AutoCloner

Multiple sequence alignment - TraesCS4B01G311100

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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	TraesCS4B01G311100	chr4B	100.000	5377	0	0	1	5377	601194048	601199424	0.000000e+00	9930.0
1	TraesCS4B01G311100	chr4D	87.934	1210	50	42	823	1953	477013349	477014541	0.000000e+00	1338.0
2	TraesCS4B01G311100	chr4D	93.476	843	40	7	3629	4459	477016002	477016841	0.000000e+00	1238.0
3	TraesCS4B01G311100	chr4D	85.020	988	81	34	2151	3128	477015072	477016002	0.000000e+00	942.0
4	TraesCS4B01G311100	chr4D	99.171	362	3	0	3264	3625	3837392	3837031	0.000000e+00	652.0
5	TraesCS4B01G311100	chr4D	98.615	361	5	0	3264	3624	417059566	417059926	1.630000e-179	640.0
6	TraesCS4B01G311100	chr4D	92.381	210	14	2	1	209	477010094	477010302	1.130000e-76	298.0
7	TraesCS4B01G311100	chr4D	96.667	120	3	1	4458	4577	477016895	477017013	1.180000e-46	198.0
8	TraesCS4B01G311100	chr4D	84.925	199	15	5	386	579	477011729	477011917	2.560000e-43	187.0
9	TraesCS4B01G311100	chr4D	83.908	174	13	7	4661	4819	300311973	300312146	9.330000e-33	152.0
10	TraesCS4B01G311100	chr4D	93.151	73	4	1	579	650	477012704	477012776	7.370000e-19	106.0
11	TraesCS4B01G311100	chr4D	97.826	46	1	0	717	762	477013170	477013215	4.460000e-11	80.5
12	TraesCS4B01G311100	chr4A	89.100	1000	62	20	991	1953	683778797	683779786	0.000000e+00	1199.0
13	TraesCS4B01G311100	chr4A	91.746	739	47	9	3629	4355	683781552	683782288	0.000000e+00	1014.0
14	TraesCS4B01G311100	chr4A	84.673	933	91	29	2207	3128	683780661	683781552	0.000000e+00	883.0
15	TraesCS4B01G311100	chr4A	97.761	134	3	0	3133	3266	477881889	477881756	1.160000e-56	231.0
16	TraesCS4B01G311100	chr4A	88.750	80	3	5	4665	4740	707668456	707668379	5.730000e-15	93.5
17	TraesCS4B01G311100	chr4A	88.608	79	5	3	4665	4740	707695928	707695851	5.730000e-15	93.5
18	TraesCS4B01G311100	chr4A	92.308	65	1	3	706	767	683778502	683778565	7.420000e-14	89.8
19	TraesCS4B01G311100	chr5B	91.737	714	42	7	1247	1953	653691834	653691131	0.000000e+00	976.0
20	TraesCS4B01G311100	chr5B	88.792	571	45	11	4814	5377	669478804	669478246	0.000000e+00	682.0
21	TraesCS4B01G311100	chr5B	96.185	367	14	0	3264	3630	610892667	610892301	7.710000e-168	601.0
22	TraesCS4B01G311100	chr5B	96.732	153	4	1	1247	1399	622453174	622453023	2.490000e-63	254.0
23	TraesCS4B01G311100	chr5B	78.698	169	16	8	4667	4819	65236003	65235839	1.590000e-15	95.3
24	TraesCS4B01G311100	chr7B	91.172	725	48	5	1244	1953	374352659	374353382	0.000000e+00	970.0
25	TraesCS4B01G311100	chr7B	88.576	569	46	7	4818	5374	27133186	27132625	0.000000e+00	673.0
