AutoCloner

Multiple sequence alignment - TraesCS6D01G029600

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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	TraesCS6D01G029600	chr6D	100.000	3195	0	0	1	3195	11485711	11488905	0.000000e+00	5901.0
1	TraesCS6D01G029600	chr6D	92.023	2783	173	22	422	3195	11344183	11341441	0.000000e+00	3864.0
2	TraesCS6D01G029600	chr6D	79.474	570	79	26	2074	2630	11340280	11339736	1.400000e-98	370.0
3	TraesCS6D01G029600	chr6D	93.750	80	5	0	1	80	11344260	11344181	1.560000e-23	121.0
4	TraesCS6D01G029600	chr6B	89.651	2290	166	38	419	2652	21170950	21168676	0.000000e+00	2850.0
5	TraesCS6D01G029600	chr6B	83.681	288	32	8	2909	3195	21168677	21168404	1.140000e-64	257.0
6	TraesCS6D01G029600	chr6A	92.257	1976	129	15	975	2938	12881401	12883364	0.000000e+00	2780.0
7	TraesCS6D01G029600	chr6A	90.544	1396	79	24	1809	3195	12598141	12596790	0.000000e+00	1797.0
8	TraesCS6D01G029600	chr6A	90.050	995	76	10	1	983	12877294	12878277	0.000000e+00	1267.0
9	TraesCS6D01G029600	chr6A	95.170	559	27	0	480	1038	12612300	12611742	0.000000e+00	883.0
10	TraesCS6D01G029600	chr6A	94.353	425	24	0	1033	1457	12603440	12603016	0.000000e+00	652.0
11	TraesCS6D01G029600	chr6A	90.281	463	39	3	1	460	12869341	12869800	4.560000e-168	601.0
12	TraesCS6D01G029600	chr6A	95.536	336	15	0	1484	1819	12603017	12602682	3.630000e-149	538.0
13	TraesCS6D01G029600	chr6A	80.818	636	99	12	795	1425	35302624	35303241	8.020000e-131	477.0
14	TraesCS6D01G029600	chr6A	88.235	289	25	3	172	456	12612578	12612295	1.420000e-88	337.0
15	TraesCS6D01G029600	chr6A	78.087	575	84	27	2074	2630	12884473	12885023	3.070000e-85	326.0
16	TraesCS6D01G029600	chr6A	94.359	195	9	1	3001	3195	12883362	12883554	6.700000e-77	298.0
17	TraesCS6D01G029600	chr6A	91.204	216	16	1	458	670	12870060	12870275	1.120000e-74	291.0
18	TraesCS6D01G029600	chr6A	76.703	279	37	10	172	450	12877220	12877470	2.590000e-26	130.0
19	TraesCS6D01G029600	chr6A	88.158	76	7	2	375	450	12869438	12869511	4.390000e-14	89.8
20	TraesCS6D01G029600	chrUn	80.173	923	151	17	578	1490	101752665	101751765	0.000000e+00	662.0

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	TraesCS6D01G029600	chr6D	11485711	11488905	3194	False	5901.000000	5901	100.000000	1	3195	1	chr6D.!!$F1	3194
1	TraesCS6D01G029600	chr6D	11339736	11344260	4524	True	1451.666667	3864	88.415667	1	3195	3	chr6D.!!$R1	3194
