AutoCloner

Multiple sequence alignment - TraesCS5A01G481900

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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	TraesCS5A01G481900	chr5A	100.000	5998	0	0	1	5998	653957182	653963179	0.000000e+00	11077.0
1	TraesCS5A01G481900	chr5A	76.866	402	60	19	2057	2437	439861393	439861004	4.740000e-46	196.0
2	TraesCS5A01G481900	chr5D	95.479	6016	222	24	1	5998	526844465	526850448	0.000000e+00	9557.0
3	TraesCS5A01G481900	chr5D	79.135	532	95	13	2440	2961	521672993	521673518	2.660000e-93	353.0
4	TraesCS5A01G481900	chr5B	93.788	3622	170	30	1	3602	662604272	662607858	0.000000e+00	5391.0
5	TraesCS5A01G481900	chr5B	93.278	2410	138	13	3598	5998	662625618	662628012	0.000000e+00	3531.0
6	TraesCS5A01G481900	chr5B	81.706	891	108	35	3094	3951	662673245	662674113	0.000000e+00	691.0
7	TraesCS5A01G481900	chr5B	83.405	699	97	13	1272	1961	662672294	662672982	1.100000e-176	630.0
8	TraesCS5A01G481900	chr5B	77.705	1063	183	37	1	1028	662754928	662755971	8.600000e-168	601.0
9	TraesCS5A01G481900	chr5B	77.069	1051	199	28	1	1019	662665872	662666912	8.720000e-158	568.0
10	TraesCS5A01G481900	chr5B	76.548	1066	198	35	1	1031	662677926	662678974	2.460000e-148	536.0
11	TraesCS5A01G481900	chr5B	78.273	695	102	31	25	680	662661017	662661701	9.360000e-108	401.0
12	TraesCS5A01G481900	chr5B	85.390	308	41	4	4994	5299	662674409	662674714	3.490000e-82	316.0
13	TraesCS5A01G481900	chr5B	87.170	265	31	3	4739	5002	662674120	662674382	1.260000e-76	298.0
14	TraesCS5A01G481900	chr5B	91.346	104	8	1	2958	3061	662673148	662673250	2.250000e-29	141.0
15	TraesCS5A01G481900	chr5B	77.692	130	28	1	3148	3276	662674655	662674784	1.790000e-10	78.7
16	TraesCS5A01G481900	chr6B	80.747	857	120	38	2062	2887	5042885	5042043	1.420000e-175	627.0
17	TraesCS5A01G481900	chr6B	80.415	868	117	34	2132	2958	688753435	688752580	3.970000e-171	612.0
18	TraesCS5A01G481900	chr2D	82.930	703	94	17	2220	2905	531769510	531768817	1.430000e-170	610.0
19	TraesCS5A01G481900	chr3D	86.450	524	57	13	2220	2731	604887029	604887550	4.060000e-156	562.0
20	TraesCS5A01G481900	chr2A	81.445	706	102	22	2220	2905	676375513	676374817	8.790000e-153	551.0
21	TraesCS5A01G481900	chr1D	80.589	747	117	25	2223	2952	475867163	475867898	8.790000e-153	551.0
22	TraesCS5A01G481900	chr1D	89.655	58	6	0	5468	5525	390322696	390322753	2.320000e-09	75.0
23	TraesCS5A01G481900	chr3B	78.974	390	62	11	2322	2692	581711015	581710627	1.290000e-61	248.0
24	TraesCS5A01G481900	chr4D	75.650	423	72	25	2293	2694	219418175	219417763	1.330000e-41	182.0
25	TraesCS5A01G481900	chr3A	76.433	157	30	6	5379	5531	435541411	435541258	1.790000e-10	78.7

