AutoCloner

Multiple sequence alignment - TraesCS7D01G466100

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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	TraesCS7D01G466100	chr7D	100.000	2624	0	0	1	2624	579962867	579960244	0.000000e+00	4846.0
1	TraesCS7D01G466100	chr7D	97.405	578	13	2	2048	2624	614693921	614694497	0.000000e+00	983.0
2	TraesCS7D01G466100	chr7D	97.064	579	15	2	2047	2624	298289552	298290129	0.000000e+00	974.0
3	TraesCS7D01G466100	chr7A	91.362	1945	93	24	168	2047	671484708	671482774	0.000000e+00	2591.0
4	TraesCS7D01G466100	chr7A	96.970	33	1	0	1	33	671485014	671484982	3.650000e-04	56.5
5	TraesCS7D01G466100	chr7B	91.896	1456	76	27	225	1654	646211187	646209748	0.000000e+00	1997.0
6	TraesCS7D01G466100	chr7B	87.679	349	13	12	1701	2047	646209738	646209418	1.910000e-101	379.0
7	TraesCS7D01G466100	chr7B	84.211	95	12	2	87	181	646211281	646211190	3.600000e-14	89.8
8	TraesCS7D01G466100	chr2D	98.443	578	8	1	2048	2624	598928967	598928390	0.000000e+00	1016.0
9	TraesCS7D01G466100	chr3D	97.755	579	12	1	2047	2624	6742286	6741708	0.000000e+00	996.0
10	TraesCS7D01G466100	chr5D	97.751	578	12	1	2048	2624	231635359	231634782	0.000000e+00	994.0
11	TraesCS7D01G466100	chr5D	94.000	600	15	2	2046	2624	314520657	314521256	0.000000e+00	889.0
12	TraesCS7D01G466100	chr6A	89.273	578	27	11	2050	2624	79037774	79037229	0.000000e+00	691.0
13	TraesCS7D01G466100	chr6A	77.817	284	39	19	1122	1392	145134357	145134085	1.260000e-33	154.0
14	TraesCS7D01G466100	chr3A	89.138	580	28	13	2048	2624	430446630	430447177	0.000000e+00	689.0
15	TraesCS7D01G466100	chr6D	95.249	421	18	2	2205	2624	80329271	80329690	0.000000e+00	665.0
16	TraesCS7D01G466100	chr6D	77.305	282	44	16	1122	1392	116953093	116952821	5.850000e-32	148.0
17	TraesCS7D01G466100	chr2A	96.296	162	6	0	2048	2209	36633799	36633960	1.550000e-67	267.0
18	TraesCS7D01G466100	chr6B	80.569	211	27	10	1124	1330	207155633	207155433	1.630000e-32	150.0

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	TraesCS7D01G466100	chr7D	579960244	579962867	2623	True	4846.000000	4846	100.000000	1	2624	1	chr7D.!!$R1	2623
1	TraesCS7D01G466100	chr7D	614693921	614694497	576	False	983.000000	983	97.405000	2048	2624	1	chr7D.!!$F2	576
2	TraesCS7D01G466100	chr7D	298289552	298290129	577	False	974.000000	974	97.064000	2047	2624	1	chr7D.!!$F1	577
3	TraesCS7D01G466100	chr7A	671482774	671485014	2240	True	1323.750000	2591	94.166000	1	2047	2	chr7A.!!$R1	2046
4	TraesCS7D01G466100	chr7B	646209418	646211281	1863	True	821.933333	1997	87.928667	87	2047	3	chr7B.!!$R1	1960
5	TraesCS7D01G466100	chr2D	598928390	598928967	577	True	1016.000000	1016	98.443000	2048	2624	1	chr2D.!!$R1	576
