AutoCloner

Multiple sequence alignment - TraesCS6D01G229600

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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	TraesCS6D01G229600	chr6D	100.000	4659	0	0	1	4659	321997591	321992933	0.000000e+00	8604.0
1	TraesCS6D01G229600	chr6D	80.337	178	26	7	477	651	421472025	421472196	4.890000e-25	126.0
2	TraesCS6D01G229600	chr6D	78.531	177	29	6	477	651	411814601	411814770	1.770000e-19	108.0
3	TraesCS6D01G229600	chr6D	95.556	45	2	0	607	651	421472284	421472328	6.470000e-09	73.1
4	TraesCS6D01G229600	chr6B	92.989	3238	146	35	799	3980	501519689	501522901	0.000000e+00	4647.0
5	TraesCS6D01G229600	chr6A	95.541	2893	82	26	1008	3857	459514856	459511968	0.000000e+00	4584.0
6	TraesCS6D01G229600	chr6A	85.563	568	45	21	3855	4420	459511753	459511221	1.130000e-155	560.0
7	TraesCS6D01G229600	chr6A	88.793	116	8	4	812	927	459515237	459515127	2.260000e-28	137.0
8	TraesCS6D01G229600	chr6A	95.918	49	1	1	917	964	459515043	459514995	1.390000e-10	78.7
9	TraesCS6D01G229600	chr3B	84.191	797	61	31	1	779	780877725	780878474	0.000000e+00	713.0
10	TraesCS6D01G229600	chr7A	84.314	765	73	16	1	749	653588151	653587418	0.000000e+00	704.0
11	TraesCS6D01G229600	chr1A	79.188	394	36	11	158	534	492187937	492188301	1.010000e-56	231.0
12	TraesCS6D01G229600	chr1A	90.132	152	12	3	1	150	492154012	492154162	1.320000e-45	195.0
13	TraesCS6D01G229600	chr5D	83.660	153	16	3	288	440	287779167	287779310	8.130000e-28	135.0
14	TraesCS6D01G229600	chr5D	83.673	147	18	4	295	440	502884174	502884315	2.920000e-27	134.0
15	TraesCS6D01G229600	chr5D	100.000	31	0	0	746	776	539723876	539723846	1.810000e-04	58.4
16	TraesCS6D01G229600	chr5A	83.673	147	15	6	295	440	631475450	631475588	3.780000e-26	130.0
17	TraesCS6D01G229600	chr5B	81.529	157	20	7	297	449	326866904	326867055	2.280000e-23	121.0
18	TraesCS6D01G229600	chr4B	79.365	189	26	10	260	445	574055512	574055334	2.280000e-23	121.0
19	TraesCS6D01G229600	chr7B	79.651	172	18	14	295	463	409166395	409166552	1.770000e-19	108.0
20	TraesCS6D01G229600	chrUn	78.505	107	20	3	676	780	56005208	56005103	3.010000e-07	67.6
21	TraesCS6D01G229600	chrUn	78.505	107	20	3	676	780	470284414	470284519	3.010000e-07	67.6

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	TraesCS6D01G229600	chr6D	321992933	321997591	4658	True	8604.000	8604	100.00000	1	4659	1	chr6D.!!$R1	4658
1	TraesCS6D01G229600	chr6B	501519689	501522901	3212	False	4647.000	4647	92.98900	799	3980	1	chr6B.!!$F1	3181
2	TraesCS6D01G229600	chr6A	459511221	459515237	4016	True	1339.925	4584	91.45375	812	4420	4	chr6A.!!$R1	3608
3	TraesCS6D01G229600	chr3B	780877725	780878474	749	False	713.000	713	84.19100	1	779	1	chr3B.!!$F1	778
4	TraesCS6D01G229600	chr7A	653587418	653588151	733	True	704.000	704	84.31400	1	749	1	chr7A.!!$R1	748

