AutoCloner

Multiple sequence alignment - TraesCS1B01G245700

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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	TraesCS1B01G245700	chr1B	100.000	2477	0	0	1	2477	434834384	434836860	0.000000e+00	4575.0
1	TraesCS1B01G245700	chr1B	89.189	74	5	3	1135	1208	435043015	435043085	3.390000e-14	89.8
2	TraesCS1B01G245700	chr1D	95.197	2415	68	16	78	2477	322164183	322166564	0.000000e+00	3773.0
3	TraesCS1B01G245700	chr1D	89.610	77	5	3	1132	1208	322262810	322262883	7.290000e-16	95.3
4	TraesCS1B01G245700	chr1D	100.000	49	0	0	1	49	322164135	322164183	9.430000e-15	91.6
5	TraesCS1B01G245700	chr1A	91.797	1597	89	16	735	2315	405868715	405870285	0.000000e+00	2185.0
6	TraesCS1B01G245700	chr1A	87.725	611	36	13	88	668	405868024	405868625	0.000000e+00	676.0
7	TraesCS1B01G245700	chr1A	89.610	77	5	3	1132	1208	406143322	406143395	7.290000e-16	95.3
8	TraesCS1B01G245700	chr1A	72.792	283	65	11	2012	2290	36128924	36129198	4.390000e-13	86.1
9	TraesCS1B01G245700	chr6D	93.293	164	7	4	2317	2477	97813584	97813746	3.180000e-59	239.0
10	TraesCS1B01G245700	chr6D	92.547	161	11	1	2314	2473	255474762	255474602	1.920000e-56	230.0
11	TraesCS1B01G245700	chr6D	77.619	210	42	5	2097	2301	156452054	156452263	3.350000e-24	122.0
12	TraesCS1B01G245700	chr5D	92.073	164	12	1	2315	2477	205290614	205290451	1.920000e-56	230.0
13	TraesCS1B01G245700	chr5D	92.500	160	9	3	2314	2471	455619636	455619794	2.480000e-55	226.0
14	TraesCS1B01G245700	chr3D	93.038	158	10	1	2315	2471	517553458	517553615	1.920000e-56	230.0
15	TraesCS1B01G245700	chr3D	91.617	167	9	5	2315	2477	24107000	24106835	2.480000e-55	226.0
16	TraesCS1B01G245700	chr2B	93.038	158	10	1	2315	2471	470075487	470075644	1.920000e-56	230.0
17	TraesCS1B01G245700	chr2B	91.515	165	13	1	2314	2477	102129643	102129479	2.480000e-55	226.0
18	TraesCS1B01G245700	chr7B	75.415	301	64	10	2024	2319	737747458	737747163	1.190000e-28	137.0
19	TraesCS1B01G245700	chr7B	74.747	297	66	9	2024	2316	737020314	737020023	9.300000e-25	124.0
20	TraesCS1B01G245700	chr7B	74.419	301	67	10	2024	2319	737320842	737320547	1.200000e-23	121.0
21	TraesCS1B01G245700	chr7B	74.086	301	68	10	2024	2319	736971516	736971221	5.600000e-22	115.0
22	TraesCS1B01G245700	chr6A	78.095	210	39	6	2101	2306	209903605	209903811	2.590000e-25	126.0
23	TraesCS1B01G245700	chrUn	84.058	69	6	4	2016	2082	23399827	23399892	7.400000e-06	62.1

