AutoCloner

Multiple sequence alignment - TraesCS6D01G073600

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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	TraesCS6D01G073600	chr6D	100.000	2913	0	0	1	2913	37661037	37658125	0.000000e+00	5380.0
1	TraesCS6D01G073600	chr6D	83.212	137	19	4	46	180	122658197	122658331	3.940000e-24	122.0
2	TraesCS6D01G073600	chr6D	90.141	71	7	0	1040	1110	77172549	77172619	3.090000e-15	93.5
3	TraesCS6D01G073600	chr6A	93.801	2694	144	11	228	2913	49083541	49080863	0.000000e+00	4028.0
4	TraesCS6D01G073600	chr6A	93.663	2525	142	10	396	2913	49079224	49076711	0.000000e+00	3760.0
5	TraesCS6D01G073600	chr6A	90.909	66	6	0	2803	2868	49081674	49081609	4.000000e-14	89.8
6	TraesCS6D01G073600	chr6B	87.680	974	116	4	1123	2094	87999497	87998526	0.000000e+00	1131.0
7	TraesCS6D01G073600	chr6B	91.209	819	66	6	2095	2913	87926425	87925613	0.000000e+00	1109.0
8	TraesCS6D01G073600	chr6B	86.957	989	116	9	1118	2096	87927459	87926474	0.000000e+00	1099.0
9	TraesCS6D01G073600	chr6B	90.842	819	67	8	2095	2913	87998475	87997665	0.000000e+00	1090.0
10	TraesCS6D01G073600	chr6B	92.676	710	45	5	411	1117	88000277	87999572	0.000000e+00	1016.0
11	TraesCS6D01G073600	chr6B	91.812	574	43	2	547	1117	87928110	87927538	0.000000e+00	797.0
12	TraesCS6D01G073600	chr6B	89.855	69	7	0	1042	1110	149876684	149876752	4.000000e-14	89.8
13	TraesCS6D01G073600	chr3B	100.000	34	0	0	429	462	731097099	731097066	2.420000e-06	63.9
14	TraesCS6D01G073600	chr7D	92.105	38	3	0	2694	2731	550554104	550554141	1.000000e-03	54.7
15	TraesCS6D01G073600	chr7D	100.000	28	0	0	2694	2721	550801497	550801524	5.000000e-03	52.8
16	TraesCS6D01G073600	chr3A	100.000	29	0	0	326	354	688593388	688593360	1.000000e-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	TraesCS6D01G073600	chr6D	37658125	37661037	2912	True	5380.000000	5380	100.000000	1	2913	1	chr6D.!!$R1	2912
1	TraesCS6D01G073600	chr6A	49076711	49083541	6830	True	2625.933333	4028	92.791000	228	2913	3	chr6A.!!$R1	2685
2	TraesCS6D01G073600	chr6B	87997665	88000277	2612	True	1079.000000	1131	90.399333	411	2913	3	chr6B.!!$R2	2502
3	TraesCS6D01G073600	chr6B	87925613	87928110	2497	True	1001.666667	1109	89.992667	547	2913	3	chr6B.!!$R1	2366

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
515	516	0.110554	GCACGCGTAATCCGTTTTGT	60.111	50.0	13.44	0.0	36.69	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2262	6558	0.036765	TGACCTAACTCGCCGCAAAT	60.037	50.0	0.0	0.0	0.0	2.32	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
58	59	9.709495	TTAAATCAAGGAGAAAATTGAACATGG	57.291	29.630	0.00	0.00	38.80	3.66
59	60	5.726980	TCAAGGAGAAAATTGAACATGGG	57.273	39.130	0.00	0.00	32.66	4.00
60	61	5.392995	TCAAGGAGAAAATTGAACATGGGA	58.607	37.500	0.00	0.00	32.66	4.37
