AutoCloner

Multiple sequence alignment - TraesCS7D01G063200

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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	TraesCS7D01G063200	chr7D	100.000	6133	0	0	1	6133	34370662	34376794	0.000000e+00	11326.0
1	TraesCS7D01G063200	chr7D	92.144	1502	78	11	4118	5589	34471550	34473041	0.000000e+00	2084.0
2	TraesCS7D01G063200	chr7D	95.623	1211	51	2	2810	4018	34756469	34755259	0.000000e+00	1941.0
3	TraesCS7D01G063200	chr7D	97.387	1110	27	2	4056	5164	34755262	34754154	0.000000e+00	1888.0
4	TraesCS7D01G063200	chr7D	95.269	782	30	2	1740	2521	34758073	34757299	0.000000e+00	1232.0
5	TraesCS7D01G063200	chr7D	92.022	727	42	7	935	1649	34470517	34471239	0.000000e+00	1007.0
6	TraesCS7D01G063200	chr7D	89.959	727	38	19	935	1649	34758880	34758177	0.000000e+00	905.0
7	TraesCS7D01G063200	chr7D	93.827	486	25	2	5590	6070	34472966	34473451	0.000000e+00	726.0
8	TraesCS7D01G063200	chr7D	90.661	514	29	4	5590	6098	34753717	34753218	0.000000e+00	665.0
9	TraesCS7D01G063200	chr7D	88.863	431	41	4	5161	5589	34754071	34753646	1.960000e-144	523.0
10	TraesCS7D01G063200	chr7D	86.224	392	24	5	1700	2091	34471379	34471740	1.240000e-106	398.0
11	TraesCS7D01G063200	chr7D	94.492	236	13	0	2578	2813	34757097	34756862	1.260000e-96	364.0
12	TraesCS7D01G063200	chr7D	91.795	195	16	0	4118	4312	34757918	34757724	7.830000e-69	272.0
13	TraesCS7D01G063200	chr7D	89.109	202	15	2	1895	2095	34755200	34755005	1.710000e-60	244.0
14	TraesCS7D01G063200	chr7D	98.630	73	1	0	5590	5662	34376178	34376250	4.990000e-26	130.0
15	TraesCS7D01G063200	chr7D	98.630	73	1	0	5517	5589	34376251	34376323	4.990000e-26	130.0
16	TraesCS7D01G063200	chr7D	96.000	50	1	1	6085	6133	34753127	34753078	5.100000e-11	80.5
17	TraesCS7D01G063200	chr7D	86.792	53	5	2	742	794	573268722	573268672	2.390000e-04	58.4
18	TraesCS7D01G063200	chr4A	93.357	3869	182	26	1740	5589	690410388	690414200	0.000000e+00	5651.0
19	TraesCS7D01G063200	chr4A	94.949	2831	124	8	2710	5524	690621655	690618828	0.000000e+00	4418.0
20	TraesCS7D01G063200	chr4A	90.000	730	37	22	935	1649	690409576	690410284	0.000000e+00	911.0
21	TraesCS7D01G063200	chr4A	88.997	718	34	20	948	1649	690623528	690622840	0.000000e+00	846.0
22	TraesCS7D01G063200	chr4A	95.059	506	24	1	2202	2707	690622254	690621750	0.000000e+00	795.0
23	TraesCS7D01G063200	chr4A	94.380	516	26	2	5621	6133	690618823	690618308	0.000000e+00	789.0
24	TraesCS7D01G063200	chr4A	91.408	547	28	4	5590	6130	690414128	690414661	0.000000e+00	732.0
25	TraesCS7D01G063200	chr4A	91.555	521	27	7	1649	2159	690622773	690622260	0.000000e+00	702.0