26	TraesCS4B01G311100	chr7B	88.401	569	47	11	4818	5374	27099925	27099364	0.000000e+00	667.0
27	TraesCS4B01G311100	chr7B	97.744	133	3	0	3138	3270	182718801	182718933	4.190000e-56	230.0
28	TraesCS4B01G311100	chr6B	91.457	714	43	8	1247	1953	152443286	152442584	0.000000e+00	965.0
29	TraesCS4B01G311100	chr6B	91.189	715	48	2	1254	1953	483680192	483679478	0.000000e+00	957.0
30	TraesCS4B01G311100	chr6B	88.951	715	50	12	1247	1956	483731563	483730873	0.000000e+00	856.0
31	TraesCS4B01G311100	chr6B	99.446	361	2	0	3264	3624	645224872	645225232	0.000000e+00	656.0
32	TraesCS4B01G311100	chr6B	89.588	461	44	4	3126	3583	495804079	495804538	2.790000e-162	582.0
33	TraesCS4B01G311100	chr6B	94.118	153	5	3	3118	3266	678328785	678328937	4.190000e-56	230.0
34	TraesCS4B01G311100	chr6B	79.114	158	16	10	4678	4819	536860812	536860656	5.730000e-15	93.5
35	TraesCS4B01G311100	chr3B	91.074	717	47	10	1244	1953	286474778	286475484	0.000000e+00	953.0
36	TraesCS4B01G311100	chr3B	90.305	722	54	6	1247	1953	205170759	205170039	0.000000e+00	931.0
37	TraesCS4B01G311100	chr3B	90.305	722	54	6	1247	1953	205835270	205834550	0.000000e+00	931.0
38	TraesCS4B01G311100	chr3B	97.507	361	9	0	3267	3627	819631211	819630851	7.650000e-173	617.0
39	TraesCS4B01G311100	chr3B	96.970	363	11	0	3264	3626	588416839	588417201	1.280000e-170	610.0
40	TraesCS4B01G311100	chr3D	89.703	573	44	11	4815	5377	435329592	435329025	0.000000e+00	717.0
41	TraesCS4B01G311100	chr3D	98.098	368	7	0	3264	3631	63771063	63770696	4.540000e-180	641.0
42	TraesCS4B01G311100	chr1B	89.649	570	43	5	4820	5374	535703827	535703259	0.000000e+00	712.0
43	TraesCS4B01G311100	chr1B	88.947	570	52	6	4815	5374	164861016	164860448	0.000000e+00	693.0
44	TraesCS4B01G311100	chr1B	98.450	129	2	0	3138	3266	649332858	649332730	1.510000e-55	228.0
45	TraesCS4B01G311100	chr1B	93.243	148	8	2	3127	3273	623687176	623687030	3.260000e-52	217.0
46	TraesCS4B01G311100	chr1A	88.652	564	53	9	4816	5374	60528032	60528589	0.000000e+00	676.0
47	TraesCS4B01G311100	chr1A	97.778	135	3	0	3140	3274	497228155	497228289	3.240000e-57	233.0
48	TraesCS4B01G311100	chr1A	94.079	152	7	2	3124	3273	505092375	505092526	4.190000e-56	230.0
49	TraesCS4B01G311100	chr1A	88.000	75	5	4	4667	4738	555643846	555643919	9.600000e-13	86.1
50	TraesCS4B01G311100	chr1A	88.000	75	5	4	4667	4738	555644676	555644749	9.600000e-13	86.1
51	TraesCS4B01G311100	chr6A	88.287	572	50	12	4815	5374	39463970	39464536	0.000000e+00	669.0
52	TraesCS4B01G311100	chr6A	96.676	361	12	0	3264	3624	395252159	395252519	7.710000e-168	601.0
