AutoCloner

Multiple sequence alignment - TraesCS3B01G531100

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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	TraesCS3B01G531100	chr3B	100.000	3047	0	0	1	3047	772227320	772230366	0.000000e+00	5627
1	TraesCS3B01G531100	chr3B	93.023	688	35	10	2364	3046	771844316	771844995	0.000000e+00	992
2	TraesCS3B01G531100	chr3B	78.431	204	36	4	2801	3003	772029189	772029385	3.190000e-25	126
3	TraesCS3B01G531100	chr3B	78.431	204	36	4	2801	3003	772074943	772075139	3.190000e-25	126
4	TraesCS3B01G531100	chr1A	98.596	2350	21	3	21	2361	584970275	584972621	0.000000e+00	4146
5	TraesCS3B01G531100	chr1A	92.846	1999	95	14	23	1978	532735357	532733364	0.000000e+00	2856
6	TraesCS3B01G531100	chr1A	92.978	1296	53	11	23	1284	12307824	12309115	0.000000e+00	1855
7	TraesCS3B01G531100	chr1A	90.729	658	41	2	1321	1978	12309363	12310000	0.000000e+00	859
8	TraesCS3B01G531100	chr5B	96.859	2356	54	8	23	2361	26737128	26734776	0.000000e+00	3923
9	TraesCS3B01G531100	chr7B	95.094	2242	88	9	18	2250	706976404	706974176	0.000000e+00	3511
10	TraesCS3B01G531100	chr1B	93.509	2357	107	16	16	2361	182058477	182060798	0.000000e+00	3463
11	TraesCS3B01G531100	chr5A	92.886	2010	99	15	8	1978	673237841	673239845	0.000000e+00	2880
12	TraesCS3B01G531100	chr2A	92.789	1997	103	13	16	1978	776173504	776175493	0.000000e+00	2852
13	TraesCS3B01G531100	chr2A	92.528	1994	105	13	19	1978	9951336	9953319	0.000000e+00	2817
14	TraesCS3B01G531100	chr2A	89.719	924	81	7	1451	2372	772968488	772969399	0.000000e+00	1168
15	TraesCS3B01G531100	chrUn	89.940	1332	98	11	1048	2361	117079696	117081009	0.000000e+00	1685
16	TraesCS3B01G531100	chrUn	90.164	915	77	8	1451	2364	290195093	290195995	0.000000e+00	1179
17	TraesCS3B01G531100	chrUn	90.132	912	77	8	1451	2361	326178300	326179199	0.000000e+00	1173
18	TraesCS3B01G531100	chrUn	90.132	912	77	8	1451	2361	327556346	327557245	0.000000e+00	1173
19	TraesCS3B01G531100	chrUn	85.828	1009	77	24	22	1006	326177276	326178242	0.000000e+00	1011
20	TraesCS3B01G531100	chrUn	87.704	675	64	8	339	1006	290194373	290195035	0.000000e+00	769
21	TraesCS3B01G531100	chr6B	90.209	909	76	6	1454	2361	20187162	20186266	0.000000e+00	1173
22	TraesCS3B01G531100	chr6B	85.813	1008	77	24	23	1006	20188188	20187223	0.000000e+00	1009
23	TraesCS3B01G531100	chr3D	89.407	708	41	12	2364	3047	578564228	578563531	0.000000e+00	861
24	TraesCS3B01G531100	chr3A	92.517	147	11	0	2901	3047	714064414	714064560	8.560000e-51	211
25	TraesCS3B01G531100	chr3A	90.551	127	9	2	2643	2766	714063705	714063831	6.760000e-37	165