26	TraesCS7D01G063200	chr4A	85.530	387	50	5	360	741	622509954	622509569	3.440000e-107	399.0
27	TraesCS7D01G063200	chr4A	94.301	193	11	0	4120	4312	690622515	690622323	4.650000e-76	296.0
28	TraesCS7D01G063200	chr4A	92.308	195	15	0	4118	4312	690410535	690410729	1.680000e-70	278.0
29	TraesCS7D01G063200	chr4A	93.590	156	9	1	2656	2811	514080164	514080010	1.330000e-56	231.0
30	TraesCS7D01G063200	chr4A	91.975	162	13	0	2651	2812	109850213	109850052	1.720000e-55	228.0
31	TraesCS7D01G063200	chr4A	95.238	42	2	0	5548	5589	690618823	690618782	3.970000e-07	67.6
32	TraesCS7D01G063200	chr7A	91.901	1494	86	21	4100	5589	35001823	35000361	0.000000e+00	2056.0
33	TraesCS7D01G063200	chr7A	94.086	1116	38	12	4125	5214	34744480	34745593	0.000000e+00	1670.0
34	TraesCS7D01G063200	chr7A	88.046	778	58	20	935	1703	35002980	35002229	0.000000e+00	889.0
35	TraesCS7D01G063200	chr7A	93.169	527	29	4	5612	6133	34963504	34962980	0.000000e+00	767.0
36	TraesCS7D01G063200	chr7A	86.030	723	58	14	929	1649	34743451	34744132	0.000000e+00	736.0
37	TraesCS7D01G063200	chr7A	90.676	547	29	11	5590	6133	35000432	34999905	0.000000e+00	708.0
38	TraesCS7D01G063200	chr7A	90.494	547	32	5	5590	6130	34745860	34746392	0.000000e+00	704.0
39	TraesCS7D01G063200	chr7A	92.837	349	20	3	5244	5589	34745589	34745935	9.180000e-138	501.0
40	TraesCS7D01G063200	chr7A	93.496	246	16	0	5264	5509	34963752	34963507	3.490000e-97	366.0
41	TraesCS7D01G063200	chr7A	90.667	225	13	1	1694	1910	35002065	35001841	6.010000e-75	292.0
42	TraesCS7D01G063200	chr7A	93.631	157	10	0	2657	2813	421785006	421785162	1.030000e-57	235.0
43	TraesCS7D01G063200	chr7A	85.354	198	24	5	495	691	460581454	460581647	3.750000e-47	200.0
44	TraesCS7D01G063200	chr7A	98.039	51	1	0	5539	5589	34963504	34963454	8.470000e-14	89.8
45	TraesCS7D01G063200	chr7A	97.619	42	1	0	5210	5251	34963791	34963750	8.530000e-09	73.1
46	TraesCS7D01G063200	chr2B	90.727	399	35	2	4301	4699	704812733	704813129	1.170000e-146	531.0
47	TraesCS7D01G063200	chr2B	88.083	386	40	5	357	741	773936943	773937323	2.610000e-123	453.0
48	TraesCS7D01G063200	chr2B	87.021	339	32	7	1151	1481	704812300	704812634	7.510000e-99	372.0
49	TraesCS7D01G063200	chr1D	89.059	393	36	5	356	741	406553752	406553360	1.200000e-131	481.0
50	TraesCS7D01G063200	chr1D	86.528	386	46	6	360	741	11134438	11134055	2.640000e-113	420.0
51	TraesCS7D01G063200	chr1D	72.222	558	130	24	2881	3425	18932829	18933374	1.380000e-31	148.0
52	TraesCS7D01G063200	chr3D	86.667	390	44	7	357	741	567264925	567265311	5.680000e-115	425.0
53	TraesCS7D01G063200	chr3D	85.788	387	49	4	360	741	41428356	41428741	7.400000e-109	405.0