53	TraesCS4B01G311100	chr3A	88.256	562	51	11	4818	5377	98955944	98955396	0.000000e+00	658.0
54	TraesCS4B01G311100	chr2B	95.513	156	6	1	1244	1399	756870875	756871029	1.160000e-61	248.0
55	TraesCS4B01G311100	chr2B	97.778	135	3	0	3139	3273	96093731	96093597	3.240000e-57	233.0
56	TraesCS4B01G311100	chr7A	86.093	151	16	3	4677	4822	512758737	512758587	2.000000e-34	158.0
57	TraesCS4B01G311100	chr2D	88.525	61	4	3	4667	4725	32026971	32026912	2.690000e-08	71.3

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	TraesCS4B01G311100	chr4B	601194048	601199424	5376	False	9930.0000	9930	100.00000	1	5377	1	chr4B.!!$F1	5376
1	TraesCS4B01G311100	chr4D	477010094	477017013	6919	False	548.4375	1338	91.42250	1	4577	8	chr4D.!!$F3	4576
2	TraesCS4B01G311100	chr4A	683778502	683782288	3786	False	796.4500	1199	89.45675	706	4355	4	chr4A.!!$F1	3649
3	TraesCS4B01G311100	chr5B	653691131	653691834	703	True	976.0000	976	91.73700	1247	1953	1	chr5B.!!$R4	706
4	TraesCS4B01G311100	chr5B	669478246	669478804	558	True	682.0000	682	88.79200	4814	5377	1	chr5B.!!$R5	563
5	TraesCS4B01G311100	chr7B	374352659	374353382	723	False	970.0000	970	91.17200	1244	1953	1	chr7B.!!$F2	709
6	TraesCS4B01G311100	chr7B	27132625	27133186	561	True	673.0000	673	88.57600	4818	5374	1	chr7B.!!$R2	556
7	TraesCS4B01G311100	chr7B	27099364	27099925	561	True	667.0000	667	88.40100	4818	5374	1	chr7B.!!$R1	556
8	TraesCS4B01G311100	chr6B	152442584	152443286	702	True	965.0000	965	91.45700	1247	1953	1	chr6B.!!$R1	706
9	TraesCS4B01G311100	chr6B	483679478	483680192	714	True	957.0000	957	91.18900	1254	1953	1	chr6B.!!$R2	699
10	TraesCS4B01G311100	chr6B	483730873	483731563	690	True	856.0000	856	88.95100	1247	1956	1	chr6B.!!$R3	709
11	TraesCS4B01G311100	chr3B	286474778	286475484	706	False	953.0000	953	91.07400	1244	1953	1	chr3B.!!$F1	709
12	TraesCS4B01G311100	chr3B	205170039	205170759	720	True	931.0000	931	90.30500	1247	1953	1	chr3B.!!$R1	706
13	TraesCS4B01G311100	chr3B	205834550	205835270	720	True	931.0000	931	90.30500	1247	1953	1	chr3B.!!$R2	706
14	TraesCS4B01G311100	chr3D	435329025	435329592	567	True	717.0000	717	89.70300	4815	5377	1	chr3D.!!$R2	562
15	TraesCS4B01G311100	chr1B	535703259	535703827	568	True	712.0000	712	89.64900	4820	5374	1	chr1B.!!$R2	554
16	TraesCS4B01G311100	chr1B	164860448	164861016	568	True	693.0000	693	88.94700	4815	5374	1	chr1B.!!$R1	559
17	TraesCS4B01G311100	chr1A	60528032	60528589	557	False	676.0000	676	88.65200	4816	5374	1	chr1A.!!$F1	558
18	TraesCS4B01G311100	chr6A	39463970	39464536	566	False	669.0000	669	88.28700	4815	5374	1	chr6A.!!$F1	559
