AutoCloner

Multiple sequence alignment - TraesCS3A01G470100

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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	TraesCS3A01G470100	chr3A	100.000	2597	0	0	1	2597	702330249	702327653	0.000000e+00	4796.0
1	TraesCS3A01G470100	chr3A	96.961	2139	45	2	459	2597	702381094	702378976	0.000000e+00	3572.0
2	TraesCS3A01G470100	chr3A	87.258	1915	163	34	724	2597	702149852	702147978	0.000000e+00	2109.0
3	TraesCS3A01G470100	chr3A	96.422	1118	22	1	459	1576	702383761	702382662	0.000000e+00	1827.0
4	TraesCS3A01G470100	chr3A	96.422	1118	22	1	459	1576	702401389	702400290	0.000000e+00	1827.0
5	TraesCS3A01G470100	chr3A	92.647	476	31	2	1	473	702384405	702383931	0.000000e+00	682.0
6	TraesCS3A01G470100	chr3A	92.647	476	31	2	1	473	702402033	702401559	0.000000e+00	682.0
7	TraesCS3A01G470100	chr3A	92.227	476	33	2	1	473	702381738	702381264	0.000000e+00	671.0
8	TraesCS3A01G470100	chr3A	88.235	527	36	13	712	1233	702116095	702115590	7.950000e-170	606.0
9	TraesCS3A01G470100	chr3A	80.835	407	61	10	1	407	702150892	702150503	1.170000e-78	303.0
10	TraesCS3A01G470100	chr3A	97.674	43	1	0	455	497	702150494	702150452	9.970000e-10	75.0
11	TraesCS3A01G470100	chrUn	96.215	2140	47	4	459	2597	312095330	312097436	0.000000e+00	3472.0
12	TraesCS3A01G470100	chrUn	87.755	1911	162	31	724	2597	268821202	268819327	0.000000e+00	2167.0
13	TraesCS3A01G470100	chrUn	87.755	1911	162	30	724	2597	268830489	268832364	0.000000e+00	2167.0
14	TraesCS3A01G470100	chrUn	97.990	398	6	1	2140	2537	479182136	479181741	0.000000e+00	689.0
15	TraesCS3A01G470100	chrUn	96.296	162	6	0	312	473	312094999	312095160	1.530000e-67	267.0
16	TraesCS3A01G470100	chrUn	92.754	69	1	1	602	666	268821660	268821592	2.130000e-16	97.1
17	TraesCS3A01G470100	chrUn	92.754	69	1	1	602	666	268830031	268830099	2.130000e-16	97.1
18	TraesCS3A01G470100	chrUn	100.000	40	0	0	458	497	268821789	268821750	9.970000e-10	75.0
19	TraesCS3A01G470100	chrUn	100.000	40	0	0	458	497	268829902	268829941	9.970000e-10	75.0
20	TraesCS3A01G470100	chr3D	87.416	1931	156	38	709	2597	566890169	566892054	0.000000e+00	2139.0
21	TraesCS3A01G470100	chr3D	82.869	1004	135	23	923	1908	567046176	567047160	0.000000e+00	867.0
22	TraesCS3A01G470100	chr3D	90.435	115	6	2	558	667	566889685	566889799	2.080000e-31	147.0

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	TraesCS3A01G470100	chr3A	702327653	702330249	2596	True	4796.0	4796	100.00000	1	2597	1	chr3A.!!$R2	2596
1	TraesCS3A01G470100	chr3A	702378976	702384405	5429	True	1688.0	3572	94.56425	1	2597	4	chr3A.!!$R4	2596
