AutoCloner

Multiple sequence alignment - TraesCS3B01G152500

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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	TraesCS3B01G152500	chr3B	100.000	2372	0	0	1	2372	144799165	144801536	0.000000e+00	4381.0
1	TraesCS3B01G152500	chr3B	99.879	825	1	0	1	825	677294214	677293390	0.000000e+00	1519.0
2	TraesCS3B01G152500	chr3B	97.979	841	1	1	1	825	677295848	677295008	0.000000e+00	1445.0
3	TraesCS3B01G152500	chr3B	94.225	710	36	3	824	1533	144781028	144781732	0.000000e+00	1079.0
4	TraesCS3B01G152500	chr3B	83.958	960	99	29	1430	2370	144777894	144778817	0.000000e+00	869.0
5	TraesCS3B01G152500	chr3B	91.985	549	40	2	824	1368	144777101	144777649	0.000000e+00	767.0
6	TraesCS3B01G152500	chr3B	86.982	507	16	21	351	825	414838722	414839210	2.090000e-145	525.0
7	TraesCS3B01G152500	chr3B	77.955	440	67	14	841	1262	143620825	143621252	5.060000e-62	248.0
8	TraesCS3B01G152500	chr3B	94.595	74	2	2	757	828	745175079	745175006	1.930000e-21	113.0
9	TraesCS3B01G152500	chr3B	95.522	67	1	2	760	824	131527922	131527988	3.220000e-19	106.0
10	TraesCS3B01G152500	chr3A	86.456	1580	164	23	827	2372	547402974	547404537	0.000000e+00	1687.0
11	TraesCS3B01G152500	chr3A	90.516	949	80	8	824	1770	547414316	547415256	0.000000e+00	1245.0
12	TraesCS3B01G152500	chr3A	87.064	688	38	11	122	759	142969565	142970251	0.000000e+00	730.0
13	TraesCS3B01G152500	chr3A	85.246	488	55	9	941	1420	547405997	547406475	9.860000e-134	486.0
14	TraesCS3B01G152500	chr3A	79.124	685	74	37	172	825	17710175	17709529	2.190000e-110	409.0
15	TraesCS3B01G152500	chr3A	89.720	107	11	0	2262	2368	547469537	547469643	1.140000e-28	137.0
16	TraesCS3B01G152500	chr6B	99.758	825	2	0	1	825	504299739	504300563	0.000000e+00	1513.0
17	TraesCS3B01G152500	chr6B	99.515	825	4	0	1	825	504300720	504301544	0.000000e+00	1502.0
18	TraesCS3B01G152500	chr6B	84.977	659	52	8	214	826	482068396	482067739	2.000000e-175	625.0
19	TraesCS3B01G152500	chr5B	99.636	825	3	0	1	825	597242619	597243443	0.000000e+00	1507.0
20	TraesCS3B01G152500	chrUn	97.428	661	1	1	181	825	435292011	435292671	0.000000e+00	1112.0
21	TraesCS3B01G152500	chr4D	90.930	430	16	9	419	827	490961797	490961370	7.410000e-155	556.0
22	TraesCS3B01G152500	chr3D	85.178	506	63	8	907	1409	94245342	94245838	2.100000e-140	508.0
23	TraesCS3B01G152500	chr3D	80.889	450	74	6	856	1298	94026160	94026604	6.280000e-91	344.0
24	TraesCS3B01G152500	chr4B	77.218	417	72	12	861	1262	50194468	50194060	3.070000e-54	222.0
25	TraesCS3B01G152500	chr2A	96.970	132	4	0	1	132	139838576	139838445	3.070000e-54	222.0
26	TraesCS3B01G152500	chr7B	95.455	132	6	0	1	132	122673007	122672876	6.640000e-51	211.0
