AutoCloner

Multiple sequence alignment - TraesCS5D01G542900

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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	TraesCS5D01G542900	chr5D	100.000	2479	0	0	1	2479	553422987	553420509	0.000000e+00	4578.0
1	TraesCS5D01G542900	chr5D	90.445	1057	62	16	950	1989	553002684	553001650	0.000000e+00	1356.0
2	TraesCS5D01G542900	chr5D	94.970	656	23	4	1	647	553003714	553003060	0.000000e+00	1020.0
3	TraesCS5D01G542900	chr5D	92.508	307	20	3	1758	2063	553420928	553420624	1.050000e-118	436.0
4	TraesCS5D01G542900	chr5D	92.508	307	20	3	2060	2364	553421230	553420925	1.050000e-118	436.0
5	TraesCS5D01G542900	chr5D	93.960	149	4	2	693	836	553003064	553002916	1.150000e-53	220.0
6	TraesCS5D01G542900	chr5D	74.603	441	76	24	950	1360	553462894	553463328	7.100000e-36	161.0
7	TraesCS5D01G542900	chr5D	75.703	391	51	21	1001	1364	553010143	553009770	3.300000e-34	156.0
8	TraesCS5D01G542900	chr5D	95.506	89	4	0	862	950	553002854	553002766	2.570000e-30	143.0
9	TraesCS5D01G542900	chr5D	94.937	79	4	0	2286	2364	553001531	553001453	9.310000e-25	124.0
10	TraesCS5D01G542900	chr5D	87.037	108	12	2	2372	2477	443339408	443339515	1.200000e-23	121.0
11	TraesCS5D01G542900	chr5D	75.824	273	44	12	1106	1364	553464880	553464616	4.330000e-23	119.0
12	TraesCS5D01G542900	chr5D	88.542	96	10	1	2383	2477	443333680	443333775	5.600000e-22	115.0
13	TraesCS5D01G542900	chr5D	91.250	80	7	0	1985	2064	553001531	553001452	2.610000e-20	110.0
14	TraesCS5D01G542900	chr5D	80.380	158	17	5	1101	1247	553468250	553468096	9.380000e-20	108.0
15	TraesCS5D01G542900	chr4A	76.607	389	49	19	1003	1364	615117654	615118027	2.530000e-40	176.0
16	TraesCS5D01G542900	chr3D	92.079	101	6	2	2378	2477	586302375	586302276	9.240000e-30	141.0
17	TraesCS5D01G542900	chr3D	90.625	96	8	1	2381	2475	357730262	357730357	2.590000e-25	126.0
18	TraesCS5D01G542900	chrUn	92.708	96	6	1	2383	2477	22759827	22759732	1.200000e-28	137.0
19	TraesCS5D01G542900	chr5B	91.837	98	7	1	2381	2477	462116205	462116302	4.300000e-28	135.0
20	TraesCS5D01G542900	chr5B	76.793	237	34	10	1001	1228	697493443	697493667	2.020000e-21	113.0
21	TraesCS5D01G542900	chr5B	82.946	129	13	4	1106	1228	697349242	697349367	9.380000e-20	108.0
22	TraesCS5D01G542900	chr2D	91.667	96	7	1	2383	2477	381559879	381559974	5.560000e-27	132.0
23	TraesCS5D01G542900	chr2D	95.122	41	2	0	862	902	45565535	45565575	5.720000e-07	65.8
24	TraesCS5D01G542900	chr1B	88.235	102	10	2	2378	2477	589076047	589076148	1.200000e-23	121.0
25	TraesCS5D01G542900	chr3B	87.755	98	11	1	2381	2477	685819007	685819104	2.020000e-21	113.0
26	TraesCS5D01G542900	chr6A	95.652	46	2	0	862	907	100300455	100300500	9.510000e-10	75.0
27	TraesCS5D01G542900	chr6A	97.561	41	1	0	862	902	100300554	100300514	1.230000e-08	71.3
28	TraesCS5D01G542900	chr2A	97.674	43	1	0	860	902	715416534	715416576	9.510000e-10	75.0
29	TraesCS5D01G542900	chr4D	97.561	41	1	0	862	902	465124193	465124153	1.230000e-08	71.3
30	TraesCS5D01G542900	chr4B	97.561	41	1	0	862	902	581904239	581904279	1.230000e-08	71.3
31	TraesCS5D01G542900	chr7D	95.349	43	2	0	862	904	100233211	100233169	4.420000e-08	69.4
32	TraesCS5D01G542900	chr2B	95.238	42	2	0	861	902	184776815	184776856	1.590000e-07	67.6
33	TraesCS5D01G542900	chr7B	97.297	37	1	0	125	161	701866902	701866938	2.060000e-06	63.9

