AutoCloner

Multiple sequence alignment - TraesCS3A01G066000

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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	TraesCS3A01G066000	chr3A	100.000	3618	0	0	1	3618	38994618	38991001	0.000000e+00	6682.0
1	TraesCS3A01G066000	chr3A	88.609	755	68	11	4	748	707352627	707353373	0.000000e+00	902.0
2	TraesCS3A01G066000	chr3A	90.774	336	29	2	1325	1658	452377035	452376700	7.130000e-122	448.0
3	TraesCS3A01G066000	chr1A	96.831	2872	89	2	748	3618	223828439	223825569	0.000000e+00	4798.0
4	TraesCS3A01G066000	chr1A	89.882	850	76	6	2775	3618	166662023	166662868	0.000000e+00	1085.0
5	TraesCS3A01G066000	chr1A	89.635	849	77	8	2775	3618	162701314	162700472	0.000000e+00	1070.0
6	TraesCS3A01G066000	chr1A	91.788	755	44	9	1	748	516588125	516588868	0.000000e+00	1035.0
7	TraesCS3A01G066000	chr1A	88.706	850	84	9	2774	3618	185846394	185847236	0.000000e+00	1027.0
8	TraesCS3A01G066000	chr1A	89.807	726	64	6	2898	3618	162650892	162650172	0.000000e+00	922.0
9	TraesCS3A01G066000	chr1D	94.253	2906	128	18	747	3618	50871362	50874262	0.000000e+00	4405.0
10	TraesCS3A01G066000	chr2D	96.619	2041	67	2	1580	3618	431523325	431521285	0.000000e+00	3386.0
11	TraesCS3A01G066000	chr2D	94.289	823	39	3	747	1561	431524136	431523314	0.000000e+00	1253.0
12	TraesCS3A01G066000	chr2D	88.782	731	64	11	1	724	33927251	33926532	0.000000e+00	880.0
13	TraesCS3A01G066000	chr7D	94.534	2177	113	5	1444	3618	324505745	324503573	0.000000e+00	3356.0
14	TraesCS3A01G066000	chr7D	91.182	567	40	6	830	1392	324506306	324505746	0.000000e+00	761.0
15	TraesCS3A01G066000	chr3D	96.366	1954	69	2	1580	3531	141488889	141490842	0.000000e+00	3214.0
16	TraesCS3A01G066000	chr3D	94.654	823	36	3	747	1561	141488078	141488900	0.000000e+00	1269.0
17	TraesCS3A01G066000	chr3D	91.406	128	8	1	1243	1367	440054412	440054285	4.800000e-39	172.0
18	TraesCS3A01G066000	chr6A	91.402	756	49	9	1	748	498010434	498009687	0.000000e+00	1022.0
19	TraesCS3A01G066000	chr2B	87.388	896	57	24	1921	2771	137214352	137213468	0.000000e+00	977.0
20	TraesCS3A01G066000	chr2B	90.806	620	40	8	134	747	162519197	162518589	0.000000e+00	813.0
21	TraesCS3A01G066000	chr2B	94.231	52	2	1	3	53	162519630	162519579	1.080000e-10	78.7
22	TraesCS3A01G066000	chrUn	89.093	761	64	12	3	754	27336532	27335782	0.000000e+00	928.0
23	TraesCS3A01G066000	chrUn	85.542	332	44	4	832	1161	377928474	377928803	9.620000e-91	344.0
24	TraesCS3A01G066000	chr7B	87.533	754	77	10	3	747	748665237	748664492	0.000000e+00	856.0
25	TraesCS3A01G066000	chr7B	89.706	340	28	5	1325	1658	600922463	600922125	9.280000e-116	427.0
26	TraesCS3A01G066000	chr7B	89.381	339	31	3	1325	1658	608180869	608180531	4.320000e-114	422.0
