AutoCloner

Multiple sequence alignment - TraesCS7D01G376300

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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	TraesCS7D01G376300	chr7D	100.000	3670	0	0	1	3670	486577423	486573754	0.000000e+00	6778.0
1	TraesCS7D01G376300	chr7D	82.023	2264	299	71	1021	3227	486630506	486628294	0.000000e+00	1827.0
2	TraesCS7D01G376300	chr7D	74.468	752	144	30	1078	1801	486242820	486242089	7.760000e-72	281.0
3	TraesCS7D01G376300	chr7A	96.459	2909	92	8	767	3670	555481403	555478501	0.000000e+00	4791.0
4	TraesCS7D01G376300	chr7A	88.179	2741	223	44	940	3632	555468529	555465842	0.000000e+00	3173.0
5	TraesCS7D01G376300	chr7A	88.831	1719	141	25	1955	3632	555474841	555473133	0.000000e+00	2063.0
6	TraesCS7D01G376300	chr7A	80.943	2120	296	61	1021	3068	555506497	555504414	0.000000e+00	1578.0
7	TraesCS7D01G376300	chr7A	88.215	874	91	10	1035	1899	555475730	555474860	0.000000e+00	1033.0
8	TraesCS7D01G376300	chr7A	86.859	799	55	15	1	769	555482440	555481662	0.000000e+00	848.0
9	TraesCS7D01G376300	chr7B	95.980	2637	72	11	846	3449	516316088	516313453	0.000000e+00	4252.0
10	TraesCS7D01G376300	chr7B	81.927	2263	308	70	1021	3227	516355614	516353397	0.000000e+00	1820.0
11	TraesCS7D01G376300	chr7B	93.173	498	33	1	313	809	516318186	516317689	0.000000e+00	730.0
12	TraesCS7D01G376300	chr7B	98.190	221	4	0	3449	3669	516313375	516313155	1.600000e-103	387.0
13	TraesCS7D01G376300	chr7B	87.234	329	40	2	1035	1362	516299141	516298814	1.240000e-99	374.0
14	TraesCS7D01G376300	chr7B	83.219	292	12	7	1	261	516318482	516318197	2.200000e-57	233.0
15	TraesCS7D01G376300	chr7B	80.952	231	33	4	3224	3447	586689359	586689133	4.870000e-39	172.0
16	TraesCS7D01G376300	chr7B	98.462	65	1	0	795	859	516317675	516317611	8.330000e-22	115.0
17	TraesCS7D01G376300	chr7B	94.643	56	3	0	3448	3503	586689101	586689046	1.820000e-13	87.9
18	TraesCS7D01G376300	chr5B	85.833	240	33	1	1613	1852	148377133	148376895	1.690000e-63	254.0
19	TraesCS7D01G376300	chr6D	78.367	245	42	6	1383	1618	470243015	470242773	8.210000e-32	148.0
20	TraesCS7D01G376300	chr6A	84.000	125	20	0	2056	2180	610510278	610510402	1.790000e-23	121.0
21	TraesCS7D01G376300	chr6B	82.946	129	22	0	2052	2180	707255271	707255143	2.320000e-22	117.0
22	TraesCS7D01G376300	chr1B	89.247	93	10	0	3355	3447	90936943	90936851	2.320000e-22	117.0
23	TraesCS7D01G376300	chr1B	92.857	56	4	0	3448	3503	90936819	90936764	8.450000e-12	82.4
24	TraesCS7D01G376300	chr5A	94.643	56	3	0	3448	3503	633676875	633676930	1.820000e-13	87.9
25	TraesCS7D01G376300	chr4B	94.643	56	3	0	3448	3503	663469782	663469837	1.820000e-13	87.9

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	TraesCS7D01G376300	chr7D	486573754	486577423	3669	True	6778.00	6778	100.0000	1	3670	1	chr7D.!!$R2	3669
