AutoCloner

Multiple sequence alignment - TraesCS3B01G169300

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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	TraesCS3B01G169300	chr3B	100.000	3395	0	0	1	3395	169627684	169631078	0.000000e+00	6270
1	TraesCS3B01G169300	chr3B	73.095	643	159	14	1034	1669	534965450	534964815	2.050000e-52	217
2	TraesCS3B01G169300	chr3A	94.200	3448	132	31	1	3395	112956446	112959878	0.000000e+00	5197
3	TraesCS3B01G169300	chr3A	73.410	692	168	16	1022	1705	542202777	542203460	9.410000e-61	244
4	TraesCS3B01G169300	chr3D	96.502	2887	70	12	1	2871	116041466	116044337	0.000000e+00	4743
5	TraesCS3B01G169300	chr3D	96.101	513	12	5	2887	3392	116044386	116044897	0.000000e+00	830
6	TraesCS3B01G169300	chr3D	73.561	643	156	14	1034	1669	409021983	409021348	2.040000e-57	233
7	TraesCS3B01G169300	chr2B	75.365	617	146	6	1049	1662	91836508	91837121	3.310000e-75	292
8	TraesCS3B01G169300	chr2A	75.200	625	151	4	1049	1671	59323948	59323326	3.310000e-75	292
9	TraesCS3B01G169300	chr2D	74.716	617	150	6	1049	1662	59007124	59007737	1.550000e-68	270

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	TraesCS3B01G169300	chr3B	169627684	169631078	3394	False	6270.0	6270	100.0000	1	3395	1	chr3B.!!$F1	3394
1	TraesCS3B01G169300	chr3B	534964815	534965450	635	True	217.0	217	73.0950	1034	1669	1	chr3B.!!$R1	635
2	TraesCS3B01G169300	chr3A	112956446	112959878	3432	False	5197.0	5197	94.2000	1	3395	1	chr3A.!!$F1	3394
3	TraesCS3B01G169300	chr3A	542202777	542203460	683	False	244.0	244	73.4100	1022	1705	1	chr3A.!!$F2	683
4	TraesCS3B01G169300	chr3D	116041466	116044897	3431	False	2786.5	4743	96.3015	1	3392	2	chr3D.!!$F1	3391
5	TraesCS3B01G169300	chr3D	409021348	409021983	635	True	233.0	233	73.5610	1034	1669	1	chr3D.!!$R1	635
6	TraesCS3B01G169300	chr2B	91836508	91837121	613	False	292.0	292	75.3650	1049	1662	1	chr2B.!!$F1	613
7	TraesCS3B01G169300	chr2A	59323326	59323948	622	True	292.0	292	75.2000	1049	1671	1	chr2A.!!$R1	622
8	TraesCS3B01G169300	chr2D	59007124	59007737	613	False	270.0	270	74.7160	1049	1662	1	chr2D.!!$F1	613

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
331	336	0.105760	ATTGTTGCACCCTCAACCCA	60.106	50.000	4.46	0.00	44.15	4.51	F
381	386	1.066858	GTCTTGGCTCGGAGACATCAA	60.067	52.381	15.56	8.51	41.45	2.57	F
669	675	1.133513	AGAAACCACAGCCATCCAACA	60.134	47.619	0.00	0.00	0.00	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1886	1906	0.244721	GTTGCCTTCACCATCCTTGC	59.755	55.000	0.00	0.00	0.00	4.01	R
1989	2009	3.432890	GGTCCTTCTCAAATAGGCCAGAG	60.433	52.174	5.01	4.11	31.82	3.35	R
2615	2642	2.620367	GGTGATGGTATGCTTGTCCCAA	60.620	50.000	0.00	0.00	0.00	4.12	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
101	102	3.424703	TGCCAGGATTCAGAAAGAAAGG	58.575	45.455	0.00	0.00	40.22	3.11
108	109	7.120432	CCAGGATTCAGAAAGAAAGGAAAGTAG	59.880	40.741	0.00	0.00	40.22	2.57
