AutoCloner

Multiple sequence alignment - TraesCS2A01G243000

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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	TraesCS2A01G243000	chr2A	100.000	3545	0	0	1	3545	338544757	338548301	0.000000e+00	6547
1	TraesCS2A01G243000	chr2A	94.421	466	26	0	3080	3545	30315035	30315500	0.000000e+00	717
2	TraesCS2A01G243000	chr2A	72.259	602	128	28	1870	2462	69314324	69314895	2.200000e-32	150
3	TraesCS2A01G243000	chr7D	96.762	3088	88	3	470	3545	379089737	379092824	0.000000e+00	5138
4	TraesCS2A01G243000	chr7D	95.682	579	25	0	1	579	541551999	541552577	0.000000e+00	931
5	TraesCS2A01G243000	chr7D	94.991	579	28	1	1	579	366571654	366571077	0.000000e+00	907
6	TraesCS2A01G243000	chr7A	96.729	2018	62	2	793	2809	427556823	427558837	0.000000e+00	3358
7	TraesCS2A01G243000	chr7A	83.224	304	40	6	2797	3092	427564625	427564925	5.830000e-68	268
8	TraesCS2A01G243000	chr7A	79.487	234	40	7	3087	3315	391901045	391901275	3.660000e-35	159
9	TraesCS2A01G243000	chr7A	80.319	188	22	8	2811	2983	90780623	90780810	1.030000e-25	128
10	TraesCS2A01G243000	chr7B	96.347	1971	54	8	793	2748	374528838	374530805	0.000000e+00	3225
11	TraesCS2A01G243000	chr7B	90.196	459	23	5	3087	3545	496786131	496786567	2.370000e-161	579
12	TraesCS2A01G243000	chr7B	89.474	209	15	3	580	785	374528325	374528529	1.260000e-64	257
13	TraesCS2A01G243000	chr7B	81.974	233	38	4	3088	3317	113064429	113064198	1.000000e-45	195
14	TraesCS2A01G243000	chr7B	85.981	107	4	3	2981	3077	374536331	374536436	1.740000e-18	104
15	TraesCS2A01G243000	chrUn	95.682	579	25	0	1	579	103839998	103839420	0.000000e+00	931
16	TraesCS2A01G243000	chrUn	78.836	189	33	7	2237	2420	114234904	114235090	1.730000e-23	121
17	TraesCS2A01G243000	chr2D	95.337	579	27	0	1	579	546397338	546397916	0.000000e+00	920
18	TraesCS2A01G243000	chr2D	95.824	455	17	1	3093	3545	73414946	73415400	0.000000e+00	734
19	TraesCS2A01G243000	chr2D	72.742	609	136	27	1870	2463	69275586	69276179	1.010000e-40	178
20	TraesCS2A01G243000	chr1D	95.337	579	25	1	1	579	300912520	300913096	0.000000e+00	918
21	TraesCS2A01G243000	chr4D	95.164	579	28	0	1	579	123772839	123773417	0.000000e+00	915
22	TraesCS2A01G243000	chr4D	94.863	584	30	0	1	584	87424345	87423762	0.000000e+00	913
23	TraesCS2A01G243000	chr4D	94.991	579	29	0	1	579	219666374	219666952	0.000000e+00	909
24	TraesCS2A01G243000	chr3D	95.164	579	28	0	1	579	398325954	398326532	0.000000e+00	915
25	TraesCS2A01G243000	chr3D	81.921	177	29	3	3090	3264	135589540	135589365	2.850000e-31	147
26	TraesCS2A01G243000	chr5B	82.110	436	61	12	3091	3524	507658083	507657663	1.210000e-94	357
27	TraesCS2A01G243000	chr5B	80.000	165	19	7	2833	2983	398074964	398075128	3.740000e-20	110
28	TraesCS2A01G243000	chr1B	76.527	622	111	23	1870	2463	522743984	522743370	1.240000e-79	307