1	TraesCS7D01G376300	chr7D	486628294	486630506	2212	True	1827.00	1827	82.0230	1021	3227	1	chr7D.!!$R3	2206
2	TraesCS7D01G376300	chr7D	486242089	486242820	731	True	281.00	281	74.4680	1078	1801	1	chr7D.!!$R1	723
3	TraesCS7D01G376300	chr7A	555465842	555468529	2687	True	3173.00	3173	88.1790	940	3632	1	chr7A.!!$R1	2692
4	TraesCS7D01G376300	chr7A	555473133	555482440	9307	True	2183.75	4791	90.0910	1	3670	4	chr7A.!!$R3	3669
5	TraesCS7D01G376300	chr7A	555504414	555506497	2083	True	1578.00	1578	80.9430	1021	3068	1	chr7A.!!$R2	2047
6	TraesCS7D01G376300	chr7B	516353397	516355614	2217	True	1820.00	1820	81.9270	1021	3227	1	chr7B.!!$R2	2206
7	TraesCS7D01G376300	chr7B	516313155	516318482	5327	True	1143.40	4252	93.8048	1	3669	5	chr7B.!!$R3	3668

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	Hairpin	End Stability	Orientation
374	409	0.036875	GTGTGGCTCTTAGGGTTGCT	59.963	55.000	0.00	0.00	3.91	F
442	477	0.395311	ATGCTCGGTACTTCCTCGGA	60.395	55.000	0.00	0.00	4.55	F
540	575	1.078426	CTCCTTTGGGTAGGTGGCG	60.078	63.158	0.00	36.63	5.69	F
966	2832	2.358619	CTTCCCCATTCCGGCCAA	59.641	61.111	2.24	0.00	4.52	F
2362	4351	2.290514	CCAAGTTCTGGCAGGAGATCAA	60.291	50.000	15.73	38.76	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1902	3864	2.955614	GCAATGAGATGCAGCAAAAGT	58.044	42.857	4.07	0.00	45.7	2.66	R
2024	4004	3.316029	CCATTGTGTCTGACTGCAAAGAA	59.684	43.478	17.24	1.12	0.0	2.52	R
2290	4279	3.641436	AGTTACAGATGGATCATGCGGTA	59.359	43.478	0.00	0.00	0.0	4.02	R
2540	4532	2.668457	CTGTAGACACTGCAATTCGTCC	59.332	50.000	0.00	0.00	0.0	4.79	R
3333	5373	7.047271	GGGCATTCCATTAAGCAAAGAATTAA	58.953	34.615	0.00	0.00	35.0	1.40	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
134	140	1.552719	GGTGGTGGGAGTCCTAGAAGT	60.553	57.143	9.58	0.00	0.00	3.01
219	252	1.232461	AGCTACCCTCCTCCCTCCTT	61.232	60.000	0.00	0.00	0.00	3.36
258	291	1.966451	CTTTTCTTGCCCGGACGCT	60.966	57.895	0.73	0.00	0.00	5.07
261	294	3.659089	TTCTTGCCCGGACGCTAGC	62.659	63.158	0.73	4.06	32.50	3.42
280	313	3.290710	AGCAACACTCTTGTTTCATGGT	58.709	40.909	0.00	0.00	43.89	3.55
286	319	2.040412	ACTCTTGTTTCATGGTCCTCCC	59.960	50.000	0.00	0.00	0.00	4.30
289	322	2.584835	TGTTTCATGGTCCTCCCTTG	57.415	50.000	0.00	0.00	39.25	3.61
374	409	0.036875	GTGTGGCTCTTAGGGTTGCT	59.963	55.000	0.00	0.00	0.00	3.91
404	439	1.334243	GGAGACGAGGTGATTACTCCG	59.666	57.143	0.00	0.00	35.38	4.63
415	450	3.248602	GTGATTACTCCGCAATCCATCAC	59.751	47.826	0.00	0.00	34.12	3.06
442	477	0.395311	ATGCTCGGTACTTCCTCGGA	60.395	55.000	0.00	0.00	0.00	4.55
540	575	1.078426	CTCCTTTGGGTAGGTGGCG	60.078	63.158	0.00	0.00	36.63	5.69
547	582	2.794028	GGGTAGGTGGCGGAGTAGC	61.794	68.421	0.00	0.00	0.00	3.58
