AutoCloner

Multiple sequence alignment - TraesCS3D01G183200

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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	TraesCS3D01G183200	chr3D	100.000	3059	0	0	1	3059	167792489	167789431	0.000000e+00	5650.0
1	TraesCS3D01G183200	chr3B	94.694	2431	87	19	664	3059	242887954	242885531	0.000000e+00	3736.0
2	TraesCS3D01G183200	chr3B	94.562	662	27	9	1	659	242890234	242889579	0.000000e+00	1014.0
3	TraesCS3D01G183200	chr3A	92.769	1867	96	24	398	2246	201474549	201476394	0.000000e+00	2663.0
4	TraesCS3D01G183200	chr3A	93.447	702	33	5	1	699	201473737	201474428	0.000000e+00	1029.0
5	TraesCS3D01G183200	chr3A	92.153	497	27	5	2561	3053	201478580	201479068	0.000000e+00	691.0
6	TraesCS3D01G183200	chr3A	94.783	115	5	1	2318	2432	201478406	201478519	8.720000e-41	178.0
7	TraesCS3D01G183200	chr3A	100.000	33	0	0	2440	2472	201478549	201478581	9.160000e-06	62.1
8	TraesCS3D01G183200	chr5B	80.198	303	49	8	382	674	588793344	588793043	1.850000e-52	217.0
9	TraesCS3D01G183200	chr5B	78.431	306	49	14	382	671	586912696	586913000	1.870000e-42	183.0
10	TraesCS3D01G183200	chr6A	80.667	300	37	11	381	671	432533241	432532954	2.390000e-51	213.0
11	TraesCS3D01G183200	chr6A	77.961	304	50	13	381	671	53063731	53063432	1.130000e-39	174.0
12	TraesCS3D01G183200	chr1A	79.934	304	46	8	381	671	507075716	507075415	3.090000e-50	209.0
13	TraesCS3D01G183200	chr7D	79.181	293	36	14	308	575	34003595	34003887	2.420000e-41	180.0
14	TraesCS3D01G183200	chr7D	88.060	67	8	0	297	363	625348674	625348608	2.530000e-11	80.5
15	TraesCS3D01G183200	chr1D	78.445	283	50	10	399	671	316617514	316617233	1.130000e-39	174.0
16	TraesCS3D01G183200	chr4D	80.081	246	32	13	383	616	401094018	401093778	1.890000e-37	167.0
17	TraesCS3D01G183200	chr5D	78.000	250	28	13	308	534	487837764	487837519	6.880000e-27	132.0
18	TraesCS3D01G183200	chr6D	88.571	70	5	3	304	373	97571697	97571631	7.030000e-12	82.4
19	TraesCS3D01G183200	chr7B	87.143	70	6	2	308	374	74850788	74850857	3.270000e-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	TraesCS3D01G183200	chr3D	167789431	167792489	3058	True	5650.00	5650	100.0000	1	3059	1	chr3D.!!$R1	3058
1	TraesCS3D01G183200	chr3B	242885531	242890234	4703	True	2375.00	3736	94.6280	1	3059	2	chr3B.!!$R1	3058
2	TraesCS3D01G183200	chr3A	201473737	201479068	5331	False	924.62	2663	94.6304	1	3053	5	chr3A.!!$F1	3052

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
901	2946	0.183014	TTAAACAGGGTCACGGGCAA	59.817	50.000	0.0	0.00	0.00	4.52	F
1838	3883	2.546494	GCATTGCCGGCGCTAGAAT	61.546	57.895	23.9	12.78	35.36	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1913	3958	1.566211	TTCCTTCTCCAGCTCCTCTG	58.434	55.0	0.0	0.0	42.49	3.35	R
2677	6691	1.590932	TCGTGCTACTCGGTCCTATC	58.409	55.0	0.0	0.0	0.00	2.08	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
145	146	3.054875	TCTGATTCTCCAATGGGTGTCAG	60.055	47.826	14.26	14.26	34.11	3.51
243	245	9.191995	GACGTTTCTGGATTTTGTAAAAATCAT	57.808	29.630	20.96	0.00	38.15	2.45
244	246	8.977505	ACGTTTCTGGATTTTGTAAAAATCATG	58.022	29.630	20.96	14.62	38.15	3.07
