AutoCloner

Multiple sequence alignment - TraesCS5D01G041600

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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	TraesCS5D01G041600	chr5D	100.000	4148	0	0	1	4148	42015832	42019979	0.000000e+00	7661
1	TraesCS5D01G041600	chr5D	91.787	3750	213	41	474	4148	440159796	440163525	0.000000e+00	5131
2	TraesCS5D01G041600	chr5D	92.416	1635	71	23	831	2449	42053515	42051918	0.000000e+00	2283
3	TraesCS5D01G041600	chr5D	79.832	476	80	9	333	794	42054072	42053599	2.390000e-87	333
4	TraesCS5D01G041600	chr5D	90.164	122	12	0	339	460	432339156	432339277	4.290000e-35	159
5	TraesCS5D01G041600	chr5A	92.622	4012	222	45	198	4148	30403674	30407672	0.000000e+00	5701
6	TraesCS5D01G041600	chr5A	94.219	3356	136	30	831	4148	555770530	555773865	0.000000e+00	5070
7	TraesCS5D01G041600	chr5B	93.929	3360	139	27	831	4148	535111100	535114436	0.000000e+00	5014
8	TraesCS5D01G041600	chr5B	93.845	3363	114	37	825	4148	36720301	36723609	0.000000e+00	4977
9	TraesCS5D01G041600	chr5B	94.833	2361	80	12	840	3192	36767815	36765489	0.000000e+00	3646
10	TraesCS5D01G041600	chr5B	89.591	807	61	12	1	800	36772053	36771263	0.000000e+00	1003
11	TraesCS5D01G041600	chr5B	89.206	806	67	6	1	797	36719425	36720219	0.000000e+00	989
12	TraesCS5D01G041600	chr5B	96.622	148	4	1	3776	3923	36765233	36765087	1.150000e-60	244
13	TraesCS5D01G041600	chr5B	98.473	131	2	0	3949	4079	36765090	36764960	8.970000e-57	231
14	TraesCS5D01G041600	chrUn	89.344	122	13	0	339	460	392770448	392770327	2.000000e-33	154
15	TraesCS5D01G041600	chr7B	89.344	122	13	0	339	460	622433732	622433853	2.000000e-33	154
16	TraesCS5D01G041600	chr4A	89.344	122	13	0	339	460	583864669	583864790	2.000000e-33	154
17	TraesCS5D01G041600	chr3D	89.344	122	13	0	339	460	581040656	581040535	2.000000e-33	154

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	TraesCS5D01G041600	chr5D	42015832	42019979	4147	False	7661	7661	100.00000	1	4148	1	chr5D.!!$F1	4147
1	TraesCS5D01G041600	chr5D	440159796	440163525	3729	False	5131	5131	91.78700	474	4148	1	chr5D.!!$F3	3674
2	TraesCS5D01G041600	chr5D	42051918	42054072	2154	True	1308	2283	86.12400	333	2449	2	chr5D.!!$R1	2116
3	TraesCS5D01G041600	chr5A	30403674	30407672	3998	False	5701	5701	92.62200	198	4148	1	chr5A.!!$F1	3950
4	TraesCS5D01G041600	chr5A	555770530	555773865	3335	False	5070	5070	94.21900	831	4148	1	chr5A.!!$F2	3317
5	TraesCS5D01G041600	chr5B	535111100	535114436	3336	False	5014	5014	93.92900	831	4148	1	chr5B.!!$F1	3317
6	TraesCS5D01G041600	chr5B	36719425	36723609	4184	False	2983	4977	91.52550	1	4148	2	chr5B.!!$F2	4147
7	TraesCS5D01G041600	chr5B	36764960	36772053	7093	True	1281	3646	94.87975	1	4079	4	chr5B.!!$R1	4078