27	TraesCS3B01G152500	chr7A	95.455	132	6	0	1	132	52252389	52252520	6.640000e-51	211.0
28	TraesCS3B01G152500	chr5A	95.455	132	6	0	1	132	495052570	495052701	6.640000e-51	211.0
29	TraesCS3B01G152500	chr5A	89.706	68	6	1	196	262	169190624	169190557	4.200000e-13	86.1

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	TraesCS3B01G152500	chr3B	144799165	144801536	2371	False	4381.0	4381	100.0000	1	2372	1	chr3B.!!$F3	2371
1	TraesCS3B01G152500	chr3B	677293390	677295848	2458	True	1482.0	1519	98.9290	1	825	2	chr3B.!!$R2	824
2	TraesCS3B01G152500	chr3B	144777101	144781732	4631	False	905.0	1079	90.0560	824	2370	3	chr3B.!!$F5	1546
3	TraesCS3B01G152500	chr3A	547414316	547415256	940	False	1245.0	1245	90.5160	824	1770	1	chr3A.!!$F2	946
4	TraesCS3B01G152500	chr3A	547402974	547406475	3501	False	1086.5	1687	85.8510	827	2372	2	chr3A.!!$F4	1545
5	TraesCS3B01G152500	chr3A	142969565	142970251	686	False	730.0	730	87.0640	122	759	1	chr3A.!!$F1	637
6	TraesCS3B01G152500	chr3A	17709529	17710175	646	True	409.0	409	79.1240	172	825	1	chr3A.!!$R1	653
7	TraesCS3B01G152500	chr6B	504299739	504301544	1805	False	1507.5	1513	99.6365	1	825	2	chr6B.!!$F1	824
8	TraesCS3B01G152500	chr6B	482067739	482068396	657	True	625.0	625	84.9770	214	826	1	chr6B.!!$R1	612
9	TraesCS3B01G152500	chr5B	597242619	597243443	824	False	1507.0	1507	99.6360	1	825	1	chr5B.!!$F1	824
10	TraesCS3B01G152500	chrUn	435292011	435292671	660	False	1112.0	1112	97.4280	181	825	1	chrUn.!!$F1	644

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
957	3695	0.250513	GATCAGCCGTCTGGGAACTT	59.749	55.0	0.0	0.0	40.69	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1773	4731	0.31812	GGTTGGATGTTGTGGCCTTG	59.682	55.0	3.32	0.0	0.0	3.61	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
857	3594	2.983592	GCCCTCCCAACACAACCG	60.984	66.667	0.00	0.00	0.00	4.44
957	3695	0.250513	GATCAGCCGTCTGGGAACTT	59.749	55.000	0.00	0.00	40.69	2.66
965	3703	1.019805	GTCTGGGAACTTGCCGTAGC	61.020	60.000	0.00	0.00	40.48	3.58
1036	3774	1.226547	GAGCTCGAGAAGTCCAGCG	60.227	63.158	18.75	0.00	36.95	5.18
1126	3867	1.452108	GATCAAGAGGGGGCAACGG	60.452	63.158	0.00	0.00	37.60	4.44
1143	3884	2.741092	GCCGTGTGGAAGGAGACA	59.259	61.111	0.00	0.00	37.49	3.41
1149	3890	0.758734	TGTGGAAGGAGACAGTGTGG	59.241	55.000	0.00	0.00	0.00	4.17
1167	3908	1.456331	GGGGCACATCTTCCATGGG	60.456	63.158	13.02	0.00	0.00	4.00
1281	4022	2.240414	TCGATATCGTAGCCCCCTCATA	59.760	50.000	23.61	0.00	40.80	2.15
1285	4026	5.395324	CGATATCGTAGCCCCCTCATATTTT	60.395	44.000	17.06	0.00	34.11	1.82
1368	4109	2.106511	CAGGGAGGAGACTTTTGTTGGA	59.893	50.000	0.00	0.00	44.43	3.53
1386	4127	3.785486	TGGATGATGAGACAATGTCGAC	58.215	45.455	9.11	9.11	37.67	4.20
