AutoCloner

Multiple sequence alignment - TraesCS5A01G507500

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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	TraesCS5A01G507500	chr5A	100.000	3924	0	0	1	3924	671915646	671911723	0.000000e+00	7247
1	TraesCS5A01G507500	chr6B	95.567	3181	127	8	747	3924	706187956	706184787	0.000000e+00	5081
2	TraesCS5A01G507500	chr6B	93.125	160	11	0	855	1014	706188115	706187956	6.560000e-58	235
3	TraesCS5A01G507500	chr4A	94.520	2938	152	8	1	2934	28974511	28971579	0.000000e+00	4525
4	TraesCS5A01G507500	chr4A	94.000	1650	86	7	1	1645	374434028	374435669	0.000000e+00	2486
5	TraesCS5A01G507500	chr4A	94.260	993	57	0	2932	3924	28971548	28970556	0.000000e+00	1519
6	TraesCS5A01G507500	chr3B	89.467	2962	258	25	1	2934	648187227	648184292	0.000000e+00	3692
7	TraesCS5A01G507500	chr3B	89.870	997	93	6	2932	3924	648184261	648183269	0.000000e+00	1275
8	TraesCS5A01G507500	chr1A	91.113	2183	171	12	8	2170	13270012	13267833	0.000000e+00	2935
9	TraesCS5A01G507500	chr1A	82.510	263	42	4	1004	1264	250648792	250648532	1.100000e-55	228
10	TraesCS5A01G507500	chr7B	93.580	1729	100	9	2	1724	304994146	304992423	0.000000e+00	2567
11	TraesCS5A01G507500	chr1D	92.254	1730	121	6	335	2052	20334354	20332626	0.000000e+00	2440
12	TraesCS5A01G507500	chr1B	93.202	559	34	3	2	557	566990944	566991501	0.000000e+00	819
13	TraesCS5A01G507500	chr1B	93.737	463	27	2	553	1014	566993531	566993992	0.000000e+00	693
14	TraesCS5A01G507500	chr2A	84.686	542	60	14	508	1045	767551360	767551882	1.620000e-143	520
15	TraesCS5A01G507500	chr2A	83.463	387	58	5	1	384	767528164	767528547	4.820000e-94	355
16	TraesCS5A01G507500	chr7A	76.566	798	185	2	997	1793	102055281	102056077	1.670000e-118	436
17	TraesCS5A01G507500	chr7A	76.617	804	176	9	996	1793	675494267	675495064	2.170000e-117	433
18	TraesCS5A01G507500	chr2D	76.485	791	178	8	1007	1793	431392367	431391581	1.300000e-114	424

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	TraesCS5A01G507500	chr5A	671911723	671915646	3923	True	7247.0	7247	100.0000	1	3924	1	chr5A.!!$R1	3923
1	TraesCS5A01G507500	chr6B	706184787	706188115	3328	True	2658.0	5081	94.3460	747	3924	2	chr6B.!!$R1	3177
2	TraesCS5A01G507500	chr4A	28970556	28974511	3955	True	3022.0	4525	94.3900	1	3924	2	chr4A.!!$R1	3923
3	TraesCS5A01G507500	chr4A	374434028	374435669	1641	False	2486.0	2486	94.0000	1	1645	1	chr4A.!!$F1	1644
4	TraesCS5A01G507500	chr3B	648183269	648187227	3958	True	2483.5	3692	89.6685	1	3924	2	chr3B.!!$R1	3923
5	TraesCS5A01G507500	chr1A	13267833	13270012	2179	True	2935.0	2935	91.1130	8	2170	1	chr1A.!!$R1	2162
6	TraesCS5A01G507500	chr7B	304992423	304994146	1723	True	2567.0	2567	93.5800	2	1724	1	chr7B.!!$R1	1722