556	591	3.552478	GGTGGCGGAGTAGCTAATTCTAC	60.552	52.174	0.00	0.00	39.28	2.59
557	592	3.067742	GTGGCGGAGTAGCTAATTCTACA	59.932	47.826	0.00	0.00	40.95	2.74
564	599	5.507482	GGAGTAGCTAATTCTACACATGCGA	60.507	44.000	0.00	0.00	40.95	5.10
614	650	3.069586	CGTTTCCTGGTGGCATATCTCTA	59.930	47.826	0.00	0.00	0.00	2.43
653	689	5.642063	GTCGAGTTTGATCTTGGTTTCCATA	59.358	40.000	0.00	0.00	31.53	2.74
708	744	3.318275	GGCACATCTTATCCTCGAGTGTA	59.682	47.826	12.31	0.62	0.00	2.90
711	747	5.986135	GCACATCTTATCCTCGAGTGTAATT	59.014	40.000	12.31	0.00	0.00	1.40
845	1172	6.162777	TGGCTTCATTTAATTTTGGCTACAC	58.837	36.000	0.00	0.00	0.00	2.90
966	2832	2.358619	CTTCCCCATTCCGGCCAA	59.641	61.111	2.24	0.00	0.00	4.52
1160	3036	2.482333	CCTACCCGCTCGTCCTCAG	61.482	68.421	0.00	0.00	0.00	3.35
1840	3781	4.864247	GTCTCAATCTCTCTCTCAACTTGC	59.136	45.833	0.00	0.00	0.00	4.01
1867	3822	6.505048	TGTTCCATCCATCATGTTCTCTAT	57.495	37.500	0.00	0.00	0.00	1.98
1869	3824	6.126681	TGTTCCATCCATCATGTTCTCTATGT	60.127	38.462	0.00	0.00	0.00	2.29
1876	3838	7.044181	TCCATCATGTTCTCTATGTTCAGAAC	58.956	38.462	6.32	6.32	45.99	3.01
2024	4004	8.784043	GTTATGATAAACCTGTCTTTGTGAACT	58.216	33.333	0.00	0.00	0.00	3.01
2289	4278	5.182950	CACATTGGTACCAATTTGCAGTCTA	59.817	40.000	33.10	7.17	43.32	2.59
2290	4279	5.951747	ACATTGGTACCAATTTGCAGTCTAT	59.048	36.000	33.10	10.02	43.32	1.98
2362	4351	2.290514	CCAAGTTCTGGCAGGAGATCAA	60.291	50.000	15.73	0.00	38.76	2.57
2540	4532	5.879223	AGCTGACAAGGTGAATGAGATAAAG	59.121	40.000	0.00	0.00	31.35	1.85
2674	4666	2.493278	ACCCTTTTGAATGCTGAATCCG	59.507	45.455	0.00	0.00	0.00	4.18
2740	4732	6.358974	TGAGGAATCATTGACTGTTGTCTA	57.641	37.500	0.00	0.00	43.29	2.59
2837	4835	9.819267	AGAGTATGTAGGAATTAAAGTTAGCAC	57.181	33.333	0.00	0.00	0.00	4.40
2876	4874	8.087982	ACTAGTGTTATTTTCATGTGTCTGTG	57.912	34.615	0.00	0.00	0.00	3.66
2955	4970	5.163426	TGTGGTTTCATTTTCTCTGCATTGT	60.163	36.000	0.00	0.00	0.00	2.71
3013	5028	7.517417	CGTTAACTATCAATTGATGGTCAGAGC	60.517	40.741	30.41	20.67	43.99	4.09
3043	5058	1.335132	TGGTTAGCCGGGATCAGGAC	61.335	60.000	2.18	2.62	37.67	3.85
3108	5137	9.507280	CATCATGTTTTGTGTATCTGGAATAAC	57.493	33.333	0.00	0.00	0.00	1.89
3325	5365	3.791953	TTTCGGGAAGTGGGAATGTTA	57.208	42.857	0.00	0.00	0.00	2.41
3333	5373	6.096282	CGGGAAGTGGGAATGTTAAAATATGT	59.904	38.462	0.00	0.00	0.00	2.29
3378	5418	7.090319	TGCCCACCATATATGTTTAGAGATT	57.910	36.000	11.73	0.00	0.00	2.40
3379	5419	6.942005	TGCCCACCATATATGTTTAGAGATTG	59.058	38.462	11.73	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	107	1.141657	CCACCACCTATCACATCCCAG	59.858	57.143	0.00	0.00	0.00	4.45
134	140	1.967779	TGATGTGAAGTCGACCAAGGA	59.032	47.619	13.01	0.00	0.00	3.36
261	294	6.997904	GGAGGACCATGAAACAAGAGTGTTG	61.998	48.000	0.00	0.00	40.90	3.33
286	319	1.071471	ACTGGACAACGCCTCCAAG	59.929	57.895	0.00	0.00	37.36	3.61
