AutoCloner

Multiple sequence alignment - TraesCS2A01G200900

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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	TraesCS2A01G200900	chr2A	100.000	3192	0	0	1	3192	173797287	173800478	0.000000e+00	5895.0
1	TraesCS2A01G200900	chr2A	94.286	35	2	0	3154	3188	553638118	553638084	2.000000e-03	54.7
2	TraesCS2A01G200900	chr2D	89.099	2165	146	35	104	2205	174245684	174247821	0.000000e+00	2608.0
3	TraesCS2A01G200900	chr2D	86.858	662	78	6	2204	2857	498515276	498515936	0.000000e+00	732.0
4	TraesCS2A01G200900	chr2D	92.727	55	4	0	51	105	560328355	560328301	2.640000e-11	80.5
5	TraesCS2A01G200900	chr2B	87.987	1257	115	22	119	1348	222122044	222123291	0.000000e+00	1452.0
6	TraesCS2A01G200900	chr2B	91.657	863	34	15	1375	2205	222123289	222124145	0.000000e+00	1160.0
7	TraesCS2A01G200900	chr2B	88.245	604	58	8	2256	2853	617935838	617936434	0.000000e+00	710.0
8	TraesCS2A01G200900	chr2B	84.682	346	44	9	2848	3188	717753825	717754166	1.420000e-88	337.0
9	TraesCS2A01G200900	chr2B	90.604	149	11	3	3018	3166	636079357	636079212	9.030000e-46	195.0
10	TraesCS2A01G200900	chr2B	92.727	55	4	0	51	105	93127328	93127382	2.640000e-11	80.5
11	TraesCS2A01G200900	chr2B	92.727	55	4	0	51	105	140217542	140217596	2.640000e-11	80.5
12	TraesCS2A01G200900	chr3D	88.408	647	64	7	2210	2853	409032359	409031721	0.000000e+00	769.0
13	TraesCS2A01G200900	chr3D	87.823	657	73	4	2201	2854	529125350	529126002	0.000000e+00	763.0
14	TraesCS2A01G200900	chr3D	86.036	666	77	6	2203	2853	61772653	61771989	0.000000e+00	701.0
15	TraesCS2A01G200900	chr7B	86.039	659	81	9	2203	2853	55468059	55468714	0.000000e+00	697.0
16	TraesCS2A01G200900	chr7B	81.867	557	94	7	171	724	748331685	748331133	2.240000e-126	462.0
17	TraesCS2A01G200900	chr7B	94.245	139	7	1	2935	3073	1477240	1477377	8.970000e-51	211.0
18	TraesCS2A01G200900	chr7A	85.022	681	89	11	2168	2839	166247459	166248135	0.000000e+00	680.0
19	TraesCS2A01G200900	chr7A	81.350	563	95	10	180	736	393325166	393325724	1.750000e-122	449.0
20	TraesCS2A01G200900	chr3A	85.915	639	74	12	2224	2853	557972991	557972360	0.000000e+00	667.0
21	TraesCS2A01G200900	chr3A	90.000	140	13	1	3053	3192	669202940	669202802	2.530000e-41	180.0
22	TraesCS2A01G200900	chr6A	84.992	653	81	12	2210	2853	87494892	87494248	0.000000e+00	647.0
23	TraesCS2A01G200900	chr6A	95.000	140	6	1	2934	3073	554386118	554386256	5.360000e-53	219.0
24	TraesCS2A01G200900	chr6A	87.931	174	18	3	3018	3189	311839849	311839677	5.400000e-48	202.0
25	TraesCS2A01G200900	chr6A	94.017	117	6	1	2855	2970	311839971	311839855	3.270000e-40	176.0
26	TraesCS2A01G200900	chr6A	94.118	51	3	0	56	106	70570949	70570999	9.490000e-11	78.7
27	TraesCS2A01G200900	chr7D	82.633	547	92	3	180	724	251355414	251354869	6.190000e-132	481.0
28	TraesCS2A01G200900	chr7D	81.754	570	97	7	171	736	595869669	595869103	1.340000e-128	470.0
