AutoCloner

Multiple sequence alignment - TraesCS3B01G194600

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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	TraesCS3B01G194600	chr3B	100.000	3509	0	0	1	3509	215309394	215312902	0.000000e+00	6481
1	TraesCS3B01G194600	chr3B	97.440	1250	31	1	2261	3509	773421037	773419788	0.000000e+00	2130
2	TraesCS3B01G194600	chr3B	95.023	1306	52	8	971	2266	221912277	221913579	0.000000e+00	2039
3	TraesCS3B01G194600	chr3B	94.564	1306	48	14	971	2266	221979757	221981049	0.000000e+00	1997
4	TraesCS3B01G194600	chr3B	93.750	1312	60	9	971	2266	215384992	215386297	0.000000e+00	1949
5	TraesCS3B01G194600	chr3B	90.659	1092	87	7	974	2058	215104600	215105683	0.000000e+00	1437
6	TraesCS3B01G194600	chr3B	92.596	986	56	12	1	972	89379221	89378239	0.000000e+00	1400
7	TraesCS3B01G194600	chr3B	89.235	1124	70	16	988	2101	221457693	221458775	0.000000e+00	1358
8	TraesCS3B01G194600	chr3B	95.429	175	6	1	2094	2266	221466768	221466942	9.590000e-71	278
9	TraesCS3B01G194600	chr3B	91.176	136	9	2	2133	2266	221750207	221750341	7.740000e-42	182
10	TraesCS3B01G194600	chr3B	88.636	132	11	3	2137	2266	215114890	215115019	1.300000e-34	158
11	TraesCS3B01G194600	chr4A	97.352	1246	32	1	2265	3509	740774560	740773315	0.000000e+00	2117
12	TraesCS3B01G194600	chr5D	97.198	1249	32	3	2263	3509	233733830	233732583	0.000000e+00	2109
13	TraesCS3B01G194600	chr5D	97.120	1250	33	3	2263	3509	274779763	274781012	0.000000e+00	2106
14	TraesCS3B01G194600	chr1B	97.191	1246	34	1	2265	3509	328666686	328665441	0.000000e+00	2106
15	TraesCS3B01G194600	chr7A	97.113	1247	34	2	2265	3509	504210546	504211792	0.000000e+00	2102
16	TraesCS3B01G194600	chr4D	97.113	1247	34	2	2265	3509	469323635	469322389	0.000000e+00	2102
17	TraesCS3B01G194600	chr6B	97.111	1246	35	1	2265	3509	662212385	662213630	0.000000e+00	2100
18	TraesCS3B01G194600	chr3D	97.040	1250	34	3	2262	3509	520593374	520592126	0.000000e+00	2100
19	TraesCS3B01G194600	chr3D	91.228	1026	65	8	1053	2056	149204949	149205971	0.000000e+00	1373
20	TraesCS3B01G194600	chr3D	91.033	1026	67	8	1053	2056	147336153	147335131	0.000000e+00	1362
21	TraesCS3B01G194600	chr3D	90.962	1029	65	9	1053	2056	149544110	149545135	0.000000e+00	1360
22	TraesCS3B01G194600	chr3D	86.987	999	82	22	1149	2111	149769974	149768988	0.000000e+00	1081
23	TraesCS3B01G194600	chr3A	88.259	1252	95	23	1053	2266	166923328	166924565	0.000000e+00	1450
24	TraesCS3B01G194600	chr3A	88.878	1007	86	10	1148	2137	159831982	159832979	0.000000e+00	1216
25	TraesCS3B01G194600	chr1D	93.245	977	51	11	1	972	464380749	464379783	0.000000e+00	1424