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	TraesCS1B01G245700	chr1B	434834384	434836860	2476	False	4575.0	4575	100.0000	1	2477	1	chr1B.!!$F1	2476
1	TraesCS1B01G245700	chr1D	322164135	322166564	2429	False	1932.3	3773	97.5985	1	2477	2	chr1D.!!$F2	2476
2	TraesCS1B01G245700	chr1A	405868024	405870285	2261	False	1430.5	2185	89.7610	88	2315	2	chr1A.!!$F3	2227

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
64	65	0.238817	GCTCGGCGTACAGGAGATAG	59.761	60.0	6.85	0.0	0.0	2.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1865	1970	0.378257	CCGATGGTCTGGAAAATGCG	59.622	55.0	0.0	0.0	0.0	4.73	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
48	49	2.395690	CGAAATCACCGCGTGCTC	59.604	61.111	4.92	1.16	32.98	4.26
49	50	2.395690	GAAATCACCGCGTGCTCG	59.604	61.111	4.92	3.31	40.37	5.03
59	60	4.111016	CGTGCTCGGCGTACAGGA	62.111	66.667	6.85	0.00	0.00	3.86
60	61	2.202623	GTGCTCGGCGTACAGGAG	60.203	66.667	6.85	0.00	0.00	3.69
61	62	2.360726	TGCTCGGCGTACAGGAGA	60.361	61.111	6.85	0.00	0.00	3.71
62	63	1.753078	TGCTCGGCGTACAGGAGAT	60.753	57.895	6.85	0.00	0.00	2.75
63	64	0.464916	TGCTCGGCGTACAGGAGATA	60.465	55.000	6.85	0.00	0.00	1.98
64	65	0.238817	GCTCGGCGTACAGGAGATAG	59.761	60.000	6.85	0.00	0.00	2.08
65	66	1.595466	CTCGGCGTACAGGAGATAGT	58.405	55.000	6.85	0.00	0.00	2.12
66	67	2.763933	CTCGGCGTACAGGAGATAGTA	58.236	52.381	6.85	0.00	0.00	1.82
67	68	3.336468	CTCGGCGTACAGGAGATAGTAT	58.664	50.000	6.85	0.00	0.00	2.12
68	69	4.502016	CTCGGCGTACAGGAGATAGTATA	58.498	47.826	6.85	0.00	0.00	1.47
69	70	5.095145	TCGGCGTACAGGAGATAGTATAT	57.905	43.478	6.85	0.00	0.00	0.86
70	71	5.494724	TCGGCGTACAGGAGATAGTATATT	58.505	41.667	6.85	0.00	0.00	1.28
71	72	5.942236	TCGGCGTACAGGAGATAGTATATTT	59.058	40.000	6.85	0.00	0.00	1.40
72	73	6.432162	TCGGCGTACAGGAGATAGTATATTTT	59.568	38.462	6.85	0.00	0.00	1.82
73	74	6.746364	CGGCGTACAGGAGATAGTATATTTTC	59.254	42.308	0.00	0.00	0.00	2.29
74	75	6.746364	GGCGTACAGGAGATAGTATATTTTCG	59.254	42.308	0.00	0.00	0.00	3.46
75	76	7.303998	GCGTACAGGAGATAGTATATTTTCGT	58.696	38.462	0.00	0.00	0.00	3.85
76	77	8.446273	GCGTACAGGAGATAGTATATTTTCGTA	58.554	37.037	0.00	0.00	0.00	3.43
116	117	3.081061	TCGATGGTCCAAAATTCCACAG	58.919	45.455	0.00	0.00	33.91	3.66
306	309	4.662961	CACGCTGACTCACGGGCA	62.663	66.667	0.00	0.00	0.00	5.36
477	506	1.081094	CGCCGTCCGGTTTCTTTATT	58.919	50.000	7.66	0.00	37.65	1.40
507	536	0.693622	TCCGGGTCATGGTTTAAGCA	59.306	50.000	0.00	0.00	0.00	3.91
