AutoCloner

Multiple sequence alignment - TraesCS6B01G453500

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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	TraesCS6B01G453500	chr6B	100.000	2824	0	0	1	2824	711724019	711726842	0.000000e+00	5216.0
1	TraesCS6B01G453500	chr6B	92.732	1197	84	3	179	1374	711655466	711654272	0.000000e+00	1725.0
2	TraesCS6B01G453500	chr6B	82.671	1812	270	28	29	1824	710318981	710317198	0.000000e+00	1567.0
3	TraesCS6B01G453500	chr6B	81.374	1208	190	20	149	1325	710222837	710224040	0.000000e+00	952.0
4	TraesCS6B01G453500	chr6B	91.408	547	45	1	1371	1915	711636617	711636071	0.000000e+00	749.0
5	TraesCS6B01G453500	chr6B	81.004	279	47	4	1449	1723	615085612	615085336	1.700000e-52	217.0
6	TraesCS6B01G453500	chr6B	77.684	354	68	8	1442	1791	711738124	711737778	3.690000e-49	206.0
7	TraesCS6B01G453500	chr6B	86.957	138	13	5	1	135	711660648	711660513	1.750000e-32	150.0
8	TraesCS6B01G453500	chr6B	100.000	33	0	0	2327	2359	711726380	711726412	8.450000e-06	62.1
9	TraesCS6B01G453500	chr1B	96.522	2358	62	7	1	2358	92326744	92324407	0.000000e+00	3882.0
10	TraesCS6B01G453500	chr1B	95.270	148	3	1	2505	2652	92324273	92324130	6.080000e-57	231.0
11	TraesCS6B01G453500	chr1B	88.350	103	7	2	2641	2738	92322096	92321994	4.940000e-23	119.0
12	TraesCS6B01G453500	chr1B	94.595	74	3	1	2736	2809	92321970	92321898	2.300000e-21	113.0
13	TraesCS6B01G453500	chr6A	96.786	2240	63	7	2	2239	613079488	613081720	0.000000e+00	3729.0
14	TraesCS6B01G453500	chr6A	90.971	886	76	3	1034	1915	612568152	612567267	0.000000e+00	1190.0
15	TraesCS6B01G453500	chr6A	82.581	1240	183	24	152	1371	608680032	608678806	0.000000e+00	1062.0
16	TraesCS6B01G453500	chr6A	82.462	1243	182	25	152	1371	608793372	608792143	0.000000e+00	1055.0
17	TraesCS6B01G453500	chr6A	93.391	696	34	5	1517	2204	613038420	613039111	0.000000e+00	1020.0
18	TraesCS6B01G453500	chr6A	87.563	394	24	11	2362	2738	613081765	613082150	1.550000e-117	433.0
19	TraesCS6B01G453500	chr6A	85.065	308	11	15	2374	2646	613039312	613039619	5.960000e-72	281.0
20	TraesCS6B01G453500	chr6A	76.845	393	77	11	1406	1791	554833215	554832830	2.850000e-50	209.0
21	TraesCS6B01G453500	chr6A	98.718	78	1	0	2246	2323	613039236	613039313	3.790000e-29	139.0
22	TraesCS6B01G453500	chr6A	98.551	69	1	0	2291	2359	613081729	613081797	3.820000e-24	122.0
23	TraesCS6B01G453500	chr6D	82.838	1818	269	27	22	1824	465347887	465346098	0.000000e+00	1589.0
24	TraesCS6B01G453500	chr6D	82.759	1247	177	27	149	1371	461820158	461818926	0.000000e+00	1077.0
25	TraesCS6B01G453500	chr6D	82.315	1244	187	22	149	1371	462026482	462025251	0.000000e+00	1048.0
