AutoCloner

Multiple sequence alignment - TraesCS4A01G418400

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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	TraesCS4A01G418400	chr4A	100.000	3819	0	0	1	3819	688376384	688372566	0.000000e+00	7053.0
1	TraesCS4A01G418400	chr4A	96.185	3827	102	18	1	3819	688328772	688324982	0.000000e+00	6218.0
2	TraesCS4A01G418400	chr4A	91.059	1935	167	3	1000	2934	687831029	687832957	0.000000e+00	2610.0
3	TraesCS4A01G418400	chr4A	90.557	1938	174	4	1000	2934	687892532	687894463	0.000000e+00	2556.0
4	TraesCS4A01G418400	chr4A	89.923	1945	174	9	990	2934	687813481	687815403	0.000000e+00	2486.0
5	TraesCS4A01G418400	chr4A	91.748	1539	123	2	1000	2538	687919347	687920881	0.000000e+00	2135.0
6	TraesCS4A01G418400	chr4A	85.098	510	67	7	3054	3562	528097636	528097135	2.630000e-141	512.0
7	TraesCS4A01G418400	chr4A	86.921	367	45	2	2568	2934	687920883	687921246	3.550000e-110	409.0
8	TraesCS4A01G418400	chr4A	94.521	73	2	1	2947	3017	732865032	732865104	1.120000e-20	111.0
9	TraesCS4A01G418400	chr7A	91.461	1944	160	4	990	2932	35696591	35698529	0.000000e+00	2665.0
10	TraesCS4A01G418400	chr7A	92.829	767	49	5	951	1712	35746323	35747088	0.000000e+00	1107.0
11	TraesCS4A01G418400	chr7D	90.205	1950	173	11	995	2932	36045154	36043211	0.000000e+00	2527.0
12	TraesCS4A01G418400	chr7D	90.492	1199	97	11	1744	2932	35552412	35553603	0.000000e+00	1567.0
13	TraesCS4A01G418400	chr7D	89.892	1019	103	0	1821	2839	35798298	35797280	0.000000e+00	1312.0
14	TraesCS4A01G418400	chr7D	88.960	933	84	13	1	928	35550477	35551395	0.000000e+00	1134.0
15	TraesCS4A01G418400	chr7D	94.645	691	34	2	953	1642	35551383	35552071	0.000000e+00	1068.0
16	TraesCS4A01G418400	chr7D	93.151	73	3	1	2947	3017	621195406	621195478	5.220000e-19	106.0
17	TraesCS4A01G418400	chr3B	83.398	512	65	12	3054	3562	463076662	463076168	1.250000e-124	457.0
18	TraesCS4A01G418400	chr3B	85.356	239	29	6	3054	3290	463077450	463077216	3.810000e-60	243.0
19	TraesCS4A01G418400	chrUn	94.656	262	11	3	3559	3819	20067469	20067210	1.650000e-108	403.0
20	TraesCS4A01G418400	chrUn	95.522	67	1	1	2953	3017	29985387	29985453	5.220000e-19	106.0
21	TraesCS4A01G418400	chrUn	100.000	32	0	0	3020	3051	433066353	433066322	4.120000e-05	60.2
22	TraesCS4A01G418400	chrUn	97.059	34	1	0	3018	3051	71517798	71517765	1.480000e-04	58.4
23	TraesCS4A01G418400	chr6D	94.636	261	11	3	3560	3819	463602259	463602001	5.940000e-108	401.0
24	TraesCS4A01G418400	chr5D	94.961	258	10	3	3560	3816	93185779	93186034	5.940000e-108	401.0
25	TraesCS4A01G418400	chr5D	94.961	258	10	3	3560	3816	376059087	376059342	5.940000e-108	401.0
26	TraesCS4A01G418400	chr5D	88.210	229	26	1	3335	3563	417674075	417674302	4.860000e-69	272.0
27	TraesCS4A01G418400	chr5D	97.059	34	1	0	3018	3051	513899636	513899603	1.480000e-04	58.4
