AutoCloner

Multiple sequence alignment - TraesCS3D01G443300

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	TraesCS3D01G443300	chr3D	100.000	2909	0	0	1	2909	552781379	552784287	0.000000e+00	5373.0
1	TraesCS3D01G443300	chr3D	91.489	47	4	0	873	919	552769863	552769909	6.730000e-07	65.8
2	TraesCS3D01G443300	chr3B	91.186	2950	148	48	1	2906	733627629	733630510	0.000000e+00	3904.0
3	TraesCS3D01G443300	chr3B	80.806	943	110	37	1003	1915	733574031	733574932	0.000000e+00	673.0
4	TraesCS3D01G443300	chr3B	97.059	34	1	0	770	803	733573780	733573813	1.130000e-04	58.4
5	TraesCS3D01G443300	chr3A	90.476	2184	108	32	1	2152	689110915	689113030	0.000000e+00	2789.0
6	TraesCS3D01G443300	chr3A	93.805	678	23	7	2238	2897	689113030	689113706	0.000000e+00	1002.0
7	TraesCS3D01G443300	chr1D	82.948	909	105	30	1003	1898	395559590	395558719	0.000000e+00	774.0
8	TraesCS3D01G443300	chr1A	82.580	907	114	22	1003	1899	489601196	489600324	0.000000e+00	760.0
9	TraesCS3D01G443300	chr7D	83.912	777	89	21	1003	1772	573898063	573898810	0.000000e+00	710.0
10	TraesCS3D01G443300	chr7D	85.000	140	13	7	1747	1886	573905459	573905590	5.060000e-28	135.0
11	TraesCS3D01G443300	chr7D	100.000	30	0	0	1853	1882	573898890	573898919	4.050000e-04	56.5
12	TraesCS3D01G443300	chr1B	83.567	785	95	20	1003	1772	526348896	526348131	0.000000e+00	704.0
13	TraesCS3D01G443300	chr1B	95.745	47	2	0	1853	1899	526348053	526348007	3.110000e-10	76.8
14	TraesCS3D01G443300	chr7B	83.548	778	85	21	1003	1772	632684677	632685419	0.000000e+00	688.0
15	TraesCS3D01G443300	chr7B	85.000	140	13	8	1747	1886	632688440	632688571	5.060000e-28	135.0
16	TraesCS3D01G443300	chr2B	76.721	799	126	31	1003	1759	759274379	759273599	9.770000e-105	390.0
17	TraesCS3D01G443300	chr5D	85.088	228	16	9	2326	2535	67965704	67965477	1.760000e-52	217.0

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	TraesCS3D01G443300	chr3D	552781379	552784287	2908	False	5373.00	5373	100.0000	1	2909	1	chr3D.!!$F2	2908
1	TraesCS3D01G443300	chr3B	733627629	733630510	2881	False	3904.00	3904	91.1860	1	2906	1	chr3B.!!$F1	2905
2	TraesCS3D01G443300	chr3B	733573780	733574932	1152	False	365.70	673	88.9325	770	1915	2	chr3B.!!$F2	1145
3	TraesCS3D01G443300	chr3A	689110915	689113706	2791	False	1895.50	2789	92.1405	1	2897	2	chr3A.!!$F1	2896
4	TraesCS3D01G443300	chr1D	395558719	395559590	871	True	774.00	774	82.9480	1003	1898	1	chr1D.!!$R1	895
5	TraesCS3D01G443300	chr1A	489600324	489601196	872	True	760.00	760	82.5800	1003	1899	1	chr1A.!!$R1	896