61	62	5.837979	TCAAGGAGAAAATTGAACATGGGAA	59.162	36.000	0.00	0.00	32.66	3.97
62	63	5.728637	AGGAGAAAATTGAACATGGGAAC	57.271	39.130	0.00	0.00	0.00	3.62
63	64	8.562671	TCAAGGAGAAAATTGAACATGGGAACA	61.563	37.037	0.00	0.00	37.32	3.18
242	243	6.750148	AGAGTTTTAGAAGTGACGACAATCT	58.250	36.000	8.88	8.88	0.00	2.40
246	247	1.344438	AGAAGTGACGACAATCTGCCA	59.656	47.619	4.18	0.00	0.00	4.92
272	273	0.868406	GCGGCAGATAGGATTTTCCG	59.132	55.000	0.00	0.00	42.75	4.30
332	333	7.664318	TGTTTCTTCCTAATTTTGGACCTCTAC	59.336	37.037	0.00	0.00	32.65	2.59
362	363	9.871175	TTAACTTACTCCCTTATTTTCCTTTGT	57.129	29.630	0.00	0.00	0.00	2.83
508	509	1.361793	TTACCAAGCACGCGTAATCC	58.638	50.000	13.44	0.16	0.00	3.01
509	510	0.802994	TACCAAGCACGCGTAATCCG	60.803	55.000	13.44	0.00	40.40	4.18
515	516	0.110554	GCACGCGTAATCCGTTTTGT	60.111	50.000	13.44	0.00	36.69	2.83
695	701	6.012508	TGGTCTCCATCTAGATTTTTCTTGGT	60.013	38.462	1.33	0.00	0.00	3.67
728	734	1.007271	CCGATCGATTGTCCCGAGG	60.007	63.158	18.66	0.00	39.55	4.63
749	755	2.014857	GGGAAGCCAGTATTTCCGTTC	58.985	52.381	0.00	0.00	43.05	3.95
766	772	5.172934	TCCGTTCGTTGCAGATTAGTAAAT	58.827	37.500	0.00	0.00	0.00	1.40
993	999	4.220821	CGTCACCTTGGCTCCATATATAGT	59.779	45.833	0.00	0.00	0.00	2.12
1035	1041	6.670695	AAAAGTCTGCACCAAATTATCCTT	57.329	33.333	0.00	0.00	0.00	3.36
1079	1085	0.743345	GCTAATCAAGGGTTCGCCGT	60.743	55.000	0.00	0.00	38.45	5.68
1147	1231	0.248949	GCCGTTAGGTCTTAGGCTCG	60.249	60.000	0.00	0.00	44.06	5.03
1212	1296	1.369091	AATCGTCGATGCTTGGTGCC	61.369	55.000	8.83	0.00	42.00	5.01
1284	1368	4.545208	TGTAAGTCCACCGATCAAATCA	57.455	40.909	0.00	0.00	0.00	2.57
1566	5807	3.767230	CAACGTCGCGCAGTCCAG	61.767	66.667	8.75	0.00	0.00	3.86
1592	5833	1.971167	GTGGCCAATGTTCTCCGCA	60.971	57.895	7.24	0.00	0.00	5.69
1711	5952	1.553706	CTTTTTGCAGGGAGGAGCAT	58.446	50.000	0.00	0.00	40.94	3.79
1889	6133	0.952497	CATGTGCGTCAAGACTGGCT	60.952	55.000	0.00	0.00	0.00	4.75
1893	6137	0.319555	TGCGTCAAGACTGGCTGTAC	60.320	55.000	0.00	0.00	0.00	2.90
1973	6218	4.738998	CCCCACCGCATCAAGCCA	62.739	66.667	0.00	0.00	41.38	4.75
2015	6260	2.261037	GCATTGCGTTGCACTATCAA	57.739	45.000	5.86	0.00	42.31	2.57
2049	6294	6.504180	CGAACGTTCATTCGCCATTATTTTTC	60.504	38.462	26.71	0.00	44.37	2.29
2097	6342	8.672823	TTTCCTTCTAAGACTTTTTACAGTCC	57.327	34.615	0.00	0.00	43.89	3.85
2261	6557	0.104882	TATATGGGTTGGGGCCGAGA	60.105	55.000	0.00	0.00	0.00	4.04
2262	6558	0.991355	ATATGGGTTGGGGCCGAGAA	60.991	55.000	0.00	0.00	0.00	2.87
2378	6674	3.233578	GACATGTATGTTGTGGCAAACG	58.766	45.455	0.00	0.00	41.95	3.60
2389	6685	0.897863	TGGCAAACGGGGAGAAATGG	60.898	55.000	0.00	0.00	0.00	3.16
2519	6815	8.600449	ATTCAGATCCAATAGTCGAAAAGATC	57.400	34.615	0.00	0.00	0.00	2.75