29	TraesCS2A01G200900	chr7D	86.186	333	39	7	2848	3177	183856214	183856542	1.410000e-93	353.0
30	TraesCS2A01G200900	chr4D	81.054	607	102	10	124	721	433088620	433089222	3.730000e-129	472.0
31	TraesCS2A01G200900	chr4D	82.098	553	86	9	171	720	67289830	67289288	8.070000e-126	460.0
32	TraesCS2A01G200900	chr4D	83.481	339	38	10	2852	3186	422502233	422501909	1.860000e-77	300.0
33	TraesCS2A01G200900	chr3B	82.601	546	82	9	179	720	4652003	4651467	1.340000e-128	470.0
34	TraesCS2A01G200900	chr6D	81.416	565	91	14	180	736	389599253	389598695	1.750000e-122	449.0
35	TraesCS2A01G200900	chr6D	92.366	131	9	1	3060	3190	149721678	149721549	5.440000e-43	185.0
36	TraesCS2A01G200900	chr1B	80.862	580	104	7	162	736	330838412	330837835	1.750000e-122	449.0
37	TraesCS2A01G200900	chr1B	94.643	56	3	0	51	106	666026947	666027002	1.580000e-13	87.9
38	TraesCS2A01G200900	chr6B	83.680	337	43	7	2854	3189	487215026	487215351	1.110000e-79	307.0
39	TraesCS2A01G200900	chr1D	82.405	341	52	6	2851	3187	200629746	200629410	1.120000e-74	291.0
40	TraesCS2A01G200900	chr5A	81.503	346	40	12	2848	3191	381813915	381814238	2.440000e-66	263.0
41	TraesCS2A01G200900	chr5A	92.366	131	8	1	3062	3190	530995048	530994918	5.440000e-43	185.0
42	TraesCS2A01G200900	chr4B	86.957	207	24	3	2870	3073	571096586	571096792	2.480000e-56	230.0
43	TraesCS2A01G200900	chr5B	96.241	133	5	0	2941	3073	670073821	670073689	5.360000e-53	219.0
44	TraesCS2A01G200900	chr5B	90.968	155	11	3	2920	3073	699386448	699386600	4.170000e-49	206.0
45	TraesCS2A01G200900	chr5B	92.857	56	4	0	51	106	623152959	623152904	7.340000e-12	82.4
46	TraesCS2A01G200900	chr5B	92.857	56	4	0	51	106	626817883	626817828	7.340000e-12	82.4
47	TraesCS2A01G200900	chr5B	92.857	56	4	0	51	106	626825612	626825557	7.340000e-12	82.4
48	TraesCS2A01G200900	chr1A	91.379	58	4	1	51	107	516661625	516661682	9.490000e-11	78.7

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	TraesCS2A01G200900	chr2A	173797287	173800478	3191	False	5895	5895	100.000	1	3192	1	chr2A.!!$F1	3191
1	TraesCS2A01G200900	chr2D	174245684	174247821	2137	False	2608	2608	89.099	104	2205	1	chr2D.!!$F1	2101
2	TraesCS2A01G200900	chr2D	498515276	498515936	660	False	732	732	86.858	2204	2857	1	chr2D.!!$F2	653
3	TraesCS2A01G200900	chr2B	222122044	222124145	2101	False	1306	1452	89.822	119	2205	2	chr2B.!!$F5	2086
4	TraesCS2A01G200900	chr2B	617935838	617936434	596	False	710	710	88.245	2256	2853	1	chr2B.!!$F3	597
5	TraesCS2A01G200900	chr3D	409031721	409032359	638	True	769	769	88.408	2210	2853	1	chr3D.!!$R2	643
6	TraesCS2A01G200900	chr3D	529125350	529126002	652	False	763	763	87.823	2201	2854	1	chr3D.!!$F1	653
7	TraesCS2A01G200900	chr3D	61771989	61772653	664	True	701	701	86.036	2203	2853	1	chr3D.!!$R1	650
8	TraesCS2A01G200900	chr7B	55468059	55468714	655	False	697	697	86.039	2203	2853	1	chr7B.!!$F2	650