19	TraesCS4B01G311100	chr3A	98955396	98955944	548	True	658.0000	658	88.25600	4818	5377	1	chr3A.!!$R1	559

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
954	3428	0.031449	CCGGAGCGAGAGAAATCTCC	59.969	60.000	0.00	0.00	43.88	3.71	F
957	3431	0.031449	GAGCGAGAGAAATCTCCCGG	59.969	60.000	14.79	0.00	43.18	5.73	F
2031	4594	0.037697	TGGTTACTCGCGATGCAAGT	60.038	50.000	10.36	6.17	0.00	3.16	F
2121	5236	1.004679	GGCTTGTGGTGGGCAAATG	60.005	57.895	0.00	0.00	0.00	2.32	F
2348	5552	1.094073	GCGAGCTGTCTTGGCATCAT	61.094	55.000	0.00	0.00	0.00	2.45	F
3158	6379	0.032813	TACTCCCTCCGTCCGGAAAT	60.033	55.000	5.23	0.00	44.66	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2323	5527	0.320247	CCAAGACAGCTCGCTGAGTT	60.320	55.0	24.30	13.70	46.30	3.01	R
2693	5914	0.321653	CTACCACAGCCCACCAGAAC	60.322	60.0	0.00	0.00	0.00	3.01	R
3139	6360	0.032813	ATTTCCGGACGGAGGGAGTA	60.033	55.0	13.64	0.00	46.06	2.59	R
3142	6363	0.032813	AGTATTTCCGGACGGAGGGA	60.033	55.0	13.64	4.95	46.06	4.20	R
3546	6767	0.034896	TCCAACGGTCAAGAGAAGGC	59.965	55.0	0.00	0.00	0.00	4.35	R
4663	7955	0.105964	AGCGGGAAAACCTTTTTGGC	59.894	50.0	0.00	0.00	40.22	4.52	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	6.358974	TGTAGAACTTCCTGTGATGATCAA	57.641	37.500	0.00	0.00	0.00	2.57
75	76	9.440761	AGGAGTATAGAATGATAGTGAACCTTT	57.559	33.333	0.00	0.00	0.00	3.11
87	88	1.173913	GAACCTTTGCCGGTTAGCAT	58.826	50.000	1.90	0.00	46.85	3.79
97	98	0.810031	CGGTTAGCATGAAGGGTCCG	60.810	60.000	0.00	0.00	0.00	4.79
98	99	1.095807	GGTTAGCATGAAGGGTCCGC	61.096	60.000	0.00	0.00	0.00	5.54
100	101	0.107703	TTAGCATGAAGGGTCCGCAG	60.108	55.000	0.00	0.00	0.00	5.18
103	104	0.179045	GCATGAAGGGTCCGCAGTAT	60.179	55.000	0.00	0.00	0.00	2.12
107	108	2.432444	TGAAGGGTCCGCAGTATTTTG	58.568	47.619	0.00	0.00	0.00	2.44
122	123	6.197842	GCAGTATTTTGTGAGCTATTGAATGC	59.802	38.462	0.00	0.00	0.00	3.56
164	165	4.708726	AAGCTAAATTGCCATCACAGAC	57.291	40.909	0.00	0.00	0.00	3.51
201	203	1.029681	GTTGTTGTTCTGTGGGGGTC	58.970	55.000	0.00	0.00	0.00	4.46
202	204	0.923358	TTGTTGTTCTGTGGGGGTCT	59.077	50.000	0.00	0.00	0.00	3.85
209	211	0.490017	TCTGTGGGGGTCTAAGGACA	59.510	55.000	0.00	0.00	43.77	4.02
210	212	0.905357	CTGTGGGGGTCTAAGGACAG	59.095	60.000	0.00	0.00	43.77	3.51
215	217	0.035343	GGGGTCTAAGGACAGGTTGC	60.035	60.000	0.00	0.00	43.77	4.17
216	218	0.391263	GGGTCTAAGGACAGGTTGCG	60.391	60.000	0.00	0.00	43.77	4.85
217	219	0.320697	GGTCTAAGGACAGGTTGCGT	59.679	55.000	0.00	0.00	43.77	5.24
227	1423	4.097863	GGTTGCGTAAGTGCCGGC	62.098	66.667	22.73	22.73	41.68	6.13
262	1458	5.804639	TGTGTGCAGAGGTTAAGTTGATAT	58.195	37.500	0.00	0.00	0.00	1.63
