AutoCloner

Multiple sequence alignment - TraesCS2A01G247100

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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	TraesCS2A01G247100	chr2A	100.000	3134	0	0	1	3134	364479914	364483047	0.000000e+00	5788.0
1	TraesCS2A01G247100	chr2A	86.503	163	15	6	2789	2947	144028186	144028345	4.160000e-39	172.0
2	TraesCS2A01G247100	chr2D	96.986	2256	34	12	1	2229	295806097	295808345	0.000000e+00	3759.0
3	TraesCS2A01G247100	chr2D	95.882	170	5	1	2965	3134	295808371	295808538	1.110000e-69	274.0
4	TraesCS2A01G247100	chr2D	78.231	147	31	1	2230	2376	397288267	397288122	3.330000e-15	93.5
5	TraesCS2A01G247100	chr2D	89.062	64	7	0	2428	2491	472444398	472444335	2.590000e-11	80.5
6	TraesCS2A01G247100	chr2D	82.353	68	10	2	2427	2493	532011286	532011220	1.210000e-04	58.4
7	TraesCS2A01G247100	chr2D	86.275	51	5	2	2427	2476	532011776	532011727	2.000000e-03	54.7
8	TraesCS2A01G247100	chr2B	98.320	1250	21	0	980	2229	352281693	352280444	0.000000e+00	2193.0
9	TraesCS2A01G247100	chr2B	95.710	1049	15	8	1	1026	352282727	352281686	0.000000e+00	1661.0
10	TraesCS2A01G247100	chr2B	95.862	145	4	1	2947	3091	352280452	352280310	1.880000e-57	233.0
11	TraesCS2A01G247100	chr2B	87.288	118	14	1	2615	2731	575882085	575881968	1.960000e-27	134.0
12	TraesCS2A01G247100	chr6D	95.708	466	17	2	1	465	437412705	437413168	0.000000e+00	747.0
13	TraesCS2A01G247100	chr6B	94.635	466	22	2	1	465	662168997	662169460	0.000000e+00	719.0
14	TraesCS2A01G247100	chr6B	92.177	294	21	1	145	438	662235932	662236223	6.250000e-112	414.0
15	TraesCS2A01G247100	chr6B	96.599	147	5	0	1	147	662223442	662223588	8.680000e-61	244.0
16	TraesCS2A01G247100	chr6B	100.000	29	0	0	452	480	662180829	662180857	2.000000e-03	54.7
17	TraesCS2A01G247100	chr6A	94.635	466	21	3	1	465	585797955	585798417	0.000000e+00	719.0
18	TraesCS2A01G247100	chr6A	80.682	264	43	6	2690	2946	172391507	172391769	6.860000e-47	198.0
19	TraesCS2A01G247100	chr7B	82.075	742	100	17	2231	2946	596743477	596742743	1.240000e-168	603.0
20	TraesCS2A01G247100	chr7D	81.622	740	96	20	2233	2951	585381710	585382430	7.540000e-161	577.0
21	TraesCS2A01G247100	chr5D	83.539	486	58	9	2468	2946	43004505	43004975	4.800000e-118	435.0
22	TraesCS2A01G247100	chr5B	82.582	488	62	11	2479	2946	602254034	602253550	2.910000e-110	409.0
23	TraesCS2A01G247100	chr5A	87.613	331	26	4	2623	2946	663381790	663382112	1.370000e-98	370.0
24	TraesCS2A01G247100	chr5A	87.324	213	26	1	2230	2442	663381460	663381671	3.120000e-60	243.0
25	TraesCS2A01G247100	chr5A	96.386	83	3	0	2536	2618	663381668	663381750	1.520000e-28	137.0
