AutoCloner

Multiple sequence alignment - TraesCS5A01G212000

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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	TraesCS5A01G212000	chr5A	100.000	3590	0	0	1	3590	427204926	427208515	0.000000e+00	6630.0
1	TraesCS5A01G212000	chr5A	93.702	2080	89	22	857	2912	427321015	427323076	0.000000e+00	3077.0
2	TraesCS5A01G212000	chr5A	91.892	814	45	8	6	815	427320125	427320921	0.000000e+00	1118.0
3	TraesCS5A01G212000	chr5D	93.468	3613	125	33	9	3589	329434248	329430715	0.000000e+00	5262.0
4	TraesCS5A01G212000	chr5D	95.872	1066	40	2	1543	2604	329276202	329275137	0.000000e+00	1722.0
5	TraesCS5A01G212000	chr5D	94.704	812	29	6	9	818	329277865	329277066	0.000000e+00	1249.0
6	TraesCS5A01G212000	chr5D	92.960	696	36	7	857	1544	329276974	329276284	0.000000e+00	1002.0
7	TraesCS5A01G212000	chr5D	95.489	399	14	1	9	407	329434729	329434335	5.060000e-178	634.0
8	TraesCS5A01G212000	chr5D	87.562	201	14	2	2657	2857	329275133	329274944	4.670000e-54	222.0
9	TraesCS5A01G212000	chr5D	97.826	46	1	0	811	856	329277039	329276994	2.970000e-11	80.5
10	TraesCS5A01G212000	chr5B	95.107	1737	71	5	1421	3146	382596364	382598097	0.000000e+00	2724.0
11	TraesCS5A01G212000	chr5B	94.390	1319	52	8	1543	2857	382381260	382379960	0.000000e+00	2006.0
12	TraesCS5A01G212000	chr5B	94.024	820	35	5	1	818	382384854	382384047	0.000000e+00	1230.0
13	TraesCS5A01G212000	chr5B	93.735	814	34	6	6	815	382594220	382595020	0.000000e+00	1205.0
14	TraesCS5A01G212000	chr5B	92.752	814	41	7	9	818	382383226	382382427	0.000000e+00	1160.0
15	TraesCS5A01G212000	chr5B	92.754	690	39	7	857	1539	382382335	382381650	0.000000e+00	987.0
16	TraesCS5A01G212000	chr5B	92.785	596	24	7	857	1436	382595115	382595707	0.000000e+00	845.0
17	TraesCS5A01G212000	chr5B	96.316	190	6	1	3231	3419	382598100	382598289	9.680000e-81	311.0
18	TraesCS5A01G212000	chr5B	97.826	46	1	0	811	856	382595050	382595095	2.970000e-11	80.5
19	TraesCS5A01G212000	chr5B	95.652	46	2	0	811	856	382382400	382382355	1.380000e-09	75.0
20	TraesCS5A01G212000	chr3B	87.263	369	37	5	903	1264	793140925	793141290	2.580000e-111	412.0
21	TraesCS5A01G212000	chr3B	83.212	137	19	3	1046	1180	85410667	85410801	4.870000e-24	122.0
22	TraesCS5A01G212000	chr2D	93.590	78	3	1	1089	1166	612497562	612497637	8.140000e-22	115.0
23	TraesCS5A01G212000	chrUn	86.408	103	13	1	1244	1345	96703870	96703972	1.050000e-20	111.0
24	TraesCS5A01G212000	chr3D	82.812	128	18	4	1055	1180	60520416	60520541	1.050000e-20	111.0
25	TraesCS5A01G212000	chr6A	93.243	74	3	2	651	723	583724402	583724330	1.360000e-19	108.0

