AutoCloner

Multiple sequence alignment - TraesCS3A01G349300

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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	TraesCS3A01G349300	chr3A	100.000	2347	0	0	1	2347	597932661	597930315	0.000000e+00	4335.0
1	TraesCS3A01G349300	chr3A	80.441	363	44	14	7	350	597966947	597967301	3.870000e-63	252.0
2	TraesCS3A01G349300	chr3D	95.102	2001	88	6	354	2347	455721789	455719792	0.000000e+00	3144.0
3	TraesCS3A01G349300	chr3D	85.588	340	29	16	4	331	455722165	455721834	2.890000e-89	339.0
4	TraesCS3A01G349300	chr3D	80.061	326	45	15	7	319	455752391	455752709	8.440000e-55	224.0
5	TraesCS3A01G349300	chr3D	83.193	119	19	1	4	122	455752161	455752278	8.870000e-20	108.0
6	TraesCS3A01G349300	chr3D	91.111	45	1	3	6	50	419152862	419152821	9.060000e-05	58.4
7	TraesCS3A01G349300	chr3B	90.998	1744	118	15	357	2073	598996513	598994782	0.000000e+00	2314.0
8	TraesCS3A01G349300	chr3B	92.169	332	9	8	36	353	598996885	598996557	9.890000e-124	453.0
9	TraesCS3A01G349300	chr3B	80.165	363	45	17	7	353	599098693	599099044	1.800000e-61	246.0
10	TraesCS3A01G349300	chr3B	96.000	50	2	0	1	50	598998799	598998750	5.380000e-12	82.4
11	TraesCS3A01G349300	chr7D	84.831	178	20	6	357	531	568765650	568765477	3.100000e-39	172.0
12	TraesCS3A01G349300	chr5A	79.426	209	28	13	151	353	109934850	109935049	1.460000e-27	134.0
13	TraesCS3A01G349300	chr5A	80.992	121	21	1	6	124	495929736	495929616	6.900000e-16	95.3
14	TraesCS3A01G349300	chr5A	77.869	122	20	5	7	122	454707223	454707103	4.190000e-08	69.4
15	TraesCS3A01G349300	chr5A	100.000	28	0	0	1662	1689	8743543	8743516	4.000000e-03	52.8
16	TraesCS3A01G349300	chr6A	79.144	187	26	11	151	333	77606759	77606582	1.470000e-22	117.0
17	TraesCS3A01G349300	chr7B	89.362	94	7	3	151	243	86162776	86162685	5.300000e-22	115.0
18	TraesCS3A01G349300	chr2D	78.421	190	29	10	148	331	17017960	17017777	1.910000e-21	113.0
19	TraesCS3A01G349300	chr2D	79.630	108	18	4	1903	2007	495787395	495787289	9.000000e-10	75.0
20	TraesCS3A01G349300	chr2A	81.818	121	13	6	7	126	120720821	120720933	2.480000e-15	93.5
21	TraesCS3A01G349300	chrUn	84.706	85	12	1	2232	2316	88050965	88051048	1.490000e-12	84.2
22	TraesCS3A01G349300	chrUn	88.000	50	5	1	7	56	271275836	271275788	9.060000e-05	58.4
23	TraesCS3A01G349300	chrUn	88.000	50	5	1	7	56	310399445	310399493	9.060000e-05	58.4
24	TraesCS3A01G349300	chr2B	78.992	119	23	2	6	124	701356337	701356453	1.930000e-11	80.5

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	TraesCS3A01G349300	chr3A	597930315	597932661	2346	True	4335.0	4335	100.000000	1	2347	1	chr3A.!!$R1	2346
1	TraesCS3A01G349300	chr3D	455719792	455722165	2373	True	1741.5	3144	90.345000	4	2347	2	chr3D.!!$R2	2343
2	TraesCS3A01G349300	chr3B	598994782	598998799	4017	True	949.8	2314	93.055667	1	2073	3	chr3B.!!$R1	2072

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
909	2849	1.451567	CAGACCGTAGCTCCTCCGA	60.452	63.158	0.0	0.0	0.0	4.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1873	3833	0.03889	TGCCCGGTGATGGATTTTCA	59.961	50.0	0.0	0.0	0.0	2.69	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
