AutoCloner

Multiple sequence alignment - TraesCS2D01G427900

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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	TraesCS2D01G427900	chr2D	100.000	8834	0	0	1	8834	539889354	539880521	0.000000e+00	16314.0
1	TraesCS2D01G427900	chr2D	96.875	64	1	1	7016	7078	592583139	592583076	1.210000e-18	106.0
2	TraesCS2D01G427900	chr2D	95.122	41	2	0	2563	2603	3013689	3013729	2.060000e-06	65.8
3	TraesCS2D01G427900	chr2B	95.922	3801	92	22	2250	6005	644157120	644153338	0.000000e+00	6102.0
4	TraesCS2D01G427900	chr2B	98.518	1012	15	0	6004	7015	644153224	644152213	0.000000e+00	1786.0
5	TraesCS2D01G427900	chr2B	94.513	1057	45	4	871	1915	644158645	644157590	0.000000e+00	1618.0
6	TraesCS2D01G427900	chr2B	90.887	1218	60	20	7077	8272	644152220	644151032	0.000000e+00	1587.0
7	TraesCS2D01G427900	chr2B	87.663	843	74	18	4	833	644159477	644158652	0.000000e+00	953.0
8	TraesCS2D01G427900	chr2B	93.558	326	6	6	1912	2235	644157507	644157195	1.040000e-128	472.0
9	TraesCS2D01G427900	chr2A	95.194	3142	84	26	1914	5010	683522688	683519569	0.000000e+00	4903.0
10	TraesCS2D01G427900	chr2A	96.560	2006	63	5	5012	7015	683519453	683517452	0.000000e+00	3317.0
11	TraesCS2D01G427900	chr2A	89.993	1529	109	20	7077	8589	683517459	683515959	0.000000e+00	1936.0
12	TraesCS2D01G427900	chr2A	94.487	1179	42	13	757	1916	683523904	683522730	0.000000e+00	1796.0
13	TraesCS2D01G427900	chr2A	85.690	594	62	16	4	587	683524937	683524357	9.810000e-169	604.0
14	TraesCS2D01G427900	chr2A	93.243	148	10	0	8685	8832	683515956	683515809	1.490000e-52	219.0
15	TraesCS2D01G427900	chr2A	82.883	222	25	8	2385	2603	2699504	2699293	4.210000e-43	187.0
16	TraesCS2D01G427900	chr2A	100.000	44	0	0	3257	3300	683521385	683521342	2.040000e-11	82.4
17	TraesCS2D01G427900	chr3D	79.710	345	50	11	2277	2603	9618016	9618358	1.920000e-56	231.0
18	TraesCS2D01G427900	chr3D	84.821	112	15	2	2500	2610	2261532	2261422	2.610000e-20	111.0
19	TraesCS2D01G427900	chr3D	96.875	64	1	1	7016	7078	390098439	390098502	1.210000e-18	106.0
20	TraesCS2D01G427900	chr5D	96.875	64	1	1	7016	7078	398804776	398804713	1.210000e-18	106.0
21	TraesCS2D01G427900	chr5D	89.024	82	9	0	2526	2607	141446312	141446393	1.570000e-17	102.0
22	TraesCS2D01G427900	chr5D	100.000	32	0	0	8743	8774	462023844	462023875	9.580000e-05	60.2
23	TraesCS2D01G427900	chr4D	96.875	64	1	1	7016	7078	216324117	216324054	1.210000e-18	106.0
24	TraesCS2D01G427900	chr1D	96.875	64	1	1	7016	7078	116458953	116459016	1.210000e-18	106.0
25	TraesCS2D01G427900	chr1B	96.875	64	1	1	7016	7078	57684789	57684852	1.210000e-18	106.0
26	TraesCS2D01G427900	chr5B	94.203	69	2	2	7016	7082	593472635	593472567	4.360000e-18	104.0
27	TraesCS2D01G427900	chr5B	94.203	69	2	2	7016	7082	593556645	593556577	4.360000e-18	104.0
28	TraesCS2D01G427900	chr5B	100.000	32	0	0	8743	8774	568176651	568176682	9.580000e-05	60.2
29	TraesCS2D01G427900	chr1A	95.161	62	2	1	7018	7078	39151552	39151613	7.300000e-16	97.1
30	TraesCS2D01G427900	chr7A	95.000	40	2	0	2565	2604	79811525	79811564	7.400000e-06	63.9
31	TraesCS2D01G427900	chr5A	100.000	32	0	0	8743	8774	582100234	582100265	9.580000e-05	60.2

