AutoCloner

Multiple sequence alignment - TraesCS4A01G224900

Loading Multiple Alignment...

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	TraesCS4A01G224900	chr4A	100.000	3034	0	0	1	3034	532832164	532835197	0.000000e+00	5603.0
1	TraesCS4A01G224900	chr4A	98.410	629	9	1	206	834	532896291	532896918	0.000000e+00	1105.0
2	TraesCS4A01G224900	chr4A	94.560	625	23	7	908	1528	532897164	532897781	0.000000e+00	955.0
3	TraesCS4A01G224900	chr4A	97.070	512	14	1	1701	2211	532897822	532898333	0.000000e+00	861.0
4	TraesCS4A01G224900	chr4A	79.478	882	159	14	1089	1963	533844309	533843443	9.300000e-170	606.0
5	TraesCS4A01G224900	chr4A	97.738	221	4	1	1	221	532896059	532896278	2.210000e-101	379.0
6	TraesCS4A01G224900	chr4A	92.857	56	3	1	1447	1502	532897774	532897828	2.510000e-11	80.5
7	TraesCS4A01G224900	chr4D	92.346	1594	82	22	562	2136	63574171	63572599	0.000000e+00	2231.0
8	TraesCS4A01G224900	chr4D	90.702	484	41	2	1656	2139	63300032	63299553	2.550000e-180	641.0
9	TraesCS4A01G224900	chr4D	79.478	882	159	14	1089	1963	62825853	62826719	9.300000e-170	606.0
10	TraesCS4A01G224900	chr4D	92.973	370	22	3	8	375	63578221	63577854	1.240000e-148	536.0
11	TraesCS4A01G224900	chr4B	93.696	1380	61	15	764	2136	94101287	94099927	0.000000e+00	2043.0
12	TraesCS4A01G224900	chr4B	79.365	882	160	16	1089	1963	92951005	92951871	4.330000e-168	601.0
13	TraesCS4A01G224900	chr4B	93.122	378	22	3	1	376	94178270	94177895	4.420000e-153	551.0
14	TraesCS4A01G224900	chr4B	84.211	209	21	6	562	769	94101755	94101558	3.090000e-45	193.0
15	TraesCS4A01G224900	chr3B	99.180	732	6	0	2303	3034	452987911	452987180	0.000000e+00	1319.0
16	TraesCS4A01G224900	chr5B	98.118	744	11	2	2291	3034	470247549	470246809	0.000000e+00	1293.0
17	TraesCS4A01G224900	chr2A	98.095	735	14	0	2300	3034	391912983	391912249	0.000000e+00	1280.0
18	TraesCS4A01G224900	chr2A	86.567	67	5	4	2291	2354	719357341	719357276	1.510000e-08	71.3
19	TraesCS4A01G224900	chr7A	94.324	740	33	7	2298	3034	524214734	524214001	0.000000e+00	1125.0
20	TraesCS4A01G224900	chr7A	95.094	693	29	5	2345	3034	49365015	49364325	0.000000e+00	1086.0
21	TraesCS4A01G224900	chr7A	93.117	741	41	7	2298	3034	552423894	552423160	0.000000e+00	1077.0
22	TraesCS4A01G224900	chr2B	92.059	743	55	4	2295	3034	197592469	197593210	0.000000e+00	1042.0
23	TraesCS4A01G224900	chr2B	83.951	81	7	6	2277	2354	53916	53993	4.200000e-09	73.1
24	TraesCS4A01G224900	chr1B	92.722	687	24	10	2316	2987	540134102	540133427	0.000000e+00	968.0
25	TraesCS4A01G224900	chr7B	89.946	368	31	6	2670	3034	256488133	256487769	1.270000e-128	470.0
26	TraesCS4A01G224900	chr7B	73.674	509	99	25	1277	1767	61113598	61113107	6.730000e-37	165.0
27	TraesCS4A01G224900	chr3D	89.674	184	15	2	2852	3034	165466463	165466643	6.540000e-57	231.0
28	TraesCS4A01G224900	chr2D	88.966	145	14	2	2467	2609	158231013	158231157	8.640000e-41	178.0
29	TraesCS4A01G224900	chr2D	72.927	410	79	26	1271	1659	87816203	87815805	2.470000e-21	113.0
30	TraesCS4A01G224900	chr1A	84.270	89	9	5	2269	2354	474154384	474154470	6.970000e-12	82.4

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	TraesCS4A01G224900	chr4A	532832164	532835197	3033	False	5603.0	5603	100.0000	1	3034	1	chr4A.!!$F1	3033
1	TraesCS4A01G224900	chr4A	532896059	532898333	2274	False	676.1	1105	96.1270	1	2211	5	chr4A.!!$F2	2210
2	TraesCS4A01G224900	chr4A	533843443	533844309	866	True	606.0	606	79.4780	1089	1963	1	chr4A.!!$R1	874
3	TraesCS4A01G224900	chr4D	63572599	63578221	5622	True	1383.5	2231	92.6595	8	2136	2	chr4D.!!$R2	2128
4	TraesCS4A01G224900	chr4D	62825853	62826719	866	False	606.0	606	79.4780	1089	1963	1	chr4D.!!$F1	874
5	TraesCS4A01G224900	chr4B	94099927	94101755	1828	True	1118.0	2043	88.9535	562	2136	2	chr4B.!!$R2	1574
6	TraesCS4A01G224900	chr4B	92951005	92951871	866	False	601.0	601	79.3650	1089	1963	1	chr4B.!!$F1	874
7	TraesCS4A01G224900	chr3B	452987180	452987911	731	True	1319.0	1319	99.1800	2303	3034	1	chr3B.!!$R1	731
8	TraesCS4A01G224900	chr5B	470246809	470247549	740	True	1293.0	1293	98.1180	2291	3034	1	chr5B.!!$R1	743
9	TraesCS4A01G224900	chr2A	391912249	391912983	734	True	1280.0	1280	98.0950	2300	3034	1	chr2A.!!$R1	734
10	TraesCS4A01G224900	chr7A	524214001	524214734	733	True	1125.0	1125	94.3240	2298	3034	1	chr7A.!!$R2	736
11	TraesCS4A01G224900	chr7A	49364325	49365015	690	True	1086.0	1086	95.0940	2345	3034	1	chr7A.!!$R1	689
12	TraesCS4A01G224900	chr7A	552423160	552423894	734	True	1077.0	1077	93.1170	2298	3034	1	chr7A.!!$R3	736
13	TraesCS4A01G224900	chr2B	197592469	197593210	741	False	1042.0	1042	92.0590	2295	3034	1	chr2B.!!$F2	739
14	TraesCS4A01G224900	chr1B	540133427	540134102	675	True	968.0	968	92.7220	2316	2987	1	chr1B.!!$R1	671

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
977	4961	0.109873	ACTACACTTCGAGAACCGCG	60.11	55.0	0.0	0.0	38.37	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2797	6816	1.679944	CCATCTGGAACCGCATCAACT	60.68	52.381	0.0	0.0	37.39	3.16	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
50	51	9.710979	TCAGTATCAAGTTTTTAAGTTTTCGTG	57.289	29.630	0.00	0.00	0.00	4.35
92	93	9.010029	TGTGAGTTTCTTCTACTTTGTTTCTTT	57.990	29.630	0.00	0.00	0.00	2.52
376	1012	6.844696	TCGGTATCACAATTTAATCTCTGC	57.155	37.500	0.00	0.00	0.00	4.26
582	4107	3.375299	CCGAATCAAATTCAGGGTGACTC	59.625	47.826	1.07	0.00	39.22	3.36
643	4171	8.845227	TGTGCTCTCATTTTTGAACTTATTGTA	58.155	29.630	0.00	0.00	0.00	2.41
805	4610	5.307196	ACTTCATCAACACACCTAACCTAGT	59.693	40.000	0.00	0.00	0.00	2.57
834	4640	8.147058	AGTAATAACCTCATTATCACTGCAGAG	58.853	37.037	23.35	13.75	31.41	3.35
