AutoCloner

Multiple sequence alignment - TraesCS5A01G374100

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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	TraesCS5A01G374100	chr5A	100.000	3263	0	0	1	3263	572055681	572052419	0.000000e+00	6026
1	TraesCS5A01G374100	chr5A	87.647	340	40	2	402	741	690020017	690019680	8.490000e-106	394
2	TraesCS5A01G374100	chr5B	95.833	2472	76	10	814	3263	553932378	553929912	0.000000e+00	3969
3	TraesCS5A01G374100	chr5D	96.388	2021	57	8	814	2821	453411098	453409081	0.000000e+00	3314
4	TraesCS5A01G374100	chr5D	85.202	446	32	7	2824	3263	453408914	453408497	8.370000e-116	427
5	TraesCS5A01G374100	chr5D	82.209	163	5	5	2872	3018	453404377	453404223	5.720000e-23	119
6	TraesCS5A01G374100	chr7D	91.067	403	35	1	1	402	271756505	271756907	7.960000e-151	544
7	TraesCS5A01G374100	chr7D	87.871	404	41	3	6	402	99421036	99420634	4.930000e-128	468
8	TraesCS5A01G374100	chr7D	90.476	336	31	1	403	738	271757093	271757427	2.990000e-120	442
9	TraesCS5A01G374100	chr7D	98.305	59	1	0	2872	2930	17613359	17613417	1.600000e-18	104
10	TraesCS5A01G374100	chr2D	90.025	401	36	1	6	402	413355794	413356194	1.740000e-142	516
11	TraesCS5A01G374100	chr2D	87.537	337	39	3	411	747	512454245	512453912	1.420000e-103	387
12	TraesCS5A01G374100	chr3A	89.604	404	40	2	1	402	454176860	454176457	2.250000e-141	512
13	TraesCS5A01G374100	chr3A	87.988	333	39	1	406	738	643177271	643177602	3.050000e-105	392
14	TraesCS5A01G374100	chr1A	89.578	403	41	1	1	402	232333126	232332724	8.080000e-141	510
15	TraesCS5A01G374100	chr7B	89.027	401	39	2	6	402	584275537	584275936	2.930000e-135	492
16	TraesCS5A01G374100	chr1B	88.778	401	39	3	6	402	642487042	642486644	1.360000e-133	486
17	TraesCS5A01G374100	chr1B	88.060	402	43	3	6	402	604625670	604626071	3.810000e-129	472
18	TraesCS5A01G374100	chr1B	87.537	337	40	2	402	738	604626250	604626584	3.950000e-104	388
19	TraesCS5A01G374100	chr4B	88.279	401	43	1	6	402	570239255	570238855	8.190000e-131	477
20	TraesCS5A01G374100	chr1D	89.053	338	34	3	402	738	218271575	218271910	1.810000e-112	416
21	TraesCS5A01G374100	chr1D	86.452	155	5	4	2872	3018	241993422	241993276	4.360000e-34	156
22	TraesCS5A01G374100	chr6B	88.131	337	34	4	402	738	64856115	64856445	2.360000e-106	396
23	TraesCS5A01G374100	chr6B	86.571	350	42	3	399	748	646144322	646143978	6.610000e-102	381
24	TraesCS5A01G374100	chr4A	87.725	334	40	1	402	735	660683170	660683502	3.950000e-104	388
25	TraesCS5A01G374100	chr3B	83.681	288	32	5	123	407	53551331	53551056	1.160000e-64	257
26	TraesCS5A01G374100	chr3D	88.158	152	4	4	2872	3017	65560631	65560488	5.600000e-38	169
27	TraesCS5A01G374100	chr3D	84.906	159	6	5	2872	3020	521727877	521728027	9.440000e-31	145
