AutoCloner

Multiple sequence alignment - TraesCS2A01G174700

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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	TraesCS2A01G174700	chr2A	100.000	1854	0	0	831	2684	133472924	133474777	0.000000e+00	3424.0
1	TraesCS2A01G174700	chr2A	100.000	420	0	0	1	420	133472094	133472513	0.000000e+00	776.0
2	TraesCS2A01G174700	chr2A	76.024	659	124	26	1988	2631	133484893	133485532	7.220000e-81	311.0
3	TraesCS2A01G174700	chr2A	75.538	650	129	19	1025	1668	133484907	133485532	2.610000e-75	292.0
4	TraesCS2A01G174700	chr2A	92.857	56	2	2	20	74	562722191	562722137	2.220000e-11	80.5
5	TraesCS2A01G174700	chr2B	95.970	1861	63	8	832	2684	180539726	180541582	0.000000e+00	3011.0
6	TraesCS2A01G174700	chr2B	92.143	280	20	2	143	420	180539446	180539725	6.960000e-106	394.0
7	TraesCS2A01G174700	chr2B	75.806	682	129	23	1025	1698	180546256	180546909	2.010000e-81	313.0
8	TraesCS2A01G174700	chr2D	94.513	1877	65	13	832	2684	126946467	126948329	0.000000e+00	2861.0
9	TraesCS2A01G174700	chr2D	87.179	429	35	8	10	420	126946040	126946466	1.120000e-128	470.0
10	TraesCS2A01G174700	chr2D	77.143	770	110	41	1915	2658	126958540	126959269	1.170000e-103	387.0
11	TraesCS2A01G174700	chr2D	76.471	680	130	20	1025	1698	126958614	126959269	2.560000e-90	342.0
12	TraesCS2A01G174700	chr5B	89.231	65	7	0	10	74	704413852	704413916	6.160000e-12	82.4
13	TraesCS2A01G174700	chr6B	84.932	73	11	0	7	79	719741667	719741739	1.030000e-09	75.0

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	TraesCS2A01G174700	chr2A	133472094	133474777	2683	False	2100.0	3424	100.0000	1	2684	2	chr2A.!!$F1	2683
1	TraesCS2A01G174700	chr2A	133484893	133485532	639	False	301.5	311	75.7810	1025	2631	2	chr2A.!!$F2	1606
2	TraesCS2A01G174700	chr2B	180539446	180541582	2136	False	1702.5	3011	94.0565	143	2684	2	chr2B.!!$F2	2541
3	TraesCS2A01G174700	chr2B	180546256	180546909	653	False	313.0	313	75.8060	1025	1698	1	chr2B.!!$F1	673
4	TraesCS2A01G174700	chr2D	126946040	126948329	2289	False	1665.5	2861	90.8460	10	2684	2	chr2D.!!$F1	2674
5	TraesCS2A01G174700	chr2D	126958540	126959269	729	False	364.5	387	76.8070	1025	2658	2	chr2D.!!$F2	1633

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
41	42	0.109319	GCGCCGGTTTGTCAAATGAT	60.109	50.0	1.9	0.0	0.0	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1853	1915	1.453379	ACGGTCGATCGTCCCTGAT	60.453	57.895	19.89	6.13	39.34	2.9	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
41	42	0.109319	GCGCCGGTTTGTCAAATGAT	60.109	50.000	1.90	0.00	0.00	2.45
45	46	3.485216	CGCCGGTTTGTCAAATGATCTAC	60.485	47.826	1.90	0.00	0.00	2.59