54	TraesCS7D01G063200	chr3D	88.439	173	18	2	4130	4301	579426311	579426140	2.240000e-49	207.0
55	TraesCS7D01G063200	chr3D	97.059	34	1	0	761	794	383591678	383591645	2.390000e-04	58.4
56	TraesCS7D01G063200	chr5D	86.528	386	46	4	360	741	519198465	519198848	2.640000e-113	420.0
57	TraesCS7D01G063200	chr5D	86.340	388	44	8	360	741	27622215	27621831	1.230000e-111	414.0
58	TraesCS7D01G063200	chr6A	85.530	387	50	5	360	741	566444715	566444330	3.440000e-107	399.0
59	TraesCS7D01G063200	chrUn	84.665	313	40	6	385	692	29282782	29283091	7.720000e-79	305.0
60	TraesCS7D01G063200	chr4B	93.789	161	8	2	2656	2816	146469215	146469373	2.210000e-59	241.0
61	TraesCS7D01G063200	chr4B	93.711	159	10	0	2651	2809	438375175	438375333	7.940000e-59	239.0
62	TraesCS7D01G063200	chr4D	94.268	157	8	1	2656	2811	74079350	74079506	7.940000e-59	239.0
63	TraesCS7D01G063200	chr7B	92.683	164	11	1	2654	2816	505937311	505937474	1.030000e-57	235.0
64	TraesCS7D01G063200	chr3A	80.090	221	25	12	4117	4320	474434030	474433812	4.950000e-31	147.0
65	TraesCS7D01G063200	chr3B	86.154	65	7	1	4239	4301	773883264	773883328	1.100000e-07	69.4
66	TraesCS7D01G063200	chr3B	88.636	44	3	1	743	786	60696207	60696248	1.100000e-02	52.8
67	TraesCS7D01G063200	chr5B	88.462	52	4	1	744	795	508373629	508373678	1.850000e-05	62.1
68	TraesCS7D01G063200	chr5A	88.235	51	4	2	744	794	566039781	566039733	6.640000e-05	60.2
69	TraesCS7D01G063200	chr2D	100.000	31	0	0	759	789	647915637	647915607	2.390000e-04	58.4
70	TraesCS7D01G063200	chr6B	90.698	43	2	2	745	787	141786817	141786857	8.590000e-04	56.5

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	TraesCS7D01G063200	chr7D	34370662	34376794	6132	False	3862.000000	11326	99.086667	1	6133	3	chr7D.!!$F1	6132
1	TraesCS7D01G063200	chr7D	34470517	34473451	2934	False	1053.750000	2084	91.054250	935	6070	4	chr7D.!!$F2	5135
2	TraesCS7D01G063200	chr7D	34753078	34758880	5802	True	811.450000	1941	92.915800	935	6133	10	chr7D.!!$R2	5198
3	TraesCS7D01G063200	chr4A	690409576	690414661	5085	False	1893.000000	5651	91.768250	935	6130	4	chr4A.!!$F1	5195
4	TraesCS7D01G063200	chr4A	690618308	690623528	5220	True	1130.514286	4418	93.497000	948	6133	7	chr4A.!!$R4	5185
5	TraesCS7D01G063200	chr7A	34999905	35002980	3075	True	986.250000	2056	90.322500	935	6133	4	chr7A.!!$R2	5198
6	TraesCS7D01G063200	chr7A	34743451	34746392	2941	False	902.750000	1670	90.861750	929	6130	4	chr7A.!!$F3	5201
7	TraesCS7D01G063200	chr7A	34962980	34963791	811	True	323.975000	767	95.580750	5210	6133	4	chr7A.!!$R1	923