26	TraesCS6B01G453500	chr6D	77.582	397	74	13	1406	1791	466525200	466525592	2.830000e-55	226.0
27	TraesCS6B01G453500	chr6D	95.122	41	1	1	1959	1999	294085201	294085162	2.350000e-06	63.9
28	TraesCS6B01G453500	chr3D	78.158	1346	200	51	416	1735	464051326	464052603	0.000000e+00	771.0
29	TraesCS6B01G453500	chr3D	97.222	36	1	0	1959	1994	26227884	26227919	8.450000e-06	62.1
30	TraesCS6B01G453500	chr2D	100.000	33	0	0	1959	1991	567483533	567483501	8.450000e-06	62.1
31	TraesCS6B01G453500	chr5A	97.143	35	1	0	1960	1994	3387888	3387854	3.040000e-05	60.2
32	TraesCS6B01G453500	chr3A	100.000	32	0	0	1959	1990	581251798	581251767	3.040000e-05	60.2
33	TraesCS6B01G453500	chr2B	100.000	32	0	0	1960	1991	680200121	680200090	3.040000e-05	60.2
34	TraesCS6B01G453500	chrUn	73.913	184	31	11	1464	1634	33026942	33026763	1.090000e-04	58.4
35	TraesCS6B01G453500	chr7A	90.698	43	3	1	2696	2738	245929495	245929454	3.930000e-04	56.5

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	TraesCS6B01G453500	chr6B	711724019	711726842	2823	False	2639.05	5216	100.000000	1	2824	2	chr6B.!!$F2	2823
1	TraesCS6B01G453500	chr6B	711654272	711655466	1194	True	1725.00	1725	92.732000	179	1374	1	chr6B.!!$R4	1195
2	TraesCS6B01G453500	chr6B	710317198	710318981	1783	True	1567.00	1567	82.671000	29	1824	1	chr6B.!!$R2	1795
3	TraesCS6B01G453500	chr6B	710222837	710224040	1203	False	952.00	952	81.374000	149	1325	1	chr6B.!!$F1	1176
4	TraesCS6B01G453500	chr6B	711636071	711636617	546	True	749.00	749	91.408000	1371	1915	1	chr6B.!!$R3	544
5	TraesCS6B01G453500	chr1B	92321898	92326744	4846	True	1086.25	3882	93.684250	1	2809	4	chr1B.!!$R1	2808
6	TraesCS6B01G453500	chr6A	613079488	613082150	2662	False	1428.00	3729	94.300000	2	2738	3	chr6A.!!$F2	2736
7	TraesCS6B01G453500	chr6A	612567267	612568152	885	True	1190.00	1190	90.971000	1034	1915	1	chr6A.!!$R4	881
8	TraesCS6B01G453500	chr6A	608678806	608680032	1226	True	1062.00	1062	82.581000	152	1371	1	chr6A.!!$R2	1219
9	TraesCS6B01G453500	chr6A	608792143	608793372	1229	True	1055.00	1055	82.462000	152	1371	1	chr6A.!!$R3	1219
10	TraesCS6B01G453500	chr6A	613038420	613039619	1199	False	480.00	1020	92.391333	1517	2646	3	chr6A.!!$F1	1129
11	TraesCS6B01G453500	chr6D	465346098	465347887	1789	True	1589.00	1589	82.838000	22	1824	1	chr6D.!!$R4	1802
12	TraesCS6B01G453500	chr6D	461818926	461820158	1232	True	1077.00	1077	82.759000	149	1371	1	chr6D.!!$R2	1222
13	TraesCS6B01G453500	chr6D	462025251	462026482	1231	True	1048.00	1048	82.315000	149	1371	1	chr6D.!!$R3	1222