28	TraesCS4A01G418400	chr4D	94.636	261	11	3	3560	3819	349727702	349727444	5.940000e-108	401.0
29	TraesCS4A01G418400	chr4D	94.636	261	11	3	3560	3819	420045008	420044750	5.940000e-108	401.0
30	TraesCS4A01G418400	chr1D	94.636	261	11	3	3560	3819	182376112	182375854	5.940000e-108	401.0
31	TraesCS4A01G418400	chr1D	94.636	261	11	3	3560	3819	327045460	327045202	5.940000e-108	401.0
32	TraesCS4A01G418400	chr1D	100.000	32	0	0	3020	3051	322476654	322476685	4.120000e-05	60.2
33	TraesCS4A01G418400	chr7B	94.521	73	2	1	2947	3017	644302646	644302718	1.120000e-20	111.0
34	TraesCS4A01G418400	chr7B	92.000	75	2	3	2947	3017	747404194	747404268	6.750000e-18	102.0
35	TraesCS4A01G418400	chr2B	94.366	71	4	0	2947	3017	697518741	697518671	4.030000e-20	110.0
36	TraesCS4A01G418400	chr5B	92.958	71	5	0	2947	3017	158819924	158819994	1.880000e-18	104.0
37	TraesCS4A01G418400	chr2D	91.549	71	5	1	2947	3017	430403251	430403320	3.140000e-16	97.1
38	TraesCS4A01G418400	chr2D	100.000	32	0	0	3020	3051	465570309	465570278	4.120000e-05	60.2
39	TraesCS4A01G418400	chr6B	100.000	32	0	0	3020	3051	132740113	132740082	4.120000e-05	60.2
40	TraesCS4A01G418400	chr6A	100.000	32	0	0	3020	3051	11114488	11114457	4.120000e-05	60.2
41	TraesCS4A01G418400	chr3A	100.000	32	0	0	3020	3051	76319692	76319661	4.120000e-05	60.2

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	TraesCS4A01G418400	chr4A	688372566	688376384	3818	True	7053.000000	7053	100.000000	1	3819	1	chr4A.!!$R3	3818
1	TraesCS4A01G418400	chr4A	688324982	688328772	3790	True	6218.000000	6218	96.185000	1	3819	1	chr4A.!!$R2	3818
2	TraesCS4A01G418400	chr4A	687831029	687832957	1928	False	2610.000000	2610	91.059000	1000	2934	1	chr4A.!!$F2	1934
3	TraesCS4A01G418400	chr4A	687892532	687894463	1931	False	2556.000000	2556	90.557000	1000	2934	1	chr4A.!!$F3	1934
4	TraesCS4A01G418400	chr4A	687813481	687815403	1922	False	2486.000000	2486	89.923000	990	2934	1	chr4A.!!$F1	1944
5	TraesCS4A01G418400	chr4A	687919347	687921246	1899	False	1272.000000	2135	89.334500	1000	2934	2	chr4A.!!$F5	1934
6	TraesCS4A01G418400	chr4A	528097135	528097636	501	True	512.000000	512	85.098000	3054	3562	1	chr4A.!!$R1	508
7	TraesCS4A01G418400	chr7A	35696591	35698529	1938	False	2665.000000	2665	91.461000	990	2932	1	chr7A.!!$F1	1942
8	TraesCS4A01G418400	chr7A	35746323	35747088	765	False	1107.000000	1107	92.829000	951	1712	1	chr7A.!!$F2	761
9	TraesCS4A01G418400	chr7D	36043211	36045154	1943	True	2527.000000	2527	90.205000	995	2932	1	chr7D.!!$R2	1937
10	TraesCS4A01G418400	chr7D	35797280	35798298	1018	True	1312.000000	1312	89.892000	1821	2839	1	chr7D.!!$R1	1018
11	TraesCS4A01G418400	chr7D	35550477	35553603	3126	False	1256.333333	1567	91.365667	1	2932	3	chr7D.!!$F2	2931
12	TraesCS4A01G418400	chr3B	463076168	463077450	1282	True	350.000000	457	84.377000	3054	3562	2	chr3B.!!$R1	508