2	TraesCS6D01G029600	chr6B	21168404	21170950	2546	True	1553.500000	2850	86.666000	419	3195	2	chr6B.!!$R1	2776
3	TraesCS6D01G029600	chr6A	12596790	12598141	1351	True	1797.000000	1797	90.544000	1809	3195	1	chr6A.!!$R1	1386
4	TraesCS6D01G029600	chr6A	12877220	12885023	7803	False	960.200000	2780	86.291200	1	3195	5	chr6A.!!$F3	3194
5	TraesCS6D01G029600	chr6A	12611742	12612578	836	True	610.000000	883	91.702500	172	1038	2	chr6A.!!$R3	866
6	TraesCS6D01G029600	chr6A	12602682	12603440	758	True	595.000000	652	94.944500	1033	1819	2	chr6A.!!$R2	786
7	TraesCS6D01G029600	chr6A	35302624	35303241	617	False	477.000000	477	80.818000	795	1425	1	chr6A.!!$F1	630
8	TraesCS6D01G029600	chr6A	12869341	12870275	934	False	327.266667	601	89.881000	1	670	3	chr6A.!!$F2	669
9	TraesCS6D01G029600	chrUn	101751765	101752665	900	True	662.000000	662	80.173000	578	1490	1	chrUn.!!$R1	912

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
188	275	0.317479	GACGTTGGAGTAGTGCAGGT	59.683	55.0	0.0	0.0	0.00	4.0	F
1430	4937	0.326048	AGGCTCTACTGGTGGCTCAT	60.326	55.0	0.0	0.0	39.58	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1684	5191	0.035439	GTCGATTTCCCTGCCTCCAA	60.035	55.0	0.0	0.0	0.0	3.53	R
3018	6573	0.249280	CGTAGCATATCCGGCACACA	60.249	55.0	0.0	0.0	0.0	3.72	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
95	170	2.670934	GGTGCAGCTGTGTGGAGG	60.671	66.667	16.64	0.00	0.00	4.30
101	182	0.886490	CAGCTGTGTGGAGGTTCACC	60.886	60.000	5.25	0.00	36.87	4.02
136	217	2.107950	TGCCCAAACCACTCTAATCG	57.892	50.000	0.00	0.00	0.00	3.34
188	275	0.317479	GACGTTGGAGTAGTGCAGGT	59.683	55.000	0.00	0.00	0.00	4.00
224	311	1.823169	GACCGTTAGGCTCACCACCA	61.823	60.000	0.00	0.00	42.76	4.17
254	341	2.567615	GGAGTTAGAAGAACAGCCCTCA	59.432	50.000	0.00	0.00	0.00	3.86
263	350	0.886490	AACAGCCCTCACAAGCTTCG	60.886	55.000	0.00	0.00	37.18	3.79
327	414	1.892819	CGTGCAGTGGAGGATGGACT	61.893	60.000	0.00	0.00	35.81	3.85
362	449	4.500116	GCGGAGGTCCAGAGCGAC	62.500	72.222	0.00	0.00	35.14	5.19
520	877	0.919710	GTGAAACTCCAGGGGGCTAT	59.080	55.000	0.00	0.00	0.00	2.97
532	889	3.070302	CAGGGGGCTATGTAGACTTCTTC	59.930	52.174	0.00	0.00	0.00	2.87
537	894	3.322541	GGCTATGTAGACTTCTTCCCTCC	59.677	52.174	0.00	0.00	0.00	4.30
685	1053	2.754658	AGTCTCTGGCCCCGTACG	60.755	66.667	8.69	8.69	0.00	3.67
