AutoCloner

Multiple sequence alignment - TraesCS3B01G151800

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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	TraesCS3B01G151800	chr3B	100.000	2000	0	0	1	2000	143572041	143570042	0.000000e+00	3694.0
1	TraesCS3B01G151800	chr3B	100.000	517	0	0	2262	2778	143569780	143569264	0.000000e+00	955.0
2	TraesCS3B01G151800	chr3B	86.141	736	89	10	962	1688	143556758	143557489	0.000000e+00	782.0
3	TraesCS3B01G151800	chr3B	95.434	438	19	1	2340	2777	754566602	754567038	0.000000e+00	697.0
4	TraesCS3B01G151800	chr3B	78.698	845	111	49	945	1756	143585754	143584946	1.490000e-137	499.0
5	TraesCS3B01G151800	chr3B	81.574	521	87	6	1167	1683	143506017	143506532	3.310000e-114	422.0
6	TraesCS3B01G151800	chr3B	87.037	216	27	1	1170	1384	143567958	143568173	2.760000e-60	243.0
7	TraesCS3B01G151800	chr3B	91.667	156	13	0	1189	1344	143523222	143523067	1.680000e-52	217.0
8	TraesCS3B01G151800	chr3D	94.156	2002	62	11	2	1954	92869798	92871793	0.000000e+00	2998.0
9	TraesCS3B01G151800	chr3D	93.636	440	26	2	2340	2777	29474871	29475310	0.000000e+00	656.0
10	TraesCS3B01G151800	chr3D	80.144	695	91	29	980	1653	92864759	92865427	2.500000e-130	475.0
11	TraesCS3B01G151800	chr3D	77.273	638	115	20	83	699	92856923	92857551	5.690000e-92	348.0
12	TraesCS3B01G151800	chr3D	89.189	259	19	6	1068	1323	92890973	92891225	5.780000e-82	315.0
13	TraesCS3B01G151800	chr3D	92.857	42	3	0	2300	2341	29472058	29472099	8.310000e-06	62.1
14	TraesCS3B01G151800	chr2B	96.347	438	16	0	2340	2777	161508376	161508813	0.000000e+00	721.0
15	TraesCS3B01G151800	chr2B	95.662	438	18	1	2340	2777	184881849	184882285	0.000000e+00	702.0
16	TraesCS3B01G151800	chr2B	94.292	438	22	2	2340	2777	797276315	797276749	0.000000e+00	667.0
17	TraesCS3B01G151800	chr2B	93.651	63	4	0	2279	2341	184880715	184880777	8.190000e-16	95.3
18	TraesCS3B01G151800	chr6B	96.119	438	16	1	2340	2777	682534954	682534518	0.000000e+00	713.0
19	TraesCS3B01G151800	chr6B	94.977	438	19	2	2340	2777	209584738	209584304	0.000000e+00	684.0
20	TraesCS3B01G151800	chr6B	95.000	80	4	0	2262	2341	209585887	209585808	2.900000e-25	126.0
21	TraesCS3B01G151800	chr6B	95.000	80	4	0	2262	2341	682536103	682536024	2.900000e-25	126.0
22	TraesCS3B01G151800	chrUn	94.977	438	21	1	2340	2777	124678649	124679085	0.000000e+00	686.0
23	TraesCS3B01G151800	chrUn	96.154	78	3	0	2264	2341	124677501	124677578	8.080000e-26	128.0
24	TraesCS3B01G151800	chr4B	94.292	438	22	2	2340	2777	522497574	522498008	0.000000e+00	667.0
25	TraesCS3B01G151800	chr4B	95.000	80	4	0	2262	2341	522496424	522496503	2.900000e-25	126.0
26	TraesCS3B01G151800	chr3A	81.305	797	101	29	980	1757	547193936	547194703	1.100000e-168	603.0
27	TraesCS3B01G151800	chr5A	95.062	81	3	1	2262	2341	535230761	535230681	2.900000e-25	126.0