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
131	132	0.391263	GCAGCGTGGCTAGGTTTACT	60.391	55.0	0.00	0.0	36.40	2.24	F
1844	2105	0.534203	GAGGTTCAAGAACACGGCCA	60.534	55.0	14.25	0.0	42.85	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2060	2321	0.603569	AACTCGTCCTGCTTCACGAT	59.396	50.000	5.29	0.0	43.75	3.73	R
3312	4380	1.474320	CCTGGTTGAGTTGGACGTGAA	60.474	52.381	0.00	0.0	0.00	3.18	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
131	132	0.391263	GCAGCGTGGCTAGGTTTACT	60.391	55.000	0.00	0.00	36.40	2.24
180	181	3.452990	TCATAACAAGCATCGGGGTAAGA	59.547	43.478	0.00	0.00	0.00	2.10
273	274	2.358003	GCCGCTGTCACAGAGCTT	60.358	61.111	9.70	0.00	34.03	3.74
291	292	0.699577	TTTCAAGGGGTGGGAGGACA	60.700	55.000	0.00	0.00	0.00	4.02
349	350	1.160137	GCCGAGTGCTTTTCTCACAT	58.840	50.000	0.00	0.00	36.93	3.21
413	415	2.271800	CTCGGCCTGTGTGAAGATAAC	58.728	52.381	0.00	0.00	0.00	1.89
436	438	3.443045	CCACAGCCGGTTGCCATC	61.443	66.667	19.28	0.00	42.71	3.51
506	508	7.376072	GGCAGATAATTTACACTTGATTTACGC	59.624	37.037	0.00	0.00	0.00	4.42
507	509	7.110216	GCAGATAATTTACACTTGATTTACGCG	59.890	37.037	3.53	3.53	0.00	6.01
529	532	5.334260	GCGTTTAAACACTAGGCAACATGTA	60.334	40.000	18.07	0.00	41.41	2.29
538	541	3.866883	AGGCAACATGTATTTTTCCCG	57.133	42.857	0.00	0.00	41.41	5.14
542	545	4.102649	GCAACATGTATTTTTCCCGTAGC	58.897	43.478	0.00	0.00	0.00	3.58
556	559	3.888323	TCCCGTAGCGGTACATGTTTATA	59.112	43.478	23.29	0.00	46.80	0.98
562	565	6.254157	CGTAGCGGTACATGTTTATAAGTGTT	59.746	38.462	23.29	0.00	0.00	3.32
563	566	7.201461	CGTAGCGGTACATGTTTATAAGTGTTT	60.201	37.037	23.29	0.00	0.00	2.83
564	567	6.837992	AGCGGTACATGTTTATAAGTGTTTG	58.162	36.000	2.30	0.00	0.00	2.93
613	616	7.861630	AGTATCCATTTAATGCGACATTACAC	58.138	34.615	10.50	3.60	0.00	2.90
619	622	3.449322	AATGCGACATTACACGTCAAC	57.551	42.857	3.68	0.00	32.72	3.18
678	682	7.843490	TCTTATCTTGTTATTTCCGTCCTTG	57.157	36.000	0.00	0.00	0.00	3.61
692	696	3.001939	CCGTCCTTGTGTTGTTTCAGTAC	59.998	47.826	0.00	0.00	0.00	2.73
721	725	3.726730	GCTGTCGTCGTCTTCATTCTATC	59.273	47.826	0.00	0.00	0.00	2.08
727	731	1.781429	CGTCTTCATTCTATCGCCGTG	59.219	52.381	0.00	0.00	0.00	4.94
756	766	6.804770	TTTTTATTAGAAAGCGTAGGCACA	57.195	33.333	10.48	0.00	43.41	4.57
767	777	1.002366	GTAGGCACATTCGTCAGCAG	58.998	55.000	0.00	0.00	0.00	4.24
790	800	7.137426	CAGAGCTGCCAATTTTATGTATTCTC	58.863	38.462	0.00	0.00	0.00	2.87
796	806	6.483307	TGCCAATTTTATGTATTCTCTCGGAG	59.517	38.462	0.00	0.00	0.00	4.63
807	817	4.785511	TTCTCTCGGAGAAAGTAAGGTG	57.214	45.455	9.32	0.00	44.37	4.00
811	821	3.700038	TCTCGGAGAAAGTAAGGTGGATC	59.300	47.826	4.96	0.00	34.09	3.36
820	830	7.565680	AGAAAGTAAGGTGGATCGATGTTATT	58.434	34.615	0.54	0.00	0.00	1.40
850	860	3.547513	GGGGCGCCCTCTCGTAAT	61.548	66.667	42.70	0.00	41.34	1.89
857	868	2.475487	GCGCCCTCTCGTAATTACATTC	59.525	50.000	15.67	0.00	0.00	2.67