711	1079	1.912043	CTCCACCACTTCTCCTCCAAT	59.088	52.381	0.00	0.00	0.00	3.16
730	1098	0.748367	TCTGACGATCTCCCCACTCG	60.748	60.000	0.00	0.00	38.34	4.18
758	1126	0.590230	GATGAAGGCGACGACGAGAG	60.590	60.000	12.29	0.00	42.66	3.20
868	1241	3.664025	TTGATCCTGCACGCCTCCG	62.664	63.158	0.00	0.00	41.14	4.63
954	1327	4.785453	CGCAAGCCCCCTGTCCTC	62.785	72.222	0.00	0.00	0.00	3.71
1000	4505	1.630126	GCTCCTCTTCATCCCTGCCA	61.630	60.000	0.00	0.00	0.00	4.92
1120	4625	2.254651	GCGTCCTCGTCGTCAACT	59.745	61.111	0.00	0.00	39.49	3.16
1237	4742	2.174319	GGAGCTTTGATCGGCGACC	61.174	63.158	13.76	1.26	0.00	4.79
1315	4821	0.530744	CGTAGGAGTTACTGCAGCCA	59.469	55.000	15.27	0.00	0.00	4.75
1430	4937	0.326048	AGGCTCTACTGGTGGCTCAT	60.326	55.000	0.00	0.00	39.58	2.90
1491	4998	2.157640	AGAGCCTAGCTGTGATCACT	57.842	50.000	25.55	9.24	39.88	3.41
1542	5049	1.070445	GAGCCGGATCATCAGTGGG	59.930	63.158	16.44	0.00	0.00	4.61
1580	5087	2.604914	GACTCGTCGTATTCTCGTACCA	59.395	50.000	0.00	0.00	0.00	3.25
1684	5191	0.251634	GCTTGCTCTGCCCTCTAACT	59.748	55.000	0.00	0.00	0.00	2.24
1800	5307	5.063944	CGATGTTTATGTCTTCCTGGTTCAG	59.936	44.000	0.00	0.00	0.00	3.02
1827	5334	5.113502	ACTTAATGCAGTGCAAGAAACTC	57.886	39.130	23.90	0.00	43.62	3.01
1860	5367	6.475402	GCTTTATGGAAAATTTGTATCACCCG	59.525	38.462	0.00	0.00	0.00	5.28
1878	5385	1.657094	CCGTACGCAAATTTCTACGCT	59.343	47.619	10.49	1.95	32.43	5.07
1899	5406	5.277345	CGCTGGTAATTGCTTATCCTTACAC	60.277	44.000	0.00	0.00	0.00	2.90
1901	5408	6.318900	GCTGGTAATTGCTTATCCTTACACTT	59.681	38.462	0.00	0.00	0.00	3.16
1903	5410	6.537301	TGGTAATTGCTTATCCTTACACTTCG	59.463	38.462	0.00	0.00	0.00	3.79
1950	5457	8.481641	GTTTTTGTAGCCTTAAAATGTTTACGG	58.518	33.333	0.19	0.19	0.00	4.02
1958	5465	7.608761	AGCCTTAAAATGTTTACGGATGACTTA	59.391	33.333	7.30	0.00	0.00	2.24
2031	5544	9.166222	TGTTATATTCTCTCCTTATTTGCCCTA	57.834	33.333	0.00	0.00	0.00	3.53
2115	5628	9.929180	GTTCACATACTTTCTATGGCTATATGA	57.071	33.333	0.00	0.00	0.00	2.15
2174	5687	4.788679	TCGTCTAGACAGTGAATGGGATA	58.211	43.478	22.37	0.00	0.00	2.59
2341	5857	5.978919	TGTCTCATGTTCATTTTGTTCTTGC	59.021	36.000	0.00	0.00	0.00	4.01
2345	5862	7.436080	TCTCATGTTCATTTTGTTCTTGCTTTC	59.564	33.333	0.00	0.00	0.00	2.62
2351	5868	4.442375	TTTTGTTCTTGCTTTCGGAACA	57.558	36.364	0.00	0.00	44.69	3.18
2422	5941	4.578928	ACTTTGTGTTGAGGGTATGTGTTC	59.421	41.667	0.00	0.00	0.00	3.18
