AutoCloner

Multiple sequence alignment - TraesCS7D01G184400

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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	TraesCS7D01G184400	chr7D	100.000	2632	0	0	1	2632	137902338	137899707	0.000000e+00	4861.0
1	TraesCS7D01G184400	chr7D	98.611	648	9	0	1	648	528900458	528901105	0.000000e+00	1147.0
2	TraesCS7D01G184400	chr7A	91.779	1265	43	22	644	1877	137917093	137915859	0.000000e+00	1703.0
3	TraesCS7D01G184400	chr7A	95.086	407	17	3	2228	2632	137914485	137914080	2.860000e-179	638.0
4	TraesCS7D01G184400	chr7A	81.513	119	20	1	1922	2038	56241862	56241980	2.160000e-16	97.1
5	TraesCS7D01G184400	chr7B	89.971	1017	47	26	646	1645	103303813	103302835	0.000000e+00	1262.0
6	TraesCS7D01G184400	chr7B	89.023	665	54	12	1972	2632	103301593	103300944	0.000000e+00	806.0
7	TraesCS7D01G184400	chr7B	92.582	337	21	3	1646	1982	103302797	103302465	5.090000e-132	481.0
8	TraesCS7D01G184400	chr3D	97.696	651	15	0	1	651	49212001	49211351	0.000000e+00	1120.0
9	TraesCS7D01G184400	chr3D	90.762	433	39	1	1	433	319439215	319438784	6.320000e-161	577.0
10	TraesCS7D01G184400	chr3D	88.934	244	18	8	410	647	319438873	319438633	2.560000e-75	292.0
11	TraesCS7D01G184400	chr2B	92.381	630	46	2	23	651	446852752	446853380	0.000000e+00	896.0
12	TraesCS7D01G184400	chr2B	94.816	463	18	3	1	459	24030078	24029618	0.000000e+00	717.0
13	TraesCS7D01G184400	chr2B	96.875	320	8	1	1	318	24015684	24016003	3.860000e-148	534.0
14	TraesCS7D01G184400	chr2B	96.562	320	9	1	1	318	23991215	23990896	1.790000e-146	529.0
15	TraesCS7D01G184400	chr2B	98.131	214	4	0	435	648	24029686	24029473	8.900000e-100	374.0
16	TraesCS7D01G184400	chr6A	93.435	457	25	3	1	454	60377867	60378321	0.000000e+00	673.0
17	TraesCS7D01G184400	chr6A	93.651	252	12	4	399	648	60378224	60378473	8.900000e-100	374.0
18	TraesCS7D01G184400	chrUn	75.150	499	72	35	153	647	80813355	80812905	1.240000e-43	187.0
19	TraesCS7D01G184400	chr5A	81.746	126	17	5	1911	2036	706053250	706053131	1.670000e-17	100.0

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	TraesCS7D01G184400	chr7D	137899707	137902338	2631	True	4861.000000	4861	100.000000	1	2632	1	chr7D.!!$R1	2631
1	TraesCS7D01G184400	chr7D	528900458	528901105	647	False	1147.000000	1147	98.611000	1	648	1	chr7D.!!$F1	647
2	TraesCS7D01G184400	chr7A	137914080	137917093	3013	True	1170.500000	1703	93.432500	644	2632	2	chr7A.!!$R1	1988
3	TraesCS7D01G184400	chr7B	103300944	103303813	2869	True	849.666667	1262	90.525333	646	2632	3	chr7B.!!$R1	1986
4	TraesCS7D01G184400	chr3D	49211351	49212001	650	True	1120.000000	1120	97.696000	1	651	1	chr3D.!!$R1	650