886	898	6.701841	AGGACATTCGTGCAGTTGTATAATAG	59.298	38.462	0.00	0.00	35.57	1.73
937	949	6.488006	ACTTTATATATCCAGTTGGCTTGCAG	59.512	38.462	0.00	0.00	34.44	4.41
945	957	2.555325	CAGTTGGCTTGCAGAAATCAGA	59.445	45.455	0.00	0.00	0.00	3.27
947	959	3.638160	AGTTGGCTTGCAGAAATCAGAAA	59.362	39.130	0.00	0.00	0.00	2.52
948	960	3.928727	TGGCTTGCAGAAATCAGAAAG	57.071	42.857	0.00	0.00	0.00	2.62
954	966	5.182001	GCTTGCAGAAATCAGAAAGAGGTTA	59.818	40.000	0.00	0.00	0.00	2.85
987	999	5.852282	AAACATGAAGCACTTGGTTTACT	57.148	34.783	0.00	0.00	35.69	2.24
988	1000	6.952773	AAACATGAAGCACTTGGTTTACTA	57.047	33.333	0.00	0.00	35.69	1.82
1056	1073	1.601171	CTCCCTCTTCTGCCACCTG	59.399	63.158	0.00	0.00	0.00	4.00
1524	1541	0.957888	GCTTCTTCCGCTTCTGGCTT	60.958	55.000	0.00	0.00	39.13	4.35
1614	1631	1.445095	CGGAGCCTTCATAGCAGCT	59.555	57.895	0.00	0.00	38.56	4.24
1844	2105	0.534203	GAGGTTCAAGAACACGGCCA	60.534	55.000	14.25	0.00	42.85	5.36
2041	2302	2.607038	CCTTGACATCGACTTCGTGTCA	60.607	50.000	22.06	22.06	46.99	3.58
2129	2393	2.364842	ATGGTCGCCAGCTCCTCT	60.365	61.111	4.90	0.00	36.75	3.69
2140	2404	0.609406	AGCTCCTCTGCACGACTACA	60.609	55.000	0.00	0.00	34.99	2.74
2194	2458	6.612456	ACTCTCTCAATCTCTTCATGAAGGAT	59.388	38.462	30.33	26.22	38.88	3.24
2883	3161	7.138736	TCGAAATTCATCAAACTTTGAGAACC	58.861	34.615	9.97	6.50	43.98	3.62
2999	3277	5.222631	CAATAAAGCAAGGTGTGTTTCTCC	58.777	41.667	0.00	0.00	29.15	3.71
3066	3344	1.523934	CGTTCGTAAGGTGCGTTTCTT	59.476	47.619	0.00	0.00	38.47	2.52
3312	4380	5.001874	GCCCTTTAGTTTAACACACTAGCT	58.998	41.667	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
205	206	6.874278	CCCATGGGTCTCATATATGTAAGA	57.126	41.667	23.93	6.35	34.12	2.10
273	274	1.073319	TGTCCTCCCACCCCTTGAA	60.073	57.895	0.00	0.00	0.00	2.69
349	350	7.517614	TGTTTCTACACAAATCTTGGCATAA	57.482	32.000	0.00	0.00	34.12	1.90
388	390	0.973632	TTCACACAGGCCGAGTACAT	59.026	50.000	0.00	0.00	0.00	2.29
476	478	4.947388	TCAAGTGTAAATTATCTGCCACCC	59.053	41.667	0.00	0.00	0.00	4.61
506	508	5.103290	ACATGTTGCCTAGTGTTTAAACG	57.897	39.130	13.45	0.24	0.00	3.60
507	509	9.471084	AAAATACATGTTGCCTAGTGTTTAAAC	57.529	29.630	11.54	11.54	0.00	2.01
538	541	7.529880	AACACTTATAAACATGTACCGCTAC	57.470	36.000	0.00	0.00	0.00	3.58
542	545	5.730802	CGCAAACACTTATAAACATGTACCG	59.269	40.000	0.00	0.00	0.00	4.02
666	670	3.697045	TGAAACAACACAAGGACGGAAAT	59.303	39.130	0.00	0.00	0.00	2.17
678	682	3.545426	GCTGTTCCGTACTGAAACAACAC	60.545	47.826	0.88	0.00	0.00	3.32
692	696	2.050351	ACGACGACAGCTGTTCCG	60.050	61.111	22.65	22.40	0.00	4.30
739	743	2.927477	CGAATGTGCCTACGCTTTCTAA	59.073	45.455	0.00	0.00	37.96	2.10
740	744	2.094390	ACGAATGTGCCTACGCTTTCTA	60.094	45.455	0.00	0.00	37.96	2.10
741	745	1.337823	ACGAATGTGCCTACGCTTTCT	60.338	47.619	0.00	0.00	37.96	2.52
767	777	7.269477	AGAGAATACATAAAATTGGCAGCTC	57.731	36.000	0.00	0.00	0.00	4.09
