AutoCloner

Multiple sequence alignment - TraesCS7A01G399300

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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	TraesCS7A01G399300	chr7A	100.000	3647	0	0	1	3647	579343730	579340084	0.000000e+00	6735.0
1	TraesCS7A01G399300	chr7A	86.362	2779	359	13	1	2774	579496751	579499514	0.000000e+00	3014.0
2	TraesCS7A01G399300	chr7A	86.790	2642	332	14	1	2629	579599496	579602133	0.000000e+00	2929.0
3	TraesCS7A01G399300	chr7A	77.911	584	67	35	2775	3328	579619017	579619568	1.270000e-79	307.0
4	TraesCS7A01G399300	chr7A	77.523	436	59	24	2775	3196	579499545	579499955	3.660000e-55	226.0
5	TraesCS7A01G399300	chr7A	92.593	54	1	2	3444	3496	81135105	81135054	1.400000e-09	75.0
6	TraesCS7A01G399300	chr7B	96.058	3247	100	7	405	3647	537162858	537166080	0.000000e+00	5262.0
7	TraesCS7A01G399300	chr7B	84.032	2768	408	24	1	2743	536990509	536993267	0.000000e+00	2632.0
8	TraesCS7A01G399300	chr7B	88.659	1402	148	8	1	1400	537215353	537216745	0.000000e+00	1698.0
9	TraesCS7A01G399300	chr7B	82.382	1016	167	10	1767	2774	537223546	537224557	0.000000e+00	874.0
10	TraesCS7A01G399300	chr7B	86.772	378	50	0	1386	1763	537217898	537218275	4.350000e-114	422.0
11	TraesCS7A01G399300	chr7B	82.174	460	63	12	3002	3449	537224971	537225423	9.560000e-101	377.0
12	TraesCS7A01G399300	chr7D	88.642	2430	276	0	200	2629	508881296	508883725	0.000000e+00	2959.0
13	TraesCS7A01G399300	chr7D	93.103	203	14	0	1	203	508833196	508833398	7.660000e-77	298.0
14	TraesCS7A01G399300	chr1D	90.141	71	3	3	3457	3524	485110610	485110541	5.020000e-14	89.8
15	TraesCS7A01G399300	chr5D	89.706	68	1	1	3457	3524	56125640	56125701	8.390000e-12	82.4
16	TraesCS7A01G399300	chr2A	88.060	67	4	4	3458	3524	675304129	675304191	3.910000e-10	76.8
17	TraesCS7A01G399300	chr6D	89.831	59	4	1	3456	3512	27037447	27037389	1.400000e-09	75.0
18	TraesCS7A01G399300	chr6D	86.885	61	5	3	3458	3518	401182239	401182182	8.450000e-07	65.8
19	TraesCS7A01G399300	chr2B	83.333	78	10	3	3450	3525	745861384	745861460	6.530000e-08	69.4
20	TraesCS7A01G399300	chr2D	82.051	78	10	4	3450	3525	610495884	610495959	3.040000e-06	63.9

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	TraesCS7A01G399300	chr7A	579340084	579343730	3646	True	6735.0	6735	100.0000	1	3647	1	chr7A.!!$R2	3646
1	TraesCS7A01G399300	chr7A	579599496	579602133	2637	False	2929.0	2929	86.7900	1	2629	1	chr7A.!!$F1	2628
2	TraesCS7A01G399300	chr7A	579496751	579499955	3204	False	1620.0	3014	81.9425	1	3196	2	chr7A.!!$F3	3195
3	TraesCS7A01G399300	chr7A	579619017	579619568	551	False	307.0	307	77.9110	2775	3328	1	chr7A.!!$F2	553
