AutoCloner

Multiple sequence alignment - TraesCS1D01G199500

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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	TraesCS1D01G199500	chr1D	100.000	6517	0	0	1	6517	282280612	282287128	0.000000e+00	12035.0
1	TraesCS1D01G199500	chr1A	97.589	6346	116	14	181	6514	354294299	354300619	0.000000e+00	10837.0
2	TraesCS1D01G199500	chr1A	95.679	162	5	2	37	197	354292756	354292916	6.480000e-65	259.0
3	TraesCS1D01G199500	chr1B	97.831	3228	61	4	2707	5929	383793943	383797166	0.000000e+00	5565.0
4	TraesCS1D01G199500	chr1B	96.246	2264	47	14	222	2470	383791702	383793942	0.000000e+00	3675.0
5	TraesCS1D01G199500	chr1B	92.979	584	35	6	5934	6517	383797217	383797794	0.000000e+00	846.0
6	TraesCS1D01G199500	chr1B	97.046	237	6	1	1	237	383791451	383791686	1.320000e-106	398.0
7	TraesCS1D01G199500	chr1B	95.722	187	8	0	92	278	144273309	144273495	1.060000e-77	302.0
8	TraesCS1D01G199500	chr1B	94.652	187	10	0	92	278	40487449	40487263	2.300000e-74	291.0
9	TraesCS1D01G199500	chr1B	80.992	242	35	4	2467	2703	178891255	178891020	1.440000e-41	182.0
10	TraesCS1D01G199500	chr7D	77.358	954	193	19	3760	4700	14882075	14881132	1.600000e-150	544.0
11	TraesCS1D01G199500	chr7D	90.698	86	6	2	2590	2674	11258137	11258221	5.340000e-21	113.0
12	TraesCS1D01G199500	chr7D	91.781	73	4	2	2637	2708	125896804	125896875	4.160000e-17	100.0
13	TraesCS1D01G199500	chr7A	77.149	954	195	19	3760	4700	14191151	14190208	3.460000e-147	532.0
14	TraesCS1D01G199500	chr7A	94.652	187	10	0	92	278	113109534	113109348	2.300000e-74	291.0
15	TraesCS1D01G199500	chr7A	90.909	44	3	1	2464	2507	19315859	19315817	2.540000e-04	58.4
16	TraesCS1D01G199500	chr4A	76.834	954	198	19	3757	4697	721384195	721385138	3.480000e-142	516.0
17	TraesCS1D01G199500	chr6B	96.296	189	7	0	90	278	708552969	708552781	1.760000e-80	311.0
18	TraesCS1D01G199500	chr5B	95.722	187	8	0	92	278	416465156	416465342	1.060000e-77	302.0
19	TraesCS1D01G199500	chr5B	94.118	187	11	0	92	278	421517577	421517763	1.070000e-72	285.0
20	TraesCS1D01G199500	chr2A	94.652	187	9	1	92	278	59043393	59043208	8.270000e-74	289.0
21	TraesCS1D01G199500	chr2A	92.857	42	2	1	2467	2508	177658674	177658634	7.060000e-05	60.2
22	TraesCS1D01G199500	chr3D	86.179	246	31	2	2465	2707	314620027	314620272	5.010000e-66	263.0
23	TraesCS1D01G199500	chr3B	88.571	210	22	2	2503	2710	97546219	97546010	3.020000e-63	254.0
24	TraesCS1D01G199500	chr3B	83.065	248	26	6	2465	2707	405231015	405230779	1.840000e-50	211.0