27	TraesCS3A01G066000	chr7B	85.241	332	45	4	832	1161	600924335	600924006	4.470000e-89	339.0
28	TraesCS3A01G066000	chr7B	84.940	332	46	4	832	1161	608182742	608182413	2.080000e-87	333.0
29	TraesCS3A01G066000	chr7B	92.913	127	5	2	1245	1367	721431401	721431527	7.980000e-42	182.0
30	TraesCS3A01G066000	chr5D	87.026	686	56	12	70	749	385980951	385980293	0.000000e+00	743.0
31	TraesCS3A01G066000	chr5D	85.818	275	32	7	478	747	124208189	124208461	5.910000e-73	285.0
32	TraesCS3A01G066000	chr1B	89.676	339	30	3	1325	1658	635830911	635831249	9.280000e-116	427.0
33	TraesCS3A01G066000	chr1B	86.145	332	42	4	832	1161	382701235	382700906	4.440000e-94	355.0
34	TraesCS3A01G066000	chr1B	92.913	127	5	2	1245	1367	101247320	101247446	7.980000e-42	182.0
35	TraesCS3A01G066000	chr5B	89.381	339	31	3	1325	1658	119152893	119153231	4.320000e-114	422.0
36	TraesCS3A01G066000	chr4B	92.126	127	6	2	1245	1367	35026844	35026718	3.710000e-40	176.0
37	TraesCS3A01G066000	chr2A	91.000	100	6	2	3519	3618	302634148	302634052	8.150000e-27	132.0

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	TraesCS3A01G066000	chr3A	38991001	38994618	3617	True	6682.00	6682	100.0000	1	3618	1	chr3A.!!$R1	3617
1	TraesCS3A01G066000	chr3A	707352627	707353373	746	False	902.00	902	88.6090	4	748	1	chr3A.!!$F1	744
2	TraesCS3A01G066000	chr1A	223825569	223828439	2870	True	4798.00	4798	96.8310	748	3618	1	chr1A.!!$R3	2870
3	TraesCS3A01G066000	chr1A	166662023	166662868	845	False	1085.00	1085	89.8820	2775	3618	1	chr1A.!!$F1	843
4	TraesCS3A01G066000	chr1A	162700472	162701314	842	True	1070.00	1070	89.6350	2775	3618	1	chr1A.!!$R2	843
5	TraesCS3A01G066000	chr1A	516588125	516588868	743	False	1035.00	1035	91.7880	1	748	1	chr1A.!!$F3	747
6	TraesCS3A01G066000	chr1A	185846394	185847236	842	False	1027.00	1027	88.7060	2774	3618	1	chr1A.!!$F2	844
7	TraesCS3A01G066000	chr1A	162650172	162650892	720	True	922.00	922	89.8070	2898	3618	1	chr1A.!!$R1	720
8	TraesCS3A01G066000	chr1D	50871362	50874262	2900	False	4405.00	4405	94.2530	747	3618	1	chr1D.!!$F1	2871
9	TraesCS3A01G066000	chr2D	431521285	431524136	2851	True	2319.50	3386	95.4540	747	3618	2	chr2D.!!$R2	2871
10	TraesCS3A01G066000	chr2D	33926532	33927251	719	True	880.00	880	88.7820	1	724	1	chr2D.!!$R1	723
11	TraesCS3A01G066000	chr7D	324503573	324506306	2733	True	2058.50	3356	92.8580	830	3618	2	chr7D.!!$R1	2788
12	TraesCS3A01G066000	chr3D	141488078	141490842	2764	False	2241.50	3214	95.5100	747	3531	2	chr3D.!!$F1	2784
13	TraesCS3A01G066000	chr6A	498009687	498010434	747	True	1022.00	1022	91.4020	1	748	1	chr6A.!!$R1	747
