AutoCloner

Multiple sequence alignment - TraesCS1B01G195500

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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	TraesCS1B01G195500	chr1B	100.000	2351	0	0	1	2351	350632254	350629904	0.000000e+00	4342
1	TraesCS1B01G195500	chr1B	89.737	419	34	7	1641	2056	669802665	669803077	5.750000e-146	527
2	TraesCS1B01G195500	chr1B	89.474	209	20	1	576	782	643042824	643043032	1.790000e-66	263
3	TraesCS1B01G195500	chr1B	88.517	209	21	3	576	782	593563261	593563468	1.390000e-62	250
4	TraesCS1B01G195500	chr1D	95.491	865	31	4	781	1639	261373340	261374202	0.000000e+00	1375
5	TraesCS1B01G195500	chr1D	89.952	418	36	4	1641	2056	458743046	458743459	3.440000e-148	534
6	TraesCS1B01G195500	chr1D	97.386	306	6	1	2047	2350	458744136	458744441	9.630000e-144	520
7	TraesCS1B01G195500	chr1D	93.510	339	9	3	1	336	261372822	261373150	2.100000e-135	492
8	TraesCS1B01G195500	chr1D	89.806	206	19	1	579	782	71764667	71764462	1.790000e-66	263
9	TraesCS1B01G195500	chr1D	89.552	201	19	2	378	577	261373148	261373347	1.080000e-63	254
10	TraesCS1B01G195500	chr1D	88.835	206	21	1	579	782	18864558	18864763	3.880000e-63	252
11	TraesCS1B01G195500	chr1D	88.462	130	14	1	575	703	486996012	486996141	3.130000e-34	156
12	TraesCS1B01G195500	chr1A	91.985	811	46	8	781	1578	338601039	338600235	0.000000e+00	1120
13	TraesCS1B01G195500	chr1A	90.777	206	17	1	579	782	566517100	566517305	8.280000e-70	274
14	TraesCS1B01G195500	chr1A	92.126	127	6	2	224	347	338601352	338601227	2.400000e-40	176
15	TraesCS1B01G195500	chr6D	90.670	418	32	5	1641	2056	148621808	148622220	1.230000e-152	549
16	TraesCS1B01G195500	chr6D	89.387	424	39	4	1635	2056	467362922	467363341	1.600000e-146	529
17	TraesCS1B01G195500	chr6D	97.394	307	6	1	2047	2351	310007841	310007535	2.680000e-144	521
18	TraesCS1B01G195500	chr6D	97.068	307	7	1	2047	2351	467364018	467364324	1.250000e-142	516
19	TraesCS1B01G195500	chr2D	90.670	418	32	5	1641	2056	527886473	527886885	1.230000e-152	549
20	TraesCS1B01G195500	chr2D	90.094	424	33	7	1636	2056	566728577	566728160	2.060000e-150	542
21	TraesCS1B01G195500	chr2D	97.068	307	7	1	2047	2351	618544866	618545172	1.250000e-142	516
22	TraesCS1B01G195500	chr2D	96.743	307	8	1	2047	2351	516844877	516845183	5.800000e-141	510
23	TraesCS1B01G195500	chr2D	96.743	307	8	1	2047	2351	565161138	565160832	5.800000e-141	510
24	TraesCS1B01G195500	chr3D	90.191	418	35	4	1641	2056	413947441	413947028	7.390000e-150	540
25	TraesCS1B01G195500	chr3D	89.524	420	36	6	1641	2058	92379868	92380281	2.070000e-145	525
26	TraesCS1B01G195500	chr3D	97.068	307	7	1	2047	2351	26669407	26669101	1.250000e-142	516
27	TraesCS1B01G195500	chr6B	89.362	423	38	5	1636	2056	572077086	572077503	2.070000e-145	525
28	TraesCS1B01G195500	chr6B	90.196	204	16	3	582	782	542504077	542503875	1.790000e-66	263
29	TraesCS1B01G195500	chr6B	88.626	211	21	2	575	782	87674524	87674314	1.080000e-63	254
30	TraesCS1B01G195500	chr4D	97.068	307	7	1	2047	2351	450521385	450521691	1.250000e-142	516
31	TraesCS1B01G195500	chr4D	96.743	307	8	1	2047	2351	508427857	508428163	5.800000e-141	510
32	TraesCS1B01G195500	chr4D	82.781	302	26	21	1026	1323	501234114	501233835	1.800000e-61	246
33	TraesCS1B01G195500	chr4D	90.419	167	15	1	1158	1323	501161638	501161472	3.930000e-53	219
34	TraesCS1B01G195500	chr5A	84.641	306	27	15	1022	1323	683125619	683125908	1.060000e-73	287
35	TraesCS1B01G195500	chr5A	88.479	217	22	1	576	789	560808246	560808462	2.320000e-65	259
36	TraesCS1B01G195500	chr3B	91.748	206	14	2	579	782	61546135	61546339	1.380000e-72	283
37	TraesCS1B01G195500	chr3B	90.291	206	18	1	579	782	62672649	62672444	3.850000e-68	268
38	TraesCS1B01G195500	chr7B	89.498	219	18	3	579	794	645396204	645395988	2.980000e-69	272
39	TraesCS1B01G195500	chr7B	90.047	211	19	1	574	782	714779749	714779959	2.980000e-69	272
40	TraesCS1B01G195500	chr5B	90.732	205	17	2	579	782	586274534	586274331	2.980000e-69	272
41	TraesCS1B01G195500	chr5B	89.320	206	19	2	579	782	387765921	387765717	3.000000e-64	255
42	TraesCS1B01G195500	chr2B	90.338	207	17	1	579	782	27548138	27547932	3.850000e-68	268
43	TraesCS1B01G195500	chrUn	89.524	210	18	3	576	782	74802855	74803063	1.790000e-66	263
44	TraesCS1B01G195500	chrUn	88.350	206	21	3	579	782	138415666	138415870	6.490000e-61	244
45	TraesCS1B01G195500	chrUn	87.923	207	21	3	579	782	138271934	138272139	8.400000e-60	241
46	TraesCS1B01G195500	chrUn	87.981	208	20	4	579	782	171112601	171112395	8.400000e-60	241
47	TraesCS1B01G195500	chrUn	87.864	206	22	3	579	782	138345952	138346156	3.020000e-59	239
48	TraesCS1B01G195500	chrUn	87.864	206	22	3	579	782	312018740	312018944	3.020000e-59	239
49	TraesCS1B01G195500	chrUn	87.379	206	24	1	579	782	73675783	73675578	3.910000e-58	235
50	TraesCS1B01G195500	chr4B	88.942	208	17	5	579	782	560238409	560238614	3.880000e-63	252
51	TraesCS1B01G195500	chr4B	82.353	306	31	16	1022	1323	645084442	645084156	6.490000e-61	244
52	TraesCS1B01G195500	chr6A	87.923	207	21	3	579	782	558457705	558457500	8.400000e-60	241
53	TraesCS1B01G195500	chr6A	87.923	207	21	3	579	782	558461025	558460820	8.400000e-60	241
54	TraesCS1B01G195500	chr4A	86.916	214	24	3	578	788	733355899	733355687	1.090000e-58	237

