AutoCloner

Multiple sequence alignment - TraesCS2B01G359200

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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	TraesCS2B01G359200	chr2B	100.000	3070	0	0	1	3070	512358905	512355836	0.000000e+00	5670.0
1	TraesCS2B01G359200	chr2B	94.336	2260	85	29	1	2233	504769126	504771369	0.000000e+00	3424.0
2	TraesCS2B01G359200	chr2B	95.630	801	33	2	2272	3070	504771979	504772779	0.000000e+00	1284.0
3	TraesCS2B01G359200	chr2B	84.035	1021	96	17	33	1030	512365222	512364246	0.000000e+00	920.0
4	TraesCS2B01G359200	chr2B	97.297	37	1	0	2238	2274	504771394	504771430	2.560000e-06	63.9
5	TraesCS2B01G359200	chr2D	88.070	2347	161	38	280	2555	427909006	427911304	0.000000e+00	2673.0
6	TraesCS2B01G359200	chr2D	88.146	2303	138	47	1	2237	427943725	427945958	0.000000e+00	2615.0
7	TraesCS2B01G359200	chr2D	88.969	1804	104	37	1	1771	427924497	427926238	0.000000e+00	2141.0
8	TraesCS2B01G359200	chr2D	86.929	1928	138	41	1	1876	427783600	427785465	0.000000e+00	2060.0
9	TraesCS2B01G359200	chr2D	87.807	1386	103	20	1	1358	427905173	427906520	0.000000e+00	1563.0
10	TraesCS2B01G359200	chr2D	86.610	829	64	20	1766	2555	427927958	427928778	0.000000e+00	872.0
11	TraesCS2B01G359200	chr2D	83.221	888	89	27	847	1704	427897825	427898682	0.000000e+00	760.0
12	TraesCS2B01G359200	chr2D	82.274	897	86	30	848	1702	427932430	427933295	0.000000e+00	708.0
13	TraesCS2B01G359200	chr2D	82.346	878	93	36	848	1704	427753232	427754068	0.000000e+00	706.0
14	TraesCS2B01G359200	chr2D	81.494	897	81	37	848	1704	427914954	427915805	0.000000e+00	658.0
15	TraesCS2B01G359200	chr2D	90.254	472	33	7	2254	2723	427949053	427949513	3.390000e-169	604.0
16	TraesCS2B01G359200	chr2D	93.985	133	8	0	2931	3063	427911655	427911787	5.190000e-48	202.0
17	TraesCS2B01G359200	chr2D	96.639	119	4	0	2812	2930	322922011	322921893	6.710000e-47	198.0
18	TraesCS2B01G359200	chr2D	85.366	205	14	6	2306	2510	427785622	427785810	6.710000e-47	198.0
19	TraesCS2B01G359200	chr2D	93.233	133	9	0	2931	3063	427929129	427929261	2.410000e-46	196.0
20	TraesCS2B01G359200	chr2D	75.769	260	37	13	241	476	427931768	427932025	1.160000e-19	108.0
21	TraesCS2B01G359200	chr2D	96.078	51	2	0	3013	3063	427949553	427949603	1.960000e-12	84.2
22	TraesCS2B01G359200	chr2A	86.182	2475	202	51	1	2408	559779473	559777072	0.000000e+00	2547.0
23	TraesCS2B01G359200	chr2A	87.056	1491	124	23	1	1459	559837696	559836243	0.000000e+00	1620.0
24	TraesCS2B01G359200	chr2A	88.586	1139	83	13	1455	2555	559834642	559833513	0.000000e+00	1339.0
25	TraesCS2B01G359200	chr2A	86.584	1051	76	25	1499	2510	559704427	559703403	0.000000e+00	1099.0