668	699	6.403200	GCTGCGAGGACTTTGAATTGTATTTA	60.403	38.462	0.00	0.00	0.00	1.40
670	701	6.428465	TGCGAGGACTTTGAATTGTATTTACA	59.572	34.615	0.00	0.00	0.00	2.41
672	703	7.360946	GCGAGGACTTTGAATTGTATTTACACT	60.361	37.037	0.00	0.00	35.64	3.55
769	838	7.931948	ACAGTACTAGTGGTATTCAATTATGCC	59.068	37.037	5.39	0.00	32.56	4.40
1212	1298	4.003788	CGGGCACTGAGGGACGTT	62.004	66.667	0.00	0.00	36.31	3.99
1490	1576	2.630098	CAGCCTAGCTAGCCAGTATTCA	59.370	50.000	15.74	0.00	36.40	2.57
1519	1605	6.432783	TCCAACAAATTGTCTGGACGATATTT	59.567	34.615	18.97	4.03	34.78	1.40
1601	1690	8.854117	GCCATGTATCTTTCCTTTTTGATATCT	58.146	33.333	3.98	0.00	0.00	1.98
1625	1714	9.822185	TCTATTTACACGTACTGACATACTAGA	57.178	33.333	0.00	0.00	0.00	2.43
1864	1969	5.694910	GTGTTTATTCGTGACTTTCTCTCCA	59.305	40.000	0.00	0.00	0.00	3.86
1865	1970	5.694910	TGTTTATTCGTGACTTTCTCTCCAC	59.305	40.000	0.00	0.00	0.00	4.02
1957	2065	2.525381	CCCCTCGGCTGCTAGGAT	60.525	66.667	18.98	0.00	34.58	3.24
1971	2079	5.750228	GCTGCTAGGATAAATTCTCCCCAAT	60.750	44.000	0.00	0.00	32.89	3.16
2014	2122	1.893137	TCGCTTCCTCTTTGTCTGCTA	59.107	47.619	0.00	0.00	0.00	3.49
2037	2145	0.902516	GCAGGGAGGAGAGTCACAGT	60.903	60.000	0.00	0.00	0.00	3.55
2086	2194	5.398012	GGTTAGGGCTTTCTAATCCTCACAT	60.398	44.000	0.00	0.00	32.62	3.21
2093	2201	3.266510	TCTAATCCTCACATGTGTGGC	57.733	47.619	32.73	0.00	45.65	5.01
2123	2231	2.289002	CAGATGGCGGCACTTATTCTTC	59.711	50.000	16.34	5.17	0.00	2.87
2130	2238	3.483738	GCGGCACTTATTCTTCGAGTTTC	60.484	47.826	0.00	0.00	0.00	2.78
2143	2251	3.431415	TCGAGTTTCTCTTCTGGATCCA	58.569	45.455	15.27	15.27	0.00	3.41
2169	2277	6.464222	TCCTACTCAAGTTTGTACATCTTGG	58.536	40.000	26.39	21.61	38.99	3.61
2240	2348	4.160252	GGTGTGGTTAGGGTTCTTATCGTA	59.840	45.833	0.00	0.00	0.00	3.43
2323	2432	3.599343	CACTGCAGCTCCATACAAGTTA	58.401	45.455	15.27	0.00	0.00	2.24
2352	2462	8.700439	AGCCTCCTCTAGTTTTATAGTTCTAG	57.300	38.462	0.00	0.00	33.41	2.43
2383	2493	7.894364	AGTTGGTCCTAGTTGACTAATTAGAGA	59.106	37.037	19.38	2.02	37.91	3.10
2422	2532	9.258826	CTTGTCCTCATAATTAGAATCTCAGTG	57.741	37.037	0.00	0.00	0.00	3.66
2439	2549	5.598830	TCTCAGTGTGGTTCTAATATCCTCC	59.401	44.000	0.00	0.00	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	5.814764	AATATACTATCTCCTGTACGCCG	57.185	43.478	0.00	0.00	0.00	6.46
49	50	6.746364	CGAAAATATACTATCTCCTGTACGCC	59.254	42.308	0.00	0.00	0.00	5.68
50	51	7.303998	ACGAAAATATACTATCTCCTGTACGC	58.696	38.462	0.00	0.00	0.00	4.42
