AutoCloner

Multiple sequence alignment - TraesCS3A01G514800

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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	TraesCS3A01G514800	chr3A	100.000	3975	0	0	1	3975	733435394	733439368	0.000000e+00	7341.0
1	TraesCS3A01G514800	chr3A	98.593	2772	33	4	1	2770	733410599	733413366	0.000000e+00	4898.0
2	TraesCS3A01G514800	chr3A	88.203	2704	221	41	726	3373	733465233	733467894	0.000000e+00	3136.0
3	TraesCS3A01G514800	chr3A	87.385	2608	249	34	728	3274	733332997	733335585	0.000000e+00	2920.0
4	TraesCS3A01G514800	chr3A	80.293	2182	338	49	775	2904	733726104	733723963	0.000000e+00	1563.0
5	TraesCS3A01G514800	chr3A	82.356	1842	269	27	782	2587	733860375	733858554	0.000000e+00	1550.0
6	TraesCS3A01G514800	chr3A	78.941	1605	285	23	870	2442	733732452	733730869	0.000000e+00	1042.0
7	TraesCS3A01G514800	chr3A	85.828	755	52	14	3221	3969	733188292	733188997	0.000000e+00	750.0
8	TraesCS3A01G514800	chr3A	90.795	239	11	4	2929	3162	733187578	733187810	3.860000e-80	309.0
9	TraesCS3A01G514800	chr3A	83.505	194	31	1	197	390	484106676	484106484	3.160000e-41	180.0
10	TraesCS3A01G514800	chr3A	97.222	36	0	1	2899	2934	733187519	733187553	4.290000e-05	60.2
11	TraesCS3A01G514800	chr3B	93.779	2845	119	13	1	2804	810969480	810972307	0.000000e+00	4220.0
12	TraesCS3A01G514800	chr3B	89.735	2075	133	44	726	2772	811040638	811042660	0.000000e+00	2579.0
13	TraesCS3A01G514800	chr3B	88.752	2027	165	27	726	2696	810977750	810979769	0.000000e+00	2422.0
14	TraesCS3A01G514800	chr3B	85.346	1085	113	20	2899	3975	810972422	810973468	0.000000e+00	1081.0
15	TraesCS3A01G514800	chr3B	86.071	761	49	14	3221	3975	810980390	810981099	0.000000e+00	765.0
16	TraesCS3A01G514800	chr3B	96.465	198	7	0	2707	2904	810979859	810980056	1.070000e-85	327.0
17	TraesCS3A01G514800	chr3B	90.438	251	13	4	2929	3174	810980151	810980395	1.780000e-83	320.0
18	TraesCS3A01G514800	chr3B	76.157	432	66	18	197	614	473185514	473185106	4.050000e-45	193.0
19	TraesCS3A01G514800	chr3B	94.737	38	2	0	2640	2677	810979822	810979859	4.290000e-05	60.2
20	TraesCS3A01G514800	chr3D	94.242	2640	101	17	1	2617	602782456	602779845	0.000000e+00	3986.0
21	TraesCS3A01G514800	chr3D	90.839	2085	120	35	726	2772	603943418	603945469	0.000000e+00	2726.0
22	TraesCS3A01G514800	chr3D	86.924	1086	100	20	2899	3975	602779667	602778615	0.000000e+00	1181.0
23	TraesCS3A01G514800	chr3D	80.694	461	74	8	3464	3910	603991552	603991093	1.060000e-90	344.0
24	TraesCS3A01G514800	chr3D	78.846	156	24	6	2832	2978	603997891	603997736	3.270000e-16	97.1
25	TraesCS3A01G514800	chr4D	78.913	460	65	17	95	534	75049153	75049600	2.340000e-72	283.0
26	TraesCS3A01G514800	chrUn	75.000	164	31	7	2705	2867	42262266	42262420	2.560000e-07	67.6