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	TraesCS5D01G542900	chr5D	553420509	553422987	2478	True	1816.666667	4578	95.005333	1	2479	3	chr5D.!!$R3	2478
1	TraesCS5D01G542900	chr5D	553001452	553003714	2262	True	495.500000	1356	93.511333	1	2364	6	chr5D.!!$R2	2363

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
945	995	0.17895	TCCAGCACCTCTGTCAGTCT	60.179	55.0	0.0	0.0	41.25	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2054	2201	0.112218	TTGGAGTGGGGACATGTTGG	59.888	55.0	0.0	0.0	46.14	3.77	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	2.117156	CGCCTTTCATGGGCTCCTG	61.117	63.158	9.42	0.00	46.73	3.86
103	104	2.488153	GCGAGGCAAAAAGTGATTAGGT	59.512	45.455	0.00	0.00	0.00	3.08
106	107	4.142816	CGAGGCAAAAAGTGATTAGGTGAG	60.143	45.833	0.00	0.00	0.00	3.51
120	121	0.737715	GGTGAGACTGCCGATGTGAC	60.738	60.000	0.00	0.00	0.00	3.67
158	159	2.287977	AAGGGTACTCTTTGGTTGGC	57.712	50.000	0.85	0.00	0.00	4.52
190	192	7.445707	AGAACACTCACCTTATCTTCTTTTTCC	59.554	37.037	0.00	0.00	0.00	3.13
257	259	9.383519	TCTCTTTTTATTTAGCGATCATCAAGT	57.616	29.630	0.00	0.00	0.00	3.16
317	319	9.950680	AAATATATTCTAAATGACCAACAAGCG	57.049	29.630	0.00	0.00	0.00	4.68
323	325	6.205784	TCTAAATGACCAACAAGCGAAAAAG	58.794	36.000	0.00	0.00	0.00	2.27
326	328	3.506810	TGACCAACAAGCGAAAAAGTTG	58.493	40.909	0.00	0.00	40.63	3.16
405	407	2.161808	AGTCGTCACTCAATGTACGAGG	59.838	50.000	0.00	0.00	44.18	4.63
448	450	6.261381	ACGAAGCTGAGGTTAACATGTTAAAA	59.739	34.615	28.05	10.80	36.86	1.52
539	548	1.632409	AGATGTGAAGTCAGGGCATGT	59.368	47.619	0.00	0.00	0.00	3.21
547	556	2.187685	CAGGGCATGTAGAGCGCA	59.812	61.111	11.47	0.00	46.12	6.09
568	577	0.247814	CCGTGCGTTCATGATGCTTC	60.248	55.000	18.04	11.63	41.04	3.86
606	615	2.172717	AGCAGGTGTACAGAACCAAACT	59.827	45.455	0.00	0.00	40.40	2.66
643	652	4.347607	CTCAAGGTCCCAATTTTCCATCT	58.652	43.478	0.00	0.00	0.00	2.90
644	653	4.750941	TCAAGGTCCCAATTTTCCATCTT	58.249	39.130	0.00	0.00	0.00	2.40
645	654	5.154418	TCAAGGTCCCAATTTTCCATCTTT	58.846	37.500	0.00	0.00	0.00	2.52
646	655	5.606329	TCAAGGTCCCAATTTTCCATCTTTT	59.394	36.000	0.00	0.00	0.00	2.27
647	656	5.488262	AGGTCCCAATTTTCCATCTTTTG	57.512	39.130	0.00	0.00	0.00	2.44
648	657	5.154418	AGGTCCCAATTTTCCATCTTTTGA	58.846	37.500	0.00	0.00	0.00	2.69
649	658	5.606329	AGGTCCCAATTTTCCATCTTTTGAA	59.394	36.000	0.00	0.00	0.00	2.69
650	659	6.273026	AGGTCCCAATTTTCCATCTTTTGAAT	59.727	34.615	0.00	0.00	0.00	2.57
651	660	6.595326	GGTCCCAATTTTCCATCTTTTGAATC	59.405	38.462	0.00	0.00	0.00	2.52