26	TraesCS2A01G247100	chr4D	81.907	409	50	7	2560	2946	337477969	337477563	1.080000e-84	324.0
27	TraesCS2A01G247100	chr4D	86.325	234	27	5	2230	2460	362783695	362783926	1.870000e-62	250.0
28	TraesCS2A01G247100	chr4D	82.490	257	36	7	2698	2946	504259833	504260088	1.890000e-52	217.0
29	TraesCS2A01G247100	chr4D	90.566	159	9	4	2463	2618	362783892	362784047	4.100000e-49	206.0
30	TraesCS2A01G247100	chr3B	78.367	490	53	25	2479	2946	749715771	749716229	5.150000e-68	268.0
31	TraesCS2A01G247100	chr3B	74.490	294	61	11	1379	1662	141735636	141735925	7.100000e-22	115.0
32	TraesCS2A01G247100	chr3B	100.000	28	0	0	2711	2738	492751630	492751603	6.000000e-03	52.8
33	TraesCS2A01G247100	chr1D	87.179	234	27	3	2230	2462	60324384	60324615	2.400000e-66	263.0
34	TraesCS2A01G247100	chr4B	83.019	265	36	9	2690	2946	36199159	36198896	6.760000e-57	231.0
35	TraesCS2A01G247100	chrUn	82.661	248	30	9	2713	2950	366418184	366417940	1.140000e-49	207.0
36	TraesCS2A01G247100	chr1A	81.648	267	34	11	2692	2947	561731224	561731486	1.140000e-49	207.0
37	TraesCS2A01G247100	chr7A	89.172	157	16	1	2792	2948	240937287	240937132	8.870000e-46	195.0
38	TraesCS2A01G247100	chr3D	88.816	152	17	0	2798	2949	574746335	574746486	1.480000e-43	187.0
39	TraesCS2A01G247100	chr3D	97.917	48	1	0	1487	1534	91696365	91696412	2.000000e-12	84.2
40	TraesCS2A01G247100	chr3A	80.625	160	27	4	1379	1536	545257734	545257891	1.530000e-23	121.0
41	TraesCS2A01G247100	chr3A	80.667	150	23	5	2228	2375	481637513	481637368	9.190000e-21	111.0
42	TraesCS2A01G247100	chr3A	86.765	68	8	1	2425	2491	642135226	642135293	1.210000e-09	75.0

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	TraesCS2A01G247100	chr2A	364479914	364483047	3133	False	5788.000000	5788	100.000000	1	3134	1	chr2A.!!$F2	3133
1	TraesCS2A01G247100	chr2D	295806097	295808538	2441	False	2016.500000	3759	96.434000	1	3134	2	chr2D.!!$F1	3133
2	TraesCS2A01G247100	chr2B	352280310	352282727	2417	True	1362.333333	2193	96.630667	1	3091	3	chr2B.!!$R2	3090
3	TraesCS2A01G247100	chr7B	596742743	596743477	734	True	603.000000	603	82.075000	2231	2946	1	chr7B.!!$R1	715
4	TraesCS2A01G247100	chr7D	585381710	585382430	720	False	577.000000	577	81.622000	2233	2951	1	chr7D.!!$F1	718
5	TraesCS2A01G247100	chr5A	663381460	663382112	652	False	250.000000	370	90.441000	2230	2946	3	chr5A.!!$F1	716

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
578	579	0.322648	ACAACTTACAGTACCCGGCC	59.677	55.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2476	2547	0.747255	CATCAGTGTAGCGCCTAGGT	59.253	55.0	11.31	0.0	0.0	3.08	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