9	TraesCS2A01G200900	chr7B	748331133	748331685	552	True	462	462	81.867	171	724	1	chr7B.!!$R1	553
10	TraesCS2A01G200900	chr7A	166247459	166248135	676	False	680	680	85.022	2168	2839	1	chr7A.!!$F1	671
11	TraesCS2A01G200900	chr7A	393325166	393325724	558	False	449	449	81.350	180	736	1	chr7A.!!$F2	556
12	TraesCS2A01G200900	chr3A	557972360	557972991	631	True	667	667	85.915	2224	2853	1	chr3A.!!$R1	629
13	TraesCS2A01G200900	chr6A	87494248	87494892	644	True	647	647	84.992	2210	2853	1	chr6A.!!$R1	643
14	TraesCS2A01G200900	chr7D	251354869	251355414	545	True	481	481	82.633	180	724	1	chr7D.!!$R1	544
15	TraesCS2A01G200900	chr7D	595869103	595869669	566	True	470	470	81.754	171	736	1	chr7D.!!$R2	565
16	TraesCS2A01G200900	chr4D	433088620	433089222	602	False	472	472	81.054	124	721	1	chr4D.!!$F1	597
17	TraesCS2A01G200900	chr4D	67289288	67289830	542	True	460	460	82.098	171	720	1	chr4D.!!$R1	549
18	TraesCS2A01G200900	chr3B	4651467	4652003	536	True	470	470	82.601	179	720	1	chr3B.!!$R1	541
19	TraesCS2A01G200900	chr6D	389598695	389599253	558	True	449	449	81.416	180	736	1	chr6D.!!$R2	556
20	TraesCS2A01G200900	chr1B	330837835	330838412	577	True	449	449	80.862	162	736	1	chr1B.!!$R1	574

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
59	60	0.036022	GAAACAGGCCTCAGCTGACT	59.964	55.0	13.74	5.84	39.73	3.41	F
677	695	0.107066	TCGTCGCAGGGTGGTCTATA	60.107	55.0	0.00	0.00	0.00	1.31	F
1005	1041	0.542702	CCAACCCAATCCTTGCACCT	60.543	55.0	0.00	0.00	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2058	2139	0.249238	CTCGCGAAATGGAGCTAGCT	60.249	55.0	19.45	19.45	0.00	3.32	R
2121	2202	0.032952	TCTACGGTTTGCTTGCGAGT	59.967	50.0	2.14	0.00	0.00	4.18	R
2595	2708	0.181350	GGCTCGTCCCCAGATGAATT	59.819	55.0	0.00	0.00	37.58	2.17	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
22	23	4.251543	CCACCACATGGGAAGTTAAAAC	57.748	45.455	0.00	0.00	45.95	2.43
23	24	3.006430	CCACCACATGGGAAGTTAAAACC	59.994	47.826	0.00	0.00	45.95	3.27
24	25	3.006430	CACCACATGGGAAGTTAAAACCC	59.994	47.826	0.00	0.00	43.51	4.11
31	32	4.316205	GGGAAGTTAAAACCCAACAGTG	57.684	45.455	0.00	0.00	42.81	3.66
32	33	3.955551	GGGAAGTTAAAACCCAACAGTGA	59.044	43.478	0.00	0.00	42.81	3.41
33	34	4.037565	GGGAAGTTAAAACCCAACAGTGAG	59.962	45.833	0.00	0.00	42.81	3.51
34	35	4.037565	GGAAGTTAAAACCCAACAGTGAGG	59.962	45.833	0.00	0.00	0.00	3.86
41	42	2.452116	CCAACAGTGAGGGAGGTGA	58.548	57.895	0.00	0.00	0.00	4.02
42	43	0.764890	CCAACAGTGAGGGAGGTGAA	59.235	55.000	0.00	0.00	0.00	3.18
43	44	1.142870	CCAACAGTGAGGGAGGTGAAA	59.857	52.381	0.00	0.00	0.00	2.69
44	45	2.222027	CAACAGTGAGGGAGGTGAAAC	58.778	52.381	0.00	0.00	0.00	2.78
45	46	1.507140	ACAGTGAGGGAGGTGAAACA	58.493	50.000	0.00	0.00	39.98	2.83
46	47	1.417890	ACAGTGAGGGAGGTGAAACAG	59.582	52.381	0.00	0.00	39.98	3.16
