AutoCloner

Multiple sequence alignment - TraesCS4B01G025900

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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	TraesCS4B01G025900	chr4B	100.000	2366	0	0	1	2366	18822110	18819745	0.000000e+00	4370.0
1	TraesCS4B01G025900	chr4B	98.473	2226	32	2	1	2224	19198040	19200265	0.000000e+00	3921.0
2	TraesCS4B01G025900	chr4B	98.383	2226	34	2	1	2224	18975303	18973078	0.000000e+00	3910.0
3	TraesCS4B01G025900	chr4B	95.678	833	22	5	1	820	19084483	19085314	0.000000e+00	1327.0
4	TraesCS4B01G025900	chrUn	97.464	2248	33	3	1	2224	52404719	52406966	0.000000e+00	3814.0
5	TraesCS4B01G025900	chrUn	98.601	2144	27	3	84	2224	342029192	342027049	0.000000e+00	3790.0
6	TraesCS4B01G025900	chrUn	98.347	1633	25	2	1	1631	151501250	151502882	0.000000e+00	2865.0
7	TraesCS4B01G025900	chrUn	97.400	1654	20	2	1	1631	378564549	378562896	0.000000e+00	2795.0
8	TraesCS4B01G025900	chrUn	96.840	633	20	0	1	633	357313716	357313084	0.000000e+00	1059.0
9	TraesCS4B01G025900	chrUn	96.696	454	14	1	1	454	324443224	324442772	0.000000e+00	754.0
10	TraesCS4B01G025900	chrUn	97.085	343	9	1	1883	2224	400549069	400549411	5.670000e-161	577.0
11	TraesCS4B01G025900	chrUn	97.085	343	9	1	1883	2224	453606338	453605996	5.670000e-161	577.0
12	TraesCS4B01G025900	chrUn	96.491	57	2	0	1937	1993	86671423	86671479	6.960000e-16	95.3
13	TraesCS4B01G025900	chr4D	88.748	791	45	17	520	1291	9997391	9996626	0.000000e+00	928.0
14	TraesCS4B01G025900	chr4D	94.304	158	7	2	2211	2366	49458993	49458836	8.450000e-60	241.0
15	TraesCS4B01G025900	chr4D	97.727	88	2	0	1287	1374	9996589	9996502	4.070000e-33	152.0
16	TraesCS4B01G025900	chr5D	96.026	151	6	0	2216	2366	565515989	565516139	1.820000e-61	246.0
17	TraesCS4B01G025900	chr5D	92.771	83	4	2	648	729	6375523	6375604	4.130000e-23	119.0
18	TraesCS4B01G025900	chr2D	96.053	152	5	1	2216	2366	643482772	643482923	1.820000e-61	246.0
19	TraesCS4B01G025900	chr2D	91.279	172	12	3	2197	2366	532366445	532366615	5.090000e-57	231.0
20	TraesCS4B01G025900	chr7D	94.410	161	5	4	2206	2366	229486135	229486291	6.530000e-61	244.0
21	TraesCS4B01G025900	chr7D	94.937	158	5	3	2212	2366	253825189	253825346	6.530000e-61	244.0
22	TraesCS4B01G025900	chr5B	95.455	154	6	1	2214	2366	699033044	699032891	6.530000e-61	244.0
23	TraesCS4B01G025900	chr5B	83.529	85	7	3	1593	1670	8543999	8543915	3.260000e-09	73.1
24	TraesCS4B01G025900	chr1A	95.455	154	5	2	2215	2366	68324406	68324559	6.530000e-61	244.0
25	TraesCS4B01G025900	chr1A	92.353	170	8	5	2199	2366	283167545	283167711	1.090000e-58	237.0
26	TraesCS4B01G025900	chr7B	84.892	139	9	5	1865	1991	643351144	643351282	1.910000e-26	130.0
27	TraesCS4B01G025900	chr1D	93.671	79	3	2	652	729	111540755	111540678	1.490000e-22	117.0
