AutoCloner

Multiple sequence alignment - TraesCS4A01G124400

Loading Multiple Alignment...

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	TraesCS4A01G124400	chr4A	100.000	4055	0	0	1	4055	157556526	157560580	0.000000e+00	7489.0
1	TraesCS4A01G124400	chr4D	96.832	3030	64	10	1027	4052	317202935	317199934	0.000000e+00	5035.0
2	TraesCS4A01G124400	chr4B	96.449	3041	78	8	1018	4054	394389026	394386012	0.000000e+00	4990.0
3	TraesCS4A01G124400	chr4B	89.798	1039	60	22	1	1023	665460441	665461449	0.000000e+00	1290.0
4	TraesCS4A01G124400	chr7D	93.353	1038	50	7	1	1023	580563501	580564534	0.000000e+00	1517.0
5	TraesCS4A01G124400	chr1B	90.655	1038	77	14	1	1023	134581187	134580155	0.000000e+00	1362.0
6	TraesCS4A01G124400	chr1B	88.436	908	99	3	41	945	60432072	60432976	0.000000e+00	1090.0
7	TraesCS4A01G124400	chr7B	85.687	1041	123	18	1	1023	14167412	14168444	0.000000e+00	1074.0
8	TraesCS4A01G124400	chr5B	84.551	602	52	19	451	1037	441690130	441690705	3.540000e-155	558.0
9	TraesCS4A01G124400	chr5B	88.820	161	18	0	294	454	441681257	441681417	8.890000e-47	198.0
10	TraesCS4A01G124400	chr2B	74.013	1039	235	25	8	1023	727677175	727678201	1.370000e-104	390.0
11	TraesCS4A01G124400	chr3A	74.000	1000	231	21	44	1023	725562277	725561287	2.960000e-101	379.0
12	TraesCS4A01G124400	chr3A	73.700	1000	234	21	44	1023	725604606	725603616	2.980000e-96	363.0
13	TraesCS4A01G124400	chr3A	80.899	89	13	4	838	925	608391045	608390960	2.620000e-07	67.6
14	TraesCS4A01G124400	chr3D	83.133	83	13	1	833	914	583307392	583307474	1.560000e-09	75.0
15	TraesCS4A01G124400	chr1D	96.970	33	0	1	883	914	56629503	56629471	2.000000e-03	54.7

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	TraesCS4A01G124400	chr4A	157556526	157560580	4054	False	7489	7489	100.000	1	4055	1	chr4A.!!$F1	4054
1	TraesCS4A01G124400	chr4D	317199934	317202935	3001	True	5035	5035	96.832	1027	4052	1	chr4D.!!$R1	3025
2	TraesCS4A01G124400	chr4B	394386012	394389026	3014	True	4990	4990	96.449	1018	4054	1	chr4B.!!$R1	3036
3	TraesCS4A01G124400	chr4B	665460441	665461449	1008	False	1290	1290	89.798	1	1023	1	chr4B.!!$F1	1022
4	TraesCS4A01G124400	chr7D	580563501	580564534	1033	False	1517	1517	93.353	1	1023	1	chr7D.!!$F1	1022
5	TraesCS4A01G124400	chr1B	134580155	134581187	1032	True	1362	1362	90.655	1	1023	1	chr1B.!!$R1	1022
6	TraesCS4A01G124400	chr1B	60432072	60432976	904	False	1090	1090	88.436	41	945	1	chr1B.!!$F1	904
7	TraesCS4A01G124400	chr7B	14167412	14168444	1032	False	1074	1074	85.687	1	1023	1	chr7B.!!$F1	1022
8	TraesCS4A01G124400	chr5B	441690130	441690705	575	False	558	558	84.551	451	1037	1	chr5B.!!$F2	586
9	TraesCS4A01G124400	chr2B	727677175	727678201	1026	False	390	390	74.013	8	1023	1	chr2B.!!$F1	1015
10	TraesCS4A01G124400	chr3A	725561287	725562277	990	True	379	379	74.000	44	1023	1	chr3A.!!$R2	979
11	TraesCS4A01G124400	chr3A	725603616	725604606	990	True	363	363	73.700	44	1023	1	chr3A.!!$R3	979

