AutoCloner

Multiple sequence alignment - TraesCS7B01G351700

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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	TraesCS7B01G351700	chr7B	100.000	2748	0	0	1	2748	608404328	608407075	0.000000e+00	5075.0
1	TraesCS7B01G351700	chr7B	84.491	1799	204	42	633	2391	608391930	608393693	0.000000e+00	1707.0
2	TraesCS7B01G351700	chr7B	85.019	1602	171	40	807	2388	608379859	608381411	0.000000e+00	1565.0
3	TraesCS7B01G351700	chr7B	84.420	1380	137	46	633	1972	608414754	608416095	0.000000e+00	1286.0
4	TraesCS7B01G351700	chr7B	95.455	198	9	0	587	784	608379669	608379866	1.590000e-82	316.0
5	TraesCS7B01G351700	chr7D	89.338	2204	178	34	233	2393	560602372	560604561	0.000000e+00	2715.0
6	TraesCS7B01G351700	chr7D	84.795	1802	212	37	633	2393	560596893	560598673	0.000000e+00	1753.0
7	TraesCS7B01G351700	chr7D	84.888	1383	127	49	633	1972	560701578	560702921	0.000000e+00	1321.0
8	TraesCS7B01G351700	chr7D	84.765	1385	129	48	633	1972	560682613	560683960	0.000000e+00	1314.0
9	TraesCS7B01G351700	chr7D	84.392	1102	121	23	1301	2388	560590253	560591317	0.000000e+00	1035.0
10	TraesCS7B01G351700	chr7A	88.631	2243	196	35	188	2392	644767848	644770069	0.000000e+00	2675.0
11	TraesCS7B01G351700	chr7A	88.437	1721	139	35	633	2321	644721677	644723369	0.000000e+00	2021.0
12	TraesCS7B01G351700	chr7A	85.907	1405	154	30	865	2243	644735005	644736391	0.000000e+00	1458.0
13	TraesCS7B01G351700	chr7A	84.771	1287	127	41	725	1972	644784927	644786183	0.000000e+00	1227.0
14	TraesCS7B01G351700	chr7A	85.985	1056	117	20	807	1845	644710397	644711438	0.000000e+00	1101.0
15	TraesCS7B01G351700	chr7A	91.785	353	27	2	2396	2746	644723585	644723937	8.840000e-135	490.0
16	TraesCS7B01G351700	chr7A	87.415	294	33	3	298	587	644709847	644710140	4.380000e-88	335.0
17	TraesCS7B01G351700	chr7A	85.666	293	38	4	2429	2719	644770139	644770429	3.440000e-79	305.0
18	TraesCS7B01G351700	chr7A	93.939	198	12	0	587	784	644710207	644710404	1.600000e-77	300.0
19	TraesCS7B01G351700	chr7A	83.333	204	20	10	4	193	644767373	644767576	2.810000e-40	176.0
20	TraesCS7B01G351700	chr7A	85.227	176	19	3	9	177	644709006	644709181	1.010000e-39	174.0
21	TraesCS7B01G351700	chr6A	80.198	101	7	10	766	866	16449590	16449503	2.280000e-06	63.9
22	TraesCS7B01G351700	chr5B	90.909	44	4	0	2613	2656	38634768	38634725	2.960000e-05	60.2

