AutoCloner

Multiple sequence alignment - TraesCS2B01G114400

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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	TraesCS2B01G114400	chr2B	100.000	2900	0	0	1	2900	77769909	77772808	0.000000e+00	5356
1	TraesCS2B01G114400	chr2B	87.125	1732	145	31	935	2656	75607135	75608798	0.000000e+00	1892
2	TraesCS2B01G114400	chr2B	93.659	1230	69	5	935	2158	76905741	76904515	0.000000e+00	1831
3	TraesCS2B01G114400	chr2B	93.214	280	15	2	2621	2900	76903831	76903556	2.690000e-110	409
4	TraesCS2B01G114400	chr2B	87.410	278	35	0	935	1212	74794423	74794700	1.300000e-83	320
5	TraesCS2B01G114400	chr2B	91.525	118	9	1	2654	2770	75608880	75608997	8.320000e-36	161
6	TraesCS2B01G114400	chr7A	99.679	934	3	0	1	934	732907411	732908344	0.000000e+00	1709
7	TraesCS2B01G114400	chr4A	99.573	937	4	0	1	937	729295135	729294199	0.000000e+00	1709
8	TraesCS2B01G114400	chr2A	99.573	936	3	1	1	935	755847015	755847950	0.000000e+00	1705
9	TraesCS2B01G114400	chr2A	86.407	1589	165	21	1082	2649	51540610	51539052	0.000000e+00	1690
10	TraesCS2B01G114400	chr2A	88.599	1228	107	12	935	2158	50916719	50917917	0.000000e+00	1461
11	TraesCS2B01G114400	chr2A	89.708	719	60	12	2192	2900	50917920	50918634	0.000000e+00	905
12	TraesCS2B01G114400	chr2A	91.776	304	17	2	2468	2770	50956199	50956495	1.610000e-112	416
13	TraesCS2B01G114400	chr2A	75.104	960	200	30	951	1889	19125494	19126435	2.080000e-111	412
14	TraesCS2B01G114400	chr2A	91.353	266	15	6	2192	2451	50923820	50924083	9.880000e-95	357
15	TraesCS2B01G114400	chr2A	81.982	444	36	14	1718	2158	50923415	50923817	1.290000e-88	337
16	TraesCS2B01G114400	chr2A	93.506	77	4	1	2645	2721	51539024	51538949	2.360000e-21	113
17	TraesCS2B01G114400	chr7B	99.572	934	4	0	1	934	423167813	423166880	0.000000e+00	1703
18	TraesCS2B01G114400	chr7B	99.572	934	4	0	1	934	537251913	537250980	0.000000e+00	1703
19	TraesCS2B01G114400	chr6B	99.572	934	4	0	1	934	555204538	555205471	0.000000e+00	1703
20	TraesCS2B01G114400	chr4B	99.572	934	4	0	1	934	481231472	481232405	0.000000e+00	1703
21	TraesCS2B01G114400	chr3A	99.572	934	4	0	1	934	119648	120581	0.000000e+00	1703
22	TraesCS2B01G114400	chr1B	99.572	934	4	0	1	934	268636233	268637166	0.000000e+00	1703
23	TraesCS2B01G114400	chr2D	89.207	1186	115	7	935	2109	49255850	49254667	0.000000e+00	1469
24	TraesCS2B01G114400	chr2D	93.812	711	35	4	2197	2900	49254632	49253924	0.000000e+00	1061
25	TraesCS2B01G114400	chr2D	90.562	498	30	9	2192	2682	47412003	47412490	0.000000e+00	643
26	TraesCS2B01G114400	chr2D	74.870	963	197	33	951	1889	17955468	17956409	2.090000e-106	396
27	TraesCS2B01G114400	chr2D	87.356	174	16	5	1972	2141	47411604	47411775	8.200000e-46	195
28	TraesCS2B01G114400	chr2D	73.333	480	107	17	940	1407	18186104	18186574	1.080000e-34	158
29	TraesCS2B01G114400	chr6A	97.931	145	3	0	935	1079	613644853	613644997	4.800000e-63	252
