AutoCloner

Multiple sequence alignment - TraesCS6B01G408800

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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	TraesCS6B01G408800	chr6B	100.000	4850	0	0	1	4850	682684097	682679248	0.000000e+00	8957.0
1	TraesCS6B01G408800	chr6B	94.519	2828	73	21	2032	4849	682718371	682715616	0.000000e+00	4289.0
2	TraesCS6B01G408800	chr6B	97.600	1958	40	3	1	1957	682720660	682718709	0.000000e+00	3349.0
3	TraesCS6B01G408800	chr6B	90.019	2064	157	25	2039	4062	682671244	682669190	0.000000e+00	2625.0
4	TraesCS6B01G408800	chr6B	88.196	1813	171	29	17	1810	682709718	682707930	0.000000e+00	2122.0
5	TraesCS6B01G408800	chr6B	89.801	1108	101	8	891	1991	682672569	682671467	0.000000e+00	1410.0
6	TraesCS6B01G408800	chr6B	87.183	710	69	10	17	721	682673594	682672902	0.000000e+00	787.0
7	TraesCS6B01G408800	chr6D	96.419	3407	90	16	750	4144	450202425	450199039	0.000000e+00	5587.0
8	TraesCS6B01G408800	chr6D	87.464	2816	242	60	2031	4789	450198570	450195809	0.000000e+00	3142.0
9	TraesCS6B01G408800	chr6D	95.349	731	22	2	1	731	450203406	450202688	0.000000e+00	1151.0
10	TraesCS6B01G408800	chr6D	88.760	258	22	6	1723	1978	450199036	450198784	4.710000e-80	309.0
11	TraesCS6B01G408800	chr6D	95.000	40	2	0	2148	2187	413352006	413352045	4.050000e-06	63.9
12	TraesCS6B01G408800	chr6A	89.745	3374	264	54	746	4067	595674174	595670831	0.000000e+00	4239.0
13	TraesCS6B01G408800	chr6A	96.404	1863	59	2	2024	3879	595693953	595692092	0.000000e+00	3062.0
14	TraesCS6B01G408800	chr6A	89.186	971	78	13	3876	4843	595692058	595691112	0.000000e+00	1186.0
15	TraesCS6B01G408800	chr6A	87.585	733	64	12	2	724	595675259	595674544	0.000000e+00	824.0
16	TraesCS6B01G408800	chr6A	78.036	560	76	24	4242	4789	595670544	595670020	4.710000e-80	309.0
17	TraesCS6B01G408800	chr6A	90.441	136	12	1	4064	4199	595670673	595670539	1.390000e-40	178.0
18	TraesCS6B01G408800	chr6A	95.000	40	2	0	2148	2187	558887860	558887899	4.050000e-06	63.9
19	TraesCS6B01G408800	chr5A	89.362	94	2	5	2314	2404	472754001	472754089	1.430000e-20	111.0
20	TraesCS6B01G408800	chr7B	82.787	122	13	6	2310	2428	61747766	61747882	8.590000e-18	102.0
21	TraesCS6B01G408800	chr2A	100.000	32	0	0	2147	2178	776463472	776463441	5.240000e-05	60.2

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	TraesCS6B01G408800	chr6B	682679248	682684097	4849	True	8957.000000	8957	100.00000	1	4850	1	chr6B.!!$R1	4849
1	TraesCS6B01G408800	chr6B	682715616	682720660	5044	True	3819.000000	4289	96.05950	1	4849	2	chr6B.!!$R4	4848
2	TraesCS6B01G408800	chr6B	682707930	682709718	1788	True	2122.000000	2122	88.19600	17	1810	1	chr6B.!!$R2	1793
3	TraesCS6B01G408800	chr6B	682669190	682673594	4404	True	1607.333333	2625	89.00100	17	4062	3	chr6B.!!$R3	4045
4	TraesCS6B01G408800	chr6D	450195809	450203406	7597	True	2547.250000	5587	91.99800	1	4789	4	chr6D.!!$R1	4788
