AutoCloner

Multiple sequence alignment - TraesCS6B01G346700

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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	TraesCS6B01G346700	chr6B	100.000	1940	0	0	834	2773	610809719	610807780	0.000000e+00	3583
1	TraesCS6B01G346700	chr6B	100.000	606	0	0	1	606	610810552	610809947	0.000000e+00	1120
2	TraesCS6B01G346700	chr6B	80.714	140	23	4	1967	2103	221401280	221401142	3.780000e-19	106
3	TraesCS6B01G346700	chr6A	92.888	1139	58	13	853	1971	552758915	552757780	0.000000e+00	1633
4	TraesCS6B01G346700	chr6A	91.456	632	23	8	1	606	552759567	552758941	0.000000e+00	839
5	TraesCS6B01G346700	chr6D	92.357	1086	54	17	853	1918	406335617	406334541	0.000000e+00	1519
6	TraesCS6B01G346700	chr6D	93.534	232	13	2	4	233	406336507	406336276	7.350000e-91	344
7	TraesCS6B01G346700	chr6D	87.444	223	10	6	402	606	406335865	406335643	9.920000e-60	241
8	TraesCS6B01G346700	chrUn	97.666	814	15	2	1964	2773	259653290	259654103	0.000000e+00	1395
9	TraesCS6B01G346700	chrUn	97.810	411	6	1	2232	2639	477614740	477615150	0.000000e+00	706
10	TraesCS6B01G346700	chrUn	81.548	168	27	4	1966	2131	62698163	62698328	4.820000e-28	135
11	TraesCS6B01G346700	chr1A	97.324	822	15	5	1957	2773	184933706	184934525	0.000000e+00	1389
12	TraesCS6B01G346700	chr7B	96.178	811	26	3	1967	2773	574513598	574512789	0.000000e+00	1321
13	TraesCS6B01G346700	chr7B	82.331	266	41	3	1519	1778	94264397	94264662	2.780000e-55	226
14	TraesCS6B01G346700	chr7B	79.392	296	55	3	1485	1774	93572083	93572378	1.300000e-48	204
15	TraesCS6B01G346700	chr7B	80.534	262	43	6	1519	1773	93865177	93865437	7.840000e-46	195
16	TraesCS6B01G346700	chr7B	78.808	302	55	8	1485	1777	94117802	94117501	7.840000e-46	195
17	TraesCS6B01G346700	chr7B	76.582	316	52	11	53	366	94268137	94267842	1.330000e-33	154
18	TraesCS6B01G346700	chr7A	89.634	820	61	8	1964	2773	32587280	32588085	0.000000e+00	1022
19	TraesCS6B01G346700	chr7A	79.195	298	53	4	1485	1773	210252822	210253119	6.060000e-47	198
20	TraesCS6B01G346700	chr7A	81.435	237	36	5	1549	1778	131776444	131776679	1.310000e-43	187
21	TraesCS6B01G346700	chr7A	78.405	301	53	6	1485	1773	130783022	130783322	4.720000e-43	185
22	TraesCS6B01G346700	chr7A	79.771	262	47	3	1519	1774	203697483	203697744	4.720000e-43	185
23	TraesCS6B01G346700	chr7A	77.409	301	56	5	1485	1773	131108855	131108555	4.750000e-38	169
24	TraesCS6B01G346700	chr7A	76.730	318	54	10	53	366	131812262	131811961	2.860000e-35	159
25	TraesCS6B01G346700	chr7D	79.412	306	55	6	1480	1778	133194221	133194525	2.800000e-50	209