434	437	3.546020	GCATCATAAAATCACGTCGGTGG	60.546	47.826	0.00	0.00	44.50	4.61
445	448	2.601067	TCGGTGGAAGGCGTGGTA	60.601	61.111	0.00	0.00	0.00	3.25
501	505	3.193263	TCAAACGCATTTTGTTGCACAT	58.807	36.364	7.47	0.00	44.47	3.21
654	660	1.623311	TCAGAAGCATTTGAGGTCGGA	59.377	47.619	0.00	0.00	0.00	4.55
767	2812	5.220643	CCATGTGAACCTGTTTTTCTTTTGC	60.221	40.000	0.00	0.00	0.00	3.68
772	2817	2.100749	ACCTGTTTTTCTTTTGCCTCCG	59.899	45.455	0.00	0.00	0.00	4.63
842	2887	6.403636	GCGATCCATGACACTCACTTAATTTT	60.404	38.462	0.00	0.00	0.00	1.82
843	2888	7.530010	CGATCCATGACACTCACTTAATTTTT	58.470	34.615	0.00	0.00	0.00	1.94
855	2900	4.840772	CACTTAATTTTTCTCTCGTGTGCG	59.159	41.667	0.00	0.00	39.92	5.34
901	2946	0.183014	TTAAACAGGGTCACGGGCAA	59.817	50.000	0.00	0.00	0.00	4.52
1485	3530	2.682494	TACCCGCGCTTCTCCCTT	60.682	61.111	5.56	0.00	0.00	3.95
1838	3883	2.546494	GCATTGCCGGCGCTAGAAT	61.546	57.895	23.90	12.78	35.36	2.40
1913	3958	1.118356	AGATCGAGGAGGATGGGCAC	61.118	60.000	0.00	0.00	0.00	5.01
2179	4228	5.396772	CCTGGTCTTTGCATAGTTAGGATGA	60.397	44.000	14.10	0.00	0.00	2.92
2180	4229	6.252599	TGGTCTTTGCATAGTTAGGATGAT	57.747	37.500	4.00	0.00	0.00	2.45
2181	4230	6.057533	TGGTCTTTGCATAGTTAGGATGATG	58.942	40.000	4.00	0.00	0.00	3.07
2240	4289	2.296073	TTTAGCCCCGGTGTGAAAAT	57.704	45.000	0.00	0.00	0.00	1.82
2312	6187	9.433317	CAATGTTTTTGCGTCGTTATCTTATAT	57.567	29.630	0.00	0.00	0.00	0.86
2339	6328	3.819564	TTGCTCGGATATGCTACAACT	57.180	42.857	0.00	0.00	0.00	3.16
2357	6346	6.220726	ACAACTGGTTAGCTTCATGTTTTT	57.779	33.333	0.00	0.00	0.00	1.94
2437	6448	2.766828	GGCCTTGAGCTTCTCTTACCTA	59.233	50.000	0.00	0.00	43.05	3.08
2473	6484	7.439655	AGAGTGACTAACAACATCTTCAACTTC	59.560	37.037	0.00	0.00	0.00	3.01
2474	6485	7.275920	AGTGACTAACAACATCTTCAACTTCT	58.724	34.615	0.00	0.00	0.00	2.85
2508	6519	4.568152	AACATCTTCAACGGTTTTCCAG	57.432	40.909	0.00	0.00	40.70	3.86
2511	6522	3.269538	TCTTCAACGGTTTTCCAGTCA	57.730	42.857	0.00	0.00	40.70	3.41
2513	6524	4.011023	TCTTCAACGGTTTTCCAGTCAAA	58.989	39.130	0.00	0.00	40.70	2.69
2529	6540	7.961351	TCCAGTCAAAACCAATATGATGTTTT	58.039	30.769	0.00	0.00	0.00	2.43
2569	6580	1.106285	GTTAATGGAGCTGCCCCAAG	58.894	55.000	7.07	0.00	37.22	3.61
2600	6611	5.356751	ACTTGATATGAAACGCCAGCAAATA	59.643	36.000	0.00	0.00	0.00	1.40
2640	6654	6.952773	AAAACTACTTCACTTTGTATGGCA	57.047	33.333	0.00	0.00	0.00	4.92
2677	6691	3.213402	GTCTCCGGGAGCTCGAGG	61.213	72.222	19.48	17.19	0.00	4.63
2786	6801	3.511595	CGGCGCACAATGAGGCAT	61.512	61.111	10.83	0.00	42.53	4.40
2883	6900	5.793817	TCTTTCATTTCTTCGTCCATCTCA	58.206	37.500	0.00	0.00	0.00	3.27
2906	6923	4.901868	TGTAGCTGACGAAAATTACCCTT	58.098	39.130	0.00	0.00	0.00	3.95
2907	6924	4.693566	TGTAGCTGACGAAAATTACCCTTG	59.306	41.667	0.00	0.00	0.00	3.61
2921	6938	8.837099	AAATTACCCTTGATGTCATCCATAAA	57.163	30.769	10.36	0.00	32.56	1.40
2960	6978	2.224018	GGCAACATGAAGACAAAAGCCA	60.224	45.455	0.00	0.00	39.35	4.75
2976	6994	9.989869	GACAAAAGCCATAAAACTAAGTAGATC	57.010	33.333	0.00	0.00	0.00	2.75
2977	6995	9.515226	ACAAAAGCCATAAAACTAAGTAGATCA	57.485	29.630	0.00	0.00	0.00	2.92