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	TraesCS7B01G351700	chr7B	608404328	608407075	2747	False	5075.0	5075	100.000000	1	2748	1	chr7B.!!$F2	2747
1	TraesCS7B01G351700	chr7B	608391930	608393693	1763	False	1707.0	1707	84.491000	633	2391	1	chr7B.!!$F1	1758
2	TraesCS7B01G351700	chr7B	608414754	608416095	1341	False	1286.0	1286	84.420000	633	1972	1	chr7B.!!$F3	1339
3	TraesCS7B01G351700	chr7B	608379669	608381411	1742	False	940.5	1565	90.237000	587	2388	2	chr7B.!!$F4	1801
4	TraesCS7B01G351700	chr7D	560596893	560604561	7668	False	2234.0	2715	87.066500	233	2393	2	chr7D.!!$F4	2160
5	TraesCS7B01G351700	chr7D	560701578	560702921	1343	False	1321.0	1321	84.888000	633	1972	1	chr7D.!!$F3	1339
6	TraesCS7B01G351700	chr7D	560682613	560683960	1347	False	1314.0	1314	84.765000	633	1972	1	chr7D.!!$F2	1339
7	TraesCS7B01G351700	chr7D	560590253	560591317	1064	False	1035.0	1035	84.392000	1301	2388	1	chr7D.!!$F1	1087
8	TraesCS7B01G351700	chr7A	644735005	644736391	1386	False	1458.0	1458	85.907000	865	2243	1	chr7A.!!$F1	1378
9	TraesCS7B01G351700	chr7A	644721677	644723937	2260	False	1255.5	2021	90.111000	633	2746	2	chr7A.!!$F4	2113
10	TraesCS7B01G351700	chr7A	644784927	644786183	1256	False	1227.0	1227	84.771000	725	1972	1	chr7A.!!$F2	1247
11	TraesCS7B01G351700	chr7A	644767373	644770429	3056	False	1052.0	2675	85.876667	4	2719	3	chr7A.!!$F5	2715
12	TraesCS7B01G351700	chr7A	644709006	644711438	2432	False	477.5	1101	88.141500	9	1845	4	chr7A.!!$F3	1836

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
71	83	1.339610	CTCATGTTTGGGGCGAAACAA	59.660	47.619	14.92	2.54	46.22	2.83	F
1256	8045	0.938168	GGACGCGAAAGAAGTCACGT	60.938	55.000	15.93	0.00	38.89	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1345	8134	2.100631	GGTGTTCAGTCCGCCGATG	61.101	63.158	0.0	0.0	0.00	3.84	R
2148	9046	4.401202	GCAGGCCTTAATAGGTTTGCTTTA	59.599	41.667	0.0	0.0	43.59	1.85	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
18	19	4.943373	ACAAACGCCCAGGGAATT	57.057	50.000	10.89	0.00	0.00	2.17
30	31	1.411977	CAGGGAATTGGCAAACACACA	59.588	47.619	3.01	0.00	0.00	3.72
33	34	2.625790	GGGAATTGGCAAACACACAGTA	59.374	45.455	3.01	0.00	0.00	2.74
35	36	4.442192	GGGAATTGGCAAACACACAGTAAA	60.442	41.667	3.01	0.00	0.00	2.01
49	50	5.289675	CACACAGTAAAAATAGAGGAGAGCG	59.710	44.000	0.00	0.00	0.00	5.03
67	72	4.413928	CCTCATGTTTGGGGCGAA	57.586	55.556	0.00	0.00	36.45	4.70
