AutoCloner

Multiple sequence alignment - TraesCS4D01G226400

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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	TraesCS4D01G226400	chr4D	100.000	2882	0	0	1	2882	385699626	385702507	0.000000e+00	5323.0
1	TraesCS4D01G226400	chr4D	93.733	1819	94	14	1	1811	385631818	385633624	0.000000e+00	2710.0
2	TraesCS4D01G226400	chr4D	90.690	1493	78	25	719	2154	385649549	385651037	0.000000e+00	1930.0
3	TraesCS4D01G226400	chr4D	93.125	1309	59	14	875	2154	385587303	385588609	0.000000e+00	1890.0
4	TraesCS4D01G226400	chr4D	87.626	792	50	20	48	827	385578971	385579726	0.000000e+00	876.0
5	TraesCS4D01G226400	chr4D	90.476	630	42	10	48	665	385640917	385641540	0.000000e+00	815.0
6	TraesCS4D01G226400	chr4D	84.634	820	108	14	998	1811	385518002	385518809	0.000000e+00	800.0
7	TraesCS4D01G226400	chr4B	89.401	2104	119	48	149	2201	472210014	472212064	0.000000e+00	2555.0
8	TraesCS4D01G226400	chr4B	81.445	1024	153	27	799	1805	472207025	472208028	0.000000e+00	804.0
9	TraesCS4D01G226400	chr4B	94.444	108	6	0	2526	2633	472212063	472212170	1.780000e-37	167.0
10	TraesCS4D01G226400	chr4B	93.478	92	6	0	2775	2866	472235914	472236005	1.390000e-28	137.0
11	TraesCS4D01G226400	chr4A	90.329	1427	71	29	491	1892	66930753	66932137	0.000000e+00	1808.0
12	TraesCS4D01G226400	chr4A	94.166	857	36	10	2032	2882	66933084	66933932	0.000000e+00	1293.0
13	TraesCS4D01G226400	chr4A	80.672	1102	175	30	799	1882	66928242	66929323	0.000000e+00	821.0
14	TraesCS4D01G226400	chr4A	92.222	90	3	2	1929	2016	66932132	66932219	1.080000e-24	124.0
15	TraesCS4D01G226400	chr4A	94.000	50	3	0	406	455	66930703	66930752	3.080000e-10	76.8

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	TraesCS4D01G226400	chr4D	385699626	385702507	2881	False	5323.000000	5323	100.0000	1	2882	1	chr4D.!!$F7	2881
1	TraesCS4D01G226400	chr4D	385631818	385633624	1806	False	2710.000000	2710	93.7330	1	1811	1	chr4D.!!$F4	1810
2	TraesCS4D01G226400	chr4D	385649549	385651037	1488	False	1930.000000	1930	90.6900	719	2154	1	chr4D.!!$F6	1435
3	TraesCS4D01G226400	chr4D	385587303	385588609	1306	False	1890.000000	1890	93.1250	875	2154	1	chr4D.!!$F3	1279
4	TraesCS4D01G226400	chr4D	385578971	385579726	755	False	876.000000	876	87.6260	48	827	1	chr4D.!!$F2	779
5	TraesCS4D01G226400	chr4D	385640917	385641540	623	False	815.000000	815	90.4760	48	665	1	chr4D.!!$F5	617
