AutoCloner

Multiple sequence alignment - TraesCS4A01G461900

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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	TraesCS4A01G461900	chr4A	100.000	2869	0	0	1	2869	726417546	726420414	0.000000e+00	5299
1	TraesCS4A01G461900	chr4A	88.344	1304	144	5	1067	2367	726315773	726317071	0.000000e+00	1559
2	TraesCS4A01G461900	chr4A	86.807	902	96	6	1380	2281	726377259	726378137	0.000000e+00	985
3	TraesCS4A01G461900	chr4A	97.628	506	12	0	2364	2869	661815219	661815724	0.000000e+00	869
4	TraesCS4A01G461900	chr4A	97.628	506	11	1	2364	2869	733340883	733340379	0.000000e+00	867
5	TraesCS4A01G461900	chr4A	91.787	621	50	1	1	620	726434688	726435308	0.000000e+00	863
6	TraesCS4A01G461900	chr4A	97.036	506	13	1	2364	2869	739526696	739527199	0.000000e+00	850
7	TraesCS4A01G461900	chr4A	77.055	1229	236	30	1071	2274	726306360	726307567	0.000000e+00	665
8	TraesCS4A01G461900	chr4A	73.870	1305	274	40	1090	2362	726307979	726309248	2.600000e-125	459
9	TraesCS4A01G461900	chr4A	73.732	986	214	23	1068	2034	718746542	718745583	7.610000e-91	344
10	TraesCS4A01G461900	chr4A	87.879	231	24	2	1056	1285	726336606	726336833	4.710000e-68	268
11	TraesCS4A01G461900	chr4A	87.000	200	26	0	1083	1282	726376954	726377153	2.880000e-55	226
12	TraesCS4A01G461900	chr4A	82.081	173	30	1	1	172	607043404	607043576	2.300000e-31	147
13	TraesCS4A01G461900	chr7D	94.701	1755	88	3	1	1753	11456328	11454577	0.000000e+00	2721
14	TraesCS4A01G461900	chr7D	88.916	1209	124	7	1163	2367	11618594	11617392	0.000000e+00	1482
15	TraesCS4A01G461900	chr7D	86.891	1068	113	8	1303	2367	4628575	4629618	0.000000e+00	1171
16	TraesCS4A01G461900	chr7D	90.248	564	48	5	1804	2365	11454570	11454012	0.000000e+00	730
17	TraesCS4A01G461900	chr7A	85.879	1303	157	8	1067	2367	10988953	10987676	0.000000e+00	1362
18	TraesCS4A01G461900	chr7A	83.862	378	59	2	1898	2274	11046126	11045750	2.720000e-95	359
19	TraesCS4A01G461900	chr1B	98.016	504	10	0	2366	2869	57805021	57805524	0.000000e+00	876
20	TraesCS4A01G461900	chr2B	97.619	504	11	1	2365	2868	95792335	95792837	0.000000e+00	863
21	TraesCS4A01G461900	chr2B	97.222	504	14	0	2366	2869	87168266	87168769	0.000000e+00	854
22	TraesCS4A01G461900	chr2B	97.041	507	14	1	2363	2869	409327730	409328235	0.000000e+00	852
23	TraesCS4A01G461900	chr5B	97.421	504	10	3	2366	2869	652623991	652624491	0.000000e+00	856
24	TraesCS4A01G461900	chr5B	86.188	181	24	1	1	180	521225386	521225566	8.110000e-46	195
25	TraesCS4A01G461900	chr6B	96.673	511	16	1	2360	2869	553061456	553061966	0.000000e+00	848
26	TraesCS4A01G461900	chr1D	87.283	173	21	1	8	179	189657910	189658082	2.260000e-46	196
27	TraesCS4A01G461900	chr5D	86.188	181	24	1	1	180	431624331	431624511	8.110000e-46	195
28	TraesCS4A01G461900	chr5A	85.165	182	25	2	1	180	546712873	546713054	4.880000e-43	185