71	83	1.339610	CTCATGTTTGGGGCGAAACAA	59.660	47.619	14.92	2.54	46.22	2.83
147	162	7.836183	GGATTGTGGGCTGGATAGAATATTTAT	59.164	37.037	0.00	0.00	0.00	1.40
156	171	7.229506	GCTGGATAGAATATTTATATGGGTGGC	59.770	40.741	0.00	0.00	0.00	5.01
171	186	3.704061	TGGGTGGCATAATTAAAGAAGGC	59.296	43.478	0.00	0.00	0.00	4.35
196	899	4.251268	TGAGTGTCAGCTGAATTGATCTG	58.749	43.478	20.19	0.00	0.00	2.90
219	922	4.452455	GTGTGATGTCCTACCAACTGAAAG	59.548	45.833	0.00	0.00	42.29	2.62
253	956	5.392767	AGGATATAAGCAGTACATGGACG	57.607	43.478	1.41	0.00	0.00	4.79
262	965	6.156748	AGCAGTACATGGACGATATTTGTA	57.843	37.500	1.41	0.00	0.00	2.41
276	979	5.296780	CGATATTTGTATGGTCTTTGCAGGT	59.703	40.000	0.00	0.00	0.00	4.00
294	997	4.213482	GCAGGTTGAGTACGAATTCAACTT	59.787	41.667	19.31	12.69	46.24	2.66
313	1018	5.464030	ACTTAAGGTCTTCACGTGTATGT	57.536	39.130	16.51	4.33	0.00	2.29
318	1023	2.096417	GGTCTTCACGTGTATGTTGTGC	60.096	50.000	16.51	0.00	33.69	4.57
335	1040	1.864711	GTGCGTGCACTCTCTTTTACA	59.135	47.619	17.32	0.00	43.12	2.41
336	1041	1.864711	TGCGTGCACTCTCTTTTACAC	59.135	47.619	16.19	0.00	0.00	2.90
387	1095	9.088987	ACACCAAAAATGACTATAAGGTGAATT	57.911	29.630	14.45	0.00	46.12	2.17
442	1150	7.593273	CGTAACATTTTTAGTTTCTGAATGGCA	59.407	33.333	0.00	0.00	33.25	4.92
456	1164	5.882557	TCTGAATGGCATTTTAGAAGTCCTC	59.117	40.000	14.93	0.00	0.00	3.71
469	1177	5.782893	AGAAGTCCTCATCTTATTCTCGG	57.217	43.478	0.00	0.00	0.00	4.63
498	1206	8.848474	TGTCCCAAAGTTCTTTTTATCTCTAG	57.152	34.615	0.00	0.00	0.00	2.43
530	1238	4.999950	CACAGCCTGATTCTTAAGTCTTGT	59.000	41.667	0.00	0.00	0.00	3.16
536	1244	5.875359	CCTGATTCTTAAGTCTTGTACCACC	59.125	44.000	1.63	0.00	0.00	4.61
538	1246	6.228258	TGATTCTTAAGTCTTGTACCACCAC	58.772	40.000	1.63	0.00	0.00	4.16
552	1262	1.458398	CACCACGGTGGCAATATGAA	58.542	50.000	26.62	0.00	42.67	2.57
553	1263	2.023673	CACCACGGTGGCAATATGAAT	58.976	47.619	26.62	0.92	42.67	2.57
554	1264	2.426738	CACCACGGTGGCAATATGAATT	59.573	45.455	26.62	0.13	42.67	2.17
593	1373	1.735571	GACACGGGCATTTGTTACGAT	59.264	47.619	0.00	0.00	0.00	3.73
656	7317	1.505477	GGGATCGCATGCTCTCTTGC	61.505	60.000	17.13	0.89	39.26	4.01
773	7441	1.893808	CCTGCCGTCCCATGCATAC	60.894	63.158	0.00	0.00	36.79	2.39
805	7541	2.973899	CGTAGCAGGCTGTCCAGT	59.026	61.111	17.16	0.00	33.74	4.00
813	7549	3.967326	AGCAGGCTGTCCAGTTATATACA	59.033	43.478	17.16	0.00	33.74	2.29
841	7577	4.320456	AGGCTGCCCACGTCACAG	62.320	66.667	16.57	4.94	34.48	3.66