25	TraesCS1D01G199500	chr4D	83.065	248	35	5	2467	2708	497279389	497279635	1.100000e-52	219.0
26	TraesCS1D01G199500	chr4B	89.474	171	17	1	2503	2672	5526025	5525855	1.420000e-51	215.0
27	TraesCS1D01G199500	chr2B	80.800	125	18	5	2591	2713	38064666	38064786	6.960000e-15	93.5
28	TraesCS1D01G199500	chr7B	97.368	38	1	0	2458	2495	302771520	302771557	1.520000e-06	65.8
29	TraesCS1D01G199500	chr5D	97.436	39	0	1	2457	2495	242650433	242650396	1.520000e-06	65.8
30	TraesCS1D01G199500	chr6D	92.683	41	2	1	2456	2495	347716127	347716087	2.540000e-04	58.4

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	TraesCS1D01G199500	chr1D	282280612	282287128	6516	False	12035	12035	100.0000	1	6517	1	chr1D.!!$F1	6516
1	TraesCS1D01G199500	chr1A	354292756	354300619	7863	False	5548	10837	96.6340	37	6514	2	chr1A.!!$F1	6477
2	TraesCS1D01G199500	chr1B	383791451	383797794	6343	False	2621	5565	96.0255	1	6517	4	chr1B.!!$F2	6516
3	TraesCS1D01G199500	chr7D	14881132	14882075	943	True	544	544	77.3580	3760	4700	1	chr7D.!!$R1	940
4	TraesCS1D01G199500	chr7A	14190208	14191151	943	True	532	532	77.1490	3760	4700	1	chr7A.!!$R1	940
5	TraesCS1D01G199500	chr4A	721384195	721385138	943	False	516	516	76.8340	3757	4697	1	chr4A.!!$F1	940

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
138	140	0.752054	CCCTCTGGTGCAAAGCAAAA	59.248	50.000	0.00	0.00	41.47	2.44	F
961	2405	2.571212	AGCAACAACATCACGAGGAAA	58.429	42.857	0.00	0.00	0.00	3.13	F
1815	3259	2.124901	TCTAAACCATGGCGGCCG	60.125	61.111	24.05	24.05	39.03	6.13	F
2951	4399	0.464452	GCCCTATCAACCGTGCTACT	59.536	55.000	0.00	0.00	0.00	2.57	F
3533	4981	0.829333	CTGATAGCACTCACTGGCCT	59.171	55.000	3.32	0.00	0.00	5.19	F
4754	6208	5.726793	TGCCCCTCTAGACTTTCTATTTCTT	59.273	40.000	0.00	0.00	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1155	2599	0.455005	CGCTGCTGATCTCTGAGTCA	59.545	55.000	4.32	7.09	0.00	3.41	R
2663	4111	1.503818	GGTCCGCACGCTTTTTGAGA	61.504	55.000	0.00	0.00	0.00	3.27	R
3368	4816	0.749091	TGATGGAATCTGGCAAGCCG	60.749	55.000	6.60	1.74	45.81	5.52	R
3980	5428	1.434188	TGCCTTCAAACCTCTGAGGA	58.566	50.000	29.71	4.61	37.67	3.71	R
4754	6208	6.317312	TGGTGAGTCTACTTTAGTAAGGGAA	58.683	40.000	0.00	0.00	35.61	3.97	R
6341	7850	4.678287	GTGAGACATGTGCAGTTTGATTTG	59.322	41.667	1.15	0.00	0.00	2.32	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
138	140	0.752054	CCCTCTGGTGCAAAGCAAAA	59.248	50.000	0.00	0.00	41.47	2.44
196	1597	6.373774	GGTGAGAAAGACATCATTGACTGATT	59.626	38.462	0.00	0.00	42.07	2.57
