AutoCloner

Multiple sequence alignment - TraesCS3D01G164300

Loading Multiple Alignment...

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	TraesCS3D01G164300	chr3D	100.000	3554	0	0	1	3554	135758818	135755265	0.000000e+00	6564
1	TraesCS3D01G164300	chr3D	94.805	77	4	0	528	604	135758223	135758147	1.730000e-23	121
2	TraesCS3D01G164300	chr3D	94.805	77	4	0	596	672	135758291	135758215	1.730000e-23	121
3	TraesCS3D01G164300	chr3B	94.963	2978	90	24	1	2956	193984095	193981156	0.000000e+00	4614
4	TraesCS3D01G164300	chr3B	86.928	153	14	2	1681	1827	193982474	193982322	2.190000e-37	167
5	TraesCS3D01G164300	chr3B	94.805	77	4	0	596	672	193983566	193983490	1.730000e-23	121
6	TraesCS3D01G164300	chr3B	95.833	72	3	0	528	599	193983498	193983427	2.240000e-22	117
7	TraesCS3D01G164300	chr3A	94.682	2971	94	22	1	2956	151325090	151322169	0.000000e+00	4553
8	TraesCS3D01G164300	chr3A	83.562	219	18	9	1681	1893	151323462	151323256	4.680000e-44	189
9	TraesCS3D01G164300	chr5D	90.307	619	53	4	2942	3554	272144946	272144329	0.000000e+00	804
10	TraesCS3D01G164300	chr5D	88.924	632	58	6	2932	3554	487455863	487455235	0.000000e+00	769
11	TraesCS3D01G164300	chr7A	89.694	621	56	5	2940	3554	629761755	629761137	0.000000e+00	785
12	TraesCS3D01G164300	chr1D	89.600	625	52	7	2942	3554	30589967	30589344	0.000000e+00	782
13	TraesCS3D01G164300	chr4D	89.583	624	51	8	2940	3554	127547053	127547671	0.000000e+00	780
14	TraesCS3D01G164300	chr4D	89.331	628	54	4	2939	3554	486785173	486784547	0.000000e+00	776
15	TraesCS3D01G164300	chr6A	89.406	623	57	6	2939	3554	453873949	453873329	0.000000e+00	776
16	TraesCS3D01G164300	chr7D	89.228	622	58	5	2939	3554	618373336	618373954	0.000000e+00	769
17	TraesCS3D01G164300	chr2D	88.558	638	62	7	2923	3554	54007689	54008321	0.000000e+00	763

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	TraesCS3D01G164300	chr3D	135755265	135758818	3553	True	2268.666667	6564	96.536667	1	3554	3	chr3D.!!$R1	3553
1	TraesCS3D01G164300	chr3B	193981156	193984095	2939	True	1254.750000	4614	93.132250	1	2956	4	chr3B.!!$R1	2955
2	TraesCS3D01G164300	chr3A	151322169	151325090	2921	True	2371.000000	4553	89.122000	1	2956	2	chr3A.!!$R1	2955
3	TraesCS3D01G164300	chr5D	272144329	272144946	617	True	804.000000	804	90.307000	2942	3554	1	chr5D.!!$R1	612
4	TraesCS3D01G164300	chr5D	487455235	487455863	628	True	769.000000	769	88.924000	2932	3554	1	chr5D.!!$R2	622
5	TraesCS3D01G164300	chr7A	629761137	629761755	618	True	785.000000	785	89.694000	2940	3554	1	chr7A.!!$R1	614
6	TraesCS3D01G164300	chr1D	30589344	30589967	623	True	782.000000	782	89.600000	2942	3554	1	chr1D.!!$R1	612
7	TraesCS3D01G164300	chr4D	127547053	127547671	618	False	780.000000	780	89.583000	2940	3554	1	chr4D.!!$F1	614
8	TraesCS3D01G164300	chr4D	486784547	486785173	626	True	776.000000	776	89.331000	2939	3554	1	chr4D.!!$R1	615