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	TraesCS3B01G531100	chr3B	772227320	772230366	3046	False	5627	5627	100.0000	1	3047	1	chr3B.!!$F4	3046
1	TraesCS3B01G531100	chr3B	771844316	771844995	679	False	992	992	93.0230	2364	3046	1	chr3B.!!$F1	682
2	TraesCS3B01G531100	chr1A	584970275	584972621	2346	False	4146	4146	98.5960	21	2361	1	chr1A.!!$F1	2340
3	TraesCS3B01G531100	chr1A	532733364	532735357	1993	True	2856	2856	92.8460	23	1978	1	chr1A.!!$R1	1955
4	TraesCS3B01G531100	chr1A	12307824	12310000	2176	False	1357	1855	91.8535	23	1978	2	chr1A.!!$F2	1955
5	TraesCS3B01G531100	chr5B	26734776	26737128	2352	True	3923	3923	96.8590	23	2361	1	chr5B.!!$R1	2338
6	TraesCS3B01G531100	chr7B	706974176	706976404	2228	True	3511	3511	95.0940	18	2250	1	chr7B.!!$R1	2232
7	TraesCS3B01G531100	chr1B	182058477	182060798	2321	False	3463	3463	93.5090	16	2361	1	chr1B.!!$F1	2345
8	TraesCS3B01G531100	chr5A	673237841	673239845	2004	False	2880	2880	92.8860	8	1978	1	chr5A.!!$F1	1970
9	TraesCS3B01G531100	chr2A	776173504	776175493	1989	False	2852	2852	92.7890	16	1978	1	chr2A.!!$F3	1962
10	TraesCS3B01G531100	chr2A	9951336	9953319	1983	False	2817	2817	92.5280	19	1978	1	chr2A.!!$F1	1959
11	TraesCS3B01G531100	chr2A	772968488	772969399	911	False	1168	1168	89.7190	1451	2372	1	chr2A.!!$F2	921
12	TraesCS3B01G531100	chrUn	117079696	117081009	1313	False	1685	1685	89.9400	1048	2361	1	chrUn.!!$F1	1313
13	TraesCS3B01G531100	chrUn	327556346	327557245	899	False	1173	1173	90.1320	1451	2361	1	chrUn.!!$F2	910
14	TraesCS3B01G531100	chrUn	326177276	326179199	1923	False	1092	1173	87.9800	22	2361	2	chrUn.!!$F4	2339
15	TraesCS3B01G531100	chrUn	290194373	290195995	1622	False	974	1179	88.9340	339	2364	2	chrUn.!!$F3	2025
16	TraesCS3B01G531100	chr6B	20186266	20188188	1922	True	1091	1173	88.0110	23	2361	2	chr6B.!!$R1	2338
17	TraesCS3B01G531100	chr3D	578563531	578564228	697	True	861	861	89.4070	2364	3047	1	chr3D.!!$R1	683

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
898	970	3.670377	GGCAAGGGTTGTGTCGCC	61.67	66.667	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2757	3107	0.253044	GGCTGATGCTGGTTAGGTGA	59.747	55.0	0.0	0.0	39.59	4.02	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
649	697	3.727723	GCTATGCTGCACGAATTTGATTC	59.272	43.478	3.57	0.00	35.94	2.52
744	794	5.704978	TGATGATTGACCATTTGTTCTTCGA	59.295	36.000	0.00	0.00	0.00	3.71
898	970	3.670377	GGCAAGGGTTGTGTCGCC	61.670	66.667	0.00	0.00	0.00	5.54
1011	1084	2.124819	CTGCCGATGCCAAGAGCT	60.125	61.111	0.00	0.00	44.23	4.09
