AutoCloner

Multiple sequence alignment - TraesCS1B01G245900

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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	TraesCS1B01G245900	chr1B	100.000	3128	0	0	1	3128	435164036	435160909	0.000000e+00	5777
1	TraesCS1B01G245900	chr1B	91.262	721	57	4	1	720	390703116	390703831	0.000000e+00	977
2	TraesCS1B01G245900	chr1B	90.833	720	59	5	1	720	679038714	679038002	0.000000e+00	957
3	TraesCS1B01G245900	chr1D	94.062	2442	98	19	723	3128	322280025	322277595	0.000000e+00	3663
4	TraesCS1B01G245900	chr1A	91.482	1444	61	14	789	2180	406176474	406175041	0.000000e+00	1929
5	TraesCS1B01G245900	chr1A	91.979	935	50	15	2204	3128	406174762	406173843	0.000000e+00	1288
6	TraesCS1B01G245900	chr1A	100.000	70	0	0	720	789	406176575	406176506	2.530000e-26	130
7	TraesCS1B01G245900	chr6B	90.055	724	62	9	1	720	527036706	527035989	0.000000e+00	929
8	TraesCS1B01G245900	chr2B	90.139	720	63	6	1	720	453657017	453656306	0.000000e+00	929
9	TraesCS1B01G245900	chr2B	88.472	720	72	6	1	720	681122250	681122958	0.000000e+00	859
10	TraesCS1B01G245900	chr3B	90.139	720	45	13	1	720	94876383	94877076	0.000000e+00	913
11	TraesCS1B01G245900	chrUn	89.043	721	70	7	1	720	153387314	153388026	0.000000e+00	885
12	TraesCS1B01G245900	chr3D	87.639	720	74	12	1	712	284993651	284994363	0.000000e+00	822
13	TraesCS1B01G245900	chr7A	86.288	722	80	13	1	720	652919152	652918448	0.000000e+00	767
14	TraesCS1B01G245900	chr5A	85.307	701	88	8	3	699	451011448	451012137	0.000000e+00	710
15	TraesCS1B01G245900	chr3A	90.909	55	5	0	1306	1360	690194620	690194566	1.200000e-09	75

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	TraesCS1B01G245900	chr1B	435160909	435164036	3127	True	5777.000000	5777	100.000	1	3128	1	chr1B.!!$R1	3127
1	TraesCS1B01G245900	chr1B	390703116	390703831	715	False	977.000000	977	91.262	1	720	1	chr1B.!!$F1	719
2	TraesCS1B01G245900	chr1B	679038002	679038714	712	True	957.000000	957	90.833	1	720	1	chr1B.!!$R2	719
3	TraesCS1B01G245900	chr1D	322277595	322280025	2430	True	3663.000000	3663	94.062	723	3128	1	chr1D.!!$R1	2405
4	TraesCS1B01G245900	chr1A	406173843	406176575	2732	True	1115.666667	1929	94.487	720	3128	3	chr1A.!!$R1	2408
5	TraesCS1B01G245900	chr6B	527035989	527036706	717	True	929.000000	929	90.055	1	720	1	chr6B.!!$R1	719
6	TraesCS1B01G245900	chr2B	453656306	453657017	711	True	929.000000	929	90.139	1	720	1	chr2B.!!$R1	719
7	TraesCS1B01G245900	chr2B	681122250	681122958	708	False	859.000000	859	88.472	1	720	1	chr2B.!!$F1	719
8	TraesCS1B01G245900	chr3B	94876383	94877076	693	False	913.000000	913	90.139	1	720	1	chr3B.!!$F1	719
9	TraesCS1B01G245900	chrUn	153387314	153388026	712	False	885.000000	885	89.043	1	720	1	chrUn.!!$F1	719
