AutoCloner

Multiple sequence alignment - TraesCS7B01G156200

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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	TraesCS7B01G156200	chr7B	100.000	2636	0	0	1	2636	211119863	211122498	0.000000e+00	4868.0
1	TraesCS7B01G156200	chr3D	91.917	1831	140	5	814	2636	555740896	555739066	0.000000e+00	2555.0
2	TraesCS7B01G156200	chr4B	90.375	1839	160	8	814	2636	568583403	568581566	0.000000e+00	2399.0
3	TraesCS7B01G156200	chr4B	88.957	163	17	1	522	684	630085084	630084923	1.600000e-47	200.0
4	TraesCS7B01G156200	chr7D	88.283	1835	196	15	816	2635	94074028	94072198	0.000000e+00	2180.0
5	TraesCS7B01G156200	chr7D	92.901	817	23	10	1	813	235167208	235167993	0.000000e+00	1155.0
6	TraesCS7B01G156200	chrUn	87.058	1839	215	15	815	2636	102570504	102572336	0.000000e+00	2056.0
7	TraesCS7B01G156200	chr5A	89.254	1554	151	9	1096	2636	482670540	482672090	0.000000e+00	1930.0
8	TraesCS7B01G156200	chr5A	90.741	54	5	0	471	524	616510847	616510794	3.640000e-09	73.1
9	TraesCS7B01G156200	chr5A	97.561	41	1	0	484	524	622200307	622200347	1.310000e-08	71.3
10	TraesCS7B01G156200	chr6A	85.365	1838	248	14	815	2636	522038855	522040687	0.000000e+00	1884.0
11	TraesCS7B01G156200	chr7A	85.079	1843	245	16	815	2636	736275852	736277685	0.000000e+00	1853.0
12	TraesCS7B01G156200	chr7A	90.758	422	31	3	392	813	250038849	250039262	8.240000e-155	556.0
13	TraesCS7B01G156200	chr7A	95.770	331	11	1	1	331	250038517	250038844	5.000000e-147	531.0
14	TraesCS7B01G156200	chr2A	92.270	1229	82	6	1420	2636	186445964	186447191	0.000000e+00	1731.0
15	TraesCS7B01G156200	chr2A	85.649	1101	138	13	1551	2636	779898553	779899648	0.000000e+00	1140.0
16	TraesCS7B01G156200	chr1B	83.025	1673	262	14	982	2635	593234741	593236410	0.000000e+00	1496.0
17	TraesCS7B01G156200	chr1B	90.385	52	5	0	473	524	3270131	3270182	4.710000e-08	69.4
18	TraesCS7B01G156200	chr3A	87.730	978	105	9	816	1781	227926420	227927394	0.000000e+00	1127.0
19	TraesCS7B01G156200	chr3A	88.199	161	17	2	522	682	490624374	490624532	9.630000e-45	191.0
20	TraesCS7B01G156200	chr1A	88.957	163	17	1	522	684	143812397	143812236	1.600000e-47	200.0
21	TraesCS7B01G156200	chr1A	88.344	163	18	1	522	684	143750790	143750629	7.440000e-46	195.0
22	TraesCS7B01G156200	chr1A	88.961	154	15	2	522	675	169712479	169712630	3.460000e-44	189.0
23	TraesCS7B01G156200	chr3B	87.952	166	18	2	522	686	480377043	480377207	7.440000e-46	195.0
24	TraesCS7B01G156200	chr3B	94.231	52	3	0	473	524	730778966	730779017	2.170000e-11	80.5
25	TraesCS7B01G156200	chr5B	88.199	161	18	1	522	682	333058798	333058639	9.630000e-45	191.0