26	TraesCS6B01G346700	chr7D	78.983	295	56	6	1485	1773	132741708	132742002	2.180000e-46	196
27	TraesCS6B01G346700	chr7D	78.523	298	55	7	1485	1773	132748610	132748907	1.310000e-43	187
28	TraesCS6B01G346700	chr7D	78.305	295	58	5	1485	1773	132197938	132198232	4.720000e-43	185
29	TraesCS6B01G346700	chr7D	77.370	327	57	11	1464	1777	131822852	131822530	7.890000e-41	178
30	TraesCS6B01G346700	chr7D	76.398	322	48	15	53	366	133199951	133199650	6.190000e-32	148
31	TraesCS6B01G346700	chr5A	91.729	133	9	2	1967	2098	36866099	36865968	1.700000e-42	183

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	TraesCS6B01G346700	chr6B	610807780	610810552	2772	True	2351.500000	3583	100.000000	1	2773	2	chr6B.!!$R2	2772
1	TraesCS6B01G346700	chr6A	552757780	552759567	1787	True	1236.000000	1633	92.172000	1	1971	2	chr6A.!!$R1	1970
2	TraesCS6B01G346700	chr6D	406334541	406336507	1966	True	701.333333	1519	91.111667	4	1918	3	chr6D.!!$R1	1914
3	TraesCS6B01G346700	chrUn	259653290	259654103	813	False	1395.000000	1395	97.666000	1964	2773	1	chrUn.!!$F2	809
4	TraesCS6B01G346700	chr1A	184933706	184934525	819	False	1389.000000	1389	97.324000	1957	2773	1	chr1A.!!$F1	816
5	TraesCS6B01G346700	chr7B	574512789	574513598	809	True	1321.000000	1321	96.178000	1967	2773	1	chr7B.!!$R3	806
6	TraesCS6B01G346700	chr7A	32587280	32588085	805	False	1022.000000	1022	89.634000	1964	2773	1	chr7A.!!$F1	809

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
142	143	1.148759	GCCTTCGCTTCATCTCGTCC	61.149	60.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1865	2169	0.528901	CAGACCCGACACGACAAACA	60.529	55.0	0.0	0.0	0.0	2.83	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
50	51	1.686052	AGGAGGCGCATCTAGAAAGAG	59.314	52.381	22.57	0.00	34.49	2.85
127	128	1.211456	CCTCCATCTCCTTGAGCCTT	58.789	55.000	0.00	0.00	0.00	4.35
142	143	1.148759	GCCTTCGCTTCATCTCGTCC	61.149	60.000	0.00	0.00	0.00	4.79
205	208	1.441738	GTTTAGGGTTTAGCGCGGAA	58.558	50.000	8.83	0.00	34.93	4.30
227	230	2.930562	GGATCCGAGGGATGGGGG	60.931	72.222	1.07	0.00	43.27	5.40
228	231	2.122369	GATCCGAGGGATGGGGGT	60.122	66.667	1.07	0.00	43.27	4.95
229	232	2.448542	ATCCGAGGGATGGGGGTG	60.449	66.667	0.00	0.00	41.43	4.61
230	233	4.815973	TCCGAGGGATGGGGGTGG	62.816	72.222	0.00	0.00	0.00	4.61
372	375	2.418910	CGTCCATGGCCGTCTCTCT	61.419	63.158	7.10	0.00	0.00	3.10
525	794	4.142425	GCCTCGTACTATCTATGGGCTTAC	60.142	50.000	0.00	0.00	35.92	2.34
530	800	6.717997	TCGTACTATCTATGGGCTTACAATGA	59.282	38.462	0.00	0.00	0.00	2.57