30	TraesCS2B01G114400	chr5A	76.285	253	49	8	1617	1865	18680053	18680298	1.090000e-24	124

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	TraesCS2B01G114400	chr2B	77769909	77772808	2899	False	5356.0	5356	100.0000	1	2900	1	chr2B.!!$F2	2899
1	TraesCS2B01G114400	chr2B	76903556	76905741	2185	True	1120.0	1831	93.4365	935	2900	2	chr2B.!!$R1	1965
2	TraesCS2B01G114400	chr2B	75607135	75608997	1862	False	1026.5	1892	89.3250	935	2770	2	chr2B.!!$F3	1835
3	TraesCS2B01G114400	chr7A	732907411	732908344	933	False	1709.0	1709	99.6790	1	934	1	chr7A.!!$F1	933
4	TraesCS2B01G114400	chr4A	729294199	729295135	936	True	1709.0	1709	99.5730	1	937	1	chr4A.!!$R1	936
5	TraesCS2B01G114400	chr2A	755847015	755847950	935	False	1705.0	1705	99.5730	1	935	1	chr2A.!!$F3	934
6	TraesCS2B01G114400	chr2A	50916719	50918634	1915	False	1183.0	1461	89.1535	935	2900	2	chr2A.!!$F4	1965
7	TraesCS2B01G114400	chr2A	51538949	51540610	1661	True	901.5	1690	89.9565	1082	2721	2	chr2A.!!$R1	1639
8	TraesCS2B01G114400	chr2A	19125494	19126435	941	False	412.0	412	75.1040	951	1889	1	chr2A.!!$F1	938
9	TraesCS2B01G114400	chr2A	50923415	50924083	668	False	347.0	357	86.6675	1718	2451	2	chr2A.!!$F5	733
10	TraesCS2B01G114400	chr7B	423166880	423167813	933	True	1703.0	1703	99.5720	1	934	1	chr7B.!!$R1	933
11	TraesCS2B01G114400	chr7B	537250980	537251913	933	True	1703.0	1703	99.5720	1	934	1	chr7B.!!$R2	933
12	TraesCS2B01G114400	chr6B	555204538	555205471	933	False	1703.0	1703	99.5720	1	934	1	chr6B.!!$F1	933
13	TraesCS2B01G114400	chr4B	481231472	481232405	933	False	1703.0	1703	99.5720	1	934	1	chr4B.!!$F1	933
14	TraesCS2B01G114400	chr3A	119648	120581	933	False	1703.0	1703	99.5720	1	934	1	chr3A.!!$F1	933
15	TraesCS2B01G114400	chr1B	268636233	268637166	933	False	1703.0	1703	99.5720	1	934	1	chr1B.!!$F1	933
16	TraesCS2B01G114400	chr2D	49253924	49255850	1926	True	1265.0	1469	91.5095	935	2900	2	chr2D.!!$R1	1965
17	TraesCS2B01G114400	chr2D	47411604	47412490	886	False	419.0	643	88.9590	1972	2682	2	chr2D.!!$F3	710
18	TraesCS2B01G114400	chr2D	17955468	17956409	941	False	396.0	396	74.8700	951	1889	1	chr2D.!!$F1	938

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
189	190	3.360867	ACTTCAAAACATGTGTGGGACA	58.639	40.909	0.00	0.0	39.53	4.02	F
1455	1474	0.895530	CCGAGCTTGAGGACCAGTTA	59.104	55.000	1.22	0.0	0.00	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1692	1714	1.615384	GCATGGTTTCCCTTGAGAGCT	60.615	52.381	0.0	0.0	37.97	4.09	R
2830	3692	0.745845	CCCTGCTCAAAGATGGACGG	60.746	60.000	0.0	0.0	0.00	4.79	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
189	190	3.360867	ACTTCAAAACATGTGTGGGACA	58.639	40.909	0.00	0.00	39.53	4.02
1414	1433	3.698040	TCTAAGTAGCCCTGTTCTTACGG	59.302	47.826	0.00	0.00	0.00	4.02
1416	1435	3.091633	AGTAGCCCTGTTCTTACGGTA	57.908	47.619	0.00	0.00	0.00	4.02