6	TraesCS3D01G443300	chr7D	573898063	573898919	856	False	383.25	710	91.9560	1003	1882	2	chr7D.!!$F2	879
7	TraesCS3D01G443300	chr1B	526348007	526348896	889	True	390.40	704	89.6560	1003	1899	2	chr1B.!!$R1	896
8	TraesCS3D01G443300	chr7B	632684677	632688571	3894	False	411.50	688	84.2740	1003	1886	2	chr7B.!!$F1	883
9	TraesCS3D01G443300	chr2B	759273599	759274379	780	True	390.00	390	76.7210	1003	1759	1	chr2B.!!$R1	756

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
257	262	0.461961	CCCTCCCAACAACGCAAAAA	59.538	50.0	0.00	0.0	0.0	1.94	F
701	725	0.820871	CCCGGAGAGAGAGGTTTCAG	59.179	60.0	0.73	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1290	1380	0.527113	CGAAGGCAATGTTGATGGCA	59.473	50.000	0.0	0.0	45.08	4.92	R
1954	2145	1.224592	CCTCAAGGAATCCCACCCG	59.775	63.158	0.0	0.0	37.39	5.28	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
56	57	2.232941	ACCATGTTATATAGCCCGGACG	59.767	50.000	0.73	0.00	0.00	4.79
85	86	3.391049	GAACACAACTCCTACACACTCC	58.609	50.000	0.00	0.00	0.00	3.85
93	94	2.690497	CTCCTACACACTCCATGACGAT	59.310	50.000	0.00	0.00	0.00	3.73
183	184	4.624364	CTGCCGGACAGTGCCACA	62.624	66.667	5.05	0.00	41.86	4.17
236	240	6.706295	ACTCAAAGAACTAGATCAAGGGAAG	58.294	40.000	0.00	0.00	0.00	3.46
237	241	6.271159	ACTCAAAGAACTAGATCAAGGGAAGT	59.729	38.462	0.00	0.00	0.00	3.01
238	242	6.702329	TCAAAGAACTAGATCAAGGGAAGTC	58.298	40.000	0.00	0.00	0.00	3.01
257	262	0.461961	CCCTCCCAACAACGCAAAAA	59.538	50.000	0.00	0.00	0.00	1.94
275	280	1.076332	AACACCATTAGCGCGAGAAC	58.924	50.000	12.10	0.00	0.00	3.01
279	284	1.209275	CCATTAGCGCGAGAACGAGG	61.209	60.000	12.10	2.23	42.66	4.63
354	359	7.284919	ACGACAAAGGATCAAAACCTTAATT	57.715	32.000	0.00	0.00	45.55	1.40
376	381	2.525105	AAAATCCGGCTACCACCATT	57.475	45.000	0.00	0.00	0.00	3.16
411	416	3.282885	GAGGTCCATGTCCCTTTTCATC	58.717	50.000	2.22	0.00	0.00	2.92
430	435	2.125147	CGGAGCTGGCGAATGGAA	60.125	61.111	0.00	0.00	0.00	3.53
440	445	1.540435	GCGAATGGAAAAAGGGGGCA	61.540	55.000	0.00	0.00	0.00	5.36
469	475	1.076727	TGAGCTCGTTGGGAGGAGA	59.923	57.895	9.64	0.00	43.36	3.71
494	500	1.947456	TCAGCGATGTCGTGCTACTAT	59.053	47.619	0.00	0.00	40.03	2.12
498	504	2.224549	GCGATGTCGTGCTACTATCTCT	59.775	50.000	4.20	0.00	42.22	3.10
644	665	9.807649	ATGATATGCCTTAACATTTTGACTTTC	57.192	29.630	0.00	0.00	0.00	2.62
669	690	6.204108	CCTAGTCAAATACGTGGTCAAACTTT	59.796	38.462	0.00	0.00	0.00	2.66
673	694	6.915843	GTCAAATACGTGGTCAAACTTTCATT	59.084	34.615	0.00	0.00	0.00	2.57
674	695	7.434013	GTCAAATACGTGGTCAAACTTTCATTT	59.566	33.333	0.00	0.00	0.00	2.32
701	725	0.820871	CCCGGAGAGAGAGGTTTCAG	59.179	60.000	0.73	0.00	0.00	3.02