26	TraesCS3B01G194600	chr2B	92.886	984	55	11	1	971	51995593	51994612	0.000000e+00	1415
27	TraesCS3B01G194600	chr2B	92.938	977	54	9	1	973	489314982	489315947	0.000000e+00	1408
28	TraesCS3B01G194600	chr2B	93.004	972	52	13	1	968	701508459	701509418	0.000000e+00	1404
29	TraesCS3B01G194600	chr2B	92.653	980	60	9	4	978	773167323	773166351	0.000000e+00	1400
30	TraesCS3B01G194600	chr7B	93.004	972	56	10	1	962	639081473	639080504	0.000000e+00	1408
31	TraesCS3B01G194600	chr7B	92.559	981	61	9	1	972	38918710	38919687	0.000000e+00	1397
32	TraesCS3B01G194600	chr2D	92.441	979	62	8	1	971	286285556	286284582	0.000000e+00	1387

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	TraesCS3B01G194600	chr3B	215309394	215312902	3508	False	6481	6481	100.000	1	3509	1	chr3B.!!$F3	3508
1	TraesCS3B01G194600	chr3B	773419788	773421037	1249	True	2130	2130	97.440	2261	3509	1	chr3B.!!$R2	1248
2	TraesCS3B01G194600	chr3B	221912277	221913579	1302	False	2039	2039	95.023	971	2266	1	chr3B.!!$F8	1295
3	TraesCS3B01G194600	chr3B	221979757	221981049	1292	False	1997	1997	94.564	971	2266	1	chr3B.!!$F9	1295
4	TraesCS3B01G194600	chr3B	215384992	215386297	1305	False	1949	1949	93.750	971	2266	1	chr3B.!!$F4	1295
5	TraesCS3B01G194600	chr3B	215104600	215105683	1083	False	1437	1437	90.659	974	2058	1	chr3B.!!$F1	1084
6	TraesCS3B01G194600	chr3B	89378239	89379221	982	True	1400	1400	92.596	1	972	1	chr3B.!!$R1	971
7	TraesCS3B01G194600	chr3B	221457693	221458775	1082	False	1358	1358	89.235	988	2101	1	chr3B.!!$F5	1113
8	TraesCS3B01G194600	chr4A	740773315	740774560	1245	True	2117	2117	97.352	2265	3509	1	chr4A.!!$R1	1244
9	TraesCS3B01G194600	chr5D	233732583	233733830	1247	True	2109	2109	97.198	2263	3509	1	chr5D.!!$R1	1246
10	TraesCS3B01G194600	chr5D	274779763	274781012	1249	False	2106	2106	97.120	2263	3509	1	chr5D.!!$F1	1246
11	TraesCS3B01G194600	chr1B	328665441	328666686	1245	True	2106	2106	97.191	2265	3509	1	chr1B.!!$R1	1244
12	TraesCS3B01G194600	chr7A	504210546	504211792	1246	False	2102	2102	97.113	2265	3509	1	chr7A.!!$F1	1244
13	TraesCS3B01G194600	chr4D	469322389	469323635	1246	True	2102	2102	97.113	2265	3509	1	chr4D.!!$R1	1244
14	TraesCS3B01G194600	chr6B	662212385	662213630	1245	False	2100	2100	97.111	2265	3509	1	chr6B.!!$F1	1244
15	TraesCS3B01G194600	chr3D	520592126	520593374	1248	True	2100	2100	97.040	2262	3509	1	chr3D.!!$R3	1247
16	TraesCS3B01G194600	chr3D	149204949	149205971	1022	False	1373	1373	91.228	1053	2056	1	chr3D.!!$F1	1003
17	TraesCS3B01G194600	chr3D	147335131	147336153	1022	True	1362	1362	91.033	1053	2056	1	chr3D.!!$R1	1003
18	TraesCS3B01G194600	chr3D	149544110	149545135	1025	False	1360	1360	90.962	1053	2056	1	chr3D.!!$F2	1003