29	TraesCS4A01G461900	chr5A	85.833	120	16	1	11	129	546888296	546888177	3.000000e-25	126
30	TraesCS4A01G461900	chr1A	85.143	175	23	2	8	179	221704113	221704287	2.940000e-40	176

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	TraesCS4A01G461900	chr4A	726417546	726420414	2868	False	5299.0	5299	100.0000	1	2869	1	chr4A.!!$F5	2868
1	TraesCS4A01G461900	chr4A	726315773	726317071	1298	False	1559.0	1559	88.3440	1067	2367	1	chr4A.!!$F3	1300
2	TraesCS4A01G461900	chr4A	661815219	661815724	505	False	869.0	869	97.6280	2364	2869	1	chr4A.!!$F2	505
3	TraesCS4A01G461900	chr4A	733340379	733340883	504	True	867.0	867	97.6280	2364	2869	1	chr4A.!!$R2	505
4	TraesCS4A01G461900	chr4A	726434688	726435308	620	False	863.0	863	91.7870	1	620	1	chr4A.!!$F6	619
5	TraesCS4A01G461900	chr4A	739526696	739527199	503	False	850.0	850	97.0360	2364	2869	1	chr4A.!!$F7	505
6	TraesCS4A01G461900	chr4A	726376954	726378137	1183	False	605.5	985	86.9035	1083	2281	2	chr4A.!!$F9	1198
7	TraesCS4A01G461900	chr4A	726306360	726309248	2888	False	562.0	665	75.4625	1071	2362	2	chr4A.!!$F8	1291
8	TraesCS4A01G461900	chr4A	718745583	718746542	959	True	344.0	344	73.7320	1068	2034	1	chr4A.!!$R1	966
9	TraesCS4A01G461900	chr7D	11454012	11456328	2316	True	1725.5	2721	92.4745	1	2365	2	chr7D.!!$R2	2364
10	TraesCS4A01G461900	chr7D	11617392	11618594	1202	True	1482.0	1482	88.9160	1163	2367	1	chr7D.!!$R1	1204
11	TraesCS4A01G461900	chr7D	4628575	4629618	1043	False	1171.0	1171	86.8910	1303	2367	1	chr7D.!!$F1	1064
12	TraesCS4A01G461900	chr7A	10987676	10988953	1277	True	1362.0	1362	85.8790	1067	2367	1	chr7A.!!$R1	1300
13	TraesCS4A01G461900	chr1B	57805021	57805524	503	False	876.0	876	98.0160	2366	2869	1	chr1B.!!$F1	503
14	TraesCS4A01G461900	chr2B	95792335	95792837	502	False	863.0	863	97.6190	2365	2868	1	chr2B.!!$F2	503
15	TraesCS4A01G461900	chr2B	87168266	87168769	503	False	854.0	854	97.2220	2366	2869	1	chr2B.!!$F1	503
16	TraesCS4A01G461900	chr2B	409327730	409328235	505	False	852.0	852	97.0410	2363	2869	1	chr2B.!!$F3	506
17	TraesCS4A01G461900	chr5B	652623991	652624491	500	False	856.0	856	97.4210	2366	2869	1	chr5B.!!$F2	503
18	TraesCS4A01G461900	chr6B	553061456	553061966	510	False	848.0	848	96.6730	2360	2869	1	chr6B.!!$F1	509

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
702	704	0.247736	CAACTCCTTCTCCGGGACTG	59.752	60.0	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2612	4281	0.248012	TTATTCTTCACCAGCGGCGA	59.752	50.0	12.98	0.0	0.0	5.54	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
172	173	1.586154	GGATGTTTGTGGGGTGCTCG	61.586	60.000	0.00	0.00	0.00	5.03
229	230	4.145807	TCATTTTGGAGGCGGTTAAAAGA	58.854	39.130	0.00	0.00	0.00	2.52
313	314	2.668212	CGGCAGCCAAAGGACGAA	60.668	61.111	13.30	0.00	0.00	3.85
337	338	3.298686	ACACTGGATATGAGTCTCCGA	57.701	47.619	0.00	0.00	34.05	4.55
