AutoCloner

Multiple sequence alignment - TraesCS3B01G598000

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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	TraesCS3B01G598000	chr3B	100.000	3368	0	0	1	3368	819947218	819950585	0.000000e+00	6220.0
1	TraesCS3B01G598000	chr3A	94.438	3398	151	16	1	3368	742783756	742787145	0.000000e+00	5193.0
2	TraesCS3B01G598000	chr3D	94.876	2693	107	19	701	3368	609231944	609234630	0.000000e+00	4180.0
3	TraesCS3B01G598000	chr3D	78.601	486	74	18	1911	2392	609239010	609239469	9.140000e-76	294.0
4	TraesCS3B01G598000	chr3D	86.301	73	10	0	1370	1442	604879439	604879511	2.790000e-11	80.5
5	TraesCS3B01G598000	chr1B	85.906	596	58	10	1	575	14127455	14128045	2.220000e-171	612.0
6	TraesCS3B01G598000	chr6A	85.569	589	72	9	1	577	57890789	57891376	3.720000e-169	604.0
7	TraesCS3B01G598000	chr6A	85.135	592	67	6	2	577	449700242	449700828	1.350000e-163	586.0
8	TraesCS3B01G598000	chr6D	82.964	587	73	17	1	577	291973037	291972468	3.880000e-139	505.0
9	TraesCS3B01G598000	chr1D	82.534	584	84	14	1	580	435464416	435464985	6.490000e-137	497.0
10	TraesCS3B01G598000	chr1D	88.038	418	36	10	1	413	430421496	430421088	1.820000e-132	483.0
11	TraesCS3B01G598000	chr1D	83.442	459	60	14	1	452	288909679	288909230	2.420000e-111	412.0
12	TraesCS3B01G598000	chr1A	81.387	591	84	17	1	580	586263672	586264247	3.060000e-125	459.0
13	TraesCS3B01G598000	chr5D	88.684	380	29	7	202	579	497927361	497927728	5.120000e-123	451.0
14	TraesCS3B01G598000	chr5D	84.286	140	20	2	2217	2355	564758192	564758054	5.860000e-28	135.0
15	TraesCS3B01G598000	chr4B	83.984	487	53	11	1	473	434588241	434587766	8.580000e-121	444.0
16	TraesCS3B01G598000	chr7B	80.920	587	68	17	1	580	139432502	139431953	1.120000e-114	424.0
17	TraesCS3B01G598000	chr2D	84.691	307	42	5	1	304	651115367	651115671	5.460000e-78	302.0
18	TraesCS3B01G598000	chr2D	88.073	109	13	0	579	687	320487151	320487259	2.730000e-26	130.0
19	TraesCS3B01G598000	chr7A	77.727	440	84	11	1959	2392	91497554	91497985	1.200000e-64	257.0
20	TraesCS3B01G598000	chr5B	74.515	412	86	18	1959	2356	708532692	708532286	9.670000e-36	161.0
21	TraesCS3B01G598000	chr5B	74.515	412	86	18	1959	2356	708570278	708569872	9.670000e-36	161.0
22	TraesCS3B01G598000	chr5B	86.207	145	20	0	2212	2356	708610507	708610363	1.250000e-34	158.0
23	TraesCS3B01G598000	chr5B	85.612	139	20	0	2217	2355	708674210	708674072	2.710000e-31	147.0
24	TraesCS3B01G598000	chr4A	82.051	195	27	6	1024	1217	606339524	606339711	3.480000e-35	159.0

