AutoCloner

Multiple sequence alignment - TraesCS4D01G021500

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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	TraesCS4D01G021500	chr4D	100.000	6575	0	0	1	6575	9222415	9228989	0.000000e+00	12142.0
1	TraesCS4D01G021500	chr4D	91.931	756	56	5	2097	2851	9241347	9242098	0.000000e+00	1053.0
2	TraesCS4D01G021500	chr4D	85.877	701	60	16	3658	4331	9242495	9243183	0.000000e+00	710.0
3	TraesCS4D01G021500	chr4D	91.051	257	21	2	4387	4641	9243409	9243665	4.880000e-91	346.0
4	TraesCS4D01G021500	chr4D	85.890	326	37	8	1658	1979	9240965	9241285	8.170000e-89	339.0
5	TraesCS4D01G021500	chr4D	83.934	361	30	14	3189	3540	9242111	9242452	2.960000e-83	320.0
6	TraesCS4D01G021500	chr4D	100.000	79	0	0	2952	3030	9225329	9225407	5.310000e-31	147.0
7	TraesCS4D01G021500	chr4D	100.000	79	0	0	2915	2993	9225366	9225444	5.310000e-31	147.0
8	TraesCS4D01G021500	chr4D	91.176	102	7	1	5488	5589	9246368	9246467	3.200000e-28	137.0
9	TraesCS4D01G021500	chr4D	83.212	137	22	1	5191	5326	9246025	9246161	2.490000e-24	124.0
10	TraesCS4D01G021500	chr4D	100.000	42	0	0	2989	3030	9225329	9225370	1.970000e-10	78.7
11	TraesCS4D01G021500	chr4D	100.000	42	0	0	2915	2956	9225403	9225444	1.970000e-10	78.7
12	TraesCS4D01G021500	chr4D	100.000	41	0	0	1305	1345	9240596	9240636	7.070000e-10	76.8
13	TraesCS4D01G021500	chr4D	90.566	53	4	1	710	761	9239438	9239490	1.180000e-07	69.4
14	TraesCS4D01G021500	chr4A	94.918	1771	47	14	1206	2956	594185756	594184009	0.000000e+00	2732.0
15	TraesCS4D01G021500	chr4A	93.806	1566	57	10	4349	5905	594181730	594180196	0.000000e+00	2318.0
16	TraesCS4D01G021500	chr4A	96.358	1373	41	6	2990	4354	594184049	594182678	0.000000e+00	2250.0
17	TraesCS4D01G021500	chr4A	89.447	995	87	15	1968	2956	594176870	594175888	0.000000e+00	1240.0
18	TraesCS4D01G021500	chr4A	93.981	432	20	3	5896	6326	594180014	594179588	0.000000e+00	649.0
19	TraesCS4D01G021500	chr4A	85.374	629	58	15	3718	4322	594175307	594174689	7.240000e-174	621.0
20	TraesCS4D01G021500	chr4A	84.821	560	52	10	2991	3540	594175926	594175390	3.490000e-147	532.0
21	TraesCS4D01G021500	chr4A	88.248	468	18	8	746	1204	594186845	594186406	5.840000e-145	525.0
22	TraesCS4D01G021500	chr4A	91.732	254	18	3	4387	4637	594174450	594174197	3.770000e-92	350.0
23	TraesCS4D01G021500	chr4A	92.797	236	17	0	4764	4999	594173692	594173457	6.310000e-90	342.0
24	TraesCS4D01G021500	chr4A	79.428	559	47	20	1437	1933	594177424	594176872	3.800000e-87	333.0
25	TraesCS4D01G021500	chr4A	92.553	188	14	0	4	191	594206218	594206031	3.020000e-68	270.0
26	TraesCS4D01G021500	chr4A	94.872	117	6	0	6459	6575	594179308	594179192	4.050000e-42	183.0
27	TraesCS4D01G021500	chr4A	100.000	41	0	0	2953	2993	594184049	594184009	7.070000e-10	76.8
28	TraesCS4D01G021500	chr4B	94.519	1715	50	11	1264	2956	17103969	17105661	0.000000e+00	2606.0