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	TraesCS3B01G151800	chr3B	143569264	143572041	2777	True	2324.50	3694	100.0000	1	2778	2	chr3B.!!$R3	2777
1	TraesCS3B01G151800	chr3B	143556758	143557489	731	False	782.00	782	86.1410	962	1688	1	chr3B.!!$F2	726
2	TraesCS3B01G151800	chr3B	143584946	143585754	808	True	499.00	499	78.6980	945	1756	1	chr3B.!!$R2	811
3	TraesCS3B01G151800	chr3B	143506017	143506532	515	False	422.00	422	81.5740	1167	1683	1	chr3B.!!$F1	516
4	TraesCS3B01G151800	chr3D	92869798	92871793	1995	False	2998.00	2998	94.1560	2	1954	1	chr3D.!!$F3	1952
5	TraesCS3B01G151800	chr3D	92864759	92865427	668	False	475.00	475	80.1440	980	1653	1	chr3D.!!$F2	673
6	TraesCS3B01G151800	chr3D	29472058	29475310	3252	False	359.05	656	93.2465	2300	2777	2	chr3D.!!$F5	477
7	TraesCS3B01G151800	chr3D	92856923	92857551	628	False	348.00	348	77.2730	83	699	1	chr3D.!!$F1	616
8	TraesCS3B01G151800	chr2B	184880715	184882285	1570	False	398.65	702	94.6565	2279	2777	2	chr2B.!!$F3	498
9	TraesCS3B01G151800	chr6B	682534518	682536103	1585	True	419.50	713	95.5595	2262	2777	2	chr6B.!!$R2	515
10	TraesCS3B01G151800	chr6B	209584304	209585887	1583	True	405.00	684	94.9885	2262	2777	2	chr6B.!!$R1	515
11	TraesCS3B01G151800	chrUn	124677501	124679085	1584	False	407.00	686	95.5655	2264	2777	2	chrUn.!!$F1	513
12	TraesCS3B01G151800	chr4B	522496424	522498008	1584	False	396.50	667	94.6460	2262	2777	2	chr4B.!!$F1	515
13	TraesCS3B01G151800	chr3A	547193936	547194703	767	False	603.00	603	81.3050	980	1757	1	chr3A.!!$F1	777

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
936	981	0.109689	GTCACCGGTTCAGACTCGAG	60.11	60.0	11.84	11.84	0.0	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2414	5306	1.403814	CTCACCCTAGAGCCGATTGA	58.596	55.0	0.0	0.0	0.0	2.57	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	73	7.063801	TCCCATATATATCAACCTGACCCTA	57.936	40.000	0.00	0.00	0.00	3.53
287	288	1.376037	CTCGACCTGAAGCAACCCC	60.376	63.158	0.00	0.00	0.00	4.95
316	317	2.592861	GGCCATGCTTAGCCCGAG	60.593	66.667	0.29	0.00	43.76	4.63
386	387	1.282157	AGGCATGTCTTGGGGAAGTAC	59.718	52.381	0.00	0.00	0.00	2.73
432	433	1.556373	CCACACATCAGCCTCCCAGA	61.556	60.000	0.00	0.00	0.00	3.86
434	435	0.545171	ACACATCAGCCTCCCAGATG	59.455	55.000	0.00	0.00	43.56	2.90
533	561	0.179073	CCTCGATGCCGGTGATTTCT	60.179	55.000	1.90	0.00	36.24	2.52
610	650	2.932614	CGGACATAAGCAAGAGGAACAG	59.067	50.000	0.00	0.00	0.00	3.16
667	707	5.293560	CGGGTATTTGGCTTTCTTGAAAAA	58.706	37.500	0.00	0.00	0.00	1.94
828	873	3.694072	AGGAGAGAGACGAGTTGATCAAG	59.306	47.826	8.80	0.00	0.00	3.02
878	923	8.182881	CAGATTTCAGACTCCAATTCAAATCTC	58.817	37.037	0.00	0.00	37.12	2.75
921	966	1.451028	GCAGGCAGGGAGATGTCAC	60.451	63.158	0.00	0.00	0.00	3.67
936	981	0.109689	GTCACCGGTTCAGACTCGAG	60.110	60.000	11.84	11.84	0.00	4.04
948	993	6.347483	GGTTCAGACTCGAGTTTGTTTAATCC	60.347	42.308	29.00	17.20	32.61	3.01
1143	1207	2.708059	GAGCAGCAACGACGACGAC	61.708	63.158	15.32	3.02	42.66	4.34