365	366	5.416271	TGGTGAAGGTAGGAATAGTTGTC	57.584	43.478	0.00	0.00	0.00	3.18
387	388	1.130561	GGTTTTTCTCCAATCGGCGAG	59.869	52.381	17.22	1.83	0.00	5.03
388	389	2.073816	GTTTTTCTCCAATCGGCGAGA	58.926	47.619	17.22	6.44	33.31	4.04
420	421	0.501435	CGACGTCGACAGTTTGGAAC	59.499	55.000	33.35	1.27	43.02	3.62
492	493	0.602905	CGTGTGGAGAAAGTGGTCCC	60.603	60.000	0.00	0.00	31.04	4.46
557	558	2.112815	CCCCCTTGAATTCGTCCGC	61.113	63.158	0.04	0.00	0.00	5.54
580	582	0.390860	ATGGAATCGAGGAAGCTCCG	59.609	55.000	0.00	0.00	42.75	4.63
591	593	0.321996	GAAGCTCCGGTTGTCTCCTT	59.678	55.000	0.00	0.00	0.00	3.36
615	617	1.982958	ACGGTGAGGTTAGGGTTTCAT	59.017	47.619	0.00	0.00	0.00	2.57
620	622	4.394729	GTGAGGTTAGGGTTTCATGTGAA	58.605	43.478	0.00	0.00	0.00	3.18
653	655	1.663695	CGGGTTCTTGTGTCAAGTGT	58.336	50.000	8.93	0.00	0.00	3.55
702	704	0.247736	CAACTCCTTCTCCGGGACTG	59.752	60.000	0.00	0.00	0.00	3.51
732	734	0.958091	GGGCATGTGCACAACAACTA	59.042	50.000	25.72	0.00	45.57	2.24
733	735	1.335872	GGGCATGTGCACAACAACTAC	60.336	52.381	25.72	9.75	45.57	2.73
751	753	2.332063	ACCCGGCTATCATTGACAAG	57.668	50.000	0.00	0.00	0.00	3.16
754	756	3.070018	CCCGGCTATCATTGACAAGATC	58.930	50.000	0.00	0.00	0.00	2.75
760	762	3.657398	ATCATTGACAAGATCAGGCCA	57.343	42.857	5.01	0.00	38.99	5.36
761	763	3.438216	TCATTGACAAGATCAGGCCAA	57.562	42.857	5.01	0.00	38.99	4.52
768	770	2.042162	ACAAGATCAGGCCAACTCCAAT	59.958	45.455	5.01	0.00	0.00	3.16
808	810	2.002586	CATGAGCTCGTTCCGTCAAAT	58.997	47.619	5.46	0.00	0.00	2.32
834	837	3.228188	ACATCAGTTTCAGGAGGCAAA	57.772	42.857	0.00	0.00	0.00	3.68
966	969	8.188799	TGTAGTGTGTATATAAGCACAAGACTC	58.811	37.037	15.82	3.24	45.59	3.36
967	970	7.170393	AGTGTGTATATAAGCACAAGACTCA	57.830	36.000	15.82	0.00	45.59	3.41
969	972	7.708322	AGTGTGTATATAAGCACAAGACTCATG	59.292	37.037	15.82	0.00	45.59	3.07
1048	1051	3.188786	GCGACAGCCGACACATCC	61.189	66.667	0.00	0.00	41.76	3.51
1262	1266	1.221021	CTCTGCAGCCTGCTCATCA	59.779	57.895	18.96	0.00	45.31	3.07
1285	1355	2.230508	ACCACGTATCAGAAGCGAAAGA	59.769	45.455	4.29	0.00	0.00	2.52
1300	1370	5.745227	AGCGAAAGAATCAAAGGGAAGATA	58.255	37.500	0.00	0.00	0.00	1.98
1309	1379	1.719253	AGGGAAGATAGCCACCCCT	59.281	57.895	6.48	0.00	42.97	4.79
1404	1474	0.807496	GAGGCCAAGACAAGACATGC	59.193	55.000	5.01	0.00	0.00	4.06
1405	1475	0.403271	AGGCCAAGACAAGACATGCT	59.597	50.000	5.01	0.00	0.00	3.79
1609	1679	1.174783	AGGTCGCTCGCTTCTTCTAA	58.825	50.000	0.00	0.00	0.00	2.10
1725	1795	5.494706	ACCCATTTTTAGTAGGGAGGATTGA	59.505	40.000	2.90	0.00	44.30	2.57
1777	1847	4.106197	CAGTTGACCAGTACTCGCTTATC	58.894	47.826	0.00	0.00	0.00	1.75
1788	1858	7.918033	CCAGTACTCGCTTATCTATGAATATGG	59.082	40.741	0.00	0.00	0.00	2.74
2068	2138	1.608025	GGTTCTGTTCGTCTGATGGCA	60.608	52.381	0.00	0.00	0.00	4.92
2125	2195	3.179443	TCATATCTCTGGCGTCAAACC	57.821	47.619	0.00	0.00	0.00	3.27