28	TraesCS4B01G025900	chr1D	92.857	70	5	0	1870	1939	435755687	435755618	4.160000e-18	102.0
29	TraesCS4B01G025900	chr7A	94.030	67	4	0	1870	1936	474294577	474294643	4.160000e-18	102.0
30	TraesCS4B01G025900	chr6D	96.552	58	2	0	1937	1994	428647350	428647293	1.940000e-16	97.1
31	TraesCS4B01G025900	chr3B	96.552	58	2	0	1937	1994	770007673	770007730	1.940000e-16	97.1
32	TraesCS4B01G025900	chr3B	92.683	41	3	0	1626	1666	829220858	829220898	2.540000e-05	60.2
33	TraesCS4B01G025900	chr1B	84.416	77	3	7	1597	1666	683390390	683390464	1.520000e-07	67.6
34	TraesCS4B01G025900	chr4A	93.023	43	3	0	1670	1712	593703074	593703116	1.960000e-06	63.9
35	TraesCS4B01G025900	chr4A	95.122	41	0	2	1627	1667	628002241	628002279	1.960000e-06	63.9

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	TraesCS4B01G025900	chr4B	18819745	18822110	2365	True	4370	4370	100.0000	1	2366	1	chr4B.!!$R1	2365
1	TraesCS4B01G025900	chr4B	19198040	19200265	2225	False	3921	3921	98.4730	1	2224	1	chr4B.!!$F2	2223
2	TraesCS4B01G025900	chr4B	18973078	18975303	2225	True	3910	3910	98.3830	1	2224	1	chr4B.!!$R2	2223
3	TraesCS4B01G025900	chr4B	19084483	19085314	831	False	1327	1327	95.6780	1	820	1	chr4B.!!$F1	819
4	TraesCS4B01G025900	chrUn	52404719	52406966	2247	False	3814	3814	97.4640	1	2224	1	chrUn.!!$F1	2223
5	TraesCS4B01G025900	chrUn	342027049	342029192	2143	True	3790	3790	98.6010	84	2224	1	chrUn.!!$R2	2140
6	TraesCS4B01G025900	chrUn	151501250	151502882	1632	False	2865	2865	98.3470	1	1631	1	chrUn.!!$F3	1630
7	TraesCS4B01G025900	chrUn	378562896	378564549	1653	True	2795	2795	97.4000	1	1631	1	chrUn.!!$R4	1630
8	TraesCS4B01G025900	chrUn	357313084	357313716	632	True	1059	1059	96.8400	1	633	1	chrUn.!!$R3	632
9	TraesCS4B01G025900	chr4D	9996502	9997391	889	True	540	928	93.2375	520	1374	2	chr4D.!!$R2	854

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
94	95	0.396435	TGCCGAGCGATGGGAATTAT	59.604	50.0	5.68	0.0	0.0	1.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2001	2087	1.619977	GGTCCCTGAACTGCTAGAGGA	60.62	57.143	0.0	0.0	0.0	3.71	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	3.056328	GAAGGGCCGCGCTTCTTT	61.056	61.111	32.17	10.50	45.72	2.52
60	61	1.590147	GACACCCGATCGACCAACT	59.410	57.895	18.66	0.00	0.00	3.16
94	95	0.396435	TGCCGAGCGATGGGAATTAT	59.604	50.000	5.68	0.00	0.00	1.28
339	340	4.018960	TCCTTCCTTTTATCTTCAGCTGCT	60.019	41.667	9.47	0.00	0.00	4.24
382	383	4.106925	CCCTCCAGGCTCCAGCAC	62.107	72.222	0.03	0.00	44.36	4.40
405	406	4.443266	AGCGACGAGAGGCCTTGC	62.443	66.667	6.77	0.00	33.32	4.01
1900	1986	6.697892	CCGCTCCTAAATACAAGTCTTTCTAG	59.302	42.308	0.00	0.00	0.00	2.43
1925	2011	7.339721	AGAGATTCCAAAAGAGACTACATACGA	59.660	37.037	0.00	0.00	0.00	3.43
2001	2087	3.256704	TGGAGGGAGTACAATTCAAGGT	58.743	45.455	0.00	0.00	0.00	3.50
