AutoCloner

Multiple sequence alignment - TraesCS7B01G121800

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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	TraesCS7B01G121800	chr7B	100.000	2903	0	0	1	2903	142285036	142282134	0.000000e+00	5361
1	TraesCS7B01G121800	chr7B	88.413	1424	103	30	619	2028	142867049	142865674	0.000000e+00	1659
2	TraesCS7B01G121800	chr7B	88.128	935	61	24	619	1544	143056093	143055200	0.000000e+00	1066
3	TraesCS7B01G121800	chr7B	86.254	873	64	26	619	1475	142780994	142780162	0.000000e+00	896
4	TraesCS7B01G121800	chr7B	89.789	568	44	8	1473	2033	142779678	142779118	0.000000e+00	715
5	TraesCS7B01G121800	chr7B	89.474	532	45	5	1502	2028	143055293	143054768	0.000000e+00	662
6	TraesCS7B01G121800	chr7B	81.690	781	100	22	2156	2902	142777777	142777006	6.880000e-171	610
7	TraesCS7B01G121800	chr7B	85.071	422	52	11	2389	2806	143054299	143053885	1.240000e-113	420
8	TraesCS7B01G121800	chr7B	83.816	414	38	15	1	387	142781837	142781426	1.640000e-97	366
9	TraesCS7B01G121800	chr7B	83.173	208	19	8	2154	2345	143054502	143054295	2.970000e-40	176
10	TraesCS7B01G121800	chr7A	89.582	2630	236	24	214	2822	178914275	178911663	0.000000e+00	3304
11	TraesCS7B01G121800	chr7A	89.202	2630	232	26	214	2822	178905680	178903082	0.000000e+00	3236
12	TraesCS7B01G121800	chr7A	87.097	1240	112	18	795	2028	179602891	179601694	0.000000e+00	1360
13	TraesCS7B01G121800	chr7A	85.766	829	58	21	619	1445	179909779	179909009	0.000000e+00	822
14	TraesCS7B01G121800	chr7A	85.042	829	64	15	619	1445	180379391	180378621	0.000000e+00	789
15	TraesCS7B01G121800	chr7A	89.430	596	57	3	949	1544	180169097	180168508	0.000000e+00	747
16	TraesCS7B01G121800	chr7A	87.500	584	52	10	1457	2033	180375202	180374633	0.000000e+00	654
17	TraesCS7B01G121800	chr7A	87.918	538	53	5	1502	2033	180168601	180168070	8.830000e-175	623
18	TraesCS7B01G121800	chr7A	88.292	521	44	8	1521	2033	179909005	179908494	2.470000e-170	608
19	TraesCS7B01G121800	chr7A	81.231	650	65	32	1	621	180170245	180169624	3.390000e-129	472
20	TraesCS7B01G121800	chr7A	81.106	651	64	33	1	621	180380286	180379665	1.580000e-127	466
21	TraesCS7B01G121800	chr7A	80.609	624	90	18	1984	2581	179908503	179907885	1.230000e-123	453
22	TraesCS7B01G121800	chr7A	86.339	366	42	6	2154	2519	179535025	179534668	2.710000e-105	392
23	TraesCS7B01G121800	chr7A	83.488	430	42	15	1	402	179603898	179603470	9.820000e-100	374
24	TraesCS7B01G121800	chr7A	84.848	363	44	8	2154	2516	180373517	180373166	3.560000e-94	355
25	TraesCS7B01G121800	chr7A	85.294	306	40	4	2267	2572	179601382	179601082	7.810000e-81	311
26	TraesCS7B01G121800	chr7A	79.402	301	16	18	619	919	180169350	180169096	1.380000e-38	171