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	TraesCS5A01G212000	chr5A	427204926	427208515	3589	False	6630.0	6630	100.0000	1	3590	1	chr5A.!!$F1	3589
1	TraesCS5A01G212000	chr5A	427320125	427323076	2951	False	2097.5	3077	92.7970	6	2912	2	chr5A.!!$F2	2906
2	TraesCS5A01G212000	chr5D	329430715	329434729	4014	True	2948.0	5262	94.4785	9	3589	2	chr5D.!!$R2	3580
3	TraesCS5A01G212000	chr5D	329274944	329277865	2921	True	855.1	1722	93.7848	9	2857	5	chr5D.!!$R1	2848
4	TraesCS5A01G212000	chr5B	382379960	382384854	4894	True	1091.6	2006	93.9144	1	2857	5	chr5B.!!$R1	2856
5	TraesCS5A01G212000	chr5B	382594220	382598289	4069	False	1033.1	2724	95.1538	6	3419	5	chr5B.!!$F1	3413

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
815	2905	0.463295	ATGCGGCTCCTGAATGAGTG	60.463	55.0	0.0	0.0	34.74	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2600	5840	0.597568	CTTCAAAGTTCATGCCGGCA	59.402	50.0	34.8	34.8	0.0	5.69	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
46	47	1.978580	GGTGGGAGTGGGACCATATAG	59.021	57.143	0.00	0.00	39.30	1.31
73	75	7.845037	TGTCACCAATTGCAATTAATCCATTA	58.155	30.769	23.69	4.99	0.00	1.90
262	264	6.467677	AGTGAATTGCTTAGGATGCGTATAT	58.532	36.000	0.00	0.00	0.00	0.86
334	336	3.355378	TGGGATAATTGAACAGGCTGTG	58.645	45.455	22.83	0.00	0.00	3.66
485	951	2.542020	TTTCGACTCAGGCATGTTCA	57.458	45.000	0.00	0.00	0.00	3.18
487	953	1.256812	TCGACTCAGGCATGTTCAGA	58.743	50.000	0.00	0.00	0.00	3.27
488	954	1.827344	TCGACTCAGGCATGTTCAGAT	59.173	47.619	0.00	0.00	0.00	2.90
489	955	1.931841	CGACTCAGGCATGTTCAGATG	59.068	52.381	0.00	0.00	0.00	2.90
490	956	2.676176	CGACTCAGGCATGTTCAGATGT	60.676	50.000	0.00	0.00	0.00	3.06
491	957	3.341823	GACTCAGGCATGTTCAGATGTT	58.658	45.455	0.00	0.00	0.00	2.71
492	958	3.341823	ACTCAGGCATGTTCAGATGTTC	58.658	45.455	0.00	0.00	0.00	3.18
493	959	3.008813	ACTCAGGCATGTTCAGATGTTCT	59.991	43.478	0.00	0.00	0.00	3.01
494	960	3.603532	TCAGGCATGTTCAGATGTTCTC	58.396	45.455	0.00	0.00	0.00	2.87
512	978	5.048504	TGTTCTCTTGCATTCTTCCATTGAC	60.049	40.000	0.00	0.00	0.00	3.18
630	1099	5.163509	TGCAGCCTTGTAATTTGTACAAACA	60.164	36.000	22.78	14.58	37.04	2.83
697	1167	9.820725	TTGTTCACTGAGAAAATGAAAATCAAT	57.179	25.926	0.00	0.00	38.13	2.57
750	1220	9.830186	ATAGCTTTCTTTGGGTATATCTCTAGA	57.170	33.333	0.00	0.00	0.00	2.43
783	1253	4.024472	GCACAACTGTTTGTTTTGTTGGTT	60.024	37.500	0.00	0.00	43.89	3.67
815	2905	0.463295	ATGCGGCTCCTGAATGAGTG	60.463	55.000	0.00	0.00	34.74	3.51
1179	3345	1.210155	GGATGTGCGCTGTGAAACC	59.790	57.895	9.73	0.00	34.36	3.27
1219	3385	6.869913	TCACTTTATCTTAACACCCAGTTACG	59.130	38.462	0.00	0.00	42.19	3.18
1248	3414	8.225603	TGGATGCTTAGATGTCTTTTATTTCC	57.774	34.615	0.00	0.00	0.00	3.13