230	1662	6.515272	AACCAAGTTGCAGTAATAAGGATG	57.485	37.500	0.00	0.00	0.00	3.51
295	1730	8.319057	TCAGGTGTGGATGATTAAGTTATACT	57.681	34.615	0.00	0.00	0.00	2.12
296	1731	8.204160	TCAGGTGTGGATGATTAAGTTATACTG	58.796	37.037	0.00	0.00	0.00	2.74
297	1732	7.987458	CAGGTGTGGATGATTAAGTTATACTGT	59.013	37.037	0.00	0.00	0.00	3.55
298	1733	9.209048	AGGTGTGGATGATTAAGTTATACTGTA	57.791	33.333	0.00	0.00	0.00	2.74
425	1867	4.785453	CTTGGCGCCTCCCCAGTC	62.785	72.222	29.70	0.00	33.13	3.51
492	1934	3.033184	ACCATTCAAATACAGCCATGGG	58.967	45.455	15.13	0.00	36.29	4.00
524	1966	5.420409	CGCTTCCTCATTACTACCTTTCTT	58.580	41.667	0.00	0.00	0.00	2.52
860	2304	9.213799	TCCAAATATGTCTTGGCAAAAATAAAC	57.786	29.630	0.00	0.00	42.68	2.01
877	2321	9.880157	AAAAATAAACCTACAGCGAGACTAATA	57.120	29.630	0.00	0.00	0.00	0.98
910	2354	9.549509	TTTTCCTTTGTTTCGTCATATTATTCG	57.450	29.630	0.00	0.00	0.00	3.34
943	2387	3.003068	CAGCCACAAGATAACAGCATAGC	59.997	47.826	0.00	0.00	0.00	2.97
961	2405	2.571212	AGCAACAACATCACGAGGAAA	58.429	42.857	0.00	0.00	0.00	3.13
965	2409	4.497340	GCAACAACATCACGAGGAAAAAGA	60.497	41.667	0.00	0.00	0.00	2.52
973	2417	5.018539	TCACGAGGAAAAAGAAGAGTCAA	57.981	39.130	0.00	0.00	0.00	3.18
977	2421	6.479001	CACGAGGAAAAAGAAGAGTCAAAGTA	59.521	38.462	0.00	0.00	0.00	2.24
1074	2518	4.641645	CCCAGCAAGCCACCGACA	62.642	66.667	0.00	0.00	0.00	4.35
1815	3259	2.124901	TCTAAACCATGGCGGCCG	60.125	61.111	24.05	24.05	39.03	6.13
1982	3426	6.128090	GGCTTACCCACTAACACAAGAATAAC	60.128	42.308	0.00	0.00	0.00	1.89
1988	3432	6.455113	CCCACTAACACAAGAATAACGAATCG	60.455	42.308	0.00	0.00	0.00	3.34
2106	3550	2.162408	GCCAGATGCTGTTAACCTTCAC	59.838	50.000	2.48	0.00	36.87	3.18
2107	3551	3.411446	CCAGATGCTGTTAACCTTCACA	58.589	45.455	2.48	0.00	0.00	3.58
2108	3552	3.189287	CCAGATGCTGTTAACCTTCACAC	59.811	47.826	2.48	0.00	0.00	3.82
2351	3798	6.837992	TGTGTTCTCTGTCACAAAACTTTAC	58.162	36.000	0.00	0.00	40.81	2.01
2506	3954	6.197096	CAGAATATAAGGTGCACGCATTTTTC	59.803	38.462	11.45	9.92	0.00	2.29
2951	4399	0.464452	GCCCTATCAACCGTGCTACT	59.536	55.000	0.00	0.00	0.00	2.57
3368	4816	1.458445	GAGTTCAAGGTCCGCGTTAAC	59.542	52.381	4.92	0.00	0.00	2.01
3533	4981	0.829333	CTGATAGCACTCACTGGCCT	59.171	55.000	3.32	0.00	0.00	5.19
4754	6208	5.726793	TGCCCCTCTAGACTTTCTATTTCTT	59.273	40.000	0.00	0.00	0.00	2.52
5783	7242	3.126514	CACAATCTCTCGCATTTGAGCTT	59.873	43.478	0.00	0.00	35.90	3.74
5922	7381	4.101741	ACCACTCCTATTCAGACCAATAGC	59.898	45.833	0.00	0.00	35.70	2.97