29	TraesCS2A01G243000	chr1B	79.474	190	24	8	2812	2986	134029840	134029651	1.730000e-23	121
30	TraesCS2A01G243000	chr2B	71.687	830	193	36	1680	2485	105896082	105896893	3.610000e-45	193
31	TraesCS2A01G243000	chr2B	80.203	197	39	0	2237	2433	470902780	470902976	7.930000e-32	148
32	TraesCS2A01G243000	chr2B	79.787	188	25	6	2811	2985	459418496	459418683	1.340000e-24	124
33	TraesCS2A01G243000	chr3A	81.503	173	31	1	3087	3258	467157544	467157716	1.330000e-29	141
34	TraesCS2A01G243000	chr3B	80.541	185	23	6	2811	2982	112100830	112101014	2.870000e-26	130
35	TraesCS2A01G243000	chr1A	78.804	184	26	6	2811	2981	309622564	309622381	1.040000e-20	111
36	TraesCS2A01G243000	chr6A	95.652	46	2	0	2936	2981	181127694	181127739	1.360000e-09	75
37	TraesCS2A01G243000	chr4B	95.652	46	2	0	2936	2981	94255413	94255368	1.360000e-09	75

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	TraesCS2A01G243000	chr2A	338544757	338548301	3544	False	6547	6547	100.0000	1	3545	1	chr2A.!!$F3	3544
1	TraesCS2A01G243000	chr7D	379089737	379092824	3087	False	5138	5138	96.7620	470	3545	1	chr7D.!!$F1	3075
2	TraesCS2A01G243000	chr7D	541551999	541552577	578	False	931	931	95.6820	1	579	1	chr7D.!!$F2	578
3	TraesCS2A01G243000	chr7D	366571077	366571654	577	True	907	907	94.9910	1	579	1	chr7D.!!$R1	578
4	TraesCS2A01G243000	chr7A	427556823	427558837	2014	False	3358	3358	96.7290	793	2809	1	chr7A.!!$F3	2016
5	TraesCS2A01G243000	chr7B	374528325	374530805	2480	False	1741	3225	92.9105	580	2748	2	chr7B.!!$F3	2168
6	TraesCS2A01G243000	chrUn	103839420	103839998	578	True	931	931	95.6820	1	579	1	chrUn.!!$R1	578
7	TraesCS2A01G243000	chr2D	546397338	546397916	578	False	920	920	95.3370	1	579	1	chr2D.!!$F3	578
8	TraesCS2A01G243000	chr1D	300912520	300913096	576	False	918	918	95.3370	1	579	1	chr1D.!!$F1	578
9	TraesCS2A01G243000	chr4D	123772839	123773417	578	False	915	915	95.1640	1	579	1	chr4D.!!$F1	578
10	TraesCS2A01G243000	chr4D	87423762	87424345	583	True	913	913	94.8630	1	584	1	chr4D.!!$R1	583
11	TraesCS2A01G243000	chr4D	219666374	219666952	578	False	909	909	94.9910	1	579	1	chr4D.!!$F2	578
12	TraesCS2A01G243000	chr3D	398325954	398326532	578	False	915	915	95.1640	1	579	1	chr3D.!!$F1	578
13	TraesCS2A01G243000	chr1B	522743370	522743984	614	True	307	307	76.5270	1870	2463	1	chr1B.!!$R2	593

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
459	460	0.720027	GAGTTAAAGTCGCCGGCTTC	59.280	55.0	26.68	16.99	0.0	3.86	F
1670	1975	0.321671	CTCCTCGCCAACTTCCTCAA	59.678	55.0	0.00	0.00	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2031	2372	0.256464	CCTGTAGGTCCTCCTCTCGT	59.744	60.0	0.00	0.00	43.94	4.18	R
3195	3565	0.110419	TTCCTTCGATTTTGCACGCG	60.110	50.0	3.53	3.53	0.00	6.01	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
53	54	6.903479	AGTTGACGAACGAAAAGTAAATTGTC	59.097	34.615	0.14	0.00	37.15	3.18
