AutoCloner

Multiple sequence alignment - TraesCS3B01G529600

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	TraesCS3B01G529600	chr3B	100.000	4201	0	0	1	4201	771160778	771164978	0.000000e+00	7758.0
1	TraesCS3B01G529600	chr3B	98.117	956	17	1	1	956	790322394	790321440	0.000000e+00	1664.0
2	TraesCS3B01G529600	chr3B	97.490	956	24	0	1	956	735947694	735948649	0.000000e+00	1633.0
3	TraesCS3B01G529600	chr3B	97.495	958	19	2	1	957	44037699	44038652	0.000000e+00	1631.0
4	TraesCS3B01G529600	chr3B	97.390	958	24	1	1	957	742678345	742677388	0.000000e+00	1629.0
5	TraesCS3B01G529600	chr3B	92.373	118	6	1	3646	3763	770973636	770973522	9.340000e-37	165.0
6	TraesCS3B01G529600	chr3B	88.182	110	8	3	3876	3982	771323342	771323235	4.410000e-25	126.0
7	TraesCS3B01G529600	chr7B	97.866	2484	48	3	1163	3644	614793264	614790784	0.000000e+00	4289.0
8	TraesCS3B01G529600	chr7B	97.492	957	20	1	1	957	629611202	629610250	0.000000e+00	1631.0
9	TraesCS3B01G529600	chr6A	94.589	2384	126	3	1033	3414	58301721	58299339	0.000000e+00	3685.0
10	TraesCS3B01G529600	chr6A	87.245	196	23	2	3447	3640	58299255	58299060	5.470000e-54	222.0
11	TraesCS3B01G529600	chr7A	94.169	2384	136	3	1033	3414	652613238	652615620	0.000000e+00	3629.0
12	TraesCS3B01G529600	chr7A	86.408	206	26	2	3441	3644	652615698	652615903	1.520000e-54	224.0
13	TraesCS3B01G529600	chr4B	92.804	2404	145	15	1033	3420	274134113	274136504	0.000000e+00	3456.0
14	TraesCS3B01G529600	chr3D	93.182	2332	156	3	1033	3362	55947128	55944798	0.000000e+00	3422.0
15	TraesCS3B01G529600	chr3D	93.182	2332	154	4	1033	3362	52815105	52812777	0.000000e+00	3421.0
16	TraesCS3B01G529600	chr3D	88.665	547	44	12	3645	4189	577820547	577820017	0.000000e+00	651.0
17	TraesCS3B01G529600	chr3D	87.956	548	43	6	3645	4186	577967381	577967911	3.570000e-175	625.0
18	TraesCS3B01G529600	chr3D	83.784	148	11	8	3869	4010	577886715	577886855	1.230000e-25	128.0
19	TraesCS3B01G529600	chr3D	96.610	59	2	0	3790	3848	577886672	577886730	9.610000e-17	99.0
20	TraesCS3B01G529600	chr3D	100.000	48	0	0	957	1004	577820614	577820567	5.790000e-14	89.8
21	TraesCS3B01G529600	chr7D	92.753	2332	163	5	1033	3362	47508119	47505792	0.000000e+00	3365.0
22	TraesCS3B01G529600	chr4A	89.789	2321	231	6	1045	3362	698339426	698341743	0.000000e+00	2968.0
23	TraesCS3B01G529600	chr4A	97.799	954	21	0	3	956	687039964	687040917	0.000000e+00	1646.0
24	TraesCS3B01G529600	chr4A	97.385	956	25	0	1	956	707443296	707442341	0.000000e+00	1628.0
25	TraesCS3B01G529600	chr1A	89.420	2344	241	7	1045	3385	550195330	550192991	0.000000e+00	2948.0
26	TraesCS3B01G529600	chr5B	98.013	956	19	0	1	956	516134454	516133499	0.000000e+00	1661.0
