AutoCloner

Multiple sequence alignment - TraesCS4B01G312500

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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	TraesCS4B01G312500	chr4B	100.000	2609	0	0	1	2609	602293337	602290729	0.000000e+00	4819
1	TraesCS4B01G312500	chr4B	90.177	1812	123	30	840	2608	194219979	194221778	0.000000e+00	2309
2	TraesCS4B01G312500	chr4B	87.630	865	55	30	1	850	194219098	194219925	0.000000e+00	957
3	TraesCS4B01G312500	chr6D	91.682	2633	154	33	1	2608	14045561	14048153	0.000000e+00	3589
4	TraesCS4B01G312500	chr5D	90.964	2634	154	39	1	2608	373747708	373750283	0.000000e+00	3469
5	TraesCS4B01G312500	chr6A	86.556	2648	258	54	1	2608	74674998	74677587	0.000000e+00	2828
6	TraesCS4B01G312500	chr5B	91.553	2060	135	19	558	2608	445131422	445133451	0.000000e+00	2804
7	TraesCS4B01G312500	chr5B	90.929	1797	118	24	854	2608	420718032	420719825	0.000000e+00	2374
8	TraesCS4B01G312500	chr5B	90.221	1810	124	29	840	2608	179227840	179229637	0.000000e+00	2313
9	TraesCS4B01G312500	chr5B	88.051	862	54	22	1	850	179226962	179227786	0.000000e+00	976
10	TraesCS4B01G312500	chr5B	87.963	864	54	26	1	850	406870655	406869828	0.000000e+00	974
11	TraesCS4B01G312500	chr5B	87.826	575	51	10	1	562	445111491	445112059	0.000000e+00	656
12	TraesCS4B01G312500	chr2D	93.764	1764	99	9	849	2608	617164184	617162428	0.000000e+00	2638
13	TraesCS4B01G312500	chr2D	93.140	860	39	12	1	850	617165088	617164239	0.000000e+00	1243
14	TraesCS4B01G312500	chr1D	93.718	1767	97	12	848	2608	485158460	485160218	0.000000e+00	2636
15	TraesCS4B01G312500	chr1D	94.416	591	27	5	263	850	485157818	485158405	0.000000e+00	904
16	TraesCS4B01G312500	chr2A	92.325	1772	104	18	848	2608	17676655	17674905	0.000000e+00	2490
17	TraesCS4B01G312500	chr2A	87.935	862	54	23	1	850	719453738	719454561	0.000000e+00	970
18	TraesCS4B01G312500	chr2A	87.703	862	58	23	1	850	43380232	43381057	0.000000e+00	961
19	TraesCS4B01G312500	chr2A	94.247	591	29	4	263	850	17677299	17676711	0.000000e+00	898
20	TraesCS4B01G312500	chr7B	90.558	1811	122	26	840	2608	68098241	68100044	0.000000e+00	2351
21	TraesCS4B01G312500	chr7B	88.079	864	52	24	1	850	528879444	528880270	0.000000e+00	977
22	TraesCS4B01G312500	chr3B	90.492	1809	123	23	840	2608	552478977	552480776	0.000000e+00	2342
23	TraesCS4B01G312500	chr3B	88.208	865	52	23	1	851	552478097	552478925	0.000000e+00	987
24	TraesCS4B01G312500	chr7A	90.387	1810	121	29	840	2608	171419456	171421253	0.000000e+00	2329
25	TraesCS4B01G312500	chr7A	85.681	866	53	35	1	850	171418592	171419402	0.000000e+00	846
26	TraesCS4B01G312500	chr1A	90.306	1795	126	29	854	2608	567477295	567475509	0.000000e+00	2307
27	TraesCS4B01G312500	chr1A	85.658	509	36	21	2131	2608	567471887	567471385	3.880000e-138	501
28	TraesCS4B01G312500	chr6B	87.963	864	53	26	1	850	704850743	704849917	0.000000e+00	972