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	TraesCS7B01G156200	chr7B	211119863	211122498	2635	False	4868.0	4868	100.000	1	2636	1	chr7B.!!$F1	2635
1	TraesCS7B01G156200	chr3D	555739066	555740896	1830	True	2555.0	2555	91.917	814	2636	1	chr3D.!!$R1	1822
2	TraesCS7B01G156200	chr4B	568581566	568583403	1837	True	2399.0	2399	90.375	814	2636	1	chr4B.!!$R1	1822
3	TraesCS7B01G156200	chr7D	94072198	94074028	1830	True	2180.0	2180	88.283	816	2635	1	chr7D.!!$R1	1819
4	TraesCS7B01G156200	chr7D	235167208	235167993	785	False	1155.0	1155	92.901	1	813	1	chr7D.!!$F1	812
5	TraesCS7B01G156200	chrUn	102570504	102572336	1832	False	2056.0	2056	87.058	815	2636	1	chrUn.!!$F1	1821
6	TraesCS7B01G156200	chr5A	482670540	482672090	1550	False	1930.0	1930	89.254	1096	2636	1	chr5A.!!$F1	1540
7	TraesCS7B01G156200	chr6A	522038855	522040687	1832	False	1884.0	1884	85.365	815	2636	1	chr6A.!!$F1	1821
8	TraesCS7B01G156200	chr7A	736275852	736277685	1833	False	1853.0	1853	85.079	815	2636	1	chr7A.!!$F1	1821
9	TraesCS7B01G156200	chr7A	250038517	250039262	745	False	543.5	556	93.264	1	813	2	chr7A.!!$F2	812
10	TraesCS7B01G156200	chr2A	186445964	186447191	1227	False	1731.0	1731	92.270	1420	2636	1	chr2A.!!$F1	1216
11	TraesCS7B01G156200	chr2A	779898553	779899648	1095	False	1140.0	1140	85.649	1551	2636	1	chr2A.!!$F2	1085
12	TraesCS7B01G156200	chr1B	593234741	593236410	1669	False	1496.0	1496	83.025	982	2635	1	chr1B.!!$F2	1653
13	TraesCS7B01G156200	chr3A	227926420	227927394	974	False	1127.0	1127	87.730	816	1781	1	chr3A.!!$F1	965

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
988	1002	0.032952	CGTGGACCTGGTTTCTTCGA	59.967	55.0	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1822	1864	1.100463	TGTCATTTGCAGCACCACGT	61.1	50.0	0.0	0.0	0.0	4.49	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
67	71	9.232473	AGTTCTCAAACTTAAGTGTTTCTCTTT	57.768	29.630	9.34	0.00	43.28	2.52
364	368	0.464036	CTGTAGCGACCTGGGCAATA	59.536	55.000	0.00	0.00	0.00	1.90
365	369	1.070758	CTGTAGCGACCTGGGCAATAT	59.929	52.381	0.00	0.00	0.00	1.28
366	370	1.488812	TGTAGCGACCTGGGCAATATT	59.511	47.619	0.00	0.00	0.00	1.28
367	371	1.873591	GTAGCGACCTGGGCAATATTG	59.126	52.381	11.27	11.27	0.00	1.90
368	372	0.255890	AGCGACCTGGGCAATATTGT	59.744	50.000	16.61	0.00	0.00	2.71
369	373	1.102978	GCGACCTGGGCAATATTGTT	58.897	50.000	16.61	0.00	0.00	2.83
370	374	1.065551	GCGACCTGGGCAATATTGTTC	59.934	52.381	16.61	9.66	0.00	3.18
371	375	1.330521	CGACCTGGGCAATATTGTTCG	59.669	52.381	16.61	10.90	0.00	3.95