2213	2283	3.333680	ACTTGTTGAATACTCATGGGGGT	59.666	43.478	0.00	0.00	0.00	4.95
2215	2285	2.093181	TGTTGAATACTCATGGGGGTCG	60.093	50.000	0.00	0.00	0.00	4.79
2273	2350	7.497773	ACCCTAGTTCAAATCTAGTTAGCTT	57.502	36.000	0.00	0.00	34.72	3.74
2274	2351	7.919151	ACCCTAGTTCAAATCTAGTTAGCTTT	58.081	34.615	0.00	0.00	34.72	3.51
2478	4147	1.351012	CCACCTAGCGACGACTACG	59.649	63.158	0.00	0.00	45.75	3.51
2499	4168	0.671796	TCACTGAAACGAGCCGAAGA	59.328	50.000	1.50	0.00	0.00	2.87
2612	4281	1.601759	AGCGCACCAGAACAGCAAT	60.602	52.632	11.47	0.00	0.00	3.56
2748	4417	3.765894	CTCCACACGCCCACCAACA	62.766	63.158	0.00	0.00	0.00	3.33
2860	4530	7.663043	AGGACACAAACCCTAACAAATTTTA	57.337	32.000	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.284657	CATGACTGCTACCTCAAGCG	58.715	55.000	0.00	0.00	45.85	4.68
172	173	2.195922	GATCGCATGAAAAATGGTGCC	58.804	47.619	0.00	0.00	34.20	5.01
205	206	5.245075	TCTTTTAACCGCCTCCAAAATGAAT	59.755	36.000	0.00	0.00	0.00	2.57
229	230	2.164338	GAAGGAGAGGAGAGTCGTTGT	58.836	52.381	0.00	0.00	0.00	3.32
313	314	4.098654	CGGAGACTCATATCCAGTGTTTCT	59.901	45.833	4.53	0.00	35.80	2.52
337	338	2.868964	TCCTACCTTCACCATAGGCT	57.131	50.000	0.00	0.00	36.23	4.58
365	366	1.135689	CGCCGATTGGAGAAAAACCAG	60.136	52.381	1.98	0.00	37.19	4.00
387	388	2.013483	CGTCGCCATCATCTCGCTC	61.013	63.158	0.00	0.00	0.00	5.03
388	389	2.026734	CGTCGCCATCATCTCGCT	59.973	61.111	0.00	0.00	0.00	4.93
409	410	3.641436	GGGGAGAATTTGTTCCAAACTGT	59.359	43.478	6.84	0.00	35.09	3.55
541	542	3.497879	GGCGGACGAATTCAAGGG	58.502	61.111	6.22	0.00	0.00	3.95
557	558	0.601311	GCTTCCTCGATTCCATCCGG	60.601	60.000	0.00	0.00	0.00	5.14
580	582	1.602377	CACCGTTTCAAGGAGACAACC	59.398	52.381	0.00	0.00	0.00	3.77
591	593	1.426751	ACCCTAACCTCACCGTTTCA	58.573	50.000	0.00	0.00	0.00	2.69
615	617	1.663388	CCTGTGCGTACGCTTCACA	60.663	57.895	36.99	30.26	42.51	3.58
636	638	4.394920	TCTGAAACACTTGACACAAGAACC	59.605	41.667	16.65	3.89	0.00	3.62
637	639	5.545658	TCTGAAACACTTGACACAAGAAC	57.454	39.130	16.65	5.37	0.00	3.01
642	644	6.511605	CGAATTGATCTGAAACACTTGACACA	60.512	38.462	0.00	0.00	0.00	3.72
653	655	4.905429	TGAACCTCCGAATTGATCTGAAA	58.095	39.130	0.00	0.00	0.00	2.69
688	690	1.889530	GACCACAGTCCCGGAGAAGG	61.890	65.000	0.73	0.00	37.00	3.46
702	704	2.187946	CATGCCCCGAGAGACCAC	59.812	66.667	0.00	0.00	0.00	4.16
728	730	2.769663	TGTCAATGATAGCCGGGTAGTT	59.230	45.455	19.61	10.70	0.00	2.24
732	734	1.837439	TCTTGTCAATGATAGCCGGGT	59.163	47.619	12.58	12.58	0.00	5.28
733	735	2.620251	TCTTGTCAATGATAGCCGGG	57.380	50.000	2.18	0.00	0.00	5.73
751	753	3.495806	CCTCTATTGGAGTTGGCCTGATC	60.496	52.174	3.32	0.00	40.30	2.92
754	756	1.839994	TCCTCTATTGGAGTTGGCCTG	59.160	52.381	3.32	0.00	40.30	4.85
768	770	1.068748	GTCGTTGTTGTCGCTCCTCTA	60.069	52.381	0.00	0.00	0.00	2.43
