AutoCloner

Multiple sequence alignment - TraesCS7D01G154200

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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	TraesCS7D01G154200	chr7D	100.000	3583	0	0	1	3583	101800154	101796572	0.000000e+00	6617
1	TraesCS7D01G154200	chr7D	80.150	1335	235	24	727	2040	143976174	143974849	0.000000e+00	970
2	TraesCS7D01G154200	chr7D	78.932	1348	245	30	730	2051	152947181	152948515	0.000000e+00	880
3	TraesCS7D01G154200	chr7D	86.373	499	55	6	535	1023	101800208	101800703	1.890000e-147	532
4	TraesCS7D01G154200	chr7D	83.918	342	40	10	2421	2752	143950214	143949878	2.690000e-81	313
5	TraesCS7D01G154200	chr7A	93.454	3437	159	32	185	3572	105768367	105764948	0.000000e+00	5040
6	TraesCS7D01G154200	chr7A	94.743	2378	106	6	1	2368	105779389	105777021	0.000000e+00	3681
7	TraesCS7D01G154200	chr7A	92.088	771	57	2	1474	2244	105773887	105773121	0.000000e+00	1083
8	TraesCS7D01G154200	chr7A	78.571	1330	255	25	725	2033	154062429	154063749	0.000000e+00	850
9	TraesCS7D01G154200	chr7A	92.489	466	17	7	3121	3582	105776152	105775701	0.000000e+00	651
10	TraesCS7D01G154200	chr7A	95.538	381	16	1	2370	2750	105776965	105776586	3.060000e-170	608
11	TraesCS7D01G154200	chr7B	95.229	2641	119	6	1	2635	59181612	59178973	0.000000e+00	4172
12	TraesCS7D01G154200	chr7B	79.007	1329	249	23	725	2033	114938744	114940062	0.000000e+00	881
13	TraesCS7D01G154200	chr7B	83.732	418	39	8	632	1023	59304957	59305371	5.650000e-98	368
14	TraesCS7D01G154200	chr7B	80.549	401	54	15	2343	2727	107823257	107823649	1.630000e-73	287
15	TraesCS7D01G154200	chr7B	79.188	394	50	21	2346	2727	114940370	114940743	9.940000e-61	244
16	TraesCS7D01G154200	chr3D	79.370	1905	294	56	660	2494	39121133	39119258	0.000000e+00	1249
17	TraesCS7D01G154200	chr3D	81.308	321	39	12	2444	2752	39031852	39031541	1.290000e-59	241
18	TraesCS7D01G154200	chr3B	79.741	1698	284	38	660	2321	61916753	61915080	0.000000e+00	1175
19	TraesCS7D01G154200	chr3B	79.191	692	110	19	1113	1774	61896885	61896198	1.960000e-122	449
20	TraesCS7D01G154200	chrUn	77.537	1340	263	26	717	2032	29901335	29900010	0.000000e+00	773

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	TraesCS7D01G154200	chr7D	101796572	101800154	3582	True	6617.00	6617	100.0000	1	3583	1	chr7D.!!$R1	3582
1	TraesCS7D01G154200	chr7D	143974849	143976174	1325	True	970.00	970	80.1500	727	2040	1	chr7D.!!$R3	1313
2	TraesCS7D01G154200	chr7D	152947181	152948515	1334	False	880.00	880	78.9320	730	2051	1	chr7D.!!$F2	1321
3	TraesCS7D01G154200	chr7A	105764948	105768367	3419	True	5040.00	5040	93.4540	185	3572	1	chr7A.!!$R1	3387
4	TraesCS7D01G154200	chr7A	105773121	105779389	6268	True	1505.75	3681	93.7145	1	3582	4	chr7A.!!$R2	3581
5	TraesCS7D01G154200	chr7A	154062429	154063749	1320	False	850.00	850	78.5710	725	2033	1	chr7A.!!$F1	1308