835	4641	4.833478	AACCTCATTATCACTGCAGAGT	57.167	40.909	23.35	8.10	0.00	3.24
840	4669	6.326064	ACCTCATTATCACTGCAGAGTAGATT	59.674	38.462	23.35	1.67	0.00	2.40
842	4671	8.028354	CCTCATTATCACTGCAGAGTAGATTAG	58.972	40.741	23.35	9.02	0.00	1.73
882	4723	4.342862	CTCCACCAGAGAGAGTTCAAAA	57.657	45.455	0.00	0.00	46.50	2.44
928	4907	1.660242	ACCCGTTACCCAACCACTAT	58.340	50.000	0.00	0.00	0.00	2.12
945	4929	6.896883	ACCACTATAAATCCTACTCAAACCC	58.103	40.000	0.00	0.00	0.00	4.11
976	4960	1.719780	CAACTACACTTCGAGAACCGC	59.280	52.381	0.00	0.00	38.37	5.68
977	4961	0.109873	ACTACACTTCGAGAACCGCG	60.110	55.000	0.00	0.00	38.37	6.46
1290	5277	2.722201	GCCTCTCCCCGTGATCGTT	61.722	63.158	0.00	0.00	35.01	3.85
1477	5464	4.493747	GCTTCCTCGACGACCCGG	62.494	72.222	0.00	0.00	0.00	5.73
1850	5847	2.842462	ATCGGCGGCTATGACCCA	60.842	61.111	7.21	0.00	0.00	4.51
1958	5955	1.267121	CGTTCTTCCTCTTCCCTGGA	58.733	55.000	0.00	0.00	0.00	3.86
2136	6137	2.319472	GCTGCGACATTCTTTTGGTTC	58.681	47.619	0.00	0.00	0.00	3.62
2138	6139	3.188460	GCTGCGACATTCTTTTGGTTCTA	59.812	43.478	0.00	0.00	0.00	2.10
2154	6155	5.734720	TGGTTCTAGGAATTGCTAACTCAG	58.265	41.667	8.14	0.00	0.00	3.35
2194	6195	9.877222	TTAAGGATGTCATATCTAAGTACAGGA	57.123	33.333	0.00	0.00	0.00	3.86
2211	6212	8.508883	AGTACAGGACCGTCAGATTATATATC	57.491	38.462	0.00	0.00	0.00	1.63
2212	6213	8.330247	AGTACAGGACCGTCAGATTATATATCT	58.670	37.037	0.00	0.00	0.00	1.98
2213	6214	8.958506	GTACAGGACCGTCAGATTATATATCTT	58.041	37.037	0.00	0.00	0.00	2.40
2214	6215	8.423906	ACAGGACCGTCAGATTATATATCTTT	57.576	34.615	0.00	0.00	0.00	2.52
2215	6216	9.529823	ACAGGACCGTCAGATTATATATCTTTA	57.470	33.333	0.00	0.00	0.00	1.85
2246	6247	7.951347	TCGTTACCTCTTTATCTTTACCTCT	57.049	36.000	0.00	0.00	0.00	3.69
2247	6248	8.358582	TCGTTACCTCTTTATCTTTACCTCTT	57.641	34.615	0.00	0.00	0.00	2.85
2248	6249	8.810041	TCGTTACCTCTTTATCTTTACCTCTTT	58.190	33.333	0.00	0.00	0.00	2.52
2252	6253	8.682297	ACCTCTTTATCTTTACCTCTTTACCT	57.318	34.615	0.00	0.00	0.00	3.08
2253	6254	8.760735	ACCTCTTTATCTTTACCTCTTTACCTC	58.239	37.037	0.00	0.00	0.00	3.85
2254	6255	8.983789	CCTCTTTATCTTTACCTCTTTACCTCT	58.016	37.037	0.00	0.00	0.00	3.69
2260	6261	8.682297	ATCTTTACCTCTTTACCTCTTTACCT	57.318	34.615	0.00	0.00	0.00	3.08
2261	6262	9.779951	ATCTTTACCTCTTTACCTCTTTACCTA	57.220	33.333	0.00	0.00	0.00	3.08
2262	6263	9.779951	TCTTTACCTCTTTACCTCTTTACCTAT	57.220	33.333	0.00	0.00	0.00	2.57
2797	6816	4.087892	GAGCTCCAAGGCAGGCGA	62.088	66.667	0.87	0.00	34.17	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	5.502153	ACTCACACGTATAGAACATCCTC	57.498	43.478	0.00	0.00	0.00	3.71
376	1012	4.113354	GTCACGGCTATACAAGAGAAAGG	58.887	47.826	0.00	0.00	0.00	3.11
834	4640	5.479306	TGTTTGAGAGTGTGGCTAATCTAC	58.521	41.667	0.00	0.00	0.00	2.59