5	TraesCS7D01G184400	chr3D	319438633	319439215	582	True	434.500000	577	89.848000	1	647	2	chr3D.!!$R2	646
6	TraesCS7D01G184400	chr2B	446852752	446853380	628	False	896.000000	896	92.381000	23	651	1	chr2B.!!$F2	628
7	TraesCS7D01G184400	chr2B	24029473	24030078	605	True	545.500000	717	96.473500	1	648	2	chr2B.!!$R2	647
8	TraesCS7D01G184400	chr6A	60377867	60378473	606	False	523.500000	673	93.543000	1	648	2	chr6A.!!$F1	647

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
847	906	1.617804	CCTCCTCCACCACCGTTACTA	60.618	57.143	0.0	0.0	0.0	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2345	4574	0.036388	TCCCATCTGGTCAAAGCGTC	60.036	55.0	0.0	0.0	34.77	5.19	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
72	75	2.436824	GCTTGAACTCCCCCTCGC	60.437	66.667	0.00	0.00	0.00	5.03
419	423	2.283529	GCGTGGGTGAGAGGGAGAA	61.284	63.158	0.00	0.00	0.00	2.87
749	800	5.877564	GTCCTTTTATGGAGACTTCTTCCTG	59.122	44.000	0.00	0.00	36.69	3.86
750	801	5.045578	TCCTTTTATGGAGACTTCTTCCTGG	60.046	44.000	0.00	0.00	0.00	4.45
751	802	3.914426	TTATGGAGACTTCTTCCTGGC	57.086	47.619	0.00	0.00	0.00	4.85
752	803	1.963985	ATGGAGACTTCTTCCTGGCT	58.036	50.000	0.00	0.00	0.00	4.75
847	906	1.617804	CCTCCTCCACCACCGTTACTA	60.618	57.143	0.00	0.00	0.00	1.82
873	932	6.823689	TCAGGCCTTCTTGTTTATTGATCTAC	59.176	38.462	0.00	0.00	0.00	2.59
876	935	8.718656	AGGCCTTCTTGTTTATTGATCTACTAT	58.281	33.333	0.00	0.00	0.00	2.12
914	973	9.906660	CTACCTAAATCAGTTGCAATTAACAAA	57.093	29.630	0.59	0.00	33.02	2.83
915	974	8.587952	ACCTAAATCAGTTGCAATTAACAAAC	57.412	30.769	0.59	0.00	33.02	2.93
932	992	3.241701	CAAACGTCTTCTCTCTGCTCTC	58.758	50.000	0.00	0.00	0.00	3.20
1080	1144	0.754957	AGGTGCTCGAGAGGATCAGG	60.755	60.000	18.75	0.00	37.82	3.86
1116	1180	1.135141	GCGAGCTGTTCATGTCTCTCT	60.135	52.381	0.00	0.00	0.00	3.10
1140	1204	0.179032	TGCAACGAGGCTGAGGAAAA	60.179	50.000	0.00	0.00	34.04	2.29
1141	1205	0.951558	GCAACGAGGCTGAGGAAAAA	59.048	50.000	0.00	0.00	0.00	1.94
1571	1641	3.533105	ATGCCGCCGTCGTATCCA	61.533	61.111	0.00	0.00	0.00	3.41
1665	1772	6.710597	TCTAATTCCTCGTGTATAAGCACT	57.289	37.500	0.00	0.00	37.24	4.40
1669	1776	5.648178	TTCCTCGTGTATAAGCACTGTAA	57.352	39.130	0.00	0.00	37.24	2.41
1805	1912	3.367630	CCCGCTTTGTTTATGTTGCATTC	59.632	43.478	0.00	0.00	0.00	2.67
1874	1981	5.812127	GGTGTTCTCATTTTTCACTTTTGCT	59.188	36.000	0.00	0.00	0.00	3.91
1896	2003	2.969443	ACCTCATGCGTTCGAAAAAG	57.031	45.000	0.00	0.00	0.00	2.27
1916	2023	2.572104	AGGGTGTGTTTAGGATGGACTC	59.428	50.000	0.00	0.00	0.00	3.36
1982	2089	3.857665	TCTTCGCGTAAGATCAATGACAC	59.142	43.478	5.77	0.00	39.36	3.67