2	TraesCS3A01G470100	chr3A	702400290	702402033	1743	True	1254.5	1827	94.53450	1	1576	2	chr3A.!!$R5	1575
3	TraesCS3A01G470100	chr3A	702147978	702150892	2914	True	829.0	2109	88.58900	1	2597	3	chr3A.!!$R3	2596
4	TraesCS3A01G470100	chr3A	702115590	702116095	505	True	606.0	606	88.23500	712	1233	1	chr3A.!!$R1	521
5	TraesCS3A01G470100	chrUn	312094999	312097436	2437	False	1869.5	3472	96.25550	312	2597	2	chrUn.!!$F2	2285
6	TraesCS3A01G470100	chrUn	268819327	268821789	2462	True	779.7	2167	93.50300	458	2597	3	chrUn.!!$R2	2139
7	TraesCS3A01G470100	chrUn	268829902	268832364	2462	False	779.7	2167	93.50300	458	2597	3	chrUn.!!$F1	2139
8	TraesCS3A01G470100	chr3D	566889685	566892054	2369	False	1143.0	2139	88.92550	558	2597	2	chr3D.!!$F2	2039
9	TraesCS3A01G470100	chr3D	567046176	567047160	984	False	867.0	867	82.86900	923	1908	1	chr3D.!!$F1	985

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
331	335	0.038599	TGGTGCTCCGACTACCACTA	59.961	55.0	0.0	0.0	39.43	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2054	5345	0.537188	ATGTGTGGATGACCGAGGAC	59.463	55.0	0.0	0.0	39.42	3.85	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	1.296392	CACCATCTCTTGTCCGGCA	59.704	57.895	0.00	0.00	0.00	5.69
36	37	0.608640	CTCTTGTCCGGCAGTAGGTT	59.391	55.000	0.00	0.00	0.00	3.50
39	40	1.764571	TTGTCCGGCAGTAGGTTGCT	61.765	55.000	0.00	0.00	43.57	3.91
65	66	1.678627	CTCCACGTCTGGTATGAGAGG	59.321	57.143	0.00	0.00	38.90	3.69
115	116	5.247337	GGATCTCTAGTATTCCCCTCTTTGG	59.753	48.000	0.00	0.00	0.00	3.28
127	128	4.105057	TCCCCTCTTTGGTGCTTTTACTAA	59.895	41.667	0.00	0.00	0.00	2.24
129	130	5.313712	CCCTCTTTGGTGCTTTTACTAAGA	58.686	41.667	0.00	0.00	0.00	2.10
138	139	5.334569	GGTGCTTTTACTAAGAATTGCGTGA	60.335	40.000	0.00	0.00	0.00	4.35
217	221	0.673644	CTTCGACGGTTCCATGGCTT	60.674	55.000	6.96	0.00	0.00	4.35
219	223	2.877691	GACGGTTCCATGGCTTGC	59.122	61.111	6.96	0.00	0.00	4.01
331	335	0.038599	TGGTGCTCCGACTACCACTA	59.961	55.000	0.00	0.00	39.43	2.74
332	336	0.455005	GGTGCTCCGACTACCACTAC	59.545	60.000	0.00	0.00	34.61	2.73
339	343	3.012518	TCCGACTACCACTACTTGCTAC	58.987	50.000	0.00	0.00	0.00	3.58
423	427	5.006153	TGTGTAATGTATCTCGGGTTCAG	57.994	43.478	0.00	0.00	0.00	3.02
508	696	2.210116	GGGCATCAATACGGTGTACTG	58.790	52.381	0.00	0.00	0.00	2.74
510	698	3.494398	GGGCATCAATACGGTGTACTGAT	60.494	47.826	0.00	0.00	0.00	2.90
525	713	7.094762	CGGTGTACTGATCATCTGCTAATACTA	60.095	40.741	0.00	0.00	0.00	1.82
527	715	8.240682	GTGTACTGATCATCTGCTAATACTAGG	58.759	40.741	0.00	0.00	0.00	3.02
528	716	8.164070	TGTACTGATCATCTGCTAATACTAGGA	58.836	37.037	0.00	0.00	0.00	2.94