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	Hairpin	End Stability	Orientation
694	712	0.107410	TTCCGCAACACCACTCTTGT	60.107	50.000	0.00	3.16	F
766	784	0.107703	TCTAATGGTCAGCAAGGCGG	60.108	55.000	0.00	6.13	F
1566	1812	1.338107	TCAGGGTCTGTGATTCGTGT	58.662	50.000	32.61	4.49	F
2027	2289	2.846206	TGGATGGCTGTGAGGTAGATTT	59.154	45.455	0.00	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1558	1804	0.247974	GCTCATGCTGCACACGAATC	60.248	55.000	3.57	36.03	2.52	R
1656	1902	3.723260	TCATGAACACGAACAGCACTTA	58.277	40.909	0.00	0.00	2.24	R
3010	3343	1.032014	GAGCCTCACTGCACCAAAAA	58.968	50.000	0.00	0.00	1.94	R
3866	4242	0.745845	CAAGAATGTCCCCTCCGCTG	60.746	60.000	0.00	0.00	5.18	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	53	3.115390	CCTCCACTCATTTTCTCCCCTA	58.885	50.000	0.00	0.00	0.00	3.53
62	64	4.380843	TTTCTCCCCTATTCTTGCAACA	57.619	40.909	0.00	0.00	0.00	3.33
100	102	4.440525	CCATCTATGCAAACCACCATGTTC	60.441	45.833	0.00	0.00	0.00	3.18
108	110	3.902881	AACCACCATGTTCTTTGCAAA	57.097	38.095	12.14	12.14	0.00	3.68
115	117	2.016165	GTTCTTTGCAAAGCGCCGG	61.016	57.895	30.35	10.58	41.33	6.13
155	158	2.100797	CGGTCGTGATAACGGCGA	59.899	61.111	16.62	0.00	38.80	5.54
181	184	0.603569	ACGGAATCACTCGAAGCTGT	59.396	50.000	0.00	0.00	0.00	4.40
185	188	2.353208	GGAATCACTCGAAGCTGTGAGT	60.353	50.000	13.78	13.78	45.98	3.41
209	212	1.154450	CACGACGACGACCAGAGAC	60.154	63.158	15.32	0.00	42.66	3.36
235	238	1.816537	GGGCAGCAGTCACGATCTA	59.183	57.895	0.00	0.00	0.00	1.98
256	259	4.602259	CGGCACCACCACACGAGT	62.602	66.667	0.00	0.00	39.03	4.18
257	260	2.665185	GGCACCACCACACGAGTC	60.665	66.667	0.00	0.00	38.86	3.36
272	275	2.509336	GTCACTGCCATCCGACGG	60.509	66.667	7.84	7.84	0.00	4.79
326	329	1.159664	ACCACCTCAAGCTCCTCCT	59.840	57.895	0.00	0.00	0.00	3.69
392	395	7.358683	GCAAAAATAGAGTTCTGCAACATGAAC	60.359	37.037	0.00	8.16	41.84	3.18
459	462	7.409767	GCAAAAGATTCTGCAAACGATCTTTAC	60.410	37.037	18.57	13.43	37.37	2.01
462	480	7.383102	AGATTCTGCAAACGATCTTTACATT	57.617	32.000	0.00	0.00	0.00	2.71
468	486	9.906660	TCTGCAAACGATCTTTACATTATTTTT	57.093	25.926	0.00	0.00	0.00	1.94
551	569	5.938322	TGTGATCTTTAGAATTTCCGCAAC	58.062	37.500	0.00	0.00	0.00	4.17
558	576	6.429692	TCTTTAGAATTTCCGCAACAAGATCA	59.570	34.615	0.00	0.00	0.00	2.92
629	647	4.536364	AAAATACACGCTCGGATGATTG	57.464	40.909	0.00	0.00	0.00	2.67
630	648	1.502231	ATACACGCTCGGATGATTGC	58.498	50.000	0.00	0.00	0.00	3.56
631	649	0.174617	TACACGCTCGGATGATTGCA	59.825	50.000	0.00	0.00	0.00	4.08
632	650	0.673333	ACACGCTCGGATGATTGCAA	60.673	50.000	0.00	0.00	0.00	4.08
633	651	0.247814	CACGCTCGGATGATTGCAAC	60.248	55.000	0.00	0.00	0.00	4.17

Showing 1 to 25 of 423 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	53	1.467920	GCCTAGGCTGTTGCAAGAAT	58.532	50.000	27.17	0.00	41.91	2.40
100	102	4.347453	AGCCGGCGCTTTGCAAAG	62.347	61.111	30.70	30.70	45.55	2.77
155	158	3.275088	AGTGATTCCGTCGCTCGT	58.725	55.556	0.00	0.00	44.18	4.18
172	175	1.300931	GTGCCACTCACAGCTTCGA	60.301	57.895	0.00	0.00	44.98	3.71
181	184	3.220658	TCGTCGTGGTGCCACTCA	61.221	61.111	17.96	3.19	44.16	3.41
185	188	4.634133	GTCGTCGTCGTGGTGCCA	62.634	66.667	1.33	0.00	38.33	4.92
194	197	2.202324	GCGTCTCTGGTCGTCGTC	60.202	66.667	0.00	0.00	0.00	4.20
214	217	3.362399	ATCGTGACTGCTGCCCGAG	62.362	63.158	0.00	0.00	0.00	4.63
215	218	3.356639	GATCGTGACTGCTGCCCGA	62.357	63.158	0.00	0.00	0.00	5.14
272	275	1.668151	AAGGTCGAGCTTCCGTTGC	60.668	57.895	23.57	0.00	0.00	4.17
333	336	0.917533	AGCATGAAGGAGATGGTGCT	59.082	50.000	0.00	0.00	38.03	4.40
472	490	9.467258	CAGAGATTTTGTTGCAGAATTTTCTTA	57.533	29.630	0.00	0.00	34.74	2.10
522	540	7.415653	GCGGAAATTCTAAAGATCACAGGATTT	60.416	37.037	7.03	7.03	31.53	2.17
538	556	4.074970	AGTGATCTTGTTGCGGAAATTCT	58.925	39.130	0.00	0.00	0.00	2.40
607	625	4.730613	GCAATCATCCGAGCGTGTATTTTT	60.731	41.667	0.00	0.00	0.00	1.94
608	626	3.242739	GCAATCATCCGAGCGTGTATTTT	60.243	43.478	0.00	0.00	0.00	1.82
609	627	2.287915	GCAATCATCCGAGCGTGTATTT	59.712	45.455	0.00	0.00	0.00	1.40
610	628	1.867233	GCAATCATCCGAGCGTGTATT	59.133	47.619	0.00	0.00	0.00	1.89
611	629	1.202521	TGCAATCATCCGAGCGTGTAT	60.203	47.619	0.00	0.00	0.00	2.29
612	630	0.174617	TGCAATCATCCGAGCGTGTA	59.825	50.000	0.00	0.00	0.00	2.90
613	631	0.673333	TTGCAATCATCCGAGCGTGT	60.673	50.000	0.00	0.00	0.00	4.49
614	632	0.247814	GTTGCAATCATCCGAGCGTG	60.248	55.000	0.59	0.00	0.00	5.34
615	633	0.673333	TGTTGCAATCATCCGAGCGT	60.673	50.000	0.59	0.00	0.00	5.07
616	634	0.447406	TTGTTGCAATCATCCGAGCG	59.553	50.000	0.59	0.00	0.00	5.03
617	635	1.796617	GCTTGTTGCAATCATCCGAGC	60.797	52.381	0.59	6.44	42.31	5.03

Showing 1 to 25 of 372 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.