AutoCloner

Multiple sequence alignment - TraesCS3D01G206800

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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	TraesCS3D01G206800	chr3D	100.000	2540	0	0	1	2540	271436346	271438885	0.000000e+00	4691.0
1	TraesCS3D01G206800	chr3D	87.013	693	59	21	41	731	151703756	151703093	0.000000e+00	752.0
2	TraesCS3D01G206800	chr3D	72.770	852	194	29	907	1740	548627032	548626201	1.170000e-63	254.0
3	TraesCS3D01G206800	chr3D	86.331	139	17	2	2403	2540	35689972	35690109	1.570000e-32	150.0
4	TraesCS3D01G206800	chr3D	86.232	138	17	2	2404	2540	504351294	504351430	5.660000e-32	148.0
5	TraesCS3D01G206800	chr3D	92.424	66	5	0	1	66	266871750	266871685	7.480000e-16	95.3
6	TraesCS3D01G206800	chr2B	88.914	1795	172	20	763	2540	91027418	91029202	0.000000e+00	2187.0
7	TraesCS3D01G206800	chr2B	81.452	744	83	27	3	731	219487439	219488142	2.210000e-155	558.0
8	TraesCS3D01G206800	chr2B	85.714	147	18	1	2397	2540	465679401	465679547	4.380000e-33	152.0
9	TraesCS3D01G206800	chr2B	90.625	64	5	1	3	66	245097226	245097164	1.620000e-12	84.2
10	TraesCS3D01G206800	chr2B	100.000	31	0	0	1649	1679	53030696	53030726	9.810000e-05	58.4
11	TraesCS3D01G206800	chr7A	85.031	1797	253	16	751	2538	55010326	55012115	0.000000e+00	1814.0
12	TraesCS3D01G206800	chr7A	85.209	1697	235	16	854	2540	495570856	495569166	0.000000e+00	1729.0
13	TraesCS3D01G206800	chr7A	87.143	700	68	19	43	731	354825879	354825191	0.000000e+00	774.0
14	TraesCS3D01G206800	chr7A	87.083	689	61	21	43	721	354790476	354789806	0.000000e+00	754.0
15	TraesCS3D01G206800	chr7A	86.331	139	17	2	2403	2540	86094120	86093983	1.570000e-32	150.0
16	TraesCS3D01G206800	chr4D	83.796	1802	262	20	754	2540	201880227	201878441	0.000000e+00	1683.0
17	TraesCS3D01G206800	chr4D	87.055	703	69	20	41	731	174300611	174301303	0.000000e+00	774.0
18	TraesCS3D01G206800	chr4D	85.832	727	72	26	18	731	174293910	174294618	0.000000e+00	743.0
19	TraesCS3D01G206800	chr4D	84.173	139	21	1	2401	2539	506393347	506393210	1.590000e-27	134.0
20	TraesCS3D01G206800	chr5D	87.476	1054	114	11	751	1802	481185827	481186864	0.000000e+00	1199.0
21	TraesCS3D01G206800	chr7B	84.378	973	129	14	751	1719	111989656	111988703	0.000000e+00	933.0
22	TraesCS3D01G206800	chr1A	87.411	699	70	15	41	731	110557768	110558456	0.000000e+00	787.0
23	TraesCS3D01G206800	chr6D	86.448	701	77	15	41	731	212933931	212933239	0.000000e+00	752.0
24	TraesCS3D01G206800	chr6D	84.559	136	21	0	2397	2532	414275003	414275138	4.410000e-28	135.0
25	TraesCS3D01G206800	chr4B	85.484	744	83	22	3	731	296725344	296726077	0.000000e+00	752.0
26	TraesCS3D01G206800	chr4B	89.552	134	14	0	2405	2538	11588413	11588280	1.210000e-38	171.0
27	TraesCS3D01G206800	chr4B	86.567	134	18	0	2397	2530	404791410	404791277	5.660000e-32	148.0