1387	4128	3.195396	TGGATGATGAGACAATGTCGACA	59.805	43.478	22.48	22.48	37.67	4.35
1394	4135	3.494251	TGAGACAATGTCGACAACACATG	59.506	43.478	24.13	17.48	41.75	3.21
1395	4136	2.224079	AGACAATGTCGACAACACATGC	59.776	45.455	24.13	8.48	41.75	4.06
1398	4139	2.686558	ATGTCGACAACACATGCAAC	57.313	45.000	24.13	0.00	41.75	4.17
1408	4149	5.344066	ACAACACATGCAACGATTTTTGTA	58.656	33.333	0.00	0.00	0.00	2.41
1409	4150	5.231147	ACAACACATGCAACGATTTTTGTAC	59.769	36.000	0.00	0.00	0.00	2.90
1455	4379	9.945904	TGTACTTATTGTGGATGTACATACAAA	57.054	29.630	22.47	14.97	38.62	2.83
1555	4507	1.975660	TCCATTTGTTATAGCCGGGC	58.024	50.000	12.11	12.11	0.00	6.13
1563	4515	2.653953	TTATAGCCGGGCAAGCGTCC	62.654	60.000	23.09	0.00	34.64	4.79
1567	4519	2.983592	CCGGGCAAGCGTCCTTTT	60.984	61.111	0.00	0.00	33.27	2.27
1568	4520	2.561037	CCGGGCAAGCGTCCTTTTT	61.561	57.895	0.00	0.00	33.27	1.94
1569	4521	1.081442	CGGGCAAGCGTCCTTTTTC	60.081	57.895	0.00	0.00	33.27	2.29
1570	4522	1.515521	CGGGCAAGCGTCCTTTTTCT	61.516	55.000	0.00	0.00	33.27	2.52
1571	4523	1.530323	GGGCAAGCGTCCTTTTTCTA	58.470	50.000	0.00	0.00	32.39	2.10
1572	4524	2.092323	GGGCAAGCGTCCTTTTTCTAT	58.908	47.619	0.00	0.00	32.39	1.98
1648	4603	3.498397	ACAGTTCAGTTCAAACTATGGCG	59.502	43.478	0.00	0.00	37.08	5.69
1715	4671	5.771666	TCTCTCAAAACTGGCTTTCATCATT	59.228	36.000	0.00	0.00	0.00	2.57
1722	4678	5.904362	ACTGGCTTTCATCATTACTTTCC	57.096	39.130	0.00	0.00	0.00	3.13
1727	4683	8.415950	TGGCTTTCATCATTACTTTCCTTTTA	57.584	30.769	0.00	0.00	0.00	1.52
1729	4685	8.739972	GGCTTTCATCATTACTTTCCTTTTAGA	58.260	33.333	0.00	0.00	0.00	2.10
1803	4761	3.535280	ACATCCAACCCACAAAAACAC	57.465	42.857	0.00	0.00	0.00	3.32
1861	4841	3.560068	CACTTCTAACAGCGTTTCAACCT	59.440	43.478	0.00	0.00	0.00	3.50
1866	4846	2.254546	ACAGCGTTTCAACCTGATCA	57.745	45.000	12.43	0.00	33.91	2.92
1880	4860	8.722480	TCAACCTGATCAATACAAGTGAATAG	57.278	34.615	0.00	0.00	0.00	1.73
1889	4869	8.510243	TCAATACAAGTGAATAGCATCAATGT	57.490	30.769	9.91	9.91	36.33	2.71
1941	4922	2.283617	CGATCAAGGCAGAAGACATTCG	59.716	50.000	0.00	0.00	40.58	3.34
1944	4925	1.396301	CAAGGCAGAAGACATTCGAGC	59.604	52.381	0.00	0.00	40.58	5.03
1952	4933	2.434884	ACATTCGAGCAGCCACGG	60.435	61.111	9.24	0.00	0.00	4.94
1981	4962	1.027792	ACCGACGCACAACACCTTTT	61.028	50.000	0.00	0.00	0.00	2.27
1999	4980	5.221864	ACCTTTTAGGAACGAACCAGAGAAT	60.222	40.000	0.00	0.00	37.67	2.40
2030	5012	4.344102	AGCCATAATGCATTCAAGCTTCAT	59.656	37.500	16.86	0.00	34.99	2.57
2038	5020	4.278919	TGCATTCAAGCTTCATCACTTTCA	59.721	37.500	0.00	0.00	34.99	2.69
2042	5025	2.886523	CAAGCTTCATCACTTTCACCCA	59.113	45.455	0.00	0.00	0.00	4.51
2096	5080	2.706190	GCCCCACAAGGTATCAGTAGAT	59.294	50.000	0.00	0.00	38.29	1.98
