AutoCloner

Multiple sequence alignment - TraesCS5D01G489900

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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	TraesCS5D01G489900	chr5D	100.000	2566	0	0	1	2566	524916189	524918754	0.000000e+00	4739
1	TraesCS5D01G489900	chr5A	93.798	1967	97	10	143	2107	651436004	651437947	0.000000e+00	2933
2	TraesCS5D01G489900	chr5A	94.692	471	19	4	2097	2566	651445223	651445688	0.000000e+00	726
3	TraesCS5D01G489900	chr5A	84.804	204	27	2	153	356	570488181	570488380	4.330000e-48	202
4	TraesCS5D01G489900	chr5A	90.071	141	13	1	1	140	651435454	651435594	5.640000e-42	182
5	TraesCS5D01G489900	chr5A	88.889	135	14	1	383	516	651436780	651436646	5.680000e-37	165
6	TraesCS5D01G489900	chr5A	89.313	131	13	1	797	926	651436372	651436242	2.040000e-36	163
7	TraesCS5D01G489900	chr5B	94.836	1065	41	6	685	1748	659411069	659412120	0.000000e+00	1650
8	TraesCS5D01G489900	chr5B	95.424	590	22	3	1	589	659410467	659411052	0.000000e+00	935
9	TraesCS5D01G489900	chr5B	95.111	450	17	4	2118	2566	659412538	659412983	0.000000e+00	704
10	TraesCS5D01G489900	chr5B	97.115	312	8	1	1770	2080	659412218	659412529	2.260000e-145	525
11	TraesCS5D01G489900	chr4A	86.291	1510	130	41	834	2288	144626099	144627586	0.000000e+00	1570
12	TraesCS5D01G489900	chr4A	84.722	288	34	8	2283	2563	144627643	144627927	1.940000e-71	279
13	TraesCS5D01G489900	chr4D	85.869	1387	128	35	779	2134	326383958	326382609	0.000000e+00	1413
14	TraesCS5D01G489900	chr4D	84.236	203	27	4	153	354	145380113	145379915	2.610000e-45	193
15	TraesCS5D01G489900	chr4D	84.615	130	20	0	383	512	326383811	326383940	2.070000e-26	130
16	TraesCS5D01G489900	chr4B	85.024	1449	136	44	728	2134	406392831	406391422	0.000000e+00	1399
17	TraesCS5D01G489900	chr4B	82.308	130	23	0	383	512	406392624	406392753	2.090000e-21	113
18	TraesCS5D01G489900	chr2B	85.784	204	25	2	153	356	139361686	139361487	2.000000e-51	213
19	TraesCS5D01G489900	chr2B	84.236	203	27	4	153	354	54563398	54563200	2.610000e-45	193
20	TraesCS5D01G489900	chr7A	85.294	204	26	2	153	356	48781089	48781288	9.310000e-50	207
21	TraesCS5D01G489900	chr3D	84.434	212	29	2	153	364	339816557	339816764	3.350000e-49	206
22	TraesCS5D01G489900	chr2D	84.804	204	26	3	153	356	631749781	631749583	1.560000e-47	200

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	TraesCS5D01G489900	chr5D	524916189	524918754	2565	False	4739.0	4739	100.0000	1	2566	1	chr5D.!!$F1	2565
1	TraesCS5D01G489900	chr5A	651435454	651437947	2493	False	1557.5	2933	91.9345	1	2107	2	chr5A.!!$F3	2106
2	TraesCS5D01G489900	chr5B	659410467	659412983	2516	False	953.5	1650	95.6215	1	2566	4	chr5B.!!$F1	2565
3	TraesCS5D01G489900	chr4A	144626099	144627927	1828	False	924.5	1570	85.5065	834	2563	2	chr4A.!!$F1	1729