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	TraesCS2D01G427900	chr2D	539880521	539889354	8833	True	16314.000000	16314	100.000000	1	8834	1	chr2D.!!$R1	8833
1	TraesCS2D01G427900	chr2B	644151032	644159477	8445	True	2086.333333	6102	93.510167	4	8272	6	chr2B.!!$R1	8268
2	TraesCS2D01G427900	chr2A	683515809	683524937	9128	True	1836.771429	4903	93.595286	4	8832	7	chr2A.!!$R2	8828

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
849	1203	0.179000	CACATAGCCGCTCCCTTCTT	59.821	55.000	0.00	0.00	0.00	2.52	F
850	1204	0.466124	ACATAGCCGCTCCCTTCTTC	59.534	55.000	0.00	0.00	0.00	2.87	F
1446	1805	0.536460	TTCTCCCCGTGGTTGCTTTC	60.536	55.000	0.00	0.00	0.00	2.62	F
2273	2794	2.377628	TAGCCCGCTATTTCCCGCTG	62.378	60.000	0.00	0.00	0.00	5.18	F
2906	3447	0.807667	AATCGATGTCGCTCCTGTGC	60.808	55.000	0.00	0.00	39.60	4.57	F
3940	4487	2.306805	ACCTGGAAGATGTCAGAATGCA	59.693	45.455	0.00	0.00	34.07	3.96	F
5495	6193	1.808343	GATTGCACAGTCATGTCTGCA	59.192	47.619	18.24	10.66	37.65	4.41	F
6261	7078	3.370209	GGGTTCCTACTCGCCTTAATGTT	60.370	47.826	0.00	0.00	0.00	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2361	2882	2.105006	AGCTTCACACTATGCACCAG	57.895	50.000	0.00	0.00	4.00	R
2787	3328	3.814842	CACCTCACAAGCAATGAGTACAA	59.185	43.478	10.03	41.78	2.41	R
2906	3447	1.012086	CGGCATCAACATCTGGACAG	58.988	55.000	0.00	0.00	3.51	R
3940	4487	1.812571	GCCACTGGACAAATTGACGAT	59.187	47.619	0.00	0.00	3.73	R
4344	4898	1.752498	ACGGTGTAGACTTCACACACA	59.248	47.619	13.45	46.53	3.72	R
5638	6338	0.804364	CAAAGCGTGCTGGCTATCAA	59.196	50.000	0.00	43.93	2.57	R
6591	7408	0.246360	TGGTGAGTACAGGATGCACG	59.754	55.000	0.00	42.53	5.34	R
8077	8899	0.034767	TCGGACGTCATACCAGGAGT	60.035	55.000	18.91	0.00	3.85	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
26	27	6.926630	ATTTTCAGCCCTTATACAAACCAA	57.073	33.333	0.00	0.00	0.00	3.67
41	42	4.069304	CAAACCAATCAACCTTCGGACTA	58.931	43.478	0.00	0.00	0.00	2.59
65	66	1.951130	CATCTGCGTCGCGGCTATT	60.951	57.895	21.37	3.18	34.49	1.73
76	77	1.739929	CGGCTATTGTGGTGTCGCA	60.740	57.895	0.00	0.00	0.00	5.10
99	100	6.512741	GCAGTTTCCAATTTCTTCTGTACGAA	60.513	38.462	0.00	0.00	0.00	3.85
133	135	2.753055	TTCGACCATGGAATCAACGA	57.247	45.000	21.47	15.15	0.00	3.85
252	262	5.875359	GTCTCGTTCAAAGTCCATAGGAAAT	59.125	40.000	0.00	0.00	31.38	2.17
260	270	5.982890	AAGTCCATAGGAAATTGTTGTGG	57.017	39.130	0.00	0.00	31.38	4.17
323	333	1.807814	ATAGGAATCTCCAACGGGCT	58.192	50.000	0.00	0.00	39.61	5.19
338	348	1.482954	GGGCTACGACTAGAGGGTTT	58.517	55.000	0.00	0.00	0.00	3.27
499	509	2.403561	TCCCCTTTGTTTTCCTTTGGG	58.596	47.619	0.00	0.00	0.00	4.12
503	513	4.568804	CCCCTTTGTTTTCCTTTGGGTTTT	60.569	41.667	0.00	0.00	0.00	2.43
541	551	5.163673	TGCTTTCATTTTTGTTTCTTTGGCC	60.164	36.000	0.00	0.00	0.00	5.36
631	644	6.535274	ACACGTGAAACTTTTACCTGATAC	57.465	37.500	25.01	0.00	31.75	2.24
633	646	6.708949	ACACGTGAAACTTTTACCTGATACAT	59.291	34.615	25.01	0.00	31.75	2.29
636	649	7.227910	ACGTGAAACTTTTACCTGATACATGTT	59.772	33.333	2.30	0.00	31.75	2.71
641	654	7.435068	ACTTTTACCTGATACATGTTGACAC	57.565	36.000	2.30	0.00	0.00	3.67
663	676	7.976826	ACACTTTTCAAATACAAGTTGTACGA	58.023	30.769	17.79	11.73	35.42	3.43
664	677	7.906527	ACACTTTTCAAATACAAGTTGTACGAC	59.093	33.333	17.79	4.97	35.42	4.34
669	682	7.124347	TCAAATACAAGTTGTACGACCATTC	57.876	36.000	17.79	0.00	35.42	2.67
778	1118	8.832458	TCCATAAATAAAGTAAAAAGGAGGGG	57.168	34.615	0.00	0.00	0.00	4.79
810	1150	3.059099	TCAGCATGACGAGCCACA	58.941	55.556	0.00	0.00	42.56	4.17
848	1202	1.690219	CCACATAGCCGCTCCCTTCT	61.690	60.000	0.00	0.00	0.00	2.85
849	1203	0.179000	CACATAGCCGCTCCCTTCTT	59.821	55.000	0.00	0.00	0.00	2.52
850	1204	0.466124	ACATAGCCGCTCCCTTCTTC	59.534	55.000	0.00	0.00	0.00	2.87