3024	7046	0.768622	AACTCGATTTCCACCCCACA	59.231	50.000	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
129	130	3.874383	TTTTCTGACACCCATTGGAGA	57.126	42.857	3.62	0.00	34.81	3.71
145	146	4.988540	GTCTTTTTGTGGGTGCCTATTTTC	59.011	41.667	0.00	0.00	0.00	2.29
211	212	6.300354	ACAAAATCCAGAAACGTCTAACTG	57.700	37.500	0.00	0.00	30.85	3.16
276	278	3.763897	GCCCTATAATAGGCCACCAAATG	59.236	47.826	5.01	0.00	44.86	2.32
306	308	4.527038	TCAAGATTAGAAACTCCACGTCCT	59.473	41.667	0.00	0.00	0.00	3.85
419	422	1.519408	CCTTCCACCGACGTGATTTT	58.481	50.000	0.00	0.00	43.14	1.82
615	621	9.525409	GCTTCTGATATGAACAGCAAAATTTAT	57.475	29.630	0.00	0.00	35.61	1.40
632	638	3.450817	TCCGACCTCAAATGCTTCTGATA	59.549	43.478	0.00	0.00	0.00	2.15
767	2812	1.376037	GAAACTGCAGGGACGGAGG	60.376	63.158	19.93	0.00	0.00	4.30
772	2817	2.289945	ACATGAGAGAAACTGCAGGGAC	60.290	50.000	19.93	8.37	0.00	4.46
1289	3334	1.021390	CATCTGTTCCAGGGTGACGC	61.021	60.000	0.00	0.00	31.51	5.19
1290	3335	0.608130	TCATCTGTTCCAGGGTGACG	59.392	55.000	0.00	0.00	31.51	4.35
1561	3606	2.548920	CGGGGATGTTTCTGCTATCTCC	60.549	54.545	0.00	0.00	37.97	3.71
1570	3615	1.299976	GGTCTGCGGGGATGTTTCT	59.700	57.895	0.00	0.00	0.00	2.52
1670	3715	0.030908	GTCCATCTCGTAGCCTTCCG	59.969	60.000	0.00	0.00	0.00	4.30
1913	3958	1.566211	TTCCTTCTCCAGCTCCTCTG	58.434	55.000	0.00	0.00	42.49	3.35
2146	4192	3.178046	TGCAAAGACCAGGTATGTCCTA	58.822	45.455	0.00	0.00	46.24	2.94
2179	4228	6.946340	TGGTGTTGATCTTGACTATGTACAT	58.054	36.000	13.93	13.93	0.00	2.29
2180	4229	6.353404	TGGTGTTGATCTTGACTATGTACA	57.647	37.500	0.00	0.00	0.00	2.90
2181	4230	9.197694	GATATGGTGTTGATCTTGACTATGTAC	57.802	37.037	0.00	0.00	0.00	2.90
2312	6187	4.607293	AGCATATCCGAGCAATGTCTTA	57.393	40.909	0.00	0.00	0.00	2.10
2313	6188	3.482156	AGCATATCCGAGCAATGTCTT	57.518	42.857	0.00	0.00	0.00	3.01
2314	6189	3.321968	TGTAGCATATCCGAGCAATGTCT	59.678	43.478	0.00	0.00	0.00	3.41
2315	6190	3.653344	TGTAGCATATCCGAGCAATGTC	58.347	45.455	0.00	0.00	0.00	3.06
2316	6191	3.751479	TGTAGCATATCCGAGCAATGT	57.249	42.857	0.00	0.00	0.00	2.71
2357	6346	9.936759	AGTTTTGTAAACTCCATCTTTTTCAAA	57.063	25.926	0.00	0.00	33.08	2.69
2437	6448	3.318275	TGTTAGTCACTCTTGAAGCTCGT	59.682	43.478	0.00	0.00	31.90	4.18
2504	6515	7.537596	AAACATCATATTGGTTTTGACTGGA	57.462	32.000	0.00	0.00	31.09	3.86
2529	6540	4.258457	CACCATATTGGGGTTCCCTAAA	57.742	45.455	10.55	5.12	45.70	1.85
2569	6580	5.350365	TGGCGTTTCATATCAAGTGAAGTAC	59.650	40.000	0.00	0.00	36.96	2.73
2590	6601	5.266733	TGAAAGATCCAATATTTGCTGGC	57.733	39.130	0.00	0.00	32.33	4.85
2640	6654	1.669115	GACATGGCAGTGCTGACGT	60.669	57.895	16.11	7.37	42.94	4.34
2677	6691	1.590932	TCGTGCTACTCGGTCCTATC	58.409	55.000	0.00	0.00	0.00	2.08
2853	6869	5.121768	GGACGAAGAAATGAAAGAAATCCGA	59.878	40.000	0.00	0.00	0.00	4.55
2856	6872	7.756558	AGATGGACGAAGAAATGAAAGAAATC	58.243	34.615	0.00	0.00	0.00	2.17
2883	6900	5.099042	AGGGTAATTTTCGTCAGCTACAT	57.901	39.130	0.00	0.00	0.00	2.29
2976	6994	6.814644	TCACATGGGTTATCGTAGTAAAACTG	59.185	38.462	0.00	0.00	0.00	3.16
2977	6995	6.938507	TCACATGGGTTATCGTAGTAAAACT	58.061	36.000	0.00	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.