6	TraesCS7D01G154200	chr7B	59178973	59181612	2639	True	4172.00	4172	95.2290	1	2635	1	chr7B.!!$R1	2634
7	TraesCS7D01G154200	chr7B	114938744	114940743	1999	False	562.50	881	79.0975	725	2727	2	chr7B.!!$F3	2002
8	TraesCS7D01G154200	chr3D	39119258	39121133	1875	True	1249.00	1249	79.3700	660	2494	1	chr3D.!!$R2	1834
9	TraesCS7D01G154200	chr3B	61915080	61916753	1673	True	1175.00	1175	79.7410	660	2321	1	chr3B.!!$R2	1661
10	TraesCS7D01G154200	chr3B	61896198	61896885	687	True	449.00	449	79.1910	1113	1774	1	chr3B.!!$R1	661
11	TraesCS7D01G154200	chrUn	29900010	29901335	1325	True	773.00	773	77.5370	717	2032	1	chrUn.!!$R1	1315

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
642	645	0.390860	TGGGCAACGGGTCATTTTTG	59.609	50.0	0.0	0.0	37.60	2.44	F
1845	1923	0.251354	GAGCAGAGGAGCAACATGGA	59.749	55.0	0.0	0.0	36.85	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2084	2165	0.459934	TTGTTGTTGTTGCTGCTGGC	60.460	50.0	0.0	0.0	42.22	4.85	R
3355	3616	0.577269	GATTGTGTGCGAGCGTATCC	59.423	55.0	0.0	0.0	0.00	2.59	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
98	101	8.602472	ATTACCTTTCTAAATTGTATGGCCAA	57.398	30.769	10.96	0.00	0.00	4.52
171	174	7.011499	TGTTCTCTAAATTGTAGGGCTTACA	57.989	36.000	5.24	5.24	40.47	2.41
182	185	1.106285	GGGCTTACATTCAAGGGCAG	58.894	55.000	0.00	0.00	0.00	4.85
219	222	9.558648	AAACAAATTGCTTTGATTTTTCACTTC	57.441	25.926	5.51	0.00	43.71	3.01
254	257	9.171877	GATTCACTTCTAGTTGGATCATTCTTT	57.828	33.333	0.00	0.00	0.00	2.52
287	290	6.069673	ACAATGATAGTAAGACCCAATGTCCA	60.070	38.462	0.00	0.00	45.68	4.02
299	302	7.007723	AGACCCAATGTCCATTAAGTTTAACA	58.992	34.615	0.00	0.00	45.68	2.41
642	645	0.390860	TGGGCAACGGGTCATTTTTG	59.609	50.000	0.00	0.00	37.60	2.44
652	655	3.230976	GGGTCATTTTTGTTCTGGGTCT	58.769	45.455	0.00	0.00	0.00	3.85
679	682	5.451242	CCCTAAAGCTAAGCAACAACAACAA	60.451	40.000	0.00	0.00	0.00	2.83
798	806	1.404391	GCATGACATGGCTTGAAGAGG	59.596	52.381	18.25	0.00	0.00	3.69
1031	1075	6.418101	AGCATCTCCTCTCATATCTCTAGAC	58.582	44.000	0.00	0.00	0.00	2.59
1070	1114	7.681939	TTTGTAGTTACACAAATCTCCATCC	57.318	36.000	8.30	0.00	42.08	3.51
1643	1706	9.444600	CCAAGGTATTTAAACACACACTAGTAT	57.555	33.333	0.00	0.00	0.00	2.12
1657	1720	9.242477	CACACACTAGTATTACTCATGATTCAG	57.758	37.037	12.06	0.94	0.00	3.02
1845	1923	0.251354	GAGCAGAGGAGCAACATGGA	59.749	55.000	0.00	0.00	36.85	3.41
2081	2162	0.899720	TCGTTCTACCACCATGACCC	59.100	55.000	0.00	0.00	0.00	4.46
2084	2165	1.268992	TTCTACCACCATGACCCCCG	61.269	60.000	0.00	0.00	0.00	5.73
2220	2313	1.228245	GCAGGAGGACACTTTGGCA	60.228	57.895	0.00	0.00	0.00	4.92
2229	2322	2.024414	GACACTTTGGCAAGGTTGAGT	58.976	47.619	12.76	7.91	33.82	3.41
2400	2585	4.064137	GGTTTGCACCGCATTTTATTTG	57.936	40.909	0.00	0.00	38.76	2.32
2711	2909	5.712152	GATTTCCATCCACCATATGAACC	57.288	43.478	3.65	0.00	0.00	3.62
