AutoCloner

Multiple sequence alignment - TraesCS5D01G043200

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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	TraesCS5D01G043200	chr5D	100.000	5920	0	0	1832	7751	42905723	42911642	0.000000e+00	10933.0
1	TraesCS5D01G043200	chr5D	100.000	1357	0	0	1	1357	42903892	42905248	0.000000e+00	2507.0
2	TraesCS5D01G043200	chr5D	89.231	195	21	0	2	196	233750529	233750335	2.160000e-60	244.0
3	TraesCS5D01G043200	chr5D	88.776	196	21	1	2	196	208128785	208128980	1.010000e-58	239.0
4	TraesCS5D01G043200	chr5D	90.909	165	15	0	32	196	557190258	557190422	1.010000e-53	222.0
5	TraesCS5D01G043200	chr5B	92.195	4382	232	55	1834	6141	38182485	38178140	0.000000e+00	6096.0
6	TraesCS5D01G043200	chr5B	92.478	678	37	11	6139	6806	38178107	38177434	0.000000e+00	957.0
7	TraesCS5D01G043200	chr5B	88.315	368	18	8	992	1357	38183012	38182668	1.200000e-112	418.0
8	TraesCS5D01G043200	chr5B	91.964	112	8	1	893	1004	38184498	38184388	1.040000e-33	156.0
9	TraesCS5D01G043200	chr5A	94.726	1934	76	12	2982	4897	32665795	32667720	0.000000e+00	2983.0
10	TraesCS5D01G043200	chr5A	91.026	1326	88	16	5449	6751	32668354	32669671	0.000000e+00	1760.0
11	TraesCS5D01G043200	chr5A	89.083	1200	67	25	1836	2984	32664372	32665558	0.000000e+00	1432.0
12	TraesCS5D01G043200	chr5A	88.604	781	51	13	6772	7550	32669998	32670742	0.000000e+00	915.0
13	TraesCS5D01G043200	chr5A	84.336	715	91	17	193	893	514777784	514777077	0.000000e+00	680.0
14	TraesCS5D01G043200	chr5A	84.672	685	88	12	194	871	18547737	18548411	0.000000e+00	667.0
15	TraesCS5D01G043200	chr5A	89.271	494	43	6	4927	5414	32667861	32668350	1.850000e-170	610.0
16	TraesCS5D01G043200	chr5A	89.702	369	14	9	1000	1357	32663952	32664307	4.270000e-122	449.0
17	TraesCS5D01G043200	chr5A	83.824	204	23	7	7549	7750	32670904	32671099	1.330000e-42	185.0
18	TraesCS5D01G043200	chr4D	87.989	716	69	11	193	902	11134490	11133786	0.000000e+00	830.0
19	TraesCS5D01G043200	chr1D	87.658	713	56	17	193	895	437470268	437470958	0.000000e+00	800.0
20	TraesCS5D01G043200	chr1D	93.333	195	13	0	2	196	288910271	288910077	9.840000e-74	289.0
21	TraesCS5D01G043200	chr7D	86.288	722	75	14	193	907	145759105	145759809	0.000000e+00	763.0
22	TraesCS5D01G043200	chr7D	85.513	711	80	16	193	893	619996687	619997384	0.000000e+00	721.0
23	TraesCS5D01G043200	chr7D	84.653	202	30	1	2	203	109168152	109167952	4.740000e-47	200.0
24	TraesCS5D01G043200	chr7D	88.732	71	8	0	7679	7749	94646767	94646697	3.850000e-13	87.9
25	TraesCS5D01G043200	chr2D	86.275	714	75	15	193	893	374111032	374111735	0.000000e+00	754.0
26	TraesCS5D01G043200	chr2D	89.706	204	11	7	2	196	556708554	556708352	1.290000e-62	252.0
27	TraesCS5D01G043200	chr3A	85.997	707	83	11	193	893	31549889	31549193	0.000000e+00	743.0
