AutoCloner

Multiple sequence alignment - TraesCS1D01G453400

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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	TraesCS1D01G453400	chr1D	100.000	2464	0	0	1	2464	494327106	494329569	0.000000e+00	4551.0
1	TraesCS1D01G453400	chr1D	85.645	1024	114	16	776	1777	494423981	494424993	0.000000e+00	1046.0
2	TraesCS1D01G453400	chr1D	88.979	617	43	6	931	1523	494169048	494169663	0.000000e+00	739.0
3	TraesCS1D01G453400	chr1D	89.806	206	11	7	146	349	494168269	494168466	3.140000e-64	255.0
4	TraesCS1D01G453400	chr1D	83.193	238	35	3	156	391	494423287	494423521	1.920000e-51	213.0
5	TraesCS1D01G453400	chr1D	81.667	240	24	12	156	391	494348481	494348704	5.410000e-42	182.0
6	TraesCS1D01G453400	chr1D	78.571	308	34	18	348	629	494168628	494168929	9.060000e-40	174.0
7	TraesCS1D01G453400	chr1D	81.991	211	12	8	78	262	494305672	494305882	3.280000e-34	156.0
8	TraesCS1D01G453400	chr1D	91.463	82	6	1	67	148	494423166	494423246	7.200000e-21	111.0
9	TraesCS1D01G453400	chr1D	83.168	101	10	5	398	491	494423588	494423688	4.370000e-13	86.1
10	TraesCS1D01G453400	chr1A	90.769	2535	119	42	1	2463	592976978	592979469	0.000000e+00	3278.0
11	TraesCS1D01G453400	chr1A	85.352	1024	108	23	778	1777	593214584	593215589	0.000000e+00	1022.0
12	TraesCS1D01G453400	chr1A	83.902	1025	118	18	778	1777	593217682	593218684	0.000000e+00	935.0
13	TraesCS1D01G453400	chr1A	87.139	762	56	12	787	1523	592851867	592852611	0.000000e+00	826.0
14	TraesCS1D01G453400	chr1A	78.510	349	45	16	69	390	593213800	593214145	4.150000e-48	202.0
15	TraesCS1D01G453400	chr1A	91.781	146	8	3	156	298	592851424	592851568	1.490000e-47	200.0
16	TraesCS1D01G453400	chr1A	85.065	154	16	7	481	629	592851615	592851766	1.530000e-32	150.0
17	TraesCS1D01G453400	chr1A	83.133	166	24	3	156	318	592924016	592924180	5.490000e-32	148.0
18	TraesCS1D01G453400	chr1A	92.593	81	4	2	78	157	592923910	592923989	5.570000e-22	115.0
19	TraesCS1D01G453400	chr1A	83.929	112	11	5	156	264	592992850	592992957	1.560000e-17	100.0
20	TraesCS1D01G453400	chr1A	82.353	85	8	5	398	475	593214182	593214266	1.580000e-07	67.6
21	TraesCS1D01G453400	chrUn	89.488	1503	75	25	34	1465	358968868	358967378	0.000000e+00	1823.0
22	TraesCS1D01G453400	chrUn	90.476	84	5	2	76	157	290640076	290639994	9.320000e-20	108.0
23	TraesCS1D01G453400	chrUn	90.476	84	5	2	76	157	290645801	290645719	9.320000e-20	108.0
24	TraesCS1D01G453400	chrUn	90.476	84	5	2	76	157	320336388	320336470	9.320000e-20	108.0
25	TraesCS1D01G453400	chr1B	93.725	1004	52	4	1469	2463	687517610	687518611	0.000000e+00	1495.0
26	TraesCS1D01G453400	chr1B	85.449	1024	107	12	778	1777	687650802	687651807	0.000000e+00	1027.0
27	TraesCS1D01G453400	chr1B	88.482	764	59	7	787	1523	687422955	687423716	0.000000e+00	896.0
28	TraesCS1D01G453400	chr1B	79.233	626	84	23	927	1514	686853885	686853268	6.390000e-106	394.0
29	TraesCS1D01G453400	chr1B	91.093	247	12	8	146	391	687422289	687422526	2.360000e-85	326.0