10	TraesCS1B01G245900	chr3D	284993651	284994363	712	False	822.000000	822	87.639	1	712	1	chr3D.!!$F1	711
11	TraesCS1B01G245900	chr7A	652918448	652919152	704	True	767.000000	767	86.288	1	720	1	chr7A.!!$R1	719
12	TraesCS1B01G245900	chr5A	451011448	451012137	689	False	710.000000	710	85.307	3	699	1	chr5A.!!$F1	696

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
456	467	0.759959	TTTGGAGGCCGACTGTGTTA	59.240	50.0	0.0	0.0	0.0	2.41	F
1666	1784	0.172578	CGACACGGAGAGCACCAATA	59.827	55.0	0.0	0.0	0.0	1.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2086	2207	1.135689	GGCATTGTCGTCGCTGAAAAT	60.136	47.619	0.0	0.0	0.00	1.82	R
2475	2867	0.249398	ACGGACTTGTGGGCAGTATC	59.751	55.000	0.0	0.0	27.16	2.24	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
272	274	2.202388	GATGTTCGACGCCGACGA	60.202	61.111	7.70	7.70	45.50	4.20
434	445	1.068885	TGCCGGCGAACAAAACTATTG	60.069	47.619	23.90	0.00	0.00	1.90
456	467	0.759959	TTTGGAGGCCGACTGTGTTA	59.240	50.000	0.00	0.00	0.00	2.41
515	528	1.911269	TGAACTAGGACCGCTGGCA	60.911	57.895	0.00	0.00	0.00	4.92
530	548	4.126524	GCATGAACTAGGCCGACC	57.873	61.111	0.00	0.00	0.00	4.79
531	549	1.883084	GCATGAACTAGGCCGACCG	60.883	63.158	0.00	0.00	42.76	4.79
552	573	6.158598	ACCGCTAGTATTTGAAACGTTCTTA	58.841	36.000	0.00	0.00	0.00	2.10
579	603	0.982852	ATGAAGGCGGACAGGATGGA	60.983	55.000	0.00	0.00	43.62	3.41
669	693	1.152756	GCCCTGCCCAAACGGATAT	60.153	57.895	0.00	0.00	0.00	1.63
921	1003	3.508793	CAGCATCAATCAAACCCTCACTT	59.491	43.478	0.00	0.00	0.00	3.16
1034	1119	0.322975	CTGCAGTGCAAGGTACCTCT	59.677	55.000	20.22	4.78	38.41	3.69
1109	1197	1.561542	TCCAGGCCTCCTTGATTTCTC	59.438	52.381	0.00	0.00	0.00	2.87
1620	1738	2.039084	AGAAGATCCCAACAAAGTCGCT	59.961	45.455	0.00	0.00	0.00	4.93
1666	1784	0.172578	CGACACGGAGAGCACCAATA	59.827	55.000	0.00	0.00	0.00	1.90
1776	1897	3.068881	CGGCAGGAGGAGAAACCA	58.931	61.111	0.00	0.00	42.04	3.67
1898	2019	1.009389	GTGCACGTCCTGAGCTACAC	61.009	60.000	0.00	0.00	34.96	2.90
1904	2025	0.905357	GTCCTGAGCTACACCATGGT	59.095	55.000	13.00	13.00	0.00	3.55
2049	2170	4.545706	CCTTGGGCGCCGCAGATA	62.546	66.667	22.54	4.05	0.00	1.98
2086	2207	1.572085	GCGCTACTCCTACGCCGATA	61.572	60.000	0.00	0.00	46.63	2.92
2133	2254	1.593787	CAGCGTGATGTGAGGGAGT	59.406	57.895	0.00	0.00	0.00	3.85
2143	2264	5.582665	GTGATGTGAGGGAGTTGTAAGAATC	59.417	44.000	0.00	0.00	0.00	2.52
2290	2680	5.438761	AAGCAGTTTGTAAGGTGACATTC	57.561	39.130	0.00	0.00	0.00	2.67
2291	2681	3.498397	AGCAGTTTGTAAGGTGACATTCG	59.502	43.478	0.00	0.00	0.00	3.34
2301	2692	2.139917	GGTGACATTCGTGTGCTTGTA	58.860	47.619	0.00	0.00	0.00	2.41
2337	2728	6.716934	TGTAAAATTGTTAAGGCAACCTGA	57.283	33.333	0.00	0.00	36.20	3.86