1276	3443	1.686355	TGTGCCATCGTTTTTGTCCT	58.314	45.000	0.00	0.00	0.00	3.85
1379	3552	7.611770	AGAAAACTTGCTTTTCCTGTTAACTT	58.388	30.769	7.22	0.00	46.36	2.66
1380	3553	7.759886	AGAAAACTTGCTTTTCCTGTTAACTTC	59.240	33.333	7.22	0.00	46.36	3.01
1381	3554	6.775594	AACTTGCTTTTCCTGTTAACTTCT	57.224	33.333	7.22	0.00	0.00	2.85
1387	3560	9.787435	TTGCTTTTCCTGTTAACTTCTTCTATA	57.213	29.630	7.22	0.00	0.00	1.31
1664	4900	3.313249	TGTTGCTGACATGTGAAGTTCTG	59.687	43.478	1.15	0.00	32.00	3.02
1825	5061	9.923143	TTGGTATACGTGAAGATTTCTATATGG	57.077	33.333	0.00	0.00	0.00	2.74
1926	5165	0.532115	CCACTAATTTGGGGCACTGC	59.468	55.000	0.00	0.00	32.35	4.40
2028	5267	2.354259	GCTGTGGAGGATGAACTTGAG	58.646	52.381	0.00	0.00	0.00	3.02
2040	5279	4.207891	TGAACTTGAGAAGGCTATGTCC	57.792	45.455	0.00	0.00	0.00	4.02
2156	5395	1.656652	CTAAAGCCCTGACGTGATGG	58.343	55.000	0.00	0.00	0.00	3.51
2174	5413	3.202829	TGGAAGTTGGACACTTGTACC	57.797	47.619	0.00	0.00	46.53	3.34
2182	5421	6.838382	AGTTGGACACTTGTACCTAAATCTT	58.162	36.000	0.00	0.00	27.32	2.40
2397	5636	0.687354	TCCTGGGCTTCTCAGTCAAC	59.313	55.000	0.00	0.00	0.00	3.18
2478	5717	1.409064	ACTATGAAAGAGATCGGCGCA	59.591	47.619	10.83	0.00	0.00	6.09
2816	6057	7.326789	GTGTGTTATGAAATGTTGGTGATGAAG	59.673	37.037	0.00	0.00	0.00	3.02
2857	6098	7.049133	TGCCTCGTTTATTTTGCCTTATAGTA	58.951	34.615	0.00	0.00	0.00	1.82
2858	6099	7.717875	TGCCTCGTTTATTTTGCCTTATAGTAT	59.282	33.333	0.00	0.00	0.00	2.12
2871	6138	9.772973	TTGCCTTATAGTATTGTGGTTACATAG	57.227	33.333	0.00	0.00	36.53	2.23
2914	6181	6.054941	TCTGAGATGTCTTTACTGTTTTGCA	58.945	36.000	0.00	0.00	0.00	4.08
3006	6284	3.058016	ACAATTGACGCCAGAACAATCAG	60.058	43.478	13.59	0.00	33.90	2.90
3026	6304	2.243221	AGAAGCTGATTGTTAGGGCCAT	59.757	45.455	6.18	0.00	0.00	4.40
3050	6328	3.214328	CCACACCATAGATACAAAGGCC	58.786	50.000	0.00	0.00	0.00	5.19
3135	6413	0.983467	TGCTGACCAACATAGCCTCA	59.017	50.000	0.00	0.00	36.64	3.86
3162	6440	4.294970	ACCTGTTAGGGGAAATTGGAGAAT	59.705	41.667	0.00	0.00	40.58	2.40
3165	6443	6.395780	TGTTAGGGGAAATTGGAGAATACA	57.604	37.500	0.00	0.00	0.00	2.29
3185	6463	4.385825	ACACGAGCATTTCTTTACTTCCA	58.614	39.130	0.00	0.00	0.00	3.53
3188	6466	4.932200	ACGAGCATTTCTTTACTTCCAGAG	59.068	41.667	0.00	0.00	0.00	3.35
3229	6507	2.966050	ACAGAGAGTCAAAATCTCGCC	58.034	47.619	0.00	0.00	46.38	5.54
3293	6571	7.420800	CAATCATGAAGCCTATTGAGTTTACC	58.579	38.462	0.00	0.00	32.29	2.85
3299	6577	2.748465	GCCTATTGAGTTTACCGGGCAT	60.748	50.000	6.32	0.00	38.35	4.40
3362	6641	2.673043	CGTACCTGGCGTAGACACATTT	60.673	50.000	0.00	0.00	34.89	2.32
3385	6664	0.744874	GAGCAGATGGTAGCCGTGTA	59.255	55.000	0.00	0.00	0.00	2.90
3420	6699	3.693807	CATAGGTGGCAAGGCATCATAT	58.306	45.455	9.64	4.16	0.00	1.78