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	TraesCS3B01G598000	chr3B	819947218	819950585	3367	False	6220	6220	100.000	1	3368	1	chr3B.!!$F1	3367
1	TraesCS3B01G598000	chr3A	742783756	742787145	3389	False	5193	5193	94.438	1	3368	1	chr3A.!!$F1	3367
2	TraesCS3B01G598000	chr3D	609231944	609234630	2686	False	4180	4180	94.876	701	3368	1	chr3D.!!$F2	2667
3	TraesCS3B01G598000	chr1B	14127455	14128045	590	False	612	612	85.906	1	575	1	chr1B.!!$F1	574
4	TraesCS3B01G598000	chr6A	57890789	57891376	587	False	604	604	85.569	1	577	1	chr6A.!!$F1	576
5	TraesCS3B01G598000	chr6A	449700242	449700828	586	False	586	586	85.135	2	577	1	chr6A.!!$F2	575
6	TraesCS3B01G598000	chr6D	291972468	291973037	569	True	505	505	82.964	1	577	1	chr6D.!!$R1	576
7	TraesCS3B01G598000	chr1D	435464416	435464985	569	False	497	497	82.534	1	580	1	chr1D.!!$F1	579
8	TraesCS3B01G598000	chr1A	586263672	586264247	575	False	459	459	81.387	1	580	1	chr1A.!!$F1	579
9	TraesCS3B01G598000	chr7B	139431953	139432502	549	True	424	424	80.920	1	580	1	chr7B.!!$R1	579

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
996	1051	0.107654	GCAGCGATCCTAACCCAACT	60.108	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2939	3022	1.409427	GTAGGCAGTGTTCCTATCGCT	59.591	52.381	0.46	0.0	38.36	4.93	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
26	27	1.696097	ATGACGAGGCCGCCCTAAAT	61.696	55.000	5.55	0.00	43.12	1.40
131	132	2.734591	GAGGGCGGCATCATCGTA	59.265	61.111	19.44	0.00	0.00	3.43
157	158	4.790962	CGACGAGGAGGACGGGGA	62.791	72.222	0.00	0.00	34.93	4.81
292	330	2.281761	GGCATGTAGATGGCGGGG	60.282	66.667	10.76	0.00	44.46	5.73
360	403	4.102649	GGCGTAGTTTGCATGTTTTATCC	58.897	43.478	0.00	0.00	0.00	2.59
529	579	4.778143	GCGCTGGTTCGTCCCCAT	62.778	66.667	0.00	0.00	34.77	4.00
536	586	3.078196	TTCGTCCCCATGCGGCTA	61.078	61.111	0.00	0.00	0.00	3.93
543	593	1.110442	CCCCATGCGGCTATTTTTCA	58.890	50.000	0.00	0.00	0.00	2.69
589	640	5.481824	TGGAGATGCTCTAAGAAAGAAGTCA	59.518	40.000	0.00	0.00	32.46	3.41
632	683	2.420129	CCAGAGAGACAAATAACCCCCG	60.420	54.545	0.00	0.00	0.00	5.73
678	729	2.901192	ACCCCAAAATCCTTAAAACCGG	59.099	45.455	0.00	0.00	0.00	5.28
680	731	2.901192	CCCAAAATCCTTAAAACCGGGT	59.099	45.455	6.32	0.00	0.00	5.28
715	766	9.807649	CCCCTAAATCTTTCAATCTGTTAAATG	57.192	33.333	0.00	0.00	0.00	2.32
768	819	3.128589	CCTGCGTGCTGGTGTTAAATTAT	59.871	43.478	9.39	0.00	0.00	1.28
769	820	4.334203	CCTGCGTGCTGGTGTTAAATTATA	59.666	41.667	9.39	0.00	0.00	0.98