2672	6968	3.983988	GCATAGACGGTGTGTATCTCATG	59.016	47.826	0.00	0.00	0.00	3.07
2706	7002	7.329962	TCATTATTTTCGCAGTTTTAGAGTCGA	59.670	33.333	0.00	0.00	0.00	4.20
2857	7153	5.473039	CCCCTCTTTTATTCTGTTTTGCTG	58.527	41.667	0.00	0.00	0.00	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	9.709495	CCATGTTCAATTTTCTCCTTGATTTAA	57.291	29.630	0.00	0.00	31.83	1.52
33	34	8.313292	CCCATGTTCAATTTTCTCCTTGATTTA	58.687	33.333	0.00	0.00	31.83	1.40
34	35	7.016465	TCCCATGTTCAATTTTCTCCTTGATTT	59.984	33.333	0.00	0.00	31.83	2.17
35	36	6.497954	TCCCATGTTCAATTTTCTCCTTGATT	59.502	34.615	0.00	0.00	31.83	2.57
36	37	6.018469	TCCCATGTTCAATTTTCTCCTTGAT	58.982	36.000	0.00	0.00	31.83	2.57
37	38	5.392995	TCCCATGTTCAATTTTCTCCTTGA	58.607	37.500	0.00	0.00	0.00	3.02
38	39	5.726980	TCCCATGTTCAATTTTCTCCTTG	57.273	39.130	0.00	0.00	0.00	3.61
39	40	5.602145	TGTTCCCATGTTCAATTTTCTCCTT	59.398	36.000	0.00	0.00	0.00	3.36
40	41	5.147032	TGTTCCCATGTTCAATTTTCTCCT	58.853	37.500	0.00	0.00	0.00	3.69
41	42	5.467035	TGTTCCCATGTTCAATTTTCTCC	57.533	39.130	0.00	0.00	0.00	3.71
42	43	7.784633	TTTTGTTCCCATGTTCAATTTTCTC	57.215	32.000	0.00	0.00	0.00	2.87
210	211	9.537192	TCGTCACTTCTAAAACTCTAATTTTCA	57.463	29.630	0.00	0.00	33.80	2.69
211	212	9.794653	GTCGTCACTTCTAAAACTCTAATTTTC	57.205	33.333	0.00	0.00	33.80	2.29
212	213	9.321562	TGTCGTCACTTCTAAAACTCTAATTTT	57.678	29.630	0.00	0.00	35.89	1.82
213	214	8.882415	TGTCGTCACTTCTAAAACTCTAATTT	57.118	30.769	0.00	0.00	0.00	1.82
214	215	8.882415	TTGTCGTCACTTCTAAAACTCTAATT	57.118	30.769	0.00	0.00	0.00	1.40
215	216	9.141400	GATTGTCGTCACTTCTAAAACTCTAAT	57.859	33.333	0.00	0.00	0.00	1.73
216	217	8.358148	AGATTGTCGTCACTTCTAAAACTCTAA	58.642	33.333	0.00	0.00	0.00	2.10
217	218	7.808381	CAGATTGTCGTCACTTCTAAAACTCTA	59.192	37.037	0.00	0.00	0.00	2.43
218	219	6.642950	CAGATTGTCGTCACTTCTAAAACTCT	59.357	38.462	0.00	0.00	0.00	3.24
219	220	6.616682	GCAGATTGTCGTCACTTCTAAAACTC	60.617	42.308	0.00	0.00	0.00	3.01
220	221	5.177696	GCAGATTGTCGTCACTTCTAAAACT	59.822	40.000	0.00	0.00	0.00	2.66
221	222	5.374898	GCAGATTGTCGTCACTTCTAAAAC	58.625	41.667	0.00	0.00	0.00	2.43
222	223	4.451096	GGCAGATTGTCGTCACTTCTAAAA	59.549	41.667	0.00	0.00	0.00	1.52
223	224	3.994392	GGCAGATTGTCGTCACTTCTAAA	59.006	43.478	0.00	0.00	0.00	1.85
224	225	3.006430	TGGCAGATTGTCGTCACTTCTAA	59.994	43.478	0.00	0.00	0.00	2.10
225	226	2.560981	TGGCAGATTGTCGTCACTTCTA	59.439	45.455	0.00	0.00	0.00	2.10
226	227	1.344438	TGGCAGATTGTCGTCACTTCT	59.656	47.619	0.00	0.00	0.00	2.85
246	247	4.833478	AATCCTATCTGCCGCATTCTAT	57.167	40.909	0.00	0.00	0.00	1.98
332	333	7.336176	AGGAAAATAAGGGAGTAAGTTAAAGCG	59.664	37.037	0.00	0.00	0.00	4.68
401	402	9.834628	ATTTTGTCGTGTTACCTACATTTAATG	57.165	29.630	3.07	3.07	39.39	1.90