388	2323	6.572119	GCAAATCAACTGACCCAAATATGTGA	60.572	38.462	0.00	0.0	0.00	3.58
391	2326	6.065976	TCAACTGACCCAAATATGTGATCT	57.934	37.500	0.00	0.0	0.00	2.75
804	2744	5.003804	AGGGACATGTTTGTGTTGACTATC	58.996	41.667	0.00	0.0	35.79	2.08
866	2806	2.515853	TGAGCCTCCTATTCTCTCTCCA	59.484	50.000	0.00	0.0	0.00	3.86
867	2807	3.052566	TGAGCCTCCTATTCTCTCTCCAA	60.053	47.826	0.00	0.0	0.00	3.53
908	2848	3.111939	CAGACCGTAGCTCCTCCG	58.888	66.667	0.00	0.0	0.00	4.63
909	2849	1.451567	CAGACCGTAGCTCCTCCGA	60.452	63.158	0.00	0.0	0.00	4.55
910	2850	1.451747	AGACCGTAGCTCCTCCGAC	60.452	63.158	0.00	0.0	0.00	4.79
950	2890	1.920835	AGGAGGAGCCTCACCAACC	60.921	63.158	17.68	0.5	46.97	3.77
1146	3086	7.691877	GCACGTTTCTTTCAATTTTCATTGTTT	59.308	29.630	0.00	0.0	40.78	2.83
1400	3340	2.800581	CTCGTCTCCTCGTCCGTCG	61.801	68.421	0.00	0.0	41.41	5.12
1436	3377	0.250640	CACCTCCACTTGAGCAGCTT	60.251	55.000	0.00	0.0	39.98	3.74
1454	3395	0.037697	TTCAGCCTGCGACGTTGTAT	60.038	50.000	4.37	0.0	0.00	2.29
1532	3473	2.582493	CCCTTTTGGCCCGCATTGT	61.582	57.895	0.00	0.0	38.58	2.71
1547	3488	7.225734	GGCCCGCATTGTTGTTTATTTTATAAT	59.774	33.333	0.00	0.0	0.00	1.28
1548	3489	8.061268	GCCCGCATTGTTGTTTATTTTATAATG	58.939	33.333	0.00	0.0	0.00	1.90
1549	3490	8.547069	CCCGCATTGTTGTTTATTTTATAATGG	58.453	33.333	0.00	0.0	0.00	3.16
1550	3491	8.061268	CCGCATTGTTGTTTATTTTATAATGGC	58.939	33.333	0.00	0.0	0.00	4.40
1551	3492	8.598924	CGCATTGTTGTTTATTTTATAATGGCA	58.401	29.630	0.00	0.0	0.00	4.92
1620	3562	0.755686	TTGGCATGTTTGAACCACCC	59.244	50.000	0.00	0.0	0.00	4.61
1624	3566	1.963515	GCATGTTTGAACCACCCTCTT	59.036	47.619	0.00	0.0	0.00	2.85
1752	3712	1.541147	CACGGCACAACCAAAGATGAT	59.459	47.619	0.00	0.0	39.03	2.45
1763	3723	5.329035	ACCAAAGATGATGTAAACATGGC	57.671	39.130	0.00	0.0	36.57	4.40
1829	3789	5.231568	GCTACAACACATAGCTAAACTACCG	59.768	44.000	0.00	0.0	41.59	4.02
1873	3833	3.244911	ACCGAAATGATGTCCCAAGTCTT	60.245	43.478	0.00	0.0	0.00	3.01
2009	3973	1.842381	AAGAGGGGCACGGAGAAAGG	61.842	60.000	0.00	0.0	0.00	3.11
2010	3974	2.529389	AGGGGCACGGAGAAAGGT	60.529	61.111	0.00	0.0	0.00	3.50
2019	3983	1.343465	ACGGAGAAAGGTCGTGACAAT	59.657	47.619	2.00	0.0	35.70	2.71
2084	4048	3.682292	AAGAACCTCGCCGCCATCC	62.682	63.158	0.00	0.0	0.00	3.51
2159	4123	2.201022	AGGTCGTGACAACGCCTCT	61.201	57.895	2.00	0.0	46.47	3.69
2184	4148	1.080093	GGGAACGACGCTGACATCA	60.080	57.895	0.00	0.0	0.00	3.07
2196	4160	1.226888	GACATCACCGCCGTCCTAC	60.227	63.158	0.00	0.0	0.00	3.18
2207	4171	1.138247	CGTCCTACCCGAAGAACCG	59.862	63.158	0.00	0.0	0.00	4.44
2283	4247	2.334023	AGAGGAGCACAGAGAAAGGTT	58.666	47.619	0.00	0.0	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	1940	9.921637	TTCATTCCTCGCAATAAAAACTTATTT	57.078	25.926	0.00	0.00	0.00	1.40
69	1947	9.311916	CCATTAATTCATTCCTCGCAATAAAAA	57.688	29.630	0.00	0.00	0.00	1.94
81	1959	9.846248	GTCATACTAATGCCATTAATTCATTCC	57.154	33.333	13.18	0.00	33.13	3.01