26	TraesCS2B01G359200	chr2A	87.388	896	81	14	1	870	559742944	559742055	0.000000e+00	1000.0
27	TraesCS2B01G359200	chr2A	90.760	671	41	10	848	1505	559741263	559740601	0.000000e+00	876.0
28	TraesCS2B01G359200	chr2A	81.541	753	74	17	1	729	559741973	559741262	7.430000e-156	560.0
29	TraesCS2B01G359200	chr2A	89.209	278	18	6	2360	2636	559671255	559670989	1.360000e-88	337.0
30	TraesCS2B01G359200	chr2A	93.985	133	8	0	2931	3063	559670923	559670791	5.190000e-48	202.0
31	TraesCS2B01G359200	chr2A	91.367	139	12	0	2931	3069	559776460	559776322	1.120000e-44	191.0
32	TraesCS2B01G359200	chr2A	91.367	139	12	0	2931	3069	559833325	559833187	1.120000e-44	191.0
33	TraesCS2B01G359200	chr2A	87.234	94	5	4	2653	2741	559833417	559833326	1.950000e-17	100.0
34	TraesCS2B01G359200	chr5A	98.291	117	2	0	2812	2928	647032007	647032123	4.010000e-49	206.0
35	TraesCS2B01G359200	chrUn	97.479	119	3	0	2812	2930	296251392	296251274	1.440000e-48	204.0
36	TraesCS2B01G359200	chrUn	94.366	71	4	0	2743	2813	43671916	43671986	3.240000e-20	110.0
37	TraesCS2B01G359200	chrUn	94.366	71	4	0	2743	2813	388831547	388831617	3.240000e-20	110.0
38	TraesCS2B01G359200	chr6D	97.479	119	3	0	2812	2930	57923582	57923700	1.440000e-48	204.0
39	TraesCS2B01G359200	chr6D	94.366	71	4	0	2743	2813	173308567	173308497	3.240000e-20	110.0
40	TraesCS2B01G359200	chr6D	94.366	71	4	0	2743	2813	389246878	389246948	3.240000e-20	110.0
41	TraesCS2B01G359200	chr4D	97.479	119	3	0	2812	2930	123443118	123443000	1.440000e-48	204.0
42	TraesCS2B01G359200	chr7A	77.682	233	24	17	1882	2088	24375313	24375543	1.930000e-22	117.0
43	TraesCS2B01G359200	chr7A	77.682	233	24	17	1882	2088	24394283	24394513	1.930000e-22	117.0
44	TraesCS2B01G359200	chr5D	95.775	71	3	0	2743	2813	523017977	523018047	6.960000e-22	115.0
45	TraesCS2B01G359200	chr5D	94.366	71	4	0	2743	2813	503244216	503244146	3.240000e-20	110.0
46	TraesCS2B01G359200	chr5D	79.268	164	23	8	1946	2099	536034701	536034539	1.510000e-18	104.0
47	TraesCS2B01G359200	chr4A	95.775	71	3	0	2743	2813	583869968	583870038	6.960000e-22	115.0
48	TraesCS2B01G359200	chr1D	95.775	71	3	0	2743	2813	254383077	254383147	6.960000e-22	115.0
49	TraesCS2B01G359200	chr5B	79.630	162	21	9	1946	2097	508363961	508363802	4.190000e-19	106.0
50	TraesCS2B01G359200	chr3D	78.261	184	23	12	1928	2096	467328942	467328761	5.420000e-18	102.0

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	TraesCS2B01G359200	chr2B	512355836	512358905	3069	True	5670.000000	5670	100.000000	1	3070	1	chr2B.!!$R1	3069
1	TraesCS2B01G359200	chr2B	504769126	504772779	3653	False	1590.633333	3424	95.754333	1	3070	3	chr2B.!!$F1	3069