2354	2745	2.749621	CCTGACCATCAGTGCCTTTAAC	59.250	50.000	5.18	0.00	42.80	2.01
2390	2782	7.945134	TCTCTTTCCTCTTTTCATTTTCTTGG	58.055	34.615	0.00	0.00	0.00	3.61
2396	2788	7.885297	TCCTCTTTTCATTTTCTTGGTGTATG	58.115	34.615	0.00	0.00	0.00	2.39
2460	2852	4.863548	TGGCATGAATCCTGAATTTCTCT	58.136	39.130	0.00	0.00	0.00	3.10
2469	2861	6.830873	ATCCTGAATTTCTCTCAAACTTGG	57.169	37.500	0.00	0.00	0.00	3.61
2475	2867	6.757947	TGAATTTCTCTCAAACTTGGCAAAAG	59.242	34.615	0.00	0.00	0.00	2.27
2499	2896	0.394488	TGCCCACAAGTCCGTTCAAA	60.394	50.000	0.00	0.00	0.00	2.69
2503	2900	2.032924	CCCACAAGTCCGTTCAAAGAAC	59.967	50.000	0.00	0.00	0.00	3.01
2530	2928	3.599730	TTGTCATGAGCTCGTGATTCT	57.400	42.857	34.87	0.97	43.04	2.40
2602	3003	4.516698	GGTCAACATGTTCATGTCAAGACT	59.483	41.667	25.79	10.59	34.31	3.24
2616	3017	3.995199	TCAAGACTGACTTAACTGCCAG	58.005	45.455	0.00	0.00	37.03	4.85
2639	3040	5.068329	AGCTCCAAAAAGAAAAAGAGACTGG	59.932	40.000	0.00	0.00	0.00	4.00
2717	3118	3.005578	AGGACTGTAAAGACCGAAGTGAC	59.994	47.826	0.00	0.00	0.00	3.67
2723	3124	1.512926	AAGACCGAAGTGACACATGC	58.487	50.000	8.59	0.00	0.00	4.06
2762	3163	3.120991	CGAATCGAGACAACACTTTCCAC	60.121	47.826	0.00	0.00	0.00	4.02
2785	3186	5.410746	ACGCATTAACCTGATCATGATCATC	59.589	40.000	32.96	12.83	45.74	2.92
2843	3244	4.793216	CCCTCTTAATTCATTTTTCGTGCG	59.207	41.667	0.00	0.00	0.00	5.34
2856	3257	0.105224	TCGTGCGTTCAGAAAAGGGA	59.895	50.000	0.00	0.00	0.00	4.20
2877	3278	3.477210	AACAAGAGAAGGCTCGAGTTT	57.523	42.857	15.13	9.12	45.98	2.66
2908	3309	2.950309	CTCTTCCTCATTGAATGGCCTG	59.050	50.000	3.32	0.00	0.00	4.85
2937	3338	0.687427	ACCACCCAGCAAAAGCAACT	60.687	50.000	0.00	0.00	0.00	3.16
3035	3436	1.725665	CATCTGCATGGCAAGACCG	59.274	57.895	0.00	0.00	43.94	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
434	445	0.804989	CACAGTCGGCCTCCAAAATC	59.195	55.000	0.00	0.00	0.00	2.17
456	467	3.437795	CTACACGTCCTCGCCGGT	61.438	66.667	1.90	0.00	41.18	5.28
494	507	1.585006	CAGCGGTCCTAGTTCACGT	59.415	57.895	0.00	0.00	0.00	4.49
515	528	0.754217	TAGCGGTCGGCCTAGTTCAT	60.754	55.000	3.66	0.00	45.17	2.57
528	546	4.563061	AGAACGTTTCAAATACTAGCGGT	58.437	39.130	0.46	0.00	0.00	5.68
529	547	5.526010	AAGAACGTTTCAAATACTAGCGG	57.474	39.130	0.46	0.00	0.00	5.52
530	548	8.985694	CAAATAAGAACGTTTCAAATACTAGCG	58.014	33.333	0.46	0.00	0.00	4.26
552	573	3.056607	CCTGTCCGCCTTCATTTTCAAAT	60.057	43.478	0.00	0.00	0.00	2.32
579	603	2.112815	GCGGCCGCATCCTTTTACT	61.113	57.895	43.55	0.00	41.49	2.24
624	648	2.682494	GTGTCCGGGCCTGTCCTA	60.682	66.667	11.58	0.00	34.39	2.94
669	693	2.730928	GACGTTCGTTTTGTCCGGATTA	59.269	45.455	7.81	0.00	0.00	1.75
921	1003	0.322322	AGTAACGCCGGATTGTTGGA	59.678	50.000	5.05	0.00	0.00	3.53
1034	1119	1.150536	GACAGTGCTGGGTTTGGGA	59.849	57.895	4.11	0.00	34.19	4.37
