00	0.00	3.51
3375	4145	5.003804	AGACCACATTACAGACATTTGACC	58.996	41.667	0.00	0.00	0.00	4.02
3427	4197	7.182060	ACACTAACATTTGGGATATTTGAGGT	58.818	34.615	0.00	0.00	0.00	3.85
3428	4198	8.333235	ACACTAACATTTGGGATATTTGAGGTA	58.667	33.333	0.00	0.00	0.00	3.08
3429	4199	8.621286	CACTAACATTTGGGATATTTGAGGTAC	58.379	37.037	0.00	0.00	0.00	3.34
3497	4270	4.435651	GCTCGGTTCATTTTCTTTACTCCG	60.436	45.833	0.00	0.00	37.29	4.63
3591	4364	7.386059	TCTCAGTTCAGAGCATGTTTGTAATA	58.614	34.615	0.00	0.00	35.59	0.98
3707	4498	9.574516	ACATTATAAGTTGAAGTTTCAGGTTCT	57.425	29.630	0.00	0.00	38.61	3.01
3824	4629	3.254657	TGCATACAAGTGTTTTACCAGCC	59.745	43.478	0.00	0.00	0.00	4.85
3833	4638	8.466798	ACAAGTGTTTTACCAGCCATAATATTC	58.533	33.333	0.00	0.00	0.00	1.75
3975	4780	8.466798	GTTCCATATGGTAAAAACTATGCAACT	58.533	33.333	21.28	0.00	36.34	3.16
3982	4787	6.099341	GGTAAAAACTATGCAACTCAATGGG	58.901	40.000	0.00	0.00	0.00	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	7.519008	GCATTAATCAAGGAAGGATCAGTTACG	60.519	40.741	0.00	0.00	0.00	3.18
209	210	4.089923	GTGCTTTATGGAAATTCGCACAAC	59.910	41.667	13.71	0.00	40.93	3.32
222	223	5.375417	TCACAATGTGAAGTGCTTTATGG	57.625	39.130	14.37	0.00	39.78	2.74
235	236	3.242837	CGGCTTATGACCATCACAATGTG	60.243	47.826	7.12	7.12	34.45	3.21
258	259	3.555168	CCCAAGCGACTAGTGATATTCCC	60.555	52.174	0.00	0.00	0.00	3.97
261	262	3.451178	ACACCCAAGCGACTAGTGATATT	59.549	43.478	0.00	0.00	32.76	1.28
300	1044	0.531532	CATTAGGTCCTGAGCTGCCG	60.532	60.000	9.03	0.00	39.78	5.69
336	1081	0.455005	CCTAACCTCTCGGTCGTTCC	59.545	60.000	0.00	0.00	44.73	3.62
388	1133	3.722101	AGCCCATATACCTTTAGCTTGGT	59.278	43.478	10.00	10.00	40.12	3.67
578	1323	4.184629	GAGCACGATGTGGAATTTACTCT	58.815	43.478	0.00	0.00	33.64	3.24
634	1379	5.831103	AGAAAAAGGATAGGGATGAGCAAA	58.169	37.500	0.00	0.00	0.00	3.68
655	1400	5.824624	AGATGAGCAAGTGTTCTTCAAAAGA	59.175	36.000	11.72	0.00	33.81	2.52
713	1458	0.523966	CGGATAGAGGGATGAGCGTC	59.476	60.000	0.00	0.00	0.00	5.19
782	1529	1.674221	GCTGGGCCTAGCAATATCTCG	60.674	57.143	34.00	0.00	43.17	4.04
810	1557	0.669625	CGGAGTCGGTTTCCTTCACC	60.670	60.000	0.00	0.00	32.34	4.02
945	1692	3.074369	TTCGCCTCGGCATCCAGA	61.074	61.111	8.87	0.00	42.06	3.86
957	1704	0.030908	CCTGATAGTCCGAGTTCGCC	59.969	60.000	0.00	0.00	38.18	5.54
959	1706	1.025812	AGCCTGATAGTCCGAGTTCG	58.974	55.000	0.00	0.00	39.44	3.95
971	1718	0.249398	AGGACGCGTTTAAGCCTGAT	59.751	50.000	15.53	0.00	0.00	2.90
1048	1795	5.133491	AGAATTATGAAGGAAGAAGGGAGGG	59.867	44.000	0.00	0.00	0.00	4.30