50	51	5.390613	GGTTTGTCAAATGATCTACAACCG	58.609	41.667	0.40	0.00	31.92	4.44
52	53	3.006940	TGTCAAATGATCTACAACCGGC	58.993	45.455	0.00	0.00	0.00	6.13
53	54	2.030457	GTCAAATGATCTACAACCGGCG	59.970	50.000	0.00	0.00	0.00	6.46
73	75	2.561569	GCCTGAAGCGCTAAATAGGAA	58.438	47.619	24.61	1.94	0.00	3.36
84	86	2.083167	AAATAGGAAACGCCGTCGAA	57.917	45.000	0.00	0.00	43.43	3.71
93	95	2.490685	GCCGTCGAAGTCTCCCTC	59.509	66.667	0.00	0.00	0.00	4.30
94	96	3.066233	GCCGTCGAAGTCTCCCTCC	62.066	68.421	0.00	0.00	0.00	4.30
100	102	1.195115	CGAAGTCTCCCTCCATTCCA	58.805	55.000	0.00	0.00	0.00	3.53
101	103	1.555075	CGAAGTCTCCCTCCATTCCAA	59.445	52.381	0.00	0.00	0.00	3.53
103	105	3.549794	GAAGTCTCCCTCCATTCCAATG	58.450	50.000	0.00	0.00	36.17	2.82
130	132	7.120579	TGCCGACTAAGACATGTCAATAAAATT	59.879	33.333	27.02	13.12	33.18	1.82
138	140	8.451908	AGACATGTCAATAAAATTAGGTAGCC	57.548	34.615	27.02	0.00	0.00	3.93
139	141	8.275040	AGACATGTCAATAAAATTAGGTAGCCT	58.725	33.333	27.02	0.00	37.71	4.58
140	142	8.823220	ACATGTCAATAAAATTAGGTAGCCTT	57.177	30.769	0.00	0.00	34.61	4.35
141	143	9.255029	ACATGTCAATAAAATTAGGTAGCCTTT	57.745	29.630	0.00	0.00	34.61	3.11
167	185	8.095452	ACAAGATTATGGGCCTCTATATTAGG	57.905	38.462	4.53	0.40	37.17	2.69
261	281	5.221048	CGAGATTCCATTGGACCCAAAATAC	60.221	44.000	4.45	0.36	39.55	1.89
272	292	1.475213	CCCAAAATACGGAGGAGCCTC	60.475	57.143	8.03	8.03	42.04	4.70
400	421	4.394712	CTGACAGCGGACCCCACC	62.395	72.222	0.00	0.00	0.00	4.61
875	897	4.360405	CCCCCTCCCCCACGTTTG	62.360	72.222	0.00	0.00	0.00	2.93
900	924	0.399806	AGCTCCCTTCCATCTCTCCC	60.400	60.000	0.00	0.00	0.00	4.30
901	925	1.414866	GCTCCCTTCCATCTCTCCCC	61.415	65.000	0.00	0.00	0.00	4.81
902	926	0.766288	CTCCCTTCCATCTCTCCCCC	60.766	65.000	0.00	0.00	0.00	5.40
903	927	1.004758	CCCTTCCATCTCTCCCCCA	59.995	63.158	0.00	0.00	0.00	4.96
929	953	3.327404	TTCTTCCTCCCCACGCCC	61.327	66.667	0.00	0.00	0.00	6.13
956	980	1.306739	CCGGGACCTAGGGTTTCCT	60.307	63.158	14.81	0.00	46.96	3.36
1323	1358	3.790437	CTCTCCATGCGCCAGGGT	61.790	66.667	14.36	0.00	36.61	4.34
1644	1691	6.016610	AGTCGGAGATATTAGAGAGCTTTGAC	60.017	42.308	0.00	0.00	40.67	3.18
1654	1701	3.286751	GCTTTGACACGCCCAGCA	61.287	61.111	0.00	0.00	0.00	4.41
1684	1731	3.172050	CCATCGTTCGACTACAAGTGAG	58.828	50.000	0.00	0.00	0.00	3.51
1795	1855	5.914898	ATTTATTACTTGGTGTTGAGGCC	57.085	39.130	0.00	0.00	0.00	5.19
1868	1930	5.821470	TCCTTATATATCAGGGACGATCGAC	59.179	44.000	24.34	16.38	0.00	4.20
2093	2161	1.160137	CACTTTCTCAAGGGCCTTCG	58.840	55.000	17.86	12.36	33.82	3.79
2156	2224	3.664025	CTCGCATGAACGCCCCTCA	62.664	63.158	0.00	0.00	0.00	3.86
2163	2231	3.952628	GAACGCCCCTCAACTCGGG	62.953	68.421	0.00	0.00	42.82	5.14