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	TraesCS1B01G195500	chr1B	350629904	350632254	2350	True	4342.0	4342	100.0000	1	2351	1	chr1B.!!$R1	2350
1	TraesCS1B01G195500	chr1D	261372822	261374202	1380	False	707.0	1375	92.8510	1	1639	3	chr1D.!!$F3	1638
2	TraesCS1B01G195500	chr1D	458743046	458744441	1395	False	527.0	534	93.6690	1641	2350	2	chr1D.!!$F4	709
3	TraesCS1B01G195500	chr1A	338600235	338601352	1117	True	648.0	1120	92.0555	224	1578	2	chr1A.!!$R1	1354
4	TraesCS1B01G195500	chr6D	467362922	467364324	1402	False	522.5	529	93.2275	1635	2351	2	chr6D.!!$F2	716
5	TraesCS1B01G195500	chr6A	558457500	558461025	3525	True	241.0	241	87.9230	579	782	2	chr6A.!!$R1	203

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
570	579	0.955428	TCTCGTGGCCACAAAGCATC	60.955	55.0	34.16	6.15	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1750	1807	0.109412	AATCGACGACTGGGACGAAC	60.109	55.0	0.0	0.0	38.22	3.95	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
101	102	1.240256	GTCTCGTGACTGTCTGGAGT	58.760	55.000	20.24	0.00	39.94	3.85
122	123	0.968901	TGGACCGCTATGTCGACCTT	60.969	55.000	14.12	3.01	36.07	3.50
123	124	1.027357	GGACCGCTATGTCGACCTTA	58.973	55.000	14.12	4.14	36.07	2.69
213	214	6.604735	CATGTAATGCAGGTAAGTCCTTAC	57.395	41.667	8.39	8.39	39.97	2.34
214	215	6.349300	CATGTAATGCAGGTAAGTCCTTACT	58.651	40.000	14.89	1.64	39.97	2.24
215	216	7.497595	CATGTAATGCAGGTAAGTCCTTACTA	58.502	38.462	14.89	3.08	39.97	1.82
218	219	7.835682	TGTAATGCAGGTAAGTCCTTACTAGTA	59.164	37.037	14.89	0.00	45.67	1.82
221	222	6.962182	TGCAGGTAAGTCCTTACTAGTACTA	58.038	40.000	14.89	1.89	45.67	1.82
222	223	7.580910	TGCAGGTAAGTCCTTACTAGTACTAT	58.419	38.462	14.89	0.00	45.67	2.12
237	238	7.163441	ACTAGTACTATCTAGCTAACAGCCTC	58.837	42.308	2.33	0.00	43.77	4.70
304	311	1.732259	GTCCACCGTGTTGCTCTTATG	59.268	52.381	0.00	0.00	0.00	1.90
336	343	2.505118	GCTCTGACACCGAGCGAC	60.505	66.667	1.35	0.00	43.69	5.19
337	344	2.983930	GCTCTGACACCGAGCGACT	61.984	63.158	1.35	0.00	43.69	4.18
338	345	1.154131	CTCTGACACCGAGCGACTG	60.154	63.158	0.00	0.00	0.00	3.51
339	346	1.578206	CTCTGACACCGAGCGACTGA	61.578	60.000	0.00	0.00	0.00	3.41
340	347	1.442857	CTGACACCGAGCGACTGAC	60.443	63.158	0.00	0.00	0.00	3.51
341	348	2.502080	GACACCGAGCGACTGACG	60.502	66.667	0.00	0.00	45.66	4.35
342	349	2.962827	GACACCGAGCGACTGACGA	61.963	63.158	3.29	0.00	45.77	4.20
343	350	2.254703	GACACCGAGCGACTGACGAT	62.255	60.000	3.29	0.00	45.46	3.73
344	351	1.869574	CACCGAGCGACTGACGATG	60.870	63.158	3.29	0.00	41.91	3.84
345	352	2.951745	CCGAGCGACTGACGATGC	60.952	66.667	3.29	0.00	41.91	3.91
346	353	2.101185	CGAGCGACTGACGATGCT	59.899	61.111	3.29	0.00	41.91	3.79
347	354	1.515088	CGAGCGACTGACGATGCTT	60.515	57.895	3.29	0.00	41.91	3.91
348	355	1.073216	CGAGCGACTGACGATGCTTT	61.073	55.000	3.29	0.00	41.91	3.51
349	356	1.071605	GAGCGACTGACGATGCTTTT	58.928	50.000	3.29	0.00	41.91	2.27

