AutoCloner

Multiple sequence alignment - TraesCS4A01G479300

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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	TraesCS4A01G479300	chr4A	100.000	3250	0	0	1	3250	736141560	736144809	0.000000e+00	6002
1	TraesCS4A01G479300	chr4A	87.927	2402	231	31	1	2395	736803878	736806227	0.000000e+00	2774
2	TraesCS4A01G479300	chr4A	88.652	2203	195	22	1	2199	736458745	736456594	0.000000e+00	2632
3	TraesCS4A01G479300	chr4A	88.092	1923	212	7	1	1919	734577458	734579367	0.000000e+00	2266
4	TraesCS4A01G479300	chr4A	88.028	1846	206	5	1	1844	736039074	736040906	0.000000e+00	2170
5	TraesCS4A01G479300	chr4A	94.080	1419	79	5	67	1484	736790563	736791977	0.000000e+00	2150
6	TraesCS4A01G479300	chr4A	87.339	1785	207	8	1	1783	736869458	736871225	0.000000e+00	2026
7	TraesCS4A01G479300	chr4A	90.871	1205	77	10	2068	3250	736049492	736050685	0.000000e+00	1585
8	TraesCS4A01G479300	chr4A	92.807	709	47	3	1214	1919	735520556	735519849	0.000000e+00	1024
9	TraesCS4A01G479300	chr4A	85.042	956	103	13	1888	2820	734579390	734580328	0.000000e+00	937
10	TraesCS4A01G479300	chr4A	85.157	667	85	8	1888	2553	735762000	735762653	0.000000e+00	671
11	TraesCS4A01G479300	chr4A	86.270	488	51	9	2758	3239	735490101	735489624	1.730000e-142	516
12	TraesCS4A01G479300	chr4A	86.871	457	33	10	2284	2716	735491010	735490557	1.360000e-133	486
13	TraesCS4A01G479300	chr4A	87.360	356	34	7	2877	3226	734580340	734580690	6.530000e-107	398
14	TraesCS4A01G479300	chr7D	89.206	2418	240	8	1	2411	575927564	575925161	0.000000e+00	3000
15	TraesCS4A01G479300	chr7D	93.902	1935	102	9	1	1932	5656166	5654245	0.000000e+00	2905
16	TraesCS4A01G479300	chr7D	88.000	875	53	9	2143	2995	5652756	5651912	0.000000e+00	987
17	TraesCS4A01G479300	chr7D	86.525	705	61	17	2386	3065	5435169	5434474	0.000000e+00	745
18	TraesCS4A01G479300	chr7D	88.722	266	18	7	2993	3250	5651849	5651588	6.770000e-82	315
19	TraesCS4A01G479300	chr7A	88.678	2420	250	12	1	2415	666796988	666794588	0.000000e+00	2929
20	TraesCS4A01G479300	chr2D	82.735	2450	364	46	1	2427	637639854	637637441	0.000000e+00	2126
21	TraesCS4A01G479300	chr2B	82.353	2414	373	39	1	2395	795053994	795051615	0.000000e+00	2049
22	TraesCS4A01G479300	chr2A	84.965	1849	247	18	1	1843	762310100	762311923	0.000000e+00	1845

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	TraesCS4A01G479300	chr4A	736141560	736144809	3249	False	6002.000000	6002	100.000000	1	3250	1	chr4A.!!$F4	3249
1	TraesCS4A01G479300	chr4A	736803878	736806227	2349	False	2774.000000	2774	87.927000	1	2395	1	chr4A.!!$F6	2394
2	TraesCS4A01G479300	chr4A	736456594	736458745	2151	True	2632.000000	2632	88.652000	1	2199	1	chr4A.!!$R2	2198