372	376	1.065551	GACCTGGGCAATATTGTTCGC	59.934	52.381	16.61	9.66	0.00	4.70
373	377	1.102154	CCTGGGCAATATTGTTCGCA	58.898	50.000	16.61	13.27	0.00	5.10
374	378	1.202290	CCTGGGCAATATTGTTCGCAC	60.202	52.381	16.61	4.15	0.00	5.34
375	379	0.449786	TGGGCAATATTGTTCGCACG	59.550	50.000	16.61	0.00	0.00	5.34
376	380	0.730265	GGGCAATATTGTTCGCACGA	59.270	50.000	16.61	0.00	0.00	4.35
377	381	1.333619	GGGCAATATTGTTCGCACGAT	59.666	47.619	16.61	0.00	0.00	3.73
378	382	2.602217	GGGCAATATTGTTCGCACGATC	60.602	50.000	16.61	0.00	0.00	3.69
379	383	2.602217	GGCAATATTGTTCGCACGATCC	60.602	50.000	16.61	1.97	0.00	3.36
380	384	2.602217	GCAATATTGTTCGCACGATCCC	60.602	50.000	16.61	0.00	0.00	3.85
381	385	2.872245	CAATATTGTTCGCACGATCCCT	59.128	45.455	7.32	0.00	0.00	4.20
382	386	1.934589	TATTGTTCGCACGATCCCTG	58.065	50.000	0.00	0.00	0.00	4.45
383	387	0.744414	ATTGTTCGCACGATCCCTGG	60.744	55.000	0.00	0.00	0.00	4.45
384	388	1.822114	TTGTTCGCACGATCCCTGGA	61.822	55.000	0.00	0.00	0.00	3.86
385	389	1.519455	GTTCGCACGATCCCTGGAG	60.519	63.158	0.00	0.00	0.00	3.86
386	390	1.680989	TTCGCACGATCCCTGGAGA	60.681	57.895	0.00	0.00	0.00	3.71
387	391	1.667154	TTCGCACGATCCCTGGAGAG	61.667	60.000	0.00	0.00	0.00	3.20
388	392	2.818132	GCACGATCCCTGGAGAGG	59.182	66.667	0.00	0.00	39.42	3.69
389	393	2.818132	CACGATCCCTGGAGAGGC	59.182	66.667	0.00	0.00	38.17	4.70
390	394	2.060383	CACGATCCCTGGAGAGGCA	61.060	63.158	0.00	0.00	38.17	4.75
422	426	3.305629	GCACGATCTCTTTCTACTGCAAG	59.694	47.826	0.00	0.00	42.29	4.01
469	474	6.880822	TTTCCTCGAATATTGTTCGTACTG	57.119	37.500	14.04	5.10	42.09	2.74
494	499	9.480861	TGTATACTCCCTCTATTCCAGAATATG	57.519	37.037	4.17	0.00	33.29	1.78
511	516	7.339212	CCAGAATATGAGGTGTATTGGTTTTCA	59.661	37.037	0.00	0.00	0.00	2.69
634	639	6.215845	ACTTGGTCAAATATGCACTTGTTTC	58.784	36.000	0.00	0.00	0.00	2.78
823	828	3.055094	GTGCAGAAAAGTATCCCCTCTCA	60.055	47.826	0.00	0.00	0.00	3.27
867	876	1.292541	GACGACTTTTCTCCCCGCT	59.707	57.895	0.00	0.00	0.00	5.52
988	1002	0.032952	CGTGGACCTGGTTTCTTCGA	59.967	55.000	0.00	0.00	0.00	3.71
1071	1091	2.746279	TGGAAGAGTTGGGCTTGAAA	57.254	45.000	0.00	0.00	0.00	2.69
1094	1114	0.318275	GACGATCTCCAGGATGTCGC	60.318	60.000	18.73	10.86	34.33	5.19
1166	1186	2.435372	AGGGTTCACACTGAAAAGCA	57.565	45.000	0.00	0.00	38.22	3.91
1236	1256	3.321682	TGGCAAAGGAAGTGAAAATCAGG	59.678	43.478	0.00	0.00	0.00	3.86
1291	1311	2.203209	GCCTCGGCGATTGGGAAT	60.203	61.111	16.81	0.00	0.00	3.01
1309	1329	1.056700	ATGCGTTATGGAGGAGGGCT	61.057	55.000	0.00	0.00	0.00	5.19
1486	1506	5.363562	TGGTGAATTCATCTATGCTGAGT	57.636	39.130	19.21	0.00	0.00	3.41