27	TraesCS7B01G121800	chr7D	92.670	2142	103	17	126	2236	176444890	176442772	0.000000e+00	3037
28	TraesCS7B01G121800	chr7D	86.526	1425	112	35	619	2034	176579474	176578121	0.000000e+00	1495
29	TraesCS7B01G121800	chr7D	85.449	646	70	10	2185	2822	176442776	176442147	0.000000e+00	651
30	TraesCS7B01G121800	chr7D	82.426	643	56	28	6	619	176580346	176579732	2.580000e-140	508
31	TraesCS7B01G121800	chr7D	81.077	650	66	29	1	622	176471736	176471116	1.580000e-127	466
32	TraesCS7B01G121800	chr7D	91.608	143	9	1	1	140	176452432	176452290	8.210000e-46	195

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	TraesCS7B01G121800	chr7B	142282134	142285036	2902	True	5361.000000	5361	100.00000	1	2903	1	chr7B.!!$R1	2902
1	TraesCS7B01G121800	chr7B	142865674	142867049	1375	True	1659.000000	1659	88.41300	619	2028	1	chr7B.!!$R2	1409
2	TraesCS7B01G121800	chr7B	142777006	142781837	4831	True	646.750000	896	85.38725	1	2902	4	chr7B.!!$R3	2901
3	TraesCS7B01G121800	chr7B	143053885	143056093	2208	True	581.000000	1066	86.46150	619	2806	4	chr7B.!!$R4	2187
4	TraesCS7B01G121800	chr7A	178911663	178914275	2612	True	3304.000000	3304	89.58200	214	2822	1	chr7A.!!$R2	2608
5	TraesCS7B01G121800	chr7A	178903082	178905680	2598	True	3236.000000	3236	89.20200	214	2822	1	chr7A.!!$R1	2608
6	TraesCS7B01G121800	chr7A	179601082	179603898	2816	True	681.666667	1360	85.29300	1	2572	3	chr7A.!!$R4	2571
7	TraesCS7B01G121800	chr7A	179907885	179909779	1894	True	627.666667	822	84.88900	619	2581	3	chr7A.!!$R5	1962
8	TraesCS7B01G121800	chr7A	180373166	180380286	7120	True	566.000000	789	84.62400	1	2516	4	chr7A.!!$R7	2515
9	TraesCS7B01G121800	chr7A	180168070	180170245	2175	True	503.250000	747	84.49525	1	2033	4	chr7A.!!$R6	2032
10	TraesCS7B01G121800	chr7D	176442147	176444890	2743	True	1844.000000	3037	89.05950	126	2822	2	chr7D.!!$R3	2696
11	TraesCS7B01G121800	chr7D	176578121	176580346	2225	True	1001.500000	1495	84.47600	6	2034	2	chr7D.!!$R4	2028
12	TraesCS7B01G121800	chr7D	176471116	176471736	620	True	466.000000	466	81.07700	1	622	1	chr7D.!!$R2	621

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
35	36	0.036732	TGTTGAGGCTCCATGGTGTC	59.963	55.0	12.58	11.46	0.00	3.67	F
1654	6056	0.099436	GTACGCCGTCTGGATAACGT	59.901	55.0	0.00	0.00	38.44	3.99	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1855	6267	1.002868	ATTCTTCTGCTGCTGGCGT	60.003	52.632	6.69	0.0	45.43	5.68	R
2854	9099	0.458543	CGACCGATGACTGTTCTGGG	60.459	60.000	0.00	0.0	0.00	4.45	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
29	30	3.962718	CCCATATTTTGTTGAGGCTCCAT	59.037	43.478	12.86	0.00	0.00	3.41
35	36	0.036732	TGTTGAGGCTCCATGGTGTC	59.963	55.000	12.58	11.46	0.00	3.67
39	40	0.107945	GAGGCTCCATGGTGTCTGAC	60.108	60.000	24.91	8.40	0.00	3.51