2169	5153	6.002062	GGTCAGAAAATGAACAAGGTACAG	57.998	41.667	0.00	0.00	45.69	2.74
2195	5179	6.405065	GGAAATCAACTATCTCAGCAATTGCA	60.405	38.462	30.89	11.90	45.16	4.08
2209	5193	6.486657	TCAGCAATTGCACCCTAGATATAAAC	59.513	38.462	30.89	0.00	45.16	2.01
2213	5197	7.978975	GCAATTGCACCCTAGATATAAACAAAA	59.021	33.333	25.36	0.00	41.59	2.44
2220	5204	9.620660	CACCCTAGATATAAACAAAACACAAAC	57.379	33.333	0.00	0.00	0.00	2.93
2233	5217	5.923733	AAACACAAACCAAAGTACATGGA	57.076	34.783	20.82	0.00	40.56	3.41
2236	5220	2.882137	ACAAACCAAAGTACATGGACGG	59.118	45.455	20.82	0.19	40.56	4.79
2271	5255	6.546034	GGTAGATTTGCAGCCCTCTTATAAAA	59.454	38.462	0.00	0.00	0.00	1.52
2279	5263	6.095440	TGCAGCCCTCTTATAAAACAAATCTC	59.905	38.462	0.00	0.00	0.00	2.75
2280	5264	6.095440	GCAGCCCTCTTATAAAACAAATCTCA	59.905	38.462	0.00	0.00	0.00	3.27
2297	5281	1.762957	CTCAGGATAACCGGACACCAT	59.237	52.381	9.46	0.00	41.83	3.55
2304	5288	0.320946	AACCGGACACCATAACCACG	60.321	55.000	9.46	0.00	0.00	4.94
2307	5291	1.375013	GGACACCATAACCACGCGT	60.375	57.895	5.58	5.58	0.00	6.01
2330	5314	6.411203	CGTGACTATGATGTCAAGTACTAACG	59.589	42.308	0.00	0.00	46.77	3.18
2353	5337	3.629398	CAGGAAGGTCTCAATACAATGCC	59.371	47.826	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
834	3568	1.826487	GTGTTGGGAGGGCGTTTGT	60.826	57.895	0.00	0.00	0.00	2.83
857	3594	0.957888	GCTGGCTCCTGTGGTTCTTC	60.958	60.000	0.00	0.00	0.00	2.87
965	3703	2.172419	CGCTACCAAAACACGGCG	59.828	61.111	4.80	4.80	36.89	6.46
1126	3867	1.374758	CTGTCTCCTTCCACACGGC	60.375	63.158	0.00	0.00	0.00	5.68
1149	3890	1.456331	CCCATGGAAGATGTGCCCC	60.456	63.158	15.22	0.00	0.00	5.80
1167	3908	2.887568	CACCTCTCCACGCATCGC	60.888	66.667	0.00	0.00	0.00	4.58
1192	3933	1.789576	ATGGGGCAACTTCCCTTCGT	61.790	55.000	0.00	0.00	45.80	3.85
1281	4022	4.222588	TCTTCCAATTCCATCGCCAAAAAT	59.777	37.500	0.00	0.00	0.00	1.82
1285	4026	2.091541	GTCTTCCAATTCCATCGCCAA	58.908	47.619	0.00	0.00	0.00	4.52
1368	4109	4.389992	GTGTTGTCGACATTGTCTCATCAT	59.610	41.667	20.80	0.00	41.10	2.45
1386	4127	4.775440	ACAAAAATCGTTGCATGTGTTG	57.225	36.364	0.00	0.00	31.29	3.33
1387	4128	5.587289	AGTACAAAAATCGTTGCATGTGTT	58.413	33.333	0.00	0.00	31.29	3.32
1416	4157	8.573885	CCACAATAAGTACATCCGATAGTCTAA	58.426	37.037	0.00	0.00	0.00	2.10
1417	4158	7.940688	TCCACAATAAGTACATCCGATAGTCTA	59.059	37.037	0.00	0.00	0.00	2.59
1423	4164	6.174720	ACATCCACAATAAGTACATCCGAT	57.825	37.500	0.00	0.00	0.00	4.18
1529	4454	4.201812	CGGCTATAACAAATGGATATGCGG	60.202	45.833	0.00	0.00	0.00	5.69
1533	4458	4.263727	TGCCCGGCTATAACAAATGGATAT	60.264	41.667	11.61	0.00	0.00	1.63
1585	4537	7.992754	AATTGCAGAGTTCTTTACAATCTCT	57.007	32.000	0.00	0.00	36.15	3.10
1634	4589	0.793861	TCACGCGCCATAGTTTGAAC	59.206	50.000	5.73	0.00	0.00	3.18
