AutoCloner

Multiple sequence alignment - TraesCS6A01G062400

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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	TraesCS6A01G062400	chr6A	100.000	2222	0	0	1	2222	33404848	33402627	0.000000e+00	4104.0
1	TraesCS6A01G062400	chr6A	87.191	648	75	7	1	643	33530505	33529861	0.000000e+00	730.0
2	TraesCS6A01G062400	chr6A	92.279	272	17	2	1	271	33305847	33305579	1.240000e-102	383.0
3	TraesCS6A01G062400	chr5B	98.074	1558	28	2	665	2222	640414837	640416392	0.000000e+00	2710.0
4	TraesCS6A01G062400	chr5B	80.465	645	101	19	643	1266	672101060	672101700	9.290000e-129	470.0
5	TraesCS6A01G062400	chr5A	98.072	1556	28	2	667	2222	475377613	475379166	0.000000e+00	2706.0
6	TraesCS6A01G062400	chr5A	82.775	209	25	6	1854	2059	255588758	255588558	2.270000e-40	176.0
7	TraesCS6A01G062400	chr5A	82.775	209	25	6	1854	2059	257331878	257331678	2.270000e-40	176.0
8	TraesCS6A01G062400	chr5A	100.000	29	0	0	992	1020	6207326	6207354	1.000000e-03	54.7
9	TraesCS6A01G062400	chrUn	97.561	1558	32	3	665	2222	62068747	62070298	0.000000e+00	2662.0
10	TraesCS6A01G062400	chrUn	99.030	722	6	1	1501	2222	428748801	428749521	0.000000e+00	1293.0
11	TraesCS6A01G062400	chr6D	87.461	646	77	3	1	642	29093997	29094642	0.000000e+00	741.0
12	TraesCS6A01G062400	chr6D	76.145	524	103	15	108	620	29152370	29152882	2.830000e-64	255.0
13	TraesCS6A01G062400	chr6B	86.822	645	77	7	1	641	60615581	60614941	0.000000e+00	713.0
14	TraesCS6A01G062400	chr6B	85.736	645	84	7	1	641	60632274	60631634	0.000000e+00	675.0
15	TraesCS6A01G062400	chr6B	85.983	585	72	7	64	641	60657724	60657143	3.130000e-173	617.0
16	TraesCS6A01G062400	chr6B	85.484	434	45	8	190	620	59829166	59829584	9.420000e-119	436.0
17	TraesCS6A01G062400	chr6B	74.803	635	126	27	5	620	60584380	60583761	2.830000e-64	255.0
18	TraesCS6A01G062400	chr6B	87.943	141	16	1	1	140	59828718	59828858	4.910000e-37	165.0
19	TraesCS6A01G062400	chr2D	85.857	601	73	8	675	1266	83846736	83847333	1.450000e-176	628.0
20	TraesCS6A01G062400	chr2D	77.992	518	86	13	665	1165	430218607	430219113	1.290000e-77	300.0
21	TraesCS6A01G062400	chr1A	83.010	618	78	19	663	1266	157082957	157083561	3.250000e-148	534.0
22	TraesCS6A01G062400	chr2A	78.116	361	63	11	250	604	762930490	762930840	4.810000e-52	215.0
23	TraesCS6A01G062400	chr7A	91.429	70	6	0	1329	1398	701403688	701403757	1.820000e-16	97.1
24	TraesCS6A01G062400	chr7D	91.176	68	6	0	1331	1398	611348668	611348735	2.350000e-15	93.5