40	41	1.448540	GGCTCCATGGTGTCTGACG	60.449	63.158	12.58	0.00	0.00	4.35
41	42	2.103042	GCTCCATGGTGTCTGACGC	61.103	63.158	12.58	12.78	0.00	5.19
44	45	1.184970	TCCATGGTGTCTGACGCTGA	61.185	55.000	19.60	8.40	0.00	4.26
53	60	2.159558	TGTCTGACGCTGATACTCGTTC	60.160	50.000	2.98	0.00	39.22	3.95
69	76	2.076863	CGTTCCCATTTGACTCAGGAC	58.923	52.381	0.00	0.00	0.00	3.85
145	168	7.147794	ACGTTAATATCACCATGTCTTGTAGGA	60.148	37.037	0.00	0.00	0.00	2.94
148	171	4.908601	ATCACCATGTCTTGTAGGAACA	57.091	40.909	0.00	0.00	0.00	3.18
187	210	7.438459	AGACGAATTCAAAATAGAGGGATTACG	59.562	37.037	6.22	0.00	0.00	3.18
248	271	7.339482	AGAGGTCTTGGTTTAATTCAGTATCC	58.661	38.462	0.00	0.00	0.00	2.59
272	295	7.563188	TCCCCTAATAGCATTTTATTTCAGCAA	59.437	33.333	0.00	0.00	0.00	3.91
370	405	7.733402	TTTTTGACATTACTACACACCTACC	57.267	36.000	0.00	0.00	0.00	3.18
453	490	9.997172	AGATTTATTTTAGATCCAGTCCCTTTT	57.003	29.630	0.00	0.00	0.00	2.27
598	652	7.153985	CCACTGATTTGGTTGTCATTATGTTT	58.846	34.615	0.00	0.00	0.00	2.83
623	959	6.155475	AGCTTTGTTGCCTTGTGTTTAATA	57.845	33.333	0.00	0.00	0.00	0.98
715	1055	2.032071	CCCTCACCACCAACGGTC	59.968	66.667	0.00	0.00	37.07	4.79
834	1180	6.174720	TCTCAACTAAATGGACACTTGTCT	57.825	37.500	9.20	0.00	44.20	3.41
852	1198	3.311322	TGTCTGTTTGATCGGAAACACAC	59.689	43.478	7.14	8.15	40.18	3.82
957	1343	3.507622	ACTCAATCAGCAAAGCCCTAAAC	59.492	43.478	0.00	0.00	0.00	2.01
988	1380	1.004745	CTACCTGCATTGGACCTTGGT	59.995	52.381	0.00	0.00	0.00	3.67
1098	1498	2.256591	GCTGATGCCCATCGCGAAT	61.257	57.895	15.24	0.00	42.08	3.34
1455	5268	1.378119	CCAGGCTCAGATGCAGCAA	60.378	57.895	4.07	0.00	38.77	3.91
1471	5770	1.226745	CAACCGATGTACGCGCCTA	60.227	57.895	5.73	0.00	41.07	3.93
1654	6056	0.099436	GTACGCCGTCTGGATAACGT	59.901	55.000	0.00	0.00	38.44	3.99
1702	6104	1.301401	CAGGTGTTCGGCGGAGAAA	60.301	57.895	7.21	0.00	0.00	2.52
1778	6187	2.738521	CGCAGGTAGCAGCAACGT	60.739	61.111	10.05	0.00	46.13	3.99
1781	6190	1.696832	GCAGGTAGCAGCAACGTAGC	61.697	60.000	4.24	0.00	44.79	3.58
2002	6478	6.015265	TGTGTGTGTACTGCTTACCTAATGTA	60.015	38.462	0.00	0.00	0.00	2.29
2019	6495	6.207810	CCTAATGTAGGCTTGTCCTCTAGTAG	59.792	46.154	0.00	0.00	43.20	2.57
2023	6499	3.018149	AGGCTTGTCCTCTAGTAGTTCG	58.982	50.000	0.00	0.00	43.20	3.95
2076	6635	6.704050	TGCTTAATTTGGTTTCCTTACTTTGC	59.296	34.615	0.00	0.00	0.00	3.68
2078	6637	4.617253	ATTTGGTTTCCTTACTTTGCCC	57.383	40.909	0.00	0.00	0.00	5.36
2189	6851	6.856938	CACAATATTTTGGGTTGCAAATTGTG	59.143	34.615	23.96	23.96	35.57	3.33
2201	6910	3.127895	TGCAAATTGTGGCTCCGTATAAC	59.872	43.478	0.00	0.00	0.00	1.89
2202	6911	3.127895	GCAAATTGTGGCTCCGTATAACA	59.872	43.478	0.00	0.00	0.00	2.41
2207	8092	2.498078	TGTGGCTCCGTATAACATCACA	59.502	45.455	0.00	0.00	0.00	3.58