421	422	1.073964	CACGTCTGCATCTGACCAAG	58.926	55.000	0.00	0.00	0.00	3.61
499	500	2.226200	CACTGAATGCGTCCATGAAACA	59.774	45.455	0.00	0.00	0.00	2.83
543	544	2.289444	CCGAGGACACCAACACATACTT	60.289	50.000	0.00	0.00	0.00	2.24
575	576	5.291971	ACAAGTTACAACTTACAGTACCCG	58.708	41.667	7.02	0.00	46.89	5.28
576	577	4.525912	AGTTACAACTTACAGTACCCGG	57.474	45.455	0.00	0.00	35.21	5.73
577	578	2.995939	GTTACAACTTACAGTACCCGGC	59.004	50.000	0.00	0.00	0.00	6.13
578	579	0.322648	ACAACTTACAGTACCCGGCC	59.677	55.000	0.00	0.00	0.00	6.13
579	580	0.392060	CAACTTACAGTACCCGGCCC	60.392	60.000	0.00	0.00	0.00	5.80
660	661	8.311109	TGTACCAATAGTAGTATACATGCATGG	58.689	37.037	29.41	11.39	46.26	3.66
685	686	0.476338	TTTACTGGGCCTGCTTCACA	59.524	50.000	10.71	0.00	0.00	3.58
826	827	8.627208	AGATGCTTTGGATATTTCGAATATGT	57.373	30.769	0.00	0.00	0.00	2.29
861	884	7.956420	AACTGAAATGAAACGTGTACATCTA	57.044	32.000	0.00	0.00	0.00	1.98
1050	1115	1.657094	GACGACGACAAACACACAACT	59.343	47.619	0.00	0.00	0.00	3.16
1146	1216	1.069765	CTCACCACGGTTCACTGCT	59.930	57.895	0.00	0.00	0.00	4.24
1626	1696	5.392811	CGACTTTACTCGGGTGTTTATCTCT	60.393	44.000	0.00	0.00	0.00	3.10
1710	1780	1.591703	CTCTGAGCTGGGCAACGTA	59.408	57.895	0.00	0.00	37.60	3.57
2165	2235	0.107116	GCCTCCGACTCCTCAGTCTA	60.107	60.000	0.90	0.00	46.31	2.59
2220	2290	4.020396	TGGCATTGCAATACCAAAACTCAT	60.020	37.500	26.06	0.00	28.93	2.90
2221	2291	4.330620	GGCATTGCAATACCAAAACTCATG	59.669	41.667	21.73	3.84	0.00	3.07
2222	2292	5.170021	GCATTGCAATACCAAAACTCATGA	58.830	37.500	12.53	0.00	0.00	3.07
2223	2293	5.638657	GCATTGCAATACCAAAACTCATGAA	59.361	36.000	12.53	0.00	0.00	2.57
2224	2294	6.147492	GCATTGCAATACCAAAACTCATGAAA	59.853	34.615	12.53	0.00	0.00	2.69
2225	2295	7.148373	GCATTGCAATACCAAAACTCATGAAAT	60.148	33.333	12.53	0.00	0.00	2.17
2226	2296	8.723311	CATTGCAATACCAAAACTCATGAAATT	58.277	29.630	12.53	0.00	0.00	1.82
2227	2297	9.941325	ATTGCAATACCAAAACTCATGAAATTA	57.059	25.926	11.02	0.00	0.00	1.40
2228	2298	8.755696	TGCAATACCAAAACTCATGAAATTAC	57.244	30.769	0.00	0.00	0.00	1.89
2327	2397	1.077787	CCCTTTCATGTAGCGCCCA	60.078	57.895	2.29	0.55	0.00	5.36
2331	2401	1.539388	CTTTCATGTAGCGCCCAACAA	59.461	47.619	2.29	0.00	0.00	2.83
2332	2402	1.832883	TTCATGTAGCGCCCAACAAT	58.167	45.000	2.29	0.00	0.00	2.71
2371	2441	1.473257	GTGCAACACCTGACTGACAGA	60.473	52.381	10.08	0.00	42.60	3.41
2385	2455	4.267536	ACTGACAGACGCTATACACCTAA	58.732	43.478	10.08	0.00	0.00	2.69
2394	2464	2.545322	GCTATACACCTAACCAGCGTCC	60.545	54.545	0.00	0.00	0.00	4.79
2397	2467	0.470766	ACACCTAACCAGCGTCCAAA	59.529	50.000	0.00	0.00	0.00	3.28