7	TraesCS5A01G507500	chr1D	20332626	20334354	1728	True	2440.0	2440	92.2540	335	2052	1	chr1D.!!$R1	1717
8	TraesCS5A01G507500	chr1B	566990944	566993992	3048	False	756.0	819	93.4695	2	1014	2	chr1B.!!$F1	1012
9	TraesCS5A01G507500	chr2A	767551360	767551882	522	False	520.0	520	84.6860	508	1045	1	chr2A.!!$F2	537
10	TraesCS5A01G507500	chr7A	102055281	102056077	796	False	436.0	436	76.5660	997	1793	1	chr7A.!!$F1	796
11	TraesCS5A01G507500	chr7A	675494267	675495064	797	False	433.0	433	76.6170	996	1793	1	chr7A.!!$F2	797
12	TraesCS5A01G507500	chr2D	431391581	431392367	786	True	424.0	424	76.4850	1007	1793	1	chr2D.!!$R1	786

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
418	425	0.034574	TAAGATGTGCCCCATGCGTT	60.035	50.000	45.60	4.84	F
700	2749	0.178891	TCTCCATCTATCCCTGCCCC	60.179	60.000	0.00	5.80	F
1866	3924	1.133976	GTGCCAATCTAGAGCCCATGT	60.134	52.381	0.00	3.21	F
2404	4478	0.877071	CTGTTGCCCTGTGATGACAC	59.123	55.000	46.09	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2039	4099	0.252789	TCCCCCGTGGTAGGAAATCA	60.253	55.000	0.00	34.77	2.57	R
2206	4268	1.202698	AGGGAGCATGTATCTTTCGCC	60.203	52.381	0.00	0.00	5.54	R
2893	4967	0.602638	TTGCTAACCCAGAGTGCACG	60.603	55.000	12.01	33.13	5.34	R
3891	6002	0.677288	TACTGTATCCGAATGGGCCG	59.323	55.000	0.00	35.24	6.13	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
147	150	1.746727	CTCGCAGCTGACATGTACGC	61.747	60.000	20.43	4.34	0.00	4.42
148	151	2.697425	GCAGCTGACATGTACGCG	59.303	61.111	20.43	3.53	0.00	6.01
149	152	2.802667	GCAGCTGACATGTACGCGG	61.803	63.158	20.43	6.48	0.00	6.46
150	153	2.509336	AGCTGACATGTACGCGGC	60.509	61.111	12.47	3.20	0.00	6.53
151	154	3.564027	GCTGACATGTACGCGGCC	61.564	66.667	12.47	0.00	0.00	6.13
152	155	3.254654	CTGACATGTACGCGGCCG	61.255	66.667	24.05	24.05	41.14	6.13
230	235	2.260869	CCCTGTGGAGCAACGTTGG	61.261	63.158	28.33	10.04	0.00	3.77
312	317	3.982576	CGCAAGTTGGTTTCCTTTAGT	57.017	42.857	4.75	0.00	0.00	2.24
321	326	7.114095	AGTTGGTTTCCTTTAGTTACAGTTCA	58.886	34.615	0.00	0.00	0.00	3.18
387	394	4.037208	GTCTTGCCCATGATATTGACAAGG	59.963	45.833	0.00	0.00	34.26	3.61
388	395	3.668141	TGCCCATGATATTGACAAGGT	57.332	42.857	0.00	0.00	0.00	3.50
412	419	1.562475	GGGTTAGTAAGATGTGCCCCA	59.438	52.381	0.00	0.00	0.00	4.96
418	425	0.034574	TAAGATGTGCCCCATGCGTT	60.035	50.000	0.00	0.00	45.60	4.84
429	436	2.491693	CCCCATGCGTTCAGTACATTTT	59.508	45.455	0.00	0.00	0.00	1.82
433	440	3.889196	TGCGTTCAGTACATTTTCCAC	57.111	42.857	0.00	0.00	0.00	4.02
501	516	3.563808	TGGTTGGAACATTTCAAGTCGAG	59.436	43.478	0.00	0.00	39.30	4.04
504	519	3.664107	TGGAACATTTCAAGTCGAGGAG	58.336	45.455	0.00	0.00	0.00	3.69
514	529	2.035155	TCGAGGAGGCGTTCAGGA	59.965	61.111	0.00	0.00	0.00	3.86