1983	2090	3.224884	TCGCGTAAGATCAATGACACA	57.775	42.857	5.77	0.00	43.02	3.72
1984	2091	3.580731	TCGCGTAAGATCAATGACACAA	58.419	40.909	5.77	0.00	43.02	3.33
1985	2092	3.991121	TCGCGTAAGATCAATGACACAAA	59.009	39.130	5.77	0.00	43.02	2.83
1990	2980	6.086765	GCGTAAGATCAATGACACAAAACTTG	59.913	38.462	0.00	0.00	43.02	3.16
1994	2984	6.684686	AGATCAATGACACAAAACTTGGATG	58.315	36.000	0.00	0.00	34.12	3.51
1996	2986	6.951062	TCAATGACACAAAACTTGGATGTA	57.049	33.333	0.00	0.00	34.12	2.29
2002	2992	8.402798	TGACACAAAACTTGGATGTACAATAT	57.597	30.769	0.00	0.00	34.12	1.28
2009	2999	9.816354	AAAACTTGGATGTACAATATTTATGGC	57.184	29.630	0.00	0.00	0.00	4.40
2011	3001	8.710749	ACTTGGATGTACAATATTTATGGCAT	57.289	30.769	4.88	4.88	0.00	4.40
2139	3564	2.281484	GCCGTGAACAAGCAGGGA	60.281	61.111	7.23	0.00	44.47	4.20
2154	3579	3.483869	GGAGCGAGCCCAAGGGAT	61.484	66.667	9.92	1.00	37.50	3.85
2155	3580	2.203126	GAGCGAGCCCAAGGGATG	60.203	66.667	9.92	0.00	37.50	3.51
2205	4432	3.891400	CGGCGGCACAATGATGGG	61.891	66.667	10.53	0.00	0.00	4.00
2212	4439	1.138036	CACAATGATGGGCAGCACG	59.862	57.895	0.00	0.00	0.00	5.34
2213	4440	2.048023	ACAATGATGGGCAGCACGG	61.048	57.895	0.00	0.00	0.00	4.94
2214	4441	2.440796	AATGATGGGCAGCACGGG	60.441	61.111	0.00	0.00	0.00	5.28
2366	4595	1.004745	ACGCTTTGACCAGATGGGAAT	59.995	47.619	3.48	0.00	41.15	3.01
2475	4705	1.706287	CTCCGTCGCACGAGATGAGA	61.706	60.000	9.75	0.00	46.05	3.27
2488	4718	0.721718	GATGAGAAAACAGGCCGTCG	59.278	55.000	0.00	0.00	0.00	5.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
396	400	4.379243	CTCTCACCCACGCGGCTT	62.379	66.667	12.47	0.00	33.26	4.35
619	666	6.881570	TCCCTCCGTAAACTTTTATAAGAGG	58.118	40.000	7.83	6.36	36.65	3.69
749	800	0.613012	AATGGGTGAGAAGCCAAGCC	60.613	55.000	0.10	0.00	0.00	4.35
750	801	1.260544	AAATGGGTGAGAAGCCAAGC	58.739	50.000	0.10	0.00	0.00	4.01
751	802	2.095059	CGAAAATGGGTGAGAAGCCAAG	60.095	50.000	0.10	0.00	0.00	3.61
752	803	1.885887	CGAAAATGGGTGAGAAGCCAA	59.114	47.619	0.10	0.00	0.00	4.52
847	906	6.430007	AGATCAATAAACAAGAAGGCCTGAT	58.570	36.000	5.69	0.00	0.00	2.90
914	973	1.271652	TGGAGAGCAGAGAGAAGACGT	60.272	52.381	0.00	0.00	0.00	4.34
915	974	1.401552	CTGGAGAGCAGAGAGAAGACG	59.598	57.143	0.00	0.00	0.00	4.18
932	992	5.344743	TTGTCTACCTTATCTTGCTCTGG	57.655	43.478	0.00	0.00	0.00	3.86
1080	1144	0.381801	TCGCGAGGAAATACGTACCC	59.618	55.000	3.71	0.00	0.00	3.69
1116	1180	0.390340	CTCAGCCTCGTTGCAGCTAA	60.390	55.000	0.00	0.00	34.38	3.09
1140	1204	3.575687	CCCTTCTCTGCAACCAAAGATTT	59.424	43.478	0.00	0.00	0.00	2.17
1141	1205	3.160269	CCCTTCTCTGCAACCAAAGATT	58.840	45.455	0.00	0.00	0.00	2.40