770	821	5.224562	TGCGTGCTGGTGTTAAATTATAC	57.775	39.130	0.00	0.00	0.00	1.47
771	822	4.695928	TGCGTGCTGGTGTTAAATTATACA	59.304	37.500	0.00	0.00	0.00	2.29
772	823	5.163804	TGCGTGCTGGTGTTAAATTATACAG	60.164	40.000	0.00	0.00	0.00	2.74
974	1029	2.851102	ATCGCCCCATCCTCCCTG	60.851	66.667	0.00	0.00	0.00	4.45
990	1045	2.202878	TGCCGCAGCGATCCTAAC	60.203	61.111	18.75	0.00	44.31	2.34
992	1047	2.280186	CCGCAGCGATCCTAACCC	60.280	66.667	18.75	0.00	0.00	4.11
994	1049	1.153449	CGCAGCGATCCTAACCCAA	60.153	57.895	9.98	0.00	0.00	4.12
995	1050	1.429148	CGCAGCGATCCTAACCCAAC	61.429	60.000	9.98	0.00	0.00	3.77
996	1051	0.107654	GCAGCGATCCTAACCCAACT	60.108	55.000	0.00	0.00	0.00	3.16
1003	1058	3.065371	CGATCCTAACCCAACTGAAATGC	59.935	47.826	0.00	0.00	0.00	3.56
1009	1064	1.508088	CCAACTGAAATGCTCGGGC	59.492	57.895	0.00	0.00	34.34	6.13
1137	1213	1.975407	GGACGACCTCCTCCACGAA	60.975	63.158	0.00	0.00	35.89	3.85
1140	1216	0.246635	ACGACCTCCTCCACGAAATG	59.753	55.000	0.00	0.00	0.00	2.32
1169	1245	1.903877	CTCAATGCCCTGGAGACGGT	61.904	60.000	0.00	0.00	33.66	4.83
1233	1309	4.830765	GCGCCGTGCCTGGACATA	62.831	66.667	0.00	0.00	37.76	2.29
1621	1697	1.873165	GGCGCCGATGAGTTTTTCA	59.127	52.632	12.58	0.00	40.85	2.69
1658	1734	3.091545	CTCCTGCTCTTGTCTCTCTTCT	58.908	50.000	0.00	0.00	0.00	2.85
1684	1760	4.623932	GGCACCTCCTATGATGTTGATA	57.376	45.455	0.00	0.00	0.00	2.15
1755	1831	4.659115	CATCCATTCAGCTATCCATTGGA	58.341	43.478	8.08	8.08	36.32	3.53
1756	1832	4.362470	TCCATTCAGCTATCCATTGGAG	57.638	45.455	11.78	0.00	34.05	3.86
1757	1833	3.975982	TCCATTCAGCTATCCATTGGAGA	59.024	43.478	11.78	5.63	34.05	3.71
1811	1887	0.654683	CTTGCCGCTCTCTACAATGC	59.345	55.000	0.00	0.00	0.00	3.56
1891	1967	6.092533	GCATCCATTTTATCCTGTGGTTTTTG	59.907	38.462	0.00	0.00	33.47	2.44
1897	1973	9.439500	CATTTTATCCTGTGGTTTTTGAATGAT	57.561	29.630	0.00	0.00	0.00	2.45
2063	2139	2.694213	GAAACCTGGAGAAGCTCACTC	58.306	52.381	0.00	11.05	31.08	3.51
2301	2377	3.393687	TGCCTCTATCCACCTATTGGTT	58.606	45.455	0.00	0.00	46.05	3.67
2347	2423	4.022068	GGAATCTGCCAAACAACAAGATCA	60.022	41.667	0.00	0.00	0.00	2.92
2393	2469	2.686405	ACCGCGTGAGAATACACTATCA	59.314	45.455	4.92	0.00	38.47	2.15
2549	2625	3.467483	AGGGTAGGGAGTGATCATACTCA	59.533	47.826	13.61	0.00	46.97	3.41
2586	2662	7.965045	ACTCTTGTGTAGATCGAAAATTAAGC	58.035	34.615	0.00	0.00	30.92	3.09
2622	2698	6.147164	TCAAGTTTGAGAAATAGTGGCTTACG	59.853	38.462	0.00	0.00	32.50	3.18
2796	2879	6.708285	AGTTTTTAACGGAGGAGTATGACAT	58.292	36.000	0.00	0.00	36.23	3.06