858	7595	4.038162	GTCACAGAGACTTGTTCCTACACT	59.962	45.833	0.00	0.00	44.09	3.55
860	7597	3.253677	ACAGAGACTTGTTCCTACACTCG	59.746	47.826	0.00	0.00	32.84	4.18
872	7639	4.784177	TCCTACACTCGACCATATGTACA	58.216	43.478	0.00	0.00	0.00	2.90
954	7729	4.082081	CAGCATAGCAACCAATTCCAAAGA	60.082	41.667	0.00	0.00	0.00	2.52
1256	8045	0.938168	GGACGCGAAAGAAGTCACGT	60.938	55.000	15.93	0.00	38.89	4.49
1345	8134	2.173382	GCCGTCAATGTCGCACAC	59.827	61.111	0.00	0.00	0.00	3.82
1757	8546	6.365839	CAAGCACAGTTCTAAGTATGTGTTG	58.634	40.000	6.10	5.84	43.84	3.33
1920	8735	9.072375	TCTTATTTAATGTTGATGTGTTGTGGA	57.928	29.630	0.00	0.00	0.00	4.02
1989	8812	6.374053	TGTGTAATATTGATGTGTTGTGGGAG	59.626	38.462	0.00	0.00	0.00	4.30
1994	8817	7.991084	ATATTGATGTGTTGTGGGAGATATG	57.009	36.000	0.00	0.00	0.00	1.78
1996	8819	3.200605	TGATGTGTTGTGGGAGATATGCT	59.799	43.478	0.00	0.00	0.00	3.79
2012	8908	9.807649	GGAGATATGCTTATTGTTTGTTTCAAT	57.192	29.630	0.00	0.00	38.72	2.57
2196	9095	8.170553	GCTTGGTATGCAGAATTTTAAAACATG	58.829	33.333	1.97	3.91	0.00	3.21
2197	9096	8.545229	TTGGTATGCAGAATTTTAAAACATGG	57.455	30.769	1.97	0.00	0.00	3.66
2225	9125	7.886629	TTTAATGCAAGCTCAAATAGAGGAT	57.113	32.000	0.00	0.00	44.86	3.24
2418	9474	9.859427	ATCATTGTATATGTTGGTCAAACTTTG	57.141	29.630	0.00	0.00	39.70	2.77
2507	9564	8.826710	TGATTTCTTATGGCACTAAATACTTCG	58.173	33.333	0.00	0.00	0.00	3.79
2604	9662	1.003928	TGGCTGCTCTCACATCATGTT	59.996	47.619	0.00	0.00	0.00	2.71
2610	9668	4.640364	TGCTCTCACATCATGTTGTTACA	58.360	39.130	6.68	0.00	38.95	2.41
2641	9699	4.896482	AGCTAGTACATCAAACCCTCTAGG	59.104	45.833	0.00	0.00	43.78	3.02
2661	9719	3.044235	GGAACCTTTTGCAATCCTTGG	57.956	47.619	0.00	1.12	0.00	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.540267	CAATTCCCTGGGCGTTTGTA	58.460	50.000	8.22	0.00	0.00	2.41
1	2	1.184970	CCAATTCCCTGGGCGTTTGT	61.185	55.000	8.22	0.00	32.32	2.83
2	3	1.591183	CCAATTCCCTGGGCGTTTG	59.409	57.895	8.22	11.00	32.32	2.93
18	19	6.238897	CCTCTATTTTTACTGTGTGTTTGCCA	60.239	38.462	0.00	0.00	0.00	4.92
30	31	3.707102	AGGCGCTCTCCTCTATTTTTACT	59.293	43.478	7.64	0.00	0.00	2.24
49	50	1.531739	TTTCGCCCCAAACATGAGGC	61.532	55.000	0.00	2.54	42.18	4.70
67	72	4.771577	TCATATGCCCACACAATCTTTGTT	59.228	37.500	0.00	0.00	43.23	2.83
71	83	7.844493	AAATATCATATGCCCACACAATCTT	57.156	32.000	0.00	0.00	0.00	2.40
147	162	5.538433	GCCTTCTTTAATTATGCCACCCATA	59.462	40.000	0.00	0.00	35.34	2.74
