AutoCloner

Multiple sequence alignment - TraesCS4A01G170300

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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	TraesCS4A01G170300	chr4A	100.000	2324	0	0	1	2324	429496362	429498685	0.000000e+00	4292.0
1	TraesCS4A01G170300	chr4A	95.948	2295	64	6	1	2279	490349399	490351680	0.000000e+00	3696.0
2	TraesCS4A01G170300	chr4A	95.726	2293	81	6	1	2279	52462309	52460020	0.000000e+00	3675.0
3	TraesCS4A01G170300	chr4A	96.795	780	24	1	1500	2279	326295911	326295133	0.000000e+00	1301.0
4	TraesCS4A01G170300	chr4A	97.778	45	1	0	2280	2324	521295516	521295560	6.880000e-11	78.7
5	TraesCS4A01G170300	chr3A	96.528	2304	60	8	1	2287	513304536	513306836	0.000000e+00	3794.0
6	TraesCS4A01G170300	chr5A	96.464	2291	65	5	1	2279	133827282	133829568	0.000000e+00	3768.0
7	TraesCS4A01G170300	chr5A	96.421	2291	69	3	1	2279	501876991	501879280	0.000000e+00	3764.0
8	TraesCS4A01G170300	chr1A	96.332	2290	60	4	1	2277	575427288	575429566	0.000000e+00	3742.0
9	TraesCS4A01G170300	chr1A	95.997	2298	67	9	1	2279	50632955	50630664	0.000000e+00	3711.0
10	TraesCS4A01G170300	chr6A	96.070	2290	65	5	1	2279	401372788	401375063	0.000000e+00	3707.0
11	TraesCS4A01G170300	chr7A	96.419	1955	56	4	1	1942	153030976	153029023	0.000000e+00	3210.0
12	TraesCS4A01G170300	chr7A	93.233	1389	53	4	1	1378	49616019	49614661	0.000000e+00	2006.0
13	TraesCS4A01G170300	chr7A	97.059	34	0	1	2281	2314	725117804	725117772	3.230000e-04	56.5
14	TraesCS4A01G170300	chr6B	95.680	1389	37	6	1	1378	703926365	703927741	0.000000e+00	2211.0
15	TraesCS4A01G170300	chr7B	95.248	1389	42	4	1	1378	553271980	553270605	0.000000e+00	2178.0
16	TraesCS4A01G170300	chr7B	94.888	1389	48	3	1	1378	549109758	549108382	0.000000e+00	2150.0
17	TraesCS4A01G170300	chr7B	94.744	1389	50	4	1	1378	164824257	164825633	0.000000e+00	2139.0
18	TraesCS4A01G170300	chr7B	90.909	44	4	0	2281	2324	348003586	348003543	2.490000e-05	60.2
19	TraesCS4A01G170300	chr4B	95.104	1389	45	3	1	1378	7005297	7006673	0.000000e+00	2167.0
20	TraesCS4A01G170300	chrUn	94.816	1389	49	3	1	1378	38472687	38474063	0.000000e+00	2145.0
21	TraesCS4A01G170300	chr5B	95.147	680	22	2	1	669	61819024	61819703	0.000000e+00	1062.0
22	TraesCS4A01G170300	chr3B	93.824	680	23	3	1	669	765162403	765161732	0.000000e+00	1005.0
23	TraesCS4A01G170300	chr7D	100.000	45	0	0	2280	2324	274865971	274865927	1.480000e-12	84.2
24	TraesCS4A01G170300	chr2D	100.000	45	0	0	2280	2324	568100254	568100210	1.480000e-12	84.2
25	TraesCS4A01G170300	chr1B	93.182	44	3	0	2281	2324	1803059	1803102	5.360000e-07	65.8

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	TraesCS4A01G170300	chr4A	429496362	429498685	2323	False	4292	4292	100.000	1	2324	1	chr4A.!!$F1	2323
1	TraesCS4A01G170300	chr4A	490349399	490351680	2281	False	3696	3696	95.948	1	2279	1	chr4A.!!$F2	2278