3	TraesCS4A01G479300	chr4A	736039074	736040906	1832	False	2170.000000	2170	88.028000	1	1844	1	chr4A.!!$F2	1843
4	TraesCS4A01G479300	chr4A	736790563	736791977	1414	False	2150.000000	2150	94.080000	67	1484	1	chr4A.!!$F5	1417
5	TraesCS4A01G479300	chr4A	736869458	736871225	1767	False	2026.000000	2026	87.339000	1	1783	1	chr4A.!!$F7	1782
6	TraesCS4A01G479300	chr4A	736049492	736050685	1193	False	1585.000000	1585	90.871000	2068	3250	1	chr4A.!!$F3	1182
7	TraesCS4A01G479300	chr4A	734577458	734580690	3232	False	1200.333333	2266	86.831333	1	3226	3	chr4A.!!$F8	3225
8	TraesCS4A01G479300	chr4A	735519849	735520556	707	True	1024.000000	1024	92.807000	1214	1919	1	chr4A.!!$R1	705
9	TraesCS4A01G479300	chr4A	735762000	735762653	653	False	671.000000	671	85.157000	1888	2553	1	chr4A.!!$F1	665
10	TraesCS4A01G479300	chr4A	735489624	735491010	1386	True	501.000000	516	86.570500	2284	3239	2	chr4A.!!$R3	955
11	TraesCS4A01G479300	chr7D	575925161	575927564	2403	True	3000.000000	3000	89.206000	1	2411	1	chr7D.!!$R2	2410
12	TraesCS4A01G479300	chr7D	5651588	5656166	4578	True	1402.333333	2905	90.208000	1	3250	3	chr7D.!!$R3	3249
13	TraesCS4A01G479300	chr7D	5434474	5435169	695	True	745.000000	745	86.525000	2386	3065	1	chr7D.!!$R1	679
14	TraesCS4A01G479300	chr7A	666794588	666796988	2400	True	2929.000000	2929	88.678000	1	2415	1	chr7A.!!$R1	2414
15	TraesCS4A01G479300	chr2D	637637441	637639854	2413	True	2126.000000	2126	82.735000	1	2427	1	chr2D.!!$R1	2426
16	TraesCS4A01G479300	chr2B	795051615	795053994	2379	True	2049.000000	2049	82.353000	1	2395	1	chr2B.!!$R1	2394
17	TraesCS4A01G479300	chr2A	762310100	762311923	1823	False	1845.000000	1845	84.965000	1	1843	1	chr2A.!!$F1	1842

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
843	846	1.157585	GAGGCCTCGAAAAGTTGGAC	58.842	55.0	19.06	0.0	0.0	4.02	F
2200	3541	0.317160	CAACCTACAGCGGAGACACA	59.683	55.0	0.00	0.0	0.0	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2246	3587	0.174389	CTCTCCTCGCAGCAAGCTAA	59.826	55.000	0.00	0.0	42.61	3.09	R
3148	5047	4.714632	GGTACCTGCATATCTTTTAGCCA	58.285	43.478	4.06	0.0	0.00	4.75	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
153	154	3.134804	CCTAGTGATTGGGATTTCCTCGT	59.865	47.826	0.00	0.00	36.20	4.18
293	295	6.042322	AGGTAAAAACAAAATAACTGGGACCC	59.958	38.462	2.45	2.45	0.00	4.46
572	574	3.260884	TGATCTTTCCGCTAACTCCTTGT	59.739	43.478	0.00	0.00	0.00	3.16
708	711	3.660501	AGCGCAATCGACCTATCAATA	57.339	42.857	11.47	0.00	38.10	1.90
843	846	1.157585	GAGGCCTCGAAAAGTTGGAC	58.842	55.000	19.06	0.00	0.00	4.02
1164	1193	8.341173	GGATGCTACTTAATGAAGACAAGAATG	58.659	37.037	0.00	0.00	36.45	2.67
1227	1256	4.987408	AGAGATGCATGAGAGGATATCG	57.013	45.455	2.46	0.00	33.52	2.92