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	TraesCS3A01G514800	chr3A	733435394	733439368	3974	False	7341.000000	7341	100.000000	1	3975	1	chr3A.!!$F3	3974
1	TraesCS3A01G514800	chr3A	733410599	733413366	2767	False	4898.000000	4898	98.593000	1	2770	1	chr3A.!!$F2	2769
2	TraesCS3A01G514800	chr3A	733465233	733467894	2661	False	3136.000000	3136	88.203000	726	3373	1	chr3A.!!$F4	2647
3	TraesCS3A01G514800	chr3A	733332997	733335585	2588	False	2920.000000	2920	87.385000	728	3274	1	chr3A.!!$F1	2546
4	TraesCS3A01G514800	chr3A	733723963	733726104	2141	True	1563.000000	1563	80.293000	775	2904	1	chr3A.!!$R2	2129
5	TraesCS3A01G514800	chr3A	733858554	733860375	1821	True	1550.000000	1550	82.356000	782	2587	1	chr3A.!!$R4	1805
6	TraesCS3A01G514800	chr3A	733730869	733732452	1583	True	1042.000000	1042	78.941000	870	2442	1	chr3A.!!$R3	1572
7	TraesCS3A01G514800	chr3A	733187519	733188997	1478	False	373.066667	750	91.281667	2899	3969	3	chr3A.!!$F5	1070
8	TraesCS3A01G514800	chr3B	810969480	810973468	3988	False	2650.500000	4220	89.562500	1	3975	2	chr3B.!!$F2	3974
9	TraesCS3A01G514800	chr3B	811040638	811042660	2022	False	2579.000000	2579	89.735000	726	2772	1	chr3B.!!$F1	2046
10	TraesCS3A01G514800	chr3B	810977750	810981099	3349	False	778.840000	2422	91.292600	726	3975	5	chr3B.!!$F3	3249
11	TraesCS3A01G514800	chr3D	603943418	603945469	2051	False	2726.000000	2726	90.839000	726	2772	1	chr3D.!!$F1	2046
12	TraesCS3A01G514800	chr3D	602778615	602782456	3841	True	2583.500000	3986	90.583000	1	3975	2	chr3D.!!$R3	3974

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
671	683	2.030562	CGAGCGTGTCCCCTTGTT	59.969	61.111	0.0	0.0	0.0	2.83	F
1668	1733	1.204146	GTCTCCTTCTGCCCCATACA	58.796	55.000	0.0	0.0	0.0	2.29	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1762	1830	3.308401	AGGGGCATCCAAATTAATGTCC	58.692	45.455	9.46	9.46	45.12	4.02	R
3532	4323	0.397675	TGACGAGGATGAGGAGGCAT	60.398	55.000	0.00	0.00	0.00	4.40	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
671	683	2.030562	CGAGCGTGTCCCCTTGTT	59.969	61.111	0.00	0.00	0.00	2.83
1419	1484	5.107375	GCAAAACTTACCATAACGAGTTCGA	60.107	40.000	8.72	0.00	43.02	3.71
1668	1733	1.204146	GTCTCCTTCTGCCCCATACA	58.796	55.000	0.00	0.00	0.00	2.29
1762	1830	1.604604	ATGTTGTTGGGGACGTTGAG	58.395	50.000	0.00	0.00	0.00	3.02
1912	1980	2.949447	AGTGACATCAAAACCCTTGCT	58.051	42.857	0.00	0.00	0.00	3.91
2231	2308	3.261897	TCTCCCTTCCTCAGTCATTCAAC	59.738	47.826	0.00	0.00	0.00	3.18
2696	2824	4.247258	GTGCATTTGAGGCAAATCATCAA	58.753	39.130	2.62	0.00	41.40	2.57
2944	3238	3.895232	TGAAGCCTGAATCAGTCTACC	57.105	47.619	9.63	0.00	0.00	3.18
2960	3254	6.490040	TCAGTCTACCTTTTGGAAATCAAAGG	59.510	38.462	8.79	8.79	45.00	3.11
2980	3274	8.246180	TCAAAGGATTTATCAGATTGCTTTCAC	58.754	33.333	0.00	0.00	35.03	3.18
2998	3292	7.088905	GCTTTCACATTTGAATGAGTCTTCAT	58.911	34.615	10.48	0.00	45.92	2.57
3060	3362	9.817809	AGTGAAATATTTGTATATCACTGTCGT	57.182	29.630	14.50	0.00	33.70	4.34
3148	3451	4.037208	CACACTTGGAATGCCTGGATTATC	59.963	45.833	0.00	0.00	34.31	1.75
3185	3963	9.537192	TTTATGAGTATATAAGTGAAACACGGG	57.463	33.333	0.00	0.00	41.43	5.28
3201	3985	4.700700	ACACGGGTATAGCCATTTACTTC	58.299	43.478	20.55	0.00	39.65	3.01
3202	3986	4.162698	ACACGGGTATAGCCATTTACTTCA	59.837	41.667	20.55	0.00	39.65	3.02
3250	4034	1.280421	GAGCACCCTTGAAGGACTGAT	59.720	52.381	13.97	6.06	37.67	2.90
3262	4046	4.039245	TGAAGGACTGATCGAGTTTCACTT	59.961	41.667	0.00	0.00	33.83	3.16
3266	4050	4.321304	GGACTGATCGAGTTTCACTTGAGA	60.321	45.833	0.00	0.00	41.60	3.27
3401	4192	7.759489	TGGTTTAAGCACCATATCATTATCC	57.241	36.000	0.00	0.00	42.27	2.59
3402	4193	7.526041	TGGTTTAAGCACCATATCATTATCCT	58.474	34.615	0.00	0.00	42.27	3.24
3403	4194	8.004215	TGGTTTAAGCACCATATCATTATCCTT	58.996	33.333	0.00	0.00	42.27	3.36
3404	4195	8.299570	GGTTTAAGCACCATATCATTATCCTTG	58.700	37.037	0.00	0.00	36.73	3.61
3436	4227	2.027745	TCTCCACATTCTCCTGACAAGC	60.028	50.000	0.00	0.00	0.00	4.01
3443	4234	3.997064	CTCCTGACAAGCCGCCTCG	62.997	68.421	0.00	0.00	0.00	4.63
3509	4300	2.979151	CTCATCATCTTCGTCATCGCTC	59.021	50.000	0.00	0.00	36.96	5.03
3532	4323	5.887035	TCCACACATTGCAATCATCATTAGA	59.113	36.000	9.53	0.00	0.00	2.10
3564	4355	1.205655	CCTCGTCATCACTCCACACAT	59.794	52.381	0.00	0.00	0.00	3.21
3585	4376	2.917933	TGGAATCGTCATCACCCATTC	58.082	47.619	0.00	0.00	0.00	2.67
3619	4410	3.194861	TGCGCTTGATATTGGTGACTAC	58.805	45.455	9.73	0.00	0.00	2.73
3656	4447	0.905357	CAAAGTCACCTCCGAGGGAT	59.095	55.000	18.99	0.00	40.58	3.85
3667	4458	1.701292	TCCGAGGGATATGACGTCCTA	59.299	52.381	14.12	8.19	36.00	2.94
3675	4466	5.046304	AGGGATATGACGTCCTAATTCCATG	60.046	44.000	14.12	0.00	36.00	3.66
3706	4497	4.079844	TCTCCAAGGAATGCAATGTCCATA	60.080	41.667	14.78	0.00	36.28	2.74
3762	4554	1.410932	CCAAACACCTTTCCCCAGACA	60.411	52.381	0.00	0.00	0.00	3.41
3779	4572	3.747529	CAGACAAACAAAAATGATGGGGC	59.252	43.478	0.00	0.00	0.00	5.80
3787	4580	1.560505	AAATGATGGGGCAGTTCACC	58.439	50.000	0.00	0.00	0.00	4.02
3834	4627	3.052620	CTGGAGTCGACCGCACGAT	62.053	63.158	13.01	0.00	43.93	3.73
3860	4653	4.865365	CCTTACGAATCTCAAACCACTCTC	59.135	45.833	0.00	0.00	0.00	3.20
3868	4663	1.202879	TCAAACCACTCTCGGGCATTT	60.203	47.619	0.00	0.00	0.00	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
467	468	2.994995	TGGACTGGTCGACGCCAT	60.995	61.111	9.92	0.00	37.96	4.40
1419	1484	0.330604	AAGCATGAGCATCCACCTGT	59.669	50.000	0.00	0.00	45.49	4.00
1762	1830	3.308401	AGGGGCATCCAAATTAATGTCC	58.692	45.455	9.46	9.46	45.12	4.02
1912	1980	5.067413	CACCCTCAGTAAAGAGTCGCTAATA	59.933	44.000	0.00	0.00	33.75	0.98
2231	2308	8.805175	TGCCATAAATATAAGAATGAACATGGG	58.195	33.333	0.00	0.00	31.82	4.00