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
651	656	0.179009	TCATTCCCCATGCAGCTAGC	60.179	55.0	6.62	6.62	45.96	3.42	F
1405	1422	0.178903	ACTCTACACCTCCCTGCCAA	60.179	55.0	0.00	0.00	0.00	4.52	F
2311	2328	0.179073	CAGGCCGGATGAGGTTACTG	60.179	60.0	5.05	0.00	0.00	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2520	2537	0.251564	TCATCGCCAACCCCACAATT	60.252	50.000	0.00	2.32	R
2535	2552	1.234821	TTGTCACAAGGCCGTTCATC	58.765	50.000	0.00	2.92	R
3243	3261	1.402968	GTCGCTGATGCCATGTGAATT	59.597	47.619	35.36	2.17	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
175	176	7.093552	GCCATAGAGAAGCTGAGGATATTAAGA	60.094	40.741	0.00	0.00	0.00	2.10
325	326	3.016736	CCGAGACCACTGCCATTAAAAT	58.983	45.455	0.00	0.00	0.00	1.82
327	328	3.242413	CGAGACCACTGCCATTAAAATCG	60.242	47.826	0.00	0.00	0.00	3.34
363	364	2.500229	CAAGTTTTAGCGGTGGGAAGA	58.500	47.619	0.00	0.00	0.00	2.87
578	583	3.329542	ATGAAGGTGTGGGCGCGAT	62.330	57.895	12.10	0.00	0.00	4.58
651	656	0.179009	TCATTCCCCATGCAGCTAGC	60.179	55.000	6.62	6.62	45.96	3.42
727	732	0.538746	GGGCTTTCCTCGGGTTGAAA	60.539	55.000	0.00	0.00	0.00	2.69
747	752	3.268023	ACAGAATCGGATTCCTCAACC	57.732	47.619	23.45	1.72	40.13	3.77
776	781	3.536956	ATCATGTACGGGTCAAACGAT	57.463	42.857	0.00	0.00	34.93	3.73
803	809	1.271656	GGATGAAGCAGCAGCAACTTT	59.728	47.619	3.17	0.00	45.49	2.66
824	830	1.202417	CGCCGAGTGTGTGGATCTATT	60.202	52.381	0.00	0.00	0.00	1.73
872	878	4.732285	AACATTGTTCACGCTCTTGTAG	57.268	40.909	0.00	0.00	0.00	2.74
956	973	2.509336	CGAGCCTCGTTTCCGCAT	60.509	61.111	5.82	0.00	34.72	4.73
962	979	0.871722	CCTCGTTTCCGCATTTGTGA	59.128	50.000	0.00	0.00	0.00	3.58
1254	1271	2.726351	CCTCCTCTTCACCTCCGCC	61.726	68.421	0.00	0.00	0.00	6.13
1314	1331	3.432588	CTCCGACTCGTCCGCTGT	61.433	66.667	0.00	0.00	0.00	4.40
1405	1422	0.178903	ACTCTACACCTCCCTGCCAA	60.179	55.000	0.00	0.00	0.00	4.52
1791	1808	1.375523	GGTGTTTGACGAGGCCGAT	60.376	57.895	0.00	0.00	39.50	4.18
1875	1892	1.210155	GGCGTTGCACATGTTCTCC	59.790	57.895	0.00	0.00	0.00	3.71
2071	2088	0.892755	CCTGGATGTTGTTGCAGCAT	59.107	50.000	3.36	0.00	37.97	3.79
2311	2328	0.179073	CAGGCCGGATGAGGTTACTG	60.179	60.000	5.05	0.00	0.00	2.74
2475	2492	1.927487	TGGAAGCTGCAATGGATGTT	58.073	45.000	1.02	0.00	0.00	2.71
2520	2537	1.825090	CACCTTGCTGGAATGCTGTA	58.175	50.000	3.40	0.00	39.71	2.74
2535	2552	0.525761	CTGTAATTGTGGGGTTGGCG	59.474	55.000	0.00	0.00	0.00	5.69
2553	2570	0.948623	CGATGAACGGCCTTGTGACA	60.949	55.000	0.00	0.00	38.46	3.58
2691	2708	3.611057	GCCACTTCTTCAAGTTGATGCAG	60.611	47.826	14.15	14.15	41.24	4.41
3010	3027	2.079158	CCATGAAGCAACGACATGTCT	58.921	47.619	22.95	8.01	39.47	3.41
3080	3097	0.390866	AGCAGTTGATCGCACCTCAG	60.391	55.000	0.00	0.00	0.00	3.35
3390	3411	2.040544	CACGCCATGGTCAGGGTTC	61.041	63.158	14.67	0.00	34.16	3.62
3842	3864	6.547402	AGAATATTTGATTAGGAAGGGAGGC	58.453	40.000	0.00	0.00	0.00	4.70
3926	3948	9.542462	TCACATAGCTATGGTTACTAATTTCAC	57.458	33.333	31.87	0.00	38.00	3.18
3927	3949	9.325198	CACATAGCTATGGTTACTAATTTCACA	57.675	33.333	31.87	0.00	38.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
175	176	7.760794	TGCATGAAAGCAATCGAAAATTAGATT	59.239	29.630	0.00	0.00	42.46	2.40