785	795	4.160626	CCACCTTACTTTCTCCGAGAGAAT	59.839	45.833	14.49	6.23	46.20	2.40
790	800	3.489398	CGATCCACCTTACTTTCTCCGAG	60.489	52.174	0.00	0.00	0.00	4.63
796	806	7.494625	TGAATAACATCGATCCACCTTACTTTC	59.505	37.037	0.00	0.00	0.00	2.62
804	814	3.496130	CAGCTGAATAACATCGATCCACC	59.504	47.826	8.42	0.00	0.00	4.61
805	815	3.496130	CCAGCTGAATAACATCGATCCAC	59.504	47.826	17.39	0.00	0.00	4.02
806	816	3.494924	CCCAGCTGAATAACATCGATCCA	60.495	47.826	17.39	0.00	0.00	3.41
807	817	3.070018	CCCAGCTGAATAACATCGATCC	58.930	50.000	17.39	0.00	0.00	3.36
811	821	1.597742	CCCCCAGCTGAATAACATCG	58.402	55.000	17.39	0.00	0.00	3.84
844	854	5.408880	TGTCCTGTGGAATGTAATTACGA	57.591	39.130	10.92	1.21	41.22	3.43
845	855	6.509517	CGAATGTCCTGTGGAATGTAATTACG	60.510	42.308	10.92	0.00	41.22	3.18
846	856	6.315393	ACGAATGTCCTGTGGAATGTAATTAC	59.685	38.462	8.75	8.75	36.07	1.89
847	857	6.315144	CACGAATGTCCTGTGGAATGTAATTA	59.685	38.462	0.00	0.00	36.07	1.40
848	858	5.123820	CACGAATGTCCTGTGGAATGTAATT	59.876	40.000	0.00	0.00	40.93	1.40
849	859	4.635765	CACGAATGTCCTGTGGAATGTAAT	59.364	41.667	0.00	0.00	31.38	1.89
850	860	4.000325	CACGAATGTCCTGTGGAATGTAA	59.000	43.478	0.00	0.00	31.38	2.41
857	868	0.603707	ACTGCACGAATGTCCTGTGG	60.604	55.000	0.00	0.00	34.24	4.17
886	898	4.436584	CGATTCAAATGTTGTCTCTGCTCC	60.437	45.833	0.00	0.00	0.00	4.70
964	976	6.952773	AGTAAACCAAGTGCTTCATGTTTA	57.047	33.333	0.00	0.00	0.00	2.01
987	999	2.668945	CGTGAACATTGTGCGTGGTATA	59.331	45.455	0.00	0.00	0.00	1.47
988	1000	1.463056	CGTGAACATTGTGCGTGGTAT	59.537	47.619	0.00	0.00	0.00	2.73
1098	1115	1.129809	GCATTTCACCGACGTCACG	59.870	57.895	17.16	7.24	0.00	4.35
1221	1238	1.081242	GTCGTAGGCGTCCGTGAAA	60.081	57.895	0.00	0.00	39.49	2.69
1614	1631	0.608130	ACACCTGCATAGCGAAGACA	59.392	50.000	0.00	0.00	0.00	3.41
1844	2105	1.840737	AGCTGGTCAGTCTCATACGT	58.159	50.000	0.00	0.00	0.00	3.57
1849	2110	2.061220	CCCAAGCTGGTCAGTCTCA	58.939	57.895	0.00	0.00	35.17	3.27
2060	2321	0.603569	AACTCGTCCTGCTTCACGAT	59.396	50.000	5.29	0.00	43.75	3.73
2129	2393	2.139917	GAACCAACATGTAGTCGTGCA	58.860	47.619	0.00	0.00	34.22	4.57
2194	2458	3.270027	CCAGCCGATGTTGTTGAAGATA	58.730	45.455	0.00	0.00	0.00	1.98
2883	3161	6.808008	AGTCCAAACATGTCAAAGATACAG	57.192	37.500	0.00	0.00	0.00	2.74
3312	4380	1.474320	CCTGGTTGAGTTGGACGTGAA	60.474	52.381	0.00	0.00	0.00	3.18
3607	4676	6.495872	TGGAACTTTAGCCTCTTACAAGACTA	59.504	38.462	0.00	0.00	0.00	2.59
3608	4677	5.307196	TGGAACTTTAGCCTCTTACAAGACT	59.693	40.000	0.00	0.00	0.00	3.24
3711	4780	4.447138	TGAGGAGAGAGAGGACTAATCC	57.553	50.000	0.00	0.00	46.69	3.01
3712	4781	6.976934	AAATGAGGAGAGAGAGGACTAATC	57.023	41.667	0.00	0.00	0.00	1.75
3713	4782	9.445973	AATTAAATGAGGAGAGAGAGGACTAAT	57.554	33.333	0.00	0.00	0.00	1.73
3714	4783	8.846423	AATTAAATGAGGAGAGAGAGGACTAA	57.154	34.615	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.