6	TraesCS4D01G226400	chr4D	385518002	385518809	807	False	800.000000	800	84.6340	998	1811	1	chr4D.!!$F1	813
7	TraesCS4D01G226400	chr4B	472207025	472212170	5145	False	1175.333333	2555	88.4300	149	2633	3	chr4B.!!$F2	2484
8	TraesCS4D01G226400	chr4A	66928242	66933932	5690	False	824.560000	1808	90.2778	406	2882	5	chr4A.!!$F1	2476

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
21	22	3.90215	GCATCATGCAGAAATCATCCAG	58.098	45.455	4.2	0.0	44.26	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1895	4876	0.035725	TCGAAGAGGCCACGAGTAGA	60.036	55.0	5.01	0.0	0.0	2.59	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
21	22	3.902150	GCATCATGCAGAAATCATCCAG	58.098	45.455	4.20	0.00	44.26	3.86
30	31	4.825634	GCAGAAATCATCCAGATCCAATCA	59.174	41.667	0.00	0.00	35.39	2.57
136	137	7.745748	ATGATATCATGTGGTGGAAGATTCCTC	60.746	40.741	17.51	8.89	40.55	3.71
141	142	4.762289	GTGGTGGAAGATTCCTCTACAT	57.238	45.455	19.28	0.00	45.71	2.29
142	143	4.446371	GTGGTGGAAGATTCCTCTACATG	58.554	47.826	19.28	0.00	45.71	3.21
145	146	8.816414	GTGGTGGAAGATTCCTCTACATGCAT	62.816	46.154	19.28	0.00	45.71	3.96
149	150	6.471146	GGAAGATTCCTCTACATGCATACAT	58.529	40.000	0.00	0.00	44.11	2.29
151	152	8.263640	GGAAGATTCCTCTACATGCATACATAT	58.736	37.037	0.00	0.00	44.11	1.78
152	153	9.096160	GAAGATTCCTCTACATGCATACATATG	57.904	37.037	0.00	0.00	33.67	1.78
177	3049	6.744537	GCTCATATTGAAACACATGACTTGAC	59.255	38.462	0.00	0.00	0.00	3.18
301	3176	7.810658	ACAAAGAATATGCTTCACAGTTACAG	58.189	34.615	0.00	0.00	0.00	2.74
1062	3979	0.410663	TTCTCCTCCCTTCCCACGTA	59.589	55.000	0.00	0.00	0.00	3.57
1068	3985	2.125106	CCTTCCCACGTAGCAGCC	60.125	66.667	0.00	0.00	0.00	4.85
1371	4288	1.002011	GTGGAAAGGGCTGGAGGTC	60.002	63.158	0.00	0.00	0.00	3.85
1545	4462	3.367743	CAACACTGCGGCATGCCT	61.368	61.111	33.07	13.08	45.60	4.75
1605	4522	1.001248	TCCGATCGGAAAGGGGAGT	59.999	57.895	33.96	0.00	42.05	3.85
1617	4534	0.842467	AGGGGAGTAGCAACTTGCCT	60.842	55.000	10.25	1.23	46.52	4.75
1848	4777	1.398390	GCTAATTTGGGTCTCAGCGTG	59.602	52.381	0.00	0.00	0.00	5.34
1856	4785	1.237285	GGTCTCAGCGTGGCAATTGT	61.237	55.000	7.40	0.00	0.00	2.71
1895	4876	4.019231	GGGTCTCTGAATTTGGTACTTCCT	60.019	45.833	0.00	0.00	37.07	3.36
1896	4877	5.179533	GGTCTCTGAATTTGGTACTTCCTC	58.820	45.833	0.00	0.00	37.07	3.71
1897	4878	5.046231	GGTCTCTGAATTTGGTACTTCCTCT	60.046	44.000	0.00	0.00	37.07	3.69
