AutoCloner

Multiple sequence alignment - TraesCS2A01G151400

Loading Multiple Alignment...

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	TraesCS2A01G151400	chr2A	100.000	2487	0	0	1	2487	99150707	99153193	0.000000e+00	4593.0
1	TraesCS2A01G151400	chr2A	98.794	995	9	1	909	1903	99150267	99149276	0.000000e+00	1768.0
2	TraesCS2A01G151400	chr2B	95.405	1001	37	4	909	1900	150939695	150940695	0.000000e+00	1585.0
3	TraesCS2A01G151400	chr2B	94.028	854	44	4	15	864	150939388	150938538	0.000000e+00	1288.0
4	TraesCS2A01G151400	chr2B	96.102	590	21	1	1900	2487	797475518	797476107	0.000000e+00	961.0
5	TraesCS2A01G151400	chr2B	90.224	624	41	13	15	624	5326799	5327416	0.000000e+00	797.0
6	TraesCS2A01G151400	chr2B	90.033	612	47	8	15	614	633252991	633253600	0.000000e+00	780.0
7	TraesCS2A01G151400	chr2D	95.906	855	28	4	15	864	99734299	99735151	0.000000e+00	1378.0
8	TraesCS2A01G151400	chr2D	93.631	738	38	3	909	1637	99733982	99733245	0.000000e+00	1094.0
9	TraesCS2A01G151400	chr2D	97.291	443	10	1	2047	2487	77604848	77604406	0.000000e+00	750.0
10	TraesCS2A01G151400	chr2D	96.711	152	4	1	1900	2051	77629565	77629415	4.110000e-63	252.0
11	TraesCS2A01G151400	chr2D	81.226	261	32	8	1646	1903	99733052	99732806	7.020000e-46	195.0
12	TraesCS2A01G151400	chr5D	97.627	590	12	1	1900	2487	50621738	50622327	0.000000e+00	1011.0
13	TraesCS2A01G151400	chr7B	90.240	625	41	13	15	624	120370087	120370706	0.000000e+00	798.0
14	TraesCS2A01G151400	chr4B	89.789	617	44	7	15	618	515892436	515893046	0.000000e+00	773.0
15	TraesCS2A01G151400	chr4B	89.331	628	47	15	14	624	48007038	48007662	0.000000e+00	771.0
16	TraesCS2A01G151400	chr4B	94.444	54	3	0	1917	1970	227189167	227189114	1.590000e-12	84.2
17	TraesCS2A01G151400	chrUn	100.000	412	0	0	1297	1708	477541466	477541055	0.000000e+00	761.0
18	TraesCS2A01G151400	chrUn	91.169	385	34	0	234	618	37014841	37014457	7.880000e-145	523.0
19	TraesCS2A01G151400	chrUn	88.739	222	11	3	15	223	37015126	37014906	2.450000e-65	259.0
20	TraesCS2A01G151400	chr6B	96.774	403	11	1	2087	2487	87650483	87650885	0.000000e+00	671.0
21	TraesCS2A01G151400	chr5B	85.099	604	60	17	1894	2475	661829962	661830557	7.660000e-165	590.0
22	TraesCS2A01G151400	chr1B	93.258	356	23	1	270	624	634027210	634026855	7.880000e-145	523.0
23	TraesCS2A01G151400	chr1A	93.870	261	12	1	1900	2160	534853598	534853854	8.340000e-105	390.0
24	TraesCS2A01G151400	chr1A	87.681	276	31	2	2215	2487	534853854	534854129	3.990000e-83	318.0
25	TraesCS2A01G151400	chr4A	88.506	261	18	4	1975	2234	100237354	100237105	3.110000e-79	305.0
