AutoCloner

Multiple sequence alignment - TraesCS6A01G176200

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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	TraesCS6A01G176200	chr6A	100.000	2930	0	0	1	2930	192831844	192828915	0.000000e+00	5411.0
1	TraesCS6A01G176200	chr6A	97.500	40	0	1	2288	2326	192829501	192829462	1.880000e-07	67.6
2	TraesCS6A01G176200	chr6A	97.500	40	0	1	2344	2383	192829557	192829519	1.880000e-07	67.6
3	TraesCS6A01G176200	chr6B	96.467	2236	66	11	617	2846	275925156	275927384	0.000000e+00	3679.0
4	TraesCS6A01G176200	chr6B	89.706	204	19	2	1	204	275922451	275922652	2.900000e-65	259.0
5	TraesCS6A01G176200	chr6B	91.329	173	10	2	263	431	275923891	275924062	6.310000e-57	231.0
6	TraesCS6A01G176200	chr6B	91.176	102	6	3	519	620	275924932	275925030	5.090000e-28	135.0
7	TraesCS6A01G176200	chr6B	97.500	40	1	0	2287	2326	275926880	275926919	5.240000e-08	69.4
8	TraesCS6A01G176200	chr6D	97.512	1728	33	6	617	2335	151506646	151508372	0.000000e+00	2944.0
9	TraesCS6A01G176200	chr6D	94.701	585	29	2	2344	2927	151508324	151508907	0.000000e+00	907.0
10	TraesCS6A01G176200	chr6D	92.834	628	31	6	1	620	151505885	151506506	0.000000e+00	898.0
11	TraesCS6A01G176200	chr6D	91.837	98	7	1	2834	2930	200382181	200382084	5.090000e-28	135.0
12	TraesCS6A01G176200	chr3A	94.681	94	4	1	2835	2927	10313751	10313844	8.460000e-31	145.0
13	TraesCS6A01G176200	chr7D	91.837	98	7	1	2834	2930	346011372	346011275	5.090000e-28	135.0
14	TraesCS6A01G176200	chr2A	90.816	98	8	1	2834	2930	560829680	560829583	2.370000e-26	130.0
15	TraesCS6A01G176200	chr5B	88.462	104	10	2	2828	2930	390539676	390539778	1.100000e-24	124.0
16	TraesCS6A01G176200	chr1D	89.109	101	10	1	2831	2930	296733969	296733869	1.100000e-24	124.0
17	TraesCS6A01G176200	chr3D	89.691	97	9	1	2835	2930	228918718	228918622	3.970000e-24	122.0
18	TraesCS6A01G176200	chr5A	87.629	97	12	0	2834	2930	670608940	670608844	2.390000e-21	113.0

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	TraesCS6A01G176200	chr6A	192828915	192831844	2929	True	1848.733333	5411	98.333333	1	2930	3	chr6A.!!$R1	2929
1	TraesCS6A01G176200	chr6B	275922451	275927384	4933	False	874.680000	3679	93.235600	1	2846	5	chr6B.!!$F1	2845
2	TraesCS6A01G176200	chr6D	151505885	151508907	3022	False	1583.000000	2944	95.015667	1	2927	3	chr6D.!!$F1	2926

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
82	83	0.110295	ATTGCAGGCCACACACTACA	59.890	50.000	5.01	0.00	0.00	2.74	F
609	2616	1.202371	ACACACACTCGATCGTGTTGT	60.202	47.619	19.39	20.63	45.27	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	4027	0.253044	GGTTCCATCTGTAGCTGGCA	59.747	55.000	0.0	0.0	31.68	4.92	R
2060	4217	1.065199	ACAATCCTGATGCGGACATGT	60.065	47.619	0.0	0.0	36.35	3.21	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
25	26	3.514706	TGGAACCAACTATTAGGCGTGTA	59.485	43.478	0.00	0.00	0.00	2.90
82	83	0.110295	ATTGCAGGCCACACACTACA	59.890	50.000	5.01	0.00	0.00	2.74
138	139	7.831691	TCTTTGGATGAGGTATTTGTGAAAA	57.168	32.000	0.00	0.00	0.00	2.29
145	146	6.142818	TGAGGTATTTGTGAAAACCAAGTG	57.857	37.500	0.00	0.00	34.29	3.16