6	TraesCS7D01G466100	chr3D	6741708	6742286	578	True	996.000000	996	97.755000	2047	2624	1	chr3D.!!$R1	577
7	TraesCS7D01G466100	chr5D	231634782	231635359	577	True	994.000000	994	97.751000	2048	2624	1	chr5D.!!$R1	576
8	TraesCS7D01G466100	chr5D	314520657	314521256	599	False	889.000000	889	94.000000	2046	2624	1	chr5D.!!$F1	578
9	TraesCS7D01G466100	chr6A	79037229	79037774	545	True	691.000000	691	89.273000	2050	2624	1	chr6A.!!$R1	574
10	TraesCS7D01G466100	chr3A	430446630	430447177	547	False	689.000000	689	89.138000	2048	2624	1	chr3A.!!$F1	576

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
560	709	0.669625	GTTGTCCGTTCCTCTTCCCG	60.67	60.0	0.0	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2019	2228	0.314935	CGCATGCAATTATGTCCCCC	59.685	55.0	19.57	0.0	0.0	5.4	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
29	30	8.966069	TTGTGGACGGATATAACAATCAATTA	57.034	30.769	0.00	0.00	0.00	1.40
35	65	8.579850	ACGGATATAACAATCAATTATGCCAT	57.420	30.769	0.00	0.00	0.00	4.40
46	76	4.652881	TCAATTATGCCATATGGGTGCAAA	59.347	37.500	23.30	11.51	38.69	3.68
51	81	2.570752	TGCCATATGGGTGCAAATGTTT	59.429	40.909	23.30	0.00	39.65	2.83
59	89	5.344743	TGGGTGCAAATGTTTTTCTTGTA	57.655	34.783	0.00	0.00	0.00	2.41
79	109	7.812191	TCTTGTATATCAATTGGTTGCAAACAC	59.188	33.333	18.78	2.58	41.23	3.32
95	168	2.335316	ACACGGCTTGTACCAGAAAA	57.665	45.000	0.00	0.00	36.32	2.29
98	171	3.004315	ACACGGCTTGTACCAGAAAATTG	59.996	43.478	0.00	0.00	36.32	2.32
137	210	4.854173	TGATGTGCATGTAATAGGTTGGT	58.146	39.130	0.00	0.00	0.00	3.67
189	329	7.895759	ACAAGGCTAAATCATATTTTGTGTGT	58.104	30.769	0.00	0.00	0.00	3.72
213	353	7.445707	TGTTAACTGCAATGAGTGGTTGTAATA	59.554	33.333	7.22	0.00	0.00	0.98
214	354	5.880054	ACTGCAATGAGTGGTTGTAATAC	57.120	39.130	0.00	0.00	0.00	1.89
223	363	5.935789	TGAGTGGTTGTAATACTTTGGCTAC	59.064	40.000	0.00	0.00	0.00	3.58
367	510	3.181490	GGTTTTTACATGATTCTCCGGCC	60.181	47.826	0.00	0.00	0.00	6.13
368	511	3.358111	TTTTACATGATTCTCCGGCCA	57.642	42.857	2.24	0.00	0.00	5.36
462	606	2.524394	ATCCATCCGTCTCCCCCG	60.524	66.667	0.00	0.00	0.00	5.73
560	709	0.669625	GTTGTCCGTTCCTCTTCCCG	60.670	60.000	0.00	0.00	0.00	5.14
944	1107	0.673644	TAGCTCCCAAAGACGCAAGC	60.674	55.000	0.00	0.00	45.62	4.01
954	1117	2.047465	ACGCAAGCAGAGCTGAGG	60.047	61.111	0.85	0.00	39.62	3.86
955	1118	3.497932	CGCAAGCAGAGCTGAGGC	61.498	66.667	0.85	0.00	39.62	4.70
971	1143	1.970114	GGCTGAGCAAAGCAGAGCA	60.970	57.895	6.82	0.00	45.43	4.26
1050	1222	1.372997	CAACTGGACCGACGACCTG	60.373	63.158	0.00	6.42	0.00	4.00
1063	1235	1.061570	GACCTGTACCGCTACGACG	59.938	63.158	0.00	0.00	0.00	5.12
1314	1489	3.781307	TTCACCGGCATCCCCTCG	61.781	66.667	0.00	0.00	0.00	4.63
1427	1617	1.458777	TGTCCTTCGACCACCACCT	60.459	57.895	0.00	0.00	38.32	4.00