8	TraesCS7D01G063200	chr2B	704812300	704813129	829	False	451.500000	531	88.874000	1151	4699	2	chr2B.!!$F2	3548

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
288	289	0.032267	GGGAGCTGCGGTACATACTC	59.968	60.0	0.00	0.0	32.92	2.59	F
875	876	0.039035	AACCGCTAGAAATGGGCCAA	59.961	50.0	11.89	0.0	0.00	4.52	F
883	884	0.109132	GAAATGGGCCAACTGAAGCG	60.109	55.0	11.89	0.0	0.00	4.68	F
2567	3056	0.323178	CACCTCTTCCTGCCAATGCT	60.323	55.0	0.00	0.0	38.71	3.79	F
2644	3133	0.613260	TTTGGCATCTCTGTACGCCT	59.387	50.0	8.41	0.0	45.13	5.52	F
3905	4501	0.107945	GGATGCTCTGAAACTCGGCT	60.108	55.0	0.00	0.0	0.00	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1336	1385	0.921347	CTCGGTGAGGAATAAACGCG	59.079	55.000	3.53	3.53	0.00	6.01	R
2602	3091	0.957395	ATGCTTGGCTTGAGTGGTCG	60.957	55.000	0.00	0.00	0.00	4.79	R
2838	3431	2.425143	TTTGATCATGGAGGGCAGAC	57.575	50.000	0.00	0.00	0.00	3.51	R
3598	4194	0.038159	AACTGGAGTGCGAGCAGTAC	60.038	55.000	8.14	8.14	35.57	2.73	R
4088	4684	0.678395	AGTATCAGCCGCCAGAGATG	59.322	55.000	0.00	0.00	0.00	2.90	R
5848	9330	1.203050	AGTGGCCTGGTTATTTGCAGT	60.203	47.619	3.32	0.00	0.00	4.40	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
49	50	8.810652	TGTAGAAAATGATAACAAGCAAAACC	57.189	30.769	0.00	0.00	0.00	3.27
50	51	8.637986	TGTAGAAAATGATAACAAGCAAAACCT	58.362	29.630	0.00	0.00	0.00	3.50
140	141	9.554395	AAGAAAGAAAGGAAAACAAAAAGAACA	57.446	25.926	0.00	0.00	0.00	3.18
141	142	9.554395	AGAAAGAAAGGAAAACAAAAAGAACAA	57.446	25.926	0.00	0.00	0.00	2.83
144	145	9.554395	AAGAAAGGAAAACAAAAAGAACAAAGA	57.446	25.926	0.00	0.00	0.00	2.52
145	146	9.554395	AGAAAGGAAAACAAAAAGAACAAAGAA	57.446	25.926	0.00	0.00	0.00	2.52
148	149	9.944663	AAGGAAAACAAAAAGAACAAAGAAAAC	57.055	25.926	0.00	0.00	0.00	2.43
149	150	8.564574	AGGAAAACAAAAAGAACAAAGAAAACC	58.435	29.630	0.00	0.00	0.00	3.27
150	151	7.532546	GGAAAACAAAAAGAACAAAGAAAACCG	59.467	33.333	0.00	0.00	0.00	4.44
151	152	6.474819	AACAAAAAGAACAAAGAAAACCGG	57.525	33.333	0.00	0.00	0.00	5.28
152	153	4.390603	ACAAAAAGAACAAAGAAAACCGGC	59.609	37.500	0.00	0.00	0.00	6.13
153	154	4.465632	AAAAGAACAAAGAAAACCGGCT	57.534	36.364	0.00	0.00	0.00	5.52
154	155	3.710326	AAGAACAAAGAAAACCGGCTC	57.290	42.857	0.00	0.00	0.00	4.70
155	156	1.602377	AGAACAAAGAAAACCGGCTCG	59.398	47.619	0.00	0.00	0.00	5.03
156	157	1.600485	GAACAAAGAAAACCGGCTCGA	59.400	47.619	0.00	0.00	0.00	4.04
157	158	1.670791	ACAAAGAAAACCGGCTCGAA	58.329	45.000	0.00	0.00	0.00	3.71
158	159	2.227194	ACAAAGAAAACCGGCTCGAAT	58.773	42.857	0.00	0.00	0.00	3.34
159	160	2.225727	ACAAAGAAAACCGGCTCGAATC	59.774	45.455	0.00	0.00	0.00	2.52