29	TraesCS4D01G021500	chr4B	95.317	1516	54	9	4349	5850	17106813	17108325	0.000000e+00	2390.0
30	TraesCS4D01G021500	chr4B	97.297	518	14	0	3837	4354	17105773	17106290	0.000000e+00	880.0
31	TraesCS4D01G021500	chr4B	86.309	745	69	15	2990	3718	17250246	17250973	0.000000e+00	780.0
32	TraesCS4D01G021500	chr4B	80.573	978	119	42	1425	2359	17248772	17249721	0.000000e+00	688.0
33	TraesCS4D01G021500	chr4B	82.895	836	70	38	393	1204	17102551	17103337	0.000000e+00	684.0
34	TraesCS4D01G021500	chr4B	87.958	573	50	10	2398	2956	17249719	17250286	0.000000e+00	658.0
35	TraesCS4D01G021500	chr4B	74.715	878	107	58	5099	5900	17251236	17252074	1.080000e-72	285.0
36	TraesCS4D01G021500	chr4B	89.756	205	6	1	5852	6056	17108424	17108613	1.420000e-61	248.0
37	TraesCS4D01G021500	chr4B	96.503	143	5	0	2989	3131	17105620	17105762	3.060000e-58	237.0
38	TraesCS4D01G021500	chr4B	87.879	66	4	2	714	775	17242738	17242803	2.540000e-09	75.0
39	TraesCS4D01G021500	chr5D	77.605	643	89	31	3	601	479446179	479446810	8.170000e-89	339.0
40	TraesCS4D01G021500	chr5D	90.541	74	6	1	6010	6083	537902153	537902081	5.430000e-16	97.1
41	TraesCS4D01G021500	chr5D	93.220	59	4	0	6345	6403	487403605	487403547	3.270000e-13	87.9
42	TraesCS4D01G021500	chr5D	91.935	62	3	2	6352	6411	418431148	418431087	1.170000e-12	86.1
43	TraesCS4D01G021500	chr2B	94.915	59	3	0	6347	6405	730560853	730560911	7.020000e-15	93.5
44	TraesCS4D01G021500	chr7B	93.333	60	4	0	6346	6405	438379364	438379423	9.080000e-14	89.8
45	TraesCS4D01G021500	chrUn	93.333	60	2	2	6354	6411	43583010	43582951	3.270000e-13	87.9
46	TraesCS4D01G021500	chrUn	88.732	71	5	3	6343	6411	1181914	1181983	4.220000e-12	84.2
47	TraesCS4D01G021500	chr3D	90.769	65	4	2	6349	6411	508385199	508385263	1.170000e-12	86.1
48	TraesCS4D01G021500	chr5A	89.552	67	4	3	6347	6411	640692680	640692745	1.520000e-11	82.4
49	TraesCS4D01G021500	chr1B	88.571	70	5	3	6344	6411	524160441	524160509	1.520000e-11	82.4
50	TraesCS4D01G021500	chr1A	85.246	61	7	2	619	678	372911560	372911501	1.980000e-05	62.1

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	TraesCS4D01G021500	chr4D	9222415	9228989	6574	False	2518.680000	12142	100.00000	1	6575	5	chr4D.!!$F1	6574
1	TraesCS4D01G021500	chr4D	9239438	9246467	7029	False	352.800000	1053	89.29300	710	5589	9	chr4D.!!$F2	4879
2	TraesCS4D01G021500	chr4A	594173457	594186845	13388	True	934.753846	2732	91.21400	746	6575	13	chr4A.!!$R2	5829
3	TraesCS4D01G021500	chr4B	17102551	17108613	6062	False	1174.166667	2606	92.71450	393	6056	6	chr4B.!!$F2	5663
4	TraesCS4D01G021500	chr4B	17248772	17252074	3302	False	602.750000	780	82.38875	1425	5900	4	chr4B.!!$F3	4475
5	TraesCS4D01G021500	chr5D	479446179	479446810	631	False	339.000000	339	77.60500	3	601	1	chr5D.!!$F1	598