1710	2012	1.512926	AGATGCGTGTCCAAGTTCAC	58.487	50.000	0.00	0.00	0.00	3.18
1716	2018	1.365699	GTGTCCAAGTTCACGTGTGT	58.634	50.000	16.51	0.00	0.00	3.72
1718	2020	0.027586	GTCCAAGTTCACGTGTGTGC	59.972	55.000	16.51	4.51	46.01	4.57
1719	2021	0.107897	TCCAAGTTCACGTGTGTGCT	60.108	50.000	16.51	6.76	46.01	4.40
1720	2022	0.027979	CCAAGTTCACGTGTGTGCTG	59.972	55.000	16.51	7.79	46.01	4.41
1721	2023	0.726827	CAAGTTCACGTGTGTGCTGT	59.273	50.000	16.51	0.00	46.01	4.40
1722	2024	1.130373	CAAGTTCACGTGTGTGCTGTT	59.870	47.619	16.51	0.00	46.01	3.16
1723	2025	1.448985	AGTTCACGTGTGTGCTGTTT	58.551	45.000	16.51	0.00	46.01	2.83
1724	2026	1.396996	AGTTCACGTGTGTGCTGTTTC	59.603	47.619	16.51	0.00	46.01	2.78
1831	2148	5.199982	AGATACTCTGTTTGAGGAGGAGA	57.800	43.478	0.00	0.00	46.72	3.71
2090	2414	4.091424	GCTAGATGTTGCGTTTTTAGCAG	58.909	43.478	0.00	0.00	46.01	4.24
2099	2423	7.419204	TGTTGCGTTTTTAGCAGTATAAAGTT	58.581	30.769	0.00	0.00	46.01	2.66
2101	2425	8.748582	GTTGCGTTTTTAGCAGTATAAAGTTTT	58.251	29.630	0.00	0.00	46.01	2.43
2102	2426	8.859517	TGCGTTTTTAGCAGTATAAAGTTTTT	57.140	26.923	0.00	0.00	40.01	1.94
2196	2523	0.251916	AACTGTAATGGCGCCAGCTA	59.748	50.000	35.36	24.42	44.37	3.32
2448	2776	4.890581	AGCATCAAGGTAGACAGTAGTAGG	59.109	45.833	0.00	0.00	0.00	3.18
2483	2812	0.849094	TGGTAACCAGGCCCAATCCT	60.849	55.000	0.00	0.00	36.78	3.24
2505	2834	5.221803	CCTGATGGGAGCTGTACAATATCTT	60.222	44.000	0.00	0.00	37.23	2.40
2525	2854	4.337555	TCTTACGGTACTGAGCATAGGTTC	59.662	45.833	9.17	0.00	0.00	3.62
2554	2883	2.353704	CCATGGTGCTGAACTTCGTCTA	60.354	50.000	2.57	0.00	0.00	2.59
2647	2985	7.734865	ACATGGATGAGGACCTATGTATAGAAA	59.265	37.037	5.22	0.00	32.18	2.52
2649	2987	8.742125	TGGATGAGGACCTATGTATAGAAATT	57.258	34.615	0.00	0.00	32.05	1.82
2650	2988	8.816894	TGGATGAGGACCTATGTATAGAAATTC	58.183	37.037	0.00	0.00	32.05	2.17
2651	2989	9.041354	GGATGAGGACCTATGTATAGAAATTCT	57.959	37.037	0.00	0.00	32.05	2.40
2740	3090	3.923461	CCGTTTGCAAGAAACTGAACAAA	59.077	39.130	0.00	0.00	0.00	2.83
2757	3107	8.416329	ACTGAACAAAAGCAAGAAACAATCTAT	58.584	29.630	0.00	0.00	37.42	1.98
2758	3108	8.801715	TGAACAAAAGCAAGAAACAATCTATC	57.198	30.769	0.00	0.00	37.42	2.08
2759	3109	8.412456	TGAACAAAAGCAAGAAACAATCTATCA	58.588	29.630	0.00	0.00	37.42	2.15
2761	3111	7.147976	ACAAAAGCAAGAAACAATCTATCACC	58.852	34.615	0.00	0.00	37.42	4.02
2762	3112	7.014615	ACAAAAGCAAGAAACAATCTATCACCT	59.985	33.333	0.00	0.00	37.42	4.00
2763	3113	8.514594	CAAAAGCAAGAAACAATCTATCACCTA	58.485	33.333	0.00	0.00	37.42	3.08