28	TraesCS3D01G206800	chr4B	87.200	125	15	1	2398	2522	612849179	612849302	9.470000e-30	141.0
29	TraesCS3D01G206800	chr4B	84.058	138	22	0	2403	2540	31853186	31853323	1.590000e-27	134.0
30	TraesCS3D01G206800	chr5A	85.070	710	82	15	41	731	146289483	146288779	0.000000e+00	702.0
31	TraesCS3D01G206800	chr5A	73.009	226	58	3	1214	1437	709747656	709747880	2.710000e-10	76.8
32	TraesCS3D01G206800	chr2D	85.933	327	26	8	3	326	381499940	381500249	5.240000e-87	331.0
33	TraesCS3D01G206800	chr2D	85.401	137	20	0	2402	2538	594570305	594570169	2.630000e-30	143.0
34	TraesCS3D01G206800	chr5B	71.642	871	219	27	933	1785	303923855	303922995	5.500000e-52	215.0
35	TraesCS3D01G206800	chr5B	84.783	138	19	2	2403	2539	249087442	249087306	1.230000e-28	137.0
36	TraesCS3D01G206800	chr6B	86.429	140	19	0	2401	2540	64974750	64974611	1.220000e-33	154.0
37	TraesCS3D01G206800	chr6B	94.828	58	3	0	3	60	191543445	191543502	9.680000e-15	91.6
38	TraesCS3D01G206800	chr1B	85.926	135	16	3	2407	2540	161574663	161574795	9.470000e-30	141.0
39	TraesCS3D01G206800	chrUn	82.812	128	20	2	2403	2529	235730210	235730336	2.070000e-21	113.0
40	TraesCS3D01G206800	chr3A	96.491	57	2	0	3	59	365691250	365691306	7.480000e-16	95.3

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	TraesCS3D01G206800	chr3D	271436346	271438885	2539	False	4691	4691	100.000	1	2540	1	chr3D.!!$F2	2539
1	TraesCS3D01G206800	chr3D	151703093	151703756	663	True	752	752	87.013	41	731	1	chr3D.!!$R1	690
2	TraesCS3D01G206800	chr3D	548626201	548627032	831	True	254	254	72.770	907	1740	1	chr3D.!!$R3	833
3	TraesCS3D01G206800	chr2B	91027418	91029202	1784	False	2187	2187	88.914	763	2540	1	chr2B.!!$F2	1777
4	TraesCS3D01G206800	chr2B	219487439	219488142	703	False	558	558	81.452	3	731	1	chr2B.!!$F3	728
5	TraesCS3D01G206800	chr7A	55010326	55012115	1789	False	1814	1814	85.031	751	2538	1	chr7A.!!$F1	1787
6	TraesCS3D01G206800	chr7A	495569166	495570856	1690	True	1729	1729	85.209	854	2540	1	chr7A.!!$R4	1686
7	TraesCS3D01G206800	chr7A	354825191	354825879	688	True	774	774	87.143	43	731	1	chr7A.!!$R3	688
8	TraesCS3D01G206800	chr7A	354789806	354790476	670	True	754	754	87.083	43	721	1	chr7A.!!$R2	678
9	TraesCS3D01G206800	chr4D	201878441	201880227	1786	True	1683	1683	83.796	754	2540	1	chr4D.!!$R1	1786
10	TraesCS3D01G206800	chr4D	174300611	174301303	692	False	774	774	87.055	41	731	1	chr4D.!!$F2	690
11	TraesCS3D01G206800	chr4D	174293910	174294618	708	False	743	743	85.832	18	731	1	chr4D.!!$F1	713
12	TraesCS3D01G206800	chr5D	481185827	481186864	1037	False	1199	1199	87.476	751	1802	1	chr5D.!!$F1	1051
13	TraesCS3D01G206800	chr7B	111988703	111989656	953	True	933	933	84.378	751	1719	1	chr7B.!!$R1	968
14	TraesCS3D01G206800	chr1A	110557768	110558456	688	False	787	787	87.411	41	731	1	chr1A.!!$F1	690
