AutoCloner

Multiple sequence alignment - TraesCS1D01G411600

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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	TraesCS1D01G411600	chr1D	100.000	2801	0	0	1	2801	473033158	473035958	0.000000e+00	5173
1	TraesCS1D01G411600	chr1D	85.943	811	109	5	993	1802	452265065	452264259	0.000000e+00	861
2	TraesCS1D01G411600	chr1B	91.587	2627	109	47	230	2801	657505904	657508473	0.000000e+00	3524
3	TraesCS1D01G411600	chr1B	92.568	296	7	3	1	295	657505633	657505914	7.220000e-111	411
4	TraesCS1D01G411600	chr1B	92.000	225	18	0	2192	2416	563710862	563710638	1.620000e-82	316
5	TraesCS1D01G411600	chr1A	94.960	1369	48	2	547	1894	566688312	566689680	0.000000e+00	2126
6	TraesCS1D01G411600	chr1A	83.642	917	136	12	892	1802	547216708	547215800	0.000000e+00	850
7	TraesCS1D01G411600	chr1A	83.642	917	136	12	892	1802	547238606	547237698	0.000000e+00	850
8	TraesCS1D01G411600	chr1A	93.603	469	30	0	1903	2371	566689661	566690129	0.000000e+00	701
9	TraesCS1D01G411600	chr1A	89.083	458	20	9	2360	2801	566690146	566690589	2.450000e-150	542
10	TraesCS1D01G411600	chr1A	90.315	413	35	3	143	554	566687713	566688121	1.140000e-148	536
11	TraesCS1D01G411600	chr1A	94.667	150	4	1	2	147	566687540	566687689	2.170000e-56	230
12	TraesCS1D01G411600	chr7B	86.118	814	111	2	993	1805	118891407	118892219	0.000000e+00	876
13	TraesCS1D01G411600	chr7B	85.855	813	115	0	993	1805	118821371	118822183	0.000000e+00	865
14	TraesCS1D01G411600	chr7D	85.855	813	115	0	993	1805	156455339	156456151	0.000000e+00	865
15	TraesCS1D01G411600	chrUn	83.533	917	137	12	892	1802	246249635	246248727	0.000000e+00	845
16	TraesCS1D01G411600	chrUn	80.386	311	50	7	2044	2352	318163724	318164025	2.810000e-55	226
17	TraesCS1D01G411600	chrUn	80.386	311	50	7	2044	2352	318170692	318170993	2.810000e-55	226
18	TraesCS1D01G411600	chr2D	88.112	429	50	1	2040	2468	54671793	54672220	2.490000e-140	508
19	TraesCS1D01G411600	chr4A	80.607	428	70	9	2044	2468	714827211	714827628	4.500000e-83	318
20	TraesCS1D01G411600	chr4A	92.000	225	18	0	2192	2416	503614954	503614730	1.620000e-82	316
21	TraesCS1D01G411600	chr7A	92.000	225	18	0	2192	2416	714590778	714590554	1.620000e-82	316
22	TraesCS1D01G411600	chr5A	92.000	225	18	0	2192	2416	427318196	427318420	1.620000e-82	316
23	TraesCS1D01G411600	chr6B	91.556	225	19	0	2192	2416	623718823	623719047	7.530000e-81	311
24	TraesCS1D01G411600	chr3B	91.556	225	19	0	2192	2416	9101517	9101293	7.530000e-81	311

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	TraesCS1D01G411600	chr1D	473033158	473035958	2800	False	5173.0	5173	100.0000	1	2801	1	chr1D.!!$F1	2800
1	TraesCS1D01G411600	chr1D	452264259	452265065	806	True	861.0	861	85.9430	993	1802	1	chr1D.!!$R1	809
2	TraesCS1D01G411600	chr1B	657505633	657508473	2840	False	1967.5	3524	92.0775	1	2801	2	chr1B.!!$F1	2800
3	TraesCS1D01G411600	chr1A	547215800	547216708	908	True	850.0	850	83.6420	892	1802	1	chr1A.!!$R1	910
4	TraesCS1D01G411600	chr1A	547237698	547238606	908	True	850.0	850	83.6420	892	1802	1	chr1A.!!$R2	910
5	TraesCS1D01G411600	chr1A	566687540	566690589	3049	False	827.0	2126	92.5256	2	2801	5	chr1A.!!$F1	2799
6	TraesCS1D01G411600	chr7B	118891407	118892219	812	False	876.0	876	86.1180	993	1805	1	chr7B.!!$F2	812
7	TraesCS1D01G411600	chr7B	118821371	118822183	812	False	865.0	865	85.8550	993	1805	1	chr7B.!!$F1	812
8	TraesCS1D01G411600	chr7D	156455339	156456151	812	False	865.0	865	85.8550	993	1805	1	chr7D.!!$F1	812
9	TraesCS1D01G411600	chrUn	246248727	246249635	908	True	845.0	845	83.5330	892	1802	1	chrUn.!!$R1	910

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
317	418	0.250252	ATGTCATGTGTGTGCCGACA	60.25	50.0	0.0	0.0	40.59	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2127	2456	0.105964	CACCCGAAGAAGACACCACA	59.894	55.0	0.0	0.0	0.0	4.17	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
96	97	4.566004	TCCTTATATAACCTGCATGCGTC	58.434	43.478	14.09	0.00	0.00	5.19
137	142	8.884726	GTCTTTATTTTTAGTAGAGAAGCAGGG	58.115	37.037	0.00	0.00	0.00	4.45
138	143	8.822805	TCTTTATTTTTAGTAGAGAAGCAGGGA	58.177	33.333	0.00	0.00	0.00	4.20
139	144	9.449719	CTTTATTTTTAGTAGAGAAGCAGGGAA	57.550	33.333	0.00	0.00	0.00	3.97
140	145	8.788325	TTATTTTTAGTAGAGAAGCAGGGAAC	57.212	34.615	0.00	0.00	0.00	3.62
141	146	6.435292	TTTTTAGTAGAGAAGCAