AutoCloner

Multiple sequence alignment - TraesCS7D01G164300

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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	TraesCS7D01G164300	chr7D	100.000	3432	0	0	1	3432	113582075	113585506	0.000000e+00	6338.0
1	TraesCS7D01G164300	chr7D	88.430	1573	130	25	991	2523	500776216	500777776	0.000000e+00	1849.0
2	TraesCS7D01G164300	chr7D	93.875	751	43	2	5	754	500774287	500775035	0.000000e+00	1129.0
3	TraesCS7D01G164300	chr7D	89.081	751	77	4	5	753	523127613	523126866	0.000000e+00	928.0
4	TraesCS7D01G164300	chr7D	89.452	730	73	4	26	754	523056458	523055732	0.000000e+00	918.0
5	TraesCS7D01G164300	chr7D	88.431	752	84	2	5	755	523133270	523132521	0.000000e+00	904.0
6	TraesCS7D01G164300	chr7D	95.610	205	6	1	787	991	500775981	500776182	3.300000e-85	326.0
7	TraesCS7D01G164300	chr7D	98.182	55	1	0	2539	2593	113584558	113584612	2.820000e-16	97.1
8	TraesCS7D01G164300	chr7B	94.540	2271	88	15	1040	3293	73176689	73178940	0.000000e+00	3474.0
9	TraesCS7D01G164300	chr7B	91.465	1570	100	14	991	2538	528873874	528875431	0.000000e+00	2126.0
10	TraesCS7D01G164300	chr7B	88.336	1689	148	20	887	2538	664398977	664397301	0.000000e+00	1982.0
11	TraesCS7D01G164300	chr7B	95.916	759	15	5	3	753	73174708	73175458	0.000000e+00	1216.0
12	TraesCS7D01G164300	chr7B	94.290	753	37	6	5	755	528872183	528872931	0.000000e+00	1147.0
13	TraesCS7D01G164300	chr7B	89.096	752	79	2	5	755	557491063	557490314	0.000000e+00	931.0
14	TraesCS7D01G164300	chr7B	98.008	251	4	1	787	1036	73176251	73176501	5.260000e-118	435.0
15	TraesCS7D01G164300	chr7B	92.248	258	16	2	2538	2795	528875376	528875629	2.520000e-96	363.0
16	TraesCS7D01G164300	chr7B	90.347	259	17	3	2537	2795	73140246	73140496	1.970000e-87	333.0
17	TraesCS7D01G164300	chr7B	92.683	205	6	4	787	991	528873645	528873840	1.560000e-73	287.0
18	TraesCS7D01G164300	chr7B	88.816	152	8	3	2795	2946	73140539	73140681	9.790000e-41	178.0
19	TraesCS7D01G164300	chr7B	90.385	104	6	1	2538	2641	664397356	664397257	2.150000e-27	134.0
20	TraesCS7D01G164300	chr7B	98.182	55	1	0	2539	2593	73178131	73178185	2.820000e-16	97.1
21	TraesCS7D01G164300	chr7B	97.436	39	1	0	2795	2833	528875672	528875710	2.210000e-07	67.6
22	TraesCS7D01G164300	chr7A	95.359	1659	63	8	1261	2913	619305129	619306779	0.000000e+00	2625.0
23	TraesCS7D01G164300	chr7A	88.345	1776	159	32	787	2538	566790298	566792049	0.000000e+00	2089.0
24	TraesCS7D01G164300	chr7A	86.857	1575	150	25	991	2523	566989673	566991232	0.000000e+00	1709.0
25	TraesCS7D01G164300	chr7A	94.800	750	36	2	7	755	566788785	566789532	0.000000e+00	1166.0
26	TraesCS7D01G164300	chr7A	89.589	730	72	4	26	754	603331099	603330373	0.000000e+00	924.0
27	TraesCS7D01G164300	chr7A	94.048	420	18	2	2811	3223	619306779	619307198	6.250000e-177	630.0
28	TraesCS7D01G164300	chr7A	91.532	248	13	6	2538	2783	566791994	566792235	5.490000e-88	335.0
29	TraesCS7D01G164300	chr7A	88.048	251	20	5	2538	2783	566911924	566912169	4.330000e-74	289.0
30	TraesCS7D01G164300	chr7A	89.873	158	9	2	817	974	566910176	566910326	2.700000e-46	196.0
31	TraesCS7D01G164300	chr7A	83.761	117	10	6	3290	3400	619307509	619307622	6.060000e-18	102.0
32	TraesCS7D01G164300	chr7A	100.000	32	0	0	3031	3062	619307236	619307267	3.700000e-05	60.2
33	TraesCS7D01G164300	chr3A	89.086	1576	136	17	992	2538	732404542	732402974	0.000000e+00	1925.0
34	TraesCS7D01G164300	chr3A	82.424	165	14	10	817	975	732404762	732404607	2.780000e-26	130.0
35	TraesCS7D01G164300	chrUn	87.861	1557	153	15	991	2522	86612154	86613699	0.000000e+00	1796.0
36	TraesCS7D01G164300	chrUn	87.302	189	11	5	787	969	86611915	86612096	1.610000e-48	204.0
37	TraesCS7D01G164300	chr3B	87.642	1586	145	22	991	2537	810194225	810192652	0.000000e+00	1796.0
38	TraesCS7D01G164300	chr3B	86.234	1155	118	19	991	2122	806058477	806057341	0.000000e+00	1214.0
39	TraesCS7D01G164300	chr3D	86.904	1153	111	21	991	2122	598726091	598724958	0.000000e+00	1256.0

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	TraesCS7D01G164300	chr7D	113582075	113585506	3431	False	3217.550000	6338	99.091000	1	3432	2	chr7D.!!$F1	3431
1	TraesCS7D01G164300	chr7D	500774287	500777776	3489	False	1101.333333	1849	92.638333	5	2523	3	chr7D.!!$F2	2518
2	TraesCS7D01G164300	chr7D	523126866	523127613	747	True	928.000000	928	89.081000	5	753	1	chr7D.!!$R2	748
3	TraesCS7D01G164300	chr7D	523055732	523056458	726	True	918.000000	918	89.452000	26	754	1	chr7D.!!$R1	728
4	TraesCS7D01G164300	chr7D	523132521	523133270	749	True	904.000000	904	88.431000	5	755	1	chr7D.!!$R3	750
5	TraesCS7D01G164300	chr7B	73174708	73178940	4232	False	1305.525000	3474	96.661500	3	3293	4	chr7B.!!$F2	3290
6	TraesCS7D01G164300	chr7B	664397257	664398977	1720	True	1058.000000	1982	89.360500	887	2641	2	chr7B.!!$R2	1754
7	TraesCS7D01G164300	chr7B	557490314	557491063	749	True	931.000000	931	89.096000	5	755	1	chr7B.!!$R1	750
8	TraesCS7D01G164300	chr7B	528872183	528875710	3527	False	798.120000	2126	93.624400	5	2833	5	chr7B.!!$F3	2828
9	TraesCS7D01G164300	chr7A	566989673	566991232	1559	False	1709.000000	1709	86.857000	991	2523	1	chr7A.!!$F1	1532
10	TraesCS7D01G164300	chr7A	566788785	566792235	3450	False	1196.666667	2089	91.559000	7	2783	3	chr7A.!!$F2	2776
11	TraesCS7D01G164300	chr7A	603330373	603331099	726	True	924.000000	924	89.589000	26	754	1	chr7A.!!$R1	728
12	TraesCS7D01G164300	chr7A	619305129	619307622	2493	False	854.300000	2625	93.292000	1261	3400	4	chr7A.!!$F4	2139
13	TraesCS7D01G164300	chr7A	566910176	566912169	1993	False	242.500000	289	88.960500	817	2783	2	chr7A.!!$F3	1966
14	TraesCS7D01G164300	chr3A	732402974	732404762	1788	True	1027.500000	1925	85.755000	817	2538	2	chr3A.!!$R1	1721
15	TraesCS7D01G164300	chrUn	86611915	86613699	1784	False	1000.000000	1796	87.581500	787	2522	2	chrUn.!!$F1	1735
16	TraesCS7D01G164300	chr3B	810192652	810194225	1573	True	1796.000000	1796	87.642000	991	2537	1	chr3B.!!$R2	1546
17	TraesCS7D01G164300	chr3B	806057341	806058477	1136	True	1214.000000	1214	86.234000	991	2122	1	chr3B.!!$R1	1131
18	TraesCS7D01G164300	chr3D	598724958	598726091	1133	True	1256.000000	1256	86.904000	991	2122	1	chr3D.!!$R1	1131

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
654	656	0.039437	GAAGGACGTCTGCGACAGAA	60.039	55.0	16.46	0.0	42.46	3.02	F
1906	3200	0.179059	TATCGGTTGCACGCCATCAT	60.179	50.0	7.21	0.0	0.00	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2293	3595	1.225855	CAGTGTACAAAAGCTCCGCA	58.774	50.000	0.00	0.0	0.00	5.69	R
3361	5149	1.604593	TGGCCTCCTGCAAAAGCTC	60.605	57.895	3.32	0.0	43.89	4.09	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	1.283793	CGCTGAACAAGGCCACAAG	59.716	57.895	5.01	0.00	0.00	3.16
135	137	1.284297	CGCTCGCTCACATTGTGTCA	61.284	55.000	16.06	0.00	34.79	3.58
586	588	1.153745	CCTTCTTCTCCGACCAGCG	60.154	63.158	0.00	0.00	40.47	5.18
654	656	0.039437	GAAGGACGTCTGCGACAGAA	60.039	55.000	16.46	0.00	42.46	3.02
767	1555	1.538512	GCGGAGGTTAACTGAAAACCC	59.461	52.381	5.42	4.91	46.33	4.11
774	1562	3.995048	GGTTAACTGAAAACCCGAGAGAG	59.005	47.826	5.42	0.00	40.49	3.20
1053	2273	2.622436	CTCCTCGTTCTGAATCCCAAC	58.378	52.381	0.00	0.00	0.00	3.77
1906	3200	0.179059	TATCGGTTGCACGCCATCAT	60.179	50.000	7.21	0.00	0.00	2.45
1963	3257	3.451141	TTGAAAACTTGGGTGCATCAC	57.549	42.857	0.00	0.00	0.00	3.06
1980	3274	7.090808	GTGCATCACTCCATAACGATAATCTA	58.909	38.462	0.00	0.00	0.00	1.98
2140	3442	3.722908	TTCGATGGGGGTTTGATTGTA	57.277	42.857	0.00	0.00	0.00	2.41
2293	3595	0.108424	GACAGCAAGGCGAGTCATCT	60.108	55.000	10.48	0.00	37.98	2.90
2580	3940	7.004086	AGTTTCATGTATTTCAAAGACTGGGA	58.996	34.615	0.00	0.00	0.00	4.37
2685	4046	7.828508	AATGTCATATGCCACATCTACAATT	57.171	32.000	9.73	0.00	31.79	2.32
2686	4047	7.828508	ATGTCATATGCCACATCTACAATTT	57.171	32.000	4.59	0.00	0.00	1.82
2766	4136	3.196469	TGGCAATTTCACACCTGTTGAAA	59.804	39.130	0.31	0.31	36.23	2.69
2790	4161	7.690952	ATTTTTGTTGTCGGCTTATAGGTAA	57.309	32.000	0.00	0.00	0.00	2.85
3025	4550	4.037923	TGCTGAGTTTCAGTTTTGGAATCC	59.962	41.667	7.80	0.00	45.94	3.01
3082	4607	4.565166	CACTATGCACAAAATTCAGCCATG	59.435	41.667	0.00	0.00	0.00	3.66
3139	4670	9.683069	AGATTCAATTGTATTGAACACAGAAAC	57.317	29.630	14.93	0.00	40.70	2.78
3144	4675	5.651172	TGTATTGAACACAGAAACGACAG	57.349	39.130	0.00	0.00	31.43	3.51
3153	4684	5.784177	ACACAGAAACGACAGATACTCAAT	58.216	37.500	0.00	0.00	0.00	2.57
3226	4770	3.646715	TTCCTTGGGCCACCTCGG	61.647	66.667	5.23	4.71	37.76	4.63
3249	4793	1.439353	CCATTGGGTTCGCAGGATCG	61.439	60.000	0.00	0.00	0.00	3.69
3302	5077	1.134965	CAGGTGATTGTCCTCTCCGTC	60.135	57.143	0.00	0.00	34.66	4.79

Showing 1 to 25 of 40 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	0.602905	GTGGCCTTGTTCAGCGTACT	60.603	55.000	3.32	0.00	2.73
1	2	0.882927	TGTGGCCTTGTTCAGCGTAC	60.883	55.000	3.32	0.00	3.67
22	23	1.225704	CTTGAGCATCCAGGGGTCC	59.774	63.158	0.00	31.96	4.46
586	588	1.741770	ACGAAGCGGCTGTTGATCC	60.742	57.895	1.81	0.00	3.36
654	656	2.561885	CGTCCTCTCAACGACGCT	59.438	61.111	0.00	44.54	5.07
848	1807	2.954611	GACCGGCAAAGCAAGTCC	59.045	61.111	0.00	0.00	3.85
1327	2565	5.664457	ACCGGGGATTACATAGTACTTCTTT	59.336	40.000	6.32	0.00	2.52
1348	2605	2.557317	AGGGTTAATTACGATGCACCG	58.443	47.619	0.00	0.00	4.94
1906	3200	2.433604	TGTAGTTGTTGGTTCGGGTGTA	59.566	45.455	0.00	0.00	2.90
2188	3490	3.056749	ACAACTCTGAGCCTTTACCTACG	60.057	47.826	4.19	0.00	3.51
2293	3595	1.225855	CAGTGTACAAAAGCTCCGCA	58.774	50.000	0.00	0.00	5.69
2614	3974	7.077605	TCTTCACAAAAGAAGATGCAAATACG	58.922	34.615	2.50	46.62	3.06
2744	4113	2.382882	TCAACAGGTGTGAAATTGCCA	58.617	42.857	0.00	0.00	4.92
2766	4136	7.690952	TTACCTATAAGCCGACAACAAAAAT	57.309	32.000	0.00	0.00	1.82
2790	4161	4.233287	ACCCTCCTTAGTCCTGAGTTAGAT	59.767	45.833	0.00	0.00	1.98
2854	4369	3.125487	TGAACACGAACACGAACACAAAT	59.875	39.130	0.00	0.00	2.32
3025	4550	9.978044	TGATCTTATCATGTGAAGATGAACTAG	57.022	33.333	21.69	41.43	2.57
3082	4607	6.586082	GTGGTGTTTGAATCATGGATTTGTAC	59.414	38.462	0.00	31.89	2.90
3139	4670	5.869344	TCCAAACTTCATTGAGTATCTGTCG	59.131	40.000	0.00	34.92	4.35
3153	4684	8.293867	CGTTTTCCTATGTTTATCCAAACTTCA	58.706	33.333	2.33	43.73	3.02
3226	4770	3.039202	CTGCGAACCCAATGGCGTC	62.039	63.158	0.00	33.59	5.19
3355	5143	4.766088	CTGCAAAAGCTCGCCGCC	62.766	66.667	0.00	40.39	6.13
3356	5144	4.766088	CCTGCAAAAGCTCGCCGC	62.766	66.667	0.00	39.57	6.53
3357	5145	3.031964	CTCCTGCAAAAGCTCGCCG	62.032	63.158	0.00	0.00	6.46
3358	5146	2.694760	CCTCCTGCAAAAGCTCGCC	61.695	63.158	0.00	0.00	5.54

Showing 1 to 25 of 30 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.