30	TraesCS1D01G453400	chr1B	78.470	353	45	14	67	391	687650024	687650373	4.150000e-48	202.0

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	TraesCS1D01G453400	chr1D	494327106	494329569	2463	False	4551.000000	4551	100.000000	1	2464	1	chr1D.!!$F2	2463
1	TraesCS1D01G453400	chr1D	494168269	494169663	1394	False	389.333333	739	85.785333	146	1523	3	chr1D.!!$F4	1377
2	TraesCS1D01G453400	chr1D	494423166	494424993	1827	False	364.025000	1046	85.867250	67	1777	4	chr1D.!!$F5	1710
3	TraesCS1D01G453400	chr1A	592976978	592979469	2491	False	3278.000000	3278	90.769000	1	2463	1	chr1A.!!$F1	2462
4	TraesCS1D01G453400	chr1A	593213800	593218684	4884	False	556.650000	1022	82.529250	69	1777	4	chr1A.!!$F5	1708
5	TraesCS1D01G453400	chr1A	592851424	592852611	1187	False	392.000000	826	87.995000	156	1523	3	chr1A.!!$F3	1367
6	TraesCS1D01G453400	chrUn	358967378	358968868	1490	True	1823.000000	1823	89.488000	34	1465	1	chrUn.!!$R3	1431
7	TraesCS1D01G453400	chr1B	687517610	687518611	1001	False	1495.000000	1495	93.725000	1469	2463	1	chr1B.!!$F1	994
8	TraesCS1D01G453400	chr1B	687650024	687651807	1783	False	614.500000	1027	81.959500	67	1777	2	chr1B.!!$F3	1710
9	TraesCS1D01G453400	chr1B	687422289	687423716	1427	False	611.000000	896	89.787500	146	1523	2	chr1B.!!$F2	1377
10	TraesCS1D01G453400	chr1B	686853268	686853885	617	True	394.000000	394	79.233000	927	1514	1	chr1B.!!$R1	587

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
154	190	0.588252	GAAAGCAAGTGCAAGCTCGA	59.412	50.0	9.64	0.0	45.16	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1465	1979	0.811616	GGATGGATCGAGCAAGCGTT	60.812	55.0	1.84	0.0	0.0	4.84	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
27	28	3.429085	GTGTCATAATCGGCAAGCTTTG	58.571	45.455	0.00	0.00	0.00	2.77
51	54	2.864343	GCGATATAAACAGAACAGCGGT	59.136	45.455	0.00	0.00	0.00	5.68
54	57	2.851263	ATAAACAGAACAGCGGTGGA	57.149	45.000	20.20	0.00	0.00	4.02
142	146	3.075283	TCCCTGGTGGAATTAGAAAGCAA	59.925	43.478	0.00	0.00	41.40	3.91
143	147	3.445096	CCCTGGTGGAATTAGAAAGCAAG	59.555	47.826	0.00	0.00	35.39	4.01
144	148	4.082125	CCTGGTGGAATTAGAAAGCAAGT	58.918	43.478	0.00	0.00	34.57	3.16
149	182	4.919754	GTGGAATTAGAAAGCAAGTGCAAG	59.080	41.667	6.00	0.00	45.16	4.01
152	188	3.904136	TTAGAAAGCAAGTGCAAGCTC	57.096	42.857	9.64	0.29	45.16	4.09
153	189	0.590195	AGAAAGCAAGTGCAAGCTCG	59.410	50.000	9.64	0.00	45.16	5.03
154	190	0.588252	GAAAGCAAGTGCAAGCTCGA	59.412	50.000	9.64	0.00	45.16	4.04
324	371	3.117131	TCATAGCCACTGTCCTCCATCTA	60.117	47.826	0.00	0.00	0.00	1.98
391	601	6.364706	GCCTACAAGATCGATCTAGATTGTTG	59.635	42.308	26.91	24.29	35.76	3.33
392	602	7.429633	CCTACAAGATCGATCTAGATTGTTGT	58.570	38.462	26.91	24.91	39.39	3.32
393	603	7.923344	CCTACAAGATCGATCTAGATTGTTGTT	59.077	37.037	26.91	15.80	38.23	2.83
560	911	3.377172	ACTGTACCTCTTGCAACAACAAC	59.623	43.478	0.00	0.00	0.00	3.32
562	913	3.759086	TGTACCTCTTGCAACAACAACAA	59.241	39.130	0.00	0.00	0.00	2.83