2	TraesCS4A01G170300	chr4A	52460020	52462309	2289	True	3675	3675	95.726	1	2279	1	chr4A.!!$R1	2278
3	TraesCS4A01G170300	chr4A	326295133	326295911	778	True	1301	1301	96.795	1500	2279	1	chr4A.!!$R2	779
4	TraesCS4A01G170300	chr3A	513304536	513306836	2300	False	3794	3794	96.528	1	2287	1	chr3A.!!$F1	2286
5	TraesCS4A01G170300	chr5A	133827282	133829568	2286	False	3768	3768	96.464	1	2279	1	chr5A.!!$F1	2278
6	TraesCS4A01G170300	chr5A	501876991	501879280	2289	False	3764	3764	96.421	1	2279	1	chr5A.!!$F2	2278
7	TraesCS4A01G170300	chr1A	575427288	575429566	2278	False	3742	3742	96.332	1	2277	1	chr1A.!!$F1	2276
8	TraesCS4A01G170300	chr1A	50630664	50632955	2291	True	3711	3711	95.997	1	2279	1	chr1A.!!$R1	2278
9	TraesCS4A01G170300	chr6A	401372788	401375063	2275	False	3707	3707	96.070	1	2279	1	chr6A.!!$F1	2278
10	TraesCS4A01G170300	chr7A	153029023	153030976	1953	True	3210	3210	96.419	1	1942	1	chr7A.!!$R2	1941
11	TraesCS4A01G170300	chr7A	49614661	49616019	1358	True	2006	2006	93.233	1	1378	1	chr7A.!!$R1	1377
12	TraesCS4A01G170300	chr6B	703926365	703927741	1376	False	2211	2211	95.680	1	1378	1	chr6B.!!$F1	1377
13	TraesCS4A01G170300	chr7B	553270605	553271980	1375	True	2178	2178	95.248	1	1378	1	chr7B.!!$R3	1377
14	TraesCS4A01G170300	chr7B	549108382	549109758	1376	True	2150	2150	94.888	1	1378	1	chr7B.!!$R2	1377
15	TraesCS4A01G170300	chr7B	164824257	164825633	1376	False	2139	2139	94.744	1	1378	1	chr7B.!!$F1	1377
16	TraesCS4A01G170300	chr4B	7005297	7006673	1376	False	2167	2167	95.104	1	1378	1	chr4B.!!$F1	1377
17	TraesCS4A01G170300	chrUn	38472687	38474063	1376	False	2145	2145	94.816	1	1378	1	chrUn.!!$F1	1377
18	TraesCS4A01G170300	chr5B	61819024	61819703	679	False	1062	1062	95.147	1	669	1	chr5B.!!$F1	668
19	TraesCS4A01G170300	chr3B	765161732	765162403	671	True	1005	1005	93.824	1	669	1	chr3B.!!$R1	668

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
154	166	0.108615	CTGGTGGAGCCTAAGACACG	60.109	60.0	0.0	0.0	38.35	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1889	1915	0.475475	CTTATCTGCATGGGCCTGGA	59.525	55.0	4.53	0.67	40.13	3.86	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
154	166	0.108615	CTGGTGGAGCCTAAGACACG	60.109	60.000	0.00	0.00	38.35	4.49
198	211	3.853831	TGCTTTATGTTCTGCACATGG	57.146	42.857	3.13	0.00	46.37	3.66
531	544	1.919240	TTCGGAGCCAGTCAAGACTA	58.081	50.000	1.86	0.00	40.20	2.59
544	557	7.255208	GCCAGTCAAGACTACTATAGTAAGTCC	60.255	44.444	24.08	15.75	40.20	3.85
545	558	7.994334	CCAGTCAAGACTACTATAGTAAGTCCT	59.006	40.741	24.08	16.28	40.20	3.85
940	954	3.360867	TCTCTTGCTTGGTTTGGTTTGA	58.639	40.909	0.00	0.00	0.00	2.69
954	968	9.231297	TGGTTTGGTTTGAAAAATGTGAAATAA	57.769	25.926	0.00	0.00	0.00	1.40
995	1009	4.655963	TCATTTTCCTCCATATGCTAGCC	58.344	43.478	13.29	0.00	0.00	3.93
1023	1037	2.336341	AAAAATGAAGGACGCGCCA	58.664	47.368	19.30	5.45	40.02	5.69