27	TraesCS3B01G529600	chr2B	97.492	957	20	1	1	957	776682523	776683475	0.000000e+00	1631.0
28	TraesCS3B01G529600	chr3A	87.590	556	44	12	3645	4189	713551268	713550727	4.610000e-174	621.0
29	TraesCS3B01G529600	chr5A	86.275	204	25	3	3447	3648	475420693	475420491	7.070000e-53	219.0

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	TraesCS3B01G529600	chr3B	771160778	771164978	4200	False	7758.0	7758	100.0000	1	4201	1	chr3B.!!$F3	4200
1	TraesCS3B01G529600	chr3B	790321440	790322394	954	True	1664.0	1664	98.1170	1	956	1	chr3B.!!$R4	955
2	TraesCS3B01G529600	chr3B	735947694	735948649	955	False	1633.0	1633	97.4900	1	956	1	chr3B.!!$F2	955
3	TraesCS3B01G529600	chr3B	44037699	44038652	953	False	1631.0	1631	97.4950	1	957	1	chr3B.!!$F1	956
4	TraesCS3B01G529600	chr3B	742677388	742678345	957	True	1629.0	1629	97.3900	1	957	1	chr3B.!!$R1	956
5	TraesCS3B01G529600	chr7B	614790784	614793264	2480	True	4289.0	4289	97.8660	1163	3644	1	chr7B.!!$R1	2481
6	TraesCS3B01G529600	chr7B	629610250	629611202	952	True	1631.0	1631	97.4920	1	957	1	chr7B.!!$R2	956
7	TraesCS3B01G529600	chr6A	58299060	58301721	2661	True	1953.5	3685	90.9170	1033	3640	2	chr6A.!!$R1	2607
8	TraesCS3B01G529600	chr7A	652613238	652615903	2665	False	1926.5	3629	90.2885	1033	3644	2	chr7A.!!$F1	2611
9	TraesCS3B01G529600	chr4B	274134113	274136504	2391	False	3456.0	3456	92.8040	1033	3420	1	chr4B.!!$F1	2387
10	TraesCS3B01G529600	chr3D	55944798	55947128	2330	True	3422.0	3422	93.1820	1033	3362	1	chr3D.!!$R2	2329
11	TraesCS3B01G529600	chr3D	52812777	52815105	2328	True	3421.0	3421	93.1820	1033	3362	1	chr3D.!!$R1	2329
12	TraesCS3B01G529600	chr3D	577967381	577967911	530	False	625.0	625	87.9560	3645	4186	1	chr3D.!!$F1	541
13	TraesCS3B01G529600	chr3D	577820017	577820614	597	True	370.4	651	94.3325	957	4189	2	chr3D.!!$R3	3232
14	TraesCS3B01G529600	chr7D	47505792	47508119	2327	True	3365.0	3365	92.7530	1033	3362	1	chr7D.!!$R1	2329
15	TraesCS3B01G529600	chr4A	698339426	698341743	2317	False	2968.0	2968	89.7890	1045	3362	1	chr4A.!!$F2	2317
16	TraesCS3B01G529600	chr4A	687039964	687040917	953	False	1646.0	1646	97.7990	3	956	1	chr4A.!!$F1	953
17	TraesCS3B01G529600	chr4A	707442341	707443296	955	True	1628.0	1628	97.3850	1	956	1	chr4A.!!$R1	955
18	TraesCS3B01G529600	chr1A	550192991	550195330	2339	True	2948.0	2948	89.4200	1045	3385	1	chr1A.!!$R1	2340
19	TraesCS3B01G529600	chr5B	516133499	516134454	955	True	1661.0	1661	98.0130	1	956	1	chr5B.!!$R1	955
20	TraesCS3B01G529600	chr2B	776682523	776683475	952	False	1631.0	1631	97.4920	1	957	1	chr2B.!!$F1	956