14	TraesCS3A01G066000	chr2B	137213468	137214352	884	True	977.00	977	87.3880	1921	2771	1	chr2B.!!$R1	850
15	TraesCS3A01G066000	chr2B	162518589	162519630	1041	True	445.85	813	92.5185	3	747	2	chr2B.!!$R2	744
16	TraesCS3A01G066000	chrUn	27335782	27336532	750	True	928.00	928	89.0930	3	754	1	chrUn.!!$R1	751
17	TraesCS3A01G066000	chr7B	748664492	748665237	745	True	856.00	856	87.5330	3	747	1	chr7B.!!$R1	744
18	TraesCS3A01G066000	chr7B	600922125	600924335	2210	True	383.00	427	87.4735	832	1658	2	chr7B.!!$R2	826
19	TraesCS3A01G066000	chr7B	608180531	608182742	2211	True	377.50	422	87.1605	832	1658	2	chr7B.!!$R3	826
20	TraesCS3A01G066000	chr5D	385980293	385980951	658	True	743.00	743	87.0260	70	749	1	chr5D.!!$R1	679

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
924	1250	1.067142	GCCCCTCGATCGCATATACAA	60.067	52.381	11.09	0.0	0.0	2.41	F
1375	3084	0.463620	GCCTTTGTTTTCTGTGCCCA	59.536	50.000	0.00	0.0	0.0	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2570	4347	1.609320	GGCGAGCTCTTTCTCCACTTT	60.609	52.381	12.85	0.0	0.00	2.66	R
3155	4950	0.166814	GTCTTCTCATGCAACACGCC	59.833	55.000	0.00	0.0	41.33	5.68	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
313	620	3.719268	ATCCCACTTGTACAGCATTGA	57.281	42.857	0.00	0.00	0.00	2.57
373	686	2.671963	GTGTTCGAACCTGGGGGC	60.672	66.667	24.78	0.00	35.63	5.80
374	687	3.172106	TGTTCGAACCTGGGGGCA	61.172	61.111	24.78	1.10	35.63	5.36
375	688	2.359975	GTTCGAACCTGGGGGCAG	60.360	66.667	17.68	0.00	35.63	4.85
376	689	2.852075	TTCGAACCTGGGGGCAGT	60.852	61.111	0.00	0.00	35.63	4.40
377	690	3.190738	TTCGAACCTGGGGGCAGTG	62.191	63.158	0.00	0.00	35.63	3.66
418	732	7.254151	GCGTCCTAATTTCTCTCTGTTGTATTC	60.254	40.741	0.00	0.00	0.00	1.75
426	740	2.012673	CTCTGTTGTATTCTGCCCTGC	58.987	52.381	0.00	0.00	0.00	4.85
443	757	2.037208	CCGGGTGGGGCTCAATTT	59.963	61.111	0.00	0.00	0.00	1.82
445	759	1.191489	CCGGGTGGGGCTCAATTTTT	61.191	55.000	0.00	0.00	0.00	1.94
534	851	5.123186	TCAGGTCGTTTTCGCAAAATATCAT	59.877	36.000	0.00	0.00	43.73	2.45
589	907	2.280592	GAGTCCCACGCCACGTTT	60.281	61.111	0.00	0.00	38.32	3.60
592	910	4.858680	TCCCACGCCACGTTTGCA	62.859	61.111	7.52	0.00	38.32	4.08
664	982	1.955663	CGCCCAAGCCAAGTTTTGC	60.956	57.895	0.00	0.00	34.57	3.68
726	1044	4.402155	TGACTTTTCTTGCCAAGTTCACAT	59.598	37.500	4.04	0.00	33.22	3.21
761	1079	9.201989	TGTAATTCACTCTACATAATCTGTCCT	57.798	33.333	0.00	0.00	39.39	3.85
852	1170	3.162666	TCATAAGTCAGACCCGAACAGT	58.837	45.455	0.00	0.00	0.00	3.55
861	1179	1.444895	CCCGAACAGTTACCGACGG	60.445	63.158	13.61	13.61	40.03	4.79
872	1190	3.070015	AGTTACCGACGGGAGAAAAGAAA	59.930	43.478	20.00	0.00	36.97	2.52
876	1195	2.225727	CCGACGGGAGAAAAGAAAAAGG	59.774	50.000	5.81	0.00	34.06	3.11