5946	7451	6.358030	GCGATATCATAGAAATGTTTGTGCAC	59.642	38.462	10.75	10.75	34.50	4.57
5995	7500	9.472361	GATAGTGCTAAAACGGATACAGAAATA	57.528	33.333	0.00	0.00	0.00	1.40
6073	7578	7.093945	TGGGAAATTCCTAAACTGCAAATAGTC	60.094	37.037	12.28	0.00	36.57	2.59
6129	7638	9.647797	TCAAACTTATGTAACGATGATACACTT	57.352	29.630	0.00	0.00	36.19	3.16
6225	7734	6.393171	ACCTGCAATTTCTTTCAAATCTAGC	58.607	36.000	0.00	0.00	0.00	3.42
6267	7776	7.631717	AAATCATTTAGGTGTAAGCCTCTTC	57.368	36.000	0.00	0.00	39.94	2.87
6341	7850	0.247736	ACTGCCTCATTCTCGGTGTC	59.752	55.000	0.00	0.00	0.00	3.67
6510	8019	2.282180	GTTGGGCGCTTCAAGGGA	60.282	61.111	7.64	0.00	0.00	4.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	98	1.670811	CAAGTCGTGCAGTGAAAACCT	59.329	47.619	0.00	0.00	0.00	3.50
97	99	1.268539	CCAAGTCGTGCAGTGAAAACC	60.269	52.381	0.00	0.00	0.00	3.27
138	140	7.091443	TGACCGTGTAATTTGTTTTTGTCTTT	58.909	30.769	0.00	0.00	0.00	2.52
196	1597	3.764434	TGCAACTTGGTTTTACCTTGTCA	59.236	39.130	0.00	0.00	39.58	3.58
230	1662	8.451908	AATTCTTTTATACATCTGCCACTACC	57.548	34.615	0.00	0.00	0.00	3.18
294	1729	4.498682	GGATGCCTGCTTGCTTAATTACAG	60.499	45.833	0.00	0.00	0.00	2.74
295	1730	3.381272	GGATGCCTGCTTGCTTAATTACA	59.619	43.478	0.00	0.00	0.00	2.41
296	1731	3.381272	TGGATGCCTGCTTGCTTAATTAC	59.619	43.478	0.00	0.00	0.00	1.89
297	1732	3.630168	TGGATGCCTGCTTGCTTAATTA	58.370	40.909	0.00	0.00	0.00	1.40
298	1733	2.459644	TGGATGCCTGCTTGCTTAATT	58.540	42.857	0.00	0.00	0.00	1.40
355	1790	5.632244	GCATGATGCATACATTCATACCA	57.368	39.130	13.36	0.00	44.26	3.25
524	1966	1.108727	GGCAATGGCGATGGAATGGA	61.109	55.000	0.00	0.00	42.47	3.41
722	2165	1.985473	TGCATGCAGGTTGTTTCTCT	58.015	45.000	18.46	0.00	0.00	3.10
723	2166	2.416431	GGATGCATGCAGGTTGTTTCTC	60.416	50.000	26.69	14.46	0.00	2.87
724	2167	1.547372	GGATGCATGCAGGTTGTTTCT	59.453	47.619	26.69	5.33	0.00	2.52
860	2304	6.682746	ACATTGATATTAGTCTCGCTGTAGG	58.317	40.000	0.00	0.00	0.00	3.18
877	2321	6.568869	TGACGAAACAAAGGAAAACATTGAT	58.431	32.000	0.00	0.00	32.37	2.57
899	2343	6.345096	TGATCTGCAGGACGAATAATATGA	57.655	37.500	15.13	0.00	0.00	2.15
910	2354	0.321919	TTGTGGCTGATCTGCAGGAC	60.322	55.000	23.84	16.90	45.03	3.85
943	2387	5.168526	TCTTTTTCCTCGTGATGTTGTTG	57.831	39.130	0.00	0.00	0.00	3.33
961	2405	6.018669	CGTGCTCTTTACTTTGACTCTTCTTT	60.019	38.462	0.00	0.00	0.00	2.52
965	2409	4.694339	ACGTGCTCTTTACTTTGACTCTT	58.306	39.130	0.00	0.00	0.00	2.85
973	2417	2.094854	CCTCCGTACGTGCTCTTTACTT	60.095	50.000	15.21	0.00	0.00	2.24
977	2421	0.526662	CTCCTCCGTACGTGCTCTTT	59.473	55.000	15.21	0.00	0.00	2.52