608	1011	6.331369	TCCTTAATTTGTTTCTTCTGCCTG	57.669	37.500	0.00	0.00	0.00	4.85
641	1100	2.102588	ACCGCTGGTACATACAAGATCC	59.897	50.000	0.00	0.00	38.20	3.36
708	1167	9.173021	CCTATATATGTTGAACTTGTTGTTGGA	57.827	33.333	0.00	0.00	39.30	3.53
939	1402	9.732130	ATCTCCTTGAAAATATTATCTAGGTGC	57.268	33.333	0.00	0.00	38.95	5.01
1119	1586	2.690497	GGCTAAGAATGGGAAAGAAGCC	59.310	50.000	0.00	0.00	41.27	4.35
1194	1661	1.228154	GCCCATAATGACCGGTCCC	60.228	63.158	31.19	9.46	0.00	4.46
1222	1699	5.108385	ACTTGCTTGAGTTAATTTGACGG	57.892	39.130	0.00	0.00	0.00	4.79
1225	1703	5.508200	TGCTTGAGTTAATTTGACGGTTT	57.492	34.783	0.00	0.00	0.00	3.27
1465	1979	6.922957	GTCATCAACAGGAAAAACAATTAGCA	59.077	34.615	0.00	0.00	0.00	3.49
1508	2022	4.442706	TGGAGGAAGAAATTAAGCTAGCG	58.557	43.478	9.55	0.00	0.00	4.26
1562	2076	9.573133	GCTATGCATTATATTATTGTTGGGTTC	57.427	33.333	3.54	0.00	0.00	3.62
1596	2110	2.038659	GAGGTCAAGCAGAGAGGCTAT	58.961	52.381	0.00	0.00	45.07	2.97
1635	2149	9.696417	CATTGGGATCGATGTAATGTGCAACAA	62.696	40.741	0.54	0.00	38.96	2.83
1693	5298	5.172687	TGATTTATGCTTCAGGGTGTGTA	57.827	39.130	0.00	0.00	0.00	2.90
1801	5406	8.641499	GTTTCTGGAAACATGAAACAAATACA	57.359	30.769	17.90	0.00	46.30	2.29
1804	5409	8.815141	TCTGGAAACATGAAACAAATACAATG	57.185	30.769	0.00	0.00	41.51	2.82
1913	5519	3.486383	ACCAACGTGACTTCAAATGGAT	58.514	40.909	4.23	0.00	32.62	3.41
1922	5528	2.498481	ACTTCAAATGGATGTGGGCATG	59.502	45.455	0.00	0.00	35.07	4.06
1951	5557	5.660417	TGCCATCCCAACAAATACATACATT	59.340	36.000	0.00	0.00	0.00	2.71
1984	5590	3.745797	GCAACCCTCCTCCATAAGCTTAG	60.746	52.174	12.54	0.00	0.00	2.18
2005	5611	3.353557	GGGTTCACAATTCCCTCCTTAC	58.646	50.000	0.00	0.00	38.29	2.34
2030	5636	6.150474	CCTACCAAAACCACAAGATATTTCGT	59.850	38.462	0.00	0.00	0.00	3.85
2057	5663	6.530120	TGGGTAGGCATACAACATACTTATG	58.470	40.000	11.12	0.00	35.37	1.90
2070	5676	8.993424	ACAACATACTTATGACTATTCCTTCCT	58.007	33.333	3.19	0.00	37.15	3.36
2125	5732	2.006888	TCTTGCGCCATTTAGTAGCAC	58.993	47.619	4.18	0.00	37.57	4.40
2264	5879	3.548770	TGGATGGCATCTCATTTGTCTC	58.451	45.455	25.48	6.75	0.00	3.36
2298	5913	4.692523	AACCCCTCATATCAAAACCCTT	57.307	40.909	0.00	0.00	0.00	3.95
2355	5970	8.816640	ATTCACCACAAATTCAATAGTTCAAC	57.183	30.769	0.00	0.00	0.00	3.18
2357	5972	7.776107	TCACCACAAATTCAATAGTTCAACAA	58.224	30.769	0.00	0.00	0.00	2.83
2419	6034	4.518970	ACACAAGCCAAAGTGAAATACGAT	59.481	37.500	0.00	0.00	39.03	3.73
2463	6078	1.835483	ATGAATCATTCCGCGCTCGC	61.835	55.000	5.56	3.90	37.85	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.316196	GCTTGCCGATTATGACACGC	60.316	55.000	0.00	0.00	0.00	5.34
9	10	2.945008	CCTCAAAGCTTGCCGATTATGA	59.055	45.455	0.00	0.00	0.00	2.15
27	28	3.182572	CGCTGTTCTGTTTATATCGCCTC	59.817	47.826	0.00	0.00	0.00	4.70
51	54	4.901197	TGGAGTAACTACTTGCATTCCA	57.099	40.909	0.00	0.00	36.50	3.53
54	57	9.632638	AAATGATATGGAGTAACTACTTGCATT	57.367	29.630	0.00	0.00	36.50	3.56
142	146	2.196749	CATTCGTATCGAGCTTGCACT	58.803	47.619	0.00	0.00	37.14	4.40