230	231	4.503296	GCTTCCGGTCATATGATTAGTGGT	60.503	45.833	9.02	0.00	0.00	4.16
260	261	1.217057	AGCAACCATGATCCCCCACT	61.217	55.000	0.00	0.00	0.00	4.00
305	306	4.993028	TCAATGCTTGGTTTTAGGTACCT	58.007	39.130	20.57	20.57	36.60	3.08
419	420	8.759481	TTTATCATAAACATGCCCATCACTAA	57.241	30.769	0.00	0.00	0.00	2.24
441	442	5.654603	ACACGACATAACACATAGGAAGA	57.345	39.130	0.00	0.00	0.00	2.87
459	460	0.720027	GAGTTAAAGTCGCCGGCTTC	59.280	55.000	26.68	16.99	0.00	3.86
491	492	2.622942	GTGACATTGCCCTTCTTGACAA	59.377	45.455	0.00	0.00	0.00	3.18
519	520	5.300286	CACCCTTCACATTGTTCTTCTTCTT	59.700	40.000	0.00	0.00	0.00	2.52
551	552	3.456277	GCCCTCTCCCTCTTTCATAAAGA	59.544	47.826	2.39	2.39	44.82	2.52
637	640	2.965147	CCACAACCTCCACATTTTCCTT	59.035	45.455	0.00	0.00	0.00	3.36
763	767	6.357579	AGCATCATGAGGTTATCTCTAAGG	57.642	41.667	9.42	0.00	42.86	2.69
802	1107	6.692486	TGAATAAAAAGGGCGAATTTGCTTA	58.308	32.000	17.19	8.00	34.52	3.09
942	1247	2.028930	CCGACCTCTTTCTTGCAGTACT	60.029	50.000	0.00	0.00	0.00	2.73
947	1252	5.491982	ACCTCTTTCTTGCAGTACTAATGG	58.508	41.667	0.00	0.00	0.00	3.16
1227	1532	2.916181	GCCTACGGCCCGGTCTAT	60.916	66.667	8.57	0.00	44.06	1.98
1392	1697	3.120385	CGCAACATCAGCTCCGCA	61.120	61.111	0.00	0.00	0.00	5.69
1670	1975	0.321671	CTCCTCGCCAACTTCCTCAA	59.678	55.000	0.00	0.00	0.00	3.02
1785	2090	3.064987	CTTCGTCCCGCTCATCCGT	62.065	63.158	0.00	0.00	0.00	4.69
1875	2180	4.423209	GGAGGGAGGGGGCTCACT	62.423	72.222	0.00	0.00	40.27	3.41
1985	2290	3.864686	CAAGAACCCGGCGATGCG	61.865	66.667	9.30	0.00	0.00	4.73
2046	2387	4.178289	CGAGCTACGAGAGGAGGACCTA	62.178	59.091	0.00	0.00	44.36	3.08
2225	2566	1.993956	CTGGACGAGGAGATCTGGAT	58.006	55.000	0.00	0.00	0.00	3.41
2478	2822	1.667830	CACGGTTGTCATGAGGCGT	60.668	57.895	0.00	0.00	0.00	5.68
2574	2918	2.355209	GGCGAACCATCTTCTCCTTTCT	60.355	50.000	0.00	0.00	35.26	2.52
2613	2965	1.929836	CCATAGCTTCTCGTTGCTCAC	59.070	52.381	0.00	0.00	40.35	3.51
2694	3053	9.409312	CTTTTGCTAATGAAATGTAATGTGTGA	57.591	29.630	0.00	0.00	0.00	3.58
2838	3198	1.330829	GCCTTGGCGTAGTGATAAAGC	59.669	52.381	0.00	0.00	0.00	3.51
2849	3209	3.274288	AGTGATAAAGCTAGTGCCTTGC	58.726	45.455	0.00	1.54	40.80	4.01
2857	3217	0.391661	CTAGTGCCTTGCGACCATGT	60.392	55.000	0.00	0.00	0.00	3.21
2858	3218	0.673333	TAGTGCCTTGCGACCATGTG	60.673	55.000	0.00	0.00	0.00	3.21
2878	3238	0.033504	GTCACGGGCTCAAGTCTTGA	59.966	55.000	14.54	14.54	38.17	3.02
2884	3244	2.357637	CGGGCTCAAGTCTTGAAAACAA	59.642	45.455	15.97	0.00	39.58	2.83
2892	3252	8.078596	GCTCAAGTCTTGAAAACAATCACTTAT	58.921	33.333	15.97	0.00	39.58	1.73
2944	3304	1.918293	AAGGTGATCGGACCCTGCA	60.918	57.895	0.00	0.00	36.56	4.41
3023	3383	8.840867	CAAAGAGCGAAATAAACAGACAAATAC	58.159	33.333	0.00	0.00	0.00	1.89
3155	3525	4.452733	GGAGTCCAGCCGAACGGG	62.453	72.222	15.01	0.00	39.58	5.28
3214	3584	0.110419	CGCGTGCAAAATCGAAGGAA	60.110	50.000	0.00	0.00	0.00	3.36