207	2096	9.791801	ATACACACAAATACCATGCAATATCTA	57.208	29.630	0.00	0.00	0.00	1.98
388	2323	1.963515	GGGCTGGTGTTTTTGACAGAT	59.036	47.619	0.00	0.00	39.39	2.90
391	2326	1.561643	TTGGGCTGGTGTTTTTGACA	58.438	45.000	0.00	0.00	35.42	3.58
449	2385	6.438763	CCGTAGATTTTGGCTTTCATATTCC	58.561	40.000	0.00	0.00	0.00	3.01
804	2744	0.682855	TAAGCCGGGCCATTTCAAGG	60.683	55.000	17.02	0.00	0.00	3.61
866	2806	6.041069	GCATATATATCGAGGTCCTAAGGCTT	59.959	42.308	4.58	4.58	0.00	4.35
867	2807	5.536916	GCATATATATCGAGGTCCTAAGGCT	59.463	44.000	0.00	0.00	0.00	4.58
908	2848	3.296322	TTTGGTCAATTGGCATTCGTC	57.704	42.857	12.93	0.00	0.00	4.20
909	2849	3.742433	TTTTGGTCAATTGGCATTCGT	57.258	38.095	12.93	0.00	0.00	3.85
910	2850	5.291614	CCTTATTTTGGTCAATTGGCATTCG	59.708	40.000	12.93	0.00	0.00	3.34
950	2890	0.895559	GTCCTGTTTGGGCCTCCTTG	60.896	60.000	4.53	0.00	33.37	3.61
1057	2997	2.690778	GGCGGCGCTCACTTGAAAT	61.691	57.895	32.30	0.00	0.00	2.17
1118	3058	5.694674	TGAAAATTGAAAGAAACGTGCAC	57.305	34.783	6.82	6.82	0.00	4.57
1123	3063	8.997960	CCAAAACAATGAAAATTGAAAGAAACG	58.002	29.630	5.49	0.00	35.60	3.60
1146	3086	0.032403	GCAAGCAATCACACAGCCAA	59.968	50.000	0.00	0.00	0.00	4.52
1400	3340	1.007734	TGCTCAACTGACGACGACC	60.008	57.895	0.00	0.00	0.00	4.79
1436	3377	0.457853	GATACAACGTCGCAGGCTGA	60.458	55.000	20.86	0.00	0.00	4.26
1454	3395	4.081862	ACACATAGCTAAGCCGTAACTTGA	60.082	41.667	0.00	0.00	0.00	3.02
1547	3488	4.261238	CCAATACGTACTTGTGTTTTGCCA	60.261	41.667	0.00	0.00	0.00	4.92
1548	3489	4.223659	CCAATACGTACTTGTGTTTTGCC	58.776	43.478	0.00	0.00	0.00	4.52
1549	3490	4.851010	ACCAATACGTACTTGTGTTTTGC	58.149	39.130	0.00	0.00	0.00	3.68
1550	3491	7.909121	TGTAAACCAATACGTACTTGTGTTTTG	59.091	33.333	22.66	13.56	33.31	2.44
1551	3492	7.983307	TGTAAACCAATACGTACTTGTGTTTT	58.017	30.769	22.66	16.81	33.31	2.43
1552	3493	7.551035	TGTAAACCAATACGTACTTGTGTTT	57.449	32.000	22.02	22.02	34.44	2.83
1599	3541	2.224499	GGGTGGTTCAAACATGCCAAAT	60.224	45.455	0.00	0.00	32.26	2.32
1620	3562	8.866956	GCCAGAAATAACAATTGAATCAAAGAG	58.133	33.333	13.59	0.00	0.00	2.85
1624	3566	7.549842	CCATGCCAGAAATAACAATTGAATCAA	59.450	33.333	13.59	0.00	0.00	2.57
1752	3712	0.390603	CTCCGGACGCCATGTTTACA	60.391	55.000	0.00	0.00	0.00	2.41
1763	3723	3.186817	GTCATGTATCTCTACTCCGGACG	59.813	52.174	0.00	0.00	0.00	4.79
1829	3789	1.876156	CAGGTTGCTTCTCTTGGTCAC	59.124	52.381	0.00	0.00	0.00	3.67
1873	3833	0.038890	TGCCCGGTGATGGATTTTCA	59.961	50.000	0.00	0.00	0.00	2.69
2009	3973	2.076100	TCATGAAGGCATTGTCACGAC	58.924	47.619	0.00	0.00	30.68	4.34
2010	3974	2.470983	TCATGAAGGCATTGTCACGA	57.529	45.000	0.00	0.00	30.68	4.35
2054	4018	2.029828	CGAGGTTCTTCGGATAGGATGG	60.030	54.545	0.00	0.00	36.95	3.51
2159	4123	0.174845	CAGCGTCGTTCCCCTTCATA	59.825	55.000	0.00	0.00	0.00	2.15
2207	4171	0.394352	AAATCAGATGGCGGTGACCC	60.394	55.000	0.00	0.00	0.00	4.46
2272	4236	2.023673	TGTTGCCACAACCTTTCTCTG	58.976	47.619	7.91	0.00	0.00	3.35
2283	4247	0.257328	TTCTTGGAGGTGTTGCCACA	59.743	50.000	0.00	0.00	43.71	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.