179	184	5.994668	GTGGAGAAGTGAGAATTCTTCAAGT	59.005	40.000	9.87	0.00	42.53	3.16
223	228	7.920160	ATGAAAAACAAAGGAAGAAGCAAAA	57.080	28.000	0.00	0.00	0.00	2.44
271	276	1.133253	CGCAAGATGTGGAGCAACG	59.867	57.895	0.00	0.00	43.02	4.10
289	294	4.144727	ACGGCCAAACCACCCCAA	62.145	61.111	2.24	0.00	39.03	4.12
300	305	1.905894	ACCACCCCAAAAACATATGCC	59.094	47.619	1.58	0.00	0.00	4.40
329	334	3.892200	CATTGTTGCACCCTCAACC	57.108	52.632	4.46	0.00	44.15	3.77
331	336	0.105760	ATTGTTGCACCCTCAACCCA	60.106	50.000	4.46	0.00	44.15	4.51
361	366	3.304293	GGTCGATTACGGAAAACCTAACG	59.696	47.826	3.36	0.00	40.21	3.18
366	371	5.443693	CGATTACGGAAAACCTAACGTCTTG	60.444	44.000	0.00	0.00	40.38	3.02
381	386	1.066858	GTCTTGGCTCGGAGACATCAA	60.067	52.381	15.56	8.51	41.45	2.57
446	451	2.854032	CACCTCACCCACCCCACT	60.854	66.667	0.00	0.00	0.00	4.00
669	675	1.133513	AGAAACCACAGCCATCCAACA	60.134	47.619	0.00	0.00	0.00	3.33
679	685	1.880646	GCCATCCAACACAACGTACCT	60.881	52.381	0.00	0.00	0.00	3.08
943	955	1.341606	GCAGAGTAGACGCTTGTGAC	58.658	55.000	0.00	0.00	0.00	3.67
944	956	1.335964	GCAGAGTAGACGCTTGTGACA	60.336	52.381	0.00	0.00	0.00	3.58
1206	1220	2.108514	CATGCGCCTGGTTCGTCAT	61.109	57.895	4.18	0.00	0.00	3.06
1494	1508	3.326006	TCAAGGAGTGTCAGAAGCAAGAT	59.674	43.478	0.00	0.00	0.00	2.40
1623	1637	1.862827	CTTTTTGTTCTGCTTGCTGGC	59.137	47.619	0.00	0.00	0.00	4.85
1758	1772	2.226330	CTCGACCCAAATCCAAACACA	58.774	47.619	0.00	0.00	0.00	3.72
1779	1793	1.211457	AGGATCACCATGGACAAGCTC	59.789	52.381	21.47	6.19	38.94	4.09
1912	1932	2.564721	GGTGAAGGCAACAGGGCAC	61.565	63.158	0.00	0.00	46.44	5.01
1989	2009	4.013050	CCCTCTCCAAAGGTTTTGATCTC	58.987	47.826	3.24	0.00	34.34	2.75
2408	2428	8.757982	AATGGCATTTAAGTGTGATATCTTCT	57.242	30.769	6.96	0.00	0.00	2.85
2412	2432	7.712639	GGCATTTAAGTGTGATATCTTCTGAGA	59.287	37.037	3.98	0.00	36.09	3.27
2734	2790	7.237263	AGCATAGAACAGATTCCTCATATTCCT	59.763	37.037	0.00	0.00	35.18	3.36
2760	2816	3.990092	TGTTGTCTTGCGACTTGAGTAT	58.010	40.909	0.00	0.00	40.86	2.12
2829	2885	2.501723	AGTAGCACGGATTTGATGGAGT	59.498	45.455	0.00	0.00	0.00	3.85
2953	3042	2.171659	TGTTAACCACCAGAGTTGCTCA	59.828	45.455	2.48	0.00	32.06	4.26
2987	3076	3.409026	ACCTCTTCACTTGGTGATGTC	57.591	47.619	11.43	0.00	42.40	3.06
3012	3101	4.644103	AATGCATGCATCTACCAGAAAC	57.356	40.909	32.25	0.00	35.31	2.78
3029	3118	5.625251	CAGAAACGAATGATTCTGGTCAAG	58.375	41.667	3.43	0.00	45.91	3.02
3083	3172	8.574251	AACAAGCCACAATCAACTTACATATA	57.426	30.769	0.00	0.00	0.00	0.86
3119	3208	9.712359	CATGTGAAATATACAAAGTGACATCAG	57.288	33.333	0.00	0.00	0.00	2.90
3164	3253	7.831193	AGAGCTTTATCTTTGTTGTCCATACAT	59.169	33.333	0.00	0.00	34.97	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	1.270893	GGTGAGAACCTTCCAGGACAC	60.271	57.143	0.00	0.00	37.67	3.67
24	25	3.074412	ACAAATGGACGATGGTGAGAAC	58.926	45.455	0.00	0.00	0.00	3.01