19	TraesCS3B01G194600	chr3D	149768988	149769974	986	True	1081	1081	86.987	1149	2111	1	chr3D.!!$R2	962
20	TraesCS3B01G194600	chr3A	166923328	166924565	1237	False	1450	1450	88.259	1053	2266	1	chr3A.!!$F2	1213
21	TraesCS3B01G194600	chr3A	159831982	159832979	997	False	1216	1216	88.878	1148	2137	1	chr3A.!!$F1	989
22	TraesCS3B01G194600	chr1D	464379783	464380749	966	True	1424	1424	93.245	1	972	1	chr1D.!!$R1	971
23	TraesCS3B01G194600	chr2B	51994612	51995593	981	True	1415	1415	92.886	1	971	1	chr2B.!!$R1	970
24	TraesCS3B01G194600	chr2B	489314982	489315947	965	False	1408	1408	92.938	1	973	1	chr2B.!!$F1	972
25	TraesCS3B01G194600	chr2B	701508459	701509418	959	False	1404	1404	93.004	1	968	1	chr2B.!!$F2	967
26	TraesCS3B01G194600	chr2B	773166351	773167323	972	True	1400	1400	92.653	4	978	1	chr2B.!!$R2	974
27	TraesCS3B01G194600	chr7B	639080504	639081473	969	True	1408	1408	93.004	1	962	1	chr7B.!!$R1	961
28	TraesCS3B01G194600	chr7B	38918710	38919687	977	False	1397	1397	92.559	1	972	1	chr7B.!!$F1	971
29	TraesCS3B01G194600	chr2D	286284582	286285556	974	True	1387	1387	92.441	1	971	1	chr2D.!!$R1	970

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
897	929	1.089920	CTGCGGGTTGAATTCTCTGG	58.91	55.0	7.05	0.00	0.00	3.86	F
1521	1587	1.179814	AGGGAACAAGAGACGCGTCT	61.18	55.0	39.89	39.89	43.78	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2018	2151	1.004918	GCAGTACCAGAAGCACGGT	60.005	57.895	0.00	0.00	39.41	4.83	R
2624	2807	1.444933	TGGATCCCACTTGTGGTCTT	58.555	50.000	17.35	3.09	0.00	3.01	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
214	236	3.963374	CTCTCCTCTCTCTCTCTCTCTCA	59.037	52.174	0.00	0.00	0.00	3.27
274	297	1.135575	CCTGCGACATTTTTCAGAGGC	60.136	52.381	0.00	0.00	0.00	4.70
300	327	9.142515	CATGCATGTGTAGTTATTGATGTTTTT	57.857	29.630	18.91	0.00	0.00	1.94
301	328	8.741101	TGCATGTGTAGTTATTGATGTTTTTC	57.259	30.769	0.00	0.00	0.00	2.29
303	330	8.853345	GCATGTGTAGTTATTGATGTTTTTCTG	58.147	33.333	0.00	0.00	0.00	3.02
684	713	7.767198	TCAGAGTAACGGTTTAAAAGATATGGG	59.233	37.037	0.00	0.00	0.00	4.00
747	777	6.542370	CGGATGAATTACCTAAAACATCAGGT	59.458	38.462	0.00	0.00	46.88	4.00
748	778	7.067008	CGGATGAATTACCTAAAACATCAGGTT	59.933	37.037	0.00	0.00	42.68	3.50
828	859	5.867903	TGATTTCAACAAAACACTGGGAT	57.132	34.783	0.00	0.00	0.00	3.85
841	872	7.603963	AAACACTGGGATTTTTGTGTAAAAC	57.396	32.000	0.00	0.00	41.97	2.43
897	929	1.089920	CTGCGGGTTGAATTCTCTGG	58.910	55.000	7.05	0.00	0.00	3.86
941	973	3.003394	TGCCATGACGGATGAAAGAAT	57.997	42.857	0.00	0.00	36.56	2.40
1032	1073	3.672241	GCGCCAACTATTGTTCCGAAAAT	60.672	43.478	0.00	0.00	33.52	1.82