2399	2469	0.250597	ACCTAACCAGCGTCCAAACC	60.251	55.000	0.00	0.00	0.00	3.27
2438	2509	2.704725	AAGTTAATGTGCAACGCCTG	57.295	45.000	0.00	0.00	42.39	4.85
2441	2512	1.135689	GTTAATGTGCAACGCCTGAGG	60.136	52.381	0.00	0.00	42.39	3.86
2465	2536	4.844522	GCTAGACGCTACACTATACAGTGC	60.845	50.000	0.00	0.00	44.96	4.40
2625	2731	2.010286	CATGCACGCACGTGGTTTG	61.010	57.895	23.12	7.26	45.49	2.93
2694	2800	4.775780	TGTCCCTTGTATAGCTGTTAGTGT	59.224	41.667	0.00	0.00	0.00	3.55
2706	2812	2.683867	CTGTTAGTGTAGCGCCTAGACT	59.316	50.000	16.60	16.60	42.08	3.24
2709	2815	1.670791	AGTGTAGCGCCTAGACTCTC	58.329	55.000	2.29	0.00	36.06	3.20
2711	2817	0.177373	TGTAGCGCCTAGACTCTCGA	59.823	55.000	2.29	0.00	0.00	4.04
2728	2834	6.918626	ACTCTCGACGCTACACTATATAGTA	58.081	40.000	15.03	0.25	34.13	1.82
2739	2845	9.001542	GCTACACTATATAGTATAGCGCCTAAT	57.998	37.037	28.46	0.00	45.72	1.73
2771	2877	7.218145	CATTGCATGCTGACTTAGAAATTTC	57.782	36.000	20.33	10.33	0.00	2.17
2860	2973	4.735132	GCTGTCGGGCGCTACACA	62.735	66.667	7.64	6.51	0.00	3.72
2992	3122	2.026262	AGCTCCCACACGGAACAAATAT	60.026	45.455	0.00	0.00	41.40	1.28
3054	3184	6.239120	ATGTACTCATGTTTGCTTTCAAAGCT	60.239	34.615	22.58	0.00	42.31	3.74
3055	3185	8.209973	ATGTACTCATGTTTGCTTTCAAAGCTG	61.210	37.037	22.58	12.21	42.31	4.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
421	422	0.458669	CCATGGAATCAGGCACTTGC	59.541	55.000	5.56	0.00	34.60	4.01
499	500	5.193679	GGTAAGGCTGTAACAGATCCAAAT	58.806	41.667	0.00	0.00	32.44	2.32
660	661	2.033602	AGGCCCAGTAAACGGTGC	59.966	61.111	0.00	0.00	0.00	5.01
685	686	7.497909	CCTCGTGTTTTGGAGGTATGTTAATAT	59.502	37.037	0.00	0.00	43.91	1.28
826	827	6.528423	CGTTTCATTTCAGTTTGTGTTTGGTA	59.472	34.615	0.00	0.00	0.00	3.25
895	921	9.391006	GTAATACAAGTATTCCCTCAATTCACA	57.609	33.333	8.62	0.00	37.07	3.58
1074	1144	1.445582	CCGGTTCAGTGGAGTACGC	60.446	63.158	0.00	0.00	0.00	4.42
1146	1216	3.574396	CAGAGTCCTCGGAAGCCATTATA	59.426	47.826	0.00	0.00	34.09	0.98
2157	2227	3.864583	GCAGCAGAAAGACATAGACTGAG	59.135	47.826	0.00	0.00	0.00	3.35
2158	2228	3.513119	AGCAGCAGAAAGACATAGACTGA	59.487	43.478	0.00	0.00	0.00	3.41
2165	2235	3.754965	TGGTAAAGCAGCAGAAAGACAT	58.245	40.909	0.00	0.00	0.00	3.06
2224	2294	8.878769	GGTCAAATTTATCATTTTTGCCGTAAT	58.121	29.630	0.00	0.00	31.88	1.89
2225	2295	8.091449	AGGTCAAATTTATCATTTTTGCCGTAA	58.909	29.630	0.00	0.00	34.55	3.18
2226	2296	7.543868	CAGGTCAAATTTATCATTTTTGCCGTA	59.456	33.333	0.00	0.00	34.55	4.02
2227	2297	6.368516	CAGGTCAAATTTATCATTTTTGCCGT	59.631	34.615	0.00	0.00	34.55	5.68
2228	2298	6.368516	ACAGGTCAAATTTATCATTTTTGCCG	59.631	34.615	0.00	0.00	34.55	5.69