156	171	8.461222	TGACACTCAATGCCTTCTTTAATTATG	58.539	33.333	0.00	0.00	0.00	1.90
167	182	1.072806	TCAGCTGACACTCAATGCCTT	59.927	47.619	13.74	0.00	0.00	4.35
171	186	5.354513	AGATCAATTCAGCTGACACTCAATG	59.645	40.000	18.03	4.92	0.00	2.82
196	899	3.678056	TCAGTTGGTAGGACATCACAC	57.322	47.619	0.00	0.00	0.00	3.82
226	929	9.191479	GTCCATGTACTGCTTATATCCTATACT	57.809	37.037	0.00	0.00	0.00	2.12
227	930	8.129840	CGTCCATGTACTGCTTATATCCTATAC	58.870	40.741	0.00	0.00	0.00	1.47
228	931	8.050930	TCGTCCATGTACTGCTTATATCCTATA	58.949	37.037	0.00	0.00	0.00	1.31
229	932	6.890268	TCGTCCATGTACTGCTTATATCCTAT	59.110	38.462	0.00	0.00	0.00	2.57
241	944	6.929049	ACCATACAAATATCGTCCATGTACTG	59.071	38.462	0.00	0.00	30.06	2.74
253	956	6.699575	ACCTGCAAAGACCATACAAATATC	57.300	37.500	0.00	0.00	0.00	1.63
262	965	2.664402	ACTCAACCTGCAAAGACCAT	57.336	45.000	0.00	0.00	0.00	3.55
276	979	7.439381	AGACCTTAAGTTGAATTCGTACTCAA	58.561	34.615	11.96	5.15	0.00	3.02
294	997	4.986034	CACAACATACACGTGAAGACCTTA	59.014	41.667	25.01	1.93	32.23	2.69
318	1023	3.123804	ACTGTGTAAAAGAGAGTGCACG	58.876	45.455	12.01	0.00	0.00	5.34
335	1040	5.104360	AGGTTGCATCTACCATTATGACTGT	60.104	40.000	8.72	0.00	38.16	3.55
336	1041	5.371526	AGGTTGCATCTACCATTATGACTG	58.628	41.667	8.72	0.00	38.16	3.51
387	1095	8.624367	TTATCACGGTCTAATTTCCAAAAAGA	57.376	30.769	0.00	0.00	0.00	2.52
393	1101	4.819630	GGCATTATCACGGTCTAATTTCCA	59.180	41.667	0.00	0.00	0.00	3.53
442	1150	9.757227	CGAGAATAAGATGAGGACTTCTAAAAT	57.243	33.333	0.00	0.00	31.68	1.82
498	1206	0.107312	ATCAGGCTGTGGAGATGTGC	60.107	55.000	15.27	0.00	0.00	4.57
560	1270	1.403679	CCCGTGTCTTGCAACTGAAAA	59.596	47.619	0.00	0.00	0.00	2.29
562	1272	1.444119	GCCCGTGTCTTGCAACTGAA	61.444	55.000	0.00	0.00	0.00	3.02
563	1273	1.891919	GCCCGTGTCTTGCAACTGA	60.892	57.895	0.00	0.00	0.00	3.41
565	1275	0.823356	AATGCCCGTGTCTTGCAACT	60.823	50.000	0.00	0.00	38.69	3.16
574	1287	1.466950	CATCGTAACAAATGCCCGTGT	59.533	47.619	0.00	0.00	0.00	4.49
577	1290	2.911819	AACATCGTAACAAATGCCCG	57.088	45.000	0.00	0.00	0.00	6.13
593	1373	2.125431	GTAGGCCCGCGCTTAACA	60.125	61.111	5.56	0.00	34.44	2.41
621	1401	2.502068	TCCCTCCACATGGATCTCAT	57.498	50.000	0.00	0.00	44.46	2.90
656	7317	2.541346	CCACATCGATCGACCAAGAATG	59.459	50.000	22.06	15.15	0.00	2.67
773	7441	5.687730	GCCTGCTACGCATATGTATGTATAG	59.312	44.000	4.29	6.86	38.13	1.31
