AutoCloner

Multiple sequence alignment - TraesCS2D01G449700

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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	TraesCS2D01G449700	chr2D	100.000	4611	0	0	1	4611	559306479	559301869	0.000000e+00	8516.0
1	TraesCS2D01G449700	chr2D	87.387	1998	208	19	1907	3881	559211974	559209998	0.000000e+00	2254.0
2	TraesCS2D01G449700	chr2D	85.312	1348	129	26	771	2071	559212979	559211654	0.000000e+00	1328.0
3	TraesCS2D01G449700	chr2D	76.294	734	147	17	2068	2789	559211429	559210711	2.620000e-97	366.0
4	TraesCS2D01G449700	chr2D	86.667	330	44	0	1743	2072	559304575	559304246	2.620000e-97	366.0
5	TraesCS2D01G449700	chr2D	81.223	458	51	26	3990	4416	559209803	559209350	2.060000e-88	337.0
6	TraesCS2D01G449700	chr2D	84.699	183	28	0	1729	1911	559211444	559211262	2.830000e-42	183.0
7	TraesCS2D01G449700	chr2D	79.167	168	30	3	2224	2387	559210889	559210723	1.360000e-20	111.0
8	TraesCS2D01G449700	chr2D	100.000	28	0	0	4373	4400	28966943	28966916	8.000000e-03	52.8
9	TraesCS2D01G449700	chr2A	84.591	2570	306	38	1905	4422	699798987	699796456	0.000000e+00	2470.0
10	TraesCS2D01G449700	chr2A	93.884	1586	78	8	665	2234	699854104	699852522	0.000000e+00	2374.0
11	TraesCS2D01G449700	chr2A	88.476	1614	147	15	2142	3740	699852500	699850911	0.000000e+00	1914.0
12	TraesCS2D01G449700	chr2A	85.089	1348	136	27	771	2071	699799988	699798659	0.000000e+00	1315.0
13	TraesCS2D01G449700	chr2A	92.575	633	44	1	1	630	699854737	699854105	0.000000e+00	905.0
14	TraesCS2D01G449700	chr2A	88.319	351	41	0	1743	2093	699852851	699852501	5.520000e-114	422.0
15	TraesCS2D01G449700	chr2B	84.540	1436	147	43	3035	4422	668175004	668173596	0.000000e+00	1352.0
16	TraesCS2D01G449700	chr2B	89.276	1091	92	8	1005	2071	668183022	668181933	0.000000e+00	1343.0
17	TraesCS2D01G449700	chr2B	88.548	978	97	5	2067	3038	668181709	668180741	0.000000e+00	1171.0
18	TraesCS2D01G449700	chr2B	81.531	1267	208	11	1908	3164	668182258	668181008	0.000000e+00	1020.0
19	TraesCS2D01G449700	chr2B	78.249	731	149	5	2457	3182	668182099	668181374	1.170000e-125	460.0
20	TraesCS2D01G449700	chr2B	96.139	259	9	1	753	1010	668224563	668224305	5.520000e-114	422.0
21	TraesCS2D01G449700	chr2B	79.287	449	79	6	2067	2511	668181316	668180878	7.500000e-78	302.0
22	TraesCS2D01G449700	chr5B	91.522	519	41	1	2602	3117	339532874	339532356	0.000000e+00	712.0
23	TraesCS2D01G449700	chr5B	76.583	521	110	7	2212	2723	339532874	339532357	4.540000e-70	276.0
24	TraesCS2D01G449700	chr5A	84.733	262	40	0	1	262	401509714	401509975	3.540000e-66	263.0
25	TraesCS2D01G449700	chr7A	91.489	47	1	3	4564	4607	695373208	695373162	1.390000e-05	62.1
26	TraesCS2D01G449700	chrUn	91.111	45	2	1	4568	4610	277594211	277594255	4.980000e-05	60.2
27	TraesCS2D01G449700	chr3B	91.111	45	2	1	4568	4610	765726746	765726790	4.980000e-05	60.2
28	TraesCS2D01G449700	chr3B	96.875	32	0	1	4564	4594	636256896	636256865	8.000000e-03	52.8
29	TraesCS2D01G449700	chr7D	96.970	33	0	1	4564	4595	386644614	386644582	2.000000e-03	54.7
30	TraesCS2D01G449700	chr3A	96.970	33	0	1	4564	4595	92537125	92537093	2.000000e-03	54.7