2214	2282	1.669115	CACCTTCCACTGCACCTCG	60.669	63.158	0.00	0.00	0.00	4.63
2266	2334	2.043604	CTCCATCATAGGTGGCGCCA	62.044	60.000	29.03	29.03	40.61	5.69
2388	2456	3.053291	GCCAACCGATTCGCACCA	61.053	61.111	0.00	0.00	0.00	4.17
2500	2571	2.607750	TGTCCCCTGCAGAGGTCC	60.608	66.667	17.39	7.52	37.73	4.46
2501	2572	3.403558	GTCCCCTGCAGAGGTCCC	61.404	72.222	17.39	0.12	37.73	4.46
2541	2612	1.903404	CTGGTTTGGCGGCCTCTTT	60.903	57.895	21.46	0.00	0.00	2.52
2608	2679	4.932799	CGGAGATATTAGAGAGCTTCGAGA	59.067	45.833	0.00	0.00	29.29	4.04

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.801574	ACCCCTACCCCTTGTTAGGA	59.198	55.000	0.00	0.00	45.05	2.94
1	2	0.916809	CACCCCTACCCCTTGTTAGG	59.083	60.000	0.00	0.00	41.60	2.69
5	6	2.535331	GCACACCCCTACCCCTTGT	61.535	63.158	0.00	0.00	0.00	3.16
6	7	2.355115	GCACACCCCTACCCCTTG	59.645	66.667	0.00	0.00	0.00	3.61
33	34	2.276201	CGCCGGTTGTAGATCATTTGA	58.724	47.619	1.90	0.00	0.00	2.69
41	42	2.501223	CTTCAGGCGCCGGTTGTAGA	62.501	60.000	26.04	11.10	0.00	2.59
53	54	2.240493	TCCTATTTAGCGCTTCAGGC	57.760	50.000	18.68	0.00	37.64	4.85
66	68	1.067354	ACTTCGACGGCGTTTCCTATT	60.067	47.619	16.19	0.00	38.98	1.73
73	75	2.257676	GGAGACTTCGACGGCGTT	59.742	61.111	16.19	0.00	38.98	4.84
84	86	2.240667	CACATTGGAATGGAGGGAGACT	59.759	50.000	4.45	0.00	40.70	3.24
93	95	2.036958	TAGTCGGCACATTGGAATGG	57.963	50.000	4.45	0.00	40.70	3.16
94	96	3.063997	GTCTTAGTCGGCACATTGGAATG	59.936	47.826	0.00	0.00	42.10	2.67
100	102	3.262420	GACATGTCTTAGTCGGCACATT	58.738	45.455	18.83	0.00	0.00	2.71
101	103	2.233676	TGACATGTCTTAGTCGGCACAT	59.766	45.455	25.55	0.00	37.58	3.21
103	105	2.363788	TGACATGTCTTAGTCGGCAC	57.636	50.000	25.55	0.00	37.58	5.01
130	132	6.465321	GCCCATAATCTTGTAAAGGCTACCTA	60.465	42.308	0.00	0.00	46.24	3.08
132	134	4.519350	GCCCATAATCTTGTAAAGGCTACC	59.481	45.833	0.00	0.00	46.24	3.18
133	135	4.519350	GGCCCATAATCTTGTAAAGGCTAC	59.481	45.833	0.00	0.00	46.24	3.58
134	136	4.415512	AGGCCCATAATCTTGTAAAGGCTA	59.584	41.667	0.00	0.00	46.24	3.93
135	137	3.205282	AGGCCCATAATCTTGTAAAGGCT	59.795	43.478	0.00	0.00	46.24	4.58
136	138	3.566351	AGGCCCATAATCTTGTAAAGGC	58.434	45.455	0.00	0.00	46.24	4.35
137	139	5.053978	AGAGGCCCATAATCTTGTAAAGG	57.946	43.478	0.00	0.00	46.24	3.11
141	143	9.213777	CCTAATATAGAGGCCCATAATCTTGTA	57.786	37.037	0.00	0.00	0.00	2.41
187	205	8.487313	TCATTGTATAAAAGTGTTGCGTCTAT	57.513	30.769	0.00	0.00	0.00	1.98
191	209	6.554334	ACTCATTGTATAAAAGTGTTGCGT	57.446	33.333	0.00	0.00	0.00	5.24
192	210	7.514805	TGTACTCATTGTATAAAAGTGTTGCG	58.485	34.615	0.00	0.00	33.23	4.85
193	211	8.504005	ACTGTACTCATTGTATAAAAGTGTTGC	58.496	33.333	0.00	0.00	33.23	4.17