2232	8117	3.904800	TGTCATGTTCACGGGTCATAT	57.095	42.857	0.00	0.00	0.00	1.78
2248	8133	3.005261	GTCATATGGTCTCTCACGCTCAT	59.995	47.826	2.13	0.00	0.00	2.90
2249	8134	3.005155	TCATATGGTCTCTCACGCTCATG	59.995	47.826	2.13	0.00	0.00	3.07
2262	8147	2.420022	ACGCTCATGCAAAAGTCATACC	59.580	45.455	0.00	0.00	39.64	2.73
2395	8336	1.667236	CTTTGGCCTGCGATGACATA	58.333	50.000	3.32	0.00	0.00	2.29
2410	8352	0.930310	ACATATTGCGCGTGTAGCTG	59.070	50.000	8.43	1.45	45.59	4.24
2416	8358	3.023591	GCGCGTGTAGCTGGGAAAC	62.024	63.158	8.43	0.00	45.59	2.78
2538	8480	2.158813	ACGAACTTCCCTCTCAGCAAAA	60.159	45.455	0.00	0.00	0.00	2.44
2563	8505	2.866872	TGCATACGCAGGGGAAAAG	58.133	52.632	0.00	0.00	45.36	2.27
2586	8529	1.957186	GCAACGGTGTACCTCGCAA	60.957	57.895	0.66	0.00	0.00	4.85
2604	8547	2.202676	CGAGAGTTCTGCGGCTCC	60.203	66.667	0.00	0.00	32.47	4.70
2636	8859	1.228398	TTTGCCATTGTCGCTCCCA	60.228	52.632	0.00	0.00	0.00	4.37
2743	8966	2.687902	CTCCACGGACCCCTCCTA	59.312	66.667	0.00	0.00	33.79	2.94
2746	8969	1.075525	CCACGGACCCCTCCTATCA	60.076	63.158	0.00	0.00	33.79	2.15
2763	8986	3.838271	ATCGCACGATCCACCGCT	61.838	61.111	0.00	0.00	0.00	5.52
2822	9067	4.744570	CCGTCCGTTATCATAGCATACAT	58.255	43.478	0.00	0.00	0.00	2.29
2851	9096	3.449377	TCATCATAGCAACACCGTCCTTA	59.551	43.478	0.00	0.00	0.00	2.69
2854	9099	0.609662	TAGCAACACCGTCCTTACCC	59.390	55.000	0.00	0.00	0.00	3.69
2870	9115	1.221840	CCCCCAGAACAGTCATCGG	59.778	63.158	0.00	0.00	0.00	4.18
2874	9119	0.243907	CCAGAACAGTCATCGGTCGT	59.756	55.000	0.00	0.00	0.00	4.34
2879	9124	1.313812	ACAGTCATCGGTCGTCTCCC	61.314	60.000	0.00	0.00	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.953579	GGAGCCTCAACAAAATATGGGTAA	59.046	41.667	0.00	0.00	0.00	2.85
29	30	1.472878	GAGTATCAGCGTCAGACACCA	59.527	52.381	0.41	0.00	33.17	4.17
35	36	1.534175	GGGAACGAGTATCAGCGTCAG	60.534	57.143	0.00	0.00	40.23	3.51
39	40	2.225068	AATGGGAACGAGTATCAGCG	57.775	50.000	0.00	0.00	33.17	5.18
40	41	3.309954	GTCAAATGGGAACGAGTATCAGC	59.690	47.826	0.00	0.00	33.17	4.26
41	42	4.759782	AGTCAAATGGGAACGAGTATCAG	58.240	43.478	0.00	0.00	33.17	2.90
44	45	4.383118	CCTGAGTCAAATGGGAACGAGTAT	60.383	45.833	0.00	0.00	0.00	2.12
53	60	2.584835	TTGGTCCTGAGTCAAATGGG	57.415	50.000	0.00	0.00	0.00	4.00
69	76	9.990360	TTTGATATTGAATCATGATTGGATTGG	57.010	29.630	25.37	0.00	35.23	3.16
109	131	9.973246	CATGGTGATATTAACGTATTAGCATTC	57.027	33.333	3.56	0.00	36.95	2.67
120	143	7.207383	TCCTACAAGACATGGTGATATTAACG	58.793	38.462	0.00	0.00	0.00	3.18
187	210	7.913821	GCATAATAAACAACCAACTAAGCTACC	59.086	37.037	0.00	0.00	0.00	3.18
248	271	9.768662	ATTTGCTGAAATAAAATGCTATTAGGG	57.231	29.630	0.00	0.00	29.49	3.53
546	599	6.921857	GGCACAGGATTTTGAAGATGAATATG	59.078	38.462	0.00	0.00	0.00	1.78