14	TraesCS6B01G453500	chr3D	464051326	464052603	1277	False	771.00	771	78.158000	416	1735	1	chr3D.!!$F2	1319

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	493	0.401738	TGGAAAGCAGGACCAGAAGG	59.598	55.0	0.0	0.0	42.21	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2388	2594	0.528901	CGTCACGGTTGAGTCCACAA	60.529	55.0	0.0	0.0	30.1	3.33	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
55	56	2.577700	TGCGTGTTTATGTGGGAAAGT	58.422	42.857	0.00	0.00	0.00	2.66
56	57	3.741249	TGCGTGTTTATGTGGGAAAGTA	58.259	40.909	0.00	0.00	0.00	2.24
57	58	4.328536	TGCGTGTTTATGTGGGAAAGTAT	58.671	39.130	0.00	0.00	0.00	2.12
58	59	4.155099	TGCGTGTTTATGTGGGAAAGTATG	59.845	41.667	0.00	0.00	0.00	2.39
59	60	4.393680	GCGTGTTTATGTGGGAAAGTATGA	59.606	41.667	0.00	0.00	0.00	2.15
60	61	5.106475	GCGTGTTTATGTGGGAAAGTATGAA	60.106	40.000	0.00	0.00	0.00	2.57
61	62	6.568844	GCGTGTTTATGTGGGAAAGTATGAAA	60.569	38.462	0.00	0.00	0.00	2.69
62	63	7.021196	CGTGTTTATGTGGGAAAGTATGAAAG	58.979	38.462	0.00	0.00	0.00	2.62
63	64	7.308348	CGTGTTTATGTGGGAAAGTATGAAAGT	60.308	37.037	0.00	0.00	0.00	2.66
64	65	8.357402	GTGTTTATGTGGGAAAGTATGAAAGTT	58.643	33.333	0.00	0.00	0.00	2.66
65	66	8.573035	TGTTTATGTGGGAAAGTATGAAAGTTC	58.427	33.333	0.00	0.00	0.00	3.01
66	67	8.793592	GTTTATGTGGGAAAGTATGAAAGTTCT	58.206	33.333	0.00	0.00	0.00	3.01
208	236	6.620877	TGTAGGACAATGAAGTTGATAGGT	57.379	37.500	0.00	0.00	40.37	3.08
420	454	2.281208	GCCAACACCACCGTGCTA	60.281	61.111	0.00	0.00	44.40	3.49
454	488	1.340017	GCATACTGGAAAGCAGGACCA	60.340	52.381	0.00	0.00	0.00	4.02
459	493	0.401738	TGGAAAGCAGGACCAGAAGG	59.598	55.000	0.00	0.00	42.21	3.46
592	626	5.776744	AGTTCGTAATCTTAACCGAAGTGT	58.223	37.500	0.00	0.00	40.37	3.55
1170	1231	5.327732	ACATAATTCTGCATTATCCCCCTG	58.672	41.667	0.00	0.00	36.10	4.45
1267	1332	9.405587	GAATTTGTTCAACATTTCCGAAGAATA	57.594	29.630	0.00	0.00	0.00	1.75
1623	1718	2.158871	TGTATCTATGGGTTTCGGGCAC	60.159	50.000	0.00	0.00	0.00	5.01
1829	1924	1.376037	CTTCCCGAGTTGACAGGCC	60.376	63.158	0.00	0.00	0.00	5.19
2019	2114	9.601217	AGTTGTACAATAATAAGAGTAGCCTTG	57.399	33.333	12.26	0.00	0.00	3.61
2363	2569	9.753674	AGAGAAGATTTATCCATTGTGGTAAAA	57.246	29.630	0.00	0.00	39.03	1.52
2392	2598	9.698309	ACGTATAGAGAAGATTTATCCATTGTG	57.302	33.333	0.00	0.00	0.00	3.33
2393	2599	9.144747	CGTATAGAGAAGATTTATCCATTGTGG	57.855	37.037	0.00	0.00	39.43	4.17
2434	2641	5.243954	GCTTTCTCCTTTTGAGGGTATTGTT	59.756	40.000	0.00	0.00	41.76	2.83
2503	2721	6.434028	TGGAAAAATGGAGAACTAGATGTTGG	59.566	38.462	0.00	0.00	39.30	3.77
2529	2779	0.394762	TGGGCTGGACATGCTTGATC	60.395	55.000	6.60	0.69	0.00	2.92
