AutoCloner

Multiple sequence alignment - TraesCS5B01G276100

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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	TraesCS5B01G276100	chr5B	100.000	2354	0	0	1	2354	461696879	461694526	0.000000e+00	4348
1	TraesCS5B01G276100	chr4A	86.078	2356	308	15	6	2354	708315836	708318178	0.000000e+00	2516
2	TraesCS5B01G276100	chr4B	85.986	2362	311	16	1	2354	614060619	614062968	0.000000e+00	2510
3	TraesCS5B01G276100	chr3A	82.738	1848	296	18	65	1906	715426473	715428303	0.000000e+00	1624
4	TraesCS5B01G276100	chr3A	90.287	453	44	0	1902	2354	715435670	715436122	5.600000e-166	593
5	TraesCS5B01G276100	chr2B	89.917	1200	106	6	1161	2352	170883564	170884756	0.000000e+00	1531
6	TraesCS5B01G276100	chr2B	87.336	608	77	0	211	818	170858297	170858904	0.000000e+00	697
7	TraesCS5B01G276100	chr2B	79.683	694	130	10	1664	2352	626301579	626300892	7.560000e-135	490
8	TraesCS5B01G276100	chr2B	91.111	360	31	1	815	1174	170859363	170859721	9.780000e-134	486
9	TraesCS5B01G276100	chr1B	91.304	368	32	0	900	1267	337927815	337927448	9.710000e-139	503
10	TraesCS5B01G276100	chr1B	76.858	713	160	4	1640	2349	670558808	670559518	4.710000e-107	398
11	TraesCS5B01G276100	chr2D	79.190	716	118	19	1664	2352	370012375	370013086	3.540000e-128	468
12	TraesCS5B01G276100	chr2D	74.669	679	158	12	1640	2311	632245565	632244894	2.960000e-74	289
13	TraesCS5B01G276100	chr7D	75.294	680	152	14	1640	2311	426458647	426457976	6.320000e-81	311

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	TraesCS5B01G276100	chr5B	461694526	461696879	2353	True	4348.0	4348	100.0000	1	2354	1	chr5B.!!$R1	2353
1	TraesCS5B01G276100	chr4A	708315836	708318178	2342	False	2516.0	2516	86.0780	6	2354	1	chr4A.!!$F1	2348
2	TraesCS5B01G276100	chr4B	614060619	614062968	2349	False	2510.0	2510	85.9860	1	2354	1	chr4B.!!$F1	2353
3	TraesCS5B01G276100	chr3A	715426473	715428303	1830	False	1624.0	1624	82.7380	65	1906	1	chr3A.!!$F1	1841
4	TraesCS5B01G276100	chr2B	170883564	170884756	1192	False	1531.0	1531	89.9170	1161	2352	1	chr2B.!!$F1	1191
5	TraesCS5B01G276100	chr2B	170858297	170859721	1424	False	591.5	697	89.2235	211	1174	2	chr2B.!!$F2	963
6	TraesCS5B01G276100	chr2B	626300892	626301579	687	True	490.0	490	79.6830	1664	2352	1	chr2B.!!$R1	688
7	TraesCS5B01G276100	chr1B	670558808	670559518	710	False	398.0	398	76.8580	1640	2349	1	chr1B.!!$F1	709
8	TraesCS5B01G276100	chr2D	370012375	370013086	711	False	468.0	468	79.1900	1664	2352	1	chr2D.!!$F1	688
9	TraesCS5B01G276100	chr2D	632244894	632245565	671	True	289.0	289	74.6690	1640	2311	1	chr2D.!!$R1	671
10	TraesCS5B01G276100	chr7D	426457976	426458647	671	True	311.0	311	75.2940	1640	2311	1	chr7D.!!$R1	671

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
348	349	0.526524	GAAGCCTCTCACGTCATCCG	60.527	60.0	0.0	0.0	44.03	4.18	F