1048	1089	5.173774	CGAAAATCATCGGATTGGATTGT	57.826	39.130	4.80	0.32	42.87	2.71
1049	1090	5.581605	CGAAAATCATCGGATTGGATTGTT	58.418	37.500	4.80	3.03	42.87	2.83
1065	1106	4.968719	GGATTGTTGGGATTTAAAGGGGAT	59.031	41.667	0.00	0.00	0.00	3.85
1072	1113	3.222603	GGATTTAAAGGGGATGACGCAT	58.777	45.455	0.00	0.00	33.80	4.73
1076	1117	1.910580	AAAGGGGATGACGCATCGGT	61.911	55.000	11.83	0.00	41.35	4.69
1133	1174	1.502163	GATCTTCGCCGCCCATCTTG	61.502	60.000	0.00	0.00	0.00	3.02
1160	1226	1.299648	CCCCCATCTCGAGTTTGCA	59.700	57.895	13.13	0.00	0.00	4.08
1397	1463	1.392589	CTGTGCTGACCCAGTTTTGT	58.607	50.000	0.00	0.00	33.43	2.83
1521	1587	1.179814	AGGGAACAAGAGACGCGTCT	61.180	55.000	39.89	39.89	43.78	4.18
1601	1667	1.453155	GCTTCAAGGGCATCGAGAAA	58.547	50.000	0.00	0.00	0.00	2.52
1873	1957	2.281761	CCTTTGCGGTGGCTCACT	60.282	61.111	5.48	0.00	40.82	3.41
1978	2108	2.124983	GCCGATCCAGCAGAAGCA	60.125	61.111	0.00	0.00	45.49	3.91
2040	2173	2.047274	GCTTCTGGTACTGCGGCA	60.047	61.111	1.29	1.29	0.00	5.69
2104	2237	4.988598	CGGCAACTGGACGCTGGT	62.989	66.667	0.00	0.00	43.96	4.00
2111	2244	2.927856	TGGACGCTGGTCATGGGT	60.928	61.111	0.00	0.00	45.28	4.51
2154	2332	2.356673	CAGTGTCGCTCAGCTGCA	60.357	61.111	9.47	0.00	0.00	4.41
2178	2356	2.700371	TGTTGATCGTCCTAGCCATCAT	59.300	45.455	0.00	0.00	0.00	2.45
2728	2911	4.261909	GGAGTGTCACCTCGAAAAGTAGAA	60.262	45.833	0.00	0.00	31.98	2.10
2729	2912	4.618965	AGTGTCACCTCGAAAAGTAGAAC	58.381	43.478	0.00	0.00	0.00	3.01
2730	2913	3.739810	GTGTCACCTCGAAAAGTAGAACC	59.260	47.826	0.00	0.00	0.00	3.62
2873	3056	3.431415	AGTTCTTTCCATACCTTTGCCC	58.569	45.455	0.00	0.00	0.00	5.36
3017	3200	4.703897	TGTCTTCGTTGTCAATTCCTCTT	58.296	39.130	0.00	0.00	0.00	2.85
3273	3456	1.526887	CCTTGGAAGCGGCCATCTA	59.473	57.895	2.24	0.00	37.86	1.98
3305	3488	2.047061	AGCCGGCAATTGTCTCCTATA	58.953	47.619	31.54	0.00	0.00	1.31
3346	3529	3.214696	AGAACCCACCAATAGCATAGC	57.785	47.619	0.00	0.00	0.00	2.97
3347	3530	2.509548	AGAACCCACCAATAGCATAGCA	59.490	45.455	0.00	0.00	0.00	3.49
3432	3615	1.303561	TGGTGCATCCCTCACTTGC	60.304	57.895	0.00	0.00	34.97	4.01
3452	3635	2.672651	CATGGCCGCACTCCAACA	60.673	61.111	0.00	0.00	37.13	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
274	297	8.692110	AAAACATCAATAACTACACATGCATG	57.308	30.769	25.09	25.09	0.00	4.06
300	327	6.729100	CCCCACTATAACAATATAGGGACAGA	59.271	42.308	6.68	0.00	44.92	3.41
301	328	6.500751	ACCCCACTATAACAATATAGGGACAG	59.499	42.308	6.68	0.00	44.92	3.51
303	330	6.271624	ACACCCCACTATAACAATATAGGGAC	59.728	42.308	6.68	0.00	44.92	4.46
660	689	7.551617	CACCCATATCTTTTAAACCGTTACTCT	59.448	37.037	0.00	0.00	0.00	3.24