1430	1620	2.214216	CCTTCGACCACCACCTCCA	61.214	63.158	0.00	0.00	0.00	3.86
1434	1624	2.750350	GACCACCACCTCCACCAG	59.250	66.667	0.00	0.00	0.00	4.00
1474	1664	4.215742	CGGCATTCGGCTACGGGA	62.216	66.667	0.00	0.00	44.01	5.14
1475	1665	2.188469	GGCATTCGGCTACGGGAA	59.812	61.111	0.00	0.00	44.01	3.97
1551	1747	2.818132	GAGGACCGGATGCTCCTG	59.182	66.667	15.70	0.00	39.84	3.86
1637	1833	1.727535	CGCCTGATCGATCGAGTGATC	60.728	57.143	23.84	15.88	46.24	2.92
1686	1882	7.661847	AGTGAAAGATTTTAGAAACACGGAGAT	59.338	33.333	0.00	0.00	33.18	2.75
1697	1893	1.086696	CACGGAGATGAATTGGCGTT	58.913	50.000	0.00	0.00	0.00	4.84
1821	2028	2.227968	ATTTTGTCACTCTCGCGCGC	62.228	55.000	27.95	23.91	0.00	6.86
1868	2075	2.645838	ATGGGAGAAACCGATGGATG	57.354	50.000	0.00	0.00	40.11	3.51
1869	2076	0.546122	TGGGAGAAACCGATGGATGG	59.454	55.000	0.00	0.00	40.11	3.51
1870	2077	0.837272	GGGAGAAACCGATGGATGGA	59.163	55.000	0.00	0.00	40.11	3.41
1871	2078	1.421646	GGGAGAAACCGATGGATGGAT	59.578	52.381	0.00	0.00	40.11	3.41
1872	2079	2.498167	GGAGAAACCGATGGATGGATG	58.502	52.381	0.00	0.00	0.00	3.51
2039	2248	0.318955	GGGGACATAATTGCATGCGC	60.319	55.000	14.09	0.00	39.24	6.09
2270	2479	1.355381	TCATTGGTGCTCTGATTGGGT	59.645	47.619	0.00	0.00	0.00	4.51
2339	2549	2.030717	ACTCTAATACGATCTGCAGCCG	60.031	50.000	21.25	21.25	0.00	5.52
2347	2557	4.742201	TCTGCAGCCGTCGCTTCC	62.742	66.667	9.47	0.00	45.55	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	2.400573	ACATTTGCACCCATATGGCAT	58.599	42.857	16.97	4.88	37.39	4.40
35	65	5.923204	ACAAGAAAAACATTTGCACCCATA	58.077	33.333	0.00	0.00	0.00	2.74
39	69	8.755696	TGATATACAAGAAAAACATTTGCACC	57.244	30.769	0.00	0.00	0.00	5.01
51	81	9.202273	GTTTGCAACCAATTGATATACAAGAAA	57.798	29.630	7.12	0.00	42.02	2.52
59	89	4.493547	CCGTGTTTGCAACCAATTGATAT	58.506	39.130	7.12	0.00	38.15	1.63
79	109	3.216147	CCAATTTTCTGGTACAAGCCG	57.784	47.619	0.00	0.00	38.70	5.52
137	210	1.003331	GTGACGAAACACATTTGGCGA	60.003	47.619	0.00	0.00	40.11	5.54
181	321	5.339177	CACTCATTGCAGTTAACACACAAA	58.661	37.500	8.61	0.00	0.00	2.83
185	325	3.550820	ACCACTCATTGCAGTTAACACA	58.449	40.909	8.61	2.68	0.00	3.72
189	329	6.892658	ATTACAACCACTCATTGCAGTTAA	57.107	33.333	0.00	0.00	0.00	2.01
196	336	6.071952	AGCCAAAGTATTACAACCACTCATTG	60.072	38.462	0.00	0.00	0.00	2.82
213	353	3.354948	TCTGATGCATGTAGCCAAAGT	57.645	42.857	2.46	0.00	44.83	2.66
214	354	3.881089	TGATCTGATGCATGTAGCCAAAG	59.119	43.478	2.46	0.00	44.83	2.77
223	363	2.495084	CCCACTCTGATCTGATGCATG	58.505	52.381	2.46	0.00	0.00	4.06
329	469	8.017418	TGTAAAAACCCATCTGTCTGATTTTT	57.983	30.769	0.00	0.00	32.05	1.94
334	476	5.875224	TCATGTAAAAACCCATCTGTCTGA	58.125	37.500	0.00	0.00	0.00	3.27
346	489	3.442273	TGGCCGGAGAATCATGTAAAAAC	59.558	43.478	5.05	0.00	36.25	2.43