3421	6700	4.847198	CATAGGTGGCAAGGCATCATATA	58.153	43.478	9.64	0.00	0.00	0.86
3489	6768	4.650972	AGCAAGGGGAAAATACTGTACA	57.349	40.909	0.00	0.00	0.00	2.90
3496	6775	6.708285	AGGGGAAAATACTGTACAAGTACTG	58.292	40.000	13.53	13.53	44.20	2.74
3518	6797	5.996644	TGGAAGTCCAGTTACAAAGAGAAA	58.003	37.500	0.00	0.00	42.01	2.52
3519	6798	6.419791	TGGAAGTCCAGTTACAAAGAGAAAA	58.580	36.000	0.00	0.00	42.01	2.29
3525	6804	9.190317	AGTCCAGTTACAAAGAGAAAAGAAAAT	57.810	29.630	0.00	0.00	0.00	1.82
3533	6812	8.181904	ACAAAGAGAAAAGAAAATAGATGCCA	57.818	30.769	0.00	0.00	0.00	4.92
3589	6868	2.094494	CCTACAGTGTGCAGATCGTCTT	60.094	50.000	5.88	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	4.545610	CACCACACACGAAAAATAGCAAT	58.454	39.130	0.00	0.00	0.00	3.56
73	75	6.322969	TCCTGCAAGCAATCATTATTGATTCT	59.677	34.615	9.39	7.72	46.06	2.40
262	264	2.490509	CAATGAGACCAATCAGCAAGCA	59.509	45.455	0.00	0.00	31.44	3.91
334	336	2.955881	AAGGGCGCACTACAGGTCC	61.956	63.158	15.36	0.00	0.00	4.46
485	951	4.914983	TGGAAGAATGCAAGAGAACATCT	58.085	39.130	0.00	0.00	41.27	2.90
487	953	5.713389	TCAATGGAAGAATGCAAGAGAACAT	59.287	36.000	0.00	0.00	0.00	2.71
488	954	5.048504	GTCAATGGAAGAATGCAAGAGAACA	60.049	40.000	0.00	0.00	0.00	3.18
489	955	5.182760	AGTCAATGGAAGAATGCAAGAGAAC	59.817	40.000	0.00	0.00	0.00	3.01
490	956	5.182570	CAGTCAATGGAAGAATGCAAGAGAA	59.817	40.000	0.00	0.00	0.00	2.87
491	957	4.698780	CAGTCAATGGAAGAATGCAAGAGA	59.301	41.667	0.00	0.00	0.00	3.10
492	958	4.458295	ACAGTCAATGGAAGAATGCAAGAG	59.542	41.667	0.00	0.00	34.68	2.85
493	959	4.401022	ACAGTCAATGGAAGAATGCAAGA	58.599	39.130	0.00	0.00	34.68	3.02
494	960	4.778534	ACAGTCAATGGAAGAATGCAAG	57.221	40.909	0.00	0.00	34.68	4.01
600	1068	5.500234	ACAAATTACAAGGCTGCAGAGATA	58.500	37.500	20.43	0.00	0.00	1.98
750	1220	4.644685	ACAAACAGTTGTGCCTCTAAACAT	59.355	37.500	0.00	0.00	46.40	2.71
783	1253	1.002773	AGCCGCATGATGCTCATATCA	59.997	47.619	16.17	0.00	42.25	2.15
801	2891	2.111384	TCCCTACACTCATTCAGGAGC	58.889	52.381	0.00	0.00	38.50	4.70
804	2894	5.129485	ACAAGTATCCCTACACTCATTCAGG	59.871	44.000	0.00	0.00	0.00	3.86
971	3130	2.166664	GCTTCCGATCACTTCTGGTAGT	59.833	50.000	0.00	0.00	0.00	2.73
977	3143	0.107945	GCAGGCTTCCGATCACTTCT	60.108	55.000	0.00	0.00	0.00	2.85
1379	3552	8.201464	TCAGTGCCGTTCATTTTATATAGAAGA	58.799	33.333	0.00	0.00	0.00	2.87
1380	3553	8.365399	TCAGTGCCGTTCATTTTATATAGAAG	57.635	34.615	0.00	0.00	0.00	2.85
1381	3554	8.725405	TTCAGTGCCGTTCATTTTATATAGAA	57.275	30.769	0.00	0.00	0.00	2.10
1387	3560	5.705609	ACTTTCAGTGCCGTTCATTTTAT	57.294	34.783	0.00	0.00	0.00	1.40
1494	4342	7.413988	CGTTTCTTAATATCATGTGGCAGTCAA	60.414	37.037	0.00	0.00	0.00	3.18