468	469	3.382048	AGGTCAGAAAACGGTAGTGAC	57.618	47.619	1.99	1.99	37.41	3.67
508	509	6.912203	AGGAAACCCAAATTAAACAAAACG	57.088	33.333	0.00	0.00	0.00	3.60
509	510	9.163899	TGTAAGGAAACCCAAATTAAACAAAAC	57.836	29.630	0.00	0.00	0.00	2.43
728	734	0.255033	ACGGAAATACTGGCTTCCCC	59.745	55.000	0.00	0.00	38.31	4.81
739	745	5.172934	ACTAATCTGCAACGAACGGAAATA	58.827	37.500	0.00	0.00	0.00	1.40
749	755	9.820229	TGTTTCTTTATTTACTAATCTGCAACG	57.180	29.630	0.00	0.00	0.00	4.10
766	772	5.025986	GAAGAATTCGCCGTGTTTCTTTA	57.974	39.130	10.99	0.00	38.25	1.85
959	965	3.998672	GGTGACGCGTCCCTGGAA	61.999	66.667	34.34	13.76	0.00	3.53
993	999	2.399916	TTGCATCGACCATGACATGA	57.600	45.000	17.24	0.00	33.80	3.07
1063	1069	1.674322	CCACGGCGAACCCTTGATT	60.674	57.895	16.62	0.00	34.90	2.57
1147	1231	1.648467	GCCATTTCCTGAGCACCGTC	61.648	60.000	0.00	0.00	0.00	4.79
1252	1336	2.355756	GTGGACTTACATGATTGCGCAT	59.644	45.455	12.75	0.40	0.00	4.73
1284	1368	3.652387	TGGATAGGTACATGCATGGTGAT	59.348	43.478	29.41	15.00	0.00	3.06
1437	5678	4.140599	CGAGCTGCTTCCTCGCCT	62.141	66.667	2.53	0.00	44.53	5.52
1566	5807	3.499737	CATTGGCCACGGTCTCGC	61.500	66.667	3.88	0.00	40.63	5.03
1711	5952	0.251832	GTGTCTCACCCTCCTCCTCA	60.252	60.000	0.00	0.00	0.00	3.86
1873	6117	0.319555	TACAGCCAGTCTTGACGCAC	60.320	55.000	4.12	0.00	0.00	5.34
1889	6133	1.335597	CGAGAAGTTGACGCTGGTACA	60.336	52.381	0.00	0.00	0.00	2.90
1893	6137	0.318699	TCACGAGAAGTTGACGCTGG	60.319	55.000	0.00	0.00	0.00	4.85
1973	6218	2.396601	CATGTGCGTTTTGTCAGCAAT	58.603	42.857	0.00	0.00	42.93	3.56
2063	6308	8.768501	AAAGTCTTAGAAGGAAAGGAAATGTT	57.231	30.769	0.00	0.00	0.00	2.71
2097	6342	5.820947	TCATCCTCTCATGTTGACATCATTG	59.179	40.000	0.00	0.00	33.61	2.82
2154	6449	4.728772	ACAATTTGTCCAACATCTCCAGA	58.271	39.130	0.00	0.00	0.00	3.86
2157	6452	5.452078	TGAACAATTTGTCCAACATCTCC	57.548	39.130	1.83	0.00	0.00	3.71
2239	6535	1.783979	TCGGCCCCAACCCATATATTT	59.216	47.619	0.00	0.00	0.00	1.40
2261	6557	1.084289	GACCTAACTCGCCGCAAATT	58.916	50.000	0.00	0.00	0.00	1.82
2262	6558	0.036765	TGACCTAACTCGCCGCAAAT	60.037	50.000	0.00	0.00	0.00	2.32
2378	6674	1.381735	CTTGCCCCCATTTCTCCCC	60.382	63.158	0.00	0.00	0.00	4.81
2389	6685	0.178961	ACCTTTGTCCTTCTTGCCCC	60.179	55.000	0.00	0.00	0.00	5.80
2538	6834	3.181445	CCCACCTTTGCTAGCCATGTATA	60.181	47.826	13.29	0.00	0.00	1.47
2672	6968	1.780860	GCGAAAATAATGACATGCGCC	59.219	47.619	4.18	0.00	37.53	6.53
2767	7063	4.095410	TCGCCATCATCAATCAAACAAC	57.905	40.909	0.00	0.00	0.00	3.32
2770	7066	3.047796	GCATCGCCATCATCAATCAAAC	58.952	45.455	0.00	0.00	0.00	2.93
2774	7070	2.095532	GCTAGCATCGCCATCATCAATC	59.904	50.000	10.63	0.00	0.00	2.67
2857	7153	8.553459	TGAGGAATTGATCTACTTGAGAAAAC	57.447	34.615	0.00	0.00	37.85	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.