1562	1583	6.767524	TGTCACAAAACCACTAAAGAATGT	57.232	33.333	0.00	0.00	0.00	2.71
1801	1843	3.311110	GGTGGCAGAGGTCGTGGA	61.311	66.667	0.00	0.00	0.00	4.02
1814	1856	4.867599	GTGGACGATCCGGCGGTC	62.868	72.222	27.32	20.40	40.17	4.79
1840	1882	0.385974	GACGTGGTGCTGCAAATGAC	60.386	55.000	2.77	0.00	0.00	3.06
1843	1885	1.336148	CGTGGTGCTGCAAATGACAAT	60.336	47.619	2.77	0.00	0.00	2.71
1934	1976	1.213296	GAAGAGGGGGATGTTAGGCA	58.787	55.000	0.00	0.00	0.00	4.75
1943	1985	1.834263	GGATGTTAGGCACTCCTCAGT	59.166	52.381	0.00	0.00	43.06	3.41
1960	2004	0.325296	AGTGGAGTAAGCCCATCGGA	60.325	55.000	0.00	0.00	35.91	4.55
2077	2121	3.584848	AGCCAAGTTCAAGTGATCCTACT	59.415	43.478	0.00	0.00	0.00	2.57
2087	2131	7.062749	TCAAGTGATCCTACTAACACAAAGT	57.937	36.000	0.00	0.00	35.97	2.66
2179	2225	0.764890	TTGCCTAGTGTGGAACTGCT	59.235	50.000	0.00	0.00	40.26	4.24
2454	2502	5.948992	AGAATTAGTTCCAGTGCAAACTC	57.051	39.130	4.81	0.00	37.02	3.01
2494	2542	3.550842	GGAGAAGCACAAACGCAAGAAAT	60.551	43.478	0.00	0.00	43.62	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	103	4.439305	TTGATCTTTTGTGCATGCCTAC	57.561	40.909	16.68	8.33	0.00	3.18
267	271	6.147000	GGCTCTAGTCTCATAAAAATAGCTGC	59.853	42.308	0.00	0.00	0.00	5.25
364	368	0.744414	CCAGGGATCGTGCGAACAAT	60.744	55.000	0.00	0.00	0.00	2.71
365	369	1.375396	CCAGGGATCGTGCGAACAA	60.375	57.895	0.00	0.00	0.00	2.83
366	370	2.225791	CTCCAGGGATCGTGCGAACA	62.226	60.000	0.00	0.00	0.00	3.18
367	371	1.519455	CTCCAGGGATCGTGCGAAC	60.519	63.158	0.00	0.00	0.00	3.95
368	372	1.667154	CTCTCCAGGGATCGTGCGAA	61.667	60.000	0.00	0.00	0.00	4.70
369	373	2.044352	TCTCCAGGGATCGTGCGA	60.044	61.111	0.00	0.00	0.00	5.10
370	374	2.415010	CTCTCCAGGGATCGTGCG	59.585	66.667	0.00	0.00	0.00	5.34
371	375	2.818132	CCTCTCCAGGGATCGTGC	59.182	66.667	0.00	0.00	35.89	5.34
372	376	2.060383	TGCCTCTCCAGGGATCGTG	61.060	63.158	0.00	0.00	40.75	4.35
373	377	2.364560	TGCCTCTCCAGGGATCGT	59.635	61.111	0.00	0.00	40.75	3.73
377	381	1.075601	AAAACATGCCTCTCCAGGGA	58.924	50.000	0.00	0.00	45.85	4.20
378	382	2.806945	TAAAACATGCCTCTCCAGGG	57.193	50.000	0.00	0.00	40.75	4.45
379	383	2.874701	CGATAAAACATGCCTCTCCAGG	59.125	50.000	0.00	0.00	43.82	4.45
380	384	2.289002	GCGATAAAACATGCCTCTCCAG	59.711	50.000	0.00	0.00	0.00	3.86
381	385	2.288666	GCGATAAAACATGCCTCTCCA	58.711	47.619	0.00	0.00	0.00	3.86
382	386	2.032178	GTGCGATAAAACATGCCTCTCC	59.968	50.000	0.00	0.00	0.00	3.71
383	387	2.285834	CGTGCGATAAAACATGCCTCTC	60.286	50.000	0.00	0.00	0.00	3.20
384	388	1.665679	CGTGCGATAAAACATGCCTCT	59.334	47.619	0.00	0.00	0.00	3.69