1053	1800	4.513318	GGCGAGAATTATGAAGGAAGAAGG	59.487	45.833	0.00	0.00	0.00	3.46
1054	1801	4.513318	GGGCGAGAATTATGAAGGAAGAAG	59.487	45.833	0.00	0.00	0.00	2.85
1055	1802	4.451900	GGGCGAGAATTATGAAGGAAGAA	58.548	43.478	0.00	0.00	0.00	2.52
1059	1806	1.070134	CGGGGCGAGAATTATGAAGGA	59.930	52.381	0.00	0.00	0.00	3.36
1135	1882	1.889530	CGAGGTCAGAAGGGTGGGAC	61.890	65.000	0.00	0.00	0.00	4.46
1874	2627	3.322318	GAGCAGCTCGAAGGGCCTT	62.322	63.158	21.09	21.09	0.00	4.35
2029	2782	2.557805	GCGGTGTAGACGTCGACA	59.442	61.111	24.99	24.99	0.00	4.35
2031	2784	2.669229	TGGCGGTGTAGACGTCGA	60.669	61.111	10.46	0.94	39.10	4.20
2239	2992	0.108615	AGAAGAACTGTCGCCATCCG	60.109	55.000	0.00	0.00	38.61	4.18
2498	3251	1.095807	GTAGAATTCCTGGCACCGGC	61.096	60.000	0.00	0.00	40.13	6.13
2641	3394	2.664851	TCCGCGCTGGTGTTCTTG	60.665	61.111	16.00	0.00	39.52	3.02
2737	3499	0.028242	CGTCAAGATCCGTCTCCGAG	59.972	60.000	0.00	0.00	35.63	4.63
2785	3547	1.756408	CTTTGTGGCAATGGGGTGCA	61.756	55.000	0.00	0.00	46.81	4.57
2822	3584	2.879462	GTAGAACGGTCTGGCGCG	60.879	66.667	14.77	0.00	35.12	6.86
3029	3793	7.064016	GCCAAGAAGTACAACAATTTGACAAAA	59.936	33.333	4.41	0.00	36.48	2.44
3059	3823	6.612247	TCAAGTTGCTGAACGATTTCTTTA	57.388	33.333	0.00	0.00	37.15	1.85
3086	3850	9.495754	GATTGAGAAAACTGCTAATGTACAATC	57.504	33.333	0.00	0.00	34.48	2.67
3126	3890	5.525745	TCGAAGAAAACTGCTACATTGTTGA	59.474	36.000	2.29	0.00	0.00	3.18
3264	4028	1.614903	CCTGAATGCAAGCTTTCCACA	59.385	47.619	15.34	0.00	31.57	4.17
3293	4061	4.365514	TGGAAACTTATGTGAGGAAGCA	57.634	40.909	0.00	0.00	0.00	3.91
3309	4077	3.058777	GTCGCCGTATTTTCACTTGGAAA	60.059	43.478	0.00	0.00	43.59	3.13
3329	4097	3.006940	TCGAGGTATTGCAATTGTGGTC	58.993	45.455	18.75	7.01	0.00	4.02
3349	4119	5.700832	TCAAATGTCTGTAATGTGGTCTGTC	59.299	40.000	0.00	0.00	0.00	3.51
3355	4125	4.078537	TGGGTCAAATGTCTGTAATGTGG	58.921	43.478	0.00	0.00	0.00	4.17
3375	4145	2.800544	CACGTGTTTCTTAGACCTGTGG	59.199	50.000	7.58	0.00	0.00	4.17
3497	4270	7.362142	GGTCAGAACAAATAAGATTGACCTTCC	60.362	40.741	12.22	0.00	45.93	3.46
3634	4423	7.387948	ACACAGACTGTTGAACATTTATACCTC	59.612	37.037	5.04	0.00	0.00	3.85
3707	4498	5.629133	GCTGACAGAAACCTGGGATATGTTA	60.629	44.000	6.65	0.00	36.01	2.41
3884	4689	6.620877	ATTTCCACTAGTGTCAATCCTGTA	57.379	37.500	21.18	0.00	0.00	2.74
3975	4780	6.723298	ACTTGTATTTGTGTTTCCCATTGA	57.277	33.333	0.00	0.00	0.00	2.57
3982	4787	7.699566	TGGAACAGTACTTGTATTTGTGTTTC	58.300	34.615	0.00	0.00	39.73	2.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.