1898	4879	6.154706	GGTCTCTGAATTTGGTACTTCCTCTA	59.845	42.308	0.00	0.00	37.07	2.43
1899	4880	7.036829	GTCTCTGAATTTGGTACTTCCTCTAC	58.963	42.308	0.00	0.00	37.07	2.59
1900	4881	6.954684	TCTCTGAATTTGGTACTTCCTCTACT	59.045	38.462	0.00	0.00	37.07	2.57
1901	4882	7.122948	TCTCTGAATTTGGTACTTCCTCTACTC	59.877	40.741	0.00	0.00	37.07	2.59
1907	4888	1.404748	GTACTTCCTCTACTCGTGGCC	59.595	57.143	0.00	0.00	0.00	5.36
1932	4913	6.291377	TCTTCGATTTTTCTCATGGGGATAG	58.709	40.000	0.00	0.00	0.00	2.08
1936	4917	3.297134	TTTTCTCATGGGGATAGTGGC	57.703	47.619	0.00	0.00	0.00	5.01
1979	4962	4.584638	AACTTGGTGGTATATTCTGGCA	57.415	40.909	0.00	0.00	0.00	4.92
2003	4986	1.539869	AGCCAGAGGATGTGTGGGT	60.540	57.895	0.00	0.00	45.33	4.51
2223	6059	1.337118	GCCAGATTCTCCTCTCCGAT	58.663	55.000	0.00	0.00	0.00	4.18
2231	6067	3.517296	TCTCCTCTCCGATGAGCTTAT	57.483	47.619	0.00	0.00	38.58	1.73
2235	6071	4.075682	TCCTCTCCGATGAGCTTATACTG	58.924	47.826	0.00	0.00	38.58	2.74
2236	6072	3.366883	CCTCTCCGATGAGCTTATACTGC	60.367	52.174	0.00	0.00	38.58	4.40
2274	6110	2.276740	GGTGGATCCCTTGCCCAG	59.723	66.667	9.90	0.00	0.00	4.45
2353	6189	1.203287	GACTTTGGAGATTGGGCAAGC	59.797	52.381	0.00	0.00	0.00	4.01
2386	6222	2.876550	GGAAAGTGGTGTTTCTTACGCT	59.123	45.455	0.00	0.00	36.76	5.07
2421	6257	2.162608	ACCGACATCTATCGAGCTATGC	59.837	50.000	0.00	0.00	45.13	3.14
2428	6264	5.010516	ACATCTATCGAGCTATGCTTGTCTT	59.989	40.000	6.68	0.00	39.88	3.01
2595	6432	3.811722	TGTAGCTTCGAATTTGTGCTG	57.188	42.857	16.54	0.00	35.47	4.41
2648	6485	4.770010	AGTTACTTAGAGCAAGCTCAGTCT	59.230	41.667	22.68	10.28	44.99	3.24
2656	6493	2.297129	AAGCTCAGTCTGCCCCCTC	61.297	63.158	0.00	0.00	0.00	4.30
2682	6519	8.705594	CAAAACCTCATATCCTCTACTTTAGGA	58.294	37.037	0.00	0.00	46.96	2.94
2750	6588	0.916809	ATGTAGGGAAAAGGACGGGG	59.083	55.000	0.00	0.00	0.00	5.73
2751	6589	0.178897	TGTAGGGAAAAGGACGGGGA	60.179	55.000	0.00	0.00	0.00	4.81
2768	6606	1.057275	GGACCATTCCCCCTCTCTCC	61.057	65.000	0.00	0.00	35.57	3.71
2769	6607	1.004891	ACCATTCCCCCTCTCTCCC	59.995	63.158	0.00	0.00	0.00	4.30
2771	6609	1.348775	CCATTCCCCCTCTCTCCCAC	61.349	65.000	0.00	0.00	0.00	4.61
2812	6650	4.211125	TGAATGTTCCCTGCAACAACTAA	58.789	39.130	0.00	0.00	39.69	2.24
2813	6651	4.037446	TGAATGTTCCCTGCAACAACTAAC	59.963	41.667	0.00	0.00	39.69	2.34
2814	6652	3.290948	TGTTCCCTGCAACAACTAACT	57.709	42.857	0.00	0.00	33.21	2.24