289	322	1.823169	TACCACTGGACAACGCCTCC	61.823	60.000	0.71	0.00	0.00	4.30
298	331	2.298661	CCCCACCCTACCACTGGAC	61.299	68.421	0.71	0.00	0.00	4.02
374	409	2.678580	TCGTCTCCACCATCGCCA	60.679	61.111	0.00	0.00	0.00	5.69
404	439	1.092921	TAACGCCGGTGATGGATTGC	61.093	55.000	24.59	0.00	0.00	3.56
473	508	1.458398	CCATCGTTTGTACCATGCCA	58.542	50.000	0.00	0.00	0.00	4.92
540	575	4.681942	CGCATGTGTAGAATTAGCTACTCC	59.318	45.833	0.00	0.00	41.01	3.85
547	582	5.532557	TGAGGATCGCATGTGTAGAATTAG	58.467	41.667	6.09	0.00	38.61	1.73
556	591	1.607509	GGAGGATGAGGATCGCATGTG	60.608	57.143	0.00	0.00	38.61	3.21
557	592	0.683973	GGAGGATGAGGATCGCATGT	59.316	55.000	4.62	0.00	38.61	3.21
564	599	1.219213	AGAGAACGGGAGGATGAGGAT	59.781	52.381	0.00	0.00	0.00	3.24
614	650	2.102588	ACTCGACACAGGCTAAAACAGT	59.897	45.455	0.00	0.00	0.00	3.55
653	689	7.541783	CACATCCACAAACGAAAATATCAACAT	59.458	33.333	0.00	0.00	0.00	2.71
708	744	4.771590	ATTGAAGCATCACACACGAATT	57.228	36.364	0.00	0.00	34.61	2.17
711	747	4.566545	AAAATTGAAGCATCACACACGA	57.433	36.364	0.00	0.00	34.61	4.35
966	2832	4.202111	CGAGGATTTGGTTTGGTTTGACTT	60.202	41.667	0.00	0.00	0.00	3.01
1867	3822	5.196341	ACTCATTGACTACGTTCTGAACA	57.804	39.130	19.56	1.18	0.00	3.18
1869	3824	7.599171	TCATAACTCATTGACTACGTTCTGAA	58.401	34.615	0.00	0.00	0.00	3.02
1902	3864	2.955614	GCAATGAGATGCAGCAAAAGT	58.044	42.857	4.07	0.00	45.70	2.66
2024	4004	3.316029	CCATTGTGTCTGACTGCAAAGAA	59.684	43.478	17.24	1.12	0.00	2.52
2289	4278	4.284490	AGTTACAGATGGATCATGCGGTAT	59.716	41.667	0.00	0.00	0.00	2.73
2290	4279	3.641436	AGTTACAGATGGATCATGCGGTA	59.359	43.478	0.00	0.00	0.00	4.02
2362	4351	4.095483	GTGATCTCAAGCAACAAATCGGAT	59.905	41.667	0.00	0.00	0.00	4.18
2540	4532	2.668457	CTGTAGACACTGCAATTCGTCC	59.332	50.000	0.00	0.00	0.00	4.79
2674	4666	6.833839	TGTAAACATACAGCGAATTAACCAC	58.166	36.000	0.00	0.00	0.00	4.16
2740	4732	7.067494	ACAAGAAACTAAACAGCAAGATCTTGT	59.933	33.333	30.88	17.93	42.09	3.16
2837	4835	9.915629	AAATAACACTAGTCTCTCAAGTACTTG	57.084	33.333	26.60	26.60	41.71	3.16
2876	4874	3.310303	GCAAACTGCTGTCATATCGAC	57.690	47.619	0.00	0.00	40.96	4.20
2930	4945	5.733620	ATGCAGAGAAAATGAAACCACAT	57.266	34.783	0.00	0.00	0.00	3.21
3033	5048	1.452108	CCTTTGCCGTCCTGATCCC	60.452	63.158	0.00	0.00	0.00	3.85
3043	5058	3.689649	AGAACTACATTTAGCCTTTGCCG	59.310	43.478	0.00	0.00	38.69	5.69
3108	5137	1.133598	AGTCGATGCAATGTGCCATTG	59.866	47.619	18.26	18.26	44.23	2.82
3333	5373	7.047271	GGGCATTCCATTAAGCAAAGAATTAA	58.953	34.615	0.00	0.00	35.00	1.40
3378	5418	7.534723	AGAGTAACACCTACATAACTGTTCA	57.465	36.000	0.00	0.00	36.79	3.18
3379	5419	8.738106	AGTAGAGTAACACCTACATAACTGTTC	58.262	37.037	0.00	0.00	38.11	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.