710	734	5.451354	AGAGAGAGGTTTCAGGGTACTATC	58.549	45.833	0.00	0.00	0.00	2.08
750	774	2.905415	ATTCATCTGCCACCTTTCCA	57.095	45.000	0.00	0.00	0.00	3.53
913	977	2.764547	CCCCCTCCGTCCTCTTCC	60.765	72.222	0.00	0.00	0.00	3.46
926	991	2.360852	CTTCCCACCTGCCTGCAG	60.361	66.667	12.17	12.17	43.26	4.41
936	1001	2.813042	GCCTGCAGTCTCTGTCGC	60.813	66.667	13.81	1.97	33.43	5.19
937	1002	2.969016	CCTGCAGTCTCTGTCGCT	59.031	61.111	13.81	0.00	33.43	4.93
1290	1380	1.144936	GGAGAGCAACGCCATAGCT	59.855	57.895	0.00	0.00	42.17	3.32
1845	2032	5.723295	TCAATCTGACAGTTCGATTCATCA	58.277	37.500	1.59	0.00	0.00	3.07
1846	2033	6.343703	TCAATCTGACAGTTCGATTCATCAT	58.656	36.000	1.59	0.00	0.00	2.45
1847	2034	7.491682	TCAATCTGACAGTTCGATTCATCATA	58.508	34.615	1.59	0.00	0.00	2.15
1848	2035	8.146412	TCAATCTGACAGTTCGATTCATCATAT	58.854	33.333	1.59	0.00	0.00	1.78
1948	2135	1.739338	ATCGATGGAGGCTGTCGACC	61.739	60.000	14.12	0.00	45.72	4.79
1949	2136	2.105128	GATGGAGGCTGTCGACCG	59.895	66.667	14.12	8.02	0.00	4.79
1966	2157	2.124278	GAAGGCGGGTGGGATTCC	60.124	66.667	0.00	0.00	0.00	3.01
1967	2158	2.614013	AAGGCGGGTGGGATTCCT	60.614	61.111	2.01	0.00	0.00	3.36
1968	2159	2.211468	GAAGGCGGGTGGGATTCCTT	62.211	60.000	2.01	0.00	39.63	3.36
1969	2160	2.440247	GGCGGGTGGGATTCCTTG	60.440	66.667	2.01	0.00	0.00	3.61
1970	2161	2.674754	GCGGGTGGGATTCCTTGA	59.325	61.111	2.01	0.00	0.00	3.02
1971	2162	1.452108	GCGGGTGGGATTCCTTGAG	60.452	63.158	2.01	0.00	0.00	3.02
1972	2163	1.224592	CGGGTGGGATTCCTTGAGG	59.775	63.158	2.01	0.00	0.00	3.86
2023	2214	5.205056	ACTCCTCCTAGCATATATACCAGC	58.795	45.833	0.00	0.00	0.00	4.85
2027	2218	3.952323	TCCTAGCATATATACCAGCGGTC	59.048	47.826	3.45	0.00	37.09	4.79
2145	2345	5.581479	GCTACTATGATCTGGATGCAATCTG	59.419	44.000	0.00	0.00	44.71	2.90
2160	2360	4.874396	TGCAATCTGTCTTAGCTTCATCAG	59.126	41.667	0.00	0.00	0.00	2.90
2167	2367	5.023452	TGTCTTAGCTTCATCAGTTAGGGA	58.977	41.667	0.00	0.00	0.00	4.20
2168	2368	5.663106	TGTCTTAGCTTCATCAGTTAGGGAT	59.337	40.000	0.00	0.00	0.00	3.85
2169	2369	6.839134	TGTCTTAGCTTCATCAGTTAGGGATA	59.161	38.462	0.00	0.00	0.00	2.59
2170	2370	7.344612	TGTCTTAGCTTCATCAGTTAGGGATAA	59.655	37.037	0.00	0.00	0.00	1.75
2171	2371	8.371699	GTCTTAGCTTCATCAGTTAGGGATAAT	58.628	37.037	0.00	0.00	0.00	1.28
2172	2372	9.601810	TCTTAGCTTCATCAGTTAGGGATAATA	57.398	33.333	0.00	0.00	0.00	0.98
2365	2655	5.463061	TCATGTTATATGTGATGTCACTGCG	59.537	40.000	13.71	0.00	46.55	5.18
2394	2684	5.888105	TGGTAATCTTCGTAGCTACTTGTC	58.112	41.667	21.20	6.75	0.00	3.18