1451	1470	3.706373	GCCCGAGCTTGAGGACCA	61.706	66.667	1.22	0.00	35.50	4.02
1455	1474	0.895530	CCGAGCTTGAGGACCAGTTA	59.104	55.000	1.22	0.00	0.00	2.24
1488	1507	1.367346	TTGTACAAGCTCCATGGGGA	58.633	50.000	18.46	0.00	42.29	4.81
1498	1517	3.788142	AGCTCCATGGGGAAATCTTCTTA	59.212	43.478	18.46	0.00	44.38	2.10
1536	1555	9.529325	TTATATGAGAACTGTGATTTAGAACCG	57.471	33.333	0.00	0.00	0.00	4.44
1538	1557	3.933332	GAGAACTGTGATTTAGAACCGGG	59.067	47.826	6.32	0.00	0.00	5.73
1692	1714	5.584253	GTCTTACTGCTGAAGACTATCCA	57.416	43.478	19.19	0.00	46.16	3.41
1773	1795	4.703897	TCAAGAACAATCCCCGTGATATC	58.296	43.478	0.00	0.00	31.83	1.63
1903	1925	8.552083	AAATTTGGCTTTCAATGAATAGGTTC	57.448	30.769	0.00	0.00	34.98	3.62
1906	1928	8.593945	TTTGGCTTTCAATGAATAGGTTCTAT	57.406	30.769	0.00	0.00	34.98	1.98
1907	1929	8.593945	TTGGCTTTCAATGAATAGGTTCTATT	57.406	30.769	0.00	0.33	35.33	1.73
1973	2003	2.376518	AGGTGATGGTCCTGTGTTGATT	59.623	45.455	0.00	0.00	33.62	2.57
2022	2054	9.224267	AGTACTCTATTCGTACACTAGAACAAA	57.776	33.333	0.00	0.00	39.66	2.83
2099	2135	6.778834	TTGTCCAAAAGTATCATCATGCAT	57.221	33.333	0.00	0.00	0.00	3.96
2104	2140	8.737175	GTCCAAAAGTATCATCATGCATCATAT	58.263	33.333	0.00	0.00	0.00	1.78
2178	2426	9.921637	TTTTTCACAACTTTTCTGTTTACTCAT	57.078	25.926	0.00	0.00	0.00	2.90
2189	2437	9.809096	TTTTCTGTTTACTCATATTTTTGCACA	57.191	25.926	0.00	0.00	0.00	4.57
2190	2438	9.809096	TTTCTGTTTACTCATATTTTTGCACAA	57.191	25.926	0.00	0.00	0.00	3.33
2191	2439	8.795786	TCTGTTTACTCATATTTTTGCACAAC	57.204	30.769	0.00	0.00	0.00	3.32
2192	2440	8.629158	TCTGTTTACTCATATTTTTGCACAACT	58.371	29.630	0.00	0.00	0.00	3.16
2193	2441	9.248291	CTGTTTACTCATATTTTTGCACAACTT	57.752	29.630	0.00	0.00	0.00	2.66
2194	2442	9.593134	TGTTTACTCATATTTTTGCACAACTTT	57.407	25.926	0.00	0.00	0.00	2.66
2232	2480	8.876275	ATACATGGATCATATTTTTGCACAAC	57.124	30.769	0.00	0.00	0.00	3.32
2237	2485	8.309163	TGGATCATATTTTTGCACAACTTTTC	57.691	30.769	0.00	0.00	0.00	2.29
2270	2518	9.881649	CTCATATTTATCATGTACTAGTGCCAT	57.118	33.333	5.39	4.86	0.00	4.40
2396	2650	2.094675	AGGGATTTGGATGAACTTGCG	58.905	47.619	0.00	0.00	0.00	4.85
2454	2708	8.408043	TGTTGCTGGATTTGGATAATAATAGG	57.592	34.615	0.00	0.00	0.00	2.57
2455	2709	7.451255	TGTTGCTGGATTTGGATAATAATAGGG	59.549	37.037	0.00	0.00	0.00	3.53
2456	2710	7.341885	TGCTGGATTTGGATAATAATAGGGA	57.658	36.000	0.00	0.00	0.00	4.20
2503	2761	7.101054	ACTGCACGTTAGAAATATAGGAAACA	58.899	34.615	3.74	0.00	0.00	2.83
2548	2820	7.383102	AGAAGATAAGTGCTAACATTTGTGG	57.617	36.000	0.00	0.00	0.00	4.17
2576	2848	5.648178	AAGCATGAAAGTGTGCATGATTA	57.352	34.783	0.00	0.00	45.83	1.75
2673	3533	6.869913	ACAATTACAAACCTGCATCATTTGAG	59.130	34.615	18.89	9.12	36.91	3.02
2743	3603	1.722636	GCTGCAGCTAGTTGGGCATC	61.723	60.000	31.33	0.00	38.21	3.91
2823	3685	8.918961	TTGTTTCGAAATAAAACAAGATGTGT	57.081	26.923	16.50	0.00	46.28	3.72