28	TraesCS5A01G374100	chr3D	83.019	159	7	5	2872	3018	285757189	285757339	3.420000e-25	126
29	TraesCS5A01G374100	chrUn	98.305	59	1	0	2872	2930	28806576	28806634	1.600000e-18	104

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	TraesCS5A01G374100	chr5A	572052419	572055681	3262	True	6026.0	6026	100.0000	1	3263	1	chr5A.!!$R1	3262
1	TraesCS5A01G374100	chr5B	553929912	553932378	2466	True	3969.0	3969	95.8330	814	3263	1	chr5B.!!$R1	2449
2	TraesCS5A01G374100	chr5D	453408497	453411098	2601	True	1870.5	3314	90.7950	814	3263	2	chr5D.!!$R2	2449
3	TraesCS5A01G374100	chr7D	271756505	271757427	922	False	493.0	544	90.7715	1	738	2	chr7D.!!$F2	737
4	TraesCS5A01G374100	chr1B	604625670	604626584	914	False	430.0	472	87.7985	6	738	2	chr1B.!!$F1	732

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
459	650	0.035056	AGTGGTACGGTAGCGTAGGT	60.035	55.0	26.11	9.31	44.89	3.08	F
738	929	0.104671	GGTCTGCTGGAGATGCTCTC	59.895	60.0	1.19	5.01	42.66	3.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2188	2391	1.098129	TCATCGCTCTCCTCGTCCTG	61.098	60.000	0.0	0.0	0.0	3.86	R
2283	2486	2.305928	CCACCAACATCACAAGACCAA	58.694	47.619	0.0	0.0	0.0	3.67	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
153	155	2.508891	CGATCGCCACGAGCTTGAC	61.509	63.158	8.31	0.00	40.26	3.18
159	161	1.222115	GCCACGAGCTTGACGACTTT	61.222	55.000	8.31	0.00	38.99	2.66
195	197	2.046023	CGCCACCATGCCTTCTCA	60.046	61.111	0.00	0.00	0.00	3.27
264	270	4.116328	CGGTGAAGAGCGAGCCGA	62.116	66.667	0.00	0.00	46.19	5.54
459	650	0.035056	AGTGGTACGGTAGCGTAGGT	60.035	55.000	26.11	9.31	44.89	3.08
472	663	1.666054	CGTAGGTCCGTTCTAGCTCT	58.334	55.000	0.00	0.00	0.00	4.09
477	668	1.677966	TCCGTTCTAGCTCTGGCGT	60.678	57.895	0.00	0.00	44.37	5.68
510	701	5.845985	AATATATGCATGCTGTGTACGAC	57.154	39.130	20.33	0.00	0.00	4.34
511	702	2.959507	TATGCATGCTGTGTACGACT	57.040	45.000	20.33	0.00	0.00	4.18
518	709	2.876091	TGCTGTGTACGACTCTTATGC	58.124	47.619	0.00	0.00	0.00	3.14
564	755	3.142951	AGAACTATCTATGCGAGCGAGT	58.857	45.455	0.00	0.00	32.88	4.18
608	799	3.313274	TCTCGCACGAAACAAGTTTTC	57.687	42.857	0.00	0.00	32.11	2.29
658	849	1.345176	CTCTGTCGCCGCGATTTTC	59.655	57.895	20.03	6.45	38.42	2.29
661	852	1.626654	CTGTCGCCGCGATTTTCAGT	61.627	55.000	20.03	0.00	38.42	3.41
664	855	0.171679	TCGCCGCGATTTTCAGTCTA	59.828	50.000	12.39	0.00	0.00	2.59
670	861	4.033587	GCCGCGATTTTCAGTCTACATAAA	59.966	41.667	8.23	0.00	0.00	1.40
673	864	5.220154	CGCGATTTTCAGTCTACATAAACGT	60.220	40.000	0.00	0.00	0.00	3.99
675	866	6.034683	GCGATTTTCAGTCTACATAAACGTCT	59.965	38.462	0.00	0.00	0.00	4.18
678	869	5.970317	TTCAGTCTACATAAACGTCTCCA	57.030	39.130	0.00	0.00	0.00	3.86