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
405	450	0.030235	CATGCCATGTCCAAGATGCG	59.970	55.000	0.00	0.00	0.00	4.73	F
437	482	0.041047	CAATGATGTACGCCGGCATG	60.041	55.000	28.98	14.14	0.00	4.06	F
569	622	0.323629	CTGGTTGGACGGCCTAGAAA	59.676	55.000	9.82	0.00	34.31	2.52	F
573	626	0.326595	TTGGACGGCCTAGAAATGCA	59.673	50.000	9.82	0.00	34.31	3.96	F
574	627	0.392461	TGGACGGCCTAGAAATGCAC	60.392	55.000	9.82	0.00	34.31	4.57	F
708	761	0.734942	CCACGCTTGGTCGTTCGTAT	60.735	55.000	0.00	0.00	41.21	3.06	F
712	765	0.997196	GCTTGGTCGTTCGTATCACC	59.003	55.000	0.00	0.00	0.00	4.02	F
1376	2197	1.003839	CTGCTCGTGTTAGGGCCAA	60.004	57.895	6.18	0.00	0.00	4.52	F
2949	3878	1.482182	TGCTCCTTCAGTGCATATCGT	59.518	47.619	0.00	0.00	39.96	3.73	F
4884	6784	0.889186	TTCGAACAGGAGCCTTTGCC	60.889	55.000	0.00	0.00	38.69	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1353	2174	0.537188	CCCTAACACGAGCAGATGGT	59.463	55.000	0.00	0.00	0.00	3.55	R
1722	2619	1.843368	CAGCAGTCATTTCCCCATGT	58.157	50.000	0.00	0.00	0.00	3.21	R
1956	2854	2.252072	TTATCACTCCCGGGCTGCAC	62.252	60.000	18.49	0.00	0.00	4.57	R
2496	3420	2.408050	AGTTTCACGCACTCTAAGCAG	58.592	47.619	0.00	0.00	0.00	4.24	R
2784	3710	9.965824	AAGTATCAAGGTTTAAGAACAAACATG	57.034	29.630	0.00	0.00	39.65	3.21	R
2879	3808	6.351711	CACTCCAAGATTTCCATGAGACATA	58.648	40.000	0.00	0.00	0.00	2.29	R
2938	3867	8.718102	AAACAAGAAATACTACGATATGCACT	57.282	30.769	0.00	0.00	0.00	4.40	R
3134	4063	0.252057	TTCCGTCCAGATGACCTCCA	60.252	55.000	0.00	0.00	41.18	3.86	R
4973	6873	1.140252	GACATAAGGGCGGCTCCTTTA	59.860	52.381	22.16	7.37	44.14	1.85	R
6416	8624	0.264955	TGGTGGATCCTACTCCCTCC	59.735	60.000	14.23	3.57	37.07	4.30	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
27	28	2.810852	GCCCAAGTGAAAGTGAGAAGAG	59.189	50.000	0.00	0.00	0.00	2.85
30	31	3.470709	CAAGTGAAAGTGAGAAGAGGCA	58.529	45.455	0.00	0.00	0.00	4.75
33	34	3.389329	AGTGAAAGTGAGAAGAGGCAGAA	59.611	43.478	0.00	0.00	0.00	3.02
36	37	2.317371	AGTGAGAAGAGGCAGAAGGA	57.683	50.000	0.00	0.00	0.00	3.36
37	38	2.614259	AGTGAGAAGAGGCAGAAGGAA	58.386	47.619	0.00	0.00	0.00	3.36
46	47	3.117512	AGAGGCAGAAGGAAAAGACCAAA	60.118	43.478	0.00	0.00	0.00	3.28
82	83	1.704582	GCGTGATGCTTCGACACTC	59.295	57.895	0.00	0.00	41.73	3.51
85	86	1.008875	GTGATGCTTCGACACTCGCA	61.009	55.000	0.00	0.00	40.21	5.10
99	100	2.975851	CACTCGCATTGCAAGAAACTTC	59.024	45.455	9.69	0.00	0.00	3.01
106	107	2.631160	TGCAAGAAACTTCGAAGGGA	57.369	45.000	27.86	8.42	0.00	4.20
110	111	3.424962	GCAAGAAACTTCGAAGGGATTCG	60.425	47.826	27.86	16.46	45.09	3.34
113	114	3.006537	AGAAACTTCGAAGGGATTCGTGA	59.993	43.478	27.86	0.96	44.18	4.35
142	143	4.163427	AGGAGGTGTCAATTGAGAAGAGA	58.837	43.478	8.80	0.00	0.00	3.10
143	144	4.222588	AGGAGGTGTCAATTGAGAAGAGAG	59.777	45.833	8.80	0.00	0.00	3.20
144	145	4.221703	GGAGGTGTCAATTGAGAAGAGAGA	59.778	45.833	8.80	0.00	0.00	3.10