1357	1386	8.512138	GTTTATGTACTGTAGCAATCAAGGTTT	58.488	33.333	0.00	0.00	0.00	3.27
1453	1482	4.997395	GGAAGCTTGTCAAAGTGATCACTA	59.003	41.667	28.10	10.78	41.58	2.74
1919	2024	3.754965	AGTAGATTTCACTTGGCAAGCA	58.245	40.909	26.45	11.18	0.00	3.91
1921	2026	3.655276	AGATTTCACTTGGCAAGCAAG	57.345	42.857	26.45	16.46	35.88	4.01
1937	2043	5.564259	GCAAGCAAGATTGAATTGAGAGTGT	60.564	40.000	1.74	0.00	31.83	3.55
1949	2055	8.675705	TGAATTGAGAGTGTAATCTGTCAAAA	57.324	30.769	9.57	0.00	45.78	2.44
1982	2088	5.186996	CCATTACATGGCCAGTAACATTC	57.813	43.478	22.19	0.00	44.70	2.67
1983	2089	4.261155	CCATTACATGGCCAGTAACATTCG	60.261	45.833	22.19	12.56	44.70	3.34
1999	2109	9.015577	AGTAACATTCGTGTTTACATGTTTTTG	57.984	29.630	2.30	0.00	34.56	2.44
2006	2116	7.623770	TCGTGTTTACATGTTTTTGAGAGTAC	58.376	34.615	2.30	0.00	34.59	2.73
2010	2120	3.472652	ACATGTTTTTGAGAGTACGGCA	58.527	40.909	0.00	0.00	0.00	5.69
2014	2124	3.128349	GTTTTTGAGAGTACGGCACAGA	58.872	45.455	0.00	0.00	0.00	3.41
2019	2129	1.476891	GAGAGTACGGCACAGAATCCA	59.523	52.381	0.00	0.00	0.00	3.41
2021	2131	2.093973	AGAGTACGGCACAGAATCCAAG	60.094	50.000	0.00	0.00	0.00	3.61
2051	2161	6.040955	CCATGGATGGTCACGTATATAGCTAT	59.959	42.308	5.56	11.77	43.05	2.97
2089	2199	6.346096	TGGAAATATTTACTGGAAGGAGACG	58.654	40.000	11.70	0.00	39.30	4.18
2090	2200	6.070424	TGGAAATATTTACTGGAAGGAGACGT	60.070	38.462	11.70	0.00	39.30	4.34
2141	3481	3.862642	GCCTGGTCGAATATGTCAGGATC	60.863	52.174	11.36	0.00	45.66	3.36
2166	3507	4.754114	CCTATCCTGATAAGCTGCTGAAAC	59.246	45.833	1.35	0.00	0.00	2.78
2200	3541	0.317160	CAACCTACAGCGGAGACACA	59.683	55.000	0.00	0.00	0.00	3.72
2202	3543	1.154016	CCTACAGCGGAGACACACG	60.154	63.158	0.00	0.00	0.00	4.49
2212	3553	2.408050	GGAGACACACGGCATATCATC	58.592	52.381	0.00	0.00	0.00	2.92
2219	3560	5.340803	ACACACGGCATATCATCGATATAC	58.659	41.667	0.00	0.00	33.98	1.47
2246	3587	8.660435	TCTTATATCCTATGTTTAAGCTTGGCT	58.340	33.333	9.86	0.00	42.56	4.75
2271	3612	0.685785	TGCTGCGAGGAGAGGATTCT	60.686	55.000	0.00	0.00	36.01	2.40
2272	3613	0.463620	GCTGCGAGGAGAGGATTCTT	59.536	55.000	0.00	0.00	32.53	2.52
2281	3622	2.275318	GAGAGGATTCTTCAAGGCACG	58.725	52.381	0.00	0.00	32.53	5.34
2420	3763	1.068588	CGATCATCTTTACGGCCCTGA	59.931	52.381	0.00	0.00	0.00	3.86
2427	3770	1.774894	TTTACGGCCCTGAGGTTGCT	61.775	55.000	0.00	0.00	34.57	3.91
2450	3797	0.327924	TGTTATCCTGTGGCCTGTGG	59.672	55.000	3.32	2.92	0.00	4.17
2465	3812	0.695924	TGTGGTATTGTGGTCTGGGG	59.304	55.000	0.00	0.00	0.00	4.96
2469	3816	0.912486	GTATTGTGGTCTGGGGAGCT	59.088	55.000	0.00	0.00	40.29	4.09
2515	3907	4.460382	TCTGAAGTCAGCATTTCCATTTCC	59.540	41.667	3.30	0.00	43.46	3.13
2521	3913	2.034124	AGCATTTCCATTTCCCATCCG	58.966	47.619	0.00	0.00	0.00	4.18