325	326	0.684535	TGCTTGATGTCCAGGTTCGA	59.315	50.000	0.00	0.00	0.00	3.71
327	328	2.508526	ACTTGCTTGATGTCCAGGTTC	58.491	47.619	0.00	0.00	0.00	3.62
363	364	3.769844	GACGGATCCACCATAGATACCAT	59.230	47.826	13.41	0.00	38.90	3.55
414	415	1.064685	AGAGGCCATTTAAAGACCGGG	60.065	52.381	6.32	0.00	0.00	5.73
543	548	5.358442	ACCTTCATCTATATAGTAGGCTGCG	59.642	44.000	9.58	0.00	0.00	5.18
578	583	2.175284	TCATCCCTAATCATTGCAGCCA	59.825	45.455	0.00	0.00	0.00	4.75
586	591	3.330198	TGCCCTTCTCATCCCTAATCAT	58.670	45.455	0.00	0.00	0.00	2.45
651	656	2.811317	GCCTCGGTGAAGACTGCG	60.811	66.667	0.00	0.00	0.00	5.18
657	662	2.747855	GCCCTTGCCTCGGTGAAG	60.748	66.667	0.00	0.00	0.00	3.02
659	664	2.905996	ATTGCCCTTGCCTCGGTGA	61.906	57.895	0.00	0.00	36.33	4.02
727	732	2.418746	CGGTTGAGGAATCCGATTCTGT	60.419	50.000	18.46	8.28	46.05	3.41
747	752	3.194861	ACCCGTACATGATTCAATCACG	58.805	45.455	0.98	0.00	43.01	4.35
776	781	0.918258	TGCTGCTTCATCCCACCATA	59.082	50.000	0.00	0.00	0.00	2.74
803	809	0.678684	TAGATCCACACACTCGGCGA	60.679	55.000	10.14	10.14	0.00	5.54
824	830	1.345089	TGACCTTCCCGATCAACGAAA	59.655	47.619	0.00	0.00	45.77	3.46
923	929	1.068055	GCTCGTCCGTCCAACTAGAAA	60.068	52.381	0.00	0.00	0.00	2.52
1055	1072	0.886490	CCAGCTGCAGGTTCGAACTT	60.886	55.000	26.32	17.77	0.00	2.66
1056	1073	1.302033	CCAGCTGCAGGTTCGAACT	60.302	57.895	26.32	10.89	0.00	3.01
1080	1097	3.302344	GCGGCAAAGGGGAAGCAA	61.302	61.111	0.00	0.00	0.00	3.91
1314	1331	3.068881	CAGGAGAAGGCGTTGGGA	58.931	61.111	0.00	0.00	0.00	4.37
1375	1392	1.477295	GGTGTAGAGTGGTAGGCAGAC	59.523	57.143	0.00	0.00	0.00	3.51
1405	1422	2.044551	GTAGGAGTCGGGGGACGT	60.045	66.667	0.00	0.00	44.69	4.34
1417	1434	1.307517	GGATGGGGTGGGTGTAGGA	60.308	63.158	0.00	0.00	0.00	2.94
1791	1808	2.752354	CCACGTGAAAATATCCCTGCAA	59.248	45.455	19.30	0.00	0.00	4.08
1875	1892	0.527169	ACATCTCTCGACGCATGCAG	60.527	55.000	19.57	12.98	0.00	4.41
2071	2088	0.817634	CCGCTGTCAAACAACCTCCA	60.818	55.000	0.00	0.00	0.00	3.86
2185	2202	4.580167	CCAAGAAACATTGTCCTTGTCAGA	59.420	41.667	20.74	0.00	35.50	3.27
2311	2328	6.907212	GTGCATGCAGATATAACACTAACAAC	59.093	38.462	23.41	0.00	0.00	3.32
2475	2492	7.872483	GCTCCTTTTTCTTCCATTATGTTGAAA	59.128	33.333	0.00	0.00	0.00	2.69
2520	2537	0.251564	TCATCGCCAACCCCACAATT	60.252	50.000	0.00	0.00	0.00	2.32
2535	2552	1.234821	TTGTCACAAGGCCGTTCATC	58.765	50.000	0.00	0.00	0.00	2.92
3010	3027	7.383687	ACGACACTATATCCTGAAACTTTTGA	58.616	34.615	0.00	0.00	0.00	2.69
3080	3097	9.620259	AACTTGGACCTATCTAAGATTTTCATC	57.380	33.333	7.33	0.00	44.19	2.92
3243	3261	1.402968	GTCGCTGATGCCATGTGAATT	59.597	47.619	0.00	0.00	35.36	2.17
3293	3311	2.557920	AAGGAAGTTCTGCCTGACTG	57.442	50.000	0.00	0.00	34.00	3.51
3419	3440	2.523245	TCATTTGCTTGCACCATGGTA	58.477	42.857	19.28	0.00	0.00	3.25
3506	3527	4.823442	TCTTTTTCCATCATCATGATCCCG	59.177	41.667	4.86	0.00	34.28	5.14
3670	3691	7.120432	GCTTGGAAAGGAATTAGCCTAGATATG	59.880	40.741	0.00	0.00	46.35	1.78
3737	3758	8.728088	ATCACATTTTCGTAACAATTCTGAAC	57.272	30.769	0.00	0.00	0.00	3.18
3794	3815	6.783708	TGGTACCAAATGGAATTGTATTCC	57.216	37.500	13.60	10.78	36.10	3.01
3842	3864	8.137437	CCTGCATACCCAATAACTTTTATTCTG	58.863	37.037	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.