367	510	5.771153	TCAGCTATCTCAGAGAATGACTG	57.229	43.478	3.63	9.95	33.22	3.51
368	511	5.221028	CGTTCAGCTATCTCAGAGAATGACT	60.221	44.000	3.63	0.00	32.66	3.41
462	606	2.325082	ACGTGCGCCATTTCACCTC	61.325	57.895	4.18	0.00	0.00	3.85
484	628	3.282831	GGAAGAACCCACGTGAATTTG	57.717	47.619	19.30	0.00	0.00	2.32
560	709	0.109913	AGGAACCTTCGGTGGAAACC	59.890	55.000	1.76	0.00	35.34	3.27
721	884	2.202703	CGTTGATCCGTCGTCCCC	60.203	66.667	0.00	0.00	0.00	4.81
907	1070	2.882137	GCTACTAGGAAGAGCTCGACAT	59.118	50.000	8.37	6.83	33.28	3.06
909	1072	2.567985	AGCTACTAGGAAGAGCTCGAC	58.432	52.381	8.37	6.36	42.97	4.20
954	1117	1.209640	GTGCTCTGCTTTGCTCAGC	59.790	57.895	0.00	0.00	40.55	4.26
955	1118	0.797542	GAGTGCTCTGCTTTGCTCAG	59.202	55.000	0.00	0.00	0.00	3.35
956	1119	0.395686	AGAGTGCTCTGCTTTGCTCA	59.604	50.000	0.28	0.00	38.75	4.26
957	1120	1.077915	GAGAGTGCTCTGCTTTGCTC	58.922	55.000	6.43	0.00	40.61	4.26
1050	1222	2.023882	GGAGCGTCGTAGCGGTAC	59.976	66.667	14.72	14.72	42.89	3.34
1245	1420	1.951130	CGTGTTGAGCAGCGTCACT	60.951	57.895	9.36	0.00	0.00	3.41
1341	1516	1.079405	GCCGAAGTTGATGACGGGA	60.079	57.895	0.00	0.00	44.61	5.14
1408	1598	1.301479	GGTGGTGGTCGAAGGACAC	60.301	63.158	0.00	0.00	45.28	3.67
1434	1624	3.793144	GTGTACTGCTGCCGCTGC	61.793	66.667	14.83	14.83	38.51	5.25
1473	1663	1.968540	GGAGTGCTGCAGGTGGTTC	60.969	63.158	17.12	0.00	0.00	3.62
1474	1664	2.113986	GGAGTGCTGCAGGTGGTT	59.886	61.111	17.12	0.00	0.00	3.67
1475	1665	3.958860	GGGAGTGCTGCAGGTGGT	61.959	66.667	17.12	0.00	0.00	4.16
1637	1833	4.629634	TCCGTGCATGTGACTTAGTTAATG	59.370	41.667	4.96	0.00	0.00	1.90
1649	1845	1.511850	TCTTTCACTCCGTGCATGTG	58.488	50.000	4.96	5.57	32.98	3.21
1679	1875	1.369625	GAACGCCAATTCATCTCCGT	58.630	50.000	0.00	0.00	0.00	4.69
1686	1882	1.277326	CTCGATCGAACGCCAATTCA	58.723	50.000	19.92	0.00	0.00	2.57
1697	1893	2.432206	TCAAACACAAGCTCGATCGA	57.568	45.000	18.32	18.32	0.00	3.59
1821	2028	1.192312	CATCATAATCCGCACGAACCG	59.808	52.381	0.00	0.00	0.00	4.44
1822	2029	1.069906	GCATCATAATCCGCACGAACC	60.070	52.381	0.00	0.00	0.00	3.62
1824	2031	2.135139	GAGCATCATAATCCGCACGAA	58.865	47.619	0.00	0.00	33.17	3.85
1870	2077	2.230508	CACTTTGACAGATGCAAGCCAT	59.769	45.455	0.00	0.00	36.70	4.40
1871	2078	1.610038	CACTTTGACAGATGCAAGCCA	59.390	47.619	0.00	0.00	0.00	4.75
1872	2079	1.881973	TCACTTTGACAGATGCAAGCC	59.118	47.619	0.00	0.00	0.00	4.35
1975	2184	4.169696	TCCGCCGGCCAATCGATT	62.170	61.111	23.46	4.39	0.00	3.34
2019	2228	0.314935	CGCATGCAATTATGTCCCCC	59.685	55.000	19.57	0.00	0.00	5.40
2039	2248	2.202298	AAAAATTCGGCGCTCGCG	60.202	55.556	7.64	6.98	43.06	5.87
2339	2549	1.202428	CCTAGCAAGGTAGGAAGCGAC	60.202	57.143	18.14	0.00	42.18	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.