AutoCloner

Multiple sequence alignment - TraesCS3B01G232400

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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	TraesCS3B01G232400	chr3B	100.000	2492	0	0	1	2492	354956098	354953607	0.000000e+00	4602.0
1	TraesCS3B01G232400	chr3B	94.751	381	19	1	296	676	354954406	354954027	2.130000e-165	592.0
2	TraesCS3B01G232400	chr3B	94.751	381	19	1	1693	2072	354955803	354955423	2.130000e-165	592.0
3	TraesCS3B01G232400	chr3B	95.638	298	13	0	1	298	354972277	354971980	1.730000e-131	479.0
4	TraesCS3B01G232400	chr3B	94.966	298	15	0	1	298	554597138	554597435	3.750000e-128	468.0
5	TraesCS3B01G232400	chr3B	81.818	264	43	5	2189	2450	193145257	193145517	1.500000e-52	217.0
6	TraesCS3B01G232400	chr1B	85.313	1103	120	24	635	1717	616025798	616024718	0.000000e+00	1101.0
7	TraesCS3B01G232400	chr1B	84.972	1058	116	29	681	1706	95442376	95443422	0.000000e+00	1033.0
8	TraesCS3B01G232400	chr1B	87.500	512	53	9	1121	1630	21840380	21840882	4.620000e-162	580.0
9	TraesCS3B01G232400	chr1B	94.295	298	17	0	1	298	494913923	494914220	8.120000e-125	457.0
10	TraesCS3B01G232400	chr1B	92.617	298	22	0	1	298	326094408	326094111	1.770000e-116	429.0
11	TraesCS3B01G232400	chr1B	92.308	299	23	0	1	299	326086047	326085749	2.290000e-115	425.0
12	TraesCS3B01G232400	chr7B	84.531	1099	122	31	657	1722	730913719	730914802	0.000000e+00	1044.0
13	TraesCS3B01G232400	chr7B	85.463	853	85	27	867	1685	389136341	389137188	0.000000e+00	852.0
14	TraesCS3B01G232400	chr7B	87.885	520	51	10	1114	1630	671196299	671196809	3.550000e-168	601.0
15	TraesCS3B01G232400	chr7B	87.595	524	55	8	1114	1635	23066021	23065506	1.280000e-167	599.0
16	TraesCS3B01G232400	chr7B	95.000	300	15	0	1	300	477705603	477705304	2.900000e-129	472.0
17	TraesCS3B01G232400	chr7B	94.631	298	16	0	1	298	477714544	477714841	1.750000e-126	462.0
18	TraesCS3B01G232400	chr5A	84.481	973	115	28	668	1630	701869494	701870440	0.000000e+00	928.0
19	TraesCS3B01G232400	chr5A	86.949	590	70	6	678	1265	63939461	63938877	0.000000e+00	656.0
20	TraesCS3B01G232400	chr5A	86.387	191	23	3	2275	2462	218320256	218320066	3.250000e-49	206.0
21	TraesCS3B01G232400	chr7A	84.235	850	107	20	757	1603	625488955	625489780	0.000000e+00	802.0
22	TraesCS3B01G232400	chr7A	88.007	567	65	3	719	1284	13545987	13545423	0.000000e+00	667.0
23	TraesCS3B01G232400	chr7A	86.242	298	41	0	1	298	184675506	184675209	8.600000e-85	324.0
24	TraesCS3B01G232400	chr5D	90.706	581	36	9	699	1265	40684428	40683852	0.000000e+00	758.0
25	TraesCS3B01G232400	chr5B	85.950	726	75	15	300	1016	44038186	44038893	0.000000e+00	750.0
26	TraesCS3B01G232400	chr5B	87.458	598	66	7	659	1251	210239089	210239682	0.000000e+00	680.0
27	TraesCS3B01G232400	chr5B	87.091	519	56	9	1114	1630	682094294	682094803	5.980000e-161	577.0
28	TraesCS3B01G232400	chr5B	86.286	525	61	9	1114	1636	682132153	682132668	6.020000e-156	560.0
29	TraesCS3B01G232400	chr5B	87.244	439	40	5	1633	2066	44038125	44038552	1.040000e-133	486.0
30	TraesCS3B01G232400	chr5B	100.000	28	0	0	2031	2058	439964511	439964538	4.000000e-03	52.8
31	TraesCS3B01G232400	chr2D	89.273	578	61	1	681	1258	252170428	252171004	0.000000e+00	723.0