1065	1079	5.111293	CCAAAGTCTGCTGTTGAAATTGTT	58.889	37.500	0.00	0.00	0.00	2.83
1093	1107	2.296471	GTCCTCAAGACCGAAGTCAAGA	59.704	50.000	0.00	0.00	46.15	3.02
1429	1447	7.800155	TTGAACTTGATGTGAAGTTATGTCA	57.200	32.000	0.00	0.00	44.46	3.58
1878	1904	5.090139	TCCATTCCCAGAAAATAAAAGGCA	58.910	37.500	0.00	0.00	0.00	4.75
1965	1994	3.930504	GGCTTGGCCCATCAAGAG	58.069	61.111	0.00	0.00	44.98	2.85
1973	2002	3.491208	CCCATCAAGAGGGCTGAAG	57.509	57.895	0.00	0.00	39.96	3.02
2070	2099	2.032634	CGTGGTGTGGTCGGATTGG	61.033	63.158	0.00	0.00	0.00	3.16
2279	2312	8.559536	CACAAGTTGACATATTTCTTGTAGTGT	58.440	33.333	10.54	0.00	44.11	3.55
2280	2313	9.772973	ACAAGTTGACATATTTCTTGTAGTGTA	57.227	29.630	10.54	0.00	44.11	2.90
2283	2316	9.601217	AGTTGACATATTTCTTGTAGTGTATCC	57.399	33.333	0.00	0.00	0.00	2.59
2284	2317	9.378551	GTTGACATATTTCTTGTAGTGTATCCA	57.621	33.333	0.00	0.00	0.00	3.41
2286	2319	7.985184	TGACATATTTCTTGTAGTGTATCCACC	59.015	37.037	0.00	0.00	42.88	4.61
2287	2320	7.857456	ACATATTTCTTGTAGTGTATCCACCA	58.143	34.615	0.00	0.00	42.88	4.17
2288	2321	7.769044	ACATATTTCTTGTAGTGTATCCACCAC	59.231	37.037	0.00	0.00	42.88	4.16
2289	2322	3.861276	TCTTGTAGTGTATCCACCACG	57.139	47.619	0.00	0.00	42.88	4.94
2290	2323	3.423749	TCTTGTAGTGTATCCACCACGA	58.576	45.455	0.00	0.00	42.88	4.35
2291	2324	3.442625	TCTTGTAGTGTATCCACCACGAG	59.557	47.826	0.00	0.00	42.66	4.18
2292	2325	2.097036	TGTAGTGTATCCACCACGAGG	58.903	52.381	0.00	0.00	42.88	4.63
2293	2326	1.407979	GTAGTGTATCCACCACGAGGG	59.592	57.143	3.29	0.00	42.88	4.30
2294	2327	1.153429	GTGTATCCACCACGAGGGC	60.153	63.158	3.29	0.00	42.05	5.19
2295	2328	1.610967	TGTATCCACCACGAGGGCA	60.611	57.895	3.29	0.00	42.05	5.36
2296	2329	1.195442	TGTATCCACCACGAGGGCAA	61.195	55.000	3.29	0.00	42.05	4.52
2297	2330	0.743345	GTATCCACCACGAGGGCAAC	60.743	60.000	3.29	0.00	42.05	4.17
2298	2331	1.195442	TATCCACCACGAGGGCAACA	61.195	55.000	3.29	0.00	42.05	3.33
2299	2332	2.748058	ATCCACCACGAGGGCAACAC	62.748	60.000	3.29	0.00	42.05	3.32
2300	2333	2.978010	CACCACGAGGGCAACACC	60.978	66.667	3.29	0.00	42.05	4.16
2310	2343	2.544726	GGCAACACCCTCTTCTTCG	58.455	57.895	0.00	0.00	0.00	3.79
2311	2344	0.034896	GGCAACACCCTCTTCTTCGA	59.965	55.000	0.00	0.00	0.00	3.71
2312	2345	1.433534	GCAACACCCTCTTCTTCGAG	58.566	55.000	0.00	0.00	0.00	4.04
2313	2346	1.433534	CAACACCCTCTTCTTCGAGC	58.566	55.000	0.00	0.00	0.00	5.03
2314	2347	0.038159	AACACCCTCTTCTTCGAGCG	60.038	55.000	0.00	0.00	0.00	5.03
2315	2348	1.179814	ACACCCTCTTCTTCGAGCGT	61.180	55.000	0.00	0.00	0.00	5.07
2316	2349	0.456995	CACCCTCTTCTTCGAGCGTC	60.457	60.000	0.00	0.00	0.00	5.19
2317	2350	1.139947	CCCTCTTCTTCGAGCGTCC	59.860	63.158	0.00	0.00	0.00	4.79
2318	2351	1.595993	CCCTCTTCTTCGAGCGTCCA	61.596	60.000	0.00	0.00	0.00	4.02
2319	2352	0.179150	CCTCTTCTTCGAGCGTCCAG	60.179	60.000	0.00	0.00	0.00	3.86