Showing 1 to 25 of 216 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	7.158021	TGGTTTGTATAAGGGCTGAAAATTTG	58.842	34.615	0.00	0.00	0.00	2.32
1	2	7.309770	TGGTTTGTATAAGGGCTGAAAATTT	57.690	32.000	0.00	0.00	0.00	1.82
2	3	6.926630	TGGTTTGTATAAGGGCTGAAAATT	57.073	33.333	0.00	0.00	0.00	1.82
10	11	4.709886	AGGTTGATTGGTTTGTATAAGGGC	59.290	41.667	0.00	0.00	0.00	5.19
41	42	2.278857	GCGACGCAGATGGACGAT	60.279	61.111	16.42	0.00	0.00	3.73
65	66	0.393132	TTGGAAACTGCGACACCACA	60.393	50.000	0.00	0.00	0.00	4.17
113	114	3.046968	TCGTTGATTCCATGGTCGAAA	57.953	42.857	12.58	0.00	0.00	3.46
133	135	6.512297	AGGTTATCTGATTTTTGTTTGCGTT	58.488	32.000	0.00	0.00	0.00	4.84
171	176	4.853468	TCCTGCTGGTTTGAATATACCA	57.147	40.909	9.73	0.00	41.97	3.25
182	188	2.897326	GGTTTTGGTAATCCTGCTGGTT	59.103	45.455	9.73	6.17	34.23	3.67
215	225	4.675510	TGAACGAGACTAACAACGTCTTT	58.324	39.130	0.00	0.00	41.53	2.52
227	237	4.087182	TCCTATGGACTTTGAACGAGACT	58.913	43.478	0.00	0.00	0.00	3.24
252	262	2.413453	GCGCTTTTTGAAACCACAACAA	59.587	40.909	0.00	0.00	0.00	2.83
260	270	0.512518	GCCATGGCGCTTTTTGAAAC	59.487	50.000	23.48	0.00	0.00	2.78
338	348	1.091537	GCAAACTACGCTAATGGGCA	58.908	50.000	0.00	0.00	0.00	5.36
370	380	2.180276	ACCGAAGCAGAGTGAACCTAT	58.820	47.619	0.00	0.00	0.00	2.57
418	428	8.893727	CCAAAGAGAAACCGATGAAAAGTATAT	58.106	33.333	0.00	0.00	0.00	0.86
422	432	4.278419	CCCAAAGAGAAACCGATGAAAAGT	59.722	41.667	0.00	0.00	0.00	2.66
423	433	4.278419	ACCCAAAGAGAAACCGATGAAAAG	59.722	41.667	0.00	0.00	0.00	2.27
426	436	3.502123	ACCCAAAGAGAAACCGATGAA	57.498	42.857	0.00	0.00	0.00	2.57
473	483	6.176896	CAAAGGAAAACAAAGGGGAAAAAGA	58.823	36.000	0.00	0.00	0.00	2.52
480	490	2.123589	ACCCAAAGGAAAACAAAGGGG	58.876	47.619	0.00	0.00	39.15	4.79
605	618	5.871539	TCAGGTAAAAGTTTCACGTGTTTC	58.128	37.500	16.51	6.95	31.70	2.78
624	637	6.558771	TGAAAAGTGTCAACATGTATCAGG	57.441	37.500	0.00	0.00	0.00	3.86
631	644	8.633075	ACTTGTATTTGAAAAGTGTCAACATG	57.367	30.769	0.00	0.00	37.24	3.21

Showing 1 to 25 of 235 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.