2466	6008	7.167468	GTCCTGTTTGTAACATTTGCTGTAAAG	59.833	37.037	0.00	0.00	41.26	1.85
2468	6010	8.132362	CCTGTTTGTAACATTTGCTGTAAAGTA	58.868	33.333	0.00	0.00	41.26	2.24
2667	6218	7.559590	AAGCACATCCATAGTTAAAGCTAAG	57.440	36.000	0.00	0.00	0.00	2.18
2720	6271	9.787435	TTGCTTCTGTCTACCTTCTTTTTATTA	57.213	29.630	0.00	0.00	0.00	0.98
2778	6329	3.441572	CCTGAACCAAGTCCTTTATGCTG	59.558	47.826	0.00	0.00	0.00	4.41
2780	6331	5.235850	TGAACCAAGTCCTTTATGCTGTA	57.764	39.130	0.00	0.00	0.00	2.74
2781	6332	5.001232	TGAACCAAGTCCTTTATGCTGTAC	58.999	41.667	0.00	0.00	0.00	2.90
2782	6333	4.910458	ACCAAGTCCTTTATGCTGTACT	57.090	40.909	0.00	0.00	0.00	2.73
2783	6334	6.014070	TGAACCAAGTCCTTTATGCTGTACTA	60.014	38.462	0.00	0.00	0.00	1.82
2784	6335	5.978814	ACCAAGTCCTTTATGCTGTACTAG	58.021	41.667	0.00	0.00	0.00	2.57
2785	6336	5.104900	ACCAAGTCCTTTATGCTGTACTAGG	60.105	44.000	0.00	0.00	0.00	3.02
2816	6367	9.896263	GGAGTCTAGCTGTAATTAGTAATACAC	57.104	37.037	0.00	0.00	0.00	2.90
2944	6499	8.375506	AGTCATAAGTTCCTTCAGATTACACAA	58.624	33.333	0.00	0.00	0.00	3.33
2951	6506	4.223032	TCCTTCAGATTACACAAGGAGGTC	59.777	45.833	0.00	0.00	39.63	3.85
2974	6529	2.771943	GGATGTCAGAATACCCACAGGA	59.228	50.000	0.00	0.00	36.73	3.86
3018	6573	3.757493	GCCGGATATGCTACAGTACTAGT	59.243	47.826	5.05	0.00	0.00	2.57
3019	6574	4.379603	GCCGGATATGCTACAGTACTAGTG	60.380	50.000	5.05	0.00	0.00	2.74
3157	6712	7.096551	CACCCGGAAAAATGTGATTCTATTTT	58.903	34.615	0.73	6.46	37.92	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	104	2.146342	GCGCACATTACATAGATGCCT	58.854	47.619	0.30	0.00	32.55	4.75
95	170	1.535226	GCGGTTTTTGGTGAGGTGAAC	60.535	52.381	0.00	0.00	0.00	3.18
101	182	0.597377	GGCAAGCGGTTTTTGGTGAG	60.597	55.000	0.00	0.00	0.00	3.51
136	217	1.494721	TGTGAATCAGCCCCTAATCCC	59.505	52.381	0.00	0.00	0.00	3.85
188	275	1.974875	TCTCCTAGTTGCCGTGCGA	60.975	57.895	0.00	0.00	0.00	5.10
224	311	5.930135	TGTTCTTCTAACTCCAAGCTTCTT	58.070	37.500	0.00	0.00	0.00	2.52
263	350	0.035317	TGGATGCCCGATATCAGCAC	59.965	55.000	17.16	11.85	39.77	4.40
271	358	3.624777	GAAATATCCATGGATGCCCGAT	58.375	45.455	33.41	17.83	36.17	4.18
308	395	1.448540	GTCCATCCTCCACTGCACG	60.449	63.158	0.00	0.00	0.00	5.34
389	480	2.087462	GAGTGGTTTGGGCAGGCAAC	62.087	60.000	0.00	0.00	0.00	4.17
390	481	1.832167	GAGTGGTTTGGGCAGGCAA	60.832	57.895	0.00	0.00	0.00	4.52