1702	4658	6.916360	AAAGGAAAGTAATGATGAAAGCCA	57.084	33.333	0.00	0.00	0.00	4.75
1722	4678	8.378172	GGAAACCCCTTTGATTTTTCTAAAAG	57.622	34.615	0.00	0.00	0.00	2.27
1772	4730	1.327303	GTTGGATGTTGTGGCCTTGA	58.673	50.000	3.32	0.00	0.00	3.02
1773	4731	0.318120	GGTTGGATGTTGTGGCCTTG	59.682	55.000	3.32	0.00	0.00	3.61
1782	4740	3.517500	AGTGTTTTTGTGGGTTGGATGTT	59.482	39.130	0.00	0.00	0.00	2.71
1803	4761	2.420642	TCTGCTGCAGAGCTGTTTAAG	58.579	47.619	27.35	0.00	46.39	1.85
1848	4828	3.837213	ATTGATCAGGTTGAAACGCTG	57.163	42.857	0.00	5.71	0.00	5.18
1861	4841	8.735692	TTGATGCTATTCACTTGTATTGATCA	57.264	30.769	0.00	0.00	0.00	2.92
1866	4846	8.510243	TGACATTGATGCTATTCACTTGTATT	57.490	30.769	0.00	0.00	0.00	1.89
1880	4860	5.180868	CCTTAGGATAGCTTGACATTGATGC	59.819	44.000	0.00	0.00	0.00	3.91
1889	4869	3.235200	GGAGCTCCTTAGGATAGCTTGA	58.765	50.000	26.25	0.00	34.13	3.02
1941	4922	3.123620	CAAGCTCCGTGGCTGCTC	61.124	66.667	0.00	0.00	42.24	4.26
1944	4925	0.737715	GTACTCAAGCTCCGTGGCTG	60.738	60.000	0.20	0.00	42.24	4.85
1952	4933	1.071567	GTGCGTCGGTACTCAAGCTC	61.072	60.000	0.00	0.00	0.00	4.09
1981	4962	5.507637	AGTAGATTCTCTGGTTCGTTCCTA	58.492	41.667	0.00	0.00	0.00	2.94
1999	4980	7.255242	GCTTGAATGCATTATGGCTTTAGTAGA	60.255	37.037	12.97	0.00	32.09	2.59
2012	4993	6.519679	AAGTGATGAAGCTTGAATGCATTA	57.480	33.333	12.97	0.00	34.99	1.90
2030	5012	2.441375	TGTCTTCCATGGGTGAAAGTGA	59.559	45.455	13.02	0.00	0.00	3.41
2038	5020	3.744940	ATGACATTGTCTTCCATGGGT	57.255	42.857	13.02	0.00	33.15	4.51
2042	5025	3.758023	TGCGAAATGACATTGTCTTCCAT	59.242	39.130	17.26	0.96	33.15	3.41
2169	5153	6.501781	CAATTGCTGAGATAGTTGATTTCCC	58.498	40.000	0.00	0.00	0.00	3.97
2195	5179	8.799367	GGTTTGTGTTTTGTTTATATCTAGGGT	58.201	33.333	0.00	0.00	0.00	4.34
2209	5193	6.035542	GTCCATGTACTTTGGTTTGTGTTTTG	59.964	38.462	13.10	0.00	35.64	2.44
2213	5197	3.314080	CGTCCATGTACTTTGGTTTGTGT	59.686	43.478	13.10	0.00	35.64	3.72
2220	5204	0.322098	TGCCCGTCCATGTACTTTGG	60.322	55.000	8.62	8.62	35.45	3.28
2233	5217	3.926058	AATCTACCTTGTATTGCCCGT	57.074	42.857	0.00	0.00	0.00	5.28
2236	5220	4.734695	GCTGCAAATCTACCTTGTATTGCC	60.735	45.833	5.91	0.00	41.72	4.52
2271	5255	3.517901	TGTCCGGTTATCCTGAGATTTGT	59.482	43.478	0.00	0.00	33.67	2.83
2279	5263	3.463944	GTTATGGTGTCCGGTTATCCTG	58.536	50.000	0.00	0.00	0.00	3.86
2280	5264	2.436911	GGTTATGGTGTCCGGTTATCCT	59.563	50.000	0.00	0.00	0.00	3.24
2297	5281	2.164827	ACATCATAGTCACGCGTGGTTA	59.835	45.455	36.41	27.37	0.00	2.85
2307	5291	6.127842	TGCGTTAGTACTTGACATCATAGTCA	60.128	38.462	0.00	0.00	46.12	3.41
2330	5314	3.065925	GCATTGTATTGAGACCTTCCTGC	59.934	47.826	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.