2004	2090	3.519913	GAGGGAGTACAATTCAAGGTCCT	59.480	47.826	0.00	0.00	0.00	3.85
2124	2210	5.809562	AGTATTTCTGATTTCTGACAGCGAG	59.190	40.000	0.00	0.00	34.57	5.03
2267	2354	4.952445	GTAACGATACGTGTTTGTCACA	57.048	40.909	0.00	0.00	46.44	3.58
2268	2355	4.926629	GTAACGATACGTGTTTGTCACAG	58.073	43.478	0.00	0.00	46.44	3.66
2269	2356	3.088194	ACGATACGTGTTTGTCACAGT	57.912	42.857	0.00	0.00	46.44	3.55
2270	2357	4.227512	ACGATACGTGTTTGTCACAGTA	57.772	40.909	0.00	0.00	46.44	2.74
2271	2358	4.224433	ACGATACGTGTTTGTCACAGTAG	58.776	43.478	0.00	0.00	46.44	2.57
2272	2359	4.224433	CGATACGTGTTTGTCACAGTAGT	58.776	43.478	0.00	0.00	46.44	2.73
2273	2360	4.678287	CGATACGTGTTTGTCACAGTAGTT	59.322	41.667	0.00	0.00	46.44	2.24
2274	2361	5.164215	CGATACGTGTTTGTCACAGTAGTTC	60.164	44.000	0.00	0.00	46.44	3.01
2275	2362	2.855963	ACGTGTTTGTCACAGTAGTTCG	59.144	45.455	0.00	0.00	46.44	3.95
2276	2363	2.347292	CGTGTTTGTCACAGTAGTTCGC	60.347	50.000	0.00	0.00	46.44	4.70
2277	2364	2.864343	GTGTTTGTCACAGTAGTTCGCT	59.136	45.455	0.00	0.00	45.51	4.93
2278	2365	3.308866	GTGTTTGTCACAGTAGTTCGCTT	59.691	43.478	0.00	0.00	45.51	4.68
2279	2366	3.936453	TGTTTGTCACAGTAGTTCGCTTT	59.064	39.130	0.00	0.00	0.00	3.51
2280	2367	4.393680	TGTTTGTCACAGTAGTTCGCTTTT	59.606	37.500	0.00	0.00	0.00	2.27
2281	2368	5.106475	TGTTTGTCACAGTAGTTCGCTTTTT	60.106	36.000	0.00	0.00	0.00	1.94
2302	2389	7.583860	TTTTTGTCATGCATGTACATTCATG	57.416	32.000	30.89	30.89	45.37	3.07
2303	2390	6.512342	TTTGTCATGCATGTACATTCATGA	57.488	33.333	33.48	33.48	44.83	3.07
2307	2394	6.512342	TCATGCATGTACATTCATGACAAA	57.488	33.333	33.48	19.70	43.16	2.83
2308	2395	7.102847	TCATGCATGTACATTCATGACAAAT	57.897	32.000	33.48	8.07	43.16	2.32
2309	2396	7.548967	TCATGCATGTACATTCATGACAAATT	58.451	30.769	33.48	7.43	43.16	1.82
2310	2397	8.035984	TCATGCATGTACATTCATGACAAATTT	58.964	29.630	33.48	6.81	43.16	1.82
2311	2398	9.303537	CATGCATGTACATTCATGACAAATTTA	57.696	29.630	32.27	0.29	42.43	1.40
2313	2400	9.303537	TGCATGTACATTCATGACAAATTTATG	57.696	29.630	5.37	0.00	45.41	1.90
2314	2401	9.518906	GCATGTACATTCATGACAAATTTATGA	57.481	29.630	5.37	0.00	45.41	2.15
2336	2423	7.904558	TGACAGAATCAAGATAGTCATACCT	57.095	36.000	8.09	0.00	33.02	3.08
2337	2424	7.720442	TGACAGAATCAAGATAGTCATACCTG	58.280	38.462	8.09	0.00	33.02	4.00
2338	2425	7.343057	TGACAGAATCAAGATAGTCATACCTGT	59.657	37.037	0.00	0.00	33.02	4.00
2339	2426	7.495901	ACAGAATCAAGATAGTCATACCTGTG	58.504	38.462	0.00	0.00	0.00	3.66
2340	2427	6.423302	CAGAATCAAGATAGTCATACCTGTGC	59.577	42.308	0.00	0.00	0.00	4.57
2341	2428	6.326064	AGAATCAAGATAGTCATACCTGTGCT	59.674	38.462	0.00	0.00	0.00	4.40
2342	2429	5.268118	TCAAGATAGTCATACCTGTGCTG	57.732	43.478	0.00	0.00	0.00	4.41
2343	2430	4.711846	TCAAGATAGTCATACCTGTGCTGT	59.288	41.667	0.00	0.00	0.00	4.40