598	652	4.464069	AAACACAAGGCAACAAAGCTAA	57.536	36.364	0.00	0.00	41.41	3.09
623	959	8.090214	CAGGTCATTTTGAAACTGAAATGGTAT	58.910	33.333	0.00	0.00	41.37	2.73
834	1180	2.616376	CCTGTGTGTTTCCGATCAAACA	59.384	45.455	7.14	7.14	42.68	2.83
988	1380	2.362397	CGTTCTCCATGGCTAGAGCTAA	59.638	50.000	6.96	0.00	41.70	3.09
1455	5268	2.410469	GTAGGCGCGTACATCGGT	59.590	61.111	29.72	0.00	40.26	4.69
1471	5770	3.575351	GAACCTGCACTCGAGCCGT	62.575	63.158	13.61	0.00	0.00	5.68
1478	5777	3.325293	TCTGATTCTGAACCTGCACTC	57.675	47.619	0.00	0.00	0.00	3.51
1519	5818	3.473647	CTGCATCGGAGCTGGGGA	61.474	66.667	0.00	0.00	34.99	4.81
1702	6104	1.836999	TATTGCTGGGCCACGACACT	61.837	55.000	0.00	0.00	0.00	3.55
1778	6187	4.435436	CGTCGGCACAGGCTGCTA	62.435	66.667	15.89	0.00	46.25	3.49
1855	6267	1.002868	ATTCTTCTGCTGCTGGCGT	60.003	52.632	6.69	0.00	45.43	5.68
1856	6268	1.720301	GATTCTTCTGCTGCTGGCG	59.280	57.895	6.69	0.00	45.43	5.69
2019	6495	3.554324	TCAACAGCAAAGAGTACACGAAC	59.446	43.478	0.00	0.00	0.00	3.95
2023	6499	5.485662	AACTTCAACAGCAAAGAGTACAC	57.514	39.130	0.00	0.00	0.00	2.90
2076	6635	3.059884	CGGATCATCAATTACGAGTGGG	58.940	50.000	0.00	0.00	0.00	4.61
2078	6637	5.222631	TCATCGGATCATCAATTACGAGTG	58.777	41.667	0.00	0.00	32.82	3.51
2189	6851	3.936453	TGTTTGTGATGTTATACGGAGCC	59.064	43.478	0.00	0.00	0.00	4.70
2232	8117	1.216444	GCATGAGCGTGAGAGACCA	59.784	57.895	0.00	0.00	0.00	4.02
2248	8133	5.663106	AGATAGAGAGGGTATGACTTTTGCA	59.337	40.000	0.00	0.00	0.00	4.08
2249	8134	6.168270	AGATAGAGAGGGTATGACTTTTGC	57.832	41.667	0.00	0.00	0.00	3.68
2395	8336	2.796483	TTCCCAGCTACACGCGCAAT	62.796	55.000	5.73	0.00	45.59	3.56
2410	8352	1.072505	TCAGGCAGTTCCGTTTCCC	59.927	57.895	0.00	0.00	40.77	3.97
2416	8358	2.317609	CCAACGTCAGGCAGTTCCG	61.318	63.158	0.00	0.00	40.77	4.30
2493	8435	2.801162	CTATCGATCACGCCGCGG	60.801	66.667	24.05	24.05	39.58	6.46
2563	8505	4.084888	GGTACACCGTTGCTGCGC	62.085	66.667	0.00	0.00	0.00	6.09
2586	8529	2.569134	GAGCCGCAGAACTCTCGT	59.431	61.111	0.00	0.00	0.00	4.18
2590	8533	2.125350	CTGGGAGCCGCAGAACTC	60.125	66.667	12.05	0.00	45.41	3.01
2624	8847	2.203070	GGCGATGGGAGCGACAAT	60.203	61.111	0.00	0.00	36.61	2.71
2636	8859	4.203076	GCTACGACGGTGGGCGAT	62.203	66.667	0.00	0.00	0.00	4.58
2743	8966	1.300156	CGGTGGATCGTGCGATGAT	60.300	57.895	12.03	0.00	34.60	2.45
2746	8969	3.774959	GAGCGGTGGATCGTGCGAT	62.775	63.158	6.80	6.80	37.59	4.58
2763	8986	2.815211	GCGATGCTGTGAAGGCGA	60.815	61.111	0.00	0.00	0.00	5.54
2822	9067	2.749076	GTGTTGCTATGATGACTTGCCA	59.251	45.455	0.00	0.00	0.00	4.92
2851	9096	1.553690	CCGATGACTGTTCTGGGGGT	61.554	60.000	0.00	0.00	0.00	4.95
2854	9099	0.458543	CGACCGATGACTGTTCTGGG	60.459	60.000	0.00	0.00	0.00	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.