AutoCloner

Multiple sequence alignment - TraesCS2A01G489600

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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	TraesCS2A01G489600	chr2A	100.000	4546	0	0	1	4546	723517802	723522347	0.000000e+00	8395.0
1	TraesCS2A01G489600	chr2A	91.089	1111	60	32	879	1956	725994246	725993142	0.000000e+00	1467.0
2	TraesCS2A01G489600	chr2A	86.235	1235	103	36	2580	3769	725993003	725991791	0.000000e+00	1277.0
3	TraesCS2A01G489600	chr2A	84.615	130	7	6	2252	2377	725993199	725993079	2.870000e-22	117.0
4	TraesCS2A01G489600	chr2D	89.907	3864	236	75	1	3766	588789617	588793424	0.000000e+00	4833.0
5	TraesCS2A01G489600	chr2D	91.682	1094	57	23	879	1951	590990826	590989746	0.000000e+00	1485.0
6	TraesCS2A01G489600	chr2D	92.257	917	57	8	2688	3602	590989482	590988578	0.000000e+00	1288.0
7	TraesCS2A01G489600	chr2B	88.457	1568	98	38	994	2518	712597407	712598934	0.000000e+00	1816.0
8	TraesCS2A01G489600	chr2B	91.905	1260	66	15	2534	3766	712599376	712600626	0.000000e+00	1729.0
9	TraesCS2A01G489600	chr2B	88.101	1353	98	41	879	2213	716596020	716594713	0.000000e+00	1548.0
10	TraesCS2A01G489600	chr2B	86.069	1249	107	36	2565	3769	716594825	716593600	0.000000e+00	1280.0
11	TraesCS2A01G489600	chr2B	94.772	746	30	5	1	743	712596175	712596914	0.000000e+00	1153.0
12	TraesCS2A01G489600	chr2B	81.579	456	44	28	2102	2517	712598811	712599266	1.570000e-89	340.0
13	TraesCS2A01G489600	chr2B	92.486	173	12	1	741	913	712596943	712597114	3.510000e-61	246.0
14	TraesCS2A01G489600	chr2B	85.156	128	14	4	2252	2377	716595005	716594881	4.770000e-25	126.0
15	TraesCS2A01G489600	chr2B	86.555	119	7	1	1570	1688	12708593	12708702	6.180000e-24	122.0
16	TraesCS2A01G489600	chr2B	83.333	72	7	3	4328	4398	73560392	73560325	1.370000e-05	62.1
17	TraesCS2A01G489600	chr7A	78.548	303	50	13	300	597	552677094	552676802	7.770000e-43	185.0
18	TraesCS2A01G489600	chr7A	92.683	41	3	0	3800	3840	286826035	286825995	4.910000e-05	60.2
19	TraesCS2A01G489600	chr7A	90.698	43	3	1	3800	3842	669735845	669735886	6.350000e-04	56.5
20	TraesCS2A01G489600	chr7A	96.970	33	0	1	4366	4397	613641291	613641259	2.000000e-03	54.7
21	TraesCS2A01G489600	chr7D	81.277	235	34	8	366	597	484359984	484359757	1.000000e-41	182.0
22	TraesCS2A01G489600	chr7D	79.630	108	10	10	4298	4397	533913712	533913609	2.940000e-07	67.6
23	TraesCS2A01G489600	chr7D	97.222	36	0	1	3810	3845	159906310	159906276	4.910000e-05	60.2
24	TraesCS2A01G489600	chrUn	78.223	349	18	20	1340	1688	93957710	93958000	2.170000e-38	171.0
25	TraesCS2A01G489600	chr1D	77.650	349	20	24	1340	1688	66758884	66759174	4.710000e-35	159.0
26	TraesCS2A01G489600	chr1D	83.708	178	10	7	1340	1517	370167928	370168086	2.830000e-32	150.0
27	TraesCS2A01G489600	chr1D	81.618	136	18	7	367	500	482502702	482502832	6.220000e-19	106.0
28	TraesCS2A01G489600	chr1D	75.155	161	28	11	293	448	89703743	89703896	1.060000e-06	65.8
29	TraesCS2A01G489600	chr6A	78.903	237	43	6	294	528	550733330	550733099	2.190000e-33	154.0
30	TraesCS2A01G489600	chr6A	76.224	286	48	13	330	604	588454662	588454938	2.850000e-27	134.0
31	TraesCS2A01G489600	chr3D	77.364	349	21	20	1340	1688	21935376	21935666	2.190000e-33	154.0
32	TraesCS2A01G489600	chr3D	92.683	41	3	0	3800	3840	384646730	384646690	4.910000e-05	60.2
33	TraesCS2A01G489600	chr3A	88.235	119	5	1	1570	1688	668637761	668637870	2.850000e-27	134.0
34	TraesCS2A01G489600	chr5A	74.661	221	46	8	389	606	91323385	91323598	6.260000e-14	89.8
35	TraesCS2A01G489600	chr5B	91.489	47	3	1	3800	3846	541163212	541163167	3.800000e-06	63.9
36	TraesCS2A01G489600	chr4B	90.476	42	4	0	3800	3841	57740596	57740637	6.350000e-04	56.5
37	TraesCS2A01G489600	chr4B	92.105	38	3	0	3800	3837	119375136	119375173	2.000000e-03	54.7
38	TraesCS2A01G489600	chr4B	90.476	42	3	1	3800	3841	643987865	643987825	2.000000e-03	54.7
39	TraesCS2A01G489600	chr1B	90.476	42	4	0	3800	3841	487484908	487484949	6.350000e-04	56.5