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	TraesCS2D01G449700	chr2D	559301869	559306479	4610	True	4441.000000	8516	93.3335	1	4611	2	chr2D.!!$R3	4610
1	TraesCS2D01G449700	chr2D	559209350	559212979	3629	True	763.166667	2254	82.3470	771	4416	6	chr2D.!!$R2	3645
2	TraesCS2D01G449700	chr2A	699796456	699799988	3532	True	1892.500000	2470	84.8400	771	4422	2	chr2A.!!$R1	3651
3	TraesCS2D01G449700	chr2A	699850911	699854737	3826	True	1403.750000	2374	90.8135	1	3740	4	chr2A.!!$R2	3739
4	TraesCS2D01G449700	chr2B	668173596	668175004	1408	True	1352.000000	1352	84.5400	3035	4422	1	chr2B.!!$R1	1387
5	TraesCS2D01G449700	chr2B	668180741	668183022	2281	True	859.200000	1343	83.3782	1005	3182	5	chr2B.!!$R3	2177
6	TraesCS2D01G449700	chr5B	339532356	339532874	518	True	494.000000	712	84.0525	2212	3117	2	chr5B.!!$R1	905

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
396	397	0.036732	ATGGTTTCTGGCGCTCAAGA	59.963	50.0	7.64	5.57	0.00	3.02	F
1784	1864	0.321671	GTGGCCTGTGCAGAGAAGTA	59.678	55.0	13.38	0.00	40.13	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2105	2185	0.392193	CACAGAGGATCCACTGCACC	60.392	60.000	31.87	5.88	38.01	5.01	R
3757	4364	1.065854	GTAGCAGCAGGTGTGAAGGAT	60.066	52.381	0.66	0.00	0.00	3.24	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
43	44	1.897802	CCCGGACTACCTTGTACTTGT	59.102	52.381	0.73	0.00	0.00	3.16
49	50	4.038883	GGACTACCTTGTACTTGTCAGTGT	59.961	45.833	0.00	0.00	34.06	3.55
87	88	0.600255	CCGTCGGGAGGAACATATGC	60.600	60.000	2.34	0.00	34.06	3.14
96	97	3.561725	GGAGGAACATATGCTTGTACTGC	59.438	47.826	1.58	0.00	0.00	4.40
105	106	1.064803	TGCTTGTACTGCGTTTTGGTG	59.935	47.619	0.00	0.00	0.00	4.17
115	116	1.534385	GCGTTTTGGTGCGGTTACTTT	60.534	47.619	0.00	0.00	0.00	2.66
116	117	2.799871	CGTTTTGGTGCGGTTACTTTT	58.200	42.857	0.00	0.00	0.00	2.27
132	133	4.223320	ACTTTTAGGCAACGTCATTGTG	57.777	40.909	0.00	0.00	46.39	3.33
155	156	0.107017	CTGGTGGCCGGATTGAAGAT	60.107	55.000	5.05	0.00	29.82	2.40
162	163	2.103263	GGCCGGATTGAAGATGTAGAGT	59.897	50.000	5.05	0.00	0.00	3.24
194	195	1.374758	GGAAGAGCACCAGACCGTG	60.375	63.158	0.00	0.00	36.80	4.94
212	213	4.402851	GCAGTGGGCAATGTGAGA	57.597	55.556	0.00	0.00	43.97	3.27
222	223	3.432749	GGGCAATGTGAGAGATTGAGCTA	60.433	47.826	0.00	0.00	33.36	3.32
225	226	5.298777	GGCAATGTGAGAGATTGAGCTAAAT	59.701	40.000	0.00	0.00	33.36	1.40
228	229	7.201714	GCAATGTGAGAGATTGAGCTAAATTCT	60.202	37.037	0.00	3.33	33.36	2.40
231	232	6.070596	TGTGAGAGATTGAGCTAAATTCTCCA	60.071	38.462	21.32	17.72	30.69	3.86
234	235	5.046288	AGATTGAGCTAAATTCTCCAGGG	57.954	43.478	0.00	0.00	0.00	4.45
245	246	2.103153	TCTCCAGGGAAGTCAGTTGT	57.897	50.000	0.00	0.00	0.00	3.32
246	247	1.694150	TCTCCAGGGAAGTCAGTTGTG	59.306	52.381	0.00	0.00	0.00	3.33
254	255	2.618241	GGAAGTCAGTTGTGTGCATCAA	59.382	45.455	0.00	0.00	0.00	2.57
264	265	3.749226	TGTGTGCATCAACCTTGTATCA	58.251	40.909	0.00	0.00	0.00	2.15
301	302	1.888436	CTGCCACTGGTAGAAGCGGA	61.888	60.000	7.38	0.00	37.63	5.54
323	324	0.923358	TGGGTTGAGAAGGTGGTTGT	59.077	50.000	0.00	0.00	0.00	3.32
375	376	0.179009	CGTGGGGAATGATGAGCCAT	60.179	55.000	0.00	0.00	0.00	4.40
396	397	0.036732	ATGGTTTCTGGCGCTCAAGA	59.963	50.000	7.64	5.57	0.00	3.02