810	1033	2.111999	CTGGCTTCGAGTGTTCCCCA	62.112	60.0	0.0	0.0	0.00	4.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1154	1620	0.317799	AAATGCATCCAACGCAGCAA	59.682	45.0	0.0	0.0	43.88	3.91	R
1759	2226	1.122227	AGGCAAACAACATGGCAAGT	58.878	45.0	0.0	0.0	45.08	3.16	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	4.778143	GGCCAGCCAATCGTCGGT	62.778	66.667	3.12	0.00	35.81	4.69
60	61	3.554692	CAGCCAATCGTCGGTCGC	61.555	66.667	0.00	0.00	39.67	5.19
102	103	5.874093	GTGATTATTCACCTCTCCATCCAT	58.126	41.667	6.50	0.00	45.45	3.41
105	106	5.557576	TTATTCACCTCTCCATCCATGAG	57.442	43.478	0.00	0.00	0.00	2.90
128	129	3.365265	CACGCAAGGGCCCAAGAC	61.365	66.667	27.56	9.47	46.39	3.01
137	138	2.047179	GCCCAAGACCGTCTCCAC	60.047	66.667	0.35	0.00	0.00	4.02
138	139	2.879233	GCCCAAGACCGTCTCCACA	61.879	63.158	0.35	0.00	0.00	4.17
145	146	0.611340	GACCGTCTCCACAGGGTACT	60.611	60.000	0.00	0.00	34.59	2.73
146	147	0.611340	ACCGTCTCCACAGGGTACTC	60.611	60.000	0.00	0.00	32.60	2.59
339	340	0.829333	GCATCAGGAGAAGCCTCTCA	59.171	55.000	14.22	0.00	46.97	3.27
348	349	0.526524	GAAGCCTCTCACGTCATCCG	60.527	60.000	0.00	0.00	44.03	4.18
511	515	2.743928	CTGCCCGTGTCCTTGAGC	60.744	66.667	0.00	0.00	0.00	4.26
512	516	4.329545	TGCCCGTGTCCTTGAGCC	62.330	66.667	0.00	0.00	0.00	4.70
647	651	3.589654	CTCCTCCGCTGTCGCCAAA	62.590	63.158	0.00	0.00	0.00	3.28
669	673	3.202706	GTTCTTCCGCCATCGCCC	61.203	66.667	0.00	0.00	0.00	6.13
714	718	3.062500	CTCTCCGCTCTCGCAAGCT	62.063	63.158	7.18	0.00	40.23	3.74
804	1027	2.743718	CCACCTGGCTTCGAGTGT	59.256	61.111	0.00	0.00	0.00	3.55
810	1033	2.111999	CTGGCTTCGAGTGTTCCCCA	62.112	60.000	0.00	0.00	0.00	4.96
838	1304	2.597217	TTGTTTCCAGCGGCCCTG	60.597	61.111	12.83	12.83	41.41	4.45
1085	1551	3.322466	CCCCAAGCCGACTCCTGT	61.322	66.667	0.00	0.00	0.00	4.00
1155	1621	2.814280	ACGGAGAAGACGTCATTGTT	57.186	45.000	19.50	2.44	41.25	2.83
1206	1672	2.419198	GATCAGCTGTCGCCGGAT	59.581	61.111	14.67	0.00	36.60	4.18
1254	1720	2.398429	CTTGATGACAGCAGCGCG	59.602	61.111	0.00	0.00	31.73	6.86
1284	1750	1.147153	GGAGGCCCTCATAGCACAC	59.853	63.158	13.90	0.00	31.08	3.82
1294	1760	1.074471	ATAGCACACGGAGGGGGAT	60.074	57.895	0.00	0.00	0.00	3.85
1299	1765	4.489771	CACGGAGGGGGATGTGCC	62.490	72.222	0.00	0.00	0.00	5.01
1317	1783	0.622665	CCCTTGACCTGGAGCAGAAT	59.377	55.000	0.00	0.00	32.44	2.40
1381	1847	1.676967	GCTTCTGCTCAACCTGGGG	60.677	63.158	0.00	0.00	36.03	4.96
1411	1877	8.303876	TCAGTTTCCTATGTTAGCAAAAATTCC	58.696	33.333	0.00	0.00	0.00	3.01
1412	1878	7.273381	CAGTTTCCTATGTTAGCAAAAATTCCG	59.727	37.037	0.00	0.00	0.00	4.30
1414	1880	5.502079	TCCTATGTTAGCAAAAATTCCGGA	58.498	37.500	0.00	0.00	0.00	5.14
1435	1901	0.963962	TCTGTAGGTGTTCGGTCCAC	59.036	55.000	0.00	0.00	0.00	4.02
1450	1916	0.604578	TCCACGTGTAAGGGTGCTAC	59.395	55.000	15.65	0.00	32.85	3.58
1484	1950	1.080025	GCTAGTTGTCGTCGGCCTT	60.080	57.895	0.00	0.00	0.00	4.35
1508	1974	2.643551	CCTTGTAATCGTTGGGATGCT	58.356	47.619	0.00	0.00	34.93	3.79
1509	1975	2.614057	CCTTGTAATCGTTGGGATGCTC	59.386	50.000	0.00	0.00	34.93	4.26