25	TraesCS6A01G062400	chr7B	85.714	77	11	0	1190	1266	501559515	501559439	5.090000e-12	82.4

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	TraesCS6A01G062400	chr6A	33402627	33404848	2221	True	4104.0	4104	100.0000	1	2222	1	chr6A.!!$R2	2221
1	TraesCS6A01G062400	chr6A	33529861	33530505	644	True	730.0	730	87.1910	1	643	1	chr6A.!!$R3	642
2	TraesCS6A01G062400	chr5B	640414837	640416392	1555	False	2710.0	2710	98.0740	665	2222	1	chr5B.!!$F1	1557
3	TraesCS6A01G062400	chr5B	672101060	672101700	640	False	470.0	470	80.4650	643	1266	1	chr5B.!!$F2	623
4	TraesCS6A01G062400	chr5A	475377613	475379166	1553	False	2706.0	2706	98.0720	667	2222	1	chr5A.!!$F2	1555
5	TraesCS6A01G062400	chrUn	62068747	62070298	1551	False	2662.0	2662	97.5610	665	2222	1	chrUn.!!$F1	1557
6	TraesCS6A01G062400	chrUn	428748801	428749521	720	False	1293.0	1293	99.0300	1501	2222	1	chrUn.!!$F2	721
7	TraesCS6A01G062400	chr6D	29093997	29094642	645	False	741.0	741	87.4610	1	642	1	chr6D.!!$F1	641
8	TraesCS6A01G062400	chr6D	29152370	29152882	512	False	255.0	255	76.1450	108	620	1	chr6D.!!$F2	512
9	TraesCS6A01G062400	chr6B	60614941	60615581	640	True	713.0	713	86.8220	1	641	1	chr6B.!!$R2	640
10	TraesCS6A01G062400	chr6B	60631634	60632274	640	True	675.0	675	85.7360	1	641	1	chr6B.!!$R3	640
11	TraesCS6A01G062400	chr6B	60657143	60657724	581	True	617.0	617	85.9830	64	641	1	chr6B.!!$R4	577
12	TraesCS6A01G062400	chr6B	59828718	59829584	866	False	300.5	436	86.7135	1	620	2	chr6B.!!$F1	619
13	TraesCS6A01G062400	chr6B	60583761	60584380	619	True	255.0	255	74.8030	5	620	1	chr6B.!!$R1	615
14	TraesCS6A01G062400	chr2D	83846736	83847333	597	False	628.0	628	85.8570	675	1266	1	chr2D.!!$F1	591
15	TraesCS6A01G062400	chr2D	430218607	430219113	506	False	300.0	300	77.9920	665	1165	1	chr2D.!!$F2	500
16	TraesCS6A01G062400	chr1A	157082957	157083561	604	False	534.0	534	83.0100	663	1266	1	chr1A.!!$F1	603

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
294	560	0.03213	TCCAAGATAGACGATGCGCC	59.968	55.0	4.18	0.0	0.0	6.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2025	2344	0.876342	AGCTCTTATTGTAGCGCGCC	60.876	55.0	30.33	14.69	43.63	6.53	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
60	62	1.342082	CGACGAGTAAACACAGGCGG	61.342	60.000	0.00	0.00	0.00	6.13
80	82	1.401018	GCCGCTTGCGTAATTTGTCTT	60.401	47.619	13.97	0.00	0.00	3.01
87	89	5.743026	TTGCGTAATTTGTCTTTCACTGA	57.257	34.783	0.00	0.00	0.00	3.41
101	109	1.350684	TCACTGATGCCTACCAAAGCA	59.649	47.619	0.00	0.00	44.45	3.91