1419	1483	3.365265	CTCCACAACCTTGGGCGC	61.365	66.667	0.00	0.00	37.24	6.53
1571	1641	1.962822	CATCATGTAGCCGCCGCAT	60.963	57.895	0.00	0.00	37.52	4.73
1665	1772	0.917939	CGTACATGCGCATCGTTACA	59.082	50.000	22.51	4.98	0.00	2.41
1669	1776	1.876714	GGTCGTACATGCGCATCGT	60.877	57.895	22.51	22.63	0.00	3.73
1747	1854	0.596577	TGACGTCTTCCTCCTCGTTG	59.403	55.000	17.92	0.00	36.67	4.10
1874	1981	4.319911	CCTTTTTCGAACGCATGAGGTTTA	60.320	41.667	0.00	0.00	0.00	2.01
1896	2003	2.304761	TGAGTCCATCCTAAACACACCC	59.695	50.000	0.00	0.00	0.00	4.61
1965	2072	5.689819	AGTTTTGTGTCATTGATCTTACGC	58.310	37.500	0.00	0.00	0.00	4.42
1977	2084	6.707440	ATTGTACATCCAAGTTTTGTGTCA	57.293	33.333	0.00	0.00	0.00	3.58
1983	2090	9.816354	GCCATAAATATTGTACATCCAAGTTTT	57.184	29.630	0.00	0.00	0.00	2.43
1984	2091	8.976353	TGCCATAAATATTGTACATCCAAGTTT	58.024	29.630	0.00	0.00	0.00	2.66
1985	2092	8.532186	TGCCATAAATATTGTACATCCAAGTT	57.468	30.769	0.00	0.00	0.00	2.66
2022	3012	8.825667	TTTTTCTCAAACAGTTTTGCTAAAGT	57.174	26.923	0.00	0.00	41.78	2.66
2048	3038	2.190981	GAAATGGACTAACGCGACGAT	58.809	47.619	15.93	0.00	0.00	3.73
2051	3041	1.060698	GCTGAAATGGACTAACGCGAC	59.939	52.381	15.93	0.00	0.00	5.19
2058	3048	0.744414	GGCTGCGCTGAAATGGACTA	60.744	55.000	19.32	0.00	0.00	2.59
2139	3564	1.639635	AATCATCCCTTGGGCTCGCT	61.640	55.000	0.00	0.00	0.00	4.93
2153	3578	6.548622	CCATCCATCTAAACCTGAACAATCAT	59.451	38.462	0.00	0.00	34.37	2.45
2154	3579	5.887598	CCATCCATCTAAACCTGAACAATCA	59.112	40.000	0.00	0.00	0.00	2.57
2155	3580	5.221126	GCCATCCATCTAAACCTGAACAATC	60.221	44.000	0.00	0.00	0.00	2.67
2189	4416	4.211502	GCCCATCATTGTGCCGCC	62.212	66.667	0.00	0.00	0.00	6.13
2192	4419	2.352821	TGCTGCCCATCATTGTGCC	61.353	57.895	0.00	0.00	0.00	5.01
2194	4421	1.138036	CGTGCTGCCCATCATTGTG	59.862	57.895	0.00	0.00	0.00	3.33
2197	4424	2.440796	CCCGTGCTGCCCATCATT	60.441	61.111	0.00	0.00	0.00	2.57
2218	4445	1.877165	GAACTACCACGCTAGCCGC	60.877	63.158	9.66	0.00	41.76	6.53
2219	4446	0.801067	GTGAACTACCACGCTAGCCG	60.801	60.000	9.66	7.08	44.21	5.52
2220	4447	3.046280	GTGAACTACCACGCTAGCC	57.954	57.895	9.66	0.00	0.00	3.93
2240	4467	1.544759	CCGCCCCTGTCTTTTGTAGTT	60.545	52.381	0.00	0.00	0.00	2.24
2243	4470	1.377229	CCCGCCCCTGTCTTTTGTA	59.623	57.895	0.00	0.00	0.00	2.41
2345	4574	0.036388	TCCCATCTGGTCAAAGCGTC	60.036	55.000	0.00	0.00	34.77	5.19
2349	4578	3.194116	CCACAATTCCCATCTGGTCAAAG	59.806	47.826	0.00	0.00	34.77	2.77
2475	4705	1.098712	TGAAAGCGACGGCCTGTTTT	61.099	50.000	0.00	0.74	41.24	2.43
2488	4718	1.815003	CTCCACAGGACCAATGAAAGC	59.185	52.381	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.