682	873	4.159693	AGTCTACATAAACGTCTCCATGCA	59.840	41.667	0.00	0.00	0.00	3.96
715	906	7.585286	ACGCAGTTTATAGTTCGACAAAATA	57.415	32.000	0.00	0.00	37.78	1.40
718	909	7.953173	CGCAGTTTATAGTTCGACAAAATACAA	59.047	33.333	0.00	0.00	0.00	2.41
738	929	0.104671	GGTCTGCTGGAGATGCTCTC	59.895	60.000	1.19	5.01	42.66	3.20
739	930	0.822811	GTCTGCTGGAGATGCTCTCA	59.177	55.000	1.19	0.00	45.12	3.27
740	931	0.822811	TCTGCTGGAGATGCTCTCAC	59.177	55.000	13.06	5.59	45.12	3.51
741	932	0.528033	CTGCTGGAGATGCTCTCACG	60.528	60.000	13.06	6.22	45.12	4.35
742	933	0.967380	TGCTGGAGATGCTCTCACGA	60.967	55.000	13.06	0.00	45.12	4.35
743	934	0.248990	GCTGGAGATGCTCTCACGAG	60.249	60.000	13.06	7.93	45.12	4.18
744	935	0.385029	CTGGAGATGCTCTCACGAGG	59.615	60.000	13.06	0.00	45.12	4.63
745	936	1.039785	TGGAGATGCTCTCACGAGGG	61.040	60.000	13.06	0.00	45.12	4.30
763	954	2.978010	CGCTGCCGTGGGAACTTT	60.978	61.111	0.00	0.00	0.00	2.66
764	955	2.954611	GCTGCCGTGGGAACTTTC	59.045	61.111	0.00	0.00	0.00	2.62
765	956	2.626780	GCTGCCGTGGGAACTTTCC	61.627	63.158	0.00	0.00	46.82	3.13
783	974	3.164269	CCATCGGGGGAGGTGAGG	61.164	72.222	0.00	0.00	0.00	3.86
784	975	2.041922	CATCGGGGGAGGTGAGGA	60.042	66.667	0.00	0.00	0.00	3.71
785	976	2.136878	CATCGGGGGAGGTGAGGAG	61.137	68.421	0.00	0.00	0.00	3.69
786	977	2.325364	ATCGGGGGAGGTGAGGAGA	61.325	63.158	0.00	0.00	0.00	3.71
787	978	1.669927	ATCGGGGGAGGTGAGGAGAT	61.670	60.000	0.00	0.00	0.00	2.75
788	979	1.383248	CGGGGGAGGTGAGGAGATT	60.383	63.158	0.00	0.00	0.00	2.40
789	980	0.983378	CGGGGGAGGTGAGGAGATTT	60.983	60.000	0.00	0.00	0.00	2.17
790	981	1.299939	GGGGGAGGTGAGGAGATTTT	58.700	55.000	0.00	0.00	0.00	1.82
791	982	1.641192	GGGGGAGGTGAGGAGATTTTT	59.359	52.381	0.00	0.00	0.00	1.94
835	1027	4.683334	GCCCGCAACAGACAACGC	62.683	66.667	0.00	0.00	0.00	4.84
923	1122	0.109723	TGCACTAACCCTTGACCCAC	59.890	55.000	0.00	0.00	0.00	4.61
992	1195	2.306715	AAACCCCTCCCAAAACCGCT	62.307	55.000	0.00	0.00	0.00	5.52
1725	1928	3.429043	GCCGTACGAAGATGGTTCA	57.571	52.632	18.76	0.00	0.00	3.18
1878	2081	1.460699	GGGGTTCAGGAAGGTGCTT	59.539	57.895	0.00	0.00	0.00	3.91
1896	2099	4.115199	GCGAGGCACCCAGGGATT	62.115	66.667	14.54	0.00	0.00	3.01
2130	2333	4.219392	TGGGGAGAATGAGGATGACTAT	57.781	45.455	0.00	0.00	0.00	2.12
2283	2486	4.223700	TGAGACAAGAACCTGCATCATAGT	59.776	41.667	0.00	0.00	0.00	2.12
2311	2514	2.229792	GTGATGTTGGTGGTGATGTGT	58.770	47.619	0.00	0.00	0.00	3.72
2400	2603	6.070366	GGTACCAAACCTACTAGAAGATGGTT	60.070	42.308	7.15	8.53	45.75	3.67
2645	2850	5.295431	TGTTTTCTGTCCATAGCAAATCG	57.705	39.130	0.00	0.00	0.00	3.34
2666	2871	4.101585	TCGATTGAGGTGATCCTTGCTATT	59.898	41.667	0.00	0.00	45.24	1.73