691	2740	3.198635	CACCCACAGTTGTCTCCATCTAT	59.801	47.826	0.00	0.00	0.00	1.98
700	2749	0.178891	TCTCCATCTATCCCTGCCCC	60.179	60.000	0.00	0.00	0.00	5.80
701	2750	1.536418	TCCATCTATCCCTGCCCCG	60.536	63.158	0.00	0.00	0.00	5.73
703	2752	1.536418	CATCTATCCCTGCCCCGGA	60.536	63.158	0.73	0.00	0.00	5.14
745	2794	1.615392	CTGTTCTTCCCCTGCTTTTGG	59.385	52.381	0.00	0.00	0.00	3.28
1192	3246	3.316308	AGTTGTTGCCAAGTTCAGTGATC	59.684	43.478	0.00	0.00	29.76	2.92
1379	3433	9.423061	ACAGAATCTTAATTATGTTTTTGGCAC	57.577	29.630	13.02	0.00	43.06	5.01
1433	3487	1.908619	TGTCAAGCCATCAGAAGCCTA	59.091	47.619	0.00	0.00	0.00	3.93
1519	3573	4.768583	TGAAAATGTTTTGCTTGGAGCTT	58.231	34.783	1.29	0.00	42.97	3.74
1528	3582	6.183360	TGTTTTGCTTGGAGCTTTATCAGAAA	60.183	34.615	1.29	0.00	42.97	2.52
1797	3851	3.181445	ACTTGTTTCTGCAGGTATGTGGA	60.181	43.478	15.13	0.00	0.00	4.02
1866	3924	1.133976	GTGCCAATCTAGAGCCCATGT	60.134	52.381	0.00	0.00	0.00	3.21
2018	4078	5.249163	TGAGGAAGATGGTTGAGAAGATTGA	59.751	40.000	0.00	0.00	0.00	2.57
2039	4099	3.136641	AGTGAACATATCTCCTGGGGT	57.863	47.619	0.00	0.00	0.00	4.95
2067	4127	2.108362	CACGGGGGAGCGGTAATC	59.892	66.667	0.00	0.00	0.00	1.75
2082	4142	6.978338	AGCGGTAATCATCGTCTTCTTAATA	58.022	36.000	0.00	0.00	0.00	0.98
2103	4164	1.634702	TTGAAGTTTGCGGTTTGTGC	58.365	45.000	0.00	0.00	0.00	4.57
2172	4234	1.880027	CTGTTTGCTTTAGGTTCGGCT	59.120	47.619	0.00	0.00	0.00	5.52
2206	4268	1.093159	GCCAGCTGATTGAACTCCAG	58.907	55.000	17.39	0.00	0.00	3.86
2285	4348	1.965935	CATACCATCCACGCCAATGA	58.034	50.000	0.00	0.00	0.00	2.57
2404	4478	0.877071	CTGTTGCCCTGTGATGACAC	59.123	55.000	0.00	0.00	46.09	3.67
2643	4717	3.008157	TGCATTTTGAATGGTGAAGGCAT	59.992	39.130	3.16	0.00	34.40	4.40
2679	4753	4.202461	ACCACATCCTACAACATCAACAGT	60.202	41.667	0.00	0.00	0.00	3.55
2694	4768	4.531854	TCAACAGTCCAGAACCAATTCAA	58.468	39.130	0.00	0.00	37.29	2.69
2786	4860	4.918810	TGAAGCTTTTCCAAGAACTTCC	57.081	40.909	0.00	0.00	32.28	3.46
2893	4967	7.489239	AAGGGAAGGAAGTATATCATCTAGC	57.511	40.000	0.00	0.00	0.00	3.42
2923	4997	3.495331	TGGGTTAGCAAAGAAGCAATGA	58.505	40.909	0.00	0.00	36.85	2.57
2957	5064	1.985473	TGACAAGCAAAGCCAGATGT	58.015	45.000	0.00	0.00	0.00	3.06
2974	5081	3.713248	AGATGTCCATAGCACAGGATTCA	59.287	43.478	0.00	0.00	36.11	2.57
2997	5104	3.324846	TCGGTTATGGAGATTGCTAGCAT	59.675	43.478	20.13	8.84	0.00	3.79
3074	5181	2.202987	GGCCATCTCCTGAGTGCG	60.203	66.667	0.00	0.00	0.00	5.34
3094	5201	3.746492	GCGTCTTGTTTGGATCAACTACT	59.254	43.478	0.00	0.00	0.00	2.57
3287	5394	6.814954	AACATACACTGATGGGTCTCTAAT	57.185	37.500	0.00	0.00	0.00	1.73
3474	5581	2.158623	AGACTTGCCCAACTTGACATGA	60.159	45.455	0.00	0.00	0.00	3.07
3491	5598	3.817647	ACATGAGCTTCTCAAAAGACACC	59.182	43.478	0.00	0.00	44.04	4.16