28	TraesCS5D01G043200	chr3D	85.675	719	75	21	193	895	144255669	144256375	0.000000e+00	732.0
29	TraesCS5D01G043200	chr3D	86.000	200	25	2	11	210	95140010	95139814	2.190000e-50	211.0
30	TraesCS5D01G043200	chr3D	88.889	72	8	0	7679	7750	29244006	29244077	1.070000e-13	89.8
31	TraesCS5D01G043200	chr3D	90.000	60	6	0	7672	7731	416943334	416943393	2.320000e-10	78.7
32	TraesCS5D01G043200	chr3D	96.970	33	1	0	7672	7704	108207746	108207778	1.000000e-03	56.5
33	TraesCS5D01G043200	chr7A	90.816	196	18	0	1	196	574081505	574081700	5.960000e-66	263.0
34	TraesCS5D01G043200	chr2A	87.317	205	17	2	1	196	673146624	673146828	7.830000e-55	226.0
35	TraesCS5D01G043200	chr2A	90.141	71	6	1	7679	7749	738852275	738852206	2.980000e-14	91.6
36	TraesCS5D01G043200	chr2A	100.000	30	0	0	866	895	752819835	752819864	1.000000e-03	56.5
37	TraesCS5D01G043200	chr2B	84.236	203	30	1	1	203	212118267	212118467	6.140000e-46	196.0
38	TraesCS5D01G043200	chr2B	81.013	79	9	5	7674	7750	772349617	772349543	3.020000e-04	58.4
39	TraesCS5D01G043200	chr3B	81.043	211	31	2	2	203	621532372	621532582	8.050000e-35	159.0
40	TraesCS5D01G043200	chr3B	84.810	79	12	0	7672	7750	543153761	543153839	6.450000e-11	80.5
41	TraesCS5D01G043200	chr6D	88.312	77	7	2	7674	7750	44932770	44932696	2.980000e-14	91.6
42	TraesCS5D01G043200	chr1A	86.486	74	9	1	7678	7751	557514460	557514388	6.450000e-11	80.5
43	TraesCS5D01G043200	chrUn	90.698	43	4	0	7673	7715	347178676	347178718	3.020000e-04	58.4
44	TraesCS5D01G043200	chrUn	96.970	33	1	0	7673	7705	216139887	216139855	1.000000e-03	56.5
45	TraesCS5D01G043200	chr6B	90.698	43	4	0	7673	7715	689062537	689062579	3.020000e-04	58.4
46	TraesCS5D01G043200	chr6B	100.000	29	0	0	7674	7702	256977172	256977200	4.000000e-03	54.7

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	TraesCS5D01G043200	chr5D	42903892	42911642	7750	False	6720.000000	10933	100.000000	1	7751	2	chr5D.!!$F3	7750
1	TraesCS5D01G043200	chr5B	38177434	38184498	7064	True	1906.750000	6096	91.238000	893	6806	4	chr5B.!!$R1	5913
2	TraesCS5D01G043200	chr5A	32663952	32671099	7147	False	1190.571429	2983	89.462286	1000	7750	7	chr5A.!!$F2	6750
3	TraesCS5D01G043200	chr5A	514777077	514777784	707	True	680.000000	680	84.336000	193	893	1	chr5A.!!$R1	700
4	TraesCS5D01G043200	chr5A	18547737	18548411	674	False	667.000000	667	84.672000	194	871	1	chr5A.!!$F1	677
5	TraesCS5D01G043200	chr4D	11133786	11134490	704	True	830.000000	830	87.989000	193	902	1	chr4D.!!$R1	709
6	TraesCS5D01G043200	chr1D	437470268	437470958	690	False	800.000000	800	87.658000	193	895	1	chr1D.!!$F1	702
7	TraesCS5D01G043200	chr7D	145759105	145759809	704	False	763.000000	763	86.288000	193	907	1	chr7D.!!$F1	714
8	TraesCS5D01G043200	chr7D	619996687	619997384	697	False	721.000000	721	85.513000	193	893	1	chr7D.!!$F2	700