2819	2902	8.030692	ACATGTTTGATATCCAAATTGTGTCTG	58.969	33.333	0.00	0.00	45.48	3.51
2832	2915	8.199449	CCAAATTGTGTCTGGCAATATATCTTT	58.801	33.333	0.00	0.00	35.73	2.52
2939	3022	4.141181	CCTTGGATAGGGACATCATGGAAA	60.141	45.833	0.00	0.00	40.67	3.13
3043	3126	5.818678	ATAAACCAGGTAATGCGGAGATA	57.181	39.130	0.00	0.00	0.00	1.98
3256	3339	4.017037	TGGGTCTAATGGATGCCCTTTTTA	60.017	41.667	0.00	0.00	39.97	1.52
3307	3390	6.818644	TGAAAGTAGATCTTGTAGCCATGTTC	59.181	38.462	0.00	0.00	36.40	3.18
3344	3427	8.498054	TGAGCTTGATTTAGACATCTTTAAGG	57.502	34.615	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	1.906105	TTTAGGGCGGCCTCGTCATT	61.906	55.000	36.44	11.84	43.76	2.57
8	9	1.906105	AATTTAGGGCGGCCTCGTCA	61.906	55.000	36.44	14.98	43.76	4.35
26	27	0.543410	TGTAGTCCTCCTTCGCCCAA	60.543	55.000	0.00	0.00	0.00	4.12
509	559	2.263540	GGGACGAACCAGCGCTAA	59.736	61.111	10.99	0.00	41.20	3.09
529	579	1.136565	GCGCTGAAAAATAGCCGCA	59.863	52.632	0.00	0.00	39.08	5.69
536	586	1.984026	CCCCAGGGCGCTGAAAAAT	60.984	57.895	30.57	0.00	0.00	1.82
558	609	4.625800	GAGCATCTCCAGCCGTTT	57.374	55.556	0.00	0.00	0.00	3.60
589	640	4.388485	GCCACATTTGAGGGTGAAAAATT	58.612	39.130	0.00	0.00	37.18	1.82
632	683	6.760770	TCAAAATCACACCAAATTGAAGTTCC	59.239	34.615	0.00	0.00	0.00	3.62
678	729	8.589701	TGAAAGATTTAGGGGAAAGATTTACC	57.410	34.615	0.00	0.00	40.63	2.85
715	766	4.439776	CGGTCCATTTCACTTTCGTTTTTC	59.560	41.667	0.00	0.00	0.00	2.29
768	819	5.395546	CGGGCCCAACTAAACTATTACTGTA	60.396	44.000	24.92	0.00	0.00	2.74
769	820	4.624604	CGGGCCCAACTAAACTATTACTGT	60.625	45.833	24.92	0.00	0.00	3.55
770	821	3.875134	CGGGCCCAACTAAACTATTACTG	59.125	47.826	24.92	0.00	0.00	2.74
771	822	3.118149	CCGGGCCCAACTAAACTATTACT	60.118	47.826	24.92	0.00	0.00	2.24
772	823	3.208594	CCGGGCCCAACTAAACTATTAC	58.791	50.000	24.92	0.00	0.00	1.89
974	1029	2.967615	GGTTAGGATCGCTGCGGC	60.968	66.667	23.03	7.70	0.00	6.53
979	1034	1.568504	TCAGTTGGGTTAGGATCGCT	58.431	50.000	0.00	0.00	0.00	4.93
982	1037	4.273318	AGCATTTCAGTTGGGTTAGGATC	58.727	43.478	0.00	0.00	0.00	3.36
987	1042	2.432444	CCGAGCATTTCAGTTGGGTTA	58.568	47.619	0.00	0.00	0.00	2.85
990	1045	1.937546	GCCCGAGCATTTCAGTTGGG	61.938	60.000	0.00	0.00	39.53	4.12
992	1047	1.243342	TGGCCCGAGCATTTCAGTTG	61.243	55.000	0.00	0.00	42.56	3.16
994	1049	1.377725	CTGGCCCGAGCATTTCAGT	60.378	57.895	0.00	0.00	42.56	3.41
995	1050	2.117156	CCTGGCCCGAGCATTTCAG	61.117	63.158	0.00	0.00	42.56	3.02
996	1051	2.045045	CCTGGCCCGAGCATTTCA	60.045	61.111	0.00	0.00	42.56	2.69