3252	3622	2.347490	GGCTCCGCAGAAACTGGA	59.653	61.111	0.00	0.00	31.21	3.86
3260	3630	0.889186	GCAGAAACTGGAAAGCGGGA	60.889	55.000	0.00	0.00	31.21	5.14
3264	3634	3.756434	CAGAAACTGGAAAGCGGGATTTA	59.244	43.478	0.00	0.00	0.00	1.40
3269	3639	5.738619	ACTGGAAAGCGGGATTTAAAAAT	57.261	34.783	0.00	0.00	0.00	1.82
3272	3642	7.847096	ACTGGAAAGCGGGATTTAAAAATAAT	58.153	30.769	0.00	0.00	0.00	1.28
3276	3646	9.811995	GGAAAGCGGGATTTAAAAATAATTACT	57.188	29.630	0.00	0.00	0.00	2.24
3290	3660	0.881118	ATTACTTGCTTGTGCCACCG	59.119	50.000	0.00	0.00	38.71	4.94
3310	3680	0.442310	CCAAGTGACATTGCGTACCG	59.558	55.000	0.00	0.00	0.00	4.02
3329	3699	1.355971	GGTTCGCGAGCAACTAATCA	58.644	50.000	24.44	0.00	0.00	2.57
3349	3719	6.986137	ATCATATTCTCTCTCTCCCTCCTA	57.014	41.667	0.00	0.00	0.00	2.94
3366	3736	1.030457	CTAACTCGTACGCCATCCCT	58.970	55.000	11.24	0.00	0.00	4.20
3371	3741	0.899720	TCGTACGCCATCCCTTCTTT	59.100	50.000	11.24	0.00	0.00	2.52
3400	3770	3.181429	TGTTGGGCTGAAGAGGAGAAAAT	60.181	43.478	0.00	0.00	0.00	1.82
3491	3861	1.595109	CCCATGCGAGCGCTAATGA	60.595	57.895	22.26	4.85	42.51	2.57
3510	3880	2.166459	TGATTGAGAAGCTACTGTCCCG	59.834	50.000	0.00	0.00	0.00	5.14
3513	3883	2.457598	TGAGAAGCTACTGTCCCGAAT	58.542	47.619	0.00	0.00	0.00	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.250031	ACTTGCAATCATGGGCTTTGA	58.750	42.857	0.00	0.00	0.00	2.69
53	54	0.595095	GCTTGTTGAGTCCCTTGCAG	59.405	55.000	0.00	0.00	0.00	4.41
107	108	2.101640	ATTGGGACTTGGCAAGGTTT	57.898	45.000	29.26	10.36	0.00	3.27
230	231	2.499693	TCATGGTTGCTCGATAGTGGAA	59.500	45.455	0.00	0.00	37.58	3.53
260	261	3.135712	TCTCTTGTAGGTGTTTGCTTCCA	59.864	43.478	0.00	0.00	0.00	3.53
398	399	5.356751	GTGTTAGTGATGGGCATGTTTATGA	59.643	40.000	0.00	0.00	36.36	2.15
419	420	5.185249	ACTCTTCCTATGTGTTATGTCGTGT	59.815	40.000	0.00	0.00	0.00	4.49
441	442	1.012486	CGAAGCCGGCGACTTTAACT	61.012	55.000	23.20	0.00	0.00	2.24
459	460	0.881118	CAATGTCACCCCTTCCAACG	59.119	55.000	0.00	0.00	0.00	4.10
491	492	2.091885	AGAACAATGTGAAGGGTGGTGT	60.092	45.455	0.00	0.00	0.00	4.16
519	520	2.982130	GAGAGGGCGCTCCAAAGA	59.018	61.111	25.68	0.00	38.24	2.52
551	552	2.238395	GACCTCCTCCTCTCAAGCAAAT	59.762	50.000	0.00	0.00	0.00	2.32
637	640	4.457603	GTCAACAATGGGTACAGTGCAATA	59.542	41.667	0.00	0.00	46.01	1.90
686	689	5.047660	GGATGGCAACTTGTACCACATTTTA	60.048	40.000	0.00	0.00	35.99	1.52
763	767	9.366216	CCTTTTTATTCAGGGTTGCTAATTAAC	57.634	33.333	0.00	0.00	0.00	2.01
881	1186	1.616725	GGAAGTTGGTGGCATGGATCA	60.617	52.381	0.00	0.00	0.00	2.92
883	1188	0.324645	GGGAAGTTGGTGGCATGGAT	60.325	55.000	0.00	0.00	0.00	3.41
947	1252	0.250081	GGATTCCGGTGGAGATGCTC	60.250	60.000	0.00	0.00	31.21	4.26
1227	1532	2.749839	CCCAATGGCGCGAAGGAA	60.750	61.111	12.10	0.00	0.00	3.36
1392	1697	3.407967	CAGGTGGGCCCATACGGT	61.408	66.667	31.45	8.22	34.66	4.83