529	717	9.015367	GTACTGATCATCTGCTAATACTAGGAA	57.985	37.037	0.00	0.00	0.00	3.36
538	726	8.410673	TCTGCTAATACTAGGAAGGACATTAG	57.589	38.462	0.00	0.00	32.14	1.73
670	1222	3.249320	GTCGTTTACTTCCACTCCAAACC	59.751	47.826	0.00	0.00	0.00	3.27
752	1346	4.196971	GTCTTACAACTGTTGAACCCACT	58.803	43.478	26.00	5.26	0.00	4.00
754	1348	4.163458	TCTTACAACTGTTGAACCCACTCT	59.837	41.667	26.00	3.84	0.00	3.24
875	1470	4.142469	ACTTTGTCAAAAACTCCAACCTCG	60.142	41.667	0.00	0.00	0.00	4.63
876	1471	3.269538	TGTCAAAAACTCCAACCTCGA	57.730	42.857	0.00	0.00	0.00	4.04
877	1472	3.202906	TGTCAAAAACTCCAACCTCGAG	58.797	45.455	5.13	5.13	0.00	4.04
878	1473	3.203716	GTCAAAAACTCCAACCTCGAGT	58.796	45.455	12.31	0.00	42.41	4.18
879	1474	4.141892	TGTCAAAAACTCCAACCTCGAGTA	60.142	41.667	12.31	0.00	39.69	2.59
880	1475	4.210746	GTCAAAAACTCCAACCTCGAGTAC	59.789	45.833	12.31	0.00	39.69	2.73
881	1476	4.100498	TCAAAAACTCCAACCTCGAGTACT	59.900	41.667	12.31	0.00	39.69	2.73
882	1477	3.938289	AAACTCCAACCTCGAGTACTC	57.062	47.619	13.18	13.18	39.69	2.59
883	1478	1.836802	ACTCCAACCTCGAGTACTCC	58.163	55.000	17.23	0.00	38.82	3.85
884	1479	1.355043	ACTCCAACCTCGAGTACTCCT	59.645	52.381	17.23	0.00	38.82	3.69
885	1480	2.018515	CTCCAACCTCGAGTACTCCTC	58.981	57.143	17.23	0.00	36.80	3.71
886	1481	1.104630	CCAACCTCGAGTACTCCTCC	58.895	60.000	17.23	0.00	36.82	4.30
887	1482	1.616187	CCAACCTCGAGTACTCCTCCA	60.616	57.143	17.23	0.00	36.82	3.86
888	1483	2.168496	CAACCTCGAGTACTCCTCCAA	58.832	52.381	17.23	0.00	36.82	3.53
889	1484	1.836802	ACCTCGAGTACTCCTCCAAC	58.163	55.000	17.23	0.00	36.82	3.77
890	1485	1.104630	CCTCGAGTACTCCTCCAACC	58.895	60.000	17.23	0.00	36.82	3.77
891	1486	1.341187	CCTCGAGTACTCCTCCAACCT	60.341	57.143	17.23	0.00	36.82	3.50
892	1487	2.018515	CTCGAGTACTCCTCCAACCTC	58.981	57.143	17.23	0.00	36.82	3.85
1155	1750	2.043604	CTGTGAGTGGTGGTGGCTCA	62.044	60.000	0.00	0.00	36.97	4.26
1212	1807	3.652057	AATAGTGGTAGCCATGCAAGT	57.348	42.857	0.00	0.00	35.28	3.16
1335	4603	5.189180	GGATCTTCATATCCTTATGGTGGC	58.811	45.833	0.00	0.00	41.99	5.01
1608	4877	0.253160	ACCCCTAGTCCCTTCATGCA	60.253	55.000	0.00	0.00	0.00	3.96
1764	5052	6.912082	TCCAAGAATGTTACATGTCAATGTG	58.088	36.000	0.00	0.00	46.66	3.21
1924	5215	3.472652	ACATGTCGTTTCACTAAAGGCA	58.527	40.909	0.00	0.00	31.90	4.75
1957	5248	6.708502	TGTAACATATAAATCACATCCACCGG	59.291	38.462	0.00	0.00	0.00	5.28
1979	5270	5.108405	CGGTTTCGTTTTGCATAAACTTCTG	60.108	40.000	16.84	6.77	33.40	3.02
2054	5345	2.682856	CCACACCCCAATATCTTTCACG	59.317	50.000	0.00	0.00	0.00	4.35