2344	2431	4.927978	AGATAGTCATACCTGTGCTGTC	57.072	45.455	0.00	0.00	0.00	3.51
2345	2432	3.316588	AGATAGTCATACCTGTGCTGTCG	59.683	47.826	0.00	0.00	0.00	4.35
2346	2433	1.257743	AGTCATACCTGTGCTGTCGT	58.742	50.000	0.00	0.00	0.00	4.34
2347	2434	2.443416	AGTCATACCTGTGCTGTCGTA	58.557	47.619	0.00	0.00	0.00	3.43
2348	2435	2.423892	AGTCATACCTGTGCTGTCGTAG	59.576	50.000	0.00	0.00	0.00	3.51
2349	2436	2.422479	GTCATACCTGTGCTGTCGTAGA	59.578	50.000	0.00	0.00	0.00	2.59
2350	2437	3.086282	TCATACCTGTGCTGTCGTAGAA	58.914	45.455	0.00	0.00	39.69	2.10
2351	2438	3.128764	TCATACCTGTGCTGTCGTAGAAG	59.871	47.826	0.00	0.00	39.69	2.85
2352	2439	1.329256	ACCTGTGCTGTCGTAGAAGT	58.671	50.000	0.00	0.00	39.69	3.01
2353	2440	1.000163	ACCTGTGCTGTCGTAGAAGTG	60.000	52.381	0.00	0.00	39.69	3.16
2354	2441	1.000163	CCTGTGCTGTCGTAGAAGTGT	60.000	52.381	0.00	0.00	39.69	3.55
2355	2442	2.545952	CCTGTGCTGTCGTAGAAGTGTT	60.546	50.000	0.00	0.00	39.69	3.32
2356	2443	2.726760	CTGTGCTGTCGTAGAAGTGTTC	59.273	50.000	0.00	0.00	39.69	3.18
2357	2444	2.059541	GTGCTGTCGTAGAAGTGTTCC	58.940	52.381	0.00	0.00	39.69	3.62
2358	2445	1.684450	TGCTGTCGTAGAAGTGTTCCA	59.316	47.619	0.00	0.00	39.69	3.53
2359	2446	2.299013	TGCTGTCGTAGAAGTGTTCCAT	59.701	45.455	0.00	0.00	39.69	3.41
2360	2447	2.668457	GCTGTCGTAGAAGTGTTCCATG	59.332	50.000	0.00	0.00	39.69	3.66
2361	2448	3.614150	GCTGTCGTAGAAGTGTTCCATGA	60.614	47.826	0.00	0.00	39.69	3.07
2362	2449	3.909430	TGTCGTAGAAGTGTTCCATGAC	58.091	45.455	0.00	1.80	39.69	3.06
2363	2450	3.319689	TGTCGTAGAAGTGTTCCATGACA	59.680	43.478	6.17	6.17	42.33	3.58
2364	2451	4.021456	TGTCGTAGAAGTGTTCCATGACAT	60.021	41.667	6.17	0.00	40.63	3.06
2365	2452	4.929808	GTCGTAGAAGTGTTCCATGACATT	59.070	41.667	0.00	0.00	39.69	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	1.589716	ATCTGGCACCAAAGAAGCGC	61.590	55.000	0.00	0.00	0.00	5.92
29	30	2.662596	GTGTCGGATCTGGCACCA	59.337	61.111	25.88	4.28	0.00	4.17
32	33	3.770040	CGGGTGTCGGATCTGGCA	61.770	66.667	4.25	4.25	34.75	4.92
60	61	2.792947	GGCAGGAACCGCCGATCTA	61.793	63.158	9.89	0.00	43.43	1.98
94	95	2.809706	CGGATTCGTTCCCCGCTA	59.190	61.111	0.00	0.00	42.06	4.26
339	340	0.178950	AGAGACAGAGGAGTGCCACA	60.179	55.000	0.00	0.00	36.29	4.17
405	406	4.101448	CAACCCAGGGAGGAGGCG	62.101	72.222	14.54	0.00	41.22	5.52
1375	1460	6.257193	GGAGTTACGGAAATGTAAATCGTCAT	59.743	38.462	7.67	0.00	45.49	3.06
1376	1461	5.577945	GGAGTTACGGAAATGTAAATCGTCA	59.422	40.000	7.67	0.00	45.49	4.35
1900	1986	7.481642	TCGTATGTAGTCTCTTTTGGAATCTC	58.518	38.462	0.00	0.00	0.00	2.75
2001	2087	1.619977	GGTCCCTGAACTGCTAGAGGA	60.620	57.143	0.00	0.00	0.00	3.71
2004	2090	2.254152	ATGGTCCCTGAACTGCTAGA	57.746	50.000	0.00	0.00	0.00	2.43
2124	2210	2.640316	ACTTTGTGGAAGGTGGACTC	57.360	50.000	0.00	0.00	39.79	3.36
2257	2344	3.173668	AGCGAACTACTGTGACAAACA	57.826	42.857	0.00	0.00	37.22	2.83