9	TraesCS3D01G164300	chr6A	453873329	453873949	620	True	776.000000	776	89.406000	2939	3554	1	chr6A.!!$R1	615
10	TraesCS3D01G164300	chr7D	618373336	618373954	618	False	769.000000	769	89.228000	2939	3554	1	chr7D.!!$F1	615
11	TraesCS3D01G164300	chr2D	54007689	54008321	632	False	763.000000	763	88.558000	2923	3554	1	chr2D.!!$F1	631

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
914	924	0.03759	AATAGGGCAAACGCACAGGA	59.962	50.0	0.0	0.0	34.18	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2626	2655	0.035725	CCCTCATCAGCTTCAGCACA	60.036	55.0	0.75	0.0	45.16	4.57	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
55	56	9.752961	GTTAGAAAAATAGGAGAGAGACCATAC	57.247	37.037	0.00	0.00	0.00	2.39
56	57	7.979786	AGAAAAATAGGAGAGAGACCATACA	57.020	36.000	0.00	0.00	0.00	2.29
115	117	5.389859	TTGATGTTTAACCCATCTTGCAG	57.610	39.130	12.95	0.00	39.54	4.41
116	118	4.406456	TGATGTTTAACCCATCTTGCAGT	58.594	39.130	12.95	0.00	39.54	4.40
162	164	5.772521	ACTTTGATCTTTTGTCCATTTCGG	58.227	37.500	0.00	0.00	0.00	4.30
400	405	2.507407	ACCACCCTCGCATAAACAAT	57.493	45.000	0.00	0.00	0.00	2.71
448	453	5.335583	GGTCGATTGTTGAACCAAATCATCA	60.336	40.000	8.49	0.00	0.00	3.07
478	483	1.803922	CACGCCGCTAACGTCATCA	60.804	57.895	0.00	0.00	42.96	3.07
479	484	1.141019	ACGCCGCTAACGTCATCAT	59.859	52.632	0.00	0.00	40.28	2.45
771	781	1.460504	TACGGCTCGAGTGAGAACAT	58.539	50.000	15.13	0.00	45.57	2.71
911	921	0.885196	GGAAATAGGGCAAACGCACA	59.115	50.000	0.00	0.00	34.18	4.57
912	922	1.135402	GGAAATAGGGCAAACGCACAG	60.135	52.381	0.00	0.00	34.18	3.66
913	923	0.887933	AAATAGGGCAAACGCACAGG	59.112	50.000	0.00	0.00	34.18	4.00
914	924	0.037590	AATAGGGCAAACGCACAGGA	59.962	50.000	0.00	0.00	34.18	3.86
915	925	0.392998	ATAGGGCAAACGCACAGGAG	60.393	55.000	0.00	0.00	34.18	3.69
916	926	1.764571	TAGGGCAAACGCACAGGAGT	61.765	55.000	0.00	0.00	34.18	3.85
917	927	2.193536	GGGCAAACGCACAGGAGTT	61.194	57.895	0.00	0.00	38.78	3.01
918	928	1.008538	GGCAAACGCACAGGAGTTG	60.009	57.895	0.00	0.00	37.11	3.16
919	929	1.444119	GGCAAACGCACAGGAGTTGA	61.444	55.000	0.00	0.00	37.11	3.18
920	930	0.040958	GCAAACGCACAGGAGTTGAG	60.041	55.000	0.00	0.00	37.11	3.02
1230	1250	4.758251	CAGATGCCGCCGTCACCA	62.758	66.667	0.00	0.00	0.00	4.17
1804	1830	3.793888	GGTTCGGGAATCGGCCCT	61.794	66.667	0.00	0.00	46.44	5.19
1805	1831	2.513897	GTTCGGGAATCGGCCCTG	60.514	66.667	0.00	0.00	46.44	4.45
1969	1995	3.546397	GACTTCGCGCCGAGCTTC	61.546	66.667	0.00	0.00	45.59	3.86
2587	2613	1.305633	TGAGCCAGAGAGAGTGGGG	60.306	63.158	0.00	0.00	35.39	4.96
2722	2754	0.255890	ATGGAACCGGCAGCAATAGT	59.744	50.000	0.00	0.00	0.00	2.12
2723	2755	0.906066	TGGAACCGGCAGCAATAGTA	59.094	50.000	0.00	0.00	0.00	1.82
2724	2756	1.134521	TGGAACCGGCAGCAATAGTAG	60.135	52.381	0.00	0.00	0.00	2.57