21	TraesCS3B01G529600	chr3A	713550727	713551268	541	True	621.0	621	87.5900	3645	4189	1	chr3A.!!$R1	544

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	Hairpin	End Stability	Orientation
670	676	1.427753	GAGGGGAAAGGGGAAGAACAA	59.572	52.381	0.00	0.00	2.83	F
1004	1023	0.611714	GGGACACCCACGTAGATGTT	59.388	55.000	1.54	44.65	2.71	F
1006	1025	2.073816	GGACACCCACGTAGATGTTTG	58.926	52.381	0.00	0.00	2.93	F
2331	2366	2.371910	GCGTCAAGCTAGAGGTCTTT	57.628	50.000	0.00	44.04	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2060	2095	0.960364	AAGATGCGCCCACGACATTT	60.960	50.000	4.18	0.00	43.93	2.32	R
2152	2187	1.829222	GATTCAGTCCACTCCCCGTAA	59.171	52.381	0.00	0.00	0.00	3.18	R
2806	2859	8.739039	CCATATCTTTGTGATTAAAGTCACCAA	58.261	33.333	6.72	2.24	46.17	3.67	R
4059	4173	0.328258	AAACACGGCTTATCCCTGCT	59.672	50.000	0.00	0.00	0.00	4.24	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
63	64	3.497332	TCCGATTCACATACCTCCTAGG	58.503	50.000	0.82	0.82	42.49	3.02
119	120	7.887996	ATTTGTCATAAACACGAAATGCAAT	57.112	28.000	0.00	0.00	37.70	3.56
311	317	7.036996	TGTAAAACATTCATGAACAAGAGCA	57.963	32.000	11.07	2.55	0.00	4.26
509	515	6.816134	TCACTATACAAAGCATTGCAAGAA	57.184	33.333	11.91	0.00	40.34	2.52
544	550	7.468631	GCAATGAGAGTTGAAAGGACAAAGTTA	60.469	37.037	0.00	0.00	0.00	2.24
670	676	1.427753	GAGGGGAAAGGGGAAGAACAA	59.572	52.381	0.00	0.00	0.00	2.83
748	755	1.963515	ACGAACCGGTACTAAAGGTGT	59.036	47.619	8.00	0.00	38.44	4.16
1004	1023	0.611714	GGGACACCCACGTAGATGTT	59.388	55.000	1.54	0.00	44.65	2.71
1006	1025	2.073816	GGACACCCACGTAGATGTTTG	58.926	52.381	0.00	0.00	0.00	2.93
1025	1044	5.930837	TTTGAACCACTCAAAGTTGGATT	57.069	34.783	0.00	0.00	46.80	3.01
1026	1045	4.916983	TGAACCACTCAAAGTTGGATTG	57.083	40.909	0.00	0.00	0.00	2.67
1027	1046	3.636300	TGAACCACTCAAAGTTGGATTGG	59.364	43.478	13.77	13.77	0.00	3.16
1028	1047	3.312736	ACCACTCAAAGTTGGATTGGT	57.687	42.857	14.99	14.99	33.22	3.67
1029	1048	4.447138	ACCACTCAAAGTTGGATTGGTA	57.553	40.909	18.35	0.00	35.00	3.25
1030	1049	4.998051	ACCACTCAAAGTTGGATTGGTAT	58.002	39.130	18.35	0.00	35.00	2.73
1031	1050	5.393866	ACCACTCAAAGTTGGATTGGTATT	58.606	37.500	18.35	0.00	35.00	1.89
1131	1164	7.121611	TGGTATGATGATTATGCTTATTGGCTG	59.878	37.037	0.00	0.00	0.00	4.85
1137	1170	6.782986	TGATTATGCTTATTGGCTGGAGTAT	58.217	36.000	0.00	0.00	0.00	2.12
1278	1311	4.202503	ACAGGGAGATTTGTGACTCACATT	60.203	41.667	12.71	3.99	44.16	2.71
1693	1728	7.661437	TGTGTTCAGCTTATTAGTTGATGAGTT	59.339	33.333	0.00	0.00	40.66	3.01
1946	1981	6.038603	TGCAAGCTAAAATTATGAGCGAGAAT	59.961	34.615	0.00	0.00	41.23	2.40
2060	2095	8.402798	TCTTTGATATGGTTTCAGTTTTGCTA	57.597	30.769	0.00	0.00	0.00	3.49