1116	2560	1.260538	TGATGAAGCGCCCAGACTCT	61.261	55.000	2.29	0.00	0.00	3.24
1155	2599	0.455005	CGCTGCTGATCTCTGAGTCA	59.545	55.000	4.32	7.09	0.00	3.41
1815	3259	4.704833	TGGAGCTTGCGGGTGAGC	62.705	66.667	0.00	0.00	39.17	4.26
2106	3550	6.183360	GCATTTCTCTTTGCTAGACTACAGTG	60.183	42.308	0.00	0.00	35.95	3.66
2107	3551	5.872070	GCATTTCTCTTTGCTAGACTACAGT	59.128	40.000	0.00	0.00	35.95	3.55
2108	3552	6.105333	AGCATTTCTCTTTGCTAGACTACAG	58.895	40.000	0.00	0.00	46.92	2.74
2187	3634	8.303156	ACAACTCAGTCACTCTATATATGCATC	58.697	37.037	0.19	0.00	0.00	3.91
2253	3700	7.391620	AGCTTACTGTATAGGCACACTTTTTA	58.608	34.615	9.41	0.00	0.00	1.52
2367	3815	7.225341	GGATCTTTGCATTTTCTTTTCAACTGT	59.775	33.333	0.00	0.00	0.00	3.55
2506	3954	5.801350	TTGATGGTCAAAGCTAAATCTCG	57.199	39.130	0.00	0.00	32.71	4.04
2663	4111	1.503818	GGTCCGCACGCTTTTTGAGA	61.504	55.000	0.00	0.00	0.00	3.27
2671	4119	1.687123	AGAATATAAGGTCCGCACGCT	59.313	47.619	0.00	0.00	0.00	5.07
2951	4399	7.220030	ACTTTTCTTTAAGCACAGAGAGATCA	58.780	34.615	0.00	0.00	0.00	2.92
3368	4816	0.749091	TGATGGAATCTGGCAAGCCG	60.749	55.000	6.60	1.74	45.81	5.52
3533	4981	4.188462	GTGACGAATGAATCCATGTACCA	58.812	43.478	0.00	0.00	32.36	3.25
3866	5314	5.128919	CAGTCCAGATTAAGAATGAAGGGG	58.871	45.833	0.00	0.00	29.81	4.79
3980	5428	1.434188	TGCCTTCAAACCTCTGAGGA	58.566	50.000	29.71	4.61	37.67	3.71
4193	5641	2.042831	GGAAGCAGATGCCTTGCGT	61.043	57.895	0.14	0.00	43.38	5.24
4754	6208	6.317312	TGGTGAGTCTACTTTAGTAAGGGAA	58.683	40.000	0.00	0.00	35.61	3.97
4800	6254	6.464222	CAATCCTTTGTAGTACCTGTGAAGA	58.536	40.000	0.00	0.00	0.00	2.87
5783	7242	6.998074	AGAGTTGTGACCAAAGAATGACATTA	59.002	34.615	0.00	0.00	30.94	1.90
5922	7381	7.408910	TGTGCACAAACATTTCTATGATATCG	58.591	34.615	19.28	0.00	35.65	2.92
6079	7584	9.217278	TGAACTATGCAATGCACAATTTTATTT	57.783	25.926	11.23	0.00	43.04	1.40
6080	7585	8.774890	TGAACTATGCAATGCACAATTTTATT	57.225	26.923	11.23	0.00	43.04	1.40
6081	7586	8.774890	TTGAACTATGCAATGCACAATTTTAT	57.225	26.923	11.23	0.00	43.04	1.40
6082	7587	8.494347	GTTTGAACTATGCAATGCACAATTTTA	58.506	29.630	11.23	0.00	43.04	1.52
6087	7592	5.199024	AGTTTGAACTATGCAATGCACAA	57.801	34.783	11.23	7.12	43.04	3.33
6183	7692	8.685838	TTGCAGGTATACTTTAGTTGTTTCTT	57.314	30.769	2.25	0.00	0.00	2.52
6267	7776	8.829612	TGACACAATGCTGATGTACTATATTTG	58.170	33.333	0.00	0.00	0.00	2.32
6341	7850	4.678287	GTGAGACATGTGCAGTTTGATTTG	59.322	41.667	1.15	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.