15	TraesCS3D01G206800	chr6D	212933239	212933931	692	True	752	752	86.448	41	731	1	chr6D.!!$R1	690
16	TraesCS3D01G206800	chr4B	296725344	296726077	733	False	752	752	85.484	3	731	1	chr4B.!!$F2	728
17	TraesCS3D01G206800	chr5A	146288779	146289483	704	True	702	702	85.070	41	731	1	chr5A.!!$R1	690
18	TraesCS3D01G206800	chr5B	303922995	303923855	860	True	215	215	71.642	933	1785	1	chr5B.!!$R2	852

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
904	959	1.035932	TCCCTGTCTTCGATCCCGTC	61.036	60.0	0.0	0.0	37.05	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2264	2373	0.108019	AAACCCAGAACCGTCTCACC	59.892	55.0	0.0	0.0	28.78	4.02	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
271	279	5.004726	GCCGCTGAAAATATGTTCATGTTTC	59.995	40.000	8.80	10.51	36.92	2.78
272	280	5.516339	CCGCTGAAAATATGTTCATGTTTCC	59.484	40.000	8.80	0.00	36.92	3.13
284	293	6.578023	TGTTCATGTTTCCGGAAATCTTTTT	58.422	32.000	31.13	10.87	32.36	1.94
285	294	6.699642	TGTTCATGTTTCCGGAAATCTTTTTC	59.300	34.615	31.13	17.18	40.48	2.29
287	296	6.446318	TCATGTTTCCGGAAATCTTTTTCAG	58.554	36.000	31.13	15.41	42.55	3.02
291	300	7.324178	TGTTTCCGGAAATCTTTTTCAGAAAA	58.676	30.769	31.13	4.06	41.82	2.29
597	644	5.346011	GCATTTCGATTTTCTCCTTGTTTCC	59.654	40.000	0.00	0.00	0.00	3.13
647	698	2.910319	TGCCTAGCCTTTGACCTCTAAA	59.090	45.455	0.00	0.00	0.00	1.85
735	788	9.691362	AATCAATATTTTGGTTTGACTACACAC	57.309	29.630	0.00	0.00	32.09	3.82
736	789	8.226819	TCAATATTTTGGTTTGACTACACACA	57.773	30.769	0.00	0.00	33.44	3.72
737	790	8.349245	TCAATATTTTGGTTTGACTACACACAG	58.651	33.333	0.00	0.00	33.44	3.66
738	791	8.349245	CAATATTTTGGTTTGACTACACACAGA	58.651	33.333	0.00	0.00	0.00	3.41
739	792	6.767524	ATTTTGGTTTGACTACACACAGAA	57.232	33.333	0.00	0.00	0.00	3.02
740	793	6.767524	TTTTGGTTTGACTACACACAGAAT	57.232	33.333	0.00	0.00	0.00	2.40
741	794	7.867305	TTTTGGTTTGACTACACACAGAATA	57.133	32.000	0.00	0.00	0.00	1.75
742	795	7.867305	TTTGGTTTGACTACACACAGAATAA	57.133	32.000	0.00	0.00	0.00	1.40
743	796	7.490962	TTGGTTTGACTACACACAGAATAAG	57.509	36.000	0.00	0.00	0.00	1.73
744	797	6.588204	TGGTTTGACTACACACAGAATAAGT	58.412	36.000	0.00	0.00	0.00	2.24
745	798	6.481976	TGGTTTGACTACACACAGAATAAGTG	59.518	38.462	0.00	0.00	42.56	3.16
746	799	6.363473	GTTTGACTACACACAGAATAAGTGC	58.637	40.000	0.00	0.00	40.59	4.40
747	800	5.208463	TGACTACACACAGAATAAGTGCA	57.792	39.130	0.00	0.00	40.59	4.57
748	801	4.988540	TGACTACACACAGAATAAGTGCAC	59.011	41.667	9.40	9.40	40.59	4.57
749	802	4.315803	ACTACACACAGAATAAGTGCACC	58.684	43.478	14.63	0.00	40.59	5.01
778	831	2.956987	CGTAGGGTGACGGTTCGT	59.043	61.111	0.00	0.00	45.10	3.85
904	959	1.035932	TCCCTGTCTTCGATCCCGTC	61.036	60.000	0.00	0.00	37.05	4.79
1006	1066	3.264450	GGGTTTGAAGGAAGAGATGGAGA	59.736	47.826	0.00	0.00	0.00	3.71