2304	2374	1.676014	GCGCTACATGAAAGGGTCAGT	60.676	52.381	0.00	0.00	40.43	3.41
2327	2397	5.312895	TGTGTAGTGTGATGCCTTATTGTT	58.687	37.500	0.00	0.00	0.00	2.83
2331	2401	4.826274	ACTGTGTAGTGTGATGCCTTAT	57.174	40.909	0.00	0.00	35.34	1.73
2358	2428	1.840737	ATAGCGTCTGTCAGTCAGGT	58.159	50.000	0.00	1.43	43.76	4.00
2371	2441	1.066605	CGCTGGTTAGGTGTATAGCGT	59.933	52.381	8.12	0.00	46.14	5.07
2385	2455	1.142262	AGTTTAGGTTTGGACGCTGGT	59.858	47.619	0.00	0.00	0.00	4.00
2394	2464	6.515832	AGAATTTTCAGGCAGTTTAGGTTTG	58.484	36.000	0.00	0.00	0.00	2.93
2397	2467	7.004691	ACTTAGAATTTTCAGGCAGTTTAGGT	58.995	34.615	0.00	0.00	0.00	3.08
2441	2512	3.814283	ACTGTATAGTGTAGCGTCTAGCC	59.186	47.826	0.00	0.00	40.69	3.93
2465	2536	2.419198	CCTAGGTGCTAGGCGCTG	59.581	66.667	7.64	0.00	45.64	5.18
2476	2547	0.747255	CATCAGTGTAGCGCCTAGGT	59.253	55.000	11.31	0.00	0.00	3.08
2506	2577	7.148323	TGCTGCTTAATGCGAATCTTTTTACTA	60.148	33.333	0.00	0.00	46.63	1.82
2507	2578	6.030228	GCTGCTTAATGCGAATCTTTTTACT	58.970	36.000	0.00	0.00	46.63	2.24
2508	2579	5.799936	TGCTGCTTAATGCGAATCTTTTTAC	59.200	36.000	0.00	0.00	46.63	2.01
2514	2585	1.328680	CGTGCTGCTTAATGCGAATCT	59.671	47.619	0.00	0.00	46.63	2.40
2525	2596	1.896220	TTGGATCTTTCGTGCTGCTT	58.104	45.000	0.00	0.00	0.00	3.91
2618	2689	1.296056	CCGACGGATCACCAAACCAC	61.296	60.000	8.64	0.00	35.59	4.16
2619	2690	1.004320	CCGACGGATCACCAAACCA	60.004	57.895	8.64	0.00	35.59	3.67
2625	2731	3.186047	CGCAACCGACGGATCACC	61.186	66.667	23.38	2.91	36.29	4.02
2694	2800	0.875040	CGTCGAGAGTCTAGGCGCTA	60.875	60.000	14.26	0.00	26.94	4.26
2748	2854	6.071221	TGGAAATTTCTAAGTCAGCATGCAAT	60.071	34.615	21.98	4.32	34.76	3.56
2754	2860	3.758554	GCCTGGAAATTTCTAAGTCAGCA	59.241	43.478	17.42	4.09	0.00	4.41
2771	2877	1.619654	TCACACCTCAAAATGCCTGG	58.380	50.000	0.00	0.00	0.00	4.45
2820	2933	2.657757	CGCCACACTACACTGTGCG	61.658	63.158	7.90	1.82	40.33	5.34
2860	2973	2.286365	TTCATTCCGCTGACCCTTTT	57.714	45.000	0.00	0.00	0.00	2.27
2924	3038	9.823647	TTTCAGGCAAAAACTATAAATTTGACA	57.176	25.926	0.00	0.00	43.07	3.58
2934	3048	6.207810	TCGGTGTAATTTCAGGCAAAAACTAT	59.792	34.615	0.00	0.00	0.00	2.12
2992	3122	8.601845	TTGAGAAAATCTGAAACAAGACGATA	57.398	30.769	0.00	0.00	0.00	2.92
3054	3184	7.809546	ATCTTGTGTAATCTCTCGATCTACA	57.190	36.000	0.00	0.00	0.00	2.74
3064	3194	8.547967	TGTTCCAGTAAATCTTGTGTAATCTC	57.452	34.615	0.00	0.00	0.00	2.75
3074	3204	5.099042	AGCCGTATGTTCCAGTAAATCTT	57.901	39.130	0.00	0.00	0.00	2.40
3082	3212	2.676342	GGTGTTTAGCCGTATGTTCCAG	59.324	50.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.