2258	2345	4.531659	AAAGCGAACTACTGTGACAAAC	57.468	40.909	0.00	0.00	0.00	2.93
2259	2346	5.554822	AAAAAGCGAACTACTGTGACAAA	57.445	34.783	0.00	0.00	0.00	2.83
2287	2374	9.303537	CATAAATTTGTCATGAATGTACATGCA	57.696	29.630	19.01	19.01	44.79	3.96
2288	2375	9.518906	TCATAAATTTGTCATGAATGTACATGC	57.481	29.630	9.63	8.21	44.79	4.06
2310	2397	9.593565	AGGTATGACTATCTTGATTCTGTCATA	57.406	33.333	18.29	18.29	42.64	2.15
2311	2398	8.366401	CAGGTATGACTATCTTGATTCTGTCAT	58.634	37.037	19.47	19.47	44.19	3.06
2312	2399	7.343057	ACAGGTATGACTATCTTGATTCTGTCA	59.657	37.037	12.36	12.36	38.52	3.58
2313	2400	7.651304	CACAGGTATGACTATCTTGATTCTGTC	59.349	40.741	0.00	0.00	0.00	3.51
2314	2401	7.495901	CACAGGTATGACTATCTTGATTCTGT	58.504	38.462	0.00	0.00	0.00	3.41
2315	2402	6.423302	GCACAGGTATGACTATCTTGATTCTG	59.577	42.308	0.00	0.00	0.00	3.02
2316	2403	6.326064	AGCACAGGTATGACTATCTTGATTCT	59.674	38.462	0.00	0.00	0.00	2.40
2317	2404	6.423302	CAGCACAGGTATGACTATCTTGATTC	59.577	42.308	0.00	0.00	0.00	2.52
2318	2405	6.126940	ACAGCACAGGTATGACTATCTTGATT	60.127	38.462	0.00	0.00	0.00	2.57
2319	2406	5.365025	ACAGCACAGGTATGACTATCTTGAT	59.635	40.000	0.00	0.00	0.00	2.57
2320	2407	4.711846	ACAGCACAGGTATGACTATCTTGA	59.288	41.667	0.00	0.00	0.00	3.02
2321	2408	5.016051	ACAGCACAGGTATGACTATCTTG	57.984	43.478	0.00	0.00	0.00	3.02
2322	2409	4.202060	CGACAGCACAGGTATGACTATCTT	60.202	45.833	0.00	0.00	0.00	2.40
2323	2410	3.316588	CGACAGCACAGGTATGACTATCT	59.683	47.826	0.00	0.00	0.00	1.98
2324	2411	3.066900	ACGACAGCACAGGTATGACTATC	59.933	47.826	0.00	0.00	0.00	2.08
2325	2412	3.024547	ACGACAGCACAGGTATGACTAT	58.975	45.455	0.00	0.00	0.00	2.12
2326	2413	2.443416	ACGACAGCACAGGTATGACTA	58.557	47.619	0.00	0.00	0.00	2.59
2327	2414	1.257743	ACGACAGCACAGGTATGACT	58.742	50.000	0.00	0.00	0.00	3.41
2328	2415	2.422479	TCTACGACAGCACAGGTATGAC	59.578	50.000	0.00	0.00	0.00	3.06
2329	2416	2.718563	TCTACGACAGCACAGGTATGA	58.281	47.619	0.00	0.00	0.00	2.15
2330	2417	3.119459	ACTTCTACGACAGCACAGGTATG	60.119	47.826	0.00	0.00	0.00	2.39
2331	2418	3.090037	ACTTCTACGACAGCACAGGTAT	58.910	45.455	0.00	0.00	0.00	2.73
2332	2419	2.228103	CACTTCTACGACAGCACAGGTA	59.772	50.000	0.00	0.00	0.00	3.08
2333	2420	1.000163	CACTTCTACGACAGCACAGGT	60.000	52.381	0.00	0.00	0.00	4.00
2334	2421	1.000163	ACACTTCTACGACAGCACAGG	60.000	52.381	0.00	0.00	0.00	4.00
2335	2422	2.423926	ACACTTCTACGACAGCACAG	57.576	50.000	0.00	0.00	0.00	3.66
2336	2423	2.545113	GGAACACTTCTACGACAGCACA	60.545	50.000	0.00	0.00	0.00	4.57
2337	2424	2.059541	GGAACACTTCTACGACAGCAC	58.940	52.381	0.00	0.00	0.00	4.40
2338	2425	1.684450	TGGAACACTTCTACGACAGCA	59.316	47.619	0.00	0.00	0.00	4.41
2339	2426	2.433868	TGGAACACTTCTACGACAGC	57.566	50.000	0.00	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.