1049	1109	3.406764	GTTTGAAGCTGTCTGATGAGGT	58.593	45.455	0.00	0.00	0.00	3.85
1053	1117	1.935799	AGCTGTCTGATGAGGTGAGT	58.064	50.000	0.00	0.00	0.00	3.41
1086	1150	1.007038	CCGGTGTTCGTCGAAGGAA	60.007	57.895	8.18	0.00	37.11	3.36
1186	1254	1.151450	CTGGGAAAGGTGTGGTGCT	59.849	57.895	0.00	0.00	0.00	4.40
1194	1262	0.396435	AGGTGTGGTGCTCGATCAAA	59.604	50.000	0.00	0.00	0.00	2.69
1197	1265	0.396435	TGTGGTGCTCGATCAAAGGT	59.604	50.000	0.00	0.00	0.00	3.50
1324	1395	3.848377	TCTGGTGGTAGTAGAGGAGTACA	59.152	47.826	0.00	0.00	35.87	2.90
1341	1412	1.410004	ACATGCCTAGTAAGCGGCTA	58.590	50.000	1.35	0.00	46.42	3.93
1462	1534	5.263599	TCATTGGTAGATTTGTTGAGGCAT	58.736	37.500	0.00	0.00	0.00	4.40
1498	1571	4.922206	TGGAAGTGCAATTGGTAGATTCT	58.078	39.130	3.09	0.00	0.00	2.40
1589	1663	1.094269	AGAAGGAGGGTAGTGGGAGT	58.906	55.000	0.00	0.00	0.00	3.85
1756	1855	0.390124	AAGCAACAGTTCGGTCGGTA	59.610	50.000	0.00	0.00	0.00	4.02
1793	1892	1.841103	GCAGAGGAGGGGGAGGATC	60.841	68.421	0.00	0.00	0.00	3.36
1802	1901	2.920384	GGGAGGATCGAGGAGGGC	60.920	72.222	0.00	0.00	34.37	5.19
1805	1904	1.758514	GAGGATCGAGGAGGGCACA	60.759	63.158	0.00	0.00	0.00	4.57
1907	2006	0.962489	ACAGTCTCACGTGGAGGAAG	59.038	55.000	17.00	5.20	44.19	3.46
1913	2012	0.959553	TCACGTGGAGGAAGTCTGAC	59.040	55.000	17.00	0.00	0.00	3.51
1976	2075	1.878656	AAGAAGTGACGAGCCCGAGG	61.879	60.000	0.00	0.00	39.50	4.63
2044	2149	1.003696	CCTTGAGGGGTCCAAGAAGAC	59.996	57.143	0.00	0.00	42.57	3.01
2046	2151	2.044793	TGAGGGGTCCAAGAAGACAT	57.955	50.000	0.00	0.00	38.59	3.06
2090	2195	1.835494	CCTCGAGTGTACCTCAGGAA	58.165	55.000	12.31	0.00	40.48	3.36
2106	2211	0.034089	GGAACAGGGTGGGAAGGATG	60.034	60.000	0.00	0.00	0.00	3.51
2126	2231	4.908601	TGTAGTCATGGTTGTGGAAGAT	57.091	40.909	0.00	0.00	0.00	2.40
2143	2248	3.423058	AGATAAGGTGGAAGGTAGGCT	57.577	47.619	0.00	0.00	0.00	4.58
2246	2355	3.426117	GAAAGGGCGCGATCGGAGA	62.426	63.158	18.30	0.00	45.75	3.71
2320	2429	1.925972	GGAGGGGGAGGAGCACTTT	60.926	63.158	0.00	0.00	0.00	2.66
2328	2437	1.339535	GGAGGAGCACTTTGGGAAGAG	60.340	57.143	0.00	0.00	36.69	2.85
2330	2439	0.322906	GGAGCACTTTGGGAAGAGGG	60.323	60.000	0.00	0.00	36.69	4.30
2365	2474	0.687354	GAGTGCAGGAGTTGGGAGAA	59.313	55.000	0.00	0.00	0.00	2.87
2413	2522	4.280929	CCTATCAATGATATATCGGCCGGA	59.719	45.833	27.83	14.80	0.00	5.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
271	279	8.364129	TCAAATTTTCTGAAAAAGATTTCCGG	57.636	30.769	18.43	0.00	43.54	5.14
612	662	2.945668	GCTAGGCAATGTGGGACTAAAG	59.054	50.000	0.00	0.00	0.00	1.85
731	784	2.143122	ACGGTGCACTTATTCTGTGTG	58.857	47.619	17.98	0.00	37.70	3.82
732	785	2.413837	GACGGTGCACTTATTCTGTGT	58.586	47.619	17.98	1.77	37.70	3.72
733	786	1.732259	GGACGGTGCACTTATTCTGTG	59.268	52.381	17.98	0.00	38.36	3.66