32	TraesCS3B01G232400	chr2D	88.983	590	58	6	678	1265	573454933	573454349	0.000000e+00	723.0
33	TraesCS3B01G232400	chr4A	88.468	581	61	5	680	1258	674928797	674928221	0.000000e+00	697.0
34	TraesCS3B01G232400	chr4A	87.500	608	64	7	1471	2070	699043777	699044380	0.000000e+00	691.0
35	TraesCS3B01G232400	chr4A	87.583	604	61	8	1468	2066	736963470	736964064	0.000000e+00	688.0
36	TraesCS3B01G232400	chr4A	93.617	376	18	3	299	670	736963691	736964064	7.790000e-155	556.0
37	TraesCS3B01G232400	chr4A	91.316	380	28	2	299	674	699044002	699044380	4.750000e-142	514.0
38	TraesCS3B01G232400	chr4A	94.845	194	10	0	1873	2066	736990808	736991001	1.120000e-78	303.0
39	TraesCS3B01G232400	chr4A	94.359	195	10	1	476	670	736990808	736991001	5.210000e-77	298.0
40	TraesCS3B01G232400	chr4A	86.935	199	23	3	2253	2450	411209185	411208989	1.160000e-53	220.0
41	TraesCS3B01G232400	chr6D	87.648	591	64	7	678	1265	18304611	18305195	0.000000e+00	678.0
42	TraesCS3B01G232400	chr6D	80.556	324	50	11	2074	2390	254288262	254287945	1.150000e-58	237.0
43	TraesCS3B01G232400	chr6D	86.957	207	26	1	2245	2450	221440137	221440343	5.360000e-57	231.0
44	TraesCS3B01G232400	chrUn	87.252	604	63	8	1468	2066	335842644	335843238	0.000000e+00	676.0
45	TraesCS3B01G232400	chrUn	93.085	376	20	3	299	670	335842865	335843238	1.690000e-151	545.0
46	TraesCS3B01G232400	chrUn	84.069	408	51	8	1468	1870	382530666	382531064	5.030000e-102	381.0
47	TraesCS3B01G232400	chrUn	94.416	197	11	0	1873	2069	327028651	327028455	1.120000e-78	303.0
48	TraesCS3B01G232400	chrUn	93.939	198	11	1	476	673	327028651	327028455	5.210000e-77	298.0
49	TraesCS3B01G232400	chrUn	92.737	179	8	2	299	473	382530887	382531064	1.140000e-63	254.0
50	TraesCS3B01G232400	chr1D	85.714	301	37	6	1	298	77198516	77198219	1.860000e-81	313.0
51	TraesCS3B01G232400	chr1D	82.488	217	35	3	2235	2450	162349472	162349686	1.180000e-43	187.0
52	TraesCS3B01G232400	chr6B	84.588	279	39	4	2173	2450	367144771	367145046	8.780000e-70	274.0
53	TraesCS3B01G232400	chr2A	81.387	274	45	6	2180	2450	402154168	402153898	4.170000e-53	219.0
54	TraesCS3B01G232400	chr4D	83.621	232	34	3	2236	2466	204948300	204948528	5.400000e-52	215.0
55	TraesCS3B01G232400	chr4D	85.859	198	27	1	2254	2450	288242656	288242459	2.510000e-50	209.0
56	TraesCS3B01G232400	chr2B	83.495	103	7	9	1640	1737	638150455	638150358	1.230000e-13	87.9

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	TraesCS3B01G232400	chr3B	354953607	354956098	2491	True	1928.666667	4602	96.500667	1	2492	3	chr3B.!!$R2	2491
1	TraesCS3B01G232400	chr1B	616024718	616025798	1080	True	1101.000000	1101	85.313000	635	1717	1	chr1B.!!$R3	1082
2	TraesCS3B01G232400	chr1B	95442376	95443422	1046	False	1033.000000	1033	84.972000	681	1706	1	chr1B.!!$F2	1025
3	TraesCS3B01G232400	chr1B	21840380	21840882	502	False	580.000000	580	87.500000	1121	1630	1	chr1B.!!$F1	509
4	TraesCS3B01G232400	chr7B	730913719	730914802	1083	False	1044.000000	1044	84.531000	657	1722	1	chr7B.!!$F4	1065
5	TraesCS3B01G232400	chr7B	389136341	389137188	847	False	852.000000	852	85.463000	867	1685	1	chr7B.!!$F1	818
6	TraesCS3B01G232400	chr7B	671196299	671196809	510	False	601.000000	601	87.885000	1114	1630	1	chr7B.!!$F3	516