1535	2001	1.073199	CTCCTTTGAAGGGCCACGT	59.927	57.895	6.18	0.00	46.47	4.49
1593	2059	3.452990	TCCTGTTTGTTCCAGTGACACTA	59.547	43.478	8.02	0.00	0.00	2.74
1597	2063	5.620206	TGTTTGTTCCAGTGACACTATCAT	58.380	37.500	8.02	0.00	40.28	2.45
1610	2076	7.011576	AGTGACACTATCATCTGTACTAGTTCG	59.988	40.741	6.24	0.00	40.28	3.95
1615	2081	9.210329	CACTATCATCTGTACTAGTTCGTCTAT	57.790	37.037	0.00	0.00	0.00	1.98
1616	2082	9.210329	ACTATCATCTGTACTAGTTCGTCTATG	57.790	37.037	0.00	0.00	0.00	2.23
1620	2086	7.769507	TCATCTGTACTAGTTCGTCTATGACTT	59.230	37.037	0.00	0.00	0.00	3.01
1635	2101	7.065085	CGTCTATGACTTCATCTTTCAAATGGT	59.935	37.037	0.00	0.00	37.76	3.55
1672	2139	7.553044	GGTGCTTCCAGTTTATAATGTTAGAGT	59.447	37.037	0.00	0.00	35.97	3.24
1674	2141	9.817809	TGCTTCCAGTTTATAATGTTAGAGTAG	57.182	33.333	0.00	0.00	0.00	2.57
1689	2156	8.644318	TGTTAGAGTAGCCGATTAATTTTCTC	57.356	34.615	0.00	0.00	0.00	2.87
1725	2192	1.523758	GTCTGAACTGCCCAAATCGT	58.476	50.000	0.00	0.00	0.00	3.73
1759	2226	3.822192	CCACCATCGCCTCGTCGA	61.822	66.667	0.00	0.00	43.09	4.20
2013	2511	0.629596	TCACCTCCGTCTATGGTCCT	59.370	55.000	0.00	0.00	30.72	3.85
2061	2559	2.916702	TTGCTGAGCTTCTGAGTCAA	57.083	45.000	5.83	0.00	0.00	3.18
2097	2595	2.985847	GCTTGGCTTGCTTCCGGT	60.986	61.111	0.00	0.00	0.00	5.28
2178	2676	2.439156	AATCGCTTCAGGGCAGCC	60.439	61.111	1.26	1.26	33.29	4.85
2319	2817	6.357367	GGACACTACATTCAACTCCCATATT	58.643	40.000	0.00	0.00	0.00	1.28
2320	2818	6.828785	GGACACTACATTCAACTCCCATATTT	59.171	38.462	0.00	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	2.674084	GGTCACCCAGTTTACGCGC	61.674	63.158	5.73	0.00	0.00	6.86
36	37	4.473520	ACGATTGGCTGGCCTCCG	62.474	66.667	13.05	14.15	36.94	4.63
39	40	4.473520	CCGACGATTGGCTGGCCT	62.474	66.667	13.05	0.00	36.94	5.19
42	43	2.885644	CGACCGACGATTGGCTGG	60.886	66.667	0.00	0.00	45.77	4.85
60	61	3.121030	CTTCGCTCCAAGCCACGG	61.121	66.667	0.00	0.00	38.18	4.94
63	64	3.249189	ACCCTTCGCTCCAAGCCA	61.249	61.111	0.00	0.00	38.18	4.75
67	68	3.054728	TGAATAATCACCCTTCGCTCCAA	60.055	43.478	0.00	0.00	0.00	3.53
93	94	0.695462	TGGGGTCCTCATGGATGGAG	60.695	60.000	0.00	0.00	45.29	3.86
102	103	3.636231	CCTTGCGTGGGGTCCTCA	61.636	66.667	0.00	0.00	0.00	3.86
123	124	1.293498	CCCTGTGGAGACGGTCTTG	59.707	63.158	12.67	1.33	0.00	3.02
128	129	1.321074	GGAGTACCCTGTGGAGACGG	61.321	65.000	0.00	0.00	34.81	4.79
146	147	5.787092	GTCGATGACACCCTTCTGGAAGG	62.787	56.522	19.35	19.35	43.43	3.46
255	256	2.124612	TCCCTATCGTCACGGCGA	60.125	61.111	16.62	0.00	45.32	5.54
256	257	2.025727	GTCCCTATCGTCACGGCG	59.974	66.667	4.80	4.80	0.00	6.46
328	329	0.820871	GGATGACGTGAGAGGCTTCT	59.179	55.000	0.00	0.00	36.01	2.85
501	505	4.329545	GGGTGCGGCTCAAGGACA	62.330	66.667	0.00	0.00	0.00	4.02
621	625	4.390556	AGCGGAGGAGAGGCAGGT	62.391	66.667	0.00	0.00	0.00	4.00
669	673	1.880027	CCTTCACTTCTTTTGGACCGG	59.120	52.381	0.00	0.00	0.00	5.28
738	742	2.813042	GAGTCCAGCGCACAGAGC	60.813	66.667	11.47	0.00	40.87	4.09