2167	5459	2.063015	AATGGTGGGAAGGTGCACGA	62.063	55.000	11.45	0.00	0.00	4.35
2467	5795	7.076362	GGTTGTTCTTAGACTTTCCGAAATTC	58.924	38.462	3.59	3.59	0.00	2.17
2468	5796	7.041303	GGTTGTTCTTAGACTTTCCGAAATTCT	60.041	37.037	15.65	15.65	35.07	2.40
2469	5797	7.653767	TGTTCTTAGACTTTCCGAAATTCTC	57.346	36.000	14.99	4.24	33.22	2.87
2470	5798	7.214381	TGTTCTTAGACTTTCCGAAATTCTCA	58.786	34.615	14.99	6.11	33.22	3.27
2471	5799	7.713507	TGTTCTTAGACTTTCCGAAATTCTCAA	59.286	33.333	14.99	8.83	33.22	3.02
2472	5800	8.557029	GTTCTTAGACTTTCCGAAATTCTCAAA	58.443	33.333	14.99	6.63	33.22	2.69
2473	5801	8.848474	TCTTAGACTTTCCGAAATTCTCAAAT	57.152	30.769	14.99	0.00	33.22	2.32
2474	5802	9.284968	TCTTAGACTTTCCGAAATTCTCAAATT	57.715	29.630	14.99	0.00	36.64	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	0.037326	GACAAGAGATGGTGGCGTGA	60.037	55.000	0.00	0.00	0.00	4.35
12	13	1.194781	ACTGCCGGACAAGAGATGGT	61.195	55.000	5.05	0.00	0.00	3.55
36	37	3.695606	GACGTGGAGGAGGCAGCA	61.696	66.667	0.00	0.00	0.00	4.41
115	116	5.564127	GTCACGCAATTCTTAGTAAAAGCAC	59.436	40.000	0.00	0.00	0.00	4.40
127	128	1.568612	CGGCACTGTCACGCAATTCT	61.569	55.000	0.00	0.00	0.00	2.40
129	130	1.841663	GACGGCACTGTCACGCAATT	61.842	55.000	4.72	0.00	38.75	2.32
138	139	3.991051	CCAGACCGACGGCACTGT	61.991	66.667	27.73	7.21	31.87	3.55
157	158	4.036852	GGGAGGCTCGAGGAAATTTTATTG	59.963	45.833	15.58	0.00	0.00	1.90
204	208	1.926511	GACAGCAAGCCATGGAACCG	61.927	60.000	18.40	0.73	0.00	4.44
210	214	0.806868	ATCAACGACAGCAAGCCATG	59.193	50.000	0.00	0.00	0.00	3.66
217	221	2.286713	CCGACAAAAATCAACGACAGCA	60.287	45.455	0.00	0.00	0.00	4.41
219	223	2.307049	GCCGACAAAAATCAACGACAG	58.693	47.619	0.00	0.00	0.00	3.51
331	335	1.759445	AGCCGAGATGATGTAGCAAGT	59.241	47.619	0.00	0.00	0.00	3.16
332	336	2.223900	TGAGCCGAGATGATGTAGCAAG	60.224	50.000	0.00	0.00	0.00	4.01
339	343	1.329906	GCTTTGTGAGCCGAGATGATG	59.670	52.381	0.00	0.00	46.01	3.07
423	427	4.512484	AGATGCTCTAGCTTCAAAGGTTC	58.488	43.478	17.16	0.00	44.66	3.62
432	436	1.361993	CGGCGAGATGCTCTAGCTT	59.638	57.895	0.00	0.00	43.36	3.74
508	696	7.177568	TGTCCTTCCTAGTATTAGCAGATGATC	59.822	40.741	0.00	0.00	0.00	2.92
510	698	6.373759	TGTCCTTCCTAGTATTAGCAGATGA	58.626	40.000	0.00	0.00	0.00	2.92
525	713	4.471386	TGCTTTAGCTCTAATGTCCTTCCT	59.529	41.667	3.10	0.00	42.66	3.36
527	715	6.934048	AATGCTTTAGCTCTAATGTCCTTC	57.066	37.500	3.10	0.00	42.66	3.46
528	716	8.986929	ATAAATGCTTTAGCTCTAATGTCCTT	57.013	30.769	3.10	0.67	42.66	3.36
529	717	9.495572	GTATAAATGCTTTAGCTCTAATGTCCT	57.504	33.333	3.10	0.00	42.66	3.85
538	726	7.513968	CAAGATCCGTATAAATGCTTTAGCTC	58.486	38.462	3.10	0.00	42.66	4.09