5	TraesCS6B01G408800	chr6A	595691112	595693953	2841	True	2124.000000	3062	92.79500	2024	4843	2	chr6A.!!$R2	2819
6	TraesCS6B01G408800	chr6A	595670020	595675259	5239	True	1387.500000	4239	86.45175	2	4789	4	chr6A.!!$R1	4787

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
442	452	1.204704	TGTAGAATCACCGCTGAGTGG	59.795	52.381	11.13	11.13	38.34	4.00	F
493	503	5.526115	TGTGGTTTTGTTTTTACGTTGTCA	58.474	33.333	0.00	0.00	0.00	3.58	F
1958	2337	5.532406	TCTCCTTCCATGTTTTCAAGAACAG	59.468	40.000	0.00	0.00	42.28	3.16	F
3535	4193	1.211703	TGTTTGGAGACACTCAAGGCA	59.788	47.619	0.00	0.00	42.67	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	2390	1.271379	GGCCCTTCTACATGTGTGTGT	60.271	52.381	9.11	0.00	39.39	3.72	R
2014	2393	2.425143	ATGGCCCTTCTACATGTGTG	57.575	50.000	9.11	1.17	0.00	3.82	R
3800	7043	1.550130	TACAAGGCCCTCAACCGGAG	61.550	60.000	9.46	0.00	43.65	4.63	R
4336	7835	0.597637	CTATAGCCGGACAACGCAGG	60.598	60.000	5.05	0.00	42.52	4.85	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
296	298	2.433145	CGCCAGTGACTGCGACAT	60.433	61.111	19.49	0.00	34.71	3.06
346	350	6.736794	GCACTGATCACTTTGAAACATCCTTT	60.737	38.462	0.00	0.00	0.00	3.11
347	351	7.205297	CACTGATCACTTTGAAACATCCTTTT	58.795	34.615	0.00	0.00	0.00	2.27
348	352	7.707893	CACTGATCACTTTGAAACATCCTTTTT	59.292	33.333	0.00	0.00	0.00	1.94
431	441	5.013704	ACCCCACAACTTACATGTAGAATCA	59.986	40.000	5.56	0.00	0.00	2.57
442	452	1.204704	TGTAGAATCACCGCTGAGTGG	59.795	52.381	11.13	11.13	38.34	4.00
493	503	5.526115	TGTGGTTTTGTTTTTACGTTGTCA	58.474	33.333	0.00	0.00	0.00	3.58
923	1291	7.742089	CAGAAGAAACGTTGTTGAGCTATAAAG	59.258	37.037	0.00	0.00	0.00	1.85
984	1354	8.336806	CAGAAAATAGAAGCAAATAGAGCTCTG	58.663	37.037	26.78	11.42	42.53	3.35
1259	1631	7.121168	AGTGAAGTTGATCTTGTTTTTCAGTGA	59.879	33.333	0.00	0.00	36.40	3.41
1484	1858	9.953825	CTTTTATGTGACGTTGATAAGTCTTAC	57.046	33.333	0.00	0.00	38.16	2.34
1958	2337	5.532406	TCTCCTTCCATGTTTTCAAGAACAG	59.468	40.000	0.00	0.00	42.28	3.16
2075	2717	3.600388	AGAGGTTCAAAAGATAGGTGCG	58.400	45.455	0.00	0.00	0.00	5.34
2421	3075	6.975772	GGATATGAGTGTTGAGTCACTAGAAC	59.024	42.308	0.00	0.00	46.81	3.01
2428	3082	8.349568	AGTGTTGAGTCACTAGAACATGTATA	57.650	34.615	0.00	0.00	45.31	1.47
2432	3086	7.956328	TGAGTCACTAGAACATGTATACCTT	57.044	36.000	0.00	0.00	0.00	3.50
2461	3117	5.342806	TGAACACGCAATTAGCTATATGC	57.657	39.130	17.11	17.11	42.61	3.14
2611	3268	6.292061	GCACGAAAACATGAAACTGCAAATAA	60.292	34.615	0.00	0.00	0.00	1.40
3535	4193	1.211703	TGTTTGGAGACACTCAAGGCA	59.788	47.619	0.00	0.00	42.67	4.75
3618	4276	5.059833	CAGTATTCCAATGGTCCTTCTAGC	58.940	45.833	0.00	0.00	0.00	3.42
3708	6951	7.390996	GGCTCAAATTCATCTAGTCATGATCAT	59.609	37.037	1.18	1.18	32.69	2.45
3764	7007	2.086869	AGCAATCACATTCCGGAACAG	58.913	47.619	21.56	17.67	0.00	3.16
3800	7043	4.636206	CCAAGTCTCCAACATAAGTAAGGC	59.364	45.833	0.00	0.00	0.00	4.35