7	TraesCS3B01G232400	chr7B	23065506	23066021	515	True	599.000000	599	87.595000	1114	1635	1	chr7B.!!$R1	521
8	TraesCS3B01G232400	chr5A	701869494	701870440	946	False	928.000000	928	84.481000	668	1630	1	chr5A.!!$F1	962
9	TraesCS3B01G232400	chr5A	63938877	63939461	584	True	656.000000	656	86.949000	678	1265	1	chr5A.!!$R1	587
10	TraesCS3B01G232400	chr7A	625488955	625489780	825	False	802.000000	802	84.235000	757	1603	1	chr7A.!!$F1	846
11	TraesCS3B01G232400	chr7A	13545423	13545987	564	True	667.000000	667	88.007000	719	1284	1	chr7A.!!$R1	565
12	TraesCS3B01G232400	chr5D	40683852	40684428	576	True	758.000000	758	90.706000	699	1265	1	chr5D.!!$R1	566
13	TraesCS3B01G232400	chr5B	210239089	210239682	593	False	680.000000	680	87.458000	659	1251	1	chr5B.!!$F1	592
14	TraesCS3B01G232400	chr5B	44038125	44038893	768	False	618.000000	750	86.597000	300	2066	2	chr5B.!!$F5	1766
15	TraesCS3B01G232400	chr5B	682094294	682094803	509	False	577.000000	577	87.091000	1114	1630	1	chr5B.!!$F3	516
16	TraesCS3B01G232400	chr5B	682132153	682132668	515	False	560.000000	560	86.286000	1114	1636	1	chr5B.!!$F4	522
17	TraesCS3B01G232400	chr2D	252170428	252171004	576	False	723.000000	723	89.273000	681	1258	1	chr2D.!!$F1	577
18	TraesCS3B01G232400	chr2D	573454349	573454933	584	True	723.000000	723	88.983000	678	1265	1	chr2D.!!$R1	587
19	TraesCS3B01G232400	chr4A	674928221	674928797	576	True	697.000000	697	88.468000	680	1258	1	chr4A.!!$R2	578
20	TraesCS3B01G232400	chr4A	736963470	736964064	594	False	622.000000	688	90.600000	299	2066	2	chr4A.!!$F2	1767
21	TraesCS3B01G232400	chr4A	699043777	699044380	603	False	602.500000	691	89.408000	299	2070	2	chr4A.!!$F1	1771
22	TraesCS3B01G232400	chr6D	18304611	18305195	584	False	678.000000	678	87.648000	678	1265	1	chr6D.!!$F1	587
23	TraesCS3B01G232400	chrUn	335842644	335843238	594	False	610.500000	676	90.168500	299	2066	2	chrUn.!!$F1	1767

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
577	583	0.03213	ACTCTGCGTCAACACACGAT	59.968	50.0	0.0	0.0	42.69	3.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2415	2517	0.037232	CAAGTCCACCGGAGTTCCTC	60.037	60.0	9.46	0.0	42.79	3.71	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
63	64	8.916628	AATAGTTTTACCTACCGTTTTAACCA	57.083	30.769	0.00	0.00	0.00	3.67
64	65	6.618287	AGTTTTACCTACCGTTTTAACCAC	57.382	37.500	0.00	0.00	0.00	4.16
65	66	6.356556	AGTTTTACCTACCGTTTTAACCACT	58.643	36.000	0.00	0.00	0.00	4.00
66	67	6.828273	AGTTTTACCTACCGTTTTAACCACTT	59.172	34.615	0.00	0.00	0.00	3.16
67	68	7.990314	AGTTTTACCTACCGTTTTAACCACTTA	59.010	33.333	0.00	0.00	0.00	2.24
68	69	8.616942	GTTTTACCTACCGTTTTAACCACTTAA	58.383	33.333	0.00	0.00	0.00	1.85
69	70	7.961325	TTACCTACCGTTTTAACCACTTAAG	57.039	36.000	0.00	0.00	0.00	1.85
70	71	5.928976	ACCTACCGTTTTAACCACTTAAGT	58.071	37.500	1.12	1.12	0.00	2.24
71	72	5.759763	ACCTACCGTTTTAACCACTTAAGTG	59.240	40.000	25.79	25.79	45.23	3.16
72	73	4.556942	ACCGTTTTAACCACTTAAGTGC	57.443	40.909	27.05	12.42	44.34	4.40
73	74	3.946558	ACCGTTTTAACCACTTAAGTGCA	59.053	39.130	27.05	13.12	44.34	4.57
74	75	4.581409	ACCGTTTTAACCACTTAAGTGCAT	59.419	37.500	27.05	19.68	44.34	3.96