2152	2187	4.411540	AGCAATAGGATGTGGAGAGATTGT	59.588	41.667	0.00	0.00	0.00	2.71
2257	2292	3.564225	GGTTTGTCCAAGATGTTCTCGTT	59.436	43.478	0.00	0.00	35.97	3.85
2331	2366	2.371910	GCGTCAAGCTAGAGGTCTTT	57.628	50.000	0.00	0.00	44.04	2.52
3414	3501	8.565416	CGTCATGTTACTACTGGATGAAGTATA	58.435	37.037	0.00	0.00	32.32	1.47
3494	3599	9.751542	CTACTGGATCAAGTATCTTTCGTTTAT	57.248	33.333	10.49	0.00	34.75	1.40
3569	3676	9.826574	TGGATAAAAAGTGCTAGACGTTTATAT	57.173	29.630	0.00	2.48	35.48	0.86
3690	3798	4.451900	AGTGACCTGACAAAAGAACGAAT	58.548	39.130	0.00	0.00	0.00	3.34
3691	3799	4.881850	AGTGACCTGACAAAAGAACGAATT	59.118	37.500	0.00	0.00	0.00	2.17
3692	3800	5.357032	AGTGACCTGACAAAAGAACGAATTT	59.643	36.000	0.00	0.00	0.00	1.82
3737	3845	0.319083	CACTACGGTACAAGCCACCA	59.681	55.000	0.00	0.00	35.67	4.17
3750	3858	1.963679	CCACCATTCCAACCCGTTG	59.036	57.895	0.39	0.39	40.13	4.10
3829	3937	5.335127	CAGCATATATACCCGTAACCGTAC	58.665	45.833	0.00	0.00	0.00	3.67
3860	3968	1.135112	GCAAGAAATTAGCCAACGGGG	60.135	52.381	0.00	0.00	40.85	5.73
3867	3975	0.912487	TTAGCCAACGGGGAGTGGAT	60.912	55.000	0.00	0.00	40.01	3.41
3928	4036	5.479306	CGAGGATTTCCATGGAACGTATAT	58.521	41.667	27.04	16.87	38.89	0.86
4051	4165	5.188163	TCCACACCTAGACAATCGGAAAATA	59.812	40.000	0.00	0.00	0.00	1.40
4059	4173	5.556915	AGACAATCGGAAAATAGGTTGTCA	58.443	37.500	19.46	0.00	44.65	3.58
4073	4187	0.107703	TTGTCAGCAGGGATAAGCCG	60.108	55.000	0.00	0.00	37.63	5.52
4115	4229	7.698506	ACCCTTTTTAGGCTAAATAAGTGTC	57.301	36.000	19.65	0.00	0.00	3.67
4116	4230	6.662234	ACCCTTTTTAGGCTAAATAAGTGTCC	59.338	38.462	19.65	0.00	0.00	4.02
4150	4264	9.607988	TGAGTTTCACAAGAATTAGTGAGTTAA	57.392	29.630	7.60	0.00	44.65	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
182	183	3.979911	AGTGCCATGGTTTTGATATCCA	58.020	40.909	14.67	0.00	35.64	3.41
354	360	1.443194	CTCCGTCGTAACCACCGTG	60.443	63.158	0.00	0.00	0.00	4.94
509	515	7.768120	CCTTTCAACTCTCATTGCTAGATTAGT	59.232	37.037	0.00	0.00	0.00	2.24
544	550	7.451255	TCCATTCAAATGATCACAAAGGTTAGT	59.549	33.333	0.00	0.00	38.70	2.24
612	618	0.106719	CCTCTCTCCTCGAGCTCCTT	60.107	60.000	6.99	0.00	39.70	3.36
748	755	4.974438	AGTCTGGGGCCCGTCCAA	62.974	66.667	19.83	0.00	36.21	3.53
1004	1023	4.099266	CCAATCCAACTTTGAGTGGTTCAA	59.901	41.667	1.97	0.00	43.92	2.69
1006	1025	3.636764	ACCAATCCAACTTTGAGTGGTTC	59.363	43.478	8.74	0.00	34.74	3.62
1018	1037	2.430694	GGGGCTGAAATACCAATCCAAC	59.569	50.000	0.00	0.00	0.00	3.77
1020	1039	1.409521	CGGGGCTGAAATACCAATCCA	60.410	52.381	0.00	0.00	0.00	3.41
1021	1040	1.318576	CGGGGCTGAAATACCAATCC	58.681	55.000	0.00	0.00	0.00	3.01
1022	1041	0.668535	GCGGGGCTGAAATACCAATC	59.331	55.000	0.00	0.00	0.00	2.67