385	389	1.663643	TCGTGCGATAAAACATGCCTC	59.336	47.619	0.00	0.00	0.00	4.70
386	390	1.732941	TCGTGCGATAAAACATGCCT	58.267	45.000	0.00	0.00	0.00	4.75
387	391	2.287915	AGATCGTGCGATAAAACATGCC	59.712	45.455	7.09	0.00	34.60	4.40
388	392	3.246226	AGAGATCGTGCGATAAAACATGC	59.754	43.478	7.09	0.00	34.60	4.06
389	393	5.395325	AAGAGATCGTGCGATAAAACATG	57.605	39.130	7.09	0.00	34.60	3.21
390	394	5.812642	AGAAAGAGATCGTGCGATAAAACAT	59.187	36.000	7.09	0.00	34.60	2.71
469	474	9.702253	TCATATTCTGGAATAGAGGGAGTATAC	57.298	37.037	8.66	0.00	36.79	1.47
494	499	4.782019	TGCATGAAAACCAATACACCTC	57.218	40.909	0.00	0.00	0.00	3.85
634	639	6.907741	AGGTGTGTTTGTTTTTCCAAAAATG	58.092	32.000	0.71	0.00	39.75	2.32
799	804	1.065418	AGGGGATACTTTTCTGCACCG	60.065	52.381	0.00	0.00	0.00	4.94
800	805	2.239907	AGAGGGGATACTTTTCTGCACC	59.760	50.000	0.00	0.00	0.00	5.01
867	876	3.687551	CGGGGTAGATCAAGGTCTCTACA	60.688	52.174	10.79	0.00	43.64	2.74
960	974	2.035312	AGGTCCACGAGCGGTAGT	59.965	61.111	0.00	0.00	35.00	2.73
988	1002	4.685575	GCCATCTTCCATAGTTCTCTTGCT	60.686	45.833	0.00	0.00	0.00	3.91
1032	1046	0.829990	TCATTGCTGCCAGATCCGTA	59.170	50.000	0.00	0.00	0.00	4.02
1071	1091	2.955660	GACATCCTGGAGATCGTCTTCT	59.044	50.000	1.52	0.00	33.65	2.85
1094	1114	0.246635	AAGTTCATCGTCCTCCACCG	59.753	55.000	0.00	0.00	0.00	4.94
1236	1256	0.394565	ACAGATTATCCTCCAGCGGC	59.605	55.000	0.00	0.00	0.00	6.53
1291	1311	1.686325	GAGCCCTCCTCCATAACGCA	61.686	60.000	0.00	0.00	34.35	5.24
1309	1329	3.284793	TTTCCCTTTGAAAGTCCACGA	57.715	42.857	4.02	0.00	38.04	4.35
1509	1530	1.308998	CCCTCACACGAGCAAAGTTT	58.691	50.000	0.00	0.00	38.00	2.66
1706	1730	4.921644	TCAGGTCCTTAAAAACTAGGGG	57.078	45.455	0.00	0.00	32.20	4.79
1763	1787	2.820787	CTCTGTTACCTCGTCCTTCACT	59.179	50.000	0.00	0.00	0.00	3.41
1822	1864	1.100463	TGTCATTTGCAGCACCACGT	61.100	50.000	0.00	0.00	0.00	4.49
1840	1882	5.434408	TCCATGAACTCCTCTGAATGATTG	58.566	41.667	0.00	0.00	0.00	2.67
1843	1885	4.099633	ACTCCATGAACTCCTCTGAATGA	58.900	43.478	0.00	0.00	0.00	2.57
1943	1985	1.335132	GGTCCGATGGGCTTACTCCA	61.335	60.000	0.00	0.00	38.82	3.86
2077	2121	1.946768	GGAGCTGTGCACTTTGTGTTA	59.053	47.619	19.41	0.00	35.75	2.41
2087	2131	1.824230	AGTTTTGTTTGGAGCTGTGCA	59.176	42.857	0.00	0.00	0.00	4.57
2166	2212	2.281070	CCGCAGCAGTTCCACACT	60.281	61.111	0.00	0.00	35.35	3.55
2241	2287	8.815565	TGGGTTTCTAAGATGCATACAATAAA	57.184	30.769	0.00	0.00	0.00	1.40
2454	2502	3.116300	CTCCATAGACAAACGTGATCCG	58.884	50.000	0.00	2.55	44.03	4.18
2494	2542	7.768582	CACGCATCATATCCCAGGTTTTATATA	59.231	37.037	0.00	0.00	0.00	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.