2815	6653	4.425180	TGTTCCCTGCAACAACTAACTA	57.575	40.909	0.00	0.00	33.21	2.24
2834	6672	4.758251	CACCGCCATCTGTCGCCA	62.758	66.667	0.00	0.00	0.00	5.69
2876	6714	0.186386	ATGGCGGAGGTAGCTAGAGT	59.814	55.000	0.00	0.00	34.52	3.24
2877	6715	0.465824	TGGCGGAGGTAGCTAGAGTC	60.466	60.000	0.00	0.00	34.52	3.36
2878	6716	1.508808	GGCGGAGGTAGCTAGAGTCG	61.509	65.000	0.00	0.00	34.52	4.18
2879	6717	1.943293	CGGAGGTAGCTAGAGTCGC	59.057	63.158	0.00	0.00	0.00	5.19
2881	6719	1.508808	GGAGGTAGCTAGAGTCGCCG	61.509	65.000	0.00	0.00	0.00	6.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	3.003068	GCTGCTACACACATGATTGGATC	59.997	47.826	0.00	0.00	0.00	3.36
30	31	1.868997	GCAACGCTGCTACACACAT	59.131	52.632	2.93	0.00	45.74	3.21
123	124	7.957676	ATGTATGCATGTAGAGGAATCTTCCAC	60.958	40.741	10.16	5.11	40.85	4.02
145	146	9.558396	TCATGTGTTTCAATATGAGCATATGTA	57.442	29.630	4.29	0.00	35.91	2.29
149	150	8.400186	CAAGTCATGTGTTTCAATATGAGCATA	58.600	33.333	0.00	0.00	30.86	3.14
151	152	6.430616	TCAAGTCATGTGTTTCAATATGAGCA	59.569	34.615	0.00	0.00	30.86	4.26
152	153	6.744537	GTCAAGTCATGTGTTTCAATATGAGC	59.255	38.462	0.00	0.00	30.86	4.26
177	3049	5.924825	GTGGGCTACGTATGGAAATAAGTAG	59.075	44.000	11.92	11.92	40.01	2.57
354	3231	5.243207	TCTTAAAGCCTTGCACCTTAGTAC	58.757	41.667	0.00	0.00	0.00	2.73
522	3404	4.350368	TGTGTGTGATCCTTTTGAGCTA	57.650	40.909	0.00	0.00	0.00	3.32
1231	4148	2.711922	CGTAGCAGAAGTCGGCCCT	61.712	63.158	0.00	0.00	37.79	5.19
1288	4205	3.680786	CGACTCCCACACGCTCCA	61.681	66.667	0.00	0.00	0.00	3.86
1371	4288	0.734253	CTGAGTTGCTCCCGTCGAAG	60.734	60.000	0.00	0.00	0.00	3.79
1617	4534	1.340017	CCTCCTTCATCTTGCCCGAAA	60.340	52.381	0.00	0.00	0.00	3.46
1895	4876	0.035725	TCGAAGAGGCCACGAGTAGA	60.036	55.000	5.01	0.00	0.00	2.59
1896	4877	1.025812	ATCGAAGAGGCCACGAGTAG	58.974	55.000	5.01	0.00	43.63	2.57
1897	4878	1.471119	AATCGAAGAGGCCACGAGTA	58.529	50.000	5.01	0.00	43.63	2.59
1898	4879	0.608640	AAATCGAAGAGGCCACGAGT	59.391	50.000	5.01	7.16	43.63	4.18
1899	4880	1.726853	AAAATCGAAGAGGCCACGAG	58.273	50.000	5.01	0.00	43.63	4.18
1900	4881	2.073816	GAAAAATCGAAGAGGCCACGA	58.926	47.619	5.01	11.17	43.63	4.35
1901	4882	2.076863	AGAAAAATCGAAGAGGCCACG	58.923	47.619	5.01	5.35	43.63	4.94
1907	4888	4.517285	TCCCCATGAGAAAAATCGAAGAG	58.483	43.478	0.00	0.00	43.63	2.85
1932	4913	0.248215	CAAATCGAAGATGCCGCCAC	60.248	55.000	0.00	0.00	45.12	5.01