1194	1258	0.874390	TGTGCCTTTTGCTCGTGATC	59.126	50.000	0.00	0.00	42.00	2.92
1257	1345	0.469331	ACTCGGTCCAGTTGACAGGA	60.469	55.000	0.00	0.00	46.38	3.86
1494	1582	2.161808	CGACGTGTCCTTGTCTAGTCAT	59.838	50.000	0.00	0.00	32.93	3.06
1536	1624	0.820226	TGCAGGAGAAGATGGAGTCG	59.180	55.000	0.00	0.00	0.00	4.18
1759	1860	7.264221	CACTCCTATCACCATAGATATTCAGC	58.736	42.308	0.00	0.00	34.82	4.26
1954	2068	3.319137	TCTCAACTTGATTCCCACTCG	57.681	47.619	0.00	0.00	0.00	4.18
1955	2069	1.734465	CTCAACTTGATTCCCACTCGC	59.266	52.381	0.00	0.00	0.00	5.03
1956	2070	1.347707	TCAACTTGATTCCCACTCGCT	59.652	47.619	0.00	0.00	0.00	4.93
1957	2071	2.565391	TCAACTTGATTCCCACTCGCTA	59.435	45.455	0.00	0.00	0.00	4.26
1958	2072	3.197766	TCAACTTGATTCCCACTCGCTAT	59.802	43.478	0.00	0.00	0.00	2.97
1959	2073	3.185246	ACTTGATTCCCACTCGCTATG	57.815	47.619	0.00	0.00	0.00	2.23
1960	2074	2.766263	ACTTGATTCCCACTCGCTATGA	59.234	45.455	0.00	0.00	0.00	2.15
1961	2075	3.197766	ACTTGATTCCCACTCGCTATGAA	59.802	43.478	0.00	0.00	0.00	2.57
1962	2076	3.459232	TGATTCCCACTCGCTATGAAG	57.541	47.619	0.00	0.00	0.00	3.02
1963	2077	2.139118	GATTCCCACTCGCTATGAAGC	58.861	52.381	0.00	0.00	45.86	3.86
1984	2098	9.542462	TGAAGCATGTTTATATACAGGTAGAAC	57.458	33.333	9.23	0.00	32.70	3.01
1985	2099	9.765795	GAAGCATGTTTATATACAGGTAGAACT	57.234	33.333	9.23	0.00	32.70	3.01
1986	2100	9.547753	AAGCATGTTTATATACAGGTAGAACTG	57.452	33.333	9.23	0.00	44.03	3.16
2532	5424	0.955428	GCTTGTCGACCTTGGCATGA	60.955	55.000	14.12	0.00	0.00	3.07
2688	5580	5.772672	TGTTTGCCTGTATCACAAATAGGTT	59.227	36.000	0.00	0.00	35.87	3.50
2735	5629	4.454504	TCTTTGCCGTTTCTGTTTCTATCC	59.545	41.667	0.00	0.00	0.00	2.59
2737	5631	4.811969	TGCCGTTTCTGTTTCTATCCTA	57.188	40.909	0.00	0.00	0.00	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.454795	TCTTTCTTTGTTGGTTAATCATGGC	58.545	36.000	0.00	0.00	0.00	4.40
8	9	9.750125	ACTGATTTCTTTCTTTGTTGGTTAATC	57.250	29.630	0.00	0.00	0.00	1.75
32	33	1.375268	GGAAGCGCTCTTGCAGACT	60.375	57.895	12.06	0.00	39.99	3.24
47	48	6.339220	AGGGTCAGGTTGATATATATGGGAA	58.661	40.000	0.00	0.00	0.00	3.97
48	49	5.927465	AGGGTCAGGTTGATATATATGGGA	58.073	41.667	0.00	0.00	0.00	4.37
49	50	7.937700	ATAGGGTCAGGTTGATATATATGGG	57.062	40.000	0.00	0.00	0.00	4.00
72	73	4.280929	TCCAAGAATGTGATCGATCGGTAT	59.719	41.667	20.03	11.21	0.00	2.73
100	101	7.757624	CAGAGACTAGTGATACAAGGTTCTTTC	59.242	40.741	0.00	0.00	0.00	2.62
316	317	3.164011	CGACGTCGACCGACTTGC	61.164	66.667	33.35	8.11	42.54	4.01
416	417	0.179026	CCATCTGGGAGGCTGATGTG	60.179	60.000	10.54	1.15	40.01	3.21
432	433	1.811266	GCGAGATGTGCGTGACCAT	60.811	57.895	0.00	0.00	0.00	3.55
533	561	4.503643	CCGGAGAAAAGTTACCACCAAGTA	60.504	45.833	0.00	0.00	0.00	2.24
610	650	1.078143	ATCTTGTTCTCTGCCGGCC	60.078	57.895	26.77	7.71	0.00	6.13
795	840	2.104963	GTCTCTCTCCTCTCCTCTCCTC	59.895	59.091	0.00	0.00	0.00	3.71