1109	1197	4.363990	ACCAGAGTCTGCACGCCG	62.364	66.667	15.10	2.50	0.00	6.46
1620	1738	4.415332	GGCTTCACGGTCTCGCGA	62.415	66.667	9.26	9.26	40.63	5.87
1735	1853	2.960688	GCTTCCGCTTCCTCTGGGT	61.961	63.158	0.00	0.00	0.00	4.51
2086	2207	1.135689	GGCATTGTCGTCGCTGAAAAT	60.136	47.619	0.00	0.00	0.00	1.82
2133	2254	8.570068	AATTAAGGTTAAGCCGATTCTTACAA	57.430	30.769	0.00	0.00	43.70	2.41
2143	2264	4.630940	TGACGGTAAATTAAGGTTAAGCCG	59.369	41.667	0.00	0.00	43.70	5.52
2290	2680	1.518325	TGGGTCATTACAAGCACACG	58.482	50.000	0.00	0.00	0.00	4.49
2291	2681	2.884639	AGTTGGGTCATTACAAGCACAC	59.115	45.455	0.00	0.00	0.00	3.82
2301	2692	9.892130	TTAACAATTTTACAAAGTTGGGTCATT	57.108	25.926	12.67	2.95	39.18	2.57
2337	2728	2.108250	ACCAGTTAAAGGCACTGATGGT	59.892	45.455	4.41	0.00	43.90	3.55
2354	2745	3.326297	AGAGGAAAGAGAAACCTGACCAG	59.674	47.826	0.00	0.00	33.89	4.00
2460	2852	4.870363	GCAGTATCTTTTGCCAAGTTTGA	58.130	39.130	0.00	0.00	34.28	2.69
2469	2861	2.558359	ACTTGTGGGCAGTATCTTTTGC	59.442	45.455	0.00	0.00	39.56	3.68
2475	2867	0.249398	ACGGACTTGTGGGCAGTATC	59.751	55.000	0.00	0.00	27.16	2.24
2484	2881	2.969055	CGTTCTTTGAACGGACTTGTG	58.031	47.619	20.74	0.00	39.73	3.33
2499	2896	3.006967	AGCTCATGACAAACTACCGTTCT	59.993	43.478	0.00	0.00	31.66	3.01
2503	2900	1.920574	CGAGCTCATGACAAACTACCG	59.079	52.381	15.40	0.00	0.00	4.02
2530	2928	4.299586	TCCAACCAACTCTCATGCAATA	57.700	40.909	0.00	0.00	0.00	1.90
2602	3003	1.055849	TGGAGCTGGCAGTTAAGTCA	58.944	50.000	17.16	4.41	0.00	3.41
2616	3017	5.284864	CCAGTCTCTTTTTCTTTTTGGAGC	58.715	41.667	0.00	0.00	0.00	4.70
2639	3040	8.289618	TGACATAAAACACTGATTCAGTTAAGC	58.710	33.333	16.64	2.67	42.59	3.09
2717	3118	1.469251	GGCAATCAGAAGCAGCATGTG	60.469	52.381	0.00	0.00	39.31	3.21
2723	3124	1.660167	TCGATGGCAATCAGAAGCAG	58.340	50.000	1.12	0.00	32.61	4.24
2843	3244	6.451064	TTCTCTTGTTTCCCTTTTCTGAAC	57.549	37.500	0.00	0.00	0.00	3.18
2856	3257	3.477210	AACTCGAGCCTTCTCTTGTTT	57.523	42.857	13.61	0.00	37.19	2.83
2877	3278	2.381752	TGAGGAAGAGGACAGTGTCA	57.618	50.000	24.20	0.00	33.68	3.58
2908	3309	1.302832	CTGGGTGGTTGCTCTGGTC	60.303	63.158	0.00	0.00	0.00	4.02
2937	3338	3.334691	CGTGCCAAAAGGTGAATCTAGA	58.665	45.455	0.00	0.00	0.00	2.43
3016	3417	1.436336	GGTCTTGCCATGCAGATGC	59.564	57.895	0.00	0.00	40.61	3.91
3017	3418	1.721664	CCGGTCTTGCCATGCAGATG	61.722	60.000	0.00	0.00	40.61	2.90
3018	3419	1.452651	CCGGTCTTGCCATGCAGAT	60.453	57.895	0.00	0.00	40.61	2.90
3019	3420	2.046023	CCGGTCTTGCCATGCAGA	60.046	61.111	0.00	0.00	40.61	4.26
3020	3421	3.818787	GCCGGTCTTGCCATGCAG	61.819	66.667	1.90	0.00	40.61	4.41
3061	3462	2.172082	CTCTGGTCATGGTCATGGTCAT	59.828	50.000	10.61	0.00	39.24	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.