1023	1042	0.033601	TGCGGGGCTGAAATACCAAT	60.034	50.000	0.00	0.00	0.00	3.16
1024	1043	0.251386	TTGCGGGGCTGAAATACCAA	60.251	50.000	0.00	0.00	0.00	3.67
1025	1044	0.251386	TTTGCGGGGCTGAAATACCA	60.251	50.000	0.00	0.00	0.00	3.25
1026	1045	1.111277	ATTTGCGGGGCTGAAATACC	58.889	50.000	0.00	0.00	0.00	2.73
1027	1046	2.539476	CAATTTGCGGGGCTGAAATAC	58.461	47.619	0.00	0.00	0.00	1.89
1028	1047	1.480137	CCAATTTGCGGGGCTGAAATA	59.520	47.619	0.00	0.00	0.00	1.40
1029	1048	0.249955	CCAATTTGCGGGGCTGAAAT	59.750	50.000	0.00	0.00	0.00	2.17
1030	1049	0.829602	TCCAATTTGCGGGGCTGAAA	60.830	50.000	0.00	0.00	0.00	2.69
1031	1050	0.829602	TTCCAATTTGCGGGGCTGAA	60.830	50.000	0.00	0.00	0.00	3.02
1131	1164	2.030628	GTGCTCCTTCTCGCTATACTCC	60.031	54.545	0.00	0.00	0.00	3.85
1137	1170	1.673033	GCTTTGTGCTCCTTCTCGCTA	60.673	52.381	0.00	0.00	38.95	4.26
1278	1311	5.079689	TGTGAAAGCTATTACGATCACCA	57.920	39.130	0.00	0.00	37.07	4.17
1322	1355	8.627208	TGATTGATCTTGCTTTAATAGATCCC	57.373	34.615	0.00	0.00	42.21	3.85
1495	1529	4.389077	GTCCATCAACTCAAGGTAGTTTCG	59.611	45.833	0.00	0.00	37.61	3.46
1693	1728	6.285224	TGTTCTTTGTCGGAAACATCTCTAA	58.715	36.000	0.00	0.00	37.82	2.10
2060	2095	0.960364	AAGATGCGCCCACGACATTT	60.960	50.000	4.18	0.00	43.93	2.32
2152	2187	1.829222	GATTCAGTCCACTCCCCGTAA	59.171	52.381	0.00	0.00	0.00	3.18
2257	2292	9.661563	CAACATATTCTAGTACTTTAACCACCA	57.338	33.333	0.00	0.00	0.00	4.17
2331	2366	9.312904	AGAATCAAAGGTCTGGAAATATTTGAA	57.687	29.630	5.17	0.00	39.34	2.69
2806	2859	8.739039	CCATATCTTTGTGATTAAAGTCACCAA	58.261	33.333	6.72	2.24	46.17	3.67
3414	3501	7.092935	ACCCCAACATTTCATATGTAGCAAAAT	60.093	33.333	1.90	0.00	0.00	1.82
3542	3649	6.870971	AAACGTCTAGCACTTTTTATCCAA	57.129	33.333	0.00	0.00	0.00	3.53
3548	3655	9.988350	CAATCATATAAACGTCTAGCACTTTTT	57.012	29.630	0.00	0.00	29.63	1.94
3750	3858	1.412453	TACATCCGGTATGGGGTGCC	61.412	60.000	15.41	0.00	40.16	5.01
3860	3968	6.561614	TGTTTCTTCTGACGTATATCCACTC	58.438	40.000	0.00	0.00	0.00	3.51
3867	3975	8.570488	TGACTAGTTTGTTTCTTCTGACGTATA	58.430	33.333	0.00	0.00	0.00	1.47
3967	4075	7.294245	AGTGCCATTCTATATATATGCTCCCAT	59.706	37.037	5.44	0.00	35.44	4.00
3968	4076	6.616959	AGTGCCATTCTATATATATGCTCCCA	59.383	38.462	5.44	0.00	0.00	4.37
3972	4080	9.426534	TGTCTAGTGCCATTCTATATATATGCT	57.573	33.333	5.44	0.00	0.00	3.79
3973	4081	9.469807	GTGTCTAGTGCCATTCTATATATATGC	57.530	37.037	5.44	0.00	0.00	3.14
4051	4165	1.065126	GCTTATCCCTGCTGACAACCT	60.065	52.381	0.00	0.00	0.00	3.50
4059	4173	0.328258	AAACACGGCTTATCCCTGCT	59.672	50.000	0.00	0.00	0.00	4.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.