2553	4228	6.153756	TGATTTCAGTTGCATTGTTGATCAG	58.846	36.000	0.00	0.00	0.00	2.90
2562	4237	3.464907	CATTGTTGATCAGAGCCGATCT	58.535	45.455	0.00	0.00	42.01	2.75
2613	4288	3.431486	GGCTCTCTAGTTCATCCAACCTG	60.431	52.174	0.00	0.00	35.28	4.00
2674	4349	9.914131	CTGCTGCTACTATATCTGTGTTTAATA	57.086	33.333	0.00	0.00	0.00	0.98
2906	4995	2.156098	GTGCATCCCCAGTTCGTTAAA	58.844	47.619	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	57	3.503800	AGGAGTTGTGTTCCTTAACCC	57.496	47.619	0.00	0.00	42.40	4.11
85	86	2.535984	GGCTAACTTCGACATCGTCATG	59.464	50.000	0.54	0.00	40.80	3.07
93	94	2.875933	CAAAGGTTGGCTAACTTCGACA	59.124	45.455	13.03	0.00	36.99	4.35
209	213	6.441924	TCCCTTGATCTAGTTCTTTGAGTCAT	59.558	38.462	3.47	0.00	0.00	3.06
210	214	5.780282	TCCCTTGATCTAGTTCTTTGAGTCA	59.220	40.000	3.47	0.00	0.00	3.41
236	240	1.104577	TTTGCGTTGTTGGGAGGGAC	61.105	55.000	0.00	0.00	0.00	4.46
237	241	0.395862	TTTTGCGTTGTTGGGAGGGA	60.396	50.000	0.00	0.00	0.00	4.20
238	242	0.461961	TTTTTGCGTTGTTGGGAGGG	59.538	50.000	0.00	0.00	0.00	4.30
257	262	1.076533	CGTTCTCGCGCTAATGGTGT	61.077	55.000	5.56	0.00	0.00	4.16
275	280	1.743252	GCAAGTCTTCCCTGCCTCG	60.743	63.158	0.00	0.00	0.00	4.63
279	284	0.034670	ATGGAGCAAGTCTTCCCTGC	60.035	55.000	0.00	0.00	0.00	4.85
361	366	1.195442	TGTCAATGGTGGTAGCCGGA	61.195	55.000	5.05	0.00	0.00	5.14
364	369	0.036765	TCGTGTCAATGGTGGTAGCC	60.037	55.000	0.00	0.00	0.00	3.93
376	381	2.158885	TGGACCTCATTGTTTCGTGTCA	60.159	45.455	0.00	0.00	0.00	3.58
390	395	2.879103	TGAAAAGGGACATGGACCTC	57.121	50.000	10.45	0.95	35.64	3.85
393	398	1.401905	GCGATGAAAAGGGACATGGAC	59.598	52.381	0.00	0.00	0.00	4.02
418	423	0.532115	CCCCTTTTTCCATTCGCCAG	59.468	55.000	0.00	0.00	0.00	4.85
430	435	3.276081	CTCCCCCTGCCCCCTTTT	61.276	66.667	0.00	0.00	0.00	2.27
469	475	1.611006	AGCACGACATCGCTGATCTAT	59.389	47.619	0.14	0.00	44.43	1.98
494	500	2.356535	GGACTAGTAACCCGGACAGAGA	60.357	54.545	0.73	0.00	0.00	3.10
498	504	1.679944	CGAGGACTAGTAACCCGGACA	60.680	57.143	0.73	0.00	0.00	4.02
640	661	5.475719	TGACCACGTATTTGACTAGGAAAG	58.524	41.667	0.00	0.00	0.00	2.62
644	665	5.235516	AGTTTGACCACGTATTTGACTAGG	58.764	41.667	0.00	0.00	0.00	3.02
657	678	7.398746	GCTTTTACAAATGAAAGTTTGACCAC	58.601	34.615	6.39	0.00	40.64	4.16
669	690	3.008594	TCTCTCCGGGCTTTTACAAATGA	59.991	43.478	0.00	0.00	0.00	2.57
673	694	2.233922	CTCTCTCTCCGGGCTTTTACAA	59.766	50.000	0.00	0.00	0.00	2.41
674	695	1.825474	CTCTCTCTCCGGGCTTTTACA	59.175	52.381	0.00	0.00	0.00	2.41
701	725	3.335579	GGAAATGCCATCGATAGTACCC	58.664	50.000	0.00	0.00	36.34	3.69