2558	2809	0.532640	TCGATGATCATGGTTGCCGG	60.533	55.000	14.30	0.00	0.00	6.13
2699	4998	7.903452	CATGTGTCAGCATGTGTATATTTTC	57.097	36.000	0.00	0.00	40.81	2.29
2738	5040	7.439056	GCCCACTTTATTGATTCATAACAATGG	59.561	37.037	0.00	0.00	37.32	3.16
2739	5041	7.927629	CCCACTTTATTGATTCATAACAATGGG	59.072	37.037	0.00	8.35	37.32	4.00
2741	5043	8.199449	CACTTTATTGATTCATAACAATGGGCT	58.801	33.333	0.00	0.00	37.32	5.19
2742	5044	9.420118	ACTTTATTGATTCATAACAATGGGCTA	57.580	29.630	0.00	0.00	37.32	3.93
2743	5045	9.683069	CTTTATTGATTCATAACAATGGGCTAC	57.317	33.333	0.00	0.00	37.32	3.58
2809	5136	5.506317	CCAAATTTGGCGAGATTATGAGGTC	60.506	44.000	23.81	0.00	42.21	3.85
2810	5137	2.910688	TTGGCGAGATTATGAGGTCC	57.089	50.000	0.00	0.00	0.00	4.46
2811	5138	1.048601	TGGCGAGATTATGAGGTCCC	58.951	55.000	0.00	0.00	0.00	4.46
2812	5139	1.048601	GGCGAGATTATGAGGTCCCA	58.951	55.000	0.00	0.00	0.00	4.37
2813	5140	1.416401	GGCGAGATTATGAGGTCCCAA	59.584	52.381	0.00	0.00	0.00	4.12
2814	5141	2.484889	GCGAGATTATGAGGTCCCAAC	58.515	52.381	0.00	0.00	0.00	3.77
2815	5142	2.743938	CGAGATTATGAGGTCCCAACG	58.256	52.381	0.00	0.00	0.00	4.10
2816	5143	2.484889	GAGATTATGAGGTCCCAACGC	58.515	52.381	0.00	0.00	0.00	4.84
2817	5144	2.103263	GAGATTATGAGGTCCCAACGCT	59.897	50.000	0.00	0.00	0.00	5.07
2818	5145	2.103263	AGATTATGAGGTCCCAACGCTC	59.897	50.000	0.00	0.00	0.00	5.03
2819	5146	1.271856	TTATGAGGTCCCAACGCTCA	58.728	50.000	0.00	0.00	37.22	4.26
2820	5147	1.271856	TATGAGGTCCCAACGCTCAA	58.728	50.000	0.00	0.00	36.74	3.02
2821	5148	0.036010	ATGAGGTCCCAACGCTCAAG	60.036	55.000	0.00	0.00	36.74	3.02
2822	5149	1.376037	GAGGTCCCAACGCTCAAGG	60.376	63.158	0.00	0.00	0.00	3.61
2823	5150	3.056328	GGTCCCAACGCTCAAGGC	61.056	66.667	0.00	0.00	37.64	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	7.172532	ACGCAATTTTGATAGTACAGTTCTTCA	59.827	33.333	0.00	0.00	0.00	3.02
14	15	7.478667	CACGCAATTTTGATAGTACAGTTCTTC	59.521	37.037	0.00	0.00	0.00	2.87
57	58	9.554724	GACGCAATTTTGATTATAGAACTTTCA	57.445	29.630	0.00	0.00	0.00	2.69
58	59	9.774742	AGACGCAATTTTGATTATAGAACTTTC	57.225	29.630	0.00	0.00	0.00	2.62
61	62	9.774742	GAAAGACGCAATTTTGATTATAGAACT	57.225	29.630	0.00	0.00	0.00	3.01
62	63	9.774742	AGAAAGACGCAATTTTGATTATAGAAC	57.225	29.630	0.00	0.00	0.00	3.01
63	64	9.773328	CAGAAAGACGCAATTTTGATTATAGAA	57.227	29.630	0.00	0.00	0.00	2.10
64	65	8.946085	ACAGAAAGACGCAATTTTGATTATAGA	58.054	29.630	0.00	0.00	0.00	1.98
65	66	9.003112	CACAGAAAGACGCAATTTTGATTATAG	57.997	33.333	0.00	0.00	0.00	1.31
66	67	7.967854	CCACAGAAAGACGCAATTTTGATTATA	59.032	33.333	0.00	0.00	0.00	0.98
67	68	6.808212	CCACAGAAAGACGCAATTTTGATTAT	59.192	34.615	0.00	0.00	0.00	1.28