9	TraesCS5D01G043200	chr2D	374111032	374111735	703	False	754.000000	754	86.275000	193	893	1	chr2D.!!$F1	700
10	TraesCS5D01G043200	chr3A	31549193	31549889	696	True	743.000000	743	85.997000	193	893	1	chr3A.!!$R1	700
11	TraesCS5D01G043200	chr3D	144255669	144256375	706	False	732.000000	732	85.675000	193	895	1	chr3D.!!$F3	702

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
171	172	0.389296	TGTGGTCCATGTACTTCGCG	60.389	55.000	0.00	0.0	0.00	5.87	F
1923	3367	0.682852	TGGGTCGTTTCCGTCAATCT	59.317	50.000	0.00	0.0	35.01	2.40	F
2713	4211	0.329261	TGGGAGATGAGGCACTTTGG	59.671	55.000	0.00	0.0	41.55	3.28	F
3251	4991	1.133513	TGGATGACCAAACTGCCAACT	60.134	47.619	0.00	0.0	43.91	3.16	F
3481	5222	1.209504	TGCCATGGACAGGTACTTAGC	59.790	52.381	18.40	0.0	34.60	3.09	F
3838	5579	1.459592	CAGAAACCGTTTACTGCCTCG	59.540	52.381	0.00	0.0	0.00	4.63	F
5188	7062	1.082366	GCGTGCACCCTTGTTTACG	60.082	57.895	12.15	0.0	33.05	3.18	F
5908	7800	1.871039	AGCAATGCTGTCGTAAAACGT	59.129	42.857	7.07	0.0	39.24	3.99	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	3455	0.038526	ACGGAACACAGCTTCCTACG	60.039	55.000	0.83	0.0	38.08	3.51	R
3838	5579	0.404426	AGGGAACAAACTGTAGGCCC	59.596	55.000	0.00	0.0	36.91	5.80	R
4449	6206	1.213926	AGAGAGGGCACAAATGGATCC	59.786	52.381	4.20	4.2	0.00	3.36	R
4959	6830	1.541147	TCAAGCATCAGGAAAAAGGCG	59.459	47.619	0.00	0.0	0.00	5.52	R
5090	6964	2.354510	GCACATTTAGCGCCATACTTCA	59.645	45.455	2.29	0.0	0.00	3.02	R
5774	7656	1.210478	TGCAGGAATGCCTACCTTCTC	59.790	52.381	0.00	0.0	44.80	2.87	R
6013	7905	0.320050	TGTAGACACGCAAGCCATCA	59.680	50.000	0.00	0.0	45.62	3.07	R
7081	9328	0.320421	TTCGAAAGAGGCGGAGTTGG	60.320	55.000	0.00	0.0	43.69	3.77	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
18	19	4.598257	GACATGTGAGTGTCGGGG	57.402	61.111	1.15	0.00	39.12	5.73
19	20	1.079127	GACATGTGAGTGTCGGGGG	60.079	63.158	1.15	0.00	39.12	5.40
20	21	2.436646	CATGTGAGTGTCGGGGGC	60.437	66.667	0.00	0.00	0.00	5.80
21	22	4.082523	ATGTGAGTGTCGGGGGCG	62.083	66.667	0.00	0.00	0.00	6.13
103	104	3.838271	GCATCCGCTCGTCCCTGA	61.838	66.667	0.00	0.00	34.30	3.86
104	105	2.105128	CATCCGCTCGTCCCTGAC	59.895	66.667	0.00	0.00	0.00	3.51
113	114	2.680352	GTCCCTGACGGAGGAGCA	60.680	66.667	4.35	0.00	46.33	4.26
114	115	2.363018	TCCCTGACGGAGGAGCAG	60.363	66.667	4.35	0.00	46.33	4.24
115	116	4.154347	CCCTGACGGAGGAGCAGC	62.154	72.222	4.35	0.00	46.33	5.25
116	117	4.504916	CCTGACGGAGGAGCAGCG	62.505	72.222	0.00	0.00	46.33	5.18
117	118	4.504916	CTGACGGAGGAGCAGCGG	62.505	72.222	0.00	0.00	0.00	5.52
119	120	3.760035	GACGGAGGAGCAGCGGAA	61.760	66.667	0.00	0.00	0.00	4.30
120	121	3.991536	GACGGAGGAGCAGCGGAAC	62.992	68.421	0.00	0.00	0.00	3.62
121	122	4.069232	CGGAGGAGCAGCGGAACA	62.069	66.667	0.00	0.00	0.00	3.18