114	122	1.962807	CCAAAGCAACATGGAAGTGGA	59.037	47.619	0.00	0.00	39.12	4.02
154	162	3.050166	GCACCGCGCCATTGATTGA	62.050	57.895	0.00	0.00	32.94	2.57
176	184	3.744660	GGATTTATCCATGTCGAAGCCT	58.255	45.455	3.87	0.00	46.38	4.58
187	453	3.647771	GAAGCCTGGGGGAACGGT	61.648	66.667	0.00	0.00	33.58	4.83
188	454	3.182996	AAGCCTGGGGGAACGGTT	61.183	61.111	0.00	0.00	33.58	4.44
198	464	2.757056	GGAACGGTTATGCGGTGCC	61.757	63.158	0.00	0.00	38.70	5.01
215	481	4.444838	CGGTCGCCAATGACGGGA	62.445	66.667	0.00	0.00	39.83	5.14
221	487	1.077068	GCCAATGACGGGATCCCAA	60.077	57.895	30.42	15.56	35.37	4.12
230	496	0.328258	CGGGATCCCAAACAAGGAGT	59.672	55.000	30.42	0.00	36.67	3.85
260	526	4.690748	CGCTTCCAAAGAAAGATGAGTACA	59.309	41.667	0.00	0.00	0.00	2.90
281	547	2.124193	CCATGGCGGCATCCAAGA	60.124	61.111	23.19	0.00	39.96	3.02
282	548	1.529948	CCATGGCGGCATCCAAGAT	60.530	57.895	23.19	0.00	39.96	2.40
289	555	1.337260	GCGGCATCCAAGATAGACGAT	60.337	52.381	0.00	0.00	0.00	3.73
293	559	1.723542	CATCCAAGATAGACGATGCGC	59.276	52.381	0.00	0.00	0.00	6.09
294	560	0.032130	TCCAAGATAGACGATGCGCC	59.968	55.000	4.18	0.00	0.00	6.53
296	562	0.946221	CAAGATAGACGATGCGCCCC	60.946	60.000	4.18	0.00	0.00	5.80
312	593	3.411351	CCCCGTCTTCGTGTTGCG	61.411	66.667	0.00	0.00	43.01	4.85
387	668	1.956297	GAGCCTGTCGTCTAGCTCTA	58.044	55.000	13.91	0.00	46.50	2.43
426	707	2.282180	GGTTGTGGCGATGGTGGT	60.282	61.111	0.00	0.00	0.00	4.16
620	907	0.394565	GGTTGCTCATCTCGCCCTAT	59.605	55.000	0.00	0.00	0.00	2.57
624	911	2.807676	TGCTCATCTCGCCCTATGATA	58.192	47.619	0.00	0.00	31.95	2.15
742	1031	6.017192	CCACAAAGTGTACACAGAATCATCAA	60.017	38.462	27.06	0.00	0.00	2.57
807	1096	7.092712	CCATATTACATCAGGGGTCTATCACAT	60.093	40.741	0.00	0.00	0.00	3.21
830	1119	9.669353	ACATAAATGAACGATGCAGATTAAATC	57.331	29.630	0.00	0.00	0.00	2.17
901	1201	6.399743	GGATTTCTATCCCGTAATCTTCTCC	58.600	44.000	0.00	0.00	43.98	3.71
915	1217	1.912043	CTTCTCCCTCCCTCACAACAT	59.088	52.381	0.00	0.00	0.00	2.71
1334	1653	1.169661	TTGCTGCCGATTTTCGTGGT	61.170	50.000	0.00	0.00	38.40	4.16
1344	1663	3.621794	GATTTTCGTGGTGAGCATATGC	58.378	45.455	20.36	20.36	42.49	3.14
1654	1973	9.496710	TCCCCTGTACTGATTTACTATCTTTTA	57.503	33.333	0.60	0.00	0.00	1.52
1848	2167	1.853963	ATGGGAAGTAGCGAGAGTGT	58.146	50.000	0.00	0.00	0.00	3.55
1929	2248	7.398332	AGTTTCTGATCCTGATGGCTAAAAATT	59.602	33.333	0.00	0.00	0.00	1.82
2025	2344	5.089970	TCCATGTGTAAGAGGATCAGTTG	57.910	43.478	0.00	0.00	37.82	3.16
2125	2444	2.359848	TCCTCGGTCATATGGTTACACG	59.640	50.000	2.13	1.10	0.00	4.49