4	TraesCS7A01G399300	chr7B	537162858	537166080	3222	False	5262.0	5262	96.0580	405	3647	1	chr7B.!!$F2	3242
5	TraesCS7A01G399300	chr7B	536990509	536993267	2758	False	2632.0	2632	84.0320	1	2743	1	chr7B.!!$F1	2742
6	TraesCS7A01G399300	chr7B	537215353	537218275	2922	False	1060.0	1698	87.7155	1	1763	2	chr7B.!!$F3	1762
7	TraesCS7A01G399300	chr7B	537223546	537225423	1877	False	625.5	874	82.2780	1767	3449	2	chr7B.!!$F4	1682
8	TraesCS7A01G399300	chr7D	508881296	508883725	2429	False	2959.0	2959	88.6420	200	2629	1	chr7D.!!$F2	2429

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	Hairpin	End Stability	Orientation
507	517	0.994247	TCAGGGTTGATCATGGCAGT	59.006	50.000	0.00	4.40	F
789	799	1.677518	CGCACTTATTACCCACTGCCA	60.678	52.381	0.00	4.92	F
887	897	2.719798	CTCAAACAAGTGGAAACAGCG	58.280	47.619	44.46	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2267	3447	0.739462	TCGCATAACTTGAGGGCACG	60.739	55.000	0.00	0.00	0.0	5.34	R
2297	3477	3.009115	GGGCTGTCTGGTGGCCTA	61.009	66.667	3.32	0.00	44.7	3.93	R
2801	4027	2.102757	CTGTCCAGAGATCCATGACAGG	59.897	54.545	17.83	6.14	45.7	4.00	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
48	49	2.079925	CCAGAGTTGAAGCAGTTAGGC	58.920	52.381	0.00	0.00	0.00	3.93
63	64	5.278758	GCAGTTAGGCTACCAAATTGTTCAA	60.279	40.000	0.00	0.00	0.00	2.69
97	98	2.838202	TCACCTCTAGCCCTAAAGGTTG	59.162	50.000	0.00	0.00	40.13	3.77
105	106	1.203013	GCCCTAAAGGTTGTTGGAGGT	60.203	52.381	0.00	0.00	38.26	3.85
153	154	3.008375	CAGAGTGGGAGGATGTTCTTCAA	59.992	47.826	0.00	0.00	0.00	2.69
155	156	4.006319	GAGTGGGAGGATGTTCTTCAAAG	58.994	47.826	0.00	0.00	0.00	2.77
180	181	8.102047	AGAGATGTCCTCAATCCAAATGATATC	58.898	37.037	0.00	0.00	44.40	1.63
186	187	7.718753	GTCCTCAATCCAAATGATATCTTGACT	59.281	37.037	3.98	0.00	31.83	3.41
282	283	6.753107	AAGGGTTACCGTATTGATTCAAAG	57.247	37.500	2.68	0.00	43.47	2.77
455	456	6.210796	ACGTTATGCATGATTCATTGAATGG	58.789	36.000	16.41	7.16	31.89	3.16
456	457	6.183360	ACGTTATGCATGATTCATTGAATGGT	60.183	34.615	16.41	2.39	31.89	3.55
498	499	1.342374	GGGGAATGCTTCAGGGTTGAT	60.342	52.381	0.00	0.00	32.27	2.57
507	517	0.994247	TCAGGGTTGATCATGGCAGT	59.006	50.000	0.00	0.00	0.00	4.40
590	600	4.777366	TCTTGTGAACTATGATGGTCTCCA	59.223	41.667	0.00	0.00	38.19	3.86
789	799	1.677518	CGCACTTATTACCCACTGCCA	60.678	52.381	0.00	0.00	0.00	4.92
838	848	7.728148	TCTACAGTCCTTGTTTGTGTTGTATA	58.272	34.615	0.00	0.00	41.29	1.47
887	897	2.719798	CTCAAACAAGTGGAAACAGCG	58.280	47.619	0.00	0.00	44.46	5.18
896	906	4.701956	AGTGGAAACAGCGGAAATATTG	57.298	40.909	0.00	0.00	44.46	1.90