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
716	737	0.107897	TTGCGCACCACCTCGATAAT	60.108	50.0	11.12	0.0	0.0	1.28	F
2137	5632	0.541392	TGTGGATGGATTCTGTCGGG	59.459	55.0	0.00	0.0	0.0	5.14	F
2269	5764	2.278332	AACTTCAGAGGCTTGGGAAC	57.722	50.0	0.00	0.0	0.0	3.62	F
3021	6516	1.081892	CGTGCCAGATGTTTCAGAGG	58.918	55.0	0.00	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2559	6054	0.753111	GCGCTGATTCCAAATCCCCT	60.753	55.000	0.00	0.0	0.00	4.79	R
3000	6495	0.035317	TCTGAAACATCTGGCACGCT	59.965	50.000	0.00	0.0	0.00	5.07	R
3076	6571	1.035139	CCAGCAGCTGGTTGTTTCTT	58.965	50.000	30.97	0.0	45.82	2.52	R
3857	7476	2.987149	CGCATACAAGTGAGAAGACGTT	59.013	45.455	0.00	0.0	0.00	3.99	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
30	31	2.946947	GACAAGTGGGTCCCATGTG	58.053	57.895	19.95	18.94	35.28	3.21
57	65	3.173668	TGGGTAATCGTGTATGTCAGC	57.826	47.619	0.00	0.00	0.00	4.26
119	127	2.511659	ACTAGACAGGCACGACAACTA	58.488	47.619	0.00	0.00	0.00	2.24
136	144	4.225267	ACAACTACCCTGGAAACTCTATGG	59.775	45.833	0.00	0.00	0.00	2.74
138	146	4.695606	ACTACCCTGGAAACTCTATGGAA	58.304	43.478	0.00	0.00	0.00	3.53
146	154	4.086457	GGAAACTCTATGGAAAAGCCCAA	58.914	43.478	0.00	0.00	40.04	4.12
151	159	4.289672	ACTCTATGGAAAAGCCCAAGAAGA	59.710	41.667	0.00	0.00	40.04	2.87
192	200	4.585879	TCTATTAGGTTCCCTGCACAAAC	58.414	43.478	0.00	0.00	34.61	2.93
243	252	0.605860	TAGTCGCCGGAGAGATAGGC	60.606	60.000	8.65	0.00	46.88	3.93
254	263	3.497227	GGAGAGATAGGCGAAGTACCTCT	60.497	52.174	0.00	0.00	38.81	3.69
271	283	3.099905	CCTCTATCATCATAGCCGGGAA	58.900	50.000	2.18	0.00	33.10	3.97
350	362	7.926555	GTCAGCACACATAAACTACCTATATGT	59.073	37.037	0.00	0.00	40.04	2.29
374	386	7.611467	TGTTTTCAGCAGTTATCCACTTCATAT	59.389	33.333	0.00	0.00	30.92	1.78
479	491	2.036604	TCATGTTAGCCGAGTGTTGTCA	59.963	45.455	0.00	0.00	0.00	3.58
503	515	2.171448	GTGCCATCCAGACCTCATAACT	59.829	50.000	0.00	0.00	0.00	2.24
512	524	2.202932	CTCATAACTGGCGCCGCT	60.203	61.111	23.90	11.16	0.00	5.52
553	567	0.456221	CTAGACATTGCCGTCCTCGT	59.544	55.000	0.00	0.00	36.52	4.18
715	736	0.320858	TTTGCGCACCACCTCGATAA	60.321	50.000	11.12	0.00	0.00	1.75
716	737	0.107897	TTGCGCACCACCTCGATAAT	60.108	50.000	11.12	0.00	0.00	1.28
729	759	4.104102	ACCTCGATAATCTTGCCCCATAAA	59.896	41.667	0.00	0.00	0.00	1.40
736	766	7.382218	CGATAATCTTGCCCCATAAACATTTTC	59.618	37.037	0.00	0.00	0.00	2.29
801	860	2.801342	GCAAGACTAGGATGGAGAAGCG	60.801	54.545	0.00	0.00	0.00	4.68
826	907	6.176183	AGGTATTGTTTCTCCTTCACATGAG	58.824	40.000	0.00	0.00	0.00	2.90
827	908	6.013379	AGGTATTGTTTCTCCTTCACATGAGA	60.013	38.462	0.00	0.00	35.89	3.27
829	910	6.814506	ATTGTTTCTCCTTCACATGAGAAG	57.185	37.500	21.85	21.85	45.49	2.85