51	52	9.752274	GTACGAAAATATACTATCTCCTGTACG	57.248	37.037	0.00	0.00	0.00	3.67
54	55	8.288208	CGTGTACGAAAATATACTATCTCCTGT	58.712	37.037	0.00	0.00	43.02	4.00
55	56	7.270793	GCGTGTACGAAAATATACTATCTCCTG	59.729	40.741	8.82	0.00	43.02	3.86
56	57	7.040892	TGCGTGTACGAAAATATACTATCTCCT	60.041	37.037	8.82	0.00	43.02	3.69
57	58	7.060403	GTGCGTGTACGAAAATATACTATCTCC	59.940	40.741	8.82	0.00	43.02	3.71
58	59	7.802251	AGTGCGTGTACGAAAATATACTATCTC	59.198	37.037	8.82	0.00	43.02	2.75
59	60	7.646314	AGTGCGTGTACGAAAATATACTATCT	58.354	34.615	8.82	0.00	43.02	1.98
60	61	7.848716	AGTGCGTGTACGAAAATATACTATC	57.151	36.000	8.82	0.00	43.02	2.08
61	62	7.703621	ACAAGTGCGTGTACGAAAATATACTAT	59.296	33.333	8.82	0.00	43.02	2.12
62	63	7.028962	ACAAGTGCGTGTACGAAAATATACTA	58.971	34.615	8.82	0.00	43.02	1.82
63	64	5.865552	ACAAGTGCGTGTACGAAAATATACT	59.134	36.000	8.82	0.00	43.02	2.12
64	65	6.086319	ACAAGTGCGTGTACGAAAATATAC	57.914	37.500	8.82	0.00	43.02	1.47
65	66	5.003684	CGACAAGTGCGTGTACGAAAATATA	59.996	40.000	8.82	0.00	43.02	0.86
66	67	4.201551	CGACAAGTGCGTGTACGAAAATAT	60.202	41.667	8.82	0.00	43.02	1.28
67	68	3.119956	CGACAAGTGCGTGTACGAAAATA	59.880	43.478	8.82	0.00	43.02	1.40
68	69	2.097104	CGACAAGTGCGTGTACGAAAAT	60.097	45.455	8.82	0.00	43.02	1.82
69	70	1.255859	CGACAAGTGCGTGTACGAAAA	59.744	47.619	8.82	0.00	43.02	2.29
70	71	0.847670	CGACAAGTGCGTGTACGAAA	59.152	50.000	8.82	0.00	43.02	3.46
71	72	0.029167	TCGACAAGTGCGTGTACGAA	59.971	50.000	8.82	0.00	43.02	3.85
72	73	0.029167	TTCGACAAGTGCGTGTACGA	59.971	50.000	8.82	0.00	43.02	3.43
73	74	0.158096	GTTCGACAAGTGCGTGTACG	59.842	55.000	0.00	0.00	43.27	3.67
74	75	1.484356	AGTTCGACAAGTGCGTGTAC	58.516	50.000	0.00	0.00	0.00	2.90
75	76	3.495193	GATAGTTCGACAAGTGCGTGTA	58.505	45.455	0.00	0.00	0.00	2.90
76	77	2.325761	GATAGTTCGACAAGTGCGTGT	58.674	47.619	0.00	0.00	0.00	4.49
231	233	3.947834	GGCAGGAGTTGTATATTTGCTGT	59.052	43.478	0.00	0.00	32.41	4.40
306	309	1.632046	CGTAAGCGCGGTTGGTCATT	61.632	55.000	31.91	7.77	0.00	2.57
507	536	2.093306	TTGATCGATCGTGTGCCTTT	57.907	45.000	20.03	0.00	0.00	3.11
668	699	6.237154	AGAAGAAACGACCTACTAGTAGTGT	58.763	40.000	24.84	21.36	0.00	3.55
670	701	6.939163	TCAAGAAGAAACGACCTACTAGTAGT	59.061	38.462	24.84	14.82	0.00	2.73
672	703	7.663081	TCTTCAAGAAGAAACGACCTACTAGTA	59.337	37.037	9.93	1.89	43.79	1.82
769	838	1.966451	GACTTTGGGCACTCCGTGG	60.966	63.158	0.00	0.00	38.76	4.94