2288	2367	5.049167	CCATGTGCTCTTAGATTGACTCTC	58.951	45.833	0.00	0.00	35.28	3.20
2696	2824	3.118592	GCACATTAAGTACTCCCTCTGCT	60.119	47.826	0.00	0.00	0.00	4.24
2868	3092	7.550906	TGACGGTGTCATCACATATTTGATTAA	59.449	33.333	1.46	0.00	45.45	1.40
2960	3254	9.577110	TCAAATGTGAAAGCAATCTGATAAATC	57.423	29.630	0.00	0.00	0.00	2.17
2998	3292	9.920946	AAATAAAATAGGAGATGTAAGGAGCAA	57.079	29.630	0.00	0.00	0.00	3.91
3128	3431	4.803329	AGATAATCCAGGCATTCCAAGT	57.197	40.909	0.00	0.00	33.74	3.16
3174	3952	2.389962	TGGCTATACCCGTGTTTCAC	57.610	50.000	0.00	0.00	37.83	3.18
3216	4000	3.053693	AGGGTGCTCCTATTTGTATTGCA	60.054	43.478	4.53	0.00	45.98	4.08
3262	4046	3.909995	TGAATTTTCCCTCTGGAGTCTCA	59.090	43.478	1.47	0.00	43.07	3.27
3266	4050	6.139679	TGTTATGAATTTTCCCTCTGGAGT	57.860	37.500	0.00	0.00	43.07	3.85
3368	4159	4.993028	TGGTGCTTAAACCACTAGGAAAT	58.007	39.130	0.00	0.00	45.43	2.17
3392	4183	5.983333	AGGACAAGGACAAGGATAATGAT	57.017	39.130	0.00	0.00	0.00	2.45
3399	4190	1.978580	GGAGAAGGACAAGGACAAGGA	59.021	52.381	0.00	0.00	0.00	3.36
3400	4191	1.699634	TGGAGAAGGACAAGGACAAGG	59.300	52.381	0.00	0.00	0.00	3.61
3401	4192	2.104792	TGTGGAGAAGGACAAGGACAAG	59.895	50.000	0.00	0.00	0.00	3.16
3402	4193	2.123589	TGTGGAGAAGGACAAGGACAA	58.876	47.619	0.00	0.00	0.00	3.18
3403	4194	1.801242	TGTGGAGAAGGACAAGGACA	58.199	50.000	0.00	0.00	0.00	4.02
3404	4195	3.008485	AGAATGTGGAGAAGGACAAGGAC	59.992	47.826	0.00	0.00	0.00	3.85
3436	4227	1.941812	GACAAATATGGCGAGGCGG	59.058	57.895	0.00	0.00	0.00	6.13
3443	4234	0.450184	ACAACGCCGACAAATATGGC	59.550	50.000	0.00	0.00	45.39	4.40
3444	4235	2.477189	GGAACAACGCCGACAAATATGG	60.477	50.000	0.00	0.00	0.00	2.74
3509	4300	6.139048	TCTAATGATGATTGCAATGTGTGG	57.861	37.500	18.59	0.00	0.00	4.17
3532	4323	0.397675	TGACGAGGATGAGGAGGCAT	60.398	55.000	0.00	0.00	0.00	4.40
3564	4355	3.278574	GAATGGGTGATGACGATTCCAA	58.721	45.455	0.00	0.00	0.00	3.53
3585	4376	3.503891	TCAAGCGCATCATTCAACATTG	58.496	40.909	11.47	0.04	0.00	2.82
3619	4410	2.887649	TTTGATGGCAATGGGGTACCTG	60.888	50.000	12.72	2.91	40.86	4.00
3656	4447	4.100963	AGTGCATGGAATTAGGACGTCATA	59.899	41.667	18.91	12.53	0.00	2.15
3667	4458	4.508551	TGGAGACATAGTGCATGGAATT	57.491	40.909	0.00	0.00	39.13	2.17
3675	4466	2.615912	GCATTCCTTGGAGACATAGTGC	59.384	50.000	0.00	0.00	42.32	4.40
3706	4497	3.439857	AGTACCACCTTCACATGCATT	57.560	42.857	0.00	0.00	0.00	3.56
3762	4554	4.141528	TGAACTGCCCCATCATTTTTGTTT	60.142	37.500	0.00	0.00	0.00	2.83
3787	4580	2.821378	TGCCATCTTCATGACCAACAAG	59.179	45.455	0.00	0.00	30.57	3.16
3834	4627	4.039973	AGTGGTTTGAGATTCGTAAGGTGA	59.960	41.667	0.00	0.00	38.47	4.02
3868	4663	0.108186	AGCTTGACGCAATCATCGGA	60.108	50.000	0.00	0.00	42.61	4.55
3877	4672	2.210013	ACTCCCTGAGCTTGACGCA	61.210	57.895	0.00	0.00	42.61	5.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.