AutoCloner

Multiple sequence alignment - TraesCS1A01G309000

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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	TraesCS1A01G309000	chr1A	100.000	3292	0	0	1	3292	499810214	499806923	0.000000e+00	6080.0
1	TraesCS1A01G309000	chr1A	82.945	1331	135	46	507	1802	499928221	499926948	0.000000e+00	1116.0
2	TraesCS1A01G309000	chr1A	84.028	576	35	21	1985	2530	499926844	499926296	4.900000e-138	501.0
3	TraesCS1A01G309000	chr1A	89.835	364	22	3	1	351	499929135	499928774	1.390000e-123	453.0
4	TraesCS1A01G309000	chr1A	81.818	121	20	2	2752	2871	499929974	499929855	2.090000e-17	100.0
5	TraesCS1A01G309000	chr1B	88.982	1788	102	33	55	1793	543582208	543580467	0.000000e+00	2122.0
6	TraesCS1A01G309000	chr1B	84.540	1119	104	32	706	1793	543741404	543740324	0.000000e+00	1044.0
7	TraesCS1A01G309000	chr1B	90.117	597	26	6	1931	2519	543580420	543579849	0.000000e+00	745.0
8	TraesCS1A01G309000	chr1B	88.270	503	30	10	1933	2409	543740279	543739780	2.850000e-160	575.0
9	TraesCS1A01G309000	chr1B	87.066	317	22	7	7	307	543742258	543741945	1.130000e-89	340.0
10	TraesCS1A01G309000	chr1B	88.000	125	14	1	375	498	543741897	543741773	2.650000e-31	147.0
11	TraesCS1A01G309000	chr1B	96.774	62	2	0	1	62	543584047	543583986	1.620000e-18	104.0
12	TraesCS1A01G309000	chr1B	80.992	121	21	2	2752	2871	543743130	543743011	9.720000e-16	95.3
13	TraesCS1A01G309000	chr1B	100.000	28	0	0	858	885	543741304	543741277	6.000000e-03	52.8
14	TraesCS1A01G309000	chr1D	85.072	1380	103	47	502	1830	404261588	404260261	0.000000e+00	1312.0
15	TraesCS1A01G309000	chr1D	83.893	1341	103	48	501	1793	404240554	404239279	0.000000e+00	1175.0
16	TraesCS1A01G309000	chr1D	90.559	572	25	10	1932	2481	404239232	404238668	0.000000e+00	730.0
17	TraesCS1A01G309000	chr1D	88.798	491	36	7	3	477	404262185	404261698	4.730000e-163	584.0
18	TraesCS1A01G309000	chr1D	87.857	420	25	8	1947	2353	404260255	404259849	1.380000e-128	470.0
19	TraesCS1A01G309000	chr1D	91.949	236	18	1	71	305	404241173	404240938	2.450000e-86	329.0
20	TraesCS1A01G309000	chr1D	91.071	56	5	0	2556	2611	404259771	404259716	3.520000e-10	76.8

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	TraesCS1A01G309000	chr1A	499806923	499810214	3291	True	6080.000000	6080	100.000000	1	3292	1	chr1A.!!$R1	3291
1	TraesCS1A01G309000	chr1A	499926296	499929974	3678	True	542.500000	1116	84.656500	1	2871	4	chr1A.!!$R2	2870
2	TraesCS1A01G309000	chr1B	543579849	543584047	4198	True	990.333333	2122	91.957667	1	2519	3	chr1B.!!$R1	2518
3	TraesCS1A01G309000	chr1B	543739780	543743130	3350	True	375.683333	1044	88.144667	7	2871	6	chr1B.!!$R2	2864
4	TraesCS1A01G309000	chr1D	404238668	404241173	2505	True	744.666667	1175	88.800333	71	2481	3	chr1D.!!$R1	2410
5	TraesCS1A01G309000	chr1D	404259716	404262185	2469	True	610.700000	1312	88.199500	3	2611	4	chr1D.!!$R2	2608