2716	2921	3.495331	ACCAACTTGTTGCACATGGATA	58.505	40.909	7.89	0.00	31.85	2.59
2722	2927	2.435422	TGTTGCACATGGATACCACTG	58.565	47.619	0.00	0.00	35.80	3.66
2723	2928	2.039613	TGTTGCACATGGATACCACTGA	59.960	45.455	0.00	0.00	35.80	3.41
2761	2966	8.608844	ATTCTAAGGATTTAAATCTACAGGCG	57.391	34.615	23.85	9.46	35.73	5.52
2821	3026	8.752005	AAGGATGCCGCATAATATTAATGTAT	57.248	30.769	5.67	0.00	0.00	2.29
3005	3384	8.446599	AACTGTACTAGTAAAACTGCAAACAT	57.553	30.769	3.61	0.00	39.18	2.71
3124	3506	7.383102	ACCTTTAGCAGACAACAAGATATTG	57.617	36.000	0.00	0.00	0.00	1.90
3176	3560	2.140065	TTAGATTGAGGCTCATCGCG	57.860	50.000	19.50	0.00	40.44	5.87
3242	3627	2.238942	TGCATGATACAGGCCGTAAG	57.761	50.000	10.72	0.00	40.65	2.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	63	4.854784	GCGCGGCGTCAGATCTGA	62.855	66.667	21.67	21.67	37.24	3.27
143	145	2.329379	GATCAAAGTCGTCAAGCTCGT	58.671	47.619	0.00	0.00	0.00	4.18
153	155	1.792506	CGAGCTCGCGATCAAAGTCG	61.793	60.000	25.07	7.13	44.14	4.18
191	193	3.059982	CGGACCAGTTGCCTGAGA	58.940	61.111	0.00	0.00	41.50	3.27
264	270	0.821711	CGAGGCGAGATCTCCTCCTT	60.822	60.000	24.21	13.20	43.19	3.36
363	369	2.561885	CTCGAGGACGACACGCTT	59.438	61.111	3.91	0.00	43.81	4.68
368	374	3.429141	GACCGCTCGAGGACGACA	61.429	66.667	15.58	0.00	43.81	4.35
459	650	0.393402	TACGCCAGAGCTAGAACGGA	60.393	55.000	0.00	0.00	36.60	4.69
510	701	8.963130	CATAGTTAGTTCTTCTTCGCATAAGAG	58.037	37.037	0.00	0.00	33.49	2.85
511	702	7.435488	GCATAGTTAGTTCTTCTTCGCATAAGA	59.565	37.037	0.00	0.00	0.00	2.10
518	709	6.028368	TCTTCGCATAGTTAGTTCTTCTTCG	58.972	40.000	0.00	0.00	0.00	3.79
564	755	0.604243	TAAGCAAAAGCTCGCCGGAA	60.604	50.000	5.05	0.00	0.00	4.30
586	777	3.319238	AAACTTGTTTCGTGCGAGAAG	57.681	42.857	0.00	2.30	0.00	2.85
608	799	8.517056	ACTGTATCCAAACCCGTAAAATTTTAG	58.483	33.333	10.92	2.89	0.00	1.85
639	830	1.352156	GAAAATCGCGGCGACAGAGT	61.352	55.000	28.88	8.62	39.18	3.24
658	849	4.504461	GCATGGAGACGTTTATGTAGACTG	59.496	45.833	0.00	0.00	0.00	3.51
661	852	4.729227	TGCATGGAGACGTTTATGTAGA	57.271	40.909	0.00	0.00	0.00	2.59
664	855	4.072131	AGTTTGCATGGAGACGTTTATGT	58.928	39.130	2.17	0.00	0.00	2.29
670	861	2.247790	GCAGTTTGCATGGAGACGT	58.752	52.632	2.17	0.00	44.26	4.34
708	899	4.074970	CTCCAGCAGACCTTGTATTTTGT	58.925	43.478	0.00	0.00	0.00	2.83
710	901	4.640771	TCTCCAGCAGACCTTGTATTTT	57.359	40.909	0.00	0.00	0.00	1.82
715	906	0.035630	GCATCTCCAGCAGACCTTGT	60.036	55.000	0.00	0.00	32.26	3.16
718	909	2.210424	GAGCATCTCCAGCAGACCT	58.790	57.895	0.00	0.00	32.26	3.85
746	937	2.966309	GAAAGTTCCCACGGCAGCG	61.966	63.158	0.00	0.00	0.00	5.18
747	938	2.626780	GGAAAGTTCCCACGGCAGC	61.627	63.158	0.00	0.00	41.62	5.25
748	939	3.668386	GGAAAGTTCCCACGGCAG	58.332	61.111	0.00	0.00	41.62	4.85