2910	2953	7.195374	TGTAGTATAACCTGAAGCTTCCATT	57.805	36.000	23.42	16.11	0.00	3.16
2915	2958	1.138247	CTGAAGCTTCCATTGCGGC	59.862	57.895	23.42	0.00	35.28	6.53
2919	2962	1.187567	AAGCTTCCATTGCGGCCTTT	61.188	50.000	0.00	0.00	35.28	3.11
2933	2976	0.657368	GCCTTTGCACTCGTTGTTCG	60.657	55.000	0.00	0.00	37.99	3.95
2960	3003	1.589414	AGAGCAACTCTAATGGGGCT	58.411	50.000	0.00	0.00	39.28	5.19
2963	3006	2.436173	GAGCAACTCTAATGGGGCTACT	59.564	50.000	0.00	0.00	0.00	2.57
2994	3037	2.029964	GCCGTCAGTTTGGGTCGA	59.970	61.111	0.00	0.00	0.00	4.20
3027	3070	4.695231	CGGTCCAACGCGTCGACT	62.695	66.667	28.07	7.31	0.00	4.18
3028	3071	2.355481	GGTCCAACGCGTCGACTT	60.355	61.111	28.07	6.95	0.00	3.01
3038	3081	1.668253	GCGTCGACTTAAACGGACGG	61.668	60.000	14.70	0.00	39.24	4.79
3043	3086	0.945743	GACTTAAACGGACGGGCGTT	60.946	55.000	0.00	0.00	0.00	4.84
3187	3237	3.700350	CCTCCCCTCTCACCCCCT	61.700	72.222	0.00	0.00	0.00	4.79
3198	3250	3.110031	ACCCCCTGGCCAACAAGT	61.110	61.111	7.01	0.00	33.59	3.16
3260	3314	2.463589	TTTGCCGGCGACTCTTCCAT	62.464	55.000	23.90	0.00	0.00	3.41
3266	3320	1.219124	GCGACTCTTCCATCTGCCA	59.781	57.895	0.00	0.00	0.00	4.92
3355	3413	3.854856	GCAAACTGCTTCCCACCA	58.145	55.556	0.00	0.00	40.96	4.17
3362	3420	3.056328	GCTTCCCACCACCGCTTC	61.056	66.667	0.00	0.00	0.00	3.86
3424	3489	3.716195	CCCTGCCACATCCGACCA	61.716	66.667	0.00	0.00	0.00	4.02
3529	3597	4.735132	TCTCCTTCAACGCCCGCG	62.735	66.667	7.69	7.69	46.03	6.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	56	3.747529	GGGTGAAAATTCAAATGCACCTG	59.252	43.478	0.00	0.00	43.90	4.00
56	57	3.244526	GGGGTGAAAATTCAAATGCACCT	60.245	43.478	0.00	0.00	43.90	4.00
107	109	2.097825	GAGGGCAAATGACTGCAAGAT	58.902	47.619	0.00	0.00	44.52	2.40
115	117	2.961526	TCTACGAGAGGGCAAATGAC	57.038	50.000	0.00	0.00	0.00	3.06
116	118	3.450817	TCATTCTACGAGAGGGCAAATGA	59.549	43.478	0.00	0.00	31.29	2.57
227	230	1.135094	GGGGAGAAGATGATGAGGCA	58.865	55.000	0.00	0.00	0.00	4.75
228	231	0.034616	CGGGGAGAAGATGATGAGGC	59.965	60.000	0.00	0.00	0.00	4.70
382	386	5.163561	ACAAATATTGTTTATGCGAGGGTGG	60.164	40.000	0.00	0.00	42.22	4.61
400	405	2.791347	TCAAGGCCCGCTTACAAATA	57.209	45.000	0.00	0.00	0.00	1.40
448	453	2.591715	GGCGTGCTGGCGGATAAT	60.592	61.111	0.00	0.00	0.00	1.28
469	474	1.809619	CGTGGCCGATGATGACGTT	60.810	57.895	0.00	0.00	35.63	3.99
478	483	3.927163	GACCGACAACGTGGCCGAT	62.927	63.158	0.00	0.00	37.88	4.18
479	484	4.651008	GACCGACAACGTGGCCGA	62.651	66.667	0.00	0.00	37.88	5.54
778	788	8.844865	AGGAAATTAAAGCCATCCTCTTTTAT	57.155	30.769	0.00	0.00	35.65	1.40
779	789	8.664669	AAGGAAATTAAAGCCATCCTCTTTTA	57.335	30.769	0.00	0.00	39.56	1.52
788	798	7.882271	TGTATTGCAAAAGGAAATTAAAGCCAT	59.118	29.630	1.71	0.00	0.00	4.40
911	921	2.242196	CTCTCCTCTCCTCTCAACTCCT	59.758	54.545	0.00	0.00	0.00	3.69
912	922	2.654863	CTCTCCTCTCCTCTCAACTCC	58.345	57.143	0.00	0.00	0.00	3.85