1572	4806	3.763360	TGGCAATGTGACCTTTTGGATAG	59.237	43.478	0.00	0.00	44.07	2.08
1926	5165	4.316645	CCCTGATCACTGCAGATATCAAG	58.683	47.826	23.35	19.46	35.39	3.02
2028	5267	2.350522	CCATATGCGGACATAGCCTTC	58.649	52.381	0.00	0.00	41.97	3.46
2088	5327	1.063649	CTGCTTGACATGCGCATCC	59.936	57.895	22.51	15.83	32.62	3.51
2156	5395	6.935208	AGATTTAGGTACAAGTGTCCAACTTC	59.065	38.462	0.00	0.00	46.60	3.01
2174	5413	8.944029	CAGTAATATGATGGAGGCAAGATTTAG	58.056	37.037	0.00	0.00	0.00	1.85
2182	5421	5.307716	TCATGTCAGTAATATGATGGAGGCA	59.692	40.000	0.00	0.00	31.24	4.75
2478	5717	2.427245	CGCCGAGGACTTGGAGGAT	61.427	63.158	9.83	0.00	36.15	3.24
2553	5792	1.072331	GACTGGCCTTGAAGAAGACCA	59.928	52.381	3.32	0.00	39.27	4.02
2600	5840	0.597568	CTTCAAAGTTCATGCCGGCA	59.402	50.000	34.80	34.80	0.00	5.69
2723	5964	1.406539	CATCAACCTAAGGCATGGCAC	59.593	52.381	22.64	0.00	0.00	5.01
2816	6057	4.142600	ACGAGGCAAAAGCATTAGATCAAC	60.143	41.667	0.00	0.00	0.00	3.18
2857	6098	6.154363	CCCCATGAAAACTATGTAACCACAAT	59.846	38.462	0.00	0.00	38.42	2.71
2858	6099	5.478679	CCCCATGAAAACTATGTAACCACAA	59.521	40.000	0.00	0.00	38.42	3.33
2871	6138	4.772100	TCAGAAGAAATCCCCCATGAAAAC	59.228	41.667	0.00	0.00	0.00	2.43
2975	6253	5.912892	TCTGGCGTCAATTGTAATCATAGA	58.087	37.500	5.13	0.27	0.00	1.98
3006	6284	2.128771	TGGCCCTAACAATCAGCTTC	57.871	50.000	0.00	0.00	0.00	3.86
3026	6304	4.625324	GCCTTTGTATCTATGGTGTGGTGA	60.625	45.833	0.00	0.00	0.00	4.02
3050	6328	4.223032	AGGTGTTAGTATTGTGAGAGGGTG	59.777	45.833	0.00	0.00	0.00	4.61
3135	6413	6.011096	TCTCCAATTTCCCCTAACAGGTTTAT	60.011	38.462	0.00	0.00	31.93	1.40
3162	6440	5.543714	TGGAAGTAAAGAAATGCTCGTGTA	58.456	37.500	0.00	0.00	0.00	2.90
3165	6443	4.894784	TCTGGAAGTAAAGAAATGCTCGT	58.105	39.130	0.00	0.00	33.76	4.18
3185	6463	2.475155	TGATCATCTGTTGGGAGCTCT	58.525	47.619	14.64	0.00	0.00	4.09
3188	6466	3.204306	TCATGATCATCTGTTGGGAGC	57.796	47.619	4.86	0.00	0.00	4.70
3293	6571	2.184836	CAATGGTTGGCATGCCCG	59.815	61.111	33.44	9.45	35.87	6.13
3362	6641	0.390492	CGGCTACCATCTGCTCATCA	59.610	55.000	0.00	0.00	0.00	3.07
3385	6664	3.117888	CCACCTATGCCTACAAGACCAAT	60.118	47.826	0.00	0.00	0.00	3.16
3433	6712	2.436824	GAGCTCCTGCCGTTTCCC	60.437	66.667	0.87	0.00	40.80	3.97
3477	6756	7.876582	GGACTTCCAGTACTTGTACAGTATTTT	59.123	37.037	12.64	0.00	36.81	1.82
3496	6775	6.766467	TCTTTTCTCTTTGTAACTGGACTTCC	59.234	38.462	0.00	0.00	0.00	3.46
3519	6798	9.595823	CATGAATTCTTTTGGCATCTATTTTCT	57.404	29.630	7.05	0.00	0.00	2.52
3525	6804	5.360714	GTCCCATGAATTCTTTTGGCATCTA	59.639	40.000	7.05	0.00	0.00	1.98
3533	6812	4.636206	GCGAGTAGTCCCATGAATTCTTTT	59.364	41.667	7.05	0.00	0.00	2.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.