75	76	4.915085	CCGTTTTAACCACTTAAGTGCATG	59.085	41.667	27.05	17.20	44.34	4.06
76	77	5.506649	CCGTTTTAACCACTTAAGTGCATGT	60.507	40.000	27.05	17.80	44.34	3.21
77	78	6.293516	CCGTTTTAACCACTTAAGTGCATGTA	60.294	38.462	27.05	13.78	44.34	2.29
78	79	7.133513	CGTTTTAACCACTTAAGTGCATGTAA	58.866	34.615	27.05	17.86	44.34	2.41
79	80	7.112426	CGTTTTAACCACTTAAGTGCATGTAAC	59.888	37.037	27.05	22.67	44.34	2.50
80	81	6.563222	TTAACCACTTAAGTGCATGTAACC	57.437	37.500	27.05	0.00	44.34	2.85
81	82	4.093472	ACCACTTAAGTGCATGTAACCA	57.907	40.909	27.05	0.00	44.34	3.67
82	83	4.662278	ACCACTTAAGTGCATGTAACCAT	58.338	39.130	27.05	2.24	44.34	3.55
83	84	5.076873	ACCACTTAAGTGCATGTAACCATT	58.923	37.500	27.05	0.00	44.34	3.16
84	85	5.538433	ACCACTTAAGTGCATGTAACCATTT	59.462	36.000	27.05	0.00	44.34	2.32
85	86	6.041523	ACCACTTAAGTGCATGTAACCATTTT	59.958	34.615	27.05	0.00	44.34	1.82
86	87	7.231722	ACCACTTAAGTGCATGTAACCATTTTA	59.768	33.333	27.05	0.00	44.34	1.52
87	88	8.250332	CCACTTAAGTGCATGTAACCATTTTAT	58.750	33.333	27.05	0.00	44.34	1.40

Showing 1 to 25 of 373 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	8.783093	GTGGTTAAAACGGTAGGTAAAACTATT	58.217	33.333	0.00	0.00	0.00	1.73
39	40	8.156820	AGTGGTTAAAACGGTAGGTAAAACTAT	58.843	33.333	0.00	0.00	0.00	2.12
41	42	6.356556	AGTGGTTAAAACGGTAGGTAAAACT	58.643	36.000	0.00	0.00	0.00	2.66
42	43	6.618287	AGTGGTTAAAACGGTAGGTAAAAC	57.382	37.500	0.00	0.00	0.00	2.43
43	44	8.738645	TTAAGTGGTTAAAACGGTAGGTAAAA	57.261	30.769	0.00	0.00	0.00	1.52
44	45	7.990314	ACTTAAGTGGTTAAAACGGTAGGTAAA	59.010	33.333	7.48	0.00	0.00	2.01
45	46	7.440856	CACTTAAGTGGTTAAAACGGTAGGTAA	59.559	37.037	25.19	0.00	42.10	2.85
46	47	6.928492	CACTTAAGTGGTTAAAACGGTAGGTA	59.072	38.462	25.19	0.00	42.10	3.08
49	50	5.236911	TGCACTTAAGTGGTTAAAACGGTAG	59.763	40.000	31.42	6.60	45.72	3.18
50	51	5.121811	TGCACTTAAGTGGTTAAAACGGTA	58.878	37.500	31.42	3.68	45.72	4.02
53	54	5.516090	ACATGCACTTAAGTGGTTAAAACG	58.484	37.500	31.42	8.35	45.72	3.60
54	55	7.380333	GGTTACATGCACTTAAGTGGTTAAAAC	59.620	37.037	31.42	20.97	45.72	2.43
55	56	7.068348	TGGTTACATGCACTTAAGTGGTTAAAA	59.932	33.333	31.42	13.15	45.72	1.52
57	58	6.062749	TGGTTACATGCACTTAAGTGGTTAA	58.937	36.000	31.42	15.18	45.72	2.01
58	59	5.622180	TGGTTACATGCACTTAAGTGGTTA	58.378	37.500	31.42	15.46	45.72	2.85
60	61	4.093472	TGGTTACATGCACTTAAGTGGT	57.907	40.909	31.42	23.60	45.72	4.16
78	79	9.719355	GGAGAAACCACATTTTTATAAAATGGT	57.281	29.630	21.30	21.30	43.39	3.55
79	80	8.868916	CGGAGAAACCACATTTTTATAAAATGG	58.131	33.333	20.32	20.32	40.84	3.16
80	81	8.379902	GCGGAGAAACCACATTTTTATAAAATG	58.620	33.333	18.40	18.40	41.91	2.32
81	82	7.547722	GGCGGAGAAACCACATTTTTATAAAAT	59.452	33.333	11.33	0.21	38.90	1.82
82	83	6.869388	GGCGGAGAAACCACATTTTTATAAAA	59.131	34.615	6.54	6.54	38.90	1.52
83	84	6.015350	TGGCGGAGAAACCACATTTTTATAAA	60.015	34.615	0.00	0.00	38.90	1.40
84	85	5.477291	TGGCGGAGAAACCACATTTTTATAA	59.523	36.000	0.00	0.00	38.90	0.98
85	86	5.010933	TGGCGGAGAAACCACATTTTTATA	58.989	37.500	0.00	0.00	38.90	0.98
86	87	3.829601	TGGCGGAGAAACCACATTTTTAT	59.170	39.130	0.00	0.00	38.90	1.40

Showing 1 to 25 of 430 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.