4	TraesCS5D01G489900	chr4D	326382609	326383958	1349	True	1413.0	1413	85.8690	779	2134	1	chr4D.!!$R2	1355
5	TraesCS5D01G489900	chr4B	406391422	406392831	1409	True	1399.0	1399	85.0240	728	2134	1	chr4B.!!$R1	1406

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
726	1138	0.111253	GCCATTCGAATCCATCCCCT	59.889	55.0	7.92	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2437	3071	0.250513	AACTGACCAGAAGCGATCCC	59.749	55.0	3.76	0.0	0.0	3.85	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
89	91	3.552132	TGTAAGTGTGGAGCAACAAGA	57.448	42.857	0.00	0.00	0.00	3.02
113	115	5.356751	AGGCGATGTTTTTGCATACTATTGA	59.643	36.000	0.00	0.00	36.33	2.57
199	609	5.629125	ACCATTGGCACCAATATTTGTTTT	58.371	33.333	14.39	0.00	43.92	2.43
201	611	7.227156	ACCATTGGCACCAATATTTGTTTTAA	58.773	30.769	14.39	0.00	43.92	1.52
256	666	4.678743	GGAGCCAAGCCCGGGTTT	62.679	66.667	24.63	21.36	36.74	3.27
410	821	5.767816	ATGGTTCAAAAGTCACAACTACC	57.232	39.130	0.00	0.00	33.48	3.18
450	861	3.334691	TGCTCTACAAATTTCCTCACGG	58.665	45.455	0.00	0.00	0.00	4.94
460	871	2.203070	CCTCACGGTATGCAGGGC	60.203	66.667	0.00	0.00	0.00	5.19
472	883	0.698238	TGCAGGGCTGGACTTAACAT	59.302	50.000	0.00	0.00	0.00	2.71
597	1009	7.661536	ATAGAGCACTGTTTCCTCTGTATAA	57.338	36.000	10.83	0.00	36.66	0.98
619	1031	3.261897	AGGTTCCTACTGTTCCTGTGATG	59.738	47.826	0.00	0.00	0.00	3.07
621	1033	3.961480	TCCTACTGTTCCTGTGATGTG	57.039	47.619	0.00	0.00	0.00	3.21
622	1034	3.506398	TCCTACTGTTCCTGTGATGTGA	58.494	45.455	0.00	0.00	0.00	3.58
623	1035	4.096681	TCCTACTGTTCCTGTGATGTGAT	58.903	43.478	0.00	0.00	0.00	3.06
624	1036	4.160439	TCCTACTGTTCCTGTGATGTGATC	59.840	45.833	0.00	0.00	0.00	2.92
625	1037	3.340814	ACTGTTCCTGTGATGTGATCC	57.659	47.619	0.00	0.00	0.00	3.36
626	1038	2.026822	ACTGTTCCTGTGATGTGATCCC	60.027	50.000	0.00	0.00	0.00	3.85
627	1039	1.281867	TGTTCCTGTGATGTGATCCCC	59.718	52.381	0.00	0.00	0.00	4.81
642	1054	3.260100	CCCCCACCCAGCTCTGTT	61.260	66.667	0.00	0.00	0.00	3.16
647	1059	2.094675	CCCACCCAGCTCTGTTAATTG	58.905	52.381	0.00	0.00	0.00	2.32
653	1065	5.525378	CACCCAGCTCTGTTAATTGTATCTC	59.475	44.000	0.00	0.00	0.00	2.75
676	1088	9.503399	TCTCTCTTGATTTATGATCAATCCATG	57.497	33.333	0.00	0.00	37.40	3.66
696	1108	0.533755	CTGGAGATTCCACGGCATCC	60.534	60.000	0.00	0.00	42.67	3.51
726	1138	0.111253	GCCATTCGAATCCATCCCCT	59.889	55.000	7.92	0.00	0.00	4.79
786	1208	3.181479	CCATAGCATTTGATGTGCAAGCT	60.181	43.478	0.00	0.00	44.87	3.74
875	1297	5.527214	TGCATATCGTGAGGAAATTTGTAGG	59.473	40.000	0.00	0.00	0.00	3.18
1102	1531	6.606796	TGCCTTATTCCTTCTTGATTGCAATA	59.393	34.615	12.97	0.00	32.68	1.90
1165	1600	3.772572	TCTAGTGCTGTATGCCAGGTAAA	59.227	43.478	0.00	0.00	41.81	2.01
1436	1871	3.121929	TCAAGGGCTAAGGACATCTCT	57.878	47.619	0.00	0.00	0.00	3.10