2824	3686	8.555166	TGTTTCGAAATAAAACAAGATGTGTC	57.445	30.769	14.69	0.00	42.09	3.67
2830	3692	7.746475	CGAAATAAAACAAGATGTGTCTCCTTC	59.254	37.037	0.00	0.00	40.60	3.46
2893	3755	1.133976	GCTTATGTGCCCCATCTGACT	60.134	52.381	0.00	0.00	34.86	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
189	190	7.609532	CACCTTGATCTTTAAAGGAACTCTGAT	59.390	37.037	15.13	0.00	44.93	2.90
976	977	7.415592	TCTCAGATCTGTCATCAACTGTAAT	57.584	36.000	21.92	0.00	0.00	1.89
1414	1433	4.327680	GGCTCCCATGTAATCATCCTTAC	58.672	47.826	0.00	0.00	31.15	2.34
1416	1435	2.108952	GGGCTCCCATGTAATCATCCTT	59.891	50.000	0.00	0.00	35.81	3.36
1455	1474	7.549488	GGAGCTTGTACAATGTAAGTATTCAGT	59.451	37.037	9.13	0.00	0.00	3.41
1498	1517	8.543774	ACAGTTCTCATATAATCTCCACACTTT	58.456	33.333	0.00	0.00	0.00	2.66
1519	1538	2.878526	GCCCCGGTTCTAAATCACAGTT	60.879	50.000	0.00	0.00	0.00	3.16
1592	1611	8.871686	TTTCTTAATTTTCTTTCCTGAAGCAC	57.128	30.769	0.00	0.00	35.24	4.40
1692	1714	1.615384	GCATGGTTTCCCTTGAGAGCT	60.615	52.381	0.00	0.00	37.97	4.09
1773	1795	2.953466	TACCCAAGTCGAGAATTCCG	57.047	50.000	0.65	5.93	0.00	4.30
1878	1900	8.377799	AGAACCTATTCATTGAAAGCCAAATTT	58.622	29.630	2.68	0.00	37.29	1.82
1881	1903	6.916360	AGAACCTATTCATTGAAAGCCAAA	57.084	33.333	2.68	0.00	37.29	3.28
1955	1985	4.979335	TGTAAATCAACACAGGACCATCA	58.021	39.130	0.00	0.00	0.00	3.07
2075	2111	6.778834	TGCATGATGATACTTTTGGACAAT	57.221	33.333	0.00	0.00	0.00	2.71
2164	2412	9.809096	TTGTGCAAAAATATGAGTAAACAGAAA	57.191	25.926	0.00	0.00	0.00	2.52
2166	2414	8.629158	AGTTGTGCAAAAATATGAGTAAACAGA	58.371	29.630	0.00	0.00	0.00	3.41
2167	2415	8.801715	AGTTGTGCAAAAATATGAGTAAACAG	57.198	30.769	0.00	0.00	0.00	3.16
2168	2416	9.593134	AAAGTTGTGCAAAAATATGAGTAAACA	57.407	25.926	0.00	0.00	0.00	2.83
2243	2491	8.870116	TGGCACTAGTACATGATAAATATGAGT	58.130	33.333	0.00	0.00	0.00	3.41
2396	2650	8.981724	TTGAATGTTACAGTAGAGTACACATC	57.018	34.615	0.00	0.00	31.14	3.06
2454	2708	4.098349	TGAATGAAAATAGCATGCCACTCC	59.902	41.667	15.66	0.15	0.00	3.85
2455	2709	5.252969	TGAATGAAAATAGCATGCCACTC	57.747	39.130	15.66	3.91	0.00	3.51
2456	2710	5.186409	AGTTGAATGAAAATAGCATGCCACT	59.814	36.000	15.66	0.00	0.00	4.00
2503	2761	9.360901	TCTTCTACATCAGCAAAGAGACTATAT	57.639	33.333	0.00	0.00	0.00	0.86
2507	2765	5.991933	TCTTCTACATCAGCAAAGAGACT	57.008	39.130	0.00	0.00	0.00	3.24
2548	2820	5.801350	TGCACACTTTCATGCTTATCTAC	57.199	39.130	0.00	0.00	42.55	2.59
2576	2848	5.069516	AGTCACAGGTGCATTTTGAAAGAAT	59.930	36.000	0.00	0.00	0.00	2.40
2673	3533	3.942439	GCCCCCGGGATGAGCTAC	61.942	72.222	26.32	0.00	37.50	3.58
2814	3674	2.611518	GACGGAAGGAGACACATCTTG	58.388	52.381	0.00	0.00	34.34	3.02
2823	3685	2.497675	CTCAAAGATGGACGGAAGGAGA	59.502	50.000	0.00	0.00	0.00	3.71
2824	3686	2.898705	CTCAAAGATGGACGGAAGGAG	58.101	52.381	0.00	0.00	0.00	3.69
2830	3692	0.745845	CCCTGCTCAAAGATGGACGG	60.746	60.000	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.