2765	3115	7.617041	AGCAAGAAACAATCTATCACCTAAC	57.383	36.000	0.00	0.00	37.42	2.34
2766	3116	6.599638	AGCAAGAAACAATCTATCACCTAACC	59.400	38.462	0.00	0.00	37.42	2.85
2767	3117	6.374333	GCAAGAAACAATCTATCACCTAACCA	59.626	38.462	0.00	0.00	37.42	3.67
2768	3118	7.414540	GCAAGAAACAATCTATCACCTAACCAG	60.415	40.741	0.00	0.00	37.42	4.00
2769	3119	6.116126	AGAAACAATCTATCACCTAACCAGC	58.884	40.000	0.00	0.00	36.32	4.85
2785	3135	2.071262	AGCATCAGCCTGAGGGGAG	61.071	63.158	8.63	0.00	43.56	4.30
2909	3259	3.418022	GGGACGGTAGGGAGTAGAG	57.582	63.158	0.00	0.00	0.00	2.43
2968	3318	4.021925	GGCGAGTTGAGGCTGGGT	62.022	66.667	0.00	0.00	0.00	4.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.301401	GGCGCGGCATCCTATGTTA	60.301	57.895	29.32	0.00	0.00	2.41
1	2	2.591715	GGCGCGGCATCCTATGTT	60.592	61.111	29.32	0.00	0.00	2.71
5	6	2.363711	CTAACTGGCGCGGCATCCTA	62.364	60.000	36.23	23.48	0.00	2.94
6	7	3.740128	CTAACTGGCGCGGCATCCT	62.740	63.158	36.23	23.63	0.00	3.24
7	8	3.272334	CTAACTGGCGCGGCATCC	61.272	66.667	36.23	15.15	0.00	3.51
9	10	4.856801	CCCTAACTGGCGCGGCAT	62.857	66.667	36.23	24.41	0.00	4.40
158	168	2.032071	CTGGACCGGGCGAAACTT	59.968	61.111	6.32	0.00	0.00	2.66
649	697	5.064198	GCACAAACAAATTCATCCATCCATG	59.936	40.000	0.00	0.00	0.00	3.66
744	794	1.142936	TGGGGCTCTGCATACATCAT	58.857	50.000	0.00	0.00	0.00	2.45
1011	1084	4.572571	GACGGTGGGGTTGGTGCA	62.573	66.667	0.00	0.00	0.00	4.57
1710	2012	0.726827	ACACAGAAACAGCACACACG	59.273	50.000	0.00	0.00	0.00	4.49
1711	2013	1.795162	GCACACAGAAACAGCACACAC	60.795	52.381	0.00	0.00	0.00	3.82
1712	2014	0.451383	GCACACAGAAACAGCACACA	59.549	50.000	0.00	0.00	0.00	3.72
1713	2015	0.734889	AGCACACAGAAACAGCACAC	59.265	50.000	0.00	0.00	0.00	3.82
1714	2016	2.212652	CTAGCACACAGAAACAGCACA	58.787	47.619	0.00	0.00	0.00	4.57
1715	2017	1.532868	CCTAGCACACAGAAACAGCAC	59.467	52.381	0.00	0.00	0.00	4.40
1716	2018	1.416030	TCCTAGCACACAGAAACAGCA	59.584	47.619	0.00	0.00	0.00	4.41
1717	2019	2.169832	TCCTAGCACACAGAAACAGC	57.830	50.000	0.00	0.00	0.00	4.40
1718	2020	4.083110	CCATTTCCTAGCACACAGAAACAG	60.083	45.833	0.00	0.00	31.51	3.16
1719	2021	3.820467	CCATTTCCTAGCACACAGAAACA	59.180	43.478	0.00	0.00	31.51	2.83
1720	2022	4.072131	TCCATTTCCTAGCACACAGAAAC	58.928	43.478	0.00	0.00	31.51	2.78
1721	2023	4.326826	CTCCATTTCCTAGCACACAGAAA	58.673	43.478	0.00	0.00	33.13	2.52
1722	2024	3.869912	GCTCCATTTCCTAGCACACAGAA	60.870	47.826	0.00	0.00	36.26	3.02
1723	2025	2.355108	GCTCCATTTCCTAGCACACAGA	60.355	50.000	0.00	0.00	36.26	3.41
1724	2026	2.012673	GCTCCATTTCCTAGCACACAG	58.987	52.381	0.00	0.00	36.26	3.66