143	147	1.258982	CCATTCGTATCGAGCTTGCAC	59.741	52.381	0.00	0.00	37.14	4.57
144	148	1.136110	TCCATTCGTATCGAGCTTGCA	59.864	47.619	0.00	0.00	37.14	4.08
149	182	1.276145	GCCGTCCATTCGTATCGAGC	61.276	60.000	0.00	0.00	37.14	5.03
152	188	2.014554	CGGCCGTCCATTCGTATCG	61.015	63.158	19.50	0.00	0.00	2.92
153	189	0.663568	CTCGGCCGTCCATTCGTATC	60.664	60.000	27.15	0.00	0.00	2.24
154	190	1.105167	TCTCGGCCGTCCATTCGTAT	61.105	55.000	27.15	0.00	0.00	3.06
257	295	2.163818	TGAAACTACGGTTGCTCTGG	57.836	50.000	0.00	0.00	35.63	3.86
324	371	2.289631	TGGAAGATGCACGACAAGACAT	60.290	45.455	0.00	0.00	0.00	3.06
391	601	0.031178	CCAGAAAGTGTGCTGCCAAC	59.969	55.000	0.00	0.00	0.00	3.77
392	602	0.395586	ACCAGAAAGTGTGCTGCCAA	60.396	50.000	0.00	0.00	0.00	4.52
393	603	0.395586	AACCAGAAAGTGTGCTGCCA	60.396	50.000	0.00	0.00	0.00	4.92
539	890	3.376859	TGTTGTTGTTGCAAGAGGTACAG	59.623	43.478	0.00	0.00	0.00	2.74
560	911	9.395707	GAAGGAACAGATATATGTACGTAGTTG	57.604	37.037	2.88	0.00	45.11	3.16
641	1100	0.654683	GCAGCGCCTCTAACAATCTG	59.345	55.000	2.29	0.00	0.00	2.90
708	1167	2.393557	CCATACGCATGGCTTCGTT	58.606	52.632	0.63	0.00	45.29	3.85
973	1437	7.076842	TCAGCTAGCTAAAATAACTGCAAAG	57.923	36.000	18.86	0.00	0.00	2.77
1119	1586	3.873910	ACCCTCAAGGAACATATCAACG	58.126	45.455	0.00	0.00	39.89	4.10
1194	1661	6.147164	TCAAATTAACTCAAGCAAGTACCTCG	59.853	38.462	0.00	0.00	0.00	4.63
1202	1669	5.508200	AACCGTCAAATTAACTCAAGCAA	57.492	34.783	0.00	0.00	0.00	3.91
1248	1747	9.761504	AACATATAGAAGTGTCAATGAGATGAG	57.238	33.333	0.00	0.00	0.00	2.90
1465	1979	0.811616	GGATGGATCGAGCAAGCGTT	60.812	55.000	1.84	0.00	0.00	4.84
1562	2076	4.676924	GCTTGACCTCGAAAACAAAATGAG	59.323	41.667	0.00	0.00	0.00	2.90
1596	2110	7.494922	TCGATCCCAATGATCTAATTATGGA	57.505	36.000	2.67	0.00	46.52	3.41
1655	2169	9.817809	AGCATAAATCAACGAGAAGTAATAGAA	57.182	29.630	0.00	0.00	0.00	2.10
1747	5352	4.468095	AGAAATCGAAACCGTGAAACAG	57.532	40.909	0.00	0.00	35.74	3.16
1801	5406	4.805192	GTGATTAAATGCGCCATTCACATT	59.195	37.500	4.18	0.00	32.43	2.71
1804	5409	3.115554	GGTGATTAAATGCGCCATTCAC	58.884	45.455	4.18	9.47	32.43	3.18
1922	5528	1.337118	TTTGTTGGGATGGCAGGTTC	58.663	50.000	0.00	0.00	0.00	3.62
1951	5557	3.115390	AGGAGGGTTGCTTGCTTCTATA	58.885	45.455	0.00	0.00	0.00	1.31
1956	5562	1.075659	GGAGGAGGGTTGCTTGCTT	59.924	57.895	0.00	0.00	0.00	3.91
1984	5590	2.604912	AAGGAGGGAATTGTGAACCC	57.395	50.000	0.00	0.00	43.55	4.11
2005	5611	6.150474	ACGAAATATCTTGTGGTTTTGGTAGG	59.850	38.462	0.00	0.00	0.00	3.18
2030	5636	6.757173	AGTATGTTGTATGCCTACCCATTA	57.243	37.500	6.69	0.00	0.00	1.90
2167	5782	2.093973	CCAAGTCTGGTCGTAGATGCTT	60.094	50.000	0.00	0.00	40.67	3.91
2264	5879	1.533033	GGGGTTTGGTTGTCTGGGG	60.533	63.158	0.00	0.00	0.00	4.96
2277	5892	4.692523	AAGGGTTTTGATATGAGGGGTT	57.307	40.909	0.00	0.00	0.00	4.11
2298	5913	4.248174	TGATGGAGGTGCATGGATTTTA	57.752	40.909	0.00	0.00	0.00	1.52
2401	6016	7.624360	TGAATTATCGTATTTCACTTTGGCT	57.376	32.000	0.00	0.00	0.00	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.