AutoCloner

Multiple sequence alignment - TraesCS7B01G065200

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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	TraesCS7B01G065200	chr7B	100.000	4973	0	0	1	4973	70528228	70523256	0.000000e+00	9184.0
1	TraesCS7B01G065200	chr7D	89.548	2411	169	34	1866	4225	111066046	111063668	0.000000e+00	2979.0
2	TraesCS7B01G065200	chr7D	90.931	838	49	13	805	1629	111067088	111066265	0.000000e+00	1101.0
3	TraesCS7B01G065200	chr7D	81.714	700	110	8	84	779	111067851	111067166	7.220000e-158	568.0
4	TraesCS7B01G065200	chr7D	86.145	332	30	8	4575	4898	111063316	111062993	1.330000e-90	344.0
5	TraesCS7B01G065200	chr7A	90.823	1373	79	32	3019	4363	116128918	116127565	0.000000e+00	1794.0
6	TraesCS7B01G065200	chr7A	90.827	665	34	10	810	1467	116130720	116130076	0.000000e+00	865.0
7	TraesCS7B01G065200	chr7A	90.036	281	21	4	785	1059	116146302	116146023	1.700000e-94	357.0
8	TraesCS7B01G065200	chr7A	81.324	423	36	15	4561	4973	116127347	116126958	2.250000e-78	303.0
9	TraesCS7B01G065200	chr7A	91.667	72	6	0	342	413	116146588	116146517	3.170000e-17	100.0
10	TraesCS7B01G065200	chr6D	95.833	48	2	0	1642	1689	378290424	378290377	1.480000e-10	78.7
11	TraesCS7B01G065200	chr6B	95.833	48	2	0	1642	1689	221293184	221293137	1.480000e-10	78.7
12	TraesCS7B01G065200	chr6B	95.833	48	2	0	1642	1689	572555543	572555496	1.480000e-10	78.7
13	TraesCS7B01G065200	chr4D	94.118	51	3	0	1642	1692	329882975	329883025	1.480000e-10	78.7
14	TraesCS7B01G065200	chr3D	92.727	55	3	1	1642	1696	591338402	591338455	1.480000e-10	78.7
15	TraesCS7B01G065200	chr3B	95.833	48	2	0	1642	1689	57556456	57556409	1.480000e-10	78.7
16	TraesCS7B01G065200	chr3B	89.655	58	5	1	1642	1698	590683152	590683209	6.910000e-09	73.1
17	TraesCS7B01G065200	chr1A	90.909	55	5	0	1642	1696	102806141	102806195	1.920000e-09	75.0
18	TraesCS7B01G065200	chr5B	90.741	54	5	0	1642	1695	173565314	173565261	6.910000e-09	73.1

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	TraesCS7B01G065200	chr7B	70523256	70528228	4972	True	9184.000000	9184	100.0000	1	4973	1	chr7B.!!$R1	4972
1	TraesCS7B01G065200	chr7D	111062993	111067851	4858	True	1248.000000	2979	87.0845	84	4898	4	chr7D.!!$R1	4814
2	TraesCS7B01G065200	chr7A	116126958	116130720	3762	True	987.333333	1794	87.6580	810	4973	3	chr7A.!!$R1	4163
3	TraesCS7B01G065200	chr7A	116146023	116146588	565	True	228.500000	357	90.8515	342	1059	2	chr7A.!!$R2	717