3503	5610	3.652057	AAAGACACCCCTGGTATGATG	57.348	47.619	1.76	0.00	32.11	3.07
3555	5662	1.762370	TGAGCGACACCATCATACCAT	59.238	47.619	0.00	0.00	0.00	3.55
3569	5676	4.296912	TCATACCATGCCCCAATTTGAAT	58.703	39.130	0.00	0.00	0.00	2.57
3596	5703	1.328374	ACACGTTTTTACTGACCGCAC	59.672	47.619	0.00	0.00	0.00	5.34
3597	5704	0.939419	ACGTTTTTACTGACCGCACC	59.061	50.000	0.00	0.00	0.00	5.01
3647	5754	1.077501	CCAATGCCGACCCACTGAT	60.078	57.895	0.00	0.00	0.00	2.90
3672	5779	2.843701	CACTCCATTAGGGCTAGCTTG	58.156	52.381	15.72	5.10	36.21	4.01
3674	5781	0.106708	TCCATTAGGGCTAGCTTGCG	59.893	55.000	15.72	0.00	36.21	4.85
3856	5967	4.322650	GGGTGGTTTATGCATTTGACATGT	60.323	41.667	3.54	0.00	0.00	3.21
3891	6002	2.000447	GTCGTTTATGACCCTGCTGTC	59.000	52.381	0.00	0.00	35.77	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
152	155	0.097674	CATGTACAGCTCGCCAAAGC	59.902	55.000	0.33	0.00	42.82	3.51
230	235	4.874970	AGAAAATTGTGGCTGTGAATCAC	58.125	39.130	6.41	6.41	34.56	3.06
321	326	5.370679	ACAACTTATTTGGTTCAGTACGGT	58.629	37.500	0.00	0.00	39.84	4.83
362	367	4.795469	TGTCAATATCATGGGCAAGACAT	58.205	39.130	0.00	0.00	30.64	3.06
363	368	4.233632	TGTCAATATCATGGGCAAGACA	57.766	40.909	0.00	0.02	32.91	3.41
387	394	3.939592	GGCACATCTTACTAACCCAGAAC	59.060	47.826	0.00	0.00	0.00	3.01
388	395	3.054655	GGGCACATCTTACTAACCCAGAA	60.055	47.826	0.00	0.00	35.84	3.02
412	419	3.120338	CGTGGAAAATGTACTGAACGCAT	60.120	43.478	0.00	0.00	0.00	4.73
418	425	3.669536	TGCATCGTGGAAAATGTACTGA	58.330	40.909	0.00	0.00	0.00	3.41
429	436	1.066286	TCACATGACATGCATCGTGGA	60.066	47.619	15.49	5.81	39.52	4.02
433	440	3.364964	CCATCATCACATGACATGCATCG	60.365	47.826	15.49	2.58	43.01	3.84
501	516	1.209747	ACCTAAATCCTGAACGCCTCC	59.790	52.381	0.00	0.00	0.00	4.30
504	519	1.737793	CACACCTAAATCCTGAACGCC	59.262	52.381	0.00	0.00	0.00	5.68
514	529	1.743995	GCGGCCGTCACACCTAAAT	60.744	57.895	28.70	0.00	0.00	1.40
559	2608	3.792401	CCTCACGCATAATACCTGAACA	58.208	45.455	0.00	0.00	0.00	3.18
691	2740	3.407967	GAATGTCCGGGGCAGGGA	61.408	66.667	7.67	0.00	0.00	4.20
700	2749	2.555199	GGTTGGAGAGATGAATGTCCG	58.445	52.381	0.00	0.00	31.05	4.79
701	2750	2.422093	GGGGTTGGAGAGATGAATGTCC	60.422	54.545	0.00	0.00	0.00	4.02
703	2752	1.566231	GGGGGTTGGAGAGATGAATGT	59.434	52.381	0.00	0.00	0.00	2.71
745	2794	2.125350	CGGCTGGCTCCTTCAGAC	60.125	66.667	0.00	0.00	36.93	3.51
833	2884	0.100861	GGAGAACTCTTCCGCCGTAG	59.899	60.000	1.86	0.00	0.00	3.51
1192	3246	1.863454	CATAACTAGCTGCCGCTTGAG	59.137	52.381	17.44	8.32	46.47	3.02
1359	3413	5.046231	GGGGGTGCCAAAAACATAATTAAGA	60.046	40.000	0.00	0.00	0.00	2.10
1433	3487	1.136305	CCATTCGGGTGTACTCGATGT	59.864	52.381	7.92	0.00	35.25	3.06
1519	3573	4.627284	TTTGGGAGGACGTTTCTGATAA	57.373	40.909	0.00	0.00	0.00	1.75