63	64	1.215423	GGCAATAGGTGTCCCATCCTT	59.785	52.381	0.00	0.00	35.51	3.36
64	65	0.846693	GGCAATAGGTGTCCCATCCT	59.153	55.000	0.00	0.00	37.80	3.24
65	66	0.550914	TGGCAATAGGTGTCCCATCC	59.449	55.000	0.00	0.00	0.00	3.51
66	67	1.477558	CCTGGCAATAGGTGTCCCATC	60.478	57.143	0.00	0.00	32.99	3.51
67	68	0.552848	CCTGGCAATAGGTGTCCCAT	59.447	55.000	0.00	0.00	32.99	4.00
68	69	0.548926	TCCTGGCAATAGGTGTCCCA	60.549	55.000	0.00	0.00	38.99	4.37
69	70	0.846693	ATCCTGGCAATAGGTGTCCC	59.153	55.000	0.00	0.00	38.99	4.46
101	102	5.297776	ACATATGCATTCAGGTGCTACTTTC	59.702	40.000	3.54	0.00	45.27	2.62
108	109	3.304257	GCTGTACATATGCATTCAGGTGC	60.304	47.826	3.54	0.00	45.25	5.01
223	228	3.658398	CAACTGATGCCAACCTCCT	57.342	52.632	0.00	0.00	0.00	3.69
271	276	4.589675	TGGGGTGGTTTGGCCGTC	62.590	66.667	0.00	0.00	41.21	4.79
289	294	4.403113	TGCATGTGATGAGGCATATGTTTT	59.597	37.500	4.29	0.00	38.95	2.43
331	336	1.274167	TCCGTAATCGACCAGTTTGCT	59.726	47.619	0.00	0.00	39.71	3.91
361	366	0.532573	TGATGTCTCCGAGCCAAGAC	59.467	55.000	0.00	0.00	41.84	3.01
366	371	1.519455	CGGTTGATGTCTCCGAGCC	60.519	63.158	10.08	0.00	46.05	4.70
626	631	0.843984	GCTATTTGTAGGCAGGGGGA	59.156	55.000	0.00	0.00	0.00	4.81
669	675	6.285990	CCTAATAATAAGCCAGGTACGTTGT	58.714	40.000	0.00	0.00	0.00	3.32
679	685	1.702957	AGGCCGCCTAATAATAAGCCA	59.297	47.619	11.25	0.00	41.45	4.75
943	955	2.825532	CTGGTGGAGGTAAATTGGGTTG	59.174	50.000	0.00	0.00	0.00	3.77
944	956	2.821625	GCTGGTGGAGGTAAATTGGGTT	60.822	50.000	0.00	0.00	0.00	4.11
1206	1220	0.955428	GCAGCTGGACGATGTTTGGA	60.955	55.000	17.12	0.00	0.00	3.53
1494	1508	3.218470	GTTGTGTGCAGCAGCCCA	61.218	61.111	0.00	0.00	41.13	5.36
1539	1553	5.707066	AGCCCTTCTTGTTGATTATCTCT	57.293	39.130	0.00	0.00	0.00	3.10
1623	1637	3.107601	TGAGTCTTGGAATGGGAGGTAG	58.892	50.000	0.00	0.00	0.00	3.18
1758	1772	1.637553	AGCTTGTCCATGGTGATCCTT	59.362	47.619	12.58	0.00	34.23	3.36
1779	1793	0.888736	TGAACCACGGGTGCTCAATG	60.889	55.000	3.11	0.00	35.34	2.82
1886	1906	0.244721	GTTGCCTTCACCATCCTTGC	59.755	55.000	0.00	0.00	0.00	4.01
1912	1932	4.533919	TCAATGGGCTATTTGGTTGTTG	57.466	40.909	0.00	0.00	0.00	3.33
1989	2009	3.432890	GGTCCTTCTCAAATAGGCCAGAG	60.433	52.174	5.01	4.11	31.82	3.35
2408	2428	8.435187	AGGAGAATAGATTGTAATTGCATCTCA	58.565	33.333	18.26	0.00	33.10	3.27
2412	2432	8.658619	AGAGAGGAGAATAGATTGTAATTGCAT	58.341	33.333	0.00	0.00	0.00	3.96
2615	2642	2.620367	GGTGATGGTATGCTTGTCCCAA	60.620	50.000	0.00	0.00	0.00	4.12
2987	3076	3.379057	TCTGGTAGATGCATGCATTTGTG	59.621	43.478	32.60	19.82	36.70	3.33
3012	3101	3.438087	AGTTGCTTGACCAGAATCATTCG	59.562	43.478	0.00	0.00	34.02	3.34
3029	3118	7.066284	TGCTGAAGATTTCTTATCCTAAGTTGC	59.934	37.037	0.00	0.00	36.11	4.17
3119	3208	3.397482	TCTCTGCTTCTTTGACTTCTGC	58.603	45.455	0.00	0.00	0.00	4.26
3164	3253	8.620416	CATAAGACCGTGATTTCATATTTTCCA	58.380	33.333	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.