835	4641	5.738619	TGTTTGAGAGTGTGGCTAATCTA	57.261	39.130	0.00	0.00	0.00	1.98
840	4669	3.388024	AGACTTGTTTGAGAGTGTGGCTA	59.612	43.478	0.00	0.00	0.00	3.93
842	4671	2.545946	GAGACTTGTTTGAGAGTGTGGC	59.454	50.000	0.00	0.00	0.00	5.01
882	4723	1.494721	TGCCTCTGGTGGAGACTTTTT	59.505	47.619	0.00	0.00	44.45	1.94
887	4728	0.613292	TCTCTGCCTCTGGTGGAGAC	60.613	60.000	0.00	0.00	44.45	3.36
889	4730	0.614415	ACTCTCTGCCTCTGGTGGAG	60.614	60.000	0.00	0.00	41.51	3.86
890	4731	0.704664	TACTCTCTGCCTCTGGTGGA	59.295	55.000	0.00	0.00	0.00	4.02
891	4732	0.820871	GTACTCTCTGCCTCTGGTGG	59.179	60.000	0.00	0.00	0.00	4.61
892	4733	0.820871	GGTACTCTCTGCCTCTGGTG	59.179	60.000	0.00	0.00	0.00	4.17
893	4734	0.324830	GGGTACTCTCTGCCTCTGGT	60.325	60.000	0.00	0.00	0.00	4.00
894	4735	1.388065	CGGGTACTCTCTGCCTCTGG	61.388	65.000	0.00	0.00	0.00	3.86
928	4907	2.572556	TGCCGGGTTTGAGTAGGATTTA	59.427	45.455	2.18	0.00	0.00	1.40
945	4929	2.173382	GTAGTTGCGTTGCTGCCG	59.827	61.111	0.00	0.00	0.00	5.69
959	4943	0.797249	CCGCGGTTCTCGAAGTGTAG	60.797	60.000	19.50	0.00	42.43	2.74
1477	5464	2.202974	GTCCGCCGGGTGGTTATC	60.203	66.667	25.20	11.29	37.67	1.75
1583	5574	1.771073	CGTTCTTGAACGCAGGCACA	61.771	55.000	20.33	0.00	39.43	4.57
1622	5613	1.304282	GAAGAAGGGCTGGATGGCA	59.696	57.895	0.00	0.00	43.83	4.92
1797	5794	4.785453	GAAGGCCGGGCTGTCCAG	62.785	72.222	33.52	0.00	34.36	3.86
1912	5909	2.180017	CGTCCGGGTACTCCAACG	59.820	66.667	0.00	0.00	37.78	4.10
1958	5955	3.185365	TTGCGCGCGTCATCGAAT	61.185	55.556	32.35	0.00	39.71	3.34
2136	6137	8.402798	TCTAGATCTGAGTTAGCAATTCCTAG	57.597	38.462	5.18	0.00	0.00	3.02
2138	6139	7.508636	TCATCTAGATCTGAGTTAGCAATTCCT	59.491	37.037	5.18	0.00	0.00	3.36
2180	6181	5.363562	TCTGACGGTCCTGTACTTAGATA	57.636	43.478	5.55	0.00	0.00	1.98
2189	6190	8.423906	AAAGATATATAATCTGACGGTCCTGT	57.576	34.615	5.55	0.00	0.00	4.00
2220	6221	9.638176	AGAGGTAAAGATAAAGAGGTAACGATA	57.362	33.333	0.00	0.00	46.39	2.92
2221	6222	8.536340	AGAGGTAAAGATAAAGAGGTAACGAT	57.464	34.615	0.00	0.00	46.39	3.73
2222	6223	7.951347	AGAGGTAAAGATAAAGAGGTAACGA	57.049	36.000	0.00	0.00	46.39	3.85
2223	6224	8.999220	AAAGAGGTAAAGATAAAGAGGTAACG	57.001	34.615	0.00	0.00	46.39	3.18
2226	6227	9.779951	AGGTAAAGAGGTAAAGATAAAGAGGTA	57.220	33.333	0.00	0.00	0.00	3.08
2227	6228	8.682297	AGGTAAAGAGGTAAAGATAAAGAGGT	57.318	34.615	0.00	0.00	0.00	3.85
2228	6229	8.983789	AGAGGTAAAGAGGTAAAGATAAAGAGG	58.016	37.037	0.00	0.00	0.00	3.69
2234	6235	9.779951	AGGTAAAGAGGTAAAGAGGTAAAGATA	57.220	33.333	0.00	0.00	0.00	1.98
2235	6236	8.682297	AGGTAAAGAGGTAAAGAGGTAAAGAT	57.318	34.615	0.00	0.00	0.00	2.40
2236	6237	9.779951	ATAGGTAAAGAGGTAAAGAGGTAAAGA	57.220	33.333	0.00	0.00	0.00	2.52
2797	6816	1.679944	CCATCTGGAACCGCATCAACT	60.680	52.381	0.00	0.00	37.39	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.