747	751	1.298014	CACCAGAAGGGAGTCCAGC	59.702	63.158	12.30	0.00	41.15	4.85
802	1025	4.323477	CGGAGGCGTTGGGGAACA	62.323	66.667	0.00	0.00	0.00	3.18
810	1033	2.258726	GGAAACAAGCGGAGGCGTT	61.259	57.895	0.00	0.00	46.35	4.84
869	1335	4.366684	CCCCCGCAGCCTTCCTTT	62.367	66.667	0.00	0.00	0.00	3.11
981	1447	3.692406	GTCTTCCGACGGGCCACT	61.692	66.667	15.25	0.00	0.00	4.00
1140	1606	1.532868	GCAGCAACAATGACGTCTTCT	59.467	47.619	17.92	0.47	0.00	2.85
1151	1617	1.007502	GCATCCAACGCAGCAACAA	60.008	52.632	0.00	0.00	0.00	2.83
1154	1620	0.317799	AAATGCATCCAACGCAGCAA	59.682	45.000	0.00	0.00	43.88	3.91
1155	1621	0.388778	CAAATGCATCCAACGCAGCA	60.389	50.000	0.00	0.00	43.88	4.41
1176	1642	1.761784	AGCTGATCCTTGAAGCGATCT	59.238	47.619	18.10	3.27	41.88	2.75
1206	1672	2.819154	CGCATGGCCACGATCACA	60.819	61.111	8.16	0.00	0.00	3.58
1254	1720	2.413765	GCCTCCTCGACATCCGTC	59.586	66.667	0.00	0.00	39.75	4.79
1294	1760	3.160585	CTCCAGGTCAAGGGCACA	58.839	61.111	0.00	0.00	0.00	4.57
1299	1765	1.280133	TCATTCTGCTCCAGGTCAAGG	59.720	52.381	0.00	0.00	31.51	3.61
1381	1847	6.985188	TTGCTAACATAGGAAACTGATGAC	57.015	37.500	0.00	0.00	43.88	3.06
1411	1877	1.203994	ACCGAACACCTACAGAATCCG	59.796	52.381	0.00	0.00	0.00	4.18
1412	1878	2.418334	GGACCGAACACCTACAGAATCC	60.418	54.545	0.00	0.00	0.00	3.01
1414	1880	2.028385	GTGGACCGAACACCTACAGAAT	60.028	50.000	0.00	0.00	32.80	2.40
1435	1901	3.887716	AGTATAGGTAGCACCCTTACACG	59.112	47.826	0.00	0.00	39.75	4.49
1450	1916	4.065321	ACTAGCTTGCTTGCAGTATAGG	57.935	45.455	0.00	1.12	34.99	2.57
1484	1950	1.074084	TCCCAACGATTACAAGGCCAA	59.926	47.619	5.01	0.00	0.00	4.52
1508	1974	2.113860	CTTCAAAGGAGCGATTGGGA	57.886	50.000	0.00	0.00	0.00	4.37
1535	2001	2.284754	TGCAAGGCATAACCACAGAA	57.715	45.000	0.00	0.00	43.14	3.02
1593	2059	7.934665	AGTCATAGACGAACTAGTACAGATGAT	59.065	37.037	0.00	0.00	37.67	2.45
1597	2063	7.101700	TGAAGTCATAGACGAACTAGTACAGA	58.898	38.462	0.00	0.00	37.67	3.41
1610	2076	8.273780	ACCATTTGAAAGATGAAGTCATAGAC	57.726	34.615	0.00	0.00	36.57	2.59
1615	2081	6.515531	GCTTGACCATTTGAAAGATGAAGTCA	60.516	38.462	0.00	0.00	29.67	3.41
1616	2082	5.860716	GCTTGACCATTTGAAAGATGAAGTC	59.139	40.000	0.00	0.00	0.00	3.01
1620	2086	4.460382	GGAGCTTGACCATTTGAAAGATGA	59.540	41.667	0.00	0.00	0.00	2.92
1635	2101	3.580084	AAGCACCCTGGAGCTTGA	58.420	55.556	18.23	0.00	46.91	3.02
1674	2141	3.627577	TCCAGCTGAGAAAATTAATCGGC	59.372	43.478	17.39	9.25	44.10	5.54
1689	2156	2.046892	CCCCTGACGTTCCAGCTG	60.047	66.667	6.78	6.78	32.97	4.24
1759	2226	1.122227	AGGCAAACAACATGGCAAGT	58.878	45.000	0.00	0.00	45.08	3.16
2061	2559	4.740822	ATTCCTGGCGGCGGCTTT	62.741	61.111	33.21	11.25	39.81	3.51
2097	2595	4.561734	GCCCGGTAAATTTGGTTGAAATCA	60.562	41.667	0.00	0.00	32.76	2.57
2319	2817	3.055530	GTGAGGAGGAGAGAGCATTCAAA	60.056	47.826	0.00	0.00	0.00	2.69
2320	2818	2.499289	GTGAGGAGGAGAGAGCATTCAA	59.501	50.000	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.