391	482	1.422977	TAGAGTGGTTTGGGCAGGCA	61.423	55.000	0.00	0.00	0.00	4.75
424	515	7.417456	GGTCTTTCCAAAACCTTGTCAATTACT	60.417	37.037	0.00	0.00	35.97	2.24
427	518	5.188751	TGGTCTTTCCAAAACCTTGTCAATT	59.811	36.000	0.00	0.00	44.12	2.32
431	522	3.068165	CCTGGTCTTTCCAAAACCTTGTC	59.932	47.826	0.00	0.00	46.59	3.18
520	877	3.309265	GGAGAGGAGGGAAGAAGTCTACA	60.309	52.174	0.00	0.00	0.00	2.74
532	889	2.066999	CGGAAAGGGGAGAGGAGGG	61.067	68.421	0.00	0.00	0.00	4.30
537	894	2.354805	CCTTGTAACGGAAAGGGGAGAG	60.355	54.545	0.00	0.00	39.49	3.20
657	1025	4.057428	AGAGACTCCGGCGTGTGC	62.057	66.667	0.00	0.00	41.71	4.57
659	1027	3.374402	CCAGAGACTCCGGCGTGT	61.374	66.667	0.00	0.00	0.00	4.49
685	1053	0.036858	GAGAAGTGGTGGAGAGGCAC	60.037	60.000	0.00	0.00	0.00	5.01
711	1079	0.748367	CGAGTGGGGAGATCGTCAGA	60.748	60.000	0.00	0.00	0.00	3.27
954	1327	4.207281	TCCCTCTCGAATGCGCCG	62.207	66.667	4.18	0.37	37.46	6.46
1120	4625	4.357947	GAGCTCACACCGCGTCCA	62.358	66.667	9.40	0.00	0.00	4.02
1298	4804	0.537188	GCTGGCTGCAGTAACTCCTA	59.463	55.000	16.64	0.00	42.31	2.94
1315	4821	0.462403	GTCTCCGAGGAGTAGACGCT	60.462	60.000	17.75	0.00	42.49	5.07
1430	4937	2.764010	AGTATACCATGGTCACGCTCAA	59.236	45.455	23.76	0.34	0.00	3.02
1491	4998	4.018506	TGGATGTTCTCAATGGAAGGCTTA	60.019	41.667	0.00	0.00	0.00	3.09
1542	5049	2.438434	CCAACACCGCCATCCTCC	60.438	66.667	0.00	0.00	0.00	4.30
1580	5087	2.102578	GGTCCCACATTTGCAAGCTAT	58.897	47.619	0.00	0.00	0.00	2.97
1677	5184	1.573108	TCCCTGCCTCCAAGTTAGAG	58.427	55.000	0.00	0.00	0.00	2.43
1684	5191	0.035439	GTCGATTTCCCTGCCTCCAA	60.035	55.000	0.00	0.00	0.00	3.53
1800	5307	1.078709	TGCACTGCATTAAGTCGAGC	58.921	50.000	0.00	0.00	31.71	5.03
1827	5334	6.880529	ACAAATTTTCCATAAAGCTTCCATGG	59.119	34.615	24.50	24.50	40.55	3.66
1860	5367	2.414138	ACCAGCGTAGAAATTTGCGTAC	59.586	45.455	0.00	0.00	0.00	3.67
1878	5385	6.537301	CGAAGTGTAAGGATAAGCAATTACCA	59.463	38.462	0.00	0.00	0.00	3.25
1899	5406	1.398390	GCATTCTGGCCACTAACGAAG	59.602	52.381	0.00	0.00	0.00	3.79
1901	5408	0.323302	TGCATTCTGGCCACTAACGA	59.677	50.000	0.00	0.00	0.00	3.85
1903	5410	1.533625	TGTGCATTCTGGCCACTAAC	58.466	50.000	0.00	0.00	0.00	2.34
1993	5501	8.999431	GGAGAGAATATAACACACAAAAAGTCA	58.001	33.333	0.00	0.00	0.00	3.41
1994	5502	9.220767	AGGAGAGAATATAACACACAAAAAGTC	57.779	33.333	0.00	0.00	0.00	3.01