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	TraesCS5A01G481900	chr5A	653957182	653963179	5997	False	11077.000000	11077	100.000000	1	5998	1	chr5A.!!$F1	5997
1	TraesCS5A01G481900	chr5D	526844465	526850448	5983	False	9557.000000	9557	95.479000	1	5998	1	chr5D.!!$F2	5997
2	TraesCS5A01G481900	chr5D	521672993	521673518	525	False	353.000000	353	79.135000	2440	2961	1	chr5D.!!$F1	521
3	TraesCS5A01G481900	chr5B	662604272	662607858	3586	False	5391.000000	5391	93.788000	1	3602	1	chr5B.!!$F1	3601
4	TraesCS5A01G481900	chr5B	662625618	662628012	2394	False	3531.000000	3531	93.278000	3598	5998	1	chr5B.!!$F2	2400
5	TraesCS5A01G481900	chr5B	662754928	662755971	1043	False	601.000000	601	77.705000	1	1028	1	chr5B.!!$F5	1027
6	TraesCS5A01G481900	chr5B	662665872	662666912	1040	False	568.000000	568	77.069000	1	1019	1	chr5B.!!$F4	1018
7	TraesCS5A01G481900	chr5B	662661017	662661701	684	False	401.000000	401	78.273000	25	680	1	chr5B.!!$F3	655
8	TraesCS5A01G481900	chr5B	662672294	662678974	6680	False	384.385714	691	83.322429	1	5299	7	chr5B.!!$F6	5298
9	TraesCS5A01G481900	chr6B	5042043	5042885	842	True	627.000000	627	80.747000	2062	2887	1	chr6B.!!$R1	825
10	TraesCS5A01G481900	chr6B	688752580	688753435	855	True	612.000000	612	80.415000	2132	2958	1	chr6B.!!$R2	826
11	TraesCS5A01G481900	chr2D	531768817	531769510	693	True	610.000000	610	82.930000	2220	2905	1	chr2D.!!$R1	685
12	TraesCS5A01G481900	chr3D	604887029	604887550	521	False	562.000000	562	86.450000	2220	2731	1	chr3D.!!$F1	511
13	TraesCS5A01G481900	chr2A	676374817	676375513	696	True	551.000000	551	81.445000	2220	2905	1	chr2A.!!$R1	685
14	TraesCS5A01G481900	chr1D	475867163	475867898	735	False	551.000000	551	80.589000	2223	2952	1	chr1D.!!$F2	729

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
447	6123	1.299976	GACGGCACATCCCCTTCTT	59.700	57.895	0.00	0.0	0.0	2.52	F
803	6489	1.639722	TGGATGAACGAGGGAAGACA	58.360	50.000	0.00	0.0	0.0	3.41	F
2106	7803	1.568025	GTCCGTCGTCACTTTTGCC	59.432	57.895	0.00	0.0	0.0	4.52	F
3568	9340	1.273759	TGCCTTCTCAGAGTGCAGAT	58.726	50.000	7.63	0.0	0.0	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2026	7722	0.036765	TTGTACGAGGACCCACATGC	60.037	55.000	0.0	0.0	0.00	4.06	R
2244	7967	2.492567	CCAAAAGATCAGGGGGTTTCCA	60.493	50.000	0.0	0.0	37.22	3.53	R
4085	9860	1.347707	AGCTTGTCAGGTTGAATCGGA	59.652	47.619	0.0	0.0	0.00	4.55	R
5533	11313	0.035739	GTTACCCAAGACCGCCAGAA	59.964	55.000	0.0	0.0	0.00	3.02	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
79	5712	6.800072	TGTCATATGTAGGGTGTTGTCATA	57.200	37.500	1.90	0.00	0.00	2.15
162	5805	2.046023	TGTCGAGGGCAAGCATGG	60.046	61.111	0.00	0.00	0.00	3.66
166	5809	1.452651	CGAGGGCAAGCATGGACAT	60.453	57.895	0.00	0.00	0.00	3.06
178	5821	2.549754	GCATGGACATCCCTCAATAACG	59.450	50.000	0.00	0.00	35.38	3.18
433	6109	7.437748	AGATTCAAAATACTCTCTATGGACGG	58.562	38.462	0.00	0.00	0.00	4.79
447	6123	1.299976	GACGGCACATCCCCTTCTT	59.700	57.895	0.00	0.00	0.00	2.52
612	6290	7.897864	TGGGTAAATAAAGTTTGTACAATGGG	58.102	34.615	9.56	0.00	0.00	4.00
645	6323	9.977762	GGTAAACTTTTAGAATGGTATACAACG	57.022	33.333	5.01	0.00	0.00	4.10
733	6416	7.848223	ACAAGAAAAGGAAAAAGATGGTTTG	57.152	32.000	0.00	0.00	0.00	2.93
803	6489	1.639722	TGGATGAACGAGGGAAGACA	58.360	50.000	0.00	0.00	0.00	3.41
806	6492	2.028020	GGATGAACGAGGGAAGACAGTT	60.028	50.000	0.00	0.00	0.00	3.16
879	6565	3.132289	GGTGGCATCAGTTACTACTAGCA	59.868	47.826	0.00	0.00	31.96	3.49
1010	6698	2.106166	GGAGCTCTTCCATGGACATCAT	59.894	50.000	15.91	0.08	46.01	2.45
1021	6709	2.799176	GACATCATGGTCCCTTGCC	58.201	57.895	0.00	0.00	0.00	4.52
1056	6744	2.203070	GTCGGCGGCATGGAGAAT	60.203	61.111	6.63	0.00	0.00	2.40
1123	6811	3.709834	TACAGCATGGAGAGGGTCA	57.290	52.632	0.00	0.00	43.62	4.02
1144	6832	2.174854	ACCACAAAGACTAGCAAGGGTT	59.825	45.455	0.00	0.00	0.00	4.11
1376	7067	5.335583	CCGTCAGAAAATGGCAATCAACTTA	60.336	40.000	0.00	0.00	30.75	2.24
1444	7135	3.138304	AGTACTGTCGAAATTGCTTGCA	58.862	40.909	0.00	0.00	0.00	4.08
1812	7508	4.105697	TCCATGAGTTTCTAAACAAGGGGT	59.894	41.667	8.21	0.00	41.30	4.95
2023	7719	1.815003	CTGACAATTTGACCAGCTCCC	59.185	52.381	2.79	0.00	0.00	4.30
2037	7733	3.338250	TCCCTGGCATGTGGGTCC	61.338	66.667	16.39	0.70	43.74	4.46
2085	7782	7.906199	ATAGTAAAGTGAGGAGTGCTTCTAT	57.094	36.000	0.00	0.00	0.00	1.98
2106	7803	1.568025	GTCCGTCGTCACTTTTGCC	59.432	57.895	0.00	0.00	0.00	4.52
2602	8351	6.402981	AGGGGACAACCTTAATCAATAGTT	57.597	37.500	0.00	0.00	37.69	2.24