805	7541	2.607038	CCTGCAGAGCGCGTGTATATAA	60.607	50.000	17.39	0.00	46.97	0.98
835	7571	4.038162	AGTGTAGGAACAAGTCTCTGTGAC	59.962	45.833	1.75	1.75	45.67	3.67
841	7577	3.366171	GGTCGAGTGTAGGAACAAGTCTC	60.366	52.174	0.00	0.00	37.36	3.36
858	7595	4.584743	AGATCTTGCTGTACATATGGTCGA	59.415	41.667	7.80	0.00	0.00	4.20
860	7597	5.233988	GGAGATCTTGCTGTACATATGGTC	58.766	45.833	7.80	0.16	0.00	4.02
872	7639	7.125053	GGCTAGTATTTATAGGGAGATCTTGCT	59.875	40.741	0.00	0.00	0.00	3.91
954	7729	5.665459	AGAGTAAATTAGCAAGCAGTCGAT	58.335	37.500	0.00	0.00	0.00	3.59
1256	8045	3.611970	CAGAGAAGTAGAAGTCCTCGGA	58.388	50.000	0.00	0.00	0.00	4.55
1345	8134	2.100631	GGTGTTCAGTCCGCCGATG	61.101	63.158	0.00	0.00	0.00	3.84
1757	8546	3.619233	ACAAACAAACGTACTCATGGC	57.381	42.857	0.00	0.00	0.00	4.40
1833	8635	9.746711	CGACTTACAATGCTATAAATAGAATGC	57.253	33.333	1.08	0.00	28.99	3.56
1847	8649	5.523916	ACACAATATCCTCGACTTACAATGC	59.476	40.000	0.00	0.00	0.00	3.56
1898	8704	7.495901	TGTTCCACAACACATCAACATTAAAT	58.504	30.769	0.00	0.00	37.61	1.40
1989	8812	9.369904	ACCATTGAAACAAACAATAAGCATATC	57.630	29.630	0.00	0.00	36.40	1.63
2012	8908	9.255304	GTTAAGCATCAAAAGAACAATTTACCA	57.745	29.630	0.00	0.00	0.00	3.25
2029	8925	2.554032	ACCACTGTGCAAGTTAAGCATC	59.446	45.455	1.29	0.00	44.79	3.91
2040	8936	2.601194	TTTGCGAGGACCACTGTGCA	62.601	55.000	1.29	0.00	35.92	4.57
2145	9043	7.203218	CAGGCCTTAATAGGTTTGCTTTATTC	58.797	38.462	0.00	0.00	44.00	1.75
2148	9046	4.401202	GCAGGCCTTAATAGGTTTGCTTTA	59.599	41.667	0.00	0.00	43.59	1.85
2170	9069	7.650834	TGTTTTAAAATTCTGCATACCAAGC	57.349	32.000	3.52	0.00	0.00	4.01
2196	9095	9.837525	CTCTATTTGAGCTTGCATTAAATATCC	57.162	33.333	0.00	0.00	35.84	2.59
2197	9096	9.837525	CCTCTATTTGAGCTTGCATTAAATATC	57.162	33.333	0.00	0.00	41.35	1.63
2212	9111	6.111382	TGTGCTTTCTGATCCTCTATTTGAG	58.889	40.000	0.00	0.00	42.30	3.02
2291	9196	7.995289	TGCAATATATTTCGGAACAAACAGAT	58.005	30.769	0.00	0.00	0.00	2.90
2393	9398	8.855110	ACAAAGTTTGACCAACATATACAATGA	58.145	29.630	22.23	0.00	37.93	2.57
2604	9662	4.707934	TGTACTAGCTAGGTGCATGTAACA	59.292	41.667	24.35	10.66	45.94	2.41
2610	9668	5.360591	GTTTGATGTACTAGCTAGGTGCAT	58.639	41.667	24.35	21.66	45.94	3.96
2652	9710	8.485976	TTGTTTTCTAAAAACACCAAGGATTG	57.514	30.769	15.45	0.00	39.57	2.67
2661	9719	9.976255	GGTTTACCATTTGTTTTCTAAAAACAC	57.024	29.630	15.45	3.78	36.61	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.