766	957	3.164269	CCTCACCTCCCCCGATGG	61.164	72.222	0.00	0.00	0.00	3.51
767	958	2.041922	TCCTCACCTCCCCCGATG	60.042	66.667	0.00	0.00	0.00	3.84
768	959	1.669927	ATCTCCTCACCTCCCCCGAT	61.670	60.000	0.00	0.00	0.00	4.18
769	960	1.886730	AATCTCCTCACCTCCCCCGA	61.887	60.000	0.00	0.00	0.00	5.14
770	961	0.983378	AAATCTCCTCACCTCCCCCG	60.983	60.000	0.00	0.00	0.00	5.73
771	962	1.299939	AAAATCTCCTCACCTCCCCC	58.700	55.000	0.00	0.00	0.00	5.40
804	995	2.028130	TGCGGGCTGAAGAAAGAAAAA	58.972	42.857	0.00	0.00	0.00	1.94
805	996	1.686355	TGCGGGCTGAAGAAAGAAAA	58.314	45.000	0.00	0.00	0.00	2.29
806	997	1.336755	GTTGCGGGCTGAAGAAAGAAA	59.663	47.619	0.00	0.00	0.00	2.52
807	998	0.951558	GTTGCGGGCTGAAGAAAGAA	59.048	50.000	0.00	0.00	0.00	2.52
808	999	0.179032	TGTTGCGGGCTGAAGAAAGA	60.179	50.000	0.00	0.00	0.00	2.52
809	1000	0.239347	CTGTTGCGGGCTGAAGAAAG	59.761	55.000	0.00	0.00	0.00	2.62
810	1001	0.179032	TCTGTTGCGGGCTGAAGAAA	60.179	50.000	0.00	0.00	0.00	2.52
811	1002	0.884704	GTCTGTTGCGGGCTGAAGAA	60.885	55.000	0.00	0.00	0.00	2.52
812	1003	1.301716	GTCTGTTGCGGGCTGAAGA	60.302	57.895	0.00	0.00	0.00	2.87
895	1094	4.460873	GTTAGTGCAAGCGCCGCC	62.461	66.667	16.00	8.08	37.32	6.13
899	1098	1.210155	CAAGGGTTAGTGCAAGCGC	59.790	57.895	0.00	0.00	35.38	5.92
930	1129	2.015726	GGGAGGAGGAGGAGGAGGA	61.016	68.421	0.00	0.00	0.00	3.71
1725	1928	2.681778	CTCCTCGGAGCCAGGTGT	60.682	66.667	0.00	0.00	35.31	4.16
1797	2000	2.342406	TCTCCATCTTCTTCCCCACA	57.658	50.000	0.00	0.00	0.00	4.17
1893	2096	4.811557	AGCTTATGCGACAGGTAGAAAATC	59.188	41.667	0.00	0.00	45.42	2.17
1896	2099	3.194755	TCAGCTTATGCGACAGGTAGAAA	59.805	43.478	0.00	0.00	45.42	2.52
2097	2300	1.427809	TCTCCCCATCTGCACCATAG	58.572	55.000	0.00	0.00	0.00	2.23
2130	2333	5.214293	TCTTCTTCATCCTCCTCATCATCA	58.786	41.667	0.00	0.00	0.00	3.07
2188	2391	1.098129	TCATCGCTCTCCTCGTCCTG	61.098	60.000	0.00	0.00	0.00	3.86
2263	2466	4.095483	CCAACTATGATGCAGGTTCTTGTC	59.905	45.833	0.00	0.00	0.00	3.18
2283	2486	2.305928	CCACCAACATCACAAGACCAA	58.694	47.619	0.00	0.00	0.00	3.67
2505	2709	8.514594	CATGCTTTCAGTAATCTACCTGAAAAA	58.485	33.333	13.79	7.57	42.70	1.94
2761	2966	6.019479	CGTTCTCATTAGTAAATCAGGAGCAC	60.019	42.308	0.00	0.00	0.00	4.40
2802	3007	7.747888	TGTCACATACATTAATATTATGCGGC	58.252	34.615	12.91	0.00	31.43	6.53
2821	3026	9.317936	GATATCAGTGAGAATAACATTGTCACA	57.682	33.333	23.17	10.23	42.86	3.58
3005	3384	5.769162	GGTTAACTGTACAAACATTACCCCA	59.231	40.000	5.42	0.00	34.37	4.96
3163	3545	3.300934	AACAGCGCGATGAGCCTCA	62.301	57.895	33.25	0.00	44.76	3.86
3176	3560	6.346838	GTTTCATTGCAAGTAAATGGAACAGC	60.347	38.462	13.80	0.00	46.28	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.