Showing 1 to 25 of 393 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	2.747460	GCGACATGGCCTGCAGAA	60.747	61.111	17.39	0.00	0.00	3.02
77	78	0.521735	CACTTTTTGCCTCGCCCTAC	59.478	55.000	0.00	0.00	0.00	3.18
89	90	4.762251	GGCAGTCTCACCTAATCACTTTTT	59.238	41.667	0.00	0.00	0.00	1.94
103	104	0.678950	TTGTCACATCGGCAGTCTCA	59.321	50.000	0.00	0.00	0.00	3.27
106	107	1.021390	CCCTTGTCACATCGGCAGTC	61.021	60.000	0.00	0.00	0.00	3.51
120	121	4.010349	CCTTTAACTAGTTGCTCCCCTTG	58.990	47.826	18.56	0.00	0.00	3.61
158	159	5.799213	AGATAAGGTGAGTGTTCTGGAAAG	58.201	41.667	0.00	0.00	0.00	2.62
225	227	9.330063	TGATCGCTAAATAAAAAGAGATCATGT	57.670	29.630	12.69	0.00	46.96	3.21
232	234	9.994432	AACTTGATGATCGCTAAATAAAAAGAG	57.006	29.630	0.00	0.00	0.00	2.85
250	252	8.792633	TCCAGGTCAAACTTTTATAACTTGATG	58.207	33.333	0.00	0.00	0.00	3.07
405	407	3.064207	TCGTTACCATTGACTGCAAGAC	58.936	45.455	0.00	0.00	37.45	3.01
501	503	0.385390	CTGTCAAAGTTGGTGGCCAC	59.615	55.000	28.57	28.57	30.78	5.01
547	556	0.462581	AGCATCATGAACGCACGGAT	60.463	50.000	19.29	0.00	0.00	4.18
568	577	4.232221	CCTGCTGCAACAAACAATAAGAG	58.768	43.478	3.02	0.00	0.00	2.85
606	615	0.975556	TTGAGGCGGCTGAGATGGTA	60.976	55.000	19.63	0.00	0.00	3.25
643	652	3.186409	GTGCTACTCGTGCTGATTCAAAA	59.814	43.478	0.00	0.00	0.00	2.44
644	653	2.736721	GTGCTACTCGTGCTGATTCAAA	59.263	45.455	0.00	0.00	0.00	2.69
645	654	2.337583	GTGCTACTCGTGCTGATTCAA	58.662	47.619	0.00	0.00	0.00	2.69
646	655	1.732405	CGTGCTACTCGTGCTGATTCA	60.732	52.381	0.00	0.00	0.00	2.57
647	656	0.917259	CGTGCTACTCGTGCTGATTC	59.083	55.000	0.00	0.00	0.00	2.52
648	657	1.078759	GCGTGCTACTCGTGCTGATT	61.079	55.000	0.00	0.00	0.00	2.57
649	658	1.517257	GCGTGCTACTCGTGCTGAT	60.517	57.895	0.00	0.00	0.00	2.90
650	659	2.126463	GCGTGCTACTCGTGCTGA	60.126	61.111	0.00	0.00	0.00	4.26
651	660	2.430751	TGCGTGCTACTCGTGCTG	60.431	61.111	0.00	0.00	0.00	4.41
652	661	2.126307	CTGCGTGCTACTCGTGCT	60.126	61.111	0.00	0.00	0.00	4.40

Showing 1 to 25 of 363 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.