Showing 1 to 25 of 345 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	2.270352	GGTTTGGACCATCACACTGA	57.730	50.000	0.00	0.00	45.77	3.41
87	88	1.753956	GCACCAAAACGCAGTACAAG	58.246	50.000	0.00	0.00	45.00	3.16
96	97	2.478547	AAAGTAACCGCACCAAAACG	57.521	45.000	0.00	0.00	0.00	3.60
105	106	1.532437	ACGTTGCCTAAAAGTAACCGC	59.468	47.619	0.00	0.00	0.00	5.68
115	116	2.147958	GGACACAATGACGTTGCCTAA	58.852	47.619	7.33	0.00	41.69	2.69
116	117	1.609580	GGGACACAATGACGTTGCCTA	60.610	52.381	7.33	0.00	41.69	3.93
132	133	3.728373	AATCCGGCCACCAGGGAC	61.728	66.667	2.24	0.00	43.65	4.46
155	156	3.071892	CCCTACCAACACCAAACTCTACA	59.928	47.826	0.00	0.00	0.00	2.74
162	163	2.488347	GCTCTTCCCTACCAACACCAAA	60.488	50.000	0.00	0.00	0.00	3.28
194	195	1.303561	TCTCACATTGCCCACTGCC	60.304	57.895	0.00	0.00	40.16	4.85
208	209	6.407865	CCTGGAGAATTTAGCTCAATCTCTCA	60.408	42.308	21.33	15.01	34.07	3.27
212	213	4.723789	TCCCTGGAGAATTTAGCTCAATCT	59.276	41.667	0.00	0.00	34.07	2.40
222	223	4.141158	ACAACTGACTTCCCTGGAGAATTT	60.141	41.667	0.00	0.00	0.00	1.82
225	226	2.104792	CACAACTGACTTCCCTGGAGAA	59.895	50.000	0.00	0.00	0.00	2.87
228	229	1.140852	CACACAACTGACTTCCCTGGA	59.859	52.381	0.00	0.00	0.00	3.86
231	232	0.546122	TGCACACAACTGACTTCCCT	59.454	50.000	0.00	0.00	0.00	4.20
234	235	3.548818	GGTTGATGCACACAACTGACTTC	60.549	47.826	26.43	13.00	44.50	3.01
245	246	4.020307	TCTCTGATACAAGGTTGATGCACA	60.020	41.667	0.00	0.00	0.00	4.57
246	247	4.331168	GTCTCTGATACAAGGTTGATGCAC	59.669	45.833	0.00	0.00	0.00	4.57
254	255	3.702045	GCTAGGTGTCTCTGATACAAGGT	59.298	47.826	0.00	0.00	0.00	3.50
264	265	3.524346	GCTAGGGCTAGGTGTCTCT	57.476	57.895	0.00	0.00	33.87	3.10
289	290	0.988832	ACCCAAATCCGCTTCTACCA	59.011	50.000	0.00	0.00	0.00	3.25
301	302	2.965147	CAACCACCTTCTCAACCCAAAT	59.035	45.455	0.00	0.00	0.00	2.32
323	324	2.025226	ACTATCGAAGGTGAGGAGTGGA	60.025	50.000	0.00	0.00	0.00	4.02
334	335	4.308899	CCTTGGACAGTACTATCGAAGG	57.691	50.000	24.84	24.84	42.22	3.46

Showing 1 to 25 of 356 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.