153	154	2.098614	TGAAAACCAAGTGCTGCTTCA	58.901	42.857	0.00	0.00	34.69	3.02
154	155	2.159254	TGAAAACCAAGTGCTGCTTCAC	60.159	45.455	0.00	1.44	34.69	3.18
288	1488	7.420002	CACTCAGTTTTGATCATTGAGAACAA	58.580	34.615	22.94	2.12	38.81	2.83
483	1691	6.557291	AGAGAGCAAGCATAATTATTCTGC	57.443	37.500	7.14	7.14	36.15	4.26
486	1694	3.885297	AGCAAGCATAATTATTCTGCCGT	59.115	39.130	10.93	0.00	36.56	5.68
488	1696	4.023707	GCAAGCATAATTATTCTGCCGTCT	60.024	41.667	10.93	0.00	36.56	4.18
503	1711	2.613223	GCCGTCTCTTATTGGATAGGCC	60.613	54.545	0.00	0.00	34.49	5.19
609	2616	1.202371	ACACACACTCGATCGTGTTGT	60.202	47.619	19.39	20.63	45.27	3.32
765	2915	3.402110	TCCTTGCCGCAATATCATACTG	58.598	45.455	6.19	0.00	0.00	2.74
808	2958	5.812127	CCTTGCTTAATAATTTGCCAGTTCC	59.188	40.000	0.00	0.00	0.00	3.62
821	2971	1.571457	CCAGTTCCTCTCCTCCCTCTA	59.429	57.143	0.00	0.00	0.00	2.43
840	2990	5.304871	CCTCTACTCCCACTTATTTACTCCC	59.695	48.000	0.00	0.00	0.00	4.30
896	3046	2.047274	CGTCGTCCCTTGCCACAT	60.047	61.111	0.00	0.00	0.00	3.21
946	3098	4.082733	AGGCGGAATAAAGAAAAGCAAGAC	60.083	41.667	0.00	0.00	0.00	3.01
1578	3730	4.947147	GCACCACCGGAAGCCACA	62.947	66.667	9.46	0.00	0.00	4.17
1875	4027	4.093291	CAGCTCCCGCCTGAAGCT	62.093	66.667	0.00	0.00	40.39	3.74
2205	4362	6.795399	TCTTCCTTTTGTTTCTCATGTTCAC	58.205	36.000	0.00	0.00	0.00	3.18
2242	4399	1.078497	TGCCACCGCATAGACTTGG	60.078	57.895	0.00	0.00	41.12	3.61
2333	4490	2.237643	GGGTTGTTTGGTTCCTTGGTTT	59.762	45.455	0.00	0.00	0.00	3.27
2334	4491	3.266636	GGTTGTTTGGTTCCTTGGTTTG	58.733	45.455	0.00	0.00	0.00	2.93
2343	4500	3.576550	GGTTCCTTGGTTTGCAGGATTTA	59.423	43.478	0.00	0.00	39.05	1.40
2346	4503	5.467035	TCCTTGGTTTGCAGGATTTAAAG	57.533	39.130	0.00	0.00	33.99	1.85
2384	4541	4.135747	CAACTTGGGTTGTTTGGTTCAT	57.864	40.909	0.00	0.00	45.42	2.57
2574	4731	7.168135	GCGTTTTCTTTGAAACTGAGATCAAAT	59.832	33.333	14.82	0.00	42.72	2.32
2736	4893	8.877864	TCCACTTACCTAAAAACATCATTCAT	57.122	30.769	0.00	0.00	0.00	2.57
2789	4946	3.254166	TCCTAGACAGTACGACAACCAAC	59.746	47.826	0.00	0.00	0.00	3.77
2899	5058	3.117776	TCCACCAAGGGAGATGATGAATG	60.118	47.826	0.00	0.00	38.24	2.67
2913	5072	7.879070	AGATGATGAATGGTGGAATTAATTCG	58.121	34.615	19.41	0.00	37.67	3.34
2927	5086	7.596995	TGGAATTAATTCGGTAGTTTGCAAAAG	59.403	33.333	14.67	3.68	37.67	2.27
2928	5087	7.597369	GGAATTAATTCGGTAGTTTGCAAAAGT	59.403	33.333	14.67	6.99	37.67	2.66
2929	5088	9.615295	GAATTAATTCGGTAGTTTGCAAAAGTA	57.385	29.630	14.67	5.93	0.00	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	1.892474	GTGGCCTGCAATTTACCTTCA	59.108	47.619	3.32	0.00	0.00	3.02
58	59	0.965439	TGTGTGGCCTGCAATTTACC	59.035	50.000	3.32	0.00	0.00	2.85
61	62	1.613437	GTAGTGTGTGGCCTGCAATTT	59.387	47.619	3.32	0.00	0.00	1.82
111	112	8.421249	TTCACAAATACCTCATCCAAAGATTT	57.579	30.769	0.00	0.00	0.00	2.17
114	115	7.255801	GGTTTTCACAAATACCTCATCCAAAGA	60.256	37.037	0.00	0.00	0.00	2.52
145	146	5.979517	ACAGTTTAAATTGAAGTGAAGCAGC	59.020	36.000	16.68	0.00	32.93	5.25
153	154	8.751302	AACGTTTTGACAGTTTAAATTGAAGT	57.249	26.923	16.68	0.87	0.00	3.01