145	146	5.279708	GGAGGTGTCAATTGAGAAGAGAGAA	60.280	44.000	8.80	0.00	0.00	2.87
146	147	5.792741	AGGTGTCAATTGAGAAGAGAGAAG	58.207	41.667	8.80	0.00	0.00	2.85
147	148	5.541868	AGGTGTCAATTGAGAAGAGAGAAGA	59.458	40.000	8.80	0.00	0.00	2.87
148	149	5.868801	GGTGTCAATTGAGAAGAGAGAAGAG	59.131	44.000	8.80	0.00	0.00	2.85
149	150	6.295011	GGTGTCAATTGAGAAGAGAGAAGAGA	60.295	42.308	8.80	0.00	0.00	3.10
150	151	6.808212	GTGTCAATTGAGAAGAGAGAAGAGAG	59.192	42.308	8.80	0.00	0.00	3.20
151	152	6.718912	TGTCAATTGAGAAGAGAGAAGAGAGA	59.281	38.462	8.80	0.00	0.00	3.10
164	165	4.273318	AGAAGAGAGAGAAGAGAGGAAGC	58.727	47.826	0.00	0.00	0.00	3.86
166	167	2.238646	AGAGAGAGAAGAGAGGAAGCGA	59.761	50.000	0.00	0.00	0.00	4.93
170	171	2.491693	AGAGAAGAGAGGAAGCGACAAG	59.508	50.000	0.00	0.00	0.00	3.16

Showing 1 to 25 of 399 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	0.535102	ACTTTCACTTGGGCCGACAG	60.535	55.000	0.00	0.00	0.00	3.51
1	2	0.817634	CACTTTCACTTGGGCCGACA	60.818	55.000	0.00	0.00	0.00	4.35
6	7	2.810852	CTCTTCTCACTTTCACTTGGGC	59.189	50.000	0.00	0.00	0.00	5.36
27	28	3.056536	GGATTTGGTCTTTTCCTTCTGCC	60.057	47.826	0.00	0.00	0.00	4.85
30	31	4.835056	CCTTGGATTTGGTCTTTTCCTTCT	59.165	41.667	0.00	0.00	0.00	2.85
33	34	3.897505	CACCTTGGATTTGGTCTTTTCCT	59.102	43.478	0.00	0.00	33.75	3.36
36	37	3.922375	TCCACCTTGGATTTGGTCTTTT	58.078	40.909	0.00	0.00	42.67	2.27
37	38	3.611025	TCCACCTTGGATTTGGTCTTT	57.389	42.857	0.00	0.00	42.67	2.52
65	66	1.983907	CGAGTGTCGAAGCATCACG	59.016	57.895	0.00	0.00	43.74	4.35
79	80	2.349817	CGAAGTTTCTTGCAATGCGAGT	60.350	45.455	20.77	2.34	40.65	4.18
82	83	2.314561	TCGAAGTTTCTTGCAATGCG	57.685	45.000	0.00	0.00	0.00	4.73
85	86	3.486383	TCCCTTCGAAGTTTCTTGCAAT	58.514	40.909	23.03	0.00	0.00	3.56
106	107	1.423921	ACCTCCTTTTGGGTCACGAAT	59.576	47.619	0.00	0.00	40.87	3.34
110	111	1.133915	TGACACCTCCTTTTGGGTCAC	60.134	52.381	0.00	0.00	40.87	3.67
113	114	2.965147	CAATTGACACCTCCTTTTGGGT	59.035	45.455	0.00	0.00	40.87	4.51
121	122	4.221703	TCTCTCTTCTCAATTGACACCTCC	59.778	45.833	3.38	0.00	0.00	4.30
142	143	4.273318	GCTTCCTCTCTTCTCTCTCTTCT	58.727	47.826	0.00	0.00	0.00	2.85
143	144	3.065371	CGCTTCCTCTCTTCTCTCTCTTC	59.935	52.174	0.00	0.00	0.00	2.87
144	145	3.016736	CGCTTCCTCTCTTCTCTCTCTT	58.983	50.000	0.00	0.00	0.00	2.85
145	146	2.238646	TCGCTTCCTCTCTTCTCTCTCT	59.761	50.000	0.00	0.00	0.00	3.10
146	147	2.354821	GTCGCTTCCTCTCTTCTCTCTC	59.645	54.545	0.00	0.00	0.00	3.20
147	148	2.290641	TGTCGCTTCCTCTCTTCTCTCT	60.291	50.000	0.00	0.00	0.00	3.10
148	149	2.088423	TGTCGCTTCCTCTCTTCTCTC	58.912	52.381	0.00	0.00	0.00	3.20
149	150	2.208132	TGTCGCTTCCTCTCTTCTCT	57.792	50.000	0.00	0.00	0.00	3.10
150	151	2.490115	TCTTGTCGCTTCCTCTCTTCTC	59.510	50.000	0.00	0.00	0.00	2.87

Showing 1 to 25 of 374 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.