131	147	6.259550	ACTTATTGAGACAGGTGCAATTTC	57.740	37.500	0.00	0.00	34.41	2.17
420	454	1.912043	AGTATGCTCCTGGTTGCTTCT	59.088	47.619	13.47	7.77	0.00	2.85
454	488	4.040755	AGGTGAATGGTGTATAGCCTTCT	58.959	43.478	7.86	0.00	0.00	2.85
592	626	5.179742	GGTCATCAACGTAACAATTGGTACA	59.820	40.000	28.39	13.02	38.08	2.90
1170	1231	3.559655	GGTTTGACCCAAATCTGCAAAAC	59.440	43.478	0.00	0.00	35.74	2.43
1267	1332	3.526931	ACATCGTCCAATTCAGATCGT	57.473	42.857	0.00	0.00	0.00	3.73
1623	1718	5.163513	GGCATACCTCACAAATTTGTCTTG	58.836	41.667	20.85	13.53	39.91	3.02
1829	1924	5.940617	TCCCTCCAATCCATACTAATTGTG	58.059	41.667	0.00	0.00	32.20	3.33
2227	2433	4.832248	TGTATAGGCTCAACTTGGTCAAG	58.168	43.478	8.97	8.97	43.79	3.02
2245	2451	9.326413	GTGCTTATACCAATTTCACTACTGTAT	57.674	33.333	0.00	0.00	0.00	2.29
2366	2572	9.698309	CACAATGGATAAATCTTCTCTATACGT	57.302	33.333	0.00	0.00	0.00	3.57
2367	2573	9.144747	CCACAATGGATAAATCTTCTCTATACG	57.855	37.037	0.00	0.00	40.96	3.06
2384	2590	0.762418	ACGGTTGAGTCCACAATGGA	59.238	50.000	0.00	0.00	45.98	3.41
2385	2591	0.874390	CACGGTTGAGTCCACAATGG	59.126	55.000	0.00	0.00	39.43	3.16
2386	2592	1.531149	GTCACGGTTGAGTCCACAATG	59.469	52.381	0.00	0.00	30.10	2.82
2387	2593	1.872237	CGTCACGGTTGAGTCCACAAT	60.872	52.381	0.00	0.00	30.10	2.71
2388	2594	0.528901	CGTCACGGTTGAGTCCACAA	60.529	55.000	0.00	0.00	30.10	3.33
2389	2595	1.066752	CGTCACGGTTGAGTCCACA	59.933	57.895	0.00	0.00	30.10	4.17
2390	2596	1.663702	CCGTCACGGTTGAGTCCAC	60.664	63.158	8.54	0.00	42.73	4.02
2391	2597	2.732016	CCGTCACGGTTGAGTCCA	59.268	61.111	8.54	0.00	42.73	4.02
2434	2641	4.270834	CTCTAGTACACCTAAGCTCCACA	58.729	47.826	0.00	0.00	0.00	4.17
2481	2699	5.185828	GGCCAACATCTAGTTCTCCATTTTT	59.814	40.000	0.00	0.00	38.74	1.94
2529	2779	0.459899	TGATCATCGACCGACTTGGG	59.540	55.000	0.00	0.00	44.64	4.12
2558	2809	0.662970	GCTCTGCTGGATCGATCGAC	60.663	60.000	22.06	14.00	0.00	4.20
2606	2857	0.318275	GGCGGTCGCACATTTTCAAA	60.318	50.000	17.21	0.00	44.11	2.69
2699	4998	4.861102	AAAGTGGGCAAGATTTCTCAAG	57.139	40.909	0.00	0.00	0.00	3.02
2711	5013	7.473735	TTGTTATGAATCAATAAAGTGGGCA	57.526	32.000	0.00	0.00	0.00	5.36
2741	5043	0.921749	TATTTGGCTGCCTGGGGGTA	60.922	55.000	21.03	0.00	34.45	3.69
2742	5044	2.245379	TATTTGGCTGCCTGGGGGT	61.245	57.895	21.03	2.80	34.45	4.95
2743	5045	1.758122	GTATTTGGCTGCCTGGGGG	60.758	63.158	21.03	0.00	0.00	5.40
2794	5121	2.484889	GTTGGGACCTCATAATCTCGC	58.515	52.381	0.00	0.00	0.00	5.03
2803	5130	1.371183	CTTGAGCGTTGGGACCTCA	59.629	57.895	0.00	0.00	33.86	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.