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
941	4395	0.030504	CATGCCGCAGTGTTGACAAA	59.969	50.0	0.0	0.0	0.0	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2829	6493	0.109086	GCGTGCTCTGTCTCTTGCTA	60.109	55.0	0.0	0.0	0.0	3.49	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
25	892	4.961730	TGTCCCCCAATTTTAGAATCCATG	59.038	41.667	0.00	0.00	0.00	3.66
62	929	8.446273	CACTCTGCTTATATGGCATAAATGTAC	58.554	37.037	11.86	0.49	39.07	2.90
110	2775	2.624838	GCCATGCTATAAATGCACCAGT	59.375	45.455	0.00	0.00	43.59	4.00
307	2977	4.559153	GATGATGTGTGGGTTGAAAAAGG	58.441	43.478	0.00	0.00	0.00	3.11
460	3565	5.048507	GGACAGAAATATAACTCCACGACC	58.951	45.833	0.00	0.00	0.00	4.79
488	3627	3.435566	TCTACTATTCGCACGAGCAAAG	58.564	45.455	5.50	0.00	42.27	2.77
540	3872	3.119602	AGCTTCAGACGCGTTGTAAGATA	60.120	43.478	23.86	4.22	0.00	1.98
541	3873	3.000971	GCTTCAGACGCGTTGTAAGATAC	60.001	47.826	23.86	6.63	0.00	2.24
542	3874	4.413087	CTTCAGACGCGTTGTAAGATACT	58.587	43.478	15.53	0.00	0.00	2.12
576	3909	4.110036	TCACATATGACTCGACAACAGG	57.890	45.455	10.38	0.00	0.00	4.00
610	3944	7.765360	TGCAATCCAATATTGTCCAAGATTTTC	59.235	33.333	14.25	9.34	30.64	2.29
674	4023	7.906010	GCATGACGACACAGAGTATATATAGTC	59.094	40.741	16.80	16.80	33.81	2.59
727	4172	9.701098	ATAATGCATAATGGATGTGATCAAAAC	57.299	29.630	0.00	0.00	37.90	2.43
801	4246	1.950909	CAAGTTAAACCGGCAGTTCCA	59.049	47.619	0.00	0.00	37.88	3.53
805	4250	0.321298	TAAACCGGCAGTTCCAGAGC	60.321	55.000	0.00	0.00	37.88	4.09
941	4395	0.030504	CATGCCGCAGTGTTGACAAA	59.969	50.000	0.00	0.00	0.00	2.83
967	4432	1.071567	GAGTAGGAGTTCACACGCGC	61.072	60.000	5.73	0.00	0.00	6.86
1053	4518	0.321346	TCATCCAAAGCACAGCTCGA	59.679	50.000	0.00	0.00	38.25	4.04
1170	4674	2.126071	CGTCTTCATGGCGGTCGT	60.126	61.111	0.00	0.00	40.56	4.34
1187	4691	2.743538	TGACGACCATGCTGCTGC	60.744	61.111	8.89	8.89	40.20	5.25
1272	4776	4.063967	CCCTGACGGTGCGCTGTA	62.064	66.667	12.68	0.13	33.67	2.74
1404	4920	0.174845	TCCATACTGCTTCCGTTCCG	59.825	55.000	0.00	0.00	0.00	4.30
1409	4925	1.210931	CTGCTTCCGTTCCGTCGTA	59.789	57.895	0.00	0.00	0.00	3.43
1410	4926	0.179145	CTGCTTCCGTTCCGTCGTAT	60.179	55.000	0.00	0.00	0.00	3.06
1475	5021	2.270352	AATCGGCTTTGTGAACCTGA	57.730	45.000	0.00	0.00	0.00	3.86

Showing 1 to 25 of 581 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	892	8.348507	CCATATAAGCAGAGTGATTTTCTTTCC	58.651	37.037	0.00	0.00	0.00	3.13
62	929	5.873712	AGTGAGATGTTTGTCTGCTTAGATG	59.126	40.000	0.00	0.00	0.00	2.90
110	2775	5.128827	GGATACTCTTGATGTCCTACAACCA	59.871	44.000	0.00	0.00	0.00	3.67
307	2977	9.823098	GTGTGATGAGATAAGATTTGCATTATC	57.177	33.333	8.98	8.98	38.24	1.75
382	3325	7.571080	TTTCTTTTCTACGGTACCAAACATT	57.429	32.000	13.54	0.00	0.00	2.71
388	3331	6.222389	TCGAAATTTCTTTTCTACGGTACCA	58.778	36.000	13.54	0.00	41.37	3.25
460	3565	6.143919	TGCTCGTGCGAATAGTAGATTTAATG	59.856	38.462	4.84	0.00	43.34	1.90
468	3573	3.435566	TCTTTGCTCGTGCGAATAGTAG	58.564	45.455	12.27	1.28	41.31	2.57
488	3627	5.005012	GCAATGTCATGTGTGCATACATTTC	59.995	40.000	24.63	19.42	39.17	2.17
576	3909	9.545105	TGGACAATATTGGATTGCAAAATATTC	57.455	29.630	19.37	11.94	35.37	1.75
674	4023	7.572724	GCATAGCAGCTTTTGGACAGATATTAG	60.573	40.741	0.00	0.00	0.00	1.73
765	4210	7.254353	GGTTTAACTTGGACTTATCGTCTATGC	60.254	40.741	0.00	0.00	42.44	3.14
801	4246	0.106015	AGTTGGCCACCTTTTGCTCT	60.106	50.000	3.88	0.00	0.00	4.09
805	4250	4.756630	GCAGTTGGCCACCTTTTG	57.243	55.556	3.88	0.31	36.11	2.44
917	4365	2.268076	AACACTGCGGCATGGGAAC	61.268	57.895	1.75	0.00	0.00	3.62
941	4395	2.110188	TGTGAACTCCTACTCCACCTCT	59.890	50.000	0.00	0.00	0.00	3.69
986	4451	2.185663	TTATAGGGGAAGGAAGGCGT	57.814	50.000	0.00	0.00	0.00	5.68
1053	4518	3.119990	CGGTGTTGTGACTTGTGAACTTT	60.120	43.478	0.00	0.00	0.00	2.66
1264	4768	0.679505	GGATCCAGGTATACAGCGCA	59.320	55.000	11.47	0.00	0.00	6.09
1271	4775	1.164313	ACCTCCGGGATCCAGGTATA	58.836	55.000	27.68	10.39	38.86	1.47
1272	4776	0.471971	CACCTCCGGGATCCAGGTAT	60.472	60.000	27.68	13.41	38.57	2.73
1293	4806	4.982701	ACCAGTTGCTGCAGGGGC	62.983	66.667	17.12	2.02	41.68	5.80
1409	4925	6.426937	CCCGTATTGAAAATCGGATGAAGTAT	59.573	38.462	4.00	0.00	44.86	2.12
1410	4926	5.756347	CCCGTATTGAAAATCGGATGAAGTA	59.244	40.000	4.00	0.00	44.86	2.24
1604	5160	9.851686	TGTTCATTAGATGCCATAAGAGTTTAT	57.148	29.630	0.00	0.00	0.00	1.40

Showing 1 to 25 of 530 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.