670	1222	2.248487	CCTCGAAGTTTCCGTAGTTCG	58.752	52.381	11.09	11.09	46.92	3.95
752	1346	2.034558	TGCTAATCGTGATCGCATCAGA	59.965	45.455	7.12	0.00	40.53	3.27
754	1348	2.223805	ACTGCTAATCGTGATCGCATCA	60.224	45.455	7.12	0.00	36.84	3.07
875	1470	1.826096	GTGGAGGTTGGAGGAGTACTC	59.174	57.143	14.87	14.87	45.84	2.59
876	1471	1.552719	GGTGGAGGTTGGAGGAGTACT	60.553	57.143	0.00	0.00	0.00	2.73
877	1472	0.903236	GGTGGAGGTTGGAGGAGTAC	59.097	60.000	0.00	0.00	0.00	2.73
878	1473	0.252558	GGGTGGAGGTTGGAGGAGTA	60.253	60.000	0.00	0.00	0.00	2.59
879	1474	1.539124	GGGTGGAGGTTGGAGGAGT	60.539	63.158	0.00	0.00	0.00	3.85
880	1475	2.301738	GGGGTGGAGGTTGGAGGAG	61.302	68.421	0.00	0.00	0.00	3.69
881	1476	2.204090	GGGGTGGAGGTTGGAGGA	60.204	66.667	0.00	0.00	0.00	3.71
882	1477	3.339093	GGGGGTGGAGGTTGGAGG	61.339	72.222	0.00	0.00	0.00	4.30
883	1478	2.531685	TGGGGGTGGAGGTTGGAG	60.532	66.667	0.00	0.00	0.00	3.86
884	1479	2.531685	CTGGGGGTGGAGGTTGGA	60.532	66.667	0.00	0.00	0.00	3.53
885	1480	4.366684	GCTGGGGGTGGAGGTTGG	62.367	72.222	0.00	0.00	0.00	3.77
886	1481	2.922704	ATGCTGGGGGTGGAGGTTG	61.923	63.158	0.00	0.00	0.00	3.77
887	1482	2.535317	ATGCTGGGGGTGGAGGTT	60.535	61.111	0.00	0.00	0.00	3.50
888	1483	3.341629	CATGCTGGGGGTGGAGGT	61.342	66.667	0.00	0.00	0.00	3.85
889	1484	4.828296	GCATGCTGGGGGTGGAGG	62.828	72.222	11.37	0.00	0.00	4.30
890	1485	3.369410	ATGCATGCTGGGGGTGGAG	62.369	63.158	20.33	0.00	0.00	3.86
891	1486	3.349304	ATGCATGCTGGGGGTGGA	61.349	61.111	20.33	0.00	0.00	4.02
892	1487	3.151710	CATGCATGCTGGGGGTGG	61.152	66.667	20.33	0.00	0.00	4.61
1155	1750	1.462238	AGTTCCACTCCCAGCACCT	60.462	57.895	0.00	0.00	0.00	4.00
1212	1807	2.529136	CCACCTCCACCTCCACCA	60.529	66.667	0.00	0.00	0.00	4.17
1335	4603	3.243101	CGCTAGTATATCCACCATAGCCG	60.243	52.174	0.00	0.00	33.68	5.52
1557	4825	1.668826	ACCCAGATCCAGCACCTTTA	58.331	50.000	0.00	0.00	0.00	1.85
1608	4877	6.682537	TGGGCTCCATTATTTTAGATTCCTT	58.317	36.000	0.00	0.00	0.00	3.36
1621	4890	4.724798	AGTACATTAGGTTGGGCTCCATTA	59.275	41.667	0.00	0.00	31.53	1.90
1700	4988	9.787435	ACTAGTACATTTTCCACAAGAACAATA	57.213	29.630	0.00	0.00	32.95	1.90
1924	5215	9.851686	ATGTGATTTATATGTTACATGACTGGT	57.148	29.630	8.26	0.00	0.00	4.00
1957	5248	6.343924	CGACAGAAGTTTATGCAAAACGAAAC	60.344	38.462	14.56	9.68	35.42	2.78
2054	5345	0.537188	ATGTGTGGATGACCGAGGAC	59.463	55.000	0.00	0.00	39.42	3.85
2351	5665	5.966853	TTTTGACCCCAAAAGAAAGGAAT	57.033	34.783	0.00	0.00	44.62	3.01
2430	5750	8.157476	AGTCTAAGAACAACCACAACTATCAAT	58.843	33.333	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.