2723	2921	4.538490	ACCATATGAACCCTTACTTCCACA	59.462	41.667	3.65	0.00	0.00	4.17
2822	3048	1.265365	CACACACACACACACACACAA	59.735	47.619	0.00	0.00	0.00	3.33
2823	3049	1.950216	ACACACACACACACACACAAA	59.050	42.857	0.00	0.00	0.00	2.83
2824	3050	2.556189	ACACACACACACACACACAAAT	59.444	40.909	0.00	0.00	0.00	2.32
2825	3051	2.916089	CACACACACACACACACAAATG	59.084	45.455	0.00	0.00	0.00	2.32
2827	3053	1.543358	ACACACACACACACAAATGCA	59.457	42.857	0.00	0.00	0.00	3.96
2834	3060	3.644976	ACACAAATGCACGCGCGA	61.645	55.556	39.36	15.84	42.97	5.87
2835	3061	2.426588	CACAAATGCACGCGCGAA	60.427	55.556	39.36	21.69	42.97	4.70
2836	3062	2.008168	CACAAATGCACGCGCGAAA	61.008	52.632	39.36	21.29	42.97	3.46
2837	3063	1.298713	ACAAATGCACGCGCGAAAA	60.299	47.368	39.36	20.90	42.97	2.29
2838	3064	0.867753	ACAAATGCACGCGCGAAAAA	60.868	45.000	39.36	18.93	42.97	1.94
2839	3065	0.447101	CAAATGCACGCGCGAAAAAC	60.447	50.000	39.36	19.82	42.97	2.43
2840	3066	0.867753	AAATGCACGCGCGAAAAACA	60.868	45.000	39.36	24.63	42.97	2.83
2860	3086	0.738063	CGCCCTATAACACGTGCACA	60.738	55.000	17.22	0.39	0.00	4.57
2925	3151	5.536538	TGATGCTAACTCCTCGAATATGAGT	59.463	40.000	1.90	1.90	40.94	3.41
2929	3155	6.040955	TGCTAACTCCTCGAATATGAGTGATT	59.959	38.462	7.17	0.00	39.22	2.57
3019	3245	4.898829	ATGCGTTGAAATGCTAATGCTA	57.101	36.364	8.59	0.00	41.45	3.49
3076	3302	9.549509	CCTTGTTGCAATTTGATTTGATTTATG	57.450	29.630	0.59	0.00	0.00	1.90
3144	3405	9.770097	TCAAATCCATCTATTCTAACATCTCAC	57.230	33.333	0.00	0.00	0.00	3.51
3201	3462	6.098838	AGAGCATCAAGGATAATGTGTGAGTA	59.901	38.462	0.00	0.00	37.82	2.59
3202	3463	6.835174	AGCATCAAGGATAATGTGTGAGTAT	58.165	36.000	0.00	0.00	0.00	2.12
3203	3464	7.285566	AGCATCAAGGATAATGTGTGAGTATT	58.714	34.615	0.00	0.00	0.00	1.89
3204	3465	7.776969	AGCATCAAGGATAATGTGTGAGTATTT	59.223	33.333	0.00	0.00	0.00	1.40
3354	3615	5.049749	TGCAACTATGTTGTCACATGTACAC	60.050	40.000	0.00	0.00	43.92	2.90
3355	3616	5.608146	CAACTATGTTGTCACATGTACACG	58.392	41.667	0.00	0.00	43.92	4.49
3421	3682	4.657039	AGTGTTGAGTAAACCTAGGTCCAA	59.343	41.667	16.64	11.45	38.06	3.53
3439	3700	4.395231	GTCCAACCCAATTAACTACTCTGC	59.605	45.833	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	7.624360	AGATACGCAAATGTCCTTTGAATAA	57.376	32.000	4.92	0.00	45.96	1.40
73	74	8.602472	TTGGCCATACAATTTAGAAAGGTAAT	57.398	30.769	6.09	0.00	0.00	1.89
171	174	5.499004	TCTTAGTTGTACTGCCCTTGAAT	57.501	39.130	0.00	0.00	0.00	2.57
182	185	9.296400	TCAAAGCAATTTGTTTCTTAGTTGTAC	57.704	29.630	0.00	0.00	33.82	2.90
219	222	7.821359	TCCAACTAGAAGTGAATCAATCAAGAG	59.179	37.037	0.00	0.00	40.50	2.85
254	257	4.868171	GTCTTACTATCATTGTGTGCGGAA	59.132	41.667	0.00	0.00	0.00	4.30
582	585	6.823182	CGGATGGATACCAAGCAATAATATGA	59.177	38.462	0.00	0.00	36.95	2.15
652	655	1.074727	TGTTGCTTAGCTTTAGGGGCA	59.925	47.619	5.60	0.00	0.00	5.36
664	667	4.387256	GTGTGCTTTTGTTGTTGTTGCTTA	59.613	37.500	0.00	0.00	0.00	3.09