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	TraesCS4B01G312500	chr4B	602290729	602293337	2608	True	4819.0	4819	100.0000	1	2609	1	chr4B.!!$R1	2608
1	TraesCS4B01G312500	chr4B	194219098	194221778	2680	False	1633.0	2309	88.9035	1	2608	2	chr4B.!!$F1	2607
2	TraesCS4B01G312500	chr6D	14045561	14048153	2592	False	3589.0	3589	91.6820	1	2608	1	chr6D.!!$F1	2607
3	TraesCS4B01G312500	chr5D	373747708	373750283	2575	False	3469.0	3469	90.9640	1	2608	1	chr5D.!!$F1	2607
4	TraesCS4B01G312500	chr6A	74674998	74677587	2589	False	2828.0	2828	86.5560	1	2608	1	chr6A.!!$F1	2607
5	TraesCS4B01G312500	chr5B	445131422	445133451	2029	False	2804.0	2804	91.5530	558	2608	1	chr5B.!!$F3	2050
6	TraesCS4B01G312500	chr5B	420718032	420719825	1793	False	2374.0	2374	90.9290	854	2608	1	chr5B.!!$F1	1754
7	TraesCS4B01G312500	chr5B	179226962	179229637	2675	False	1644.5	2313	89.1360	1	2608	2	chr5B.!!$F4	2607
8	TraesCS4B01G312500	chr5B	406869828	406870655	827	True	974.0	974	87.9630	1	850	1	chr5B.!!$R1	849
9	TraesCS4B01G312500	chr5B	445111491	445112059	568	False	656.0	656	87.8260	1	562	1	chr5B.!!$F2	561
10	TraesCS4B01G312500	chr2D	617162428	617165088	2660	True	1940.5	2638	93.4520	1	2608	2	chr2D.!!$R1	2607
11	TraesCS4B01G312500	chr1D	485157818	485160218	2400	False	1770.0	2636	94.0670	263	2608	2	chr1D.!!$F1	2345
12	TraesCS4B01G312500	chr2A	17674905	17677299	2394	True	1694.0	2490	93.2860	263	2608	2	chr2A.!!$R1	2345
13	TraesCS4B01G312500	chr2A	719453738	719454561	823	False	970.0	970	87.9350	1	850	1	chr2A.!!$F2	849
14	TraesCS4B01G312500	chr2A	43380232	43381057	825	False	961.0	961	87.7030	1	850	1	chr2A.!!$F1	849
15	TraesCS4B01G312500	chr7B	68098241	68100044	1803	False	2351.0	2351	90.5580	840	2608	1	chr7B.!!$F1	1768
16	TraesCS4B01G312500	chr7B	528879444	528880270	826	False	977.0	977	88.0790	1	850	1	chr7B.!!$F2	849
17	TraesCS4B01G312500	chr3B	552478097	552480776	2679	False	1664.5	2342	89.3500	1	2608	2	chr3B.!!$F1	2607
18	TraesCS4B01G312500	chr7A	171418592	171421253	2661	False	1587.5	2329	88.0340	1	2608	2	chr7A.!!$F1	2607
19	TraesCS4B01G312500	chr1A	567471385	567477295	5910	True	1404.0	2307	87.9820	854	2608	2	chr1A.!!$R1	1754
20	TraesCS4B01G312500	chr6B	704849917	704850743	826	True	972.0	972	87.9630	1	850	1	chr6B.!!$R1	849

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
172	187	1.681229	TGAAAGAGGGGGTAGGCAAT	58.319	50.0	0.0	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1659	1862	1.627329	TCCCATCTGCCATCTATCAGC	59.373	52.381	0.0	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
95	106	8.830201	TTATCAGCTTGCAAAAATGTAAACAT	57.170	26.923	0.00	0.00	38.41	2.71
106	117	8.223100	GCAAAAATGTAAACATTAGGCAAGAAG	58.777	33.333	8.67	0.00	45.06	2.85
119	130	5.757850	AGGCAAGAAGTACTGTGAAAAAG	57.242	39.130	0.00	0.00	0.00	2.27
161	174	4.861102	AAAGCAACTTGGATGAAAGAGG	57.139	40.909	0.00	0.00	0.00	3.69
162	175	2.800250	AGCAACTTGGATGAAAGAGGG	58.200	47.619	0.00	0.00	0.00	4.30
172	187	1.681229	TGAAAGAGGGGGTAGGCAAT	58.319	50.000	0.00	0.00	0.00	3.56
366	408	6.567959	TGTTGTTGTTGTGATCTTGCAATTA	58.432	32.000	0.00	0.00	0.00	1.40
381	424	2.418609	GCAATTAGTGGGGAACAATGCC	60.419	50.000	0.00	0.00	36.03	4.40
487	541	4.168922	CATCAGTTGCAGCATGAAAAGA	57.831	40.909	2.55	0.00	33.62	2.52
492	546	6.050432	TCAGTTGCAGCATGAAAAGAAAAAT	58.950	32.000	2.55	0.00	33.62	1.82
517	579	2.439507	ACTCATGACCTGGACAAACAGT	59.560	45.455	0.00	1.56	36.75	3.55
562	624	6.912591	CACAAAGACAGTGATAACCAAAGTTC	59.087	38.462	0.00	0.00	39.30	3.01
599	661	9.865321	AAACTTTAGGAGAAAAACAAAAGTACC	57.135	29.630	0.00	0.00	36.45	3.34
796	861	8.065473	TGAAAACCATGCATATGTATGAGTTT	57.935	30.769	28.94	28.10	39.94	2.66
807	872	7.707893	GCATATGTATGAGTTTCCTGCATTTTT	59.292	33.333	4.29	0.00	35.75	1.94
868	1045	6.510960	GCAAAAACCCATGTTGTATGTTGAAC	60.511	38.462	0.00	0.00	34.13	3.18
941	1120	7.024171	GCCTGAATTTAGTTTCTTACTTGCTC	58.976	38.462	0.00	0.00	38.33	4.26
1067	1265	4.588951	TCCAGTGAACTCTACACAACAGAT	59.411	41.667	0.00	0.00	40.25	2.90
1069	1267	5.406780	CCAGTGAACTCTACACAACAGATTC	59.593	44.000	0.00	0.00	40.25	2.52
1077	1275	6.483640	ACTCTACACAACAGATTCCTCAAAAC	59.516	38.462	0.00	0.00	0.00	2.43
1080	1278	3.005791	CACAACAGATTCCTCAAAACCCC	59.994	47.826	0.00	0.00	0.00	4.95
1188	1386	2.156917	CCTGCAGCACAAGAATCTGAA	58.843	47.619	8.66	0.00	0.00	3.02
1390	1588	3.062042	GCCTTGCAGATTGGTTTTTCAG	58.938	45.455	0.00	0.00	0.00	3.02
1397	1595	6.169094	TGCAGATTGGTTTTTCAGTCAAAAA	58.831	32.000	0.00	0.00	40.93	1.94
1606	1809	9.783081	ATAAAACCAAAAAGATGAGCAAGAAAT	57.217	25.926	0.00	0.00	0.00	2.17