1536	1841	3.329542	GAAGGGCTCCATGACGGCA	62.330	63.158	0.00	0.00	33.14	5.69
1670	1975	2.158081	AGGAAGGAGAAGACCTGGAAGT	60.158	50.000	0.00	0.00	40.49	3.01
1730	2035	3.184683	GCAGCGAGACGAGCTTGG	61.185	66.667	5.79	0.00	44.06	3.61
1902	2207	4.069232	CCGGCGCTCAGGAACTCA	62.069	66.667	7.64	0.00	34.60	3.41
1985	2290	1.003051	TCCTCCCTTAGCCTGTCCC	59.997	63.158	0.00	0.00	0.00	4.46
2031	2372	0.256464	CCTGTAGGTCCTCCTCTCGT	59.744	60.000	0.00	0.00	43.94	4.18
2034	2375	0.555369	TCCCCTGTAGGTCCTCCTCT	60.555	60.000	0.00	0.00	43.94	3.69
2046	2387	2.040606	AGGTACGGCATCCCCTGT	59.959	61.111	0.00	0.00	0.00	4.00
2574	2918	4.260139	TGGTGCACTACTAAACATTCGA	57.740	40.909	17.98	0.00	0.00	3.71
2857	3217	1.407656	AAGACTTGAGCCCGTGACCA	61.408	55.000	0.00	0.00	0.00	4.02
2858	3218	0.951040	CAAGACTTGAGCCCGTGACC	60.951	60.000	9.76	0.00	0.00	4.02
2865	3225	4.978580	GTGATTGTTTTCAAGACTTGAGCC	59.021	41.667	17.06	10.07	43.41	4.70
2866	3226	5.825507	AGTGATTGTTTTCAAGACTTGAGC	58.174	37.500	17.06	12.18	43.41	4.26
2899	3259	8.090214	GGGTCTATTGTACGCAATATTTACCTA	58.910	37.037	16.85	0.00	43.97	3.08
2923	3283	1.995626	AGGGTCCGATCACCTTGGG	60.996	63.158	2.49	0.00	36.57	4.12
2928	3288	2.125106	GTGCAGGGTCCGATCACC	60.125	66.667	0.00	0.00	35.42	4.02
2944	3304	1.450312	GCATGTAGCTCCCGCTTGT	60.450	57.895	0.00	0.00	46.47	3.16
2988	3348	7.810759	TGTTTATTTCGCTCTTTGGGTTAAATC	59.189	33.333	0.00	0.00	0.00	2.17
3023	3383	7.145932	AGGTTCCAGAAAAAGAATGTATTCG	57.854	36.000	0.00	0.00	41.56	3.34
3109	3479	4.128643	GAGATGAGGATTTGAGAAGCCAG	58.871	47.826	0.00	0.00	43.86	4.85
3155	3525	1.981256	TCCAAAAGCCAGGAGTTGAC	58.019	50.000	0.00	0.00	0.00	3.18
3195	3565	0.110419	TTCCTTCGATTTTGCACGCG	60.110	50.000	3.53	3.53	0.00	6.01
3214	3584	1.202722	ACGTTTTCCCAACTCCACGAT	60.203	47.619	0.00	0.00	0.00	3.73
3264	3634	6.426633	GGTGGCACAAGCAAGTAATTATTTTT	59.573	34.615	20.82	0.00	44.16	1.94
3269	3639	2.486203	CGGTGGCACAAGCAAGTAATTA	59.514	45.455	20.82	0.00	44.16	1.40
3272	3642	1.791103	GCGGTGGCACAAGCAAGTAA	61.791	55.000	25.42	0.00	44.16	2.24
3290	3660	0.168128	GGTACGCAATGTCACTTGGC	59.832	55.000	0.00	0.00	0.00	4.52
3310	3680	1.355971	TGATTAGTTGCTCGCGAACC	58.644	50.000	11.33	4.71	0.00	3.62
3329	3699	6.521770	CGAGTTAGGAGGGAGAGAGAGAATAT	60.522	46.154	0.00	0.00	0.00	1.28
3349	3719	0.175073	GAAGGGATGGCGTACGAGTT	59.825	55.000	21.65	1.13	0.00	3.01
3366	3736	4.277476	TCAGCCCAACAAGAAGAAAAGAA	58.723	39.130	0.00	0.00	0.00	2.52
3371	3741	3.480470	CTCTTCAGCCCAACAAGAAGAA	58.520	45.455	0.00	0.00	43.97	2.52
3400	3770	1.004628	TCTTGCAGCCCAATTAGCTCA	59.995	47.619	0.00	0.10	38.95	4.26
3491	3861	2.457598	TCGGGACAGTAGCTTCTCAAT	58.542	47.619	0.00	0.00	0.00	2.57
3510	3880	5.728637	ATCCTGGAGTTTGAAAACCATTC	57.271	39.130	1.52	0.00	39.71	2.67
3513	3883	5.948742	AAAATCCTGGAGTTTGAAAACCA	57.051	34.783	20.16	5.30	39.71	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.