796	841	2.127708	GTCTCTCTCCTCTCCTCTCCT	58.872	57.143	0.00	0.00	0.00	3.69
797	842	1.202651	CGTCTCTCTCCTCTCCTCTCC	60.203	61.905	0.00	0.00	0.00	3.71
798	843	1.760613	TCGTCTCTCTCCTCTCCTCTC	59.239	57.143	0.00	0.00	0.00	3.20
799	844	1.762957	CTCGTCTCTCTCCTCTCCTCT	59.237	57.143	0.00	0.00	0.00	3.69
828	873	1.812214	GACGTCGATTCCGCATCTGC	61.812	60.000	0.00	0.00	35.37	4.26
836	881	0.169672	TCTGAACCGACGTCGATTCC	59.830	55.000	35.41	21.12	41.04	3.01
878	923	2.456119	GCGACCGGACTGCAGATTG	61.456	63.158	23.35	8.78	0.00	2.67
921	966	1.269621	ACAAACTCGAGTCTGAACCGG	60.270	52.381	25.16	0.00	0.00	5.28
936	981	6.294564	GGGAGGACTTTGAGGATTAAACAAAC	60.295	42.308	0.00	0.00	31.67	2.93
948	993	1.589414	ATGGGAGGGAGGACTTTGAG	58.411	55.000	0.00	0.00	0.00	3.02
995	1044	1.576356	CTCGCAGATCTAAAGGCCAC	58.424	55.000	5.01	0.00	33.89	5.01
1126	1181	2.729862	GTCGTCGTCGTTGCTGCT	60.730	61.111	0.00	0.00	38.33	4.24
1143	1207	0.807667	CAAGCAGAAGGATCGTCGGG	60.808	60.000	0.00	0.00	0.00	5.14
1494	1582	2.636412	CCGAGAGAGGAACACGCCA	61.636	63.158	0.00	0.00	0.00	5.69
1659	1753	1.741401	TGTGTAGCACAGCATCGCC	60.741	57.895	0.00	0.00	39.62	5.54
1818	1919	6.885735	AGTTTTGTACATGCTTTGTCAAAC	57.114	33.333	0.00	1.13	39.87	2.93
1856	1957	7.049754	AGCAGAAAAAGAATGGTCACAAAAAT	58.950	30.769	0.00	0.00	0.00	1.82
1865	1966	6.183360	TGGATTGAAAGCAGAAAAAGAATGGT	60.183	34.615	0.00	0.00	0.00	3.55
1866	1967	6.225318	TGGATTGAAAGCAGAAAAAGAATGG	58.775	36.000	0.00	0.00	0.00	3.16
1867	1968	7.900782	ATGGATTGAAAGCAGAAAAAGAATG	57.099	32.000	0.00	0.00	0.00	2.67
1868	1969	7.389607	CCAATGGATTGAAAGCAGAAAAAGAAT	59.610	33.333	0.00	0.00	40.14	2.40
1869	1970	6.707161	CCAATGGATTGAAAGCAGAAAAAGAA	59.293	34.615	0.00	0.00	40.14	2.52
1927	2041	4.350816	TGGGAATCAAGTTGAGAAGGAGAA	59.649	41.667	11.91	0.00	0.00	2.87
1928	2042	3.909995	TGGGAATCAAGTTGAGAAGGAGA	59.090	43.478	11.91	0.00	0.00	3.71
1958	2072	9.542462	GTTCTACCTGTATATAAACATGCTTCA	57.458	33.333	0.00	0.00	0.00	3.02
1959	2073	9.765795	AGTTCTACCTGTATATAAACATGCTTC	57.234	33.333	0.00	0.00	0.00	3.86
1960	2074	9.547753	CAGTTCTACCTGTATATAAACATGCTT	57.452	33.333	0.00	0.00	0.00	3.91
1961	2075	8.705594	ACAGTTCTACCTGTATATAAACATGCT	58.294	33.333	0.00	0.00	43.71	3.79
1962	2076	8.888579	ACAGTTCTACCTGTATATAAACATGC	57.111	34.615	0.00	0.00	43.71	4.06
2335	2449	3.936203	GACCTCACCACCACGGCA	61.936	66.667	0.00	0.00	39.03	5.69
2402	5294	1.583451	CGATTGAACAATGCCGCCG	60.583	57.895	4.72	0.00	0.00	6.46
2414	5306	1.403814	CTCACCCTAGAGCCGATTGA	58.596	55.000	0.00	0.00	0.00	2.57
2532	5424	2.123854	TCGCCTACTCCCGCAGAT	60.124	61.111	0.00	0.00	0.00	2.90
2709	5601	7.012421	GGATAGAAACAGAAACGGCAAAGATAT	59.988	37.037	0.00	0.00	0.00	1.63
2735	5629	7.254455	CCAGGATTACAAGAAAGCGTACAATAG	60.254	40.741	0.00	0.00	0.00	1.73
2737	5631	5.354234	CCAGGATTACAAGAAAGCGTACAAT	59.646	40.000	0.00	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.