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	TraesCS2A01G489600	chr2A	723517802	723522347	4545	False	8395.000000	8395	100.0000	1	4546	1	chr2A.!!$F1	4545
1	TraesCS2A01G489600	chr2A	725991791	725994246	2455	True	953.666667	1467	87.3130	879	3769	3	chr2A.!!$R1	2890
2	TraesCS2A01G489600	chr2D	588789617	588793424	3807	False	4833.000000	4833	89.9070	1	3766	1	chr2D.!!$F1	3765
3	TraesCS2A01G489600	chr2D	590988578	590990826	2248	True	1386.500000	1485	91.9695	879	3602	2	chr2D.!!$R1	2723
4	TraesCS2A01G489600	chr2B	712596175	712600626	4451	False	1056.800000	1816	89.8398	1	3766	5	chr2B.!!$F2	3765
5	TraesCS2A01G489600	chr2B	716593600	716596020	2420	True	984.666667	1548	86.4420	879	3769	3	chr2B.!!$R2	2890

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
892	927	0.179045	CTAGCCCATTTCCACCGGAG	60.179	60.0	9.46	0.0	31.21	4.63	F
1920	2202	0.321298	TCTTCGCCTGTGGGTTTAGC	60.321	55.0	0.00	0.0	34.45	3.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1967	2256	0.103208	ATCAGATTCAGACCGACGCC	59.897	55.0	0.0	0.0	0.0	5.68	R
3843	4675	0.033366	CACATCACACCACTCACGGA	59.967	55.0	0.0	0.0	0.0	4.69	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
110	113	4.835615	TGCAAAATAGGGCTTTCTTAACCA	59.164	37.500	0.00	0.00	0.00	3.67
163	166	8.859236	AATTATGCATAGCTTCTGATACATGT	57.141	30.769	6.50	2.69	0.00	3.21
310	313	5.021458	TCCTTTAGGGACTCTTTGATACGT	58.979	41.667	0.00	0.00	41.75	3.57
335	338	8.143835	GTGGTATTCTAAAATCATGGGAATTGG	58.856	37.037	0.00	0.00	0.00	3.16
526	530	9.599866	TCGATCAATAGTATGAATCAAACAACT	57.400	29.630	0.00	0.00	32.06	3.16
757	792	2.578940	TCAATAAACCACGGAGGGGAAT	59.421	45.455	0.00	0.00	43.89	3.01
822	857	2.817258	TGACAAATCATCCGGTGGTTTC	59.183	45.455	10.99	4.36	39.10	2.78
835	870	4.072088	GTTTCGTGAGGCGTGGCG	62.072	66.667	0.00	0.00	42.13	5.69
892	927	0.179045	CTAGCCCATTTCCACCGGAG	60.179	60.000	9.46	0.00	31.21	4.63
960	1004	0.686112	CTCCTCCCACCACTCCTCTC	60.686	65.000	0.00	0.00	0.00	3.20
968	1012	1.454847	CCACTCCTCTCCCTCCTCG	60.455	68.421	0.00	0.00	0.00	4.63
969	1013	1.454847	CACTCCTCTCCCTCCTCGG	60.455	68.421	0.00	0.00	0.00	4.63
988	1240	1.106285	GCAGATCCAATCCACCAACC	58.894	55.000	0.00	0.00	0.00	3.77
989	1241	1.341383	GCAGATCCAATCCACCAACCT	60.341	52.381	0.00	0.00	0.00	3.50
990	1242	2.648059	CAGATCCAATCCACCAACCTC	58.352	52.381	0.00	0.00	0.00	3.85
991	1243	1.566231	AGATCCAATCCACCAACCTCC	59.434	52.381	0.00	0.00	0.00	4.30
992	1244	1.566231	GATCCAATCCACCAACCTCCT	59.434	52.381	0.00	0.00	0.00	3.69
1272	1524	1.081892	CCTGCAACATCTTCTCCACG	58.918	55.000	0.00	0.00	0.00	4.94
1717	1969	3.532542	GTCACCAAGAGCAAGGTATACC	58.467	50.000	14.54	14.54	36.07	2.73
1788	2041	3.059884	CGAGCTTCTACTTGTTTGAGCA	58.940	45.455	0.00	0.00	0.00	4.26
1844	2125	7.298122	AGTATTTAGATCTTGTTGTTGTTGCG	58.702	34.615	0.00	0.00	0.00	4.85
1877	2158	0.804989	GCTTAATGGTGAAGCAGCGT	59.195	50.000	2.59	0.00	46.97	5.07
1905	2187	7.093684	GGGGTATTAGACTGGATCTGTATCTTC	60.094	44.444	0.00	0.00	38.49	2.87
1907	2189	5.440234	TTAGACTGGATCTGTATCTTCGC	57.560	43.478	0.00	0.00	38.49	4.70
1918	2200	2.568062	TGTATCTTCGCCTGTGGGTTTA	59.432	45.455	0.00	0.00	34.45	2.01