263	1459	6.941857	TGTGTGCAGAGGTTAAGTTGATATA	58.058	36.000	0.00	0.00	0.00	0.86
264	1460	7.390823	TGTGTGCAGAGGTTAAGTTGATATAA	58.609	34.615	0.00	0.00	0.00	0.98
265	1461	7.549134	TGTGTGCAGAGGTTAAGTTGATATAAG	59.451	37.037	0.00	0.00	0.00	1.73
270	1467	9.819267	GCAGAGGTTAAGTTGATATAAGTAACT	57.181	33.333	0.00	0.00	36.29	2.24
310	1511	4.619227	CGCTGGTCCGTTGGTGGT	62.619	66.667	0.00	0.00	0.00	4.16
325	1526	3.434319	GGTGTGGTGGCTGATGCG	61.434	66.667	0.00	0.00	40.82	4.73

Showing 1 to 25 of 762 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	7.134815	CCACGAGGAACAAATTATTGATCATC	58.865	38.462	0.00	4.17	42.31	2.92
29	30	6.057321	TCCTAACCACGAGGAACAAATTAT	57.943	37.500	5.68	0.00	40.25	1.28
75	76	1.077787	CCCTTCATGCTAACCGGCA	60.078	57.895	0.00	0.00	46.63	5.69
87	88	2.224670	ACAAAATACTGCGGACCCTTCA	60.225	45.455	0.00	0.00	0.00	3.02
97	98	6.197842	GCATTCAATAGCTCACAAAATACTGC	59.802	38.462	0.00	0.00	0.00	4.40
98	99	6.694411	GGCATTCAATAGCTCACAAAATACTG	59.306	38.462	0.00	0.00	0.00	2.74
100	101	5.979517	GGGCATTCAATAGCTCACAAAATAC	59.020	40.000	0.00	0.00	0.00	1.89
103	104	3.831333	TGGGCATTCAATAGCTCACAAAA	59.169	39.130	0.00	0.00	36.06	2.44
107	108	4.823989	AGTATTGGGCATTCAATAGCTCAC	59.176	41.667	0.00	0.08	41.73	3.51
122	123	7.547227	AGCTTAAATTTTACAGCAGTATTGGG	58.453	34.615	15.30	0.00	34.49	4.12
201	203	2.993899	CACTTACGCAACCTGTCCTTAG	59.006	50.000	0.00	0.00	0.00	2.18
202	204	2.868839	GCACTTACGCAACCTGTCCTTA	60.869	50.000	0.00	0.00	0.00	2.69
209	211	2.358247	CCGGCACTTACGCAACCT	60.358	61.111	0.00	0.00	0.00	3.50
210	212	4.097863	GCCGGCACTTACGCAACC	62.098	66.667	24.80	0.00	0.00	3.77
215	217	2.869503	AAGGATGGCCGGCACTTACG	62.870	60.000	30.85	0.00	39.96	3.18
216	218	0.679960	AAAGGATGGCCGGCACTTAC	60.680	55.000	30.85	16.05	39.96	2.34
217	219	0.039035	AAAAGGATGGCCGGCACTTA	59.961	50.000	30.85	11.81	39.96	2.24
244	1440	9.819267	AGTTACTTATATCAACTTAACCTCTGC	57.181	33.333	0.00	0.00	0.00	4.26
291	1492	2.340809	CACCAACGGACCAGCGTA	59.659	61.111	0.00	0.00	0.00	4.42
310	1511	2.669229	CACGCATCAGCCACCACA	60.669	61.111	0.00	0.00	37.52	4.17
330	1531	4.707200	CTGATGTACAGTGCACTGAGTGC	61.707	52.174	44.82	29.73	46.74	4.40
331	1532	2.991866	CTGATGTACAGTGCACTGAGTG	59.008	50.000	44.82	25.34	46.59	3.51
332	1533	3.309961	CTGATGTACAGTGCACTGAGT	57.690	47.619	44.82	29.56	46.59	3.41
360	1561	3.432186	CGGACCCTCAATCTATTTGCAGA	60.432	47.826	0.00	0.00	35.16	4.26
380	1581	4.025730	CGATGACAATGTTCTAATGACCGG	60.026	45.833	0.00	0.00	0.00	5.28

Showing 1 to 25 of 726 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.