3882	7162	9.717942	ATACCTTGATTCAACTAGATATTGAGC	57.282	33.333	0.00	0.00	37.38	4.26
3898	7178	8.223330	AGATATTGAGCATGGACCTAAAATCTT	58.777	33.333	0.00	0.00	0.00	2.40
3927	7229	7.777095	AGACTCTATGGTGAGTTGAAGATTAC	58.223	38.462	0.00	0.00	46.11	1.89
3930	7232	7.038302	ACTCTATGGTGAGTTGAAGATTACCAA	60.038	37.037	0.00	0.00	44.01	3.67
3932	7234	4.072131	TGGTGAGTTGAAGATTACCAAGC	58.928	43.478	0.00	0.00	35.45	4.01
3935	7237	4.997395	GTGAGTTGAAGATTACCAAGCAGA	59.003	41.667	0.00	0.00	0.00	4.26
3937	7239	4.006319	AGTTGAAGATTACCAAGCAGAGC	58.994	43.478	0.00	0.00	0.00	4.09
3941	7243	1.440145	GATTACCAAGCAGAGCCGGC	61.440	60.000	21.89	21.89	0.00	6.13
3942	7244	1.915078	ATTACCAAGCAGAGCCGGCT	61.915	55.000	33.48	33.48	45.15	5.52
4028	7358	6.313905	GTCCAATAAGATTGAATCGTGAGTGT	59.686	38.462	3.85	0.00	0.00	3.55
4062	7392	4.657436	AACAAGATAGCTTACTCTCCGG	57.343	45.455	0.00	0.00	31.81	5.14
4122	7613	5.406780	AGAAAATCATGAGTGAGAACGACAC	59.593	40.000	0.09	0.00	37.87	3.67
4193	7684	3.257561	CGCCGACGAATCCAGCTG	61.258	66.667	6.78	6.78	43.93	4.24
4198	7689	1.078848	GACGAATCCAGCTGCACCT	60.079	57.895	8.66	0.00	0.00	4.00
4207	7698	0.894141	CAGCTGCACCTGTAGAGTCT	59.106	55.000	0.00	0.00	0.00	3.24
4266	7764	3.561143	CTCGATCTCCCTCTATATGGGG	58.439	54.545	10.11	7.30	44.67	4.96
4515	8036	6.333416	GCCCTTGCCTTTTATTTTAGAGAAG	58.667	40.000	0.00	0.00	0.00	2.85
4516	8037	6.152831	GCCCTTGCCTTTTATTTTAGAGAAGA	59.847	38.462	0.00	0.00	0.00	2.87
4517	8038	7.309805	GCCCTTGCCTTTTATTTTAGAGAAGAA	60.310	37.037	0.00	0.00	0.00	2.52
4537	8058	3.584733	ATCCAGGACCTTTGCCTTATC	57.415	47.619	0.00	0.00	32.12	1.75
4538	8059	1.209504	TCCAGGACCTTTGCCTTATCG	59.790	52.381	0.00	0.00	32.12	2.92
4545	8066	1.818674	CCTTTGCCTTATCGTTGCCTT	59.181	47.619	0.00	0.00	0.00	4.35
4653	8174	9.766277	TTGCTTTGAAAACAACAAACATATTTC	57.234	25.926	0.00	0.00	34.30	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	5.486526	TGCACCAGAAACAAAGTTTCAAAT	58.513	33.333	20.71	6.19	0.00	2.32
71	72	1.555075	TGAGGTCCATAAGTCTGCACC	59.445	52.381	0.00	0.00	0.00	5.01
206	208	7.985184	TGTAGTGGCGAGATCAAAGTTATAATT	59.015	33.333	0.00	0.00	0.00	1.40
265	267	1.139163	CTGGCGGCACAAATCAAAAC	58.861	50.000	7.97	0.00	0.00	2.43
296	298	3.691575	TGAAACCACAACTCTTTGGTGA	58.308	40.909	0.00	0.00	45.84	4.02
442	452	1.740025	CACCATTTTTCGGAGGAGCTC	59.260	52.381	4.71	4.71	0.00	4.09
736	751	6.924111	ACACAACAATAAATGAATCACCTCC	58.076	36.000	0.00	0.00	0.00	4.30
737	752	7.592938	TGACACAACAATAAATGAATCACCTC	58.407	34.615	0.00	0.00	0.00	3.85
738	753	7.448161	TCTGACACAACAATAAATGAATCACCT	59.552	33.333	0.00	0.00	0.00	4.00
1253	1625	4.705507	GGGACTTGTATAGACTGTCACTGA	59.294	45.833	10.88	0.00	33.41	3.41
1259	1631	6.041069	GCTTCTATGGGACTTGTATAGACTGT	59.959	42.308	0.00	0.00	34.22	3.55
1891	2268	8.447053	GGTGAAGAAAAAGAGATAGACATGAAC	58.553	37.037	0.00	0.00	0.00	3.18
2006	2385	3.248363	CCTTCTACATGTGTGTGTGTGTG	59.752	47.826	9.11	0.00	39.39	3.82