26	TraesCS2A01G151400	chr4A	79.012	162	32	2	1900	2060	42775151	42774991	2.620000e-20	110.0
27	TraesCS2A01G151400	chr3B	91.351	185	16	0	1988	2172	592671653	592671837	1.140000e-63	254.0
28	TraesCS2A01G151400	chr3D	89.189	185	14	2	1988	2172	450886535	450886713	2.490000e-55	226.0
29	TraesCS2A01G151400	chr3D	90.909	154	8	2	1988	2141	450886268	450886415	4.190000e-48	202.0

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	TraesCS2A01G151400	chr2A	99150707	99153193	2486	False	4593.0	4593	100.0000	1	2487	1	chr2A.!!$F1	2486
1	TraesCS2A01G151400	chr2A	99149276	99150267	991	True	1768.0	1768	98.7940	909	1903	1	chr2A.!!$R1	994
2	TraesCS2A01G151400	chr2B	150939695	150940695	1000	False	1585.0	1585	95.4050	909	1900	1	chr2B.!!$F2	991
3	TraesCS2A01G151400	chr2B	150938538	150939388	850	True	1288.0	1288	94.0280	15	864	1	chr2B.!!$R1	849
4	TraesCS2A01G151400	chr2B	797475518	797476107	589	False	961.0	961	96.1020	1900	2487	1	chr2B.!!$F4	587
5	TraesCS2A01G151400	chr2B	5326799	5327416	617	False	797.0	797	90.2240	15	624	1	chr2B.!!$F1	609
6	TraesCS2A01G151400	chr2B	633252991	633253600	609	False	780.0	780	90.0330	15	614	1	chr2B.!!$F3	599
7	TraesCS2A01G151400	chr2D	99734299	99735151	852	False	1378.0	1378	95.9060	15	864	1	chr2D.!!$F1	849
8	TraesCS2A01G151400	chr2D	99732806	99733982	1176	True	644.5	1094	87.4285	909	1903	2	chr2D.!!$R3	994
9	TraesCS2A01G151400	chr5D	50621738	50622327	589	False	1011.0	1011	97.6270	1900	2487	1	chr5D.!!$F1	587
10	TraesCS2A01G151400	chr7B	120370087	120370706	619	False	798.0	798	90.2400	15	624	1	chr7B.!!$F1	609
11	TraesCS2A01G151400	chr4B	515892436	515893046	610	False	773.0	773	89.7890	15	618	1	chr4B.!!$F2	603
12	TraesCS2A01G151400	chr4B	48007038	48007662	624	False	771.0	771	89.3310	14	624	1	chr4B.!!$F1	610
13	TraesCS2A01G151400	chrUn	37014457	37015126	669	True	391.0	523	89.9540	15	618	2	chrUn.!!$R2	603
14	TraesCS2A01G151400	chr5B	661829962	661830557	595	False	590.0	590	85.0990	1894	2475	1	chr5B.!!$F1	581
15	TraesCS2A01G151400	chr1A	534853598	534854129	531	False	354.0	390	90.7755	1900	2487	2	chr1A.!!$F1	587

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
871	949	0.32336	GCCCCAGCAATACAAGTCCA	60.323	55.0	0.0	0.0	39.53	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2298	2603	4.176271	GTTTGTTTGCAACTTCTCTGCTT	58.824	39.13	0.0	0.0	40.59	3.91	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
197	210	3.572255	GCGGGGGCAAGATTTATGATTTA	59.428	43.478	0.00	0.00	0.00	1.40
386	463	2.352388	GGCGAATTGGTTGCTGTACTA	58.648	47.619	0.00	0.00	0.00	1.82