1374	1384	6.035758	GGCTGAGAAGATTGAAATTGATTTGC	59.964	38.462	0.00	0.00	0.00	3.68
1517	2694	3.883669	CTGGATTCCCTTCTCTGGAAAG	58.116	50.000	0.00	0.00	44.64	2.62
1895	3075	5.918426	TTTGGCATTGATGAGCAGAATAA	57.082	34.783	0.00	0.00	0.00	1.40
2235	3415	8.107399	TGGAATATGTACCGTACTTAGATGAG	57.893	38.462	10.03	0.00	0.00	2.90
2267	3447	6.017934	TGTCTTCAGAAACTACATTTGTCTGC	60.018	38.462	0.00	0.00	0.00	4.26
2289	3469	3.202906	GTGCCCTCAAGTTATGCGATTA	58.797	45.455	0.00	0.00	0.00	1.75
2297	3477	7.657761	CCCTCAAGTTATGCGATTATCTAAAGT	59.342	37.037	0.00	0.00	0.00	2.66
2430	3610	4.462483	TGTTCTGATTTATTGTGGCTTCCC	59.538	41.667	0.00	0.00	0.00	3.97
2451	3631	6.606069	TCCCGATATGGATGGTTTTTATTCA	58.394	36.000	0.00	0.00	42.00	2.57
2470	3650	3.349927	TCACTTCGGGTTCTCTCGATTA	58.650	45.455	0.00	0.00	35.25	1.75
2629	3809	0.329261	CCTTCCAGGATGCAAGTGGA	59.671	55.000	10.24	10.24	37.67	4.02
2630	3810	1.064166	CCTTCCAGGATGCAAGTGGAT	60.064	52.381	14.02	0.00	40.11	3.41
2633	3813	2.763039	TCCAGGATGCAAGTGGATAGA	58.237	47.619	10.24	0.00	35.36	1.98
2660	3843	8.634188	AGTAGGTGGTAAATATTAGGAGGTTT	57.366	34.615	0.00	0.00	0.00	3.27
2682	3865	7.068348	GGTTTCCCTTTTTACTATCCTGAATCC	59.932	40.741	0.00	0.00	0.00	3.01
2794	4020	2.640989	CACAGCTGTGCGTGCATT	59.359	55.556	32.39	0.00	39.39	3.56
2795	4021	1.576451	CCACAGCTGTGCGTGCATTA	61.576	55.000	36.38	0.00	44.34	1.90
2801	4027	1.818850	CTGTGCGTGCATTATTCTGC	58.181	50.000	0.00	0.00	42.62	4.26
2849	4076	7.277174	AGTTTTGCTTATTGAACTTGCTAGT	57.723	32.000	0.00	0.00	35.68	2.57
3207	4636	9.452287	GGGTATGTGTTAGTTGAATACCTTTAA	57.548	33.333	9.38	0.00	41.59	1.52
3297	4734	9.067986	AGAAAGAAGAAACCAACTTAATACCTG	57.932	33.333	0.00	0.00	0.00	4.00
3450	4889	2.436542	CCCGACACAAGGGGTCATATTA	59.563	50.000	0.00	0.00	45.14	0.98
3527	4966	6.041979	ACATTTGTTTGCAGAGGGAGTAAAAT	59.958	34.615	0.00	0.00	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	88	3.502123	TGACCTCCAACAACCTTTAGG	57.498	47.619	0.00	0.00	42.17	2.69
97	98	9.366216	GTATTTTCCATTTAAATGACCTCCAAC	57.634	33.333	26.32	13.27	38.70	3.77
105	106	9.585099	GCATCACTGTATTTTCCATTTAAATGA	57.415	29.630	26.32	11.82	38.70	2.57
153	154	6.070951	TCATTTGGATTGAGGACATCTCTT	57.929	37.500	0.00	0.00	42.86	2.85
155	156	8.102047	AGATATCATTTGGATTGAGGACATCTC	58.898	37.037	5.32	0.00	38.92	2.75
198	199	4.023536	TGTTCCGGCAAACTTTCATAACTC	60.024	41.667	0.00	0.00	0.00	3.01
282	283	5.046448	AGCTATCCACATCCAGATCAATCTC	60.046	44.000	0.00	0.00	34.22	2.75
344	345	4.078395	AGCCCCTTCCAATATCTTCCAAAT	60.078	41.667	0.00	0.00	0.00	2.32
345	346	3.272020	AGCCCCTTCCAATATCTTCCAAA	59.728	43.478	0.00	0.00	0.00	3.28