122	123	2.347490	GGAGGAGCAGCGGAACAA	59.653	61.111	0.00	0.00	0.00	2.83
123	124	1.743252	GGAGGAGCAGCGGAACAAG	60.743	63.158	0.00	0.00	0.00	3.16
124	125	2.359230	AGGAGCAGCGGAACAAGC	60.359	61.111	0.00	0.00	0.00	4.01
130	131	4.626081	AGCGGAACAAGCTGCGGT	62.626	61.111	0.00	0.00	44.22	5.68
131	132	2.740826	GCGGAACAAGCTGCGGTA	60.741	61.111	0.00	0.00	0.00	4.02
132	133	3.023591	GCGGAACAAGCTGCGGTAC	62.024	63.158	0.00	0.00	0.00	3.34
153	154	3.490759	GCCGACAGCCACACGATG	61.491	66.667	0.00	0.00	34.35	3.84
154	155	2.048222	CCGACAGCCACACGATGT	60.048	61.111	0.00	0.00	0.00	3.06
163	164	3.231734	CACACGATGTGGTCCATGT	57.768	52.632	0.00	0.00	44.27	3.21
164	165	2.378445	CACACGATGTGGTCCATGTA	57.622	50.000	0.00	0.00	44.27	2.29
165	166	1.999735	CACACGATGTGGTCCATGTAC	59.000	52.381	0.00	0.00	44.27	2.90

Showing 1 to 25 of 259 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.544825	CCCCCGACACTCACATGTCT	61.545	60.000	0.00	0.00	45.73	3.41
1	2	1.079127	CCCCCGACACTCACATGTC	60.079	63.158	0.00	0.00	44.68	3.06
2	3	3.068881	CCCCCGACACTCACATGT	58.931	61.111	0.00	0.00	34.78	3.21
3	4	2.436646	GCCCCCGACACTCACATG	60.437	66.667	0.00	0.00	0.00	3.21
4	5	4.082523	CGCCCCCGACACTCACAT	62.083	66.667	0.00	0.00	36.29	3.21
86	87	3.838271	TCAGGGACGAGCGGATGC	61.838	66.667	0.00	0.00	43.24	3.91
87	88	2.105128	GTCAGGGACGAGCGGATG	59.895	66.667	0.00	0.00	0.00	3.51
96	97	2.680352	TGCTCCTCCGTCAGGGAC	60.680	66.667	0.00	0.00	43.67	4.46
97	98	2.363018	CTGCTCCTCCGTCAGGGA	60.363	66.667	0.00	0.00	43.67	4.20
98	99	4.154347	GCTGCTCCTCCGTCAGGG	62.154	72.222	0.00	0.00	43.67	4.45
99	100	4.504916	CGCTGCTCCTCCGTCAGG	62.505	72.222	0.00	0.00	45.15	3.86
100	101	4.504916	CCGCTGCTCCTCCGTCAG	62.505	72.222	0.00	0.00	0.00	3.51
102	103	3.760035	TTCCGCTGCTCCTCCGTC	61.760	66.667	0.00	0.00	0.00	4.79
103	104	4.070552	GTTCCGCTGCTCCTCCGT	62.071	66.667	0.00	0.00	0.00	4.69
104	105	3.589654	TTGTTCCGCTGCTCCTCCG	62.590	63.158	0.00	0.00	0.00	4.63
105	106	1.743252	CTTGTTCCGCTGCTCCTCC	60.743	63.158	0.00	0.00	0.00	4.30
106	107	2.394563	GCTTGTTCCGCTGCTCCTC	61.395	63.158	0.00	0.00	0.00	3.71
107	108	2.359230	GCTTGTTCCGCTGCTCCT	60.359	61.111	0.00	0.00	0.00	3.69
108	109	2.359230	AGCTTGTTCCGCTGCTCC	60.359	61.111	0.00	0.00	36.15	4.70
109	110	2.866028	CAGCTTGTTCCGCTGCTC	59.134	61.111	0.00	0.00	46.98	4.26
113	114	3.234630	TACCGCAGCTTGTTCCGCT	62.235	57.895	0.00	0.00	38.49	5.52
114	115	2.740826	TACCGCAGCTTGTTCCGC	60.741	61.111	0.00	0.00	0.00	5.54
115	116	2.726691	CGTACCGCAGCTTGTTCCG	61.727	63.158	0.00	0.00	0.00	4.30
116	117	3.165498	CGTACCGCAGCTTGTTCC	58.835	61.111	0.00	0.00	0.00	3.62
136	137	3.490759	CATCGTGTGGCTGTCGGC	61.491	66.667	0.00	0.00	40.90	5.54

Showing 1 to 25 of 264 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.