2	TraesCS2B01G359200	chr2B	512364246	512365222	976	True	920.000000	920	84.035000	33	1030	1	chr2B.!!$R2	997
3	TraesCS2B01G359200	chr2D	427905173	427915805	10632	False	1274.000000	2673	87.839000	1	3063	4	chr2D.!!$F4	3062
4	TraesCS2B01G359200	chr2D	427783600	427785810	2210	False	1129.000000	2060	86.147500	1	2510	2	chr2D.!!$F3	2509
5	TraesCS2B01G359200	chr2D	427943725	427949603	5878	False	1101.066667	2615	91.492667	1	3063	3	chr2D.!!$F6	3062
6	TraesCS2B01G359200	chr2D	427924497	427933295	8798	False	805.000000	2141	85.371000	1	3063	5	chr2D.!!$F5	3062
7	TraesCS2B01G359200	chr2D	427897825	427898682	857	False	760.000000	760	83.221000	847	1704	1	chr2D.!!$F2	857
8	TraesCS2B01G359200	chr2D	427753232	427754068	836	False	706.000000	706	82.346000	848	1704	1	chr2D.!!$F1	856
9	TraesCS2B01G359200	chr2A	559776322	559779473	3151	True	1369.000000	2547	88.774500	1	3069	2	chr2A.!!$R4	3068
10	TraesCS2B01G359200	chr2A	559703403	559704427	1024	True	1099.000000	1099	86.584000	1499	2510	1	chr2A.!!$R1	1011
11	TraesCS2B01G359200	chr2A	559833187	559837696	4509	True	812.500000	1620	88.560750	1	3069	4	chr2A.!!$R5	3068
12	TraesCS2B01G359200	chr2A	559740601	559742944	2343	True	812.000000	1000	86.563000	1	1505	3	chr2A.!!$R3	1504

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
833	4457	0.602905	AGACCGAAAAAGGCCACTCG	60.603	55.0	5.01	7.18	33.69	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2770	13907	0.940047	GCTAGTAATCGCCGGTCAGC	60.94	60.0	1.9	0.0	0.0	4.26	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
30	31	2.372172	ACCCTGTTCCTACCAAAGACAG	59.628	50.000	0.00	0.00	37.92	3.51
75	76	0.977108	ACCCATGCGGATTTGGCAAT	60.977	50.000	0.00	0.00	44.66	3.56
83	84	1.821753	CGGATTTGGCAATAACCCACA	59.178	47.619	0.00	0.00	30.65	4.17
121	122	2.356135	CTTATGGGTTGTTGCTACGCT	58.644	47.619	0.00	0.00	0.00	5.07
184	187	9.936759	CCTCTCTCAATTATCTAAATTAGGACC	57.063	37.037	0.00	0.00	0.00	4.46
204	207	0.606944	TAGGGAATGTTGCGGCGTTT	60.607	50.000	9.37	0.00	0.00	3.60
231	234	2.969262	CCTAGATCACCCTCCCTCTTTC	59.031	54.545	0.00	0.00	0.00	2.62
288	291	6.993902	TCATTGCTTTGTCAGATAGATGCATA	59.006	34.615	0.00	0.00	0.00	3.14
360	388	2.167693	TGTATGGTCTCGTGGAATGTCC	59.832	50.000	0.00	0.00	36.96	4.02
432	460	1.610363	TGCTTGGTTATTGTTCGGCA	58.390	45.000	0.00	0.00	0.00	5.69
631	4253	5.371115	TGCTATGTCAAAAGCAACCTTAC	57.629	39.130	10.03	0.00	45.36	2.34
632	4254	5.070001	TGCTATGTCAAAAGCAACCTTACT	58.930	37.500	10.03	0.00	45.36	2.24
671	4294	1.933247	CGTGCCTCTCTCAATTCTCC	58.067	55.000	0.00	0.00	0.00	3.71
813	4437	2.124236	AAACAAACCGGCGGGACA	60.124	55.556	31.78	0.00	36.97	4.02