777	779	1.125021	CGAGCTCATGTCGTTGTTGTC	59.875	52.381	15.40	0.00	32.62	3.18
834	837	6.544928	AACTTGGAAATTGACTCCAACTTT	57.455	33.333	6.06	1.36	45.88	2.66
859	862	0.798776	CATGCACGGAAACTGACTCC	59.201	55.000	0.00	0.00	0.00	3.85
941	944	8.188799	TGAGTCTTGTGCTTATATACACACTAC	58.811	37.037	12.99	10.39	45.94	2.73
966	969	1.066143	ACGTGTCCTAGGCCTTTCATG	60.066	52.381	12.58	13.00	0.00	3.07
967	970	1.276622	ACGTGTCCTAGGCCTTTCAT	58.723	50.000	12.58	0.00	0.00	2.57
969	972	1.468736	CGTACGTGTCCTAGGCCTTTC	60.469	57.143	12.58	0.00	0.00	2.62
1143	1146	2.430751	TGCAGACGCAGCGTAGTG	60.431	61.111	23.04	21.60	45.36	2.74
1262	1266	0.885879	TCGCTTCTGATACGTGGTGT	59.114	50.000	0.00	0.00	0.00	4.16
1285	1355	3.373110	GGGTGGCTATCTTCCCTTTGATT	60.373	47.826	0.00	0.00	37.18	2.57
1300	1370	1.498176	GGTAAAGTCCAGGGGTGGCT	61.498	60.000	0.00	0.00	0.00	4.75
1309	1379	1.132657	TCCTCCCACAGGTAAAGTCCA	60.133	52.381	0.00	0.00	43.95	4.02
1404	1474	2.252260	CGTCGCAGTGGGCAAAAG	59.748	61.111	1.51	0.00	45.17	2.27
1405	1475	3.283684	CCGTCGCAGTGGGCAAAA	61.284	61.111	1.51	0.00	45.17	2.44
1522	1592	2.032071	GGTGCTACCAAGTGCCGT	59.968	61.111	1.01	0.00	38.42	5.68
1624	1694	2.986019	CTCCATCCCAATACCACCCATA	59.014	50.000	0.00	0.00	0.00	2.74
1689	1759	3.473113	AAAATGGGTATGGAGGTTGCT	57.527	42.857	0.00	0.00	0.00	3.91
1777	1847	6.851222	AAAAGCGAGTGACCATATTCATAG	57.149	37.500	0.00	0.00	0.00	2.23
1788	1858	5.554636	CAAGATCATGTAAAAGCGAGTGAC	58.445	41.667	0.00	0.00	0.00	3.67
1825	1895	1.070445	TCGAGGCTAAACCGGACAAAA	59.930	47.619	9.46	0.00	46.52	2.44
2068	2138	7.147497	TGGTACACTATCTCATCATCCAATGTT	60.147	37.037	0.00	0.00	0.00	2.71
2074	2144	5.788450	CCTTGGTACACTATCTCATCATCC	58.212	45.833	0.00	0.00	39.29	3.51
2125	2195	7.510549	AACCATAATATCATTTCCTTCACGG	57.489	36.000	0.00	0.00	0.00	4.94
2155	2225	6.592870	GGGGCTATAATACTTCAAGTCAGTT	58.407	40.000	0.00	0.00	0.00	3.16
2213	2283	3.576982	ACTACATCAAAGTCCTCAACCGA	59.423	43.478	0.00	0.00	0.00	4.69
2215	2285	5.153950	AGACTACATCAAAGTCCTCAACC	57.846	43.478	0.00	0.00	43.64	3.77
2294	2371	4.878397	CCAGTGATGGTCCTTCTTGATTAC	59.122	45.833	6.35	0.00	0.00	1.89
2295	2372	4.536090	ACCAGTGATGGTCCTTCTTGATTA	59.464	41.667	6.35	0.00	37.74	1.75
2296	2373	3.331889	ACCAGTGATGGTCCTTCTTGATT	59.668	43.478	6.35	0.00	37.74	2.57
2297	2374	2.915604	ACCAGTGATGGTCCTTCTTGAT	59.084	45.455	6.35	0.00	37.74	2.57
2301	2378	4.536090	TGAAATACCAGTGATGGTCCTTCT	59.464	41.667	2.59	0.00	42.99	2.85
2302	2379	4.843728	TGAAATACCAGTGATGGTCCTTC	58.156	43.478	2.59	8.45	42.99	3.46
2478	4147	1.656095	CTTCGGCTCGTTTCAGTGATC	59.344	52.381	0.00	0.00	0.00	2.92
2612	4281	0.248012	TTATTCTTCACCAGCGGCGA	59.752	50.000	12.98	0.00	0.00	5.54
2621	4290	6.971184	TCCTTTCGATCTACGTTATTCTTCAC	59.029	38.462	0.00	0.00	43.13	3.18
2766	4435	2.758737	CCGCCTAGTCCCCGTTCT	60.759	66.667	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.