Showing 1 to 25 of 652 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	1.910819	GTATGCATGCGGTGTTTTTCG	59.089	47.619	14.09	0.00	0.00	3.46
37	38	2.258755	GGTATGCATGCGGTGTTTTTC	58.741	47.619	14.09	0.00	0.00	2.29
38	39	1.615883	TGGTATGCATGCGGTGTTTTT	59.384	42.857	14.09	0.00	0.00	1.94
79	82	1.043022	CCCTATTTTGCATCAGGGGC	58.957	55.000	12.46	0.00	43.55	5.80
110	113	5.012664	TGACACAACCATATACAACAGAGGT	59.987	40.000	0.00	0.00	0.00	3.85
163	166	5.874810	GGATGTGCTGAACAAAGTCATACTA	59.125	40.000	0.00	0.00	43.61	1.82
310	313	8.064389	TCCAATTCCCATGATTTTAGAATACCA	58.936	33.333	0.00	0.00	0.00	3.25
500	504	9.599866	AGTTGTTTGATTCATACTATTGATCGA	57.400	29.630	8.42	0.00	0.00	3.59
728	732	2.172717	CCGTGGTTTATTGATCCCCTCT	59.827	50.000	0.00	0.00	0.00	3.69
757	792	8.640291	GGCAAAATTACGAATCGAAACATTTTA	58.360	29.630	10.55	0.00	0.00	1.52
835	870	3.435327	TCAATTGTGTATCAACGGTCAGC	59.565	43.478	5.13	0.00	38.97	4.26
892	927	2.125326	GGGTTTTATGGGGAGCGGC	61.125	63.158	0.00	0.00	0.00	6.53
960	1004	1.414061	ATTGGATCTGCCGAGGAGGG	61.414	60.000	0.00	0.00	41.48	4.30
968	1012	1.106285	GTTGGTGGATTGGATCTGCC	58.894	55.000	0.00	0.00	37.10	4.85
969	1013	1.106285	GGTTGGTGGATTGGATCTGC	58.894	55.000	0.00	0.00	0.00	4.26
988	1240	3.136750	CGCCATGGAGGAGAGGAG	58.863	66.667	18.40	0.00	40.01	3.69
989	1241	3.157252	GCGCCATGGAGGAGAGGA	61.157	66.667	18.40	0.00	40.01	3.71
990	1242	3.160047	AGCGCCATGGAGGAGAGG	61.160	66.667	18.40	0.00	40.01	3.69
991	1243	2.086251	GAGAGCGCCATGGAGGAGAG	62.086	65.000	18.40	0.00	40.01	3.20
992	1244	2.042537	AGAGCGCCATGGAGGAGA	60.043	61.111	18.40	0.00	40.01	3.71
1431	1683	2.503061	CCCTCGTGGATGAGCAGG	59.497	66.667	4.76	0.00	35.39	4.85
1500	1752	3.296709	CTCGGGGTTGTCGGTGGAG	62.297	68.421	0.00	0.00	0.00	3.86
1832	2113	5.524281	TCATCTAAACTACGCAACAACAACA	59.476	36.000	0.00	0.00	0.00	3.33
1833	2114	5.981174	TCATCTAAACTACGCAACAACAAC	58.019	37.500	0.00	0.00	0.00	3.32
1834	2115	5.178623	CCTCATCTAAACTACGCAACAACAA	59.821	40.000	0.00	0.00	0.00	2.83

Showing 1 to 25 of 615 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.