830	4454	1.001706	GACAAGACCGAAAAAGGCCAC	60.002	52.381	5.01	0.00	33.69	5.01
833	4457	0.602905	AGACCGAAAAAGGCCACTCG	60.603	55.000	5.01	7.18	33.69	4.18
899	4525	6.146021	GCCATCAAATTTTGTTCGAATTGAGT	59.854	34.615	13.29	2.60	0.00	3.41
971	4605	3.171348	GGAACCTTCCCTGCCACT	58.829	61.111	0.00	0.00	41.62	4.00
972	4606	1.303643	GGAACCTTCCCTGCCACTG	60.304	63.158	0.00	0.00	41.62	3.66
973	4607	1.973812	GAACCTTCCCTGCCACTGC	60.974	63.158	0.00	0.00	38.26	4.40
974	4608	3.513750	AACCTTCCCTGCCACTGCC	62.514	63.158	0.00	0.00	36.33	4.85
975	4609	3.970410	CCTTCCCTGCCACTGCCA	61.970	66.667	0.00	0.00	36.33	4.92
1078	4723	3.019564	CTCTGATCCACCCAACATTTCC	58.980	50.000	0.00	0.00	0.00	3.13
1122	4771	3.954904	CTCCTAGCTAGGCTACAACTTCA	59.045	47.826	31.76	11.94	43.31	3.02
1298	4950	4.785512	CACGCGCGCTCTCCTTCT	62.786	66.667	32.58	3.21	0.00	2.85
1853	8859	5.705441	TGTGTCTCTTGTGTTTTCAGTTCTT	59.295	36.000	0.00	0.00	0.00	2.52
1922	8928	5.440685	GTCGATCACTGTTTTCATCGTTTT	58.559	37.500	0.00	0.00	32.57	2.43
2088	9121	8.017418	TGAATCAATAAAACTCACCCTTTGTT	57.983	30.769	0.00	0.00	0.00	2.83
2089	9123	8.141268	TGAATCAATAAAACTCACCCTTTGTTC	58.859	33.333	0.00	0.00	0.00	3.18
2142	9176	6.212388	ACATCTATCAGAACAGTTCAGAGGTT	59.788	38.462	15.85	1.27	0.00	3.50
2236	9296	3.557577	TCATGTTGCAGAAATTCGGTG	57.442	42.857	0.00	0.00	0.00	4.94
2285	12955	2.897969	GACAGAACTGTGAGGGTAAGGA	59.102	50.000	12.29	0.00	45.05	3.36
2591	13593	6.982141	AGCACATTCACCTTGCATAATTAATG	59.018	34.615	8.99	8.99	38.81	1.90
2601	13726	6.262944	CCTTGCATAATTAATGTACTGCCAGA	59.737	38.462	0.00	0.00	37.93	3.86
2629	13754	8.915654	CAAAATTTCAGAAAACTGCCAGTATAC	58.084	33.333	0.00	0.00	0.00	1.47
2645	13770	6.663953	GCCAGTATACTTCAGGAGGTATATCA	59.336	42.308	11.07	0.00	37.89	2.15
2655	13780	5.839063	TCAGGAGGTATATCATTCGACCTTT	59.161	40.000	0.00	0.00	42.47	3.11
2741	13878	7.307811	GGTCACAGAAAAGTTGTAATCACCTAC	60.308	40.741	0.00	0.00	0.00	3.18
2748	13885	0.683828	TGTAATCACCTACGGCCCGA	60.684	55.000	11.71	0.00	0.00	5.14
2749	13886	0.031721	GTAATCACCTACGGCCCGAG	59.968	60.000	11.71	2.47	0.00	4.63
2770	13907	4.043168	GGATTCACCGCCGTATGG	57.957	61.111	0.00	0.00	38.77	2.74
2794	13931	2.475487	GACCGGCGATTACTAGCAATTC	59.525	50.000	9.30	0.00	34.54	2.17
2795	13932	2.159014	ACCGGCGATTACTAGCAATTCA	60.159	45.455	9.30	0.00	34.54	2.57
2833	13970	7.420800	GCGAGAAACAATCTATCAATTTCCAT	58.579	34.615	0.00	0.00	38.96	3.41
2885	14022	9.826574	AGAAAACATTGACTTTGTAGTGTAGTA	57.173	29.630	0.00	0.00	33.84	1.82
2917	14055	3.152400	ACGAGGCCACCGATACCC	61.152	66.667	21.82	0.00	0.00	3.69
2941	14079	3.496331	TGTGGATAGGATCATAGTGCGA	58.504	45.455	0.00	0.00	0.00	5.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	4.806247	CGGACAGTTGATGAAGAGGTTATC	59.194	45.833	0.00	0.00	0.00	1.75