1936	4917	7.186804	AGTTAAATAACAAATCGAAGATGCCG	58.813	34.615	6.13	0.00	39.09	5.69
1979	4962	3.614092	CACACATCCTCTGGCTTATTGT	58.386	45.455	0.00	0.00	0.00	2.71
2223	6059	7.075851	TCCTAGTACTAGCAGTATAAGCTCA	57.924	40.000	22.39	0.00	42.32	4.26
2231	6067	4.851843	TGTTGCTCCTAGTACTAGCAGTA	58.148	43.478	22.39	15.17	46.17	2.74
2235	6071	4.372656	CCATTGTTGCTCCTAGTACTAGC	58.627	47.826	22.39	15.60	36.77	3.42
2236	6072	4.406003	ACCCATTGTTGCTCCTAGTACTAG	59.594	45.833	21.11	21.11	0.00	2.57
2268	6104	4.342427	GCCACAATGATCTGGGCA	57.658	55.556	0.00	0.00	44.01	5.36
2269	6105	3.530067	GGCCACAATGATCTGGGC	58.470	61.111	9.16	9.16	45.01	5.36
2274	6110	1.729881	GCCTTCGGCCACAATGATC	59.270	57.895	2.24	0.00	44.06	2.92
2353	6189	0.179225	CACTTTCCATTCCGCGTTCG	60.179	55.000	4.92	0.00	0.00	3.95
2364	6200	2.614983	GCGTAAGAAACACCACTTTCCA	59.385	45.455	0.00	0.00	43.02	3.53
2447	6284	5.105106	TCAGGTATTCGATGAGGCTTTTGTA	60.105	40.000	0.00	0.00	0.00	2.41
2458	6295	5.118990	ACCAGTTTCATCAGGTATTCGATG	58.881	41.667	0.00	0.00	40.34	3.84
2459	6296	5.359194	ACCAGTTTCATCAGGTATTCGAT	57.641	39.130	0.00	0.00	31.32	3.59
2461	6298	3.551890	CGACCAGTTTCATCAGGTATTCG	59.448	47.826	0.00	0.00	33.77	3.34
2500	6337	6.220726	TGGTTATGTCGATGAGAGATCAAA	57.779	37.500	0.00	0.00	34.42	2.69
2595	6432	1.388431	CAACACAAACGCAAACACACC	59.612	47.619	0.00	0.00	0.00	4.16
2648	6485	1.377690	TATGAGGTTTTGAGGGGGCA	58.622	50.000	0.00	0.00	0.00	5.36
2656	6493	8.705594	TCCTAAAGTAGAGGATATGAGGTTTTG	58.294	37.037	0.00	0.00	38.22	2.44
2682	6519	3.071312	TGTGAGATTTTGGGCATTTTGCT	59.929	39.130	0.00	0.00	44.28	3.91
2734	6571	0.911045	GGTCCCCGTCCTTTTCCCTA	60.911	60.000	0.00	0.00	0.00	3.53
2750	6588	1.057275	GGGAGAGAGGGGGAATGGTC	61.057	65.000	0.00	0.00	0.00	4.02
2751	6589	1.004891	GGGAGAGAGGGGGAATGGT	59.995	63.158	0.00	0.00	0.00	3.55
2754	6592	0.121197	TTGTGGGAGAGAGGGGGAAT	59.879	55.000	0.00	0.00	0.00	3.01
2755	6593	0.104144	TTTGTGGGAGAGAGGGGGAA	60.104	55.000	0.00	0.00	0.00	3.97
2756	6594	0.104144	TTTTGTGGGAGAGAGGGGGA	60.104	55.000	0.00	0.00	0.00	4.81
2757	6595	0.777446	TTTTTGTGGGAGAGAGGGGG	59.223	55.000	0.00	0.00	0.00	5.40
2812	6650	1.898154	GACAGATGGCGGTGGTAGT	59.102	57.895	0.00	0.00	0.00	2.73
2813	6651	1.226974	CGACAGATGGCGGTGGTAG	60.227	63.158	0.00	0.00	44.21	3.18
2814	6652	2.889617	CGACAGATGGCGGTGGTA	59.110	61.111	0.00	0.00	44.21	3.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.