904	1181	4.572571	TTCCCCAAGCAACGCCGT	62.573	61.111	0.00	0.00	0.00	5.68
918	1196	2.466846	ACGCCGTTGTATAAATCTCCG	58.533	47.619	0.00	0.00	0.00	4.63
987	1265	2.636412	CCGACGAAGACAGGCAGGA	61.636	63.158	0.00	0.00	0.00	3.86
1014	1301	3.299503	GTGGATAATGGCATCAAGGGTT	58.700	45.455	0.00	0.00	0.00	4.11
1153	1440	2.439701	CCCTCCGGAGCTACGACA	60.440	66.667	26.87	4.62	35.47	4.35
1235	1525	2.750712	GCTTCTTCTCAGGTAGTCGTCT	59.249	50.000	0.00	0.00	0.00	4.18
1249	1539	2.456119	CGTCTTCTCGCACCATGCC	61.456	63.158	0.00	0.00	41.12	4.40
1287	1577	0.249238	GATTCATCTCTCCGCTGCGT	60.249	55.000	21.59	0.00	0.00	5.24
1330	1622	2.355126	CAGCGTGCGTGACAGAGT	60.355	61.111	0.00	0.00	0.00	3.24
1341	1633	2.555199	GTGACAGAGTTGTGCTGACTT	58.445	47.619	0.00	0.00	37.76	3.01
1342	1634	3.717707	GTGACAGAGTTGTGCTGACTTA	58.282	45.455	0.00	0.00	37.76	2.24
1613	1905	3.151022	GAGTCGGAGCAGGAGGGG	61.151	72.222	0.00	0.00	0.00	4.79
1707	1999	1.005037	ATGAAGAACGGCGTGCTCA	60.005	52.632	22.93	20.01	0.00	4.26
1774	2066	0.450983	GAGGTCAACGTCGACTAGGG	59.549	60.000	14.70	0.00	36.12	3.53
1783	2075	2.371179	ACGTCGACTAGGGAGGATCATA	59.629	50.000	14.70	0.00	36.25	2.15
1784	2076	3.009253	ACGTCGACTAGGGAGGATCATAT	59.991	47.826	14.70	0.00	36.25	1.78
1785	2077	3.375610	CGTCGACTAGGGAGGATCATATG	59.624	52.174	14.70	0.00	36.25	1.78
1786	2078	3.129638	GTCGACTAGGGAGGATCATATGC	59.870	52.174	8.70	0.00	36.25	3.14
1902	2206	1.478105	CTGGATGTGATGGTCTCGTGA	59.522	52.381	0.00	0.00	0.00	4.35
1938	2242	6.937457	ACGAGTATGAATCGATCAAACAATG	58.063	36.000	0.00	0.00	42.54	2.82
1945	2249	2.560504	TCGATCAAACAATGGATCCGG	58.439	47.619	7.39	0.00	37.26	5.14
2040	2344	2.916269	TGGTTGTGGGATTAGACATGGA	59.084	45.455	0.00	0.00	0.00	3.41
2121	2425	9.764363	GGAATTTGACAGAAAATTAACTTCCTT	57.236	29.630	0.00	0.00	39.31	3.36
2138	2442	2.115427	CCTTTGTTTGGTTCAGGGGTT	58.885	47.619	0.00	0.00	0.00	4.11
2424	2734	6.474427	CAGCTGACAGCATTTACCAAATAATG	59.526	38.462	28.43	9.40	45.56	1.90
2433	2743	8.621286	AGCATTTACCAAATAATGTACTACTGC	58.379	33.333	0.00	0.00	34.88	4.40
2551	2862	3.058016	GCAACACATGACACAGCAATACT	60.058	43.478	0.00	0.00	0.00	2.12
2624	2938	7.649533	TGAACCAATCATTCAGCATATTTCT	57.350	32.000	0.00	0.00	32.34	2.52
2701	3015	5.183904	GGAAGCACCAAATGTTCTTACTGAT	59.816	40.000	0.00	0.00	38.79	2.90
2728	3042	9.468532	GAGTTTAAAAGAAAACGAGTAGTCCTA	57.531	33.333	0.00	0.00	42.83	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	0.813821	GCCAAGGAGATGCAAGGTTC	59.186	55.000	0.00	0.00	0.00	3.62
127	128	1.139734	GCTGGACGAGATGAAGCGA	59.860	57.895	0.00	0.00	0.00	4.93