1528	3582	0.981183	TGCTGTATTTGGGAGGACGT	59.019	50.000	0.00	0.00	0.00	4.34
1797	3851	3.616219	TCACTAGTTTGTGCAAAGTGGT	58.384	40.909	13.36	13.36	43.30	4.16
1866	3924	7.589395	ACGACAACATAGAACAAATGCATTAA	58.411	30.769	13.39	0.00	0.00	1.40
2018	4078	3.200825	CACCCCAGGAGATATGTTCACTT	59.799	47.826	0.00	0.00	0.00	3.16
2039	4099	0.252789	TCCCCCGTGGTAGGAAATCA	60.253	55.000	0.00	0.00	34.77	2.57
2082	4142	2.607180	GCACAAACCGCAAACTTCAATT	59.393	40.909	0.00	0.00	0.00	2.32
2138	4200	5.757850	AGCAAACAGTGAGAGTTTTTAGG	57.242	39.130	0.00	0.00	37.10	2.69
2172	4234	3.266240	TGGCTAACAGAGAGCTCGA	57.734	52.632	8.37	0.00	39.98	4.04
2206	4268	1.202698	AGGGAGCATGTATCTTTCGCC	60.203	52.381	0.00	0.00	0.00	5.54
2404	4478	5.589855	TGGTTAGTCACAAGGCATGAATATG	59.410	40.000	0.00	0.00	37.36	1.78
2643	4717	3.137544	AGGATGTGGTTGACAGTTGGTTA	59.862	43.478	0.00	0.00	38.23	2.85
2679	4753	3.138283	AGGAGTGTTGAATTGGTTCTGGA	59.862	43.478	0.00	0.00	35.33	3.86
2694	4768	4.976540	ACCTTGCTTACTAAAGGAGTGT	57.023	40.909	8.39	0.00	44.93	3.55
2759	4833	5.595952	AGTTCTTGGAAAAGCTTCATGTTCT	59.404	36.000	0.00	0.00	32.75	3.01
2760	4834	5.836347	AGTTCTTGGAAAAGCTTCATGTTC	58.164	37.500	0.00	0.00	32.75	3.18
2786	4860	4.414337	TGGGATTGTTTTGTTTCTTGGG	57.586	40.909	0.00	0.00	0.00	4.12
2893	4967	0.602638	TTGCTAACCCAGAGTGCACG	60.603	55.000	12.01	0.00	33.13	5.34
2923	4997	2.584492	TGTCAATCTCATCGCGTGAT	57.416	45.000	5.43	5.43	35.97	3.06
2957	5064	2.037641	CCGATGAATCCTGTGCTATGGA	59.962	50.000	0.00	0.00	36.72	3.41
2974	5081	3.324846	TGCTAGCAATCTCCATAACCGAT	59.675	43.478	16.84	0.00	0.00	4.18
2997	5104	4.664150	TCATCGTACATACTGGCAATCA	57.336	40.909	0.00	0.00	0.00	2.57
3074	5181	6.073003	CCTTCAGTAGTTGATCCAAACAAGAC	60.073	42.308	0.00	0.00	35.27	3.01
3287	5394	3.317993	GGTTAGTGCTTGCCTCTGAAAAA	59.682	43.478	0.00	0.00	0.00	1.94
3474	5581	1.777272	AGGGGTGTCTTTTGAGAAGCT	59.223	47.619	0.00	0.00	0.00	3.74
3491	5598	1.806496	TCCTCCACATCATACCAGGG	58.194	55.000	0.00	0.00	0.00	4.45
3503	5610	2.103263	AGGCTCGATGTATTTCCTCCAC	59.897	50.000	0.00	0.00	0.00	4.02
3539	5646	1.229428	GGCATGGTATGATGGTGTCG	58.771	55.000	0.00	0.00	0.00	4.35
3555	5662	5.936956	GTGTCATAAAATTCAAATTGGGGCA	59.063	36.000	0.00	0.00	0.00	5.36
3569	5676	6.420588	CGGTCAGTAAAAACGTGTCATAAAA	58.579	36.000	0.00	0.00	0.00	1.52
3596	5703	1.180029	CTGCACATTCAGAAAGGGGG	58.820	55.000	0.00	0.00	36.19	5.40
3597	5704	1.815003	GTCTGCACATTCAGAAAGGGG	59.185	52.381	0.00	0.00	43.89	4.79
3647	5754	0.698238	AGCCCTAATGGAGTGCACAA	59.302	50.000	21.04	4.31	35.39	3.33
3856	5967	2.474266	GACGATTCGCTTGCGCAA	59.526	55.556	23.48	23.48	35.30	4.85
3891	6002	0.677288	TACTGTATCCGAATGGGCCG	59.323	55.000	0.00	0.00	35.24	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.