426	503	2.045242	AGCTGCTGACCTGCCATG	60.045	61.111	0.00	0.00	39.01	3.66
489	566	2.015736	AATGAGTGGATGCAGTCGTC	57.984	50.000	16.18	0.00	0.00	4.20
601	678	2.577059	CTTAGGGGCGCGAAGTGA	59.423	61.111	12.10	0.00	43.07	3.41
641	718	2.045340	GGTGGCGGCAGGTATTGT	60.045	61.111	13.91	0.00	0.00	2.71
683	760	3.733960	TGACGGCGTCGGAGTCAG	61.734	66.667	31.90	0.00	39.63	3.51
723	801	2.607892	GCAGGGGATATGCGTTCGC	61.608	63.158	10.34	10.34	33.31	4.70
824	902	2.615912	GAGCCCAAGACATTCTGCATAC	59.384	50.000	0.00	0.00	0.00	2.39
833	911	7.172190	CCAAGACATTCTGCATACGAAGATTAT	59.828	37.037	0.00	0.00	0.00	1.28
834	912	9.196552	CAAGACATTCTGCATACGAAGATTATA	57.803	33.333	0.00	0.00	0.00	0.98
870	948	2.493547	GCCCCAGCAATACAAGTCC	58.506	57.895	0.00	0.00	39.53	3.85
871	949	0.323360	GCCCCAGCAATACAAGTCCA	60.323	55.000	0.00	0.00	39.53	4.02
872	950	1.463674	CCCCAGCAATACAAGTCCAC	58.536	55.000	0.00	0.00	0.00	4.02
873	951	1.271871	CCCCAGCAATACAAGTCCACA	60.272	52.381	0.00	0.00	0.00	4.17
874	952	1.812571	CCCAGCAATACAAGTCCACAC	59.187	52.381	0.00	0.00	0.00	3.82
875	953	1.464608	CCAGCAATACAAGTCCACACG	59.535	52.381	0.00	0.00	0.00	4.49
876	954	1.464608	CAGCAATACAAGTCCACACGG	59.535	52.381	0.00	0.00	0.00	4.94
877	955	1.071699	AGCAATACAAGTCCACACGGT	59.928	47.619	0.00	0.00	0.00	4.83
878	956	1.196808	GCAATACAAGTCCACACGGTG	59.803	52.381	6.58	6.58	0.00	4.94
879	957	2.489971	CAATACAAGTCCACACGGTGT	58.510	47.619	8.21	8.21	32.34	4.16
880	958	2.875933	CAATACAAGTCCACACGGTGTT	59.124	45.455	11.82	0.00	30.74	3.32
881	959	1.942677	TACAAGTCCACACGGTGTTG	58.057	50.000	11.82	8.65	34.25	3.33
882	960	1.355210	CAAGTCCACACGGTGTTGC	59.645	57.895	11.82	4.80	0.00	4.17
883	961	1.078072	AAGTCCACACGGTGTTGCA	60.078	52.632	11.82	0.00	0.00	4.08
884	962	0.678366	AAGTCCACACGGTGTTGCAA	60.678	50.000	11.82	0.00	0.00	4.08
885	963	1.063488	GTCCACACGGTGTTGCAAC	59.937	57.895	22.83	22.83	0.00	4.17
886	964	2.115911	TCCACACGGTGTTGCAACC	61.116	57.895	26.14	16.80	36.82	3.77
892	970	4.322385	GGTGTTGCAACCGTCGGC	62.322	66.667	26.14	9.42	0.00	5.54
893	971	3.578272	GTGTTGCAACCGTCGGCA	61.578	61.111	26.14	3.19	38.46	5.69
894	972	2.593148	TGTTGCAACCGTCGGCAT	60.593	55.556	26.14	0.00	40.17	4.40
895	973	2.126888	GTTGCAACCGTCGGCATG	60.127	61.111	19.15	12.20	40.17	4.06
896	974	2.281139	TTGCAACCGTCGGCATGA	60.281	55.556	18.91	4.41	40.17	3.07
897	975	1.673993	TTGCAACCGTCGGCATGAT	60.674	52.632	18.91	0.00	40.17	2.45
898	976	1.643868	TTGCAACCGTCGGCATGATC	61.644	55.000	18.91	5.41	40.17	2.92
899	977	3.005898	CAACCGTCGGCATGATCG	58.994	61.111	12.28	0.00	0.00	3.69
900	978	2.890474	AACCGTCGGCATGATCGC	60.890	61.111	12.28	0.00	0.00	4.58