157	158	3.175240	CTGACCGTGCGCTTCTCG	61.175	66.667	9.73	8.36	42.12	4.04
158	159	1.372997	TTCTGACCGTGCGCTTCTC	60.373	57.895	9.73	0.00	0.00	2.87
159	160	1.664965	GTTCTGACCGTGCGCTTCT	60.665	57.895	9.73	0.00	0.00	2.85
160	161	0.388134	TAGTTCTGACCGTGCGCTTC	60.388	55.000	9.73	0.35	0.00	3.86
205	208	1.056700	CCATCCCTCGGATCCCTGTT	61.057	60.000	6.06	0.00	40.98	3.16
282	285	4.470170	CCGCCGACGTCGACATGA	62.470	66.667	37.65	0.00	43.02	3.07
299	302	3.195698	GGACGGCGACATGGAAGC	61.196	66.667	16.62	0.00	0.00	3.86
525	794	3.253188	CCCAATGGGCGTATAGTTCATTG	59.747	47.826	4.89	0.00	42.28	2.82
558	828	1.622607	CGATGCCTGGACCCACCTAA	61.623	60.000	0.00	0.00	39.86	2.69
875	1152	3.291584	GCTTGGGGAAGGATTTAGAAGG	58.708	50.000	0.00	0.00	0.00	3.46
904	1181	3.181458	GGGGACTGCGGAGATTTATACAA	60.181	47.826	12.26	0.00	0.00	2.41
987	1265	2.158769	TGATGCCATTATCCACGCTCTT	60.159	45.455	0.00	0.00	0.00	2.85
1014	1301	1.351017	GGGATCCTGTTGGAGAACACA	59.649	52.381	12.58	0.00	46.91	3.72
1235	1525	1.375908	GACAGGCATGGTGCGAGAA	60.376	57.895	2.31	0.00	46.21	2.87
1249	1539	1.564622	CAACGCGTTGGAGTGACAG	59.435	57.895	37.79	14.28	36.95	3.51
1330	1622	3.882288	TGCACAAGAATAAGTCAGCACAA	59.118	39.130	0.00	0.00	0.00	3.33
1341	1633	3.684305	CGGAACACATCTGCACAAGAATA	59.316	43.478	0.00	0.00	38.79	1.75
1342	1634	2.485426	CGGAACACATCTGCACAAGAAT	59.515	45.455	0.00	0.00	38.79	2.40
1774	2066	1.707427	ACTTGGGGGCATATGATCCTC	59.293	52.381	6.97	7.65	0.00	3.71
1783	2075	3.061848	CGCGAAACTTGGGGGCAT	61.062	61.111	0.00	0.00	0.00	4.40
1784	2076	4.572571	ACGCGAAACTTGGGGGCA	62.573	61.111	15.93	0.00	0.00	5.36
1785	2077	3.733960	GACGCGAAACTTGGGGGC	61.734	66.667	15.93	0.00	0.00	5.80
1786	2078	2.281208	TGACGCGAAACTTGGGGG	60.281	61.111	15.93	0.00	0.00	5.40
1865	2169	0.528901	CAGACCCGACACGACAAACA	60.529	55.000	0.00	0.00	0.00	2.83
1902	2206	5.847111	TTCATACTCGTACAGGCACTTAT	57.153	39.130	0.00	0.00	34.60	1.73
1938	2242	2.491675	AGACCAAGAAAACCGGATCC	57.508	50.000	9.46	0.00	0.00	3.36
1945	2249	6.436843	TGTCAGAAGAAAGACCAAGAAAAC	57.563	37.500	0.00	0.00	33.89	2.43
2121	2425	2.237392	CCAAAACCCCTGAACCAAACAA	59.763	45.455	0.00	0.00	0.00	2.83
2138	2442	8.694540	CATATCATTAACAACTCCCATTCCAAA	58.305	33.333	0.00	0.00	0.00	3.28
2286	2591	6.793505	TTTCCTTAGTTTGCCCAGTTTTAA	57.206	33.333	0.00	0.00	0.00	1.52
2551	2862	4.535526	TCATCTCTTTCATCAACCGTGA	57.464	40.909	0.00	0.00	38.41	4.35
2701	3015	7.983484	AGGACTACTCGTTTTCTTTTAAACTCA	59.017	33.333	0.00	0.00	36.18	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.