1092	1168	1.733399	GCTCAGACGGTCGTTGTCC	60.733	63.158	1.89	0.00	37.04	4.02
1137	1213	1.746615	ATTGAGGCGCGACAGCATT	60.747	52.632	17.71	5.49	45.49	3.56
1140	1216	4.527157	GCATTGAGGCGCGACAGC	62.527	66.667	17.71	6.24	40.74	4.40
1169	1245	3.884581	GACAGCACGCACGTACCGA	62.885	63.158	13.75	0.00	0.00	4.69
1217	1293	2.586079	CTATGTCCAGGCACGGCG	60.586	66.667	4.80	4.80	0.00	6.46
1227	1303	1.102222	ACTCCCGCTCGTCTATGTCC	61.102	60.000	0.00	0.00	0.00	4.02
1233	1309	2.637383	GGTGAACTCCCGCTCGTCT	61.637	63.158	0.00	0.00	0.00	4.18
1621	1697	6.441284	AGAGCAGGAGCATCTATAATGAAGAT	59.559	38.462	0.00	0.00	45.49	2.40
1658	1734	1.770658	CATCATAGGAGGTGCCCAAGA	59.229	52.381	0.00	0.00	37.37	3.02
1684	1760	2.812011	GTTCGTTAGGAGCAACAATGGT	59.188	45.455	0.00	0.00	40.72	3.55
1909	1985	3.824443	GGCACAACAACTATAACCCAAGT	59.176	43.478	0.00	0.00	0.00	3.16
2063	2139	4.081030	CACCTTGCAGCGACGCAG	62.081	66.667	23.70	15.97	44.14	5.18
2086	2162	6.611381	TGCTAATATTTGTTGAGTGAAGCAC	58.389	36.000	0.00	0.00	31.78	4.40
2093	2169	7.864108	TGTGCTATGCTAATATTTGTTGAGT	57.136	32.000	0.00	0.00	0.00	3.41
2197	2273	2.108168	CTCGGAAGGGTCATGAAGGTA	58.892	52.381	0.00	0.00	0.00	3.08
2301	2377	2.290896	CCACATGCCCTCCAGAAACTTA	60.291	50.000	0.00	0.00	0.00	2.24
2347	2423	4.863131	CGGCTAATCGACTTTAGTGAGTTT	59.137	41.667	7.45	0.00	32.77	2.66
2393	2469	7.976414	TTCCAAAATGAATTATCCTCACCAT	57.024	32.000	0.00	0.00	0.00	3.55
2549	2625	4.640771	ACACAAGAGTCCCACATAACAT	57.359	40.909	0.00	0.00	0.00	2.71
2669	2752	5.471456	GCCAGATATCCATTAGAGTTGTTGG	59.529	44.000	0.00	0.00	0.00	3.77
2796	2879	6.572119	GCCAGACACAATTTGGATATCAAACA	60.572	38.462	4.83	0.00	46.72	2.83
2819	2902	8.627208	TTCCTCTCATCAAAAGATATATTGCC	57.373	34.615	0.00	0.00	0.00	4.52
2832	2915	8.691194	AATATCCATCCTATTCCTCTCATCAA	57.309	34.615	0.00	0.00	0.00	2.57
2876	2959	9.362151	TGTAATCTCTTTGTTATTCCAAACCTT	57.638	29.630	0.00	0.00	31.38	3.50
2939	3022	1.409427	GTAGGCAGTGTTCCTATCGCT	59.591	52.381	0.46	0.00	38.36	4.93
2994	3077	7.921304	AGGACCATATAGCACATTAATCATCA	58.079	34.615	0.00	0.00	0.00	3.07
3011	3094	7.228590	GCATTACCTGGTTTATTAGGACCATA	58.771	38.462	3.84	0.00	44.43	2.74
3043	3126	8.220755	TGTAGTAATCTGCAACAACTTTCTTT	57.779	30.769	0.00	0.00	33.64	2.52
3256	3339	8.792830	TGATGTCCGAGAAATTTTTAGAAGAT	57.207	30.769	0.00	0.00	0.00	2.40
3273	3356	6.045318	ACAAGATCTACTTTCATGATGTCCG	58.955	40.000	0.00	0.00	36.61	4.79
3307	3390	1.302832	AAGCTCAAACCAGGCCTCG	60.303	57.895	0.00	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.