47	48	1.059913	AGTGAGGGAGGTGAAACAGG	58.940	55.000	0.00	0.00	39.98	4.00
48	49	0.606673	GTGAGGGAGGTGAAACAGGC	60.607	60.000	0.00	0.00	39.98	4.85
49	50	1.002011	GAGGGAGGTGAAACAGGCC	60.002	63.158	0.00	0.00	39.98	5.19
50	51	1.464198	AGGGAGGTGAAACAGGCCT	60.464	57.895	0.00	0.00	39.98	5.19
51	52	1.002011	GGGAGGTGAAACAGGCCTC	60.002	63.158	0.00	0.00	45.92	4.70
53	54	3.239861	GAGGTGAAACAGGCCTCAG	57.760	57.895	0.00	0.00	45.93	3.35
54	55	0.957888	GAGGTGAAACAGGCCTCAGC	60.958	60.000	0.00	8.22	45.93	4.26
55	56	1.073897	GGTGAAACAGGCCTCAGCT	59.926	57.895	0.00	0.00	39.98	4.24
56	57	1.239968	GGTGAAACAGGCCTCAGCTG	61.240	60.000	7.63	7.63	39.98	4.24
57	58	0.250467	GTGAAACAGGCCTCAGCTGA	60.250	55.000	17.19	17.19	36.34	4.26
58	59	0.250467	TGAAACAGGCCTCAGCTGAC	60.250	55.000	13.74	3.73	39.73	3.51
59	60	0.036022	GAAACAGGCCTCAGCTGACT	59.964	55.000	13.74	5.84	39.73	3.41

Showing 1 to 25 of 264 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	3.236047	GGGTTTTAACTTCCCATGTGGT	58.764	45.455	0.00	0.00	40.79	4.16
10	11	3.955551	TCACTGTTGGGTTTTAACTTCCC	59.044	43.478	0.00	0.00	41.41	3.97
11	12	4.037565	CCTCACTGTTGGGTTTTAACTTCC	59.962	45.833	0.00	0.00	0.00	3.46
12	13	4.037565	CCCTCACTGTTGGGTTTTAACTTC	59.962	45.833	7.31	0.00	38.65	3.01
13	14	3.958147	CCCTCACTGTTGGGTTTTAACTT	59.042	43.478	7.31	0.00	38.65	2.66
14	15	3.203487	TCCCTCACTGTTGGGTTTTAACT	59.797	43.478	13.39	0.00	43.74	2.24
15	16	3.558033	TCCCTCACTGTTGGGTTTTAAC	58.442	45.455	13.39	0.00	43.74	2.01
16	17	3.435890	CCTCCCTCACTGTTGGGTTTTAA	60.436	47.826	13.39	0.00	43.74	1.52
17	18	2.107552	CCTCCCTCACTGTTGGGTTTTA	59.892	50.000	13.39	0.00	43.74	1.52
18	19	1.133482	CCTCCCTCACTGTTGGGTTTT	60.133	52.381	13.39	0.00	43.74	2.43
19	20	0.478507	CCTCCCTCACTGTTGGGTTT	59.521	55.000	13.39	0.00	43.74	3.27
20	21	0.697854	ACCTCCCTCACTGTTGGGTT	60.698	55.000	13.39	0.52	43.74	4.11
21	22	1.073706	ACCTCCCTCACTGTTGGGT	60.074	57.895	13.39	0.00	43.74	4.51
22	23	1.127567	TCACCTCCCTCACTGTTGGG	61.128	60.000	8.84	8.84	44.66	4.12
23	24	0.764890	TTCACCTCCCTCACTGTTGG	59.235	55.000	0.00	0.00	0.00	3.77
24	25	2.222027	GTTTCACCTCCCTCACTGTTG	58.778	52.381	0.00	0.00	0.00	3.33
25	26	1.843851	TGTTTCACCTCCCTCACTGTT	59.156	47.619	0.00	0.00	0.00	3.16
26	27	1.417890	CTGTTTCACCTCCCTCACTGT	59.582	52.381	0.00	0.00	0.00	3.55
27	28	1.271054	CCTGTTTCACCTCCCTCACTG	60.271	57.143	0.00	0.00	0.00	3.66
28	29	1.059913	CCTGTTTCACCTCCCTCACT	58.940	55.000	0.00	0.00	0.00	3.41
29	30	0.606673	GCCTGTTTCACCTCCCTCAC	60.607	60.000	0.00	0.00	0.00	3.51
30	31	1.761174	GCCTGTTTCACCTCCCTCA	59.239	57.895	0.00	0.00	0.00	3.86
31	32	1.002011	GGCCTGTTTCACCTCCCTC	60.002	63.158	0.00	0.00	0.00	4.30
32	33	1.464198	AGGCCTGTTTCACCTCCCT	60.464	57.895	3.11	0.00	0.00	4.20
33	34	1.002011	GAGGCCTGTTTCACCTCCC	60.002	63.158	12.00	0.00	43.54	4.30

Showing 1 to 25 of 275 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.