Showing 1 to 25 of 52 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	3.055747	TGCTGACATACACGATTACCCAA	60.056	43.478	0.00	0.00	0.00	4.12
37	38	2.498078	TGCTGACATACACGATTACCCA	59.502	45.455	0.00	0.00	0.00	4.51
119	127	4.811063	GCTTTTCCATAGAGTTTCCAGGGT	60.811	45.833	0.00	0.00	0.00	4.34
179	187	0.953471	CGATCGGTTTGTGCAGGGAA	60.953	55.000	7.38	0.00	0.00	3.97
180	188	1.375396	CGATCGGTTTGTGCAGGGA	60.375	57.895	7.38	0.00	0.00	4.20
192	200	0.464036	TGGGGATCAAAGACGATCGG	59.536	55.000	20.98	0.47	42.35	4.18
243	252	5.447954	CGGCTATGATGATAGAGGTACTTCG	60.448	48.000	3.06	0.00	41.55	3.79
271	283	0.545171	CCCTGACAGTGATGATGCCT	59.455	55.000	0.00	0.00	0.00	4.75
350	362	8.579850	AATATGAAGTGGATAACTGCTGAAAA	57.420	30.769	0.00	0.00	39.81	2.29
479	491	0.977627	TGAGGTCTGGATGGCACGAT	60.978	55.000	0.00	0.00	0.00	3.73
503	515	4.695993	TGTCAATGAGCGGCGCCA	62.696	61.111	30.40	25.38	0.00	5.69
512	524	8.088365	TCTAGTCTTTCTCGATTTTGTCAATGA	58.912	33.333	0.00	0.00	0.00	2.57
553	567	2.097036	CATGAAGCATGGAAAGAGGCA	58.903	47.619	0.00	0.00	38.11	4.75
621	640	0.462937	CGTGTTCGGGATGGCCAATA	60.463	55.000	10.96	0.00	35.15	1.90
715	736	7.564660	TGATAGAAAATGTTTATGGGGCAAGAT	59.435	33.333	0.00	0.00	0.00	2.40
716	737	6.894654	TGATAGAAAATGTTTATGGGGCAAGA	59.105	34.615	0.00	0.00	0.00	3.02
736	766	8.079203	ACTCTAGCAAAGTCGTCATATTGATAG	58.921	37.037	9.84	9.84	41.00	2.08
801	860	6.173339	TCATGTGAAGGAGAAACAATACCTC	58.827	40.000	0.00	0.00	31.89	3.85
826	907	4.637977	CCTTTTTGCTAGGATCTCCACTTC	59.362	45.833	0.00	0.00	38.89	3.01
827	908	4.593956	CCTTTTTGCTAGGATCTCCACTT	58.406	43.478	0.00	0.00	38.89	3.16
829	910	2.685388	GCCTTTTTGCTAGGATCTCCAC	59.315	50.000	0.00	0.00	38.89	4.02
838	4281	2.099756	GCCCATGTAGCCTTTTTGCTAG	59.900	50.000	0.00	0.00	44.12	3.42
942	4416	0.733150	GTTAGGAAGGCGATTGGCAC	59.267	55.000	9.53	2.39	46.16	5.01
1086	4565	2.364448	GAGGGGGCGAGTTCTCCT	60.364	66.667	0.00	0.00	0.00	3.69
1109	4588	1.740285	CGGGGTATCTCCTTGACGG	59.260	63.158	0.00	0.00	36.25	4.79

Showing 1 to 25 of 50 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.