1281	1371	8.532186	AGAGTACTTCTGTTATCATGAGTGAT	57.468	34.615	0.09	0.00	40.49	3.06
1708	1986	6.145338	TGAAGGGCTAAAATACTCTAGTCG	57.855	41.667	0.00	0.00	0.00	4.18
2060	2348	5.482908	AGACTGAACTACCAATGTCATCAC	58.517	41.667	0.00	0.00	0.00	3.06
2128	2416	5.704053	TGCTTGATATCCATCTACAATGCAG	59.296	40.000	0.00	0.00	31.93	4.41
2132	2420	6.949715	TGATATCCATCTACAATGCAGCATA	58.050	36.000	8.75	0.00	31.93	3.14
2275	2580	3.812053	GGCAGAAGTACATAGCAGAATGG	59.188	47.826	0.00	0.00	35.86	3.16
2298	2603	5.938125	GGACAGCAGTTTATACCTTGAGAAA	59.062	40.000	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.142038	AGTATAATAAAAAGGGCAGCCGG	58.858	43.478	5.00	0.00	0.00	6.13
2	3	7.665974	ACATCTAGTATAATAAAAAGGGCAGCC	59.334	37.037	1.26	1.26	0.00	4.85
114	127	0.744281	AGTTCGTGGCAGTTTTTGGG	59.256	50.000	0.00	0.00	0.00	4.12
241	312	7.895767	GTCATTACGGTTGTTCTTTTTGTTTTG	59.104	33.333	0.00	0.00	0.00	2.44
242	313	7.599245	TGTCATTACGGTTGTTCTTTTTGTTTT	59.401	29.630	0.00	0.00	0.00	2.43
243	314	7.091443	TGTCATTACGGTTGTTCTTTTTGTTT	58.909	30.769	0.00	0.00	0.00	2.83
248	319	9.804758	TTTAATTGTCATTACGGTTGTTCTTTT	57.195	25.926	0.00	0.00	0.00	2.27
386	463	1.307691	AGAGGAGGCTGGGAGCATT	60.308	57.895	0.00	0.00	44.75	3.56
426	503	5.119931	TGCCAATGTGTTTTCATACTGAC	57.880	39.130	0.00	0.00	0.00	3.51
489	566	3.019564	GTTTCCCTCCATGTCTCCATTG	58.980	50.000	0.00	0.00	0.00	2.82
567	644	2.338577	AAGCAGCTGTCTGTTCTGTT	57.661	45.000	16.64	0.00	42.29	3.16
568	645	2.289320	CCTAAGCAGCTGTCTGTTCTGT	60.289	50.000	16.64	0.00	42.29	3.41
723	801	1.630244	CCGAGAAAGCACTGCCTTCG	61.630	60.000	6.71	6.84	34.57	3.79
824	902	5.939883	TGGATCATTGGGCTTATAATCTTCG	59.060	40.000	0.00	0.00	0.00	3.79
833	911	2.378038	GCAGTTGGATCATTGGGCTTA	58.622	47.619	0.00	0.00	0.00	3.09
834	912	1.188863	GCAGTTGGATCATTGGGCTT	58.811	50.000	0.00	0.00	0.00	4.35
860	938	2.875933	CAACACCGTGTGGACTTGTATT	59.124	45.455	4.57	0.00	37.94	1.89
864	942	1.355210	GCAACACCGTGTGGACTTG	59.645	57.895	10.44	3.20	37.94	3.16
865	943	0.678366	TTGCAACACCGTGTGGACTT	60.678	50.000	10.44	0.00	37.94	3.01
866	944	1.078072	TTGCAACACCGTGTGGACT	60.078	52.632	10.44	0.00	37.94	3.85
867	945	1.063488	GTTGCAACACCGTGTGGAC	59.937	57.895	24.52	2.26	37.94	4.02
868	946	2.115911	GGTTGCAACACCGTGTGGA	61.116	57.895	29.55	1.09	37.94	4.02
869	947	2.411290	GGTTGCAACACCGTGTGG	59.589	61.111	29.55	2.80	37.94	4.17
875	953	4.322385	GCCGACGGTTGCAACACC	62.322	66.667	29.55	14.61	0.00	4.16
876	954	2.903547	ATGCCGACGGTTGCAACAC	61.904	57.895	29.55	17.93	41.50	3.32