915	1241	3.917760	GACCCTGCCCCTCGATCG	61.918	72.222	9.36	9.36	0.00	3.69
924	1250	1.067142	GCCCCTCGATCGCATATACAA	60.067	52.381	11.09	0.00	0.00	2.41
1001	1327	4.109675	CCGCGTCCCTCCCCAAAT	62.110	66.667	4.92	0.00	0.00	2.32
1021	1347	2.315781	GACAGCGATGATGGAGGGCA	62.316	60.000	8.12	0.00	0.00	5.36
1375	3084	0.463620	GCCTTTGTTTTCTGTGCCCA	59.536	50.000	0.00	0.00	0.00	5.36
1500	3210	0.675083	CTGCATCAAACTGTTGGGCA	59.325	50.000	0.00	1.49	40.64	5.36
1734	3483	7.548075	TCGTTATTCTACCAAGAGAACATTTCC	59.452	37.037	0.00	0.00	38.25	3.13
1845	3594	5.422012	TGCTTGGAGATGATACTGTTCACTA	59.578	40.000	0.00	0.00	0.00	2.74
1871	3620	5.124138	CCATATTTTGTTTGTACGGTGGCTA	59.876	40.000	0.00	0.00	0.00	3.93
2522	4298	7.465960	TCCAGAGAGAGTATAATACTGATGCT	58.534	38.462	0.00	0.00	39.59	3.79
2570	4347	5.338871	GGTTCCATGAGGGTGTCTATTACAA	60.339	44.000	0.00	0.00	40.63	2.41
2654	4431	2.745698	CCTGTCAGAGTGCAGCCA	59.254	61.111	0.00	0.00	0.00	4.75
2660	4455	0.109153	TCAGAGTGCAGCCACACAAT	59.891	50.000	9.18	0.00	44.53	2.71
2687	4482	1.609501	CTGTTGAGGACCCCGGAGA	60.610	63.158	0.73	0.00	0.00	3.71
2690	4485	1.609501	TTGAGGACCCCGGAGACTG	60.610	63.158	0.73	0.00	0.00	3.51
2748	4543	9.788960	GAACTTGTTTTCTTCAGTAAATCAACT	57.211	29.630	0.00	0.00	0.00	3.16
2879	4674	1.005097	TGCCTCATTGGATGCACTTCT	59.995	47.619	0.00	0.00	39.34	2.85
3090	4885	0.599558	CCATGTTGTTGCCTGGAGTG	59.400	55.000	0.00	0.00	0.00	3.51
3155	4950	2.504244	GGAGCGTCAACGACCTCG	60.504	66.667	6.75	0.00	43.02	4.63
3186	4981	5.221501	TGCATGAGAAGACCATGAATATCGA	60.222	40.000	0.00	0.00	42.89	3.59
3367	5168	0.833287	AGCATGGCCTACAATCTCGT	59.167	50.000	3.32	0.00	0.00	4.18
3369	5170	1.871080	CATGGCCTACAATCTCGTCC	58.129	55.000	3.32	0.00	0.00	4.79
3545	5350	3.721575	TCCTATATCTGCAATTGGGTGGT	59.278	43.478	7.72	0.00	0.00	4.16
3556	5361	4.144297	CAATTGGGTGGTCTATGGTATGG	58.856	47.826	0.00	0.00	0.00	2.74
3558	5363	2.404559	TGGGTGGTCTATGGTATGGAC	58.595	52.381	0.00	0.00	39.72	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
219	526	2.366266	ACAGTCACTGCATGCCATTTTT	59.634	40.909	16.68	0.00	34.37	1.94
232	539	3.522553	GCTTAAATCGGCTACAGTCACT	58.477	45.455	0.00	0.00	0.00	3.41
313	620	1.228228	CAGGCCAGCCACCACATAT	59.772	57.895	12.03	0.00	38.92	1.78
373	686	1.967762	CAAAATGTAGCACCGCACTG	58.032	50.000	0.00	0.00	0.00	3.66
374	687	0.240945	GCAAAATGTAGCACCGCACT	59.759	50.000	0.00	0.00	0.00	4.40
375	688	1.065031	CGCAAAATGTAGCACCGCAC	61.065	55.000	0.00	0.00	0.00	5.34
376	689	1.208870	CGCAAAATGTAGCACCGCA	59.791	52.632	0.00	0.00	0.00	5.69
377	690	0.793104	GACGCAAAATGTAGCACCGC	60.793	55.000	0.00	0.00	0.00	5.68
426	740	1.191489	AAAAATTGAGCCCCACCCGG	61.191	55.000	0.00	0.00	0.00	5.73