679	682	3.953612	TCTTCATGGAAAGTGTGTGCTTT	59.046	39.130	0.00	0.00	40.94	3.51
841	850	6.300354	ACTGTGTGTTGTTTATCTTGCTAC	57.700	37.500	0.00	0.00	0.00	3.58
988	1030	8.152309	AGATGCTTAAATAGAGTGAATGCTTC	57.848	34.615	0.00	0.00	0.00	3.86
1643	1706	5.147330	ACGTGTTCCTGAATCATGAGTAA	57.853	39.130	0.09	0.00	0.00	2.24
1657	1720	2.927553	AGTATGTACGGACGTGTTCC	57.072	50.000	1.67	0.00	41.75	3.62
1845	1923	3.632145	GCAATGTACCGGATTCAAGGAAT	59.368	43.478	9.46	0.00	34.71	3.01
1923	2001	0.924090	GCTGGTACGAAGAAGATGCG	59.076	55.000	0.00	0.00	0.00	4.73
2081	2162	4.347453	GTTGTTGCTGCTGGCGGG	62.347	66.667	0.00	0.00	45.43	6.13
2084	2165	0.459934	TTGTTGTTGTTGCTGCTGGC	60.460	50.000	0.00	0.00	42.22	4.85
2336	2467	9.190858	GGTATATATCAATCGATCTTCTGATGC	57.809	37.037	16.91	4.42	32.19	3.91
2400	2585	2.799412	CAAGCTCTCTTCTCACACACAC	59.201	50.000	0.00	0.00	0.00	3.82
2763	2961	7.120432	TGTGTTAGCATTTGCATCAGTATTGTA	59.880	33.333	5.20	0.00	45.16	2.41
2774	2972	2.424956	TGTGTGTGTGTTAGCATTTGCA	59.575	40.909	5.20	0.00	45.16	4.08
2822	3048	1.298713	TGTTTTTCGCGCGTGCATT	60.299	47.368	30.98	0.00	42.97	3.56
2823	3049	2.008697	GTGTTTTTCGCGCGTGCAT	61.009	52.632	30.98	0.00	42.97	3.96
2824	3050	2.649349	GTGTTTTTCGCGCGTGCA	60.649	55.556	30.98	18.29	42.97	4.57
2825	3051	3.727864	CGTGTTTTTCGCGCGTGC	61.728	61.111	30.98	11.84	42.93	5.34
2834	3060	3.058777	CACGTGTTATAGGGCGTGTTTTT	60.059	43.478	7.58	0.00	46.30	1.94
2835	3061	2.481185	CACGTGTTATAGGGCGTGTTTT	59.519	45.455	7.58	0.00	46.30	2.43
2836	3062	2.070783	CACGTGTTATAGGGCGTGTTT	58.929	47.619	7.58	0.00	46.30	2.83
2837	3063	1.717194	CACGTGTTATAGGGCGTGTT	58.283	50.000	7.58	0.00	46.30	3.32
2838	3064	3.429043	CACGTGTTATAGGGCGTGT	57.571	52.632	7.58	0.00	46.30	4.49
2840	3066	0.738412	GTGCACGTGTTATAGGGCGT	60.738	55.000	18.38	0.00	38.14	5.68
2882	3108	1.253800	CATGTCGACGCAATCTCTTCG	59.746	52.381	11.62	0.00	0.00	3.79
2893	3119	2.120232	GGAGTTAGCATCATGTCGACG	58.880	52.381	11.62	0.00	0.00	5.12
2895	3121	2.033424	CGAGGAGTTAGCATCATGTCGA	59.967	50.000	0.00	0.00	0.00	4.20
2925	3151	7.393841	TTGCAACATCAGTGATATTCAATCA	57.606	32.000	5.03	0.00	0.00	2.57
2929	3155	9.738832	CATATTTTGCAACATCAGTGATATTCA	57.261	29.630	5.03	0.00	0.00	2.57
2963	3189	9.942850	TCTTATTCTCATCAATCAACACAACTA	57.057	29.630	0.00	0.00	0.00	2.24
2969	3195	6.263842	GGCCATCTTATTCTCATCAATCAACA	59.736	38.462	0.00	0.00	0.00	3.33
3019	3245	8.262227	TGTATACATCCGGATTTTGAACTAGTT	58.738	33.333	16.19	8.13	0.00	2.24
3210	3471	4.554292	CGGACATCATGTATCCTCAAGAG	58.446	47.826	0.00	0.00	0.00	2.85
3354	3615	1.145759	ATTGTGTGCGAGCGTATCCG	61.146	55.000	0.00	0.00	37.07	4.18
3355	3616	0.577269	GATTGTGTGCGAGCGTATCC	59.423	55.000	0.00	0.00	0.00	2.59
3421	3682	6.543735	AGAAAAGCAGAGTAGTTAATTGGGT	58.456	36.000	0.00	0.00	0.00	4.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.