877	955	2.593148	ATGCCGACGGTTGCAACA	60.593	55.556	29.55	8.98	41.50	3.33
878	956	1.922135	ATCATGCCGACGGTTGCAAC	61.922	55.000	21.59	21.59	41.50	4.17
879	957	1.643868	GATCATGCCGACGGTTGCAA	61.644	55.000	16.73	0.00	41.50	4.08
880	958	2.046411	ATCATGCCGACGGTTGCA	60.046	55.556	16.73	7.79	42.52	4.08
881	959	2.709475	GATCATGCCGACGGTTGC	59.291	61.111	16.73	1.21	0.00	4.17
882	960	3.005898	CGATCATGCCGACGGTTG	58.994	61.111	16.73	13.63	0.00	3.77
883	961	2.890474	GCGATCATGCCGACGGTT	60.890	61.111	16.73	0.09	0.00	4.44
884	962	4.891727	GGCGATCATGCCGACGGT	62.892	66.667	16.73	0.00	46.75	4.83
891	969	2.819595	ACCGTGTGGCGATCATGC	60.820	61.111	0.00	0.00	44.77	4.06
892	970	1.298157	AACACCGTGTGGCGATCATG	61.298	55.000	4.57	0.00	44.77	3.07
893	971	1.003839	AACACCGTGTGGCGATCAT	60.004	52.632	4.57	0.00	44.77	2.45
894	972	1.958715	CAACACCGTGTGGCGATCA	60.959	57.895	4.57	0.00	44.77	2.92
895	973	0.668096	TACAACACCGTGTGGCGATC	60.668	55.000	4.57	0.00	44.77	3.69
896	974	0.036765	ATACAACACCGTGTGGCGAT	60.037	50.000	4.57	0.00	44.77	4.58
897	975	0.249953	AATACAACACCGTGTGGCGA	60.250	50.000	4.57	0.00	44.77	5.54
898	976	0.589223	AAATACAACACCGTGTGGCG	59.411	50.000	4.57	0.00	39.70	5.69
899	977	2.785713	AAAATACAACACCGTGTGGC	57.214	45.000	4.57	0.00	39.70	5.01
900	978	5.007823	TCACTAAAAATACAACACCGTGTGG	59.992	40.000	4.57	4.46	37.94	4.17
901	979	6.050454	TCACTAAAAATACAACACCGTGTG	57.950	37.500	4.57	2.46	39.75	3.82
902	980	6.708949	AGATCACTAAAAATACAACACCGTGT	59.291	34.615	0.00	0.00	35.43	4.49
903	981	7.129109	AGATCACTAAAAATACAACACCGTG	57.871	36.000	0.00	0.00	0.00	4.94
904	982	7.739498	AAGATCACTAAAAATACAACACCGT	57.261	32.000	0.00	0.00	0.00	4.83
905	983	8.073768	ACAAAGATCACTAAAAATACAACACCG	58.926	33.333	0.00	0.00	0.00	4.94
1139	1225	2.636893	AGCCTCCATGCTCCTACAATAG	59.363	50.000	0.00	0.00	36.75	1.73
1140	1226	2.369860	CAGCCTCCATGCTCCTACAATA	59.630	50.000	0.00	0.00	40.32	1.90
1141	1227	1.142465	CAGCCTCCATGCTCCTACAAT	59.858	52.381	0.00	0.00	40.32	2.71
1152	1238	2.850828	GAAGCCTTGGCAGCCTCCAT	62.851	60.000	14.15	0.00	35.77	3.41
1281	1371	9.206870	GCAAAAGAACATTGGAATATTCTGAAA	57.793	29.630	14.95	8.02	32.81	2.69
1294	1384	9.672086	AAAAATCATGAATGCAAAAGAACATTG	57.328	25.926	0.00	0.00	36.65	2.82
1295	1385	9.672086	CAAAAATCATGAATGCAAAAGAACATT	57.328	25.926	0.00	0.00	39.16	2.71
2060	2348	4.620982	TGTGTCATATATGCTTGTCTCGG	58.379	43.478	7.92	0.00	0.00	4.63
2275	2580	7.435068	TTTTCTCAAGGTATAAACTGCTGTC	57.565	36.000	0.00	0.00	0.00	3.51
2298	2603	4.176271	GTTTGTTTGCAACTTCTCTGCTT	58.824	39.130	0.00	0.00	40.59	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.