75	76	2.039348	GGAAGCAAGTAGGTGTGGGTTA	59.961	50.000	0.00	0.00	0.00	2.85
83	84	2.967946	GCCCCGGAAGCAAGTAGGT	61.968	63.158	0.73	0.00	0.00	3.08
184	187	1.024579	AACGCCGCAACATTCCCTAG	61.025	55.000	0.00	0.00	0.00	3.02
204	207	1.693627	GAGGGTGATCTAGGCTTCGA	58.306	55.000	0.00	0.00	0.00	3.71
231	234	7.166142	GCGCTCTAAATGTTACTTCTACTAGTG	59.834	40.741	5.39	0.00	0.00	2.74
432	460	8.755696	ACATATGTGCGTTGATTTAATTTGTT	57.244	26.923	7.78	0.00	0.00	2.83
609	4230	5.070001	AGTAAGGTTGCTTTTGACATAGCA	58.930	37.500	8.29	8.29	45.06	3.49
611	4232	8.324163	AGTTAGTAAGGTTGCTTTTGACATAG	57.676	34.615	0.00	0.00	0.00	2.23
671	4294	4.846779	TTCTTGAGTCCCAAAATTTCCG	57.153	40.909	0.00	0.00	33.76	4.30
804	4428	3.869473	TTTCGGTCTTGTCCCGCCG	62.869	63.158	0.00	0.00	45.09	6.46
806	4430	0.237498	CTTTTTCGGTCTTGTCCCGC	59.763	55.000	0.00	0.00	45.09	6.13
813	4437	1.605753	GAGTGGCCTTTTTCGGTCTT	58.394	50.000	3.32	0.00	0.00	3.01
830	4454	2.035961	TCTGAAAACAGGTCAGACCGAG	59.964	50.000	14.32	13.10	45.11	4.63
899	4525	1.062258	GTCAAATTCGGTCGCGTGTA	58.938	50.000	5.77	0.00	0.00	2.90
972	4606	2.497770	GGCATCATGGCAGTTGGC	59.502	61.111	6.27	0.00	43.14	4.52
1078	4723	2.642254	TAGGTTCTGTGGGCGACGG	61.642	63.158	1.52	1.52	0.00	4.79
1298	4950	0.765135	TCCCTCCTGTGGTTTTCCGA	60.765	55.000	0.00	0.00	44.36	4.55
1654	6920	2.505777	CTGGAGCTGCTGTCGACG	60.506	66.667	7.01	7.05	0.00	5.12
1853	8859	1.405463	ACTAGATCGAGCGCACAATCA	59.595	47.619	11.47	0.00	0.00	2.57
1922	8928	2.910688	AGCGACAGAAGAAAACTCCA	57.089	45.000	0.00	0.00	0.00	3.86
2108	9142	3.565764	TCTGATAGATGTTGCAAGGGG	57.434	47.619	0.00	0.00	0.00	4.79
2274	12392	4.706616	AGTTTCCCTTATCCTTACCCTCA	58.293	43.478	0.00	0.00	0.00	3.86
2285	12955	7.357471	AGCATTTATGGAGAAGTTTCCCTTAT	58.643	34.615	0.00	0.00	36.35	1.73
2410	13084	7.043192	GCAATGGCTAGCAATATTTTGTACTTG	60.043	37.037	18.24	3.78	36.96	3.16
2591	13593	6.072112	TCTGAAATTTTGTTCTGGCAGTAC	57.928	37.500	16.37	16.37	0.00	2.73
2629	13754	5.478679	AGGTCGAATGATATACCTCCTGAAG	59.521	44.000	0.00	0.00	37.87	3.02
2707	13836	4.724279	ACTTTTCTGTGACCAACCCTAT	57.276	40.909	0.00	0.00	0.00	2.57
2770	13907	0.940047	GCTAGTAATCGCCGGTCAGC	60.940	60.000	1.90	0.00	0.00	4.26
2801	13938	3.266510	AGATTGTTTCTCGCCTGCATA	57.733	42.857	0.00	0.00	0.00	3.14
2833	13970	9.325248	TCATCTTCCATATGATAGGTGTGATTA	57.675	33.333	3.65	0.00	0.00	1.75
2885	14022	4.130118	GGCCTCGTGATCACTTTATGAAT	58.870	43.478	22.95	0.00	41.93	2.57
2917	14055	5.358160	TCGCACTATGATCCTATCCACATAG	59.642	44.000	0.00	0.00	44.14	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.