2556	3948	9.554395	TGTTTGTCCAGTATACATATATTGTGG	57.446	33.333	5.50	1.51	39.48	4.17
2686	4099	9.343103	CTTCTCAGATTCTTGTCATCAAAATTG	57.657	33.333	0.00	0.00	32.87	2.32
2743	4544	1.730064	CTTTGGCTGCACAAATGATGC	59.270	47.619	13.90	0.00	43.68	3.91
2812	4641	3.738830	TCTTGCTGCTGCTTTGATTTT	57.261	38.095	17.00	0.00	40.48	1.82
2826	4655	1.243902	GATTTTGGACCCAAGTGCGA	58.756	50.000	1.42	0.00	37.08	5.10
2860	4690	3.306703	GCATTTTGCATCCATTGGTTACG	59.693	43.478	1.86	0.00	44.26	3.18
2963	4795	7.513190	TGTTTTGACCGTTCAACTTTAAATG	57.487	32.000	0.00	0.00	41.64	2.32
3210	5117	7.665559	GGTAGGTGAGCATATGGAAAATATGAA	59.334	37.037	4.56	0.00	34.74	2.57
3211	5118	9.066892	GTAGGTGAGCATATGGAAAATATGAAA	57.933	33.333	4.56	0.00	34.74	2.69
3212	5119	8.537728	AGGTGAGCATATGGAAAATATGAAAA	57.462	30.769	4.56	0.00	34.74	2.29
3213	5120	9.151177	AGGTGAGCATATGGAAAATATGAAAAT	57.849	29.630	4.56	0.00	34.74	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	4.273235	GCCAAGAACCAAAAATTCAAGTGG	59.727	41.667	0.00	0.00	37.17	4.00
153	154	5.249852	AGGTTGCTACAGTTGGTTAAGGATA	59.750	40.000	0.00	0.00	0.00	2.59
223	224	4.640201	GCAGATAGGTTGGCAATAGAAACA	59.360	41.667	1.92	0.00	0.00	2.83
373	375	4.352001	AGGCTAGAAATCAGGCCAATATCA	59.648	41.667	5.01	0.00	46.23	2.15
451	453	3.762823	TGCTCAATTGTGTGATATTGCCA	59.237	39.130	5.13	0.00	32.96	4.92
550	552	3.260884	ACAAGGAGTTAGCGGAAAGATCA	59.739	43.478	0.00	0.00	0.00	2.92
586	588	4.857509	AGGAATCGTAAGTATCTCCTGC	57.142	45.455	0.00	0.00	32.04	4.85
708	711	3.823304	GGATTTCACCAGAGAGCTTGTTT	59.177	43.478	0.00	0.00	0.00	2.83
843	846	7.442666	GGTCCTGCTAAGTTATTATCAGAAAGG	59.557	40.741	1.50	0.00	37.33	3.11
1080	1106	0.521291	TGCAAAACAGTATGAGCCGC	59.479	50.000	0.00	0.00	39.69	6.53
1092	1118	4.187694	TCAAAGTTCCAACCATGCAAAAC	58.812	39.130	0.00	0.00	0.00	2.43
1164	1193	4.215399	TGATCAAGACCATTGTTCGGTTTC	59.785	41.667	0.00	0.00	36.69	2.78
1357	1386	2.813754	CTCCTCGTTTGCCAAGATTGAA	59.186	45.455	0.00	0.00	0.00	2.69
1453	1482	1.071699	ACGGTCCAAACTGCTACACAT	59.928	47.619	0.00	0.00	34.94	3.21
1498	1527	6.222038	TCCGTTGCAGATAAACTCTAAGAT	57.778	37.500	0.00	0.00	31.13	2.40
1898	1992	3.754965	TGCTTGCCAAGTGAAATCTACT	58.245	40.909	6.28	0.00	0.00	2.57
1900	1994	4.771590	CTTGCTTGCCAAGTGAAATCTA	57.228	40.909	6.28	0.00	44.74	1.98
1919	2024	9.160496	GACAGATTACACTCTCAATTCAATCTT	57.840	33.333	0.00	0.00	30.84	2.40
1921	2026	8.484641	TGACAGATTACACTCTCAATTCAATC	57.515	34.615	0.00	0.00	0.00	2.67
1937	2043	8.698973	TGGGTAGACAAAATTTTGACAGATTA	57.301	30.769	32.20	14.55	40.55	1.75
1982	2088	6.568601	CGTACTCTCAAAAACATGTAAACACG	59.431	38.462	0.00	0.00	0.00	4.49
1983	2089	6.849305	CCGTACTCTCAAAAACATGTAAACAC	59.151	38.462	0.00	0.00	0.00	3.32