1503	1941	7.781324	AGAATGGATGTTTAACTGGAATGTT	57.219	32.000	0.00	0.00	0.00	2.71
1511	1949	6.326375	TGTTTAACTGGAATGTTGTTGTGTC	58.674	36.000	0.00	0.00	0.00	3.67
1524	1962	4.112716	TGTTGTGTCGTCTTGTAAGTGA	57.887	40.909	0.00	0.00	0.00	3.41
1555	1995	2.726821	TCTGGAAATCAGGATGGTTGC	58.273	47.619	0.00	0.00	39.53	4.17
1658	2100	4.068599	GACTTTGAAAGGTCTAAGCAGCT	58.931	43.478	10.02	0.00	39.40	4.24
1659	2101	4.464947	ACTTTGAAAGGTCTAAGCAGCTT	58.535	39.130	13.46	13.46	39.40	3.74
1746	2188	8.958119	TTCAATTCTGGTTGGATAGTATACAC	57.042	34.615	5.50	0.00	0.00	2.90
1949	2482	1.264295	TGTGCCAATTATGCCAGCAA	58.736	45.000	0.00	0.00	34.79	3.91
1996	2530	7.878477	ATCATGTAAAGTCAAGCATGTTTTG	57.122	32.000	0.00	0.00	39.54	2.44
2000	2534	0.681175	AGTCAAGCATGTTTTGGGCC	59.319	50.000	0.00	0.00	0.00	5.80
2090	2630	7.448748	AAGCATTAGGAACGTTCTAAAATGT	57.551	32.000	29.48	21.33	36.14	2.71
2091	2631	6.842163	AGCATTAGGAACGTTCTAAAATGTG	58.158	36.000	29.48	20.59	34.81	3.21
2108	2648	5.618056	AATGTGTTGTGATTGAGTAGCAG	57.382	39.130	0.00	0.00	0.00	4.24
2126	2666	2.943199	GCAGCCTGCCAGGATTATATCC	60.943	54.545	16.85	0.00	43.06	2.59
2156	2714	1.819928	ACAGCAATCGGTATTGTGCA	58.180	45.000	0.00	0.00	43.75	4.57
2262	2823	6.821388	ACTTGAATGGATCCTGTAGTGATAC	58.179	40.000	14.23	0.00	0.00	2.24
2300	2927	5.193679	ACCTTAGGTTGTGGCAATATTCTC	58.806	41.667	0.00	0.00	27.29	2.87
2395	3023	9.202273	TGTATTTTGATGACATTTTAAACCTGC	57.798	29.630	0.00	0.00	0.00	4.85
2398	3026	4.793071	TGATGACATTTTAAACCTGCACG	58.207	39.130	0.00	0.00	0.00	5.34
2421	3049	7.710907	CACGGAAATAATAGATCTGTTCCTCAA	59.289	37.037	8.12	0.00	33.78	3.02
2437	3071	6.016360	TGTTCCTCAATATTATTTGGCCATCG	60.016	38.462	6.09	0.00	0.00	3.84
2450	3084	1.301244	CCATCGGGATCGCTTCTGG	60.301	63.158	8.28	7.78	35.59	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	91	5.356751	TCAATAGTATGCAAAAACATCGCCT	59.643	36.000	0.00	0.00	0.00	5.52
113	115	7.238710	ACAACCCTATTCTGAAGGTTTATGTT	58.761	34.615	9.18	0.00	40.62	2.71
215	625	2.032620	ACCGGCATCAACTAGGTAGAG	58.967	52.381	0.00	0.00	32.76	2.43
326	737	5.810095	AGTGCTAAAGGTTGAATAGCTCTT	58.190	37.500	0.00	0.00	41.25	2.85
327	738	5.046304	TGAGTGCTAAAGGTTGAATAGCTCT	60.046	40.000	7.96	7.96	44.57	4.09
410	821	2.782163	CATGTCGCTTTCTGAATGCTG	58.218	47.619	21.25	15.83	0.00	4.41
450	861	2.289565	GTTAAGTCCAGCCCTGCATAC	58.710	52.381	0.00	0.00	0.00	2.39
460	871	6.471233	TCCTATGTCTCATGTTAAGTCCAG	57.529	41.667	0.00	0.00	0.00	3.86
472	883	5.163405	GGCTCAACTGTATTCCTATGTCTCA	60.163	44.000	0.00	0.00	0.00	3.27
597	1009	2.972348	TCACAGGAACAGTAGGAACCT	58.028	47.619	0.00	0.00	0.00	3.50
625	1037	1.497309	TTAACAGAGCTGGGTGGGGG	61.497	60.000	0.00	0.00	34.19	5.40
626	1038	0.625849	ATTAACAGAGCTGGGTGGGG	59.374	55.000	0.00	0.00	34.19	4.96