206	224	2.232941	CCGGGTACACTGTACTCATTGT	59.767	50.000	17.62	0.00	39.92	2.71
207	225	2.888594	CCGGGTACACTGTACTCATTG	58.111	52.381	17.62	3.44	0.00	2.82
261	281	3.302347	AACTTGCGAGGCTCCTCCG	62.302	63.158	9.32	0.00	39.77	4.63
272	292	0.315059	GTGTGTGTCACGAACTTGCG	60.315	55.000	0.00	0.00	37.14	4.85
400	421	1.284297	GGTTTACGTGTTCCCGTCGG	61.284	60.000	3.60	3.60	42.00	4.79
830	851	1.675641	GCCGTGGCTGGATCTTGTT	60.676	57.895	2.98	0.00	38.26	2.83
842	863	1.313091	GGGGAGCTTTTTAGCCGTGG	61.313	60.000	0.00	0.00	34.90	4.94
900	924	1.004862	GAGGAAGAAGAAAGGGGTGGG	59.995	57.143	0.00	0.00	0.00	4.61
901	925	1.004862	GGAGGAAGAAGAAAGGGGTGG	59.995	57.143	0.00	0.00	0.00	4.61
902	926	1.004862	GGGAGGAAGAAGAAAGGGGTG	59.995	57.143	0.00	0.00	0.00	4.61
903	927	1.373536	GGGAGGAAGAAGAAAGGGGT	58.626	55.000	0.00	0.00	0.00	4.95
986	1018	2.506061	CCCATCTCCTCCTCCTGCG	61.506	68.421	0.00	0.00	0.00	5.18
1524	1568	3.827898	GAGCTCCCGACCTCCACG	61.828	72.222	0.87	0.00	0.00	4.94
1613	1660	3.483421	TCTAATATCTCCGACTTGCCGA	58.517	45.455	0.00	0.00	0.00	5.54
1644	1691	3.076258	TATCGGAGTGCTGGGCGTG	62.076	63.158	0.00	0.00	0.00	5.34
1795	1855	2.101770	GACTCCTAACCGCGGACG	59.898	66.667	35.90	18.67	39.67	4.79
1853	1915	1.453379	ACGGTCGATCGTCCCTGAT	60.453	57.895	19.89	6.13	39.34	2.90
1854	1916	2.045634	ACGGTCGATCGTCCCTGA	60.046	61.111	19.89	0.00	39.34	3.86
2093	2161	1.800681	GCACCATTGGGCGAGTTAC	59.199	57.895	7.78	0.00	37.90	2.50
2163	2231	2.270986	CCACACAGCAAAGCTCCCC	61.271	63.158	0.00	0.00	36.40	4.81
2190	2258	1.963515	GTGCAGTGGAAGGTGGAAAAT	59.036	47.619	0.00	0.00	0.00	1.82
2266	2334	0.545548	GAGAGAACCCCTCCAGTGGT	60.546	60.000	9.54	0.00	42.97	4.16
2278	2346	1.817099	CCTGCCGCATGGAGAGAAC	60.817	63.158	0.00	0.00	37.49	3.01
2299	2367	1.001641	AGCGGCCAGAAGCTTTGAT	60.002	52.632	2.24	0.00	41.52	2.57
2327	2395	3.799755	CGAGGAAAAAGCCGCCCG	61.800	66.667	0.00	0.00	0.00	6.13
2379	2447	0.745845	GGAGCATCTGTGGTGCGAAT	60.746	55.000	0.00	0.00	46.86	3.34
2412	2480	0.466007	CGGCCATGTTGGGATCATCA	60.466	55.000	2.24	0.00	38.19	3.07
2436	2504	0.179026	CACCTCCTCCCGTCGAGATA	60.179	60.000	0.00	0.00	41.63	1.98
2444	2512	3.787001	GGAAGCCACCTCCTCCCG	61.787	72.222	0.00	0.00	0.00	5.14
2500	2571	2.435586	CCCACTGCTTGAGCTCGG	60.436	66.667	9.64	5.68	42.66	4.63
2501	2572	2.435586	CCCCACTGCTTGAGCTCG	60.436	66.667	9.64	0.00	42.66	5.03
2541	2612	2.030027	TCTTCTCCTCCTTCTTGCCA	57.970	50.000	0.00	0.00	0.00	4.92
2575	2646	4.152647	TCTAATATCTCCGACATGCCAGT	58.847	43.478	0.00	0.00	0.00	4.00
2608	2679	4.853142	TATCGGAGGGCTGGGCGT	62.853	66.667	0.00	0.00	0.00	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.