Showing 1 to 25 of 95 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	4.340076	CAAACTTGCAATGCGCCA	57.660	50.000	4.18	0.00	41.33	5.69
101	102	1.381928	GGTCGACATAGCGGTCCAGA	61.382	60.000	18.91	0.00	34.24	3.86
122	123	4.963373	TCCTTGAAACGTGGAACTTCATA	58.037	39.130	0.75	0.00	32.11	2.15
123	124	3.815809	TCCTTGAAACGTGGAACTTCAT	58.184	40.909	0.75	0.00	32.11	2.57
165	166	9.573166	TGTAATAATCAGTGATTCTATTTGGGG	57.427	33.333	21.49	0.00	33.95	4.96
206	207	9.995003	TGTTAGCTAGATAGTACTAGTAAGGAC	57.005	37.037	8.85	0.00	41.10	3.85
208	209	8.938906	GCTGTTAGCTAGATAGTACTAGTAAGG	58.061	40.741	8.85	0.00	41.10	2.69
209	210	8.938906	GGCTGTTAGCTAGATAGTACTAGTAAG	58.061	40.741	8.85	6.32	41.99	2.34
210	211	8.658619	AGGCTGTTAGCTAGATAGTACTAGTAA	58.341	37.037	8.85	0.00	41.99	2.24
211	212	8.204903	AGGCTGTTAGCTAGATAGTACTAGTA	57.795	38.462	8.85	0.00	41.99	1.82
212	213	7.081857	AGGCTGTTAGCTAGATAGTACTAGT	57.918	40.000	8.85	0.00	41.99	2.57
213	214	6.596497	GGAGGCTGTTAGCTAGATAGTACTAG	59.404	46.154	8.85	0.00	41.99	2.57
214	215	6.272792	AGGAGGCTGTTAGCTAGATAGTACTA	59.727	42.308	4.77	4.77	41.99	1.82
215	216	5.073965	AGGAGGCTGTTAGCTAGATAGTACT	59.926	44.000	0.00	0.00	41.99	2.73
218	219	4.148838	CAGGAGGCTGTTAGCTAGATAGT	58.851	47.826	0.00	0.00	41.99	2.12
221	222	2.962421	GACAGGAGGCTGTTAGCTAGAT	59.038	50.000	0.00	0.00	41.99	1.98
222	223	2.291605	TGACAGGAGGCTGTTAGCTAGA	60.292	50.000	0.00	0.00	41.99	2.43
291	295	3.555956	CGACCCATACATAAGAGCAACAC	59.444	47.826	0.00	0.00	0.00	3.32
304	311	1.732259	CAGAGCAAACACGACCCATAC	59.268	52.381	0.00	0.00	0.00	2.39
360	367	0.464013	TCGTCAGTTCCCCGCAAAAA	60.464	50.000	0.00	0.00	0.00	1.94
361	368	0.250553	ATCGTCAGTTCCCCGCAAAA	60.251	50.000	0.00	0.00	0.00	2.44
362	369	0.953471	CATCGTCAGTTCCCCGCAAA	60.953	55.000	0.00	0.00	0.00	3.68
363	370	1.375396	CATCGTCAGTTCCCCGCAA	60.375	57.895	0.00	0.00	0.00	4.85
364	371	2.264480	CATCGTCAGTTCCCCGCA	59.736	61.111	0.00	0.00	0.00	5.69
365	372	2.292794	TAGCATCGTCAGTTCCCCGC	62.293	60.000	0.00	0.00	0.00	6.13

Showing 1 to 25 of 89 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.