160	161	1.450025	AAGAAAACCGGCTCGAATCC	58.550	50.000	0.00	0.00	0.00	3.01
161	162	0.613777	AGAAAACCGGCTCGAATCCT	59.386	50.000	0.00	0.00	0.00	3.24
162	163	1.003233	AGAAAACCGGCTCGAATCCTT	59.997	47.619	0.00	0.00	0.00	3.36
163	164	2.235402	AGAAAACCGGCTCGAATCCTTA	59.765	45.455	0.00	0.00	0.00	2.69
164	165	2.773993	AAACCGGCTCGAATCCTTAA	57.226	45.000	0.00	0.00	0.00	1.85
165	166	2.311124	AACCGGCTCGAATCCTTAAG	57.689	50.000	0.00	0.00	0.00	1.85
166	167	1.192428	ACCGGCTCGAATCCTTAAGT	58.808	50.000	0.00	0.00	0.00	2.24

Showing 1 to 25 of 519 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	9.423061	GGTTTTGCTTGTTATCATTTTCTACAT	57.577	29.630	0.00	0.00	0.00	2.29
24	25	8.637986	AGGTTTTGCTTGTTATCATTTTCTACA	58.362	29.630	0.00	0.00	0.00	2.74
114	115	9.554395	TGTTCTTTTTGTTTTCCTTTCTTTCTT	57.446	25.926	0.00	0.00	0.00	2.52
115	116	9.554395	TTGTTCTTTTTGTTTTCCTTTCTTTCT	57.446	25.926	0.00	0.00	0.00	2.52
118	119	9.554395	TCTTTGTTCTTTTTGTTTTCCTTTCTT	57.446	25.926	0.00	0.00	0.00	2.52
119	120	9.554395	TTCTTTGTTCTTTTTGTTTTCCTTTCT	57.446	25.926	0.00	0.00	0.00	2.52
122	123	9.944663	GTTTTCTTTGTTCTTTTTGTTTTCCTT	57.055	25.926	0.00	0.00	0.00	3.36
123	124	8.564574	GGTTTTCTTTGTTCTTTTTGTTTTCCT	58.435	29.630	0.00	0.00	0.00	3.36
124	125	7.532546	CGGTTTTCTTTGTTCTTTTTGTTTTCC	59.467	33.333	0.00	0.00	0.00	3.13
125	126	7.532546	CCGGTTTTCTTTGTTCTTTTTGTTTTC	59.467	33.333	0.00	0.00	0.00	2.29
126	127	7.356540	CCGGTTTTCTTTGTTCTTTTTGTTTT	58.643	30.769	0.00	0.00	0.00	2.43
127	128	6.566942	GCCGGTTTTCTTTGTTCTTTTTGTTT	60.567	34.615	1.90	0.00	0.00	2.83
128	129	5.106869	GCCGGTTTTCTTTGTTCTTTTTGTT	60.107	36.000	1.90	0.00	0.00	2.83
129	130	4.390603	GCCGGTTTTCTTTGTTCTTTTTGT	59.609	37.500	1.90	0.00	0.00	2.83
130	131	4.629634	AGCCGGTTTTCTTTGTTCTTTTTG	59.370	37.500	1.90	0.00	0.00	2.44
131	132	4.827692	AGCCGGTTTTCTTTGTTCTTTTT	58.172	34.783	1.90	0.00	0.00	1.94
132	133	4.430007	GAGCCGGTTTTCTTTGTTCTTTT	58.570	39.130	1.90	0.00	0.00	2.27
133	134	3.488553	CGAGCCGGTTTTCTTTGTTCTTT	60.489	43.478	1.90	0.00	0.00	2.52
134	135	2.032924	CGAGCCGGTTTTCTTTGTTCTT	59.967	45.455	1.90	0.00	0.00	2.52
135	136	1.602377	CGAGCCGGTTTTCTTTGTTCT	59.398	47.619	1.90	0.00	0.00	3.01
136	137	1.600485	TCGAGCCGGTTTTCTTTGTTC	59.400	47.619	1.90	0.00	0.00	3.18
137	138	1.670791	TCGAGCCGGTTTTCTTTGTT	58.329	45.000	1.90	0.00	0.00	2.83
138	139	1.670791	TTCGAGCCGGTTTTCTTTGT	58.329	45.000	1.90	0.00	0.00	2.83
139	140	2.414161	GGATTCGAGCCGGTTTTCTTTG	60.414	50.000	1.90	0.00	0.00	2.77
140	141	1.810755	GGATTCGAGCCGGTTTTCTTT	59.189	47.619	1.90	0.00	0.00	2.52

Showing 1 to 25 of 518 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.