1490	1576	4.216257	CGTCCAGACAATTTGTTGGATTCT	59.784	41.667	23.83	8.00	38.66	2.40
1519	1605	8.615211	CGGTGTATAGTGTACACATTAGAAGTA	58.385	37.037	27.06	9.05	46.96	2.24
1677	1767	9.478768	TCGGTCGCATATATAACAAAGAAAATA	57.521	29.630	0.00	0.00	0.00	1.40
1678	1768	8.280497	GTCGGTCGCATATATAACAAAGAAAAT	58.720	33.333	0.00	0.00	0.00	1.82
1679	1769	7.278203	TGTCGGTCGCATATATAACAAAGAAAA	59.722	33.333	0.00	0.00	0.00	2.29
1680	1770	6.757478	TGTCGGTCGCATATATAACAAAGAAA	59.243	34.615	0.00	0.00	0.00	2.52
1681	1771	6.274579	TGTCGGTCGCATATATAACAAAGAA	58.725	36.000	0.00	0.00	0.00	2.52
1682	1772	5.834169	TGTCGGTCGCATATATAACAAAGA	58.166	37.500	0.00	0.00	0.00	2.52
1683	1773	6.519353	TTGTCGGTCGCATATATAACAAAG	57.481	37.500	0.00	0.00	0.00	2.77
1684	1774	6.905544	TTTGTCGGTCGCATATATAACAAA	57.094	33.333	0.00	0.00	34.15	2.83
1685	1775	8.590719	TTATTTGTCGGTCGCATATATAACAA	57.409	30.769	0.00	0.00	0.00	2.83
1686	1776	8.766000	ATTATTTGTCGGTCGCATATATAACA	57.234	30.769	0.00	0.00	0.00	2.41
1864	1969	1.086696	CGATGGTCTGGAAAATGCGT	58.913	50.000	0.00	0.00	0.00	5.24
1865	1970	0.378257	CCGATGGTCTGGAAAATGCG	59.622	55.000	0.00	0.00	0.00	4.73
1906	2014	4.451900	GTGACGGAGGAATCATACCATTT	58.548	43.478	0.00	0.00	0.00	2.32
1914	2022	0.976073	GAGGGGTGACGGAGGAATCA	60.976	60.000	0.00	0.00	0.00	2.57
1957	2065	4.393680	CGACGAAACATTGGGGAGAATTTA	59.606	41.667	0.00	0.00	0.00	1.40
2014	2122	1.305718	GACTCTCCTCCCTGCCACT	60.306	63.158	0.00	0.00	0.00	4.00
2037	2145	2.103373	CTACTAGCTGGAGTGAAGGCA	58.897	52.381	3.17	0.00	0.00	4.75
2123	2231	3.876274	TGGATCCAGAAGAGAAACTCG	57.124	47.619	11.44	0.00	35.36	4.18
2143	2251	7.607991	CCAAGATGTACAAACTTGAGTAGGATT	59.392	37.037	30.29	1.85	42.12	3.01
2153	2261	6.237901	TGACTATGCCAAGATGTACAAACTT	58.762	36.000	0.00	6.25	0.00	2.66
2169	2277	1.269831	CGTAGGCTCCCTTGACTATGC	60.270	57.143	0.00	0.00	34.61	3.14
2240	2348	1.134995	ACATCTCGTGATCGTGCATGT	60.135	47.619	5.68	0.00	38.33	3.21
2302	2411	2.105006	ACTTGTATGGAGCTGCAGTG	57.895	50.000	14.98	4.30	0.00	3.66
2323	2432	6.386284	ACTATAAAACTAGAGGAGGCTCCAT	58.614	40.000	33.86	23.77	39.61	3.41
2352	2462	5.725325	AGTCAACTAGGACCAACTAGAAC	57.275	43.478	7.20	3.23	42.40	3.01
2415	2525	5.598830	GGAGGATATTAGAACCACACTGAGA	59.401	44.000	0.00	0.00	0.00	3.27
2422	2532	7.800300	ATTAGAGGGAGGATATTAGAACCAC	57.200	40.000	0.00	0.00	0.00	4.16
2439	2549	0.317938	CGTCGCCGGAGAATTAGAGG	60.318	60.000	10.32	0.00	0.00	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.