Showing 1 to 25 of 47 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	5.710513	ATGCAAGTTGCTTCAGACAATTA	57.289	34.783	27.17	4.04	45.31	1.40
21	22	4.595762	ATGCAAGTTGCTTCAGACAATT	57.404	36.364	27.17	0.00	45.31	2.32
95	106	6.262273	CCTTTTTCACAGTACTTCTTGCCTAA	59.738	38.462	0.00	0.00	0.00	2.69
106	117	3.630312	TGAGTTGCCCTTTTTCACAGTAC	59.370	43.478	0.00	0.00	0.00	2.73
119	130	0.458669	CAATCAGCCATGAGTTGCCC	59.541	55.000	0.00	0.00	39.29	5.36
161	174	5.889289	TCACAATAGTTTTATTGCCTACCCC	59.111	40.000	7.09	0.00	46.60	4.95
162	175	7.338449	TCTTCACAATAGTTTTATTGCCTACCC	59.662	37.037	7.09	0.00	46.60	3.69
172	187	8.445275	TCACTTGCTTCTTCACAATAGTTTTA	57.555	30.769	0.00	0.00	0.00	1.52
332	368	4.023450	TCACAACAACAACAACCGTTTGTA	60.023	37.500	0.00	0.00	45.69	2.41
334	370	3.309388	TCACAACAACAACAACCGTTTG	58.691	40.909	0.00	0.00	38.83	2.93
336	372	3.442273	AGATCACAACAACAACAACCGTT	59.558	39.130	0.00	0.00	35.01	4.44
338	374	3.691049	AGATCACAACAACAACAACCG	57.309	42.857	0.00	0.00	0.00	4.44
366	408	1.603455	CACGGCATTGTTCCCCACT	60.603	57.895	0.00	0.00	0.00	4.00
487	541	7.595819	TGTCCAGGTCATGAGTTTTATTTTT	57.404	32.000	0.00	0.00	0.00	1.94
492	546	5.441500	TGTTTGTCCAGGTCATGAGTTTTA	58.558	37.500	0.00	0.00	0.00	1.52
517	579	6.665474	TGTGTAGTCGCTTTTTCAAGTAAA	57.335	33.333	0.00	0.00	31.86	2.01
562	624	6.282199	TCTCCTAAAGTTTGTACTAGCAGG	57.718	41.667	0.00	0.00	33.17	4.85
599	661	8.964420	ACATATGTTTGTCCTTTTTATGTTCG	57.036	30.769	1.41	0.00	0.00	3.95
834	901	4.881920	ACATGGGTTTTTGCTTGTATCAC	58.118	39.130	0.00	0.00	0.00	3.06
914	1093	6.582672	GCAAGTAAGAAACTAAATTCAGGCAC	59.417	38.462	0.00	0.00	37.50	5.01
1031	1229	3.751479	TCACTGGATCACCAATATCGG	57.249	47.619	0.00	0.00	46.32	4.18
1032	1230	4.697514	AGTTCACTGGATCACCAATATCG	58.302	43.478	0.00	0.00	46.32	2.92
1067	1265	2.740506	AAACTCGGGGTTTTGAGGAA	57.259	45.000	0.00	0.00	44.77	3.36
1069	1267	2.156917	GGTAAACTCGGGGTTTTGAGG	58.843	52.381	11.82	0.00	44.77	3.86
1080	1278	2.165845	AGGAGAATCACCGGTAAACTCG	59.834	50.000	6.87	0.00	36.25	4.18

Showing 1 to 25 of 44 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.