734	787	1.671850	CGGACGGTGCACTTATTCTGT	60.672	52.381	17.98	0.00	0.00	3.41
735	788	0.999406	CGGACGGTGCACTTATTCTG	59.001	55.000	17.98	9.07	0.00	3.02
736	789	0.606604	ACGGACGGTGCACTTATTCT	59.393	50.000	17.98	0.00	0.00	2.40
737	790	0.997196	GACGGACGGTGCACTTATTC	59.003	55.000	17.98	7.79	0.00	1.75
738	791	0.390735	GGACGGACGGTGCACTTATT	60.391	55.000	17.98	0.00	36.89	1.40
739	792	1.217244	GGACGGACGGTGCACTTAT	59.783	57.895	17.98	1.90	36.89	1.73
740	793	2.652530	GGACGGACGGTGCACTTA	59.347	61.111	17.98	0.00	36.89	2.24
741	794	4.309950	GGGACGGACGGTGCACTT	62.310	66.667	17.98	3.72	39.01	3.16
759	812	2.505557	GAACCGTCACCCTACGCG	60.506	66.667	3.53	3.53	41.51	6.01
778	831	1.448893	GCAATCGCCGGACCTAACA	60.449	57.895	5.05	0.00	0.00	2.41
862	915	2.111932	CTCGTGCGGAGGAGAGATCG	62.112	65.000	20.37	0.00	39.22	3.69
904	959	2.364186	GCCTTTGGTGGATGGGGG	60.364	66.667	0.00	0.00	0.00	5.40
1006	1066	2.503061	CATCAGCCCTGCTACGCT	59.497	61.111	0.00	0.00	36.40	5.07
1049	1109	3.560453	CCGGATTTTCACCCCTTTACTCA	60.560	47.826	0.00	0.00	0.00	3.41
1053	1117	2.108601	ACACCGGATTTTCACCCCTTTA	59.891	45.455	9.46	0.00	0.00	1.85
1197	1265	3.234353	CCCTATCTCTGTGCAGGTGATA	58.766	50.000	0.00	0.00	0.00	2.15
1341	1412	4.832248	TGTCATTGAAGGCGTAATCTTCT	58.168	39.130	0.00	0.00	40.73	2.85
1462	1534	2.628178	CACTTCCATCCGCTCCTGTATA	59.372	50.000	0.00	0.00	0.00	1.47
1498	1571	2.288666	GCATCCGCACTTTGATCCTAA	58.711	47.619	0.00	0.00	38.36	2.69
1589	1663	1.180029	CGTTCGTCCTCCCTCCTTTA	58.820	55.000	0.00	0.00	0.00	1.85
1725	1824	1.615392	CTGTTGCTTCTCCCCCTTTTG	59.385	52.381	0.00	0.00	0.00	2.44
1793	1892	1.406065	ATCTCCATGTGCCCTCCTCG	61.406	60.000	0.00	0.00	0.00	4.63
1820	1919	0.611340	GGACTCCTCCTGTACCACGT	60.611	60.000	0.00	0.00	33.07	4.49
1907	2006	1.808411	TGCCGGATTTTGAGTCAGAC	58.192	50.000	5.05	0.00	0.00	3.51
1913	2012	0.461135	CCCCATTGCCGGATTTTGAG	59.539	55.000	5.05	0.00	0.00	3.02
1940	2039	1.308746	TTCCCCTCCCTCCATTCCC	60.309	63.158	0.00	0.00	0.00	3.97
1945	2044	0.547712	CACTTCTTCCCCTCCCTCCA	60.548	60.000	0.00	0.00	0.00	3.86
2044	2149	4.372656	GTTCTTCCCTTGATCGGTAGATG	58.627	47.826	0.00	0.00	37.19	2.90
2046	2151	2.426024	CGTTCTTCCCTTGATCGGTAGA	59.574	50.000	0.00	0.00	0.00	2.59
2090	2195	1.203440	ACTACATCCTTCCCACCCTGT	60.203	52.381	0.00	0.00	0.00	4.00
2106	2211	5.817816	CCTTATCTTCCACAACCATGACTAC	59.182	44.000	0.00	0.00	0.00	2.73
2126	2231	2.634639	TCAGCCTACCTTCCACCTTA	57.365	50.000	0.00	0.00	0.00	2.69
2143	2248	4.019950	TCTGATTGTTCTGCTTCTCCATCA	60.020	41.667	0.00	0.00	0.00	3.07
2254	2363	2.286523	CGTCTCACCCTCCTGCCTT	61.287	63.158	0.00	0.00	0.00	4.35
2264	2373	0.108019	AAACCCAGAACCGTCTCACC	59.892	55.000	0.00	0.00	28.78	4.02
2365	2474	1.581954	CTCCTGTGCGTTCGTCTCT	59.418	57.895	0.00	0.00	0.00	3.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.