448	449	2.542020	TGAAGTGCGAGACCATTCAA	57.458	45.000	0.00	0.00	0.00	2.69
455	456	2.143122	TGGAAACATGAAGTGCGAGAC	58.857	47.619	0.00	0.00	33.40	3.36
456	457	2.542020	TGGAAACATGAAGTGCGAGA	57.458	45.000	0.00	0.00	33.40	4.04
498	499	1.379916	CTCCCCAACACTGCCATGA	59.620	57.895	0.00	0.00	0.00	3.07
590	600	7.928167	TCAGAATCATAAATGTACGCAATCTCT	59.072	33.333	0.00	0.00	0.00	3.10
789	799	5.624159	TGATTGAGTCTGGAGATTGTTGTT	58.376	37.500	0.00	0.00	0.00	2.83
887	897	5.755849	TCACTTCCCTCCTTCAATATTTCC	58.244	41.667	0.00	0.00	0.00	3.13
896	906	3.579151	AGTAGTGTTCACTTCCCTCCTTC	59.421	47.826	10.74	0.00	0.00	3.46
1072	1082	0.397564	TCCCTCGGTTGTACCAAACC	59.602	55.000	5.25	5.25	45.24	3.27
1085	1095	4.576463	CCCTAATTTTGTTCAGATCCCTCG	59.424	45.833	0.00	0.00	0.00	4.63
1147	1157	2.129555	GACTTTGCAGCCTCCTCCCA	62.130	60.000	0.00	0.00	0.00	4.37
1374	1384	6.127591	CCTCCCATCTATTACAATCTCGTAGG	60.128	46.154	0.00	0.00	0.00	3.18
1432	2609	1.352156	CGCCGCACTTCAAGAGTACC	61.352	60.000	0.00	0.00	36.65	3.34
1482	2659	3.703052	GGAATCCAGCATGACCAAAGAAT	59.297	43.478	0.00	0.00	39.69	2.40
1517	2694	1.666189	GTAGGCGTTCCAGAAGCAATC	59.334	52.381	0.00	0.00	33.74	2.67
1895	3075	4.292186	AGTGTGGTAATCACTGAGCAAT	57.708	40.909	0.00	0.00	46.20	3.56
2235	3415	4.937620	TGTAGTTTCTGAAGACATGGCATC	59.062	41.667	0.00	0.00	0.00	3.91
2267	3447	0.739462	TCGCATAACTTGAGGGCACG	60.739	55.000	0.00	0.00	0.00	5.34
2289	3469	3.450904	TGTCTGGTGGCCTACTTTAGAT	58.549	45.455	3.32	0.00	0.00	1.98
2297	3477	3.009115	GGGCTGTCTGGTGGCCTA	61.009	66.667	3.32	0.00	44.70	3.93
2430	3610	7.798516	CGAAGTGAATAAAAACCATCCATATCG	59.201	37.037	0.00	0.00	0.00	2.92
2633	3813	9.909365	AACCTCCTAATATTTACCACCTACTAT	57.091	33.333	0.00	0.00	0.00	2.12
2660	3843	5.686650	GCGGATTCAGGATAGTAAAAAGGGA	60.687	44.000	0.00	0.00	0.00	4.20
2682	3865	3.824414	AAGAAAACATACCCGAAAGCG	57.176	42.857	0.00	0.00	37.24	4.68
2750	3946	9.413048	GTACCATCTAAGATCTATACAGTTTGC	57.587	37.037	0.00	0.00	0.00	3.68
2794	4020	4.040095	CAGAGATCCATGACAGGCAGAATA	59.960	45.833	0.00	0.00	0.00	1.75
2795	4021	3.047115	AGAGATCCATGACAGGCAGAAT	58.953	45.455	0.00	0.00	0.00	2.40
2801	4027	2.102757	CTGTCCAGAGATCCATGACAGG	59.897	54.545	17.83	6.14	45.70	4.00
3159	4588	7.538575	ACCCATCTGATTATTTTCTTGTTTCG	58.461	34.615	0.00	0.00	0.00	3.46
3297	4734	2.229784	GCATTACAGGCTTATGGCATCC	59.770	50.000	1.65	0.00	44.01	3.51
3416	4855	1.100510	TGTCGGGTTCCACTATCTCG	58.899	55.000	0.00	0.00	0.00	4.04
3450	4889	9.143155	ACATTTGTTTACAGAGGGAGTATTTTT	57.857	29.630	0.00	0.00	0.00	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.