2448	2776	8.190784	CCTGGTTACCATTCAAATTTCTATGAC	58.809	37.037	3.88	2.55	30.82	3.06
2483	2812	5.894298	AAGATATTGTACAGCTCCCATCA	57.106	39.130	0.00	0.00	0.00	3.07
2484	2813	5.864474	CGTAAGATATTGTACAGCTCCCATC	59.136	44.000	0.00	0.00	43.02	3.51
2505	2834	2.615447	CGAACCTATGCTCAGTACCGTA	59.385	50.000	0.00	0.00	0.00	4.02
2525	2854	0.888736	TCAGCACCATGGTTCAACCG	60.889	55.000	16.84	3.64	42.58	4.44
2554	2883	6.502158	ACCCAATTCCTAAATCTCTATCCGAT	59.498	38.462	0.00	0.00	0.00	4.18
2647	2985	9.736414	CATCTACATATCTCATGGGAAAAGAAT	57.264	33.333	0.00	0.00	0.00	2.40
2649	2987	7.513781	TCCATCTACATATCTCATGGGAAAAGA	59.486	37.037	0.00	0.00	35.61	2.52
2650	2988	7.683578	TCCATCTACATATCTCATGGGAAAAG	58.316	38.462	0.00	0.00	35.61	2.27
2651	2989	7.631510	TCCATCTACATATCTCATGGGAAAA	57.368	36.000	0.00	0.00	35.61	2.29
2665	3012	5.514484	GCTCCAATTCAGGATCCATCTACAT	60.514	44.000	15.82	0.00	36.99	2.29
2672	3019	0.464373	GCGCTCCAATTCAGGATCCA	60.464	55.000	15.82	0.00	36.99	3.41
2740	3090	7.121315	GGTTAGGTGATAGATTGTTTCTTGCTT	59.879	37.037	0.00	0.00	35.79	3.91
2757	3107	0.253044	GGCTGATGCTGGTTAGGTGA	59.747	55.000	0.00	0.00	39.59	4.02
2758	3108	0.254178	AGGCTGATGCTGGTTAGGTG	59.746	55.000	0.00	0.00	39.59	4.00
2759	3109	0.254178	CAGGCTGATGCTGGTTAGGT	59.746	55.000	9.42	0.00	39.59	3.08
2761	3111	1.474677	CCTCAGGCTGATGCTGGTTAG	60.475	57.143	19.11	2.52	39.59	2.34
2762	3112	0.543277	CCTCAGGCTGATGCTGGTTA	59.457	55.000	19.11	0.00	39.59	2.85
2763	3113	1.302285	CCTCAGGCTGATGCTGGTT	59.698	57.895	19.11	0.00	39.59	3.67
2765	3115	2.192443	CCCTCAGGCTGATGCTGG	59.808	66.667	19.11	15.21	39.59	4.85
2766	3116	2.192443	CCCCTCAGGCTGATGCTG	59.808	66.667	19.11	6.06	39.59	4.41
2767	3117	2.041762	TCCCCTCAGGCTGATGCT	59.958	61.111	19.11	0.00	39.59	3.79
2768	3118	2.509916	CTCCCCTCAGGCTGATGC	59.490	66.667	19.11	0.00	38.76	3.91
2769	3119	2.450320	CCCTCCCCTCAGGCTGATG	61.450	68.421	19.11	15.34	34.51	3.07
2785	3135	0.781920	AAGGTTTTACCCCCTGTCCC	59.218	55.000	0.00	0.00	39.75	4.46
2796	3146	0.945265	CGACGGCGACCAAGGTTTTA	60.945	55.000	16.62	0.00	40.82	1.52
2871	3221	2.995574	CTGGGTTCTCGTCCCCGT	60.996	66.667	0.00	0.00	44.44	5.28
2894	3244	1.229643	GGGCTCTACTCCCTACCGT	59.770	63.158	0.00	0.00	40.66	4.83
2905	3255	1.066858	CAAGCGAAGTTCAGGGCTCTA	60.067	52.381	3.32	0.00	33.99	2.43
2909	3259	2.563427	GCAAGCGAAGTTCAGGGC	59.437	61.111	3.32	0.00	0.00	5.19
2915	3265	1.639298	GCGATGAGGCAAGCGAAGTT	61.639	55.000	1.93	0.00	0.00	2.66
2968	3318	0.173935	CGTACCCAATACTGCGTCCA	59.826	55.000	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.