913	923	2.654863	CCTCTCCTCTCCTCTCAACTC	58.345	57.143	0.00	0.00	0.00	3.01
914	924	1.287739	CCCTCTCCTCTCCTCTCAACT	59.712	57.143	0.00	0.00	0.00	3.16
915	925	1.286553	TCCCTCTCCTCTCCTCTCAAC	59.713	57.143	0.00	0.00	0.00	3.18
916	926	1.687492	TCCCTCTCCTCTCCTCTCAA	58.313	55.000	0.00	0.00	0.00	3.02
917	927	1.780309	GATCCCTCTCCTCTCCTCTCA	59.220	57.143	0.00	0.00	0.00	3.27
918	928	1.271379	CGATCCCTCTCCTCTCCTCTC	60.271	61.905	0.00	0.00	0.00	3.20
919	929	0.771127	CGATCCCTCTCCTCTCCTCT	59.229	60.000	0.00	0.00	0.00	3.69
920	930	0.768622	TCGATCCCTCTCCTCTCCTC	59.231	60.000	0.00	0.00	0.00	3.71
1379	1399	3.717294	GCACGATGGTGGGGAGGT	61.717	66.667	10.06	0.00	44.54	3.85
2170	2196	1.134699	CAGCATCATGTGGTACGACCT	60.135	52.381	5.50	0.00	39.58	3.85
2172	2198	2.293677	TCAGCATCATGTGGTACGAC	57.706	50.000	0.33	0.33	36.63	4.34
2173	2199	2.892374	CTTCAGCATCATGTGGTACGA	58.108	47.619	0.00	0.00	36.63	3.43
2565	2591	1.685421	ACTCTCTCTGGCTCAGGGC	60.685	63.158	2.86	0.00	40.90	5.19
2566	2592	1.329171	CCACTCTCTCTGGCTCAGGG	61.329	65.000	2.86	0.00	32.35	4.45
2567	2593	1.329171	CCCACTCTCTCTGGCTCAGG	61.329	65.000	2.86	0.00	31.51	3.86
2568	2594	1.329171	CCCCACTCTCTCTGGCTCAG	61.329	65.000	0.00	0.00	0.00	3.35
2569	2595	1.305633	CCCCACTCTCTCTGGCTCA	60.306	63.158	0.00	0.00	0.00	4.26
2570	2596	1.305718	ACCCCACTCTCTCTGGCTC	60.306	63.158	0.00	0.00	0.00	4.70
2587	2613	1.015868	CTCCTTACCTCTCCGTCGAC	58.984	60.000	5.18	5.18	0.00	4.20
2626	2655	0.035725	CCCTCATCAGCTTCAGCACA	60.036	55.000	0.75	0.00	45.16	4.57
2722	2754	1.351017	CCTGCCCACTCCAGAAAACTA	59.649	52.381	0.00	0.00	32.03	2.24
2723	2755	0.111253	CCTGCCCACTCCAGAAAACT	59.889	55.000	0.00	0.00	32.03	2.66
2724	2756	0.110486	TCCTGCCCACTCCAGAAAAC	59.890	55.000	0.00	0.00	32.03	2.43
2855	2897	0.927537	GCCAAAACCAAACAACGAGC	59.072	50.000	0.00	0.00	0.00	5.03
2910	2953	4.927782	ACGAGTGCAAAGGCCGCA	62.928	61.111	0.00	0.00	40.13	5.69
2915	2958	0.657368	GCGAACAACGAGTGCAAAGG	60.657	55.000	0.00	0.00	45.77	3.11
2919	2962	1.487452	GACAGCGAACAACGAGTGCA	61.487	55.000	0.00	0.00	45.77	4.57
2960	3003	1.517694	GCCGCGGACGAAATGAGTA	60.518	57.895	33.48	0.00	43.93	2.59
2983	3026	1.375523	GTCCGCATCGACCCAAACT	60.376	57.895	0.00	0.00	0.00	2.66
2994	3037	2.625823	CCGCCTTTTGTGTCCGCAT	61.626	57.895	0.00	0.00	0.00	4.73
3022	3065	1.080569	GCCCGTCCGTTTAAGTCGA	60.081	57.895	4.18	0.00	0.00	4.20
3038	3081	1.437573	CGGACGAAAAACGAACGCC	60.438	57.895	0.00	0.00	45.77	5.68
3043	3086	3.037249	CCCGCGGACGAAAAACGA	61.037	61.111	30.73	0.00	45.77	3.85
3187	3237	0.250553	CGAGGGTTACTTGTTGGCCA	60.251	55.000	0.00	0.00	0.00	5.36
3233	3286	4.067913	CGCCGGCAAAAATGGGCT	62.068	61.111	28.98	0.00	43.38	5.19
3441	3506	2.941333	GTCCGACGAGTGTGACGA	59.059	61.111	0.00	0.00	34.70	4.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.