665	694	7.712204	AATCACCCATATCTTTTAAACCGTT	57.288	32.000	0.00	0.00	0.00	4.44
757	788	8.419442	ACACCCAAACCGTTATTTTACATTTTA	58.581	29.630	0.00	0.00	0.00	1.52
823	854	8.792830	TTTTCATGTTTTACACAAAAATCCCA	57.207	26.923	0.00	0.00	39.50	4.37
859	891	6.443792	CCGCAGTCCTGTTTTAAGTTAAAAT	58.556	36.000	20.66	4.38	39.56	1.82
897	929	7.757173	GCATTTTTCAGAAAAGTCCCTCTATTC	59.243	37.037	8.34	0.00	38.09	1.75
1032	1073	2.240921	TCCCAACAATCCAATCCGATGA	59.759	45.455	0.00	0.00	0.00	2.92
1047	1088	3.380320	CGTCATCCCCTTTAAATCCCAAC	59.620	47.826	0.00	0.00	0.00	3.77
1048	1089	3.626930	CGTCATCCCCTTTAAATCCCAA	58.373	45.455	0.00	0.00	0.00	4.12
1049	1090	2.685522	GCGTCATCCCCTTTAAATCCCA	60.686	50.000	0.00	0.00	0.00	4.37
1065	1106	2.047655	GAACCCACCGATGCGTCA	60.048	61.111	6.75	0.00	0.00	4.35
1344	1410	2.599082	GACGAACATACCTGCGAAAGAG	59.401	50.000	0.00	0.00	0.00	2.85
1397	1463	1.335132	GGATGCCGGTGAGTTCCCTA	61.335	60.000	1.90	0.00	0.00	3.53
1501	1567	0.524862	GACGCGTCTCTTGTTCCCTA	59.475	55.000	31.12	0.00	0.00	3.53
1521	1587	3.529341	ATGTCACGACGGCCAAGCA	62.529	57.895	2.24	0.00	0.00	3.91
1669	1735	2.328099	GCTTCCTGCAGGTTGACCG	61.328	63.158	31.58	15.12	42.08	4.79
1962	2077	2.178890	GCTGCTTCTGCTGGATCGG	61.179	63.158	0.00	0.00	40.48	4.18
1978	2108	2.094675	GGTTGATTATGTGTGGCTGCT	58.905	47.619	0.00	0.00	0.00	4.24
2018	2151	1.004918	GCAGTACCAGAAGCACGGT	60.005	57.895	0.00	0.00	39.41	4.83
2040	2173	3.859414	GCCTCCTCTGCTCGCCAT	61.859	66.667	0.00	0.00	0.00	4.40
2101	2234	2.187958	CAGGAAGTAGACCCATGACCA	58.812	52.381	0.00	0.00	0.00	4.02
2104	2237	2.187958	CCACAGGAAGTAGACCCATGA	58.812	52.381	0.00	0.00	0.00	3.07
2111	2244	2.300152	CAGTTGCTCCACAGGAAGTAGA	59.700	50.000	0.00	0.00	32.08	2.59
2154	2332	1.899814	TGGCTAGGACGATCAACACTT	59.100	47.619	0.00	0.00	0.00	3.16
2412	2594	5.007724	GGCAAATACTAGAACCCTCAAATCG	59.992	44.000	0.00	0.00	0.00	3.34
2624	2807	1.444933	TGGATCCCACTTGTGGTCTT	58.555	50.000	17.35	3.09	0.00	3.01
2639	2822	2.290134	CCGATGGAGATGCTTGATGGAT	60.290	50.000	0.00	0.00	0.00	3.41
2835	3018	5.511386	AGAACTCATGGTGGAAGAGAAAT	57.489	39.130	0.00	0.00	33.69	2.17
2873	3056	4.128643	GAGAGGATGATCAAGCTCAAAGG	58.871	47.826	0.00	0.00	0.00	3.11
3017	3200	2.170166	GGACCACATGATGAAGGCAAA	58.830	47.619	0.00	0.00	0.00	3.68
3305	3488	8.303876	GGTTCTTATGTGATTTATGTGTGGTTT	58.696	33.333	0.00	0.00	0.00	3.27
3346	3529	9.333497	CTTCACTATTTTGATTATGTGTGTGTG	57.667	33.333	0.00	0.00	0.00	3.82
3347	3530	9.283768	TCTTCACTATTTTGATTATGTGTGTGT	57.716	29.630	0.00	0.00	0.00	3.72
3432	3615	3.626996	TTGGAGTGCGGCCATGGAG	62.627	63.158	18.40	9.81	34.90	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.