627	1039	2.094675	CAATTAACAGAGCTGGGTGGG	58.905	52.381	0.00	0.00	34.19	4.61
630	1042	5.426833	AGAGATACAATTAACAGAGCTGGGT	59.573	40.000	0.00	0.00	34.19	4.51
653	1065	8.023706	CAGCATGGATTGATCATAAATCAAGAG	58.976	37.037	0.00	0.00	40.80	2.85
685	1097	2.764128	GGAGGAGGATGCCGTGGA	60.764	66.667	0.00	0.00	0.00	4.02
686	1098	2.370445	AAGGAGGAGGATGCCGTGG	61.370	63.158	0.00	0.00	0.00	4.94
696	1108	0.826715	TCGAATGGCTCAAGGAGGAG	59.173	55.000	0.00	0.00	37.97	3.69
726	1138	5.224441	ACTATGCTGGGGAAGAACCTAATA	58.776	41.667	0.00	0.00	38.98	0.98
786	1208	7.363181	CCATGGATTTCACAGAAAATAAGCTGA	60.363	37.037	5.56	0.00	36.07	4.26
1102	1531	8.618677	CATGAGAACATTACTAATTGCAGTCAT	58.381	33.333	0.00	0.00	34.15	3.06
1168	1603	7.707893	CACTGAAGAATTTTGACCTTCATGTTT	59.292	33.333	6.91	0.00	43.41	2.83
1169	1604	7.205297	CACTGAAGAATTTTGACCTTCATGTT	58.795	34.615	6.91	0.00	43.41	2.71
1170	1605	6.239120	CCACTGAAGAATTTTGACCTTCATGT	60.239	38.462	6.91	5.55	43.41	3.21
1333	1768	5.363562	TGAGTATGCAGTGAAGATGGAAT	57.636	39.130	0.00	0.00	0.00	3.01
1387	1822	2.514592	CTACGGCACATGGGGCAG	60.515	66.667	22.70	16.11	0.00	4.85
1436	1871	7.880713	TGAAAATGCTTGGTACTGACATAGTTA	59.119	33.333	0.00	0.00	40.89	2.24
1503	1941	4.112716	TCACTTACAAGACGACACAACA	57.887	40.909	0.00	0.00	0.00	3.33
1511	1949	7.542477	AGAAGTATGACAATCACTTACAAGACG	59.458	37.037	0.00	0.00	32.79	4.18
1524	1962	6.962182	TCCTGATTTCCAGAAGTATGACAAT	58.038	36.000	0.00	0.00	45.78	2.71
1555	1995	8.836413	TGTCTCACAGTTTTACTTAAAAGATGG	58.164	33.333	0.00	2.78	36.00	3.51
1685	2127	2.371841	ACCATCTGCAGGTAAACAGTGA	59.628	45.455	15.13	0.00	37.67	3.41
1996	2530	5.007682	TGATAAGTCTTTACTTGTTGGCCC	58.992	41.667	0.00	0.00	45.63	5.80
2000	2534	9.155975	ACTAGCATGATAAGTCTTTACTTGTTG	57.844	33.333	0.00	0.00	45.63	3.33
2090	2630	2.038952	AGGCTGCTACTCAATCACAACA	59.961	45.455	0.00	0.00	0.00	3.33
2091	2631	2.417933	CAGGCTGCTACTCAATCACAAC	59.582	50.000	0.00	0.00	0.00	3.32
2126	2666	2.353889	CCGATTGCTGTTTCAGATCCTG	59.646	50.000	0.66	0.00	32.44	3.86
2129	2669	5.065218	ACAATACCGATTGCTGTTTCAGATC	59.935	40.000	0.66	0.00	45.52	2.75
2201	2759	7.389330	CCCGGCACAAAATACATATATCTAACA	59.611	37.037	0.00	0.00	0.00	2.41
2202	2760	7.604927	TCCCGGCACAAAATACATATATCTAAC	59.395	37.037	0.00	0.00	0.00	2.34
2262	2823	5.010282	ACCTAAGGTCAAATGCCTTTAGTG	58.990	41.667	12.25	0.00	43.24	2.74
2300	2927	8.403236	TGATTGATGCTATTTCTCAGATGTTTG	58.597	33.333	0.00	0.00	0.00	2.93
2395	3023	7.210174	TGAGGAACAGATCTATTATTTCCGTG	58.790	38.462	0.00	0.00	38.04	4.94
2421	3049	4.199310	CGATCCCGATGGCCAAATAATAT	58.801	43.478	10.96	0.00	38.22	1.28
2437	3071	0.250513	AACTGACCAGAAGCGATCCC	59.749	55.000	3.76	0.00	0.00	3.85
2476	3110	3.012518	GCACACTGCTATTCAAGATGGT	58.987	45.455	0.00	0.00	40.96	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.