589	907	1.734117	CATGCTGACGAGACGTGCA	60.734	57.895	10.56	10.56	41.46	4.57
592	910	0.032130	ACAACATGCTGACGAGACGT	59.968	50.000	2.44	0.00	45.10	4.34
664	982	2.936498	GTGAGATACATTGAACCGGTGG	59.064	50.000	8.52	0.00	0.00	4.61
742	1060	5.046529	GTGCAGGACAGATTATGTAGAGTG	58.953	45.833	0.00	0.00	44.17	3.51
761	1079	0.546747	AAGGCCCAGGTAGTAGTGCA	60.547	55.000	0.00	0.00	0.00	4.57
852	1170	3.749665	TTTCTTTTCTCCCGTCGGTAA	57.250	42.857	11.06	0.00	0.00	2.85
861	1179	5.050490	GTGGCTTTCCTTTTTCTTTTCTCC	58.950	41.667	0.00	0.00	0.00	3.71
872	1190	2.564721	GCGCTGGTGGCTTTCCTTT	61.565	57.895	0.00	0.00	39.13	3.11
876	1195	3.435186	GAGGCGCTGGTGGCTTTC	61.435	66.667	7.64	0.00	45.90	2.62
915	1241	2.143925	GCGGGAAGGAGTTGTATATGC	58.856	52.381	0.00	0.00	0.00	3.14
1001	1327	1.825341	CCCTCCATCATCGCTGTCA	59.175	57.895	0.00	0.00	0.00	3.58
1375	3084	1.182667	TCCAATCCGACGACACAGAT	58.817	50.000	0.00	0.00	0.00	2.90
1412	3121	0.744874	GCTCCGACATGTAGTGGCTA	59.255	55.000	0.00	0.00	31.78	3.93
1500	3210	1.980765	TGAATCCAGGCTCTCACAGTT	59.019	47.619	0.00	0.00	0.00	3.16
1574	3287	3.880846	GGCCAAGGCGAATCAGCG	61.881	66.667	4.80	0.00	43.06	5.18
1734	3483	8.506168	TTCATATTGCCTAGAAACCAAAGTAG	57.494	34.615	0.00	0.00	0.00	2.57
1845	3594	5.393678	GCCACCGTACAAACAAAATATGGAT	60.394	40.000	0.00	0.00	0.00	3.41
1863	3612	2.283351	GCGTTACAAAGTATAGCCACCG	59.717	50.000	0.00	0.00	0.00	4.94
1871	3620	5.018539	TCCATGCTAGCGTTACAAAGTAT	57.981	39.130	6.73	0.00	0.00	2.12
1929	3678	4.588528	AGAGCTGCAATTTTCTTTACCCAA	59.411	37.500	1.02	0.00	0.00	4.12
2188	3960	5.373222	AGTGAACAGCAGTACAAATTGGTA	58.627	37.500	0.00	0.00	0.00	3.25
2522	4298	9.367160	ACCTTTTTCTTCTCTGAAATAAATGGA	57.633	29.630	16.39	0.00	36.07	3.41
2570	4347	1.609320	GGCGAGCTCTTTCTCCACTTT	60.609	52.381	12.85	0.00	0.00	2.66
2687	4482	3.807368	GGTGGCTACCTGTCCAGT	58.193	61.111	12.81	0.00	43.97	4.00
2761	4556	7.436320	AAATTTGGATGGTATTAACTGGCAT	57.564	32.000	0.00	0.00	0.00	4.40
3022	4817	4.752101	GCTAAGGACATGATATCACACCAC	59.248	45.833	7.78	0.00	0.00	4.16
3155	4950	0.166814	GTCTTCTCATGCAACACGCC	59.833	55.000	0.00	0.00	41.33	5.68
3166	4961	5.852282	TGTCGATATTCATGGTCTTCTCA	57.148	39.130	0.00	0.00	0.00	3.27
3186	4981	4.697352	GCACATCACCTACATCTTTCTTGT	59.303	41.667	0.00	0.00	0.00	3.16
3260	5060	6.807720	TGCAACACAAATTGATATGACATGAC	59.192	34.615	0.00	0.00	0.00	3.06
3367	5168	2.995077	GCACATGGATGGTGGGGGA	61.995	63.158	0.00	0.00	36.76	4.81
3369	5170	2.442643	GGCACATGGATGGTGGGG	60.443	66.667	0.00	0.00	36.76	4.96
3556	5361	4.705023	ACCATGGTTGCTTATAAACTGGTC	59.295	41.667	13.00	0.00	28.98	4.02
3558	5363	4.462483	ACACCATGGTTGCTTATAAACTGG	59.538	41.667	16.84	0.61	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.