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
477	483	0.038526	TCGTGGGAGCTCGAGAAAAC	60.039	55.0	18.75	5.41	0.00	2.43	F
569	575	0.311165	TCGCCTATGAAGAGTAGCGC	59.689	55.0	0.00	0.00	0.00	5.92	F
722	729	0.322816	TGCTTCAATGGTGAGGGCTC	60.323	55.0	0.00	0.00	36.16	4.70	F
1806	1955	0.831307	ACGGATTTGGGGCTCTAGTC	59.169	55.0	0.00	0.00	0.00	2.59	F
2934	3165	0.033405	CGGTCCCTCCTACTTCCTCA	60.033	60.0	0.00	0.00	0.00	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1304	1399	0.104671	CCTGCAACCAACCAACCAAG	59.895	55.0	0.00	3.61	R
1483	1578	0.388659	TGGATGCACAAACTGTTGCC	59.611	50.0	38.39	4.52	R
1823	1972	0.823356	ACACGCCCTTGCAACTTGAT	60.823	50.0	37.32	2.57	R
3293	4035	0.037975	GGTCATGGCAAGGTGCTTTG	60.038	55.0	44.28	2.77	R
4438	5284	0.182299	TTGGACACATGACACTGGCA	59.818	50.0	0.00	4.92	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	2.959275	CGCACTCGTTCCTGGATAC	58.041	57.895	0.00	0.00	0.00	2.24
24	25	1.641577	GCACTCGTTCCTGGATACAC	58.358	55.000	0.00	0.00	46.17	2.90
25	26	1.909376	CACTCGTTCCTGGATACACG	58.091	55.000	12.09	12.09	46.17	4.49
26	27	1.471287	CACTCGTTCCTGGATACACGA	59.529	52.381	18.11	18.11	46.17	4.35
28	29	2.118313	TCGTTCCTGGATACACGAGA	57.882	50.000	15.94	0.00	46.17	4.04
29	30	2.439409	TCGTTCCTGGATACACGAGAA	58.561	47.619	15.94	0.00	46.17	2.87
30	31	2.821378	TCGTTCCTGGATACACGAGAAA	59.179	45.455	15.94	0.00	46.17	2.52
31	32	3.446161	TCGTTCCTGGATACACGAGAAAT	59.554	43.478	15.94	0.00	46.17	2.17
32	33	3.551890	CGTTCCTGGATACACGAGAAATG	59.448	47.826	12.82	0.00	46.17	2.32
33	34	3.819564	TCCTGGATACACGAGAAATGG	57.180	47.619	0.00	0.00	46.17	3.16
34	35	2.158957	TCCTGGATACACGAGAAATGGC	60.159	50.000	0.00	0.00	46.17	4.40
35	36	2.213499	CTGGATACACGAGAAATGGCC	58.787	52.381	0.00	0.00	46.17	5.36
36	37	1.837439	TGGATACACGAGAAATGGCCT	59.163	47.619	3.32	0.00	46.17	5.19
37	38	2.158957	TGGATACACGAGAAATGGCCTC	60.159	50.000	3.32	0.00	46.17	4.70
42	43	2.089854	CGAGAAATGGCCTCGTTGG	58.910	57.895	3.32	0.00	45.89	3.77
43	44	1.369091	CGAGAAATGGCCTCGTTGGG	61.369	60.000	3.32	0.00	45.89	4.12
44	45	1.000896	AGAAATGGCCTCGTTGGGG	60.001	57.895	3.32	0.00	36.00	4.96
45	46	1.304134	GAAATGGCCTCGTTGGGGT	60.304	57.895	3.32	0.00	36.00	4.95
46	47	0.898326	GAAATGGCCTCGTTGGGGTT	60.898	55.000	3.32	0.00	36.00	4.11
47	48	1.184970	AAATGGCCTCGTTGGGGTTG	61.185	55.000	3.32	0.00	36.00	3.77
48	49	4.966787	TGGCCTCGTTGGGGTTGC	62.967	66.667	3.32	0.00	36.00	4.17
50	51	4.966787	GCCTCGTTGGGGTTGCCA	62.967	66.667	0.05	0.00	36.00	4.92
51	52	2.035626	CCTCGTTGGGGTTGCCAT	59.964	61.111	0.00	0.00	0.00	4.40
52	53	2.342650	CCTCGTTGGGGTTGCCATG	61.343	63.158	0.00	0.00	0.00	3.66
53	54	2.282816	TCGTTGGGGTTGCCATGG	60.283	61.111	7.63	7.63	0.00	3.66

Showing 1 to 25 of 465 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.172578	TGTATCCAGGAACGAGTGCG	59.827	55.000	0.00	0.00	44.79	5.34
5	6	1.641577	GTGTATCCAGGAACGAGTGC	58.358	55.000	0.00	0.00	0.00	4.40
6	7	1.471287	TCGTGTATCCAGGAACGAGTG	59.529	52.381	10.31	0.00	39.90	3.51
7	8	1.830279	TCGTGTATCCAGGAACGAGT	58.170	50.000	10.31	0.00	39.90	4.18
9	10	2.118313	TCTCGTGTATCCAGGAACGA	57.882	50.000	13.16	13.16	42.30	3.85
10	11	2.933495	TTCTCGTGTATCCAGGAACG	57.067	50.000	5.89	5.89	35.24	3.95
11	12	3.871594	CCATTTCTCGTGTATCCAGGAAC	59.128	47.826	0.00	0.00	35.24	3.62
12	13	3.681594	GCCATTTCTCGTGTATCCAGGAA	60.682	47.826	0.00	0.00	35.24	3.36
13	14	2.158957	GCCATTTCTCGTGTATCCAGGA	60.159	50.000	0.00	0.00	34.51	3.86
14	15	2.213499	GCCATTTCTCGTGTATCCAGG	58.787	52.381	0.00	0.00	0.00	4.45
15	16	2.158900	AGGCCATTTCTCGTGTATCCAG	60.159	50.000	5.01	0.00	0.00	3.86
16	17	1.837439	AGGCCATTTCTCGTGTATCCA	59.163	47.619	5.01	0.00	0.00	3.41
17	18	2.484889	GAGGCCATTTCTCGTGTATCC	58.515	52.381	5.01	0.00	0.00	2.59
18	19	2.128035	CGAGGCCATTTCTCGTGTATC	58.872	52.381	5.01	0.00	46.16	2.24
19	20	2.225068	CGAGGCCATTTCTCGTGTAT	57.775	50.000	5.01	0.00	46.16	2.29
20	21	3.733236	CGAGGCCATTTCTCGTGTA	57.267	52.632	5.01	0.00	46.16	2.90
21	22	4.598257	CGAGGCCATTTCTCGTGT	57.402	55.556	5.01	0.00	46.16	4.49
25	26	1.032114	CCCCAACGAGGCCATTTCTC	61.032	60.000	5.01	0.00	35.39	2.87
26	27	1.000896	CCCCAACGAGGCCATTTCT	60.001	57.895	5.01	0.00	35.39	2.52
27	28	0.898326	AACCCCAACGAGGCCATTTC	60.898	55.000	5.01	0.00	35.39	2.17
28	29	1.155155	AACCCCAACGAGGCCATTT	59.845	52.632	5.01	0.00	35.39	2.32
29	30	1.606313	CAACCCCAACGAGGCCATT	60.606	57.895	5.01	0.00	35.39	3.16
30	31	2.035626	CAACCCCAACGAGGCCAT	59.964	61.111	5.01	0.00	35.39	4.40
31	32	4.966787	GCAACCCCAACGAGGCCA	62.967	66.667	5.01	0.00	35.39	5.36
33	34	4.966787	TGGCAACCCCAACGAGGC	62.967	66.667	0.00	0.00	41.82	4.70

Showing 1 to 25 of 466 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.