2320	2353	0.805614	CTCTTCTTCGAGCGTCCAGA	59.194	55.000	0.00	0.00	0.00	3.86
2321	2354	0.805614	TCTTCTTCGAGCGTCCAGAG	59.194	55.000	0.00	0.00	0.00	3.35
2322	2355	0.800300	CTTCTTCGAGCGTCCAGAGC	60.800	60.000	0.00	0.00	0.00	4.09
2323	2356	1.524008	TTCTTCGAGCGTCCAGAGCA	61.524	55.000	0.00	0.00	37.01	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
154	166	4.096382	TCAAACAAAGCAGAGACAAACCTC	59.904	41.667	0.00	0.00	0.00	3.85
198	211	4.863689	CAGCATGATCTAGCACTAGCATAC	59.136	45.833	11.56	0.00	41.10	2.39
531	544	7.275920	CAAAGCATGGAAGGACTTACTATAGT	58.724	38.462	10.87	10.87	0.00	2.12
544	557	0.971386	AACAGGGCAAAGCATGGAAG	59.029	50.000	0.00	0.00	0.00	3.46
545	558	1.070445	CAAACAGGGCAAAGCATGGAA	59.930	47.619	0.00	0.00	0.00	3.53
734	748	5.647658	TGAGCCGATCATCAAACTAACATTT	59.352	36.000	0.00	0.00	31.12	2.32
954	968	6.460103	AATGATAGGCATTAGTGGGAGATT	57.540	37.500	0.00	0.00	45.16	2.40
1023	1037	1.903183	GGCTCTTCACCTTCTGGTACT	59.097	52.381	0.00	0.00	46.60	2.73
1065	1079	2.036387	TCGGTCTTGAGGACTTGTTCA	58.964	47.619	0.00	0.00	43.97	3.18
1429	1447	5.889853	TCCACATAAGTTCACGACCTACTAT	59.110	40.000	0.00	0.00	0.00	2.12
1878	1904	3.197927	TGGGCCTGGACCAATAATTTT	57.802	42.857	21.88	0.00	38.06	1.82
1889	1915	0.475475	CTTATCTGCATGGGCCTGGA	59.525	55.000	4.53	0.67	40.13	3.86
1965	1994	4.410400	CCCGGTCCACTTCAGCCC	62.410	72.222	0.00	0.00	0.00	5.19
1973	2002	0.759346	ATAGAATCAGCCCGGTCCAC	59.241	55.000	0.00	0.00	0.00	4.02
2279	2312	1.195442	TGTTGCCCTCGTGGTGGATA	61.195	55.000	2.33	0.00	36.04	2.59
2280	2313	2.351276	GTTGCCCTCGTGGTGGAT	59.649	61.111	2.33	0.00	36.04	3.41
2281	2314	3.164977	TGTTGCCCTCGTGGTGGA	61.165	61.111	2.33	0.00	36.04	4.02
2282	2315	2.978010	GTGTTGCCCTCGTGGTGG	60.978	66.667	2.33	0.00	36.04	4.61
2283	2316	2.978010	GGTGTTGCCCTCGTGGTG	60.978	66.667	2.33	0.00	36.04	4.17
2292	2325	0.034896	TCGAAGAAGAGGGTGTTGCC	59.965	55.000	0.00	0.00	0.00	4.52
2293	2326	1.433534	CTCGAAGAAGAGGGTGTTGC	58.566	55.000	0.00	0.00	34.09	4.17
2294	2327	1.433534	GCTCGAAGAAGAGGGTGTTG	58.566	55.000	0.00	0.00	38.63	3.33
2295	2328	0.038159	CGCTCGAAGAAGAGGGTGTT	60.038	55.000	3.35	0.00	43.52	3.32
2296	2329	1.587054	CGCTCGAAGAAGAGGGTGT	59.413	57.895	3.35	0.00	43.52	4.16
2297	2330	4.485554	CGCTCGAAGAAGAGGGTG	57.514	61.111	3.35	0.00	43.52	4.61
2300	2333	0.179150	CTGGACGCTCGAAGAAGAGG	60.179	60.000	0.00	0.00	38.63	3.69
2301	2334	0.805614	TCTGGACGCTCGAAGAAGAG	59.194	55.000	0.00	0.00	41.03	2.85
2302	2335	0.805614	CTCTGGACGCTCGAAGAAGA	59.194	55.000	0.00	0.00	34.09	2.87
2303	2336	0.800300	GCTCTGGACGCTCGAAGAAG	60.800	60.000	0.00	0.00	34.09	2.85
2304	2337	1.213013	GCTCTGGACGCTCGAAGAA	59.787	57.895	0.00	0.00	34.09	2.52
2305	2338	1.971695	TGCTCTGGACGCTCGAAGA	60.972	57.895	0.00	0.00	0.00	2.87
2306	2339	2.568612	TGCTCTGGACGCTCGAAG	59.431	61.111	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.