750	774	6.534793	ACAAGACGTGCAATTTCAGAAATTTT	59.465	30.769	17.12	6.11	38.97	1.82
814	865	2.280797	TCAGCCTGCACGTTGACC	60.281	61.111	0.00	0.00	0.00	4.02
936	1001	1.351153	GTTTTCCGAAGAGGCGAGAG	58.649	55.000	0.00	0.00	40.77	3.20
937	1002	0.037605	GGTTTTCCGAAGAGGCGAGA	60.038	55.000	0.00	0.00	40.77	4.04
1290	1380	0.527113	CGAAGGCAATGTTGATGGCA	59.473	50.000	0.00	0.00	45.08	4.92
1845	2032	9.872721	CTAATCTGCAGTGAGATGAACATATAT	57.127	33.333	14.67	0.00	32.77	0.86
1846	2033	7.816513	GCTAATCTGCAGTGAGATGAACATATA	59.183	37.037	14.67	0.00	32.77	0.86
1847	2034	6.649973	GCTAATCTGCAGTGAGATGAACATAT	59.350	38.462	14.67	0.00	32.77	1.78
1848	2035	5.987953	GCTAATCTGCAGTGAGATGAACATA	59.012	40.000	14.67	0.00	32.77	2.29
1900	2087	3.274288	AGTTGTAAGCTGGCTAATCTGC	58.726	45.455	0.00	0.00	0.00	4.26
1948	2135	2.513897	GAATCCCACCCGCCTTCG	60.514	66.667	0.00	0.00	0.00	3.79
1949	2136	2.124278	GGAATCCCACCCGCCTTC	60.124	66.667	0.00	0.00	0.00	3.46
1954	2145	1.224592	CCTCAAGGAATCCCACCCG	59.775	63.158	0.00	0.00	37.39	5.28
1964	2155	2.165167	CAGCAATTCAAGCCTCAAGGA	58.835	47.619	0.00	0.00	37.39	3.36
1966	2157	3.487042	CGATCAGCAATTCAAGCCTCAAG	60.487	47.826	0.00	0.00	0.00	3.02
1967	2158	2.421073	CGATCAGCAATTCAAGCCTCAA	59.579	45.455	0.00	0.00	0.00	3.02
1968	2159	2.011947	CGATCAGCAATTCAAGCCTCA	58.988	47.619	0.00	0.00	0.00	3.86
1969	2160	2.283298	TCGATCAGCAATTCAAGCCTC	58.717	47.619	0.00	0.00	0.00	4.70
1970	2161	2.408271	TCGATCAGCAATTCAAGCCT	57.592	45.000	0.00	0.00	0.00	4.58
1971	2162	3.705043	ATTCGATCAGCAATTCAAGCC	57.295	42.857	0.00	0.00	0.00	4.35
1972	2163	5.172771	GCTTAATTCGATCAGCAATTCAAGC	59.827	40.000	0.00	6.79	32.17	4.01
2023	2214	4.454161	AGAGATCATAGATGAAGTCGACCG	59.546	45.833	13.01	0.00	40.69	4.79
2027	2218	9.599866	ACTATCTAGAGATCATAGATGAAGTCG	57.400	37.037	21.82	10.91	39.68	4.18
2145	2345	5.599999	TCCCTAACTGATGAAGCTAAGAC	57.400	43.478	0.00	0.00	0.00	3.01
2363	2653	4.550255	GCTACGAAGATTACCAAACATCGC	60.550	45.833	0.00	0.00	32.46	4.58
2365	2655	6.979238	AGTAGCTACGAAGATTACCAAACATC	59.021	38.462	17.99	0.00	0.00	3.06
2394	2684	2.017113	GCTCCCAGTCCCAAATAACCG	61.017	57.143	0.00	0.00	0.00	4.44
2553	4228	5.797934	CGATTGATAAGAACTAGATCGGCTC	59.202	44.000	0.00	0.00	33.35	4.70
2613	4288	9.774742	GACCAAACTTAACTGATATCAATCAAC	57.225	33.333	6.90	0.00	41.57	3.18
2674	4349	4.227197	AGAATATCCACAGTTCTCCGGAT	58.773	43.478	3.57	0.00	41.20	4.18
2716	4391	2.289569	TGCATGTCAGCATCACACTACA	60.290	45.455	0.00	0.00	40.11	2.74
2826	4506	4.328983	GCAAATGCCATCACAGAAAATGAG	59.671	41.667	0.00	0.00	34.31	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.