1999	2109	1.476891	TGGATTCTGTGCCGTACTCTC	59.523	52.381	0.00	0.00	0.00	3.20
2006	2116	2.409870	GGGCTTGGATTCTGTGCCG	61.410	63.158	0.00	0.00	44.07	5.69
2010	2120	1.064166	CATGGAGGGCTTGGATTCTGT	60.064	52.381	0.00	0.00	0.00	3.41
2014	2124	1.133262	CATCCATGGAGGGCTTGGATT	60.133	52.381	21.33	0.00	45.76	3.01
2037	2147	5.168569	CAACACCCCATAGCTATATACGTG	58.831	45.833	5.77	12.20	0.00	4.49
2051	2161	2.685106	TTTCCAATAGCAACACCCCA	57.315	45.000	0.00	0.00	0.00	4.96
2087	2197	4.635765	CCATCCATGAAATTGTCAGTACGT	59.364	41.667	0.00	0.00	40.43	3.57
2089	2199	5.415701	ACACCATCCATGAAATTGTCAGTAC	59.584	40.000	0.00	0.00	40.43	2.73
2090	2200	5.415389	CACACCATCCATGAAATTGTCAGTA	59.585	40.000	0.00	0.00	40.43	2.74
2141	3481	1.274728	AGCAGCTTATCAGGATAGGCG	59.725	52.381	15.05	11.87	46.87	5.52
2200	3541	6.701145	AAGAGTATATCGATGATATGCCGT	57.299	37.500	8.54	0.00	38.01	5.68
2219	3560	8.940952	GCCAAGCTTAAACATAGGATATAAGAG	58.059	37.037	0.00	0.00	0.00	2.85
2246	3587	0.174389	CTCTCCTCGCAGCAAGCTAA	59.826	55.000	0.00	0.00	42.61	3.09
2260	3601	2.637947	GTGCCTTGAAGAATCCTCTCC	58.362	52.381	0.00	0.00	0.00	3.71
2261	3602	2.275318	CGTGCCTTGAAGAATCCTCTC	58.725	52.381	0.00	0.00	0.00	3.20
2262	3603	1.065854	CCGTGCCTTGAAGAATCCTCT	60.066	52.381	0.00	0.00	0.00	3.69
2263	3604	1.066143	TCCGTGCCTTGAAGAATCCTC	60.066	52.381	0.00	0.00	0.00	3.71
2264	3605	0.984230	TCCGTGCCTTGAAGAATCCT	59.016	50.000	0.00	0.00	0.00	3.24
2271	3612	2.559698	TCTTCATTCCGTGCCTTGAA	57.440	45.000	0.00	0.00	0.00	2.69
2272	3613	2.027285	TCATCTTCATTCCGTGCCTTGA	60.027	45.455	0.00	0.00	0.00	3.02
2281	3622	6.042777	TGACTACATCGTTCATCTTCATTCC	58.957	40.000	0.00	0.00	0.00	3.01
2420	3763	4.565652	CCACAGGATAACAACTAGCAACCT	60.566	45.833	0.00	0.00	0.00	3.50
2427	3770	2.910319	ACAGGCCACAGGATAACAACTA	59.090	45.455	5.01	0.00	0.00	2.24
2450	3797	0.912486	AGCTCCCCAGACCACAATAC	59.088	55.000	0.00	0.00	0.00	1.89
2465	3812	2.204237	CCAAAGCCACAAAACAAGCTC	58.796	47.619	0.00	0.00	33.56	4.09
2469	3816	1.065854	CACCCCAAAGCCACAAAACAA	60.066	47.619	0.00	0.00	0.00	2.83
2515	3907	7.444183	ACTGGACAAACATATAATAACGGATGG	59.556	37.037	0.00	0.00	0.00	3.51
2556	3948	5.153950	AGACAATACAACTTCAGGGAGAC	57.846	43.478	0.00	0.00	0.00	3.36
2686	4099	7.617041	ACATACTATTGAAACCAAAGAGCTC	57.383	36.000	5.27	5.27	0.00	4.09
2743	4544	5.694006	GGAGATGATAAGATCACAAGAACCG	59.306	44.000	0.00	0.00	43.01	4.44
2812	4641	0.400213	ATTTCTCGCACTTGGGTCCA	59.600	50.000	0.00	0.00	0.00	4.02
2826	4655	3.818180	TGCAAAATGCCACCAAATTTCT	58.182	36.364	0.00	0.00	44.23	2.52
2860	4690	6.854496	AATTGCATTGACAATATTCATGCC	57.146	33.333	0.00	0.00	39.32	4.40
3148	5047	4.714632	GGTACCTGCATATCTTTTAGCCA	58.285	43.478	4.06	0.00	0.00	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.