251	252	7.849804	TCAAAACTGAGTGCCTTATCTAATC	57.150	36.000	0.00	0.00	0.00	1.75
264	1464	7.572523	TTGTTCTCAATGATCAAAACTGAGT	57.427	32.000	18.99	0.00	35.93	3.41
267	1467	8.133627	ACTCTTTGTTCTCAATGATCAAAACTG	58.866	33.333	0.00	0.00	41.21	3.16
288	1488	2.569134	GTCGAGCCGCTGACTCTT	59.431	61.111	0.00	0.00	32.37	2.85
340	1540	6.374333	TGTCCTACCTGACAAATTTTATCAGC	59.626	38.462	18.15	8.49	42.06	4.26
341	1541	7.921786	TGTCCTACCTGACAAATTTTATCAG	57.078	36.000	17.17	17.17	42.06	2.90
483	1691	2.632996	TGGCCTATCCAATAAGAGACGG	59.367	50.000	3.32	0.00	43.21	4.79
579	2582	2.563620	TCGAGTGTGTGTTTAGGGCATA	59.436	45.455	0.00	0.00	0.00	3.14
609	2616	1.226745	CCACCGCGCGTCTTGTATA	60.227	57.895	29.95	0.00	0.00	1.47
773	2923	1.247567	TAAGCAAGGAAAGCTGTGGC	58.752	50.000	0.00	0.00	42.53	5.01
808	2958	1.133606	GTGGGAGTAGAGGGAGGAGAG	60.134	61.905	0.00	0.00	0.00	3.20
821	2971	3.120898	GGGGGAGTAAATAAGTGGGAGT	58.879	50.000	0.00	0.00	0.00	3.85
840	2990	0.597377	GTGGCAACGAAAGCAAAGGG	60.597	55.000	0.00	0.00	42.51	3.95
896	3046	7.962995	ATCTTATCTACAGACAAACCTCTCA	57.037	36.000	0.00	0.00	0.00	3.27
946	3098	1.067985	TGCTCAGCTCTCTCTCGTTTG	60.068	52.381	0.00	0.00	0.00	2.93
983	3135	0.315568	CATGCTCCCGACCTAGCTAC	59.684	60.000	0.00	0.00	39.53	3.58
1251	3403	4.847516	CGGCGCGATCCGTTCTCA	62.848	66.667	12.10	0.00	44.18	3.27
1578	3730	1.078710	AAGGTAGACGGTGAGCCCT	59.921	57.895	0.00	0.00	0.00	5.19
1875	4027	0.253044	GGTTCCATCTGTAGCTGGCA	59.747	55.000	0.00	0.00	31.68	4.92
1879	4031	1.207791	CCTGGGTTCCATCTGTAGCT	58.792	55.000	0.00	0.00	30.82	3.32
2060	4217	1.065199	ACAATCCTGATGCGGACATGT	60.065	47.619	0.00	0.00	36.35	3.21
2126	4283	7.013178	TGCAAAATCAGTTATGAGACACAAGAA	59.987	33.333	0.00	0.00	39.29	2.52
2205	4362	4.122776	GGCACAGGTTGATGACTAGTATG	58.877	47.826	0.00	0.00	0.00	2.39
2234	4391	8.160765	TGGATTGTTCAAGATTAACCAAGTCTA	58.839	33.333	0.00	0.00	0.00	2.59
2237	4394	7.781324	ATGGATTGTTCAAGATTAACCAAGT	57.219	32.000	0.00	0.00	0.00	3.16
2333	4490	6.647334	TTCATGTGTTCTTTAAATCCTGCA	57.353	33.333	0.00	0.00	0.00	4.41
2334	4491	8.031277	AGAATTCATGTGTTCTTTAAATCCTGC	58.969	33.333	8.44	0.00	30.84	4.85
2343	4500	9.903682	CAAGTTGATAGAATTCATGTGTTCTTT	57.096	29.630	16.49	11.10	36.23	2.52
2346	4503	7.094205	ACCCAAGTTGATAGAATTCATGTGTTC	60.094	37.037	8.44	0.00	0.00	3.18
2420	4577	5.275067	TGTGCTTGAACTTTAATTTGGCT	57.725	34.783	0.00	0.00	0.00	4.75
2434	4591	8.791675	TCTAACAATACATTTTCATGTGCTTGA	58.208	29.630	14.45	0.00	43.92	3.02
2438	4595	9.793252	AGAATCTAACAATACATTTTCATGTGC	57.207	29.630	0.00	0.00	43.92	4.57
2574	4731	6.591001	CAAAGGAAAAAGGGAGGAAATTTCA	58.409	36.000	19.49	0.00	32.91	2.69
2666	4823	2.834113	TCAAAGGAGAAGTAGAGGGGG	58.166	52.381	0.00	0.00	0.00	5.40
2789	4946	5.469373	TGCGCTTACATATCAAAAGTCAG	57.531	39.130	9.73	0.00	0.00	3.51
2879	5038	3.220110	CCATTCATCATCTCCCTTGGTG	58.780	50.000	0.00	0.00	0.00	4.17
2893	5052	7.060421	ACTACCGAATTAATTCCACCATTCAT	58.940	34.615	20.01	1.39	33.28	2.57
2899	5058	5.106078	TGCAAACTACCGAATTAATTCCACC	60.106	40.000	20.01	0.00	33.28	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.