Showing 1 to 25 of 73 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	5712	1.115467	GAGACCCTCCACGTGATGAT	58.885	55.000	19.30	0.00	0.00	2.45
152	5791	1.076485	AGGGATGTCCATGCTTGCC	60.076	57.895	0.86	0.00	38.24	4.52
153	5792	0.394762	TGAGGGATGTCCATGCTTGC	60.395	55.000	0.86	0.00	38.24	4.01
154	5793	2.133281	TTGAGGGATGTCCATGCTTG	57.867	50.000	0.86	0.00	38.24	4.01
155	5794	4.210331	GTTATTGAGGGATGTCCATGCTT	58.790	43.478	0.86	0.00	38.24	3.91
156	5795	3.745480	CGTTATTGAGGGATGTCCATGCT	60.745	47.826	0.86	0.00	38.24	3.79
157	5796	2.549754	CGTTATTGAGGGATGTCCATGC	59.450	50.000	0.86	0.00	38.24	4.06
162	5805	6.436843	AAATGTTCGTTATTGAGGGATGTC	57.563	37.500	0.00	0.00	0.00	3.06
166	5809	4.520874	TGCAAAATGTTCGTTATTGAGGGA	59.479	37.500	0.00	0.00	0.00	4.20
178	5821	2.222007	TGTGTGGCTGCAAAATGTTC	57.778	45.000	0.50	0.00	0.00	3.18
385	6059	4.038080	GGCCTGCCGGTGTTTTCG	62.038	66.667	1.90	0.00	0.00	3.46
433	6109	0.681243	GGTGGAAGAAGGGGATGTGC	60.681	60.000	0.00	0.00	0.00	4.57
447	6123	2.506231	TGTGTGACTTAAAGGTGGTGGA	59.494	45.455	0.00	0.00	0.00	4.02
599	6277	2.556622	CCACCAGACCCATTGTACAAAC	59.443	50.000	13.23	2.65	0.00	2.93
612	6290	6.489022	ACCATTCTAAAAGTTTACCACCAGAC	59.511	38.462	0.00	0.00	0.00	3.51
733	6416	8.777578	ATGAAAGGGGTTAATAAATAAGGGTC	57.222	34.615	0.00	0.00	0.00	4.46
803	6489	7.490840	TCATTCATTTTGTGTGACATTGAACT	58.509	30.769	0.00	0.00	30.30	3.01
806	6492	8.890124	AAATCATTCATTTTGTGTGACATTGA	57.110	26.923	0.00	0.00	29.60	2.57
840	6526	0.409484	ACCAGCCAGTTGCCCTAATT	59.591	50.000	0.00	0.00	42.71	1.40
1021	6709	1.750399	CGCCATTCCACTCAAGGGG	60.750	63.158	0.00	0.00	0.00	4.79
1064	6752	2.619849	CCATGGGCATCATCCCTATCAC	60.620	54.545	2.85	0.00	46.67	3.06
1123	6811	1.774856	ACCCTTGCTAGTCTTTGTGGT	59.225	47.619	0.00	0.00	0.00	4.16
1144	6832	1.208052	GTTGCTCTCCATGCTGTAGGA	59.792	52.381	0.00	0.00	0.00	2.94
1206	6894	4.080582	CCAATGGTAATAGGTGGTCACTCA	60.081	45.833	0.00	0.00	0.00	3.41
1376	7067	3.702548	TCATATTCTTGCAAGCTGCCATT	59.297	39.130	21.99	3.42	44.23	3.16

Showing 1 to 25 of 80 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.