2007	2386	3.466836	CCTTCTACATGTGTGTGTGTGT	58.533	45.455	9.11	0.00	39.39	3.72
2009	2388	2.810400	GCCCTTCTACATGTGTGTGTGT	60.810	50.000	9.11	0.00	39.39	3.72
2011	2390	1.271379	GGCCCTTCTACATGTGTGTGT	60.271	52.381	9.11	0.00	39.39	3.72
2014	2393	2.425143	ATGGCCCTTCTACATGTGTG	57.575	50.000	9.11	1.17	0.00	3.82
2016	2395	6.469782	AAAATAATGGCCCTTCTACATGTG	57.530	37.500	9.11	0.00	0.00	3.21
2075	2717	6.173339	TGGTAGAGACTCATTCCATTTCAAC	58.827	40.000	5.02	0.00	0.00	3.18
2150	2792	5.402997	TTTGATTGAGTTAATGCATGCCA	57.597	34.783	16.68	3.52	0.00	4.92
2360	3011	9.832445	CTTACACCCAACATATTCTAATGTAGT	57.168	33.333	0.00	0.00	39.16	2.73
2421	3075	7.334749	CGTGTTCATAAACGAAGGTATACATG	58.665	38.462	5.01	0.00	42.32	3.21
2428	3082	2.485903	TGCGTGTTCATAAACGAAGGT	58.514	42.857	0.00	0.00	42.32	3.50
2432	3086	4.643953	GCTAATTGCGTGTTCATAAACGA	58.356	39.130	0.00	0.00	42.32	3.85
2461	3117	8.881743	AGACGTCTCTAACTTGTACTACTATTG	58.118	37.037	13.58	0.00	0.00	1.90
2611	3268	6.255215	GCGTGTGCACAACATAATACTTTAT	58.745	36.000	23.59	0.00	41.97	1.40
2862	3519	6.141844	CGATGCATCTGAAATGAATTAACAGC	59.858	38.462	23.73	0.00	0.00	4.40
3046	3703	7.435068	TTTCTAATACAAGACACTTTGGCTC	57.565	36.000	0.00	0.00	31.94	4.70
3103	3760	4.142600	GGGTTCACTGTTCATCTGTATTGC	60.143	45.833	0.00	0.00	0.00	3.56
3618	4276	4.503007	CCTATAACTTCACATGGTTCGTCG	59.497	45.833	0.00	0.00	0.00	5.12
3708	6951	4.852134	ATTGTATGTTTGAGCAGCAACA	57.148	36.364	0.00	0.00	35.91	3.33
3764	7007	4.113354	GGAGACTTGGTCGTGATGATAAC	58.887	47.826	0.00	0.00	37.67	1.89
3800	7043	1.550130	TACAAGGCCCTCAACCGGAG	61.550	60.000	9.46	0.00	43.65	4.63
3882	7162	8.919145	AGAGTCTAGTAAGATTTTAGGTCCATG	58.081	37.037	0.00	0.00	33.30	3.66
3941	7243	5.424252	TGATTAGGCCCCTAATATTACCGAG	59.576	44.000	17.26	0.00	45.88	4.63
3942	7244	5.343715	TGATTAGGCCCCTAATATTACCGA	58.656	41.667	17.26	0.00	45.88	4.69
4122	7613	1.868469	TTTCGTCCAAACTGGTACGG	58.132	50.000	13.77	0.00	39.64	4.02
4186	7677	0.542938	ACTCTACAGGTGCAGCTGGA	60.543	55.000	40.06	34.71	0.00	3.86
4193	7684	0.739112	GCAGCAGACTCTACAGGTGC	60.739	60.000	0.00	0.00	46.21	5.01
4238	7736	3.148279	GGGAGATCGAGGTGGCGT	61.148	66.667	0.00	0.00	0.00	5.68
4266	7764	2.125106	CGCCCTGGCTGGTACTTC	60.125	66.667	9.73	0.00	39.32	3.01
4283	7782	2.772189	CAGCTACACGCGAACAGC	59.228	61.111	15.93	17.45	45.59	4.40
4336	7835	0.597637	CTATAGCCGGACAACGCAGG	60.598	60.000	5.05	0.00	42.52	4.85
4515	8036	2.222227	AAGGCAAAGGTCCTGGATTC	57.778	50.000	0.00	0.00	33.43	2.52
4516	8037	3.685550	CGATAAGGCAAAGGTCCTGGATT	60.686	47.826	0.00	0.00	33.43	3.01
4517	8038	2.158755	CGATAAGGCAAAGGTCCTGGAT	60.159	50.000	0.00	0.00	33.43	3.41
4653	8174	9.980780	AAACCTGAAATAATTTTGTGTTTTTCG	57.019	25.926	0.00	0.00	0.00	3.46
4659	8180	9.612066	ATTGACAAACCTGAAATAATTTTGTGT	57.388	25.926	2.90	0.00	39.79	3.72

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.