2002	5515	8.560374	GGCAAATAAGGAGAGAATATAACACAC	58.440	37.037	0.00	0.00	0.00	3.82
2014	5527	8.432805	TCTATCTTTTAGGGCAAATAAGGAGAG	58.567	37.037	0.00	0.00	0.00	3.20
2115	5628	2.661718	CCGTTGGGCCTGGTAATTAAT	58.338	47.619	4.53	0.00	0.00	1.40
2116	5629	2.131776	CCGTTGGGCCTGGTAATTAA	57.868	50.000	4.53	0.00	0.00	1.40
2117	5630	3.886324	CCGTTGGGCCTGGTAATTA	57.114	52.632	4.53	0.00	0.00	1.40
2118	5631	4.755656	CCGTTGGGCCTGGTAATT	57.244	55.556	4.53	0.00	0.00	1.40
2174	5687	0.677288	TACGCTTGTGGTACAGCAGT	59.323	50.000	4.08	5.18	41.80	4.40
2279	5792	2.989253	GCAACCAACGGGGGAAGG	60.989	66.667	1.25	0.00	42.91	3.46
2341	5857	2.788786	GCACAACACAATGTTCCGAAAG	59.211	45.455	0.00	0.00	38.77	2.62
2345	5862	1.757574	CAGCACAACACAATGTTCCG	58.242	50.000	0.00	0.00	38.77	4.30
2351	5868	2.864882	GCATCTTGCAGCACAACACAAT	60.865	45.455	0.00	0.00	44.26	2.71
2422	5941	1.738099	CGCTCCCAACCTGAGTTCG	60.738	63.158	0.00	0.00	32.45	3.95
2632	6182	8.630054	ACTATGGATGTGCTTTTTAACTACAA	57.370	30.769	0.00	0.00	0.00	2.41
2667	6218	6.231951	GTCTCCCCCTTAAAGCATTCTATAC	58.768	44.000	0.00	0.00	0.00	1.47
2778	6329	5.070847	ACAGCTAGACTCCTAGTCCTAGTAC	59.929	48.000	3.49	0.00	46.18	2.73
2780	6331	4.042174	ACAGCTAGACTCCTAGTCCTAGT	58.958	47.826	3.49	0.00	46.18	2.57
2781	6332	4.699925	ACAGCTAGACTCCTAGTCCTAG	57.300	50.000	3.49	6.39	46.18	3.02
2782	6333	6.766997	ATTACAGCTAGACTCCTAGTCCTA	57.233	41.667	3.49	0.00	46.18	2.94
2783	6334	5.656549	ATTACAGCTAGACTCCTAGTCCT	57.343	43.478	3.49	0.00	46.18	3.85
2784	6335	6.999871	ACTAATTACAGCTAGACTCCTAGTCC	59.000	42.308	3.49	0.00	46.18	3.85
2785	6336	9.558396	TTACTAATTACAGCTAGACTCCTAGTC	57.442	37.037	0.00	0.00	45.38	2.59
2816	6367	9.167311	ACTAGTTTTCAACTTAGCCATATGAAG	57.833	33.333	3.65	2.67	42.81	3.02
2944	6499	2.630889	TTCTGACATCCTGACCTCCT	57.369	50.000	0.00	0.00	0.00	3.69
2951	6506	3.432749	CCTGTGGGTATTCTGACATCCTG	60.433	52.174	0.00	0.00	0.00	3.86
2974	6529	1.883275	CGGATCTCTCTGCCTTCGTAT	59.117	52.381	0.00	0.00	0.00	3.06
3018	6573	0.249280	CGTAGCATATCCGGCACACA	60.249	55.000	0.00	0.00	0.00	3.72
3019	6574	0.944311	CCGTAGCATATCCGGCACAC	60.944	60.000	0.00	0.00	34.62	3.82
3166	6721	9.295825	TGTGACATGATCCTAAATAAAAACACT	57.704	29.630	0.00	0.00	0.00	3.55
3167	6722	9.341899	GTGTGACATGATCCTAAATAAAAACAC	57.658	33.333	0.00	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.