2196	2515	4.647564	AATCCTAATTCGGATGGAGCAT	57.352	40.909	12.01	0.00	42.89	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.140325	ACCGGTATATGGGCAATCTTG	57.860	47.619	4.49	0.00	0.00	3.02
60	62	0.168128	AGACAAATTACGCAAGCGGC	59.832	50.000	19.30	0.00	44.69	6.53
80	82	2.224744	TGCTTTGGTAGGCATCAGTGAA	60.225	45.455	0.00	0.00	33.23	3.18
87	89	1.826720	CCATGTTGCTTTGGTAGGCAT	59.173	47.619	0.00	0.00	38.30	4.40
101	109	1.002087	GACGTCCTCCACTTCCATGTT	59.998	52.381	3.51	0.00	0.00	2.71
133	141	1.876497	AATCAATGGCGCGGTGCTTT	61.876	50.000	13.85	5.07	45.43	3.51
154	162	7.721088	CCAGGCTTCGACATGGATAAATCCT	62.721	48.000	10.28	0.00	44.28	3.24
165	173	1.923395	TTCCCCCAGGCTTCGACAT	60.923	57.895	0.00	0.00	0.00	3.06
173	181	1.453197	CATAACCGTTCCCCCAGGC	60.453	63.158	0.00	0.00	0.00	4.85
176	184	2.269562	CGCATAACCGTTCCCCCA	59.730	61.111	0.00	0.00	0.00	4.96
198	464	3.733344	ATCCCGTCATTGGCGACCG	62.733	63.158	13.09	0.00	31.91	4.79
206	472	2.446435	CTTGTTTGGGATCCCGTCATT	58.554	47.619	26.03	0.00	39.42	2.57
207	473	1.340991	CCTTGTTTGGGATCCCGTCAT	60.341	52.381	26.03	0.00	39.42	3.06
215	481	2.716424	TCTCCAACTCCTTGTTTGGGAT	59.284	45.455	0.66	0.00	36.63	3.85
221	487	0.759346	AGCGTCTCCAACTCCTTGTT	59.241	50.000	0.00	0.00	39.92	2.83
312	593	2.964389	GCCCGAGCGCTTCTCATC	60.964	66.667	13.26	0.00	41.98	2.92
314	595	3.939837	CTTGCCCGAGCGCTTCTCA	62.940	63.158	13.26	4.83	44.31	3.27
330	611	3.782443	GGCCCCGGATCGTGTCTT	61.782	66.667	0.73	0.00	0.00	3.01
363	644	1.305201	CTAGACGACAGGCTCTCCTC	58.695	60.000	0.00	0.00	41.93	3.71
373	654	3.908643	TCTTCCTAGAGCTAGACGACA	57.091	47.619	6.11	0.00	35.21	4.35
387	668	0.910088	CCCCTCCTCGGTTTCTTCCT	60.910	60.000	0.00	0.00	0.00	3.36
470	751	2.431430	CTCGTCTGCAAGCGCTGA	60.431	61.111	12.58	0.00	43.07	4.26
603	890	1.413118	TCATAGGGCGAGATGAGCAA	58.587	50.000	0.00	0.00	36.08	3.91
696	985	1.806542	CGTGTCTGTTGGGGAATTCAG	59.193	52.381	7.93	0.00	0.00	3.02
807	1096	9.935682	GAAGATTTAATCTGCATCGTTCATTTA	57.064	29.630	8.34	0.00	40.13	1.40
901	1201	1.746615	CGGCATGTTGTGAGGGAGG	60.747	63.158	0.00	0.00	0.00	4.30
915	1217	0.967887	CAAGAGGAGGAGAGACGGCA	60.968	60.000	0.00	0.00	0.00	5.69
1244	1563	1.536943	GGTCAGCAGAGGAGAACGGT	61.537	60.000	0.00	0.00	0.00	4.83
1654	1973	9.474313	TCTTTGGCCACTAATAAATATGAACTT	57.526	29.630	3.88	0.00	0.00	2.66
1848	2167	3.980022	TCCATAGCCAAATCATAGTCCCA	59.020	43.478	0.00	0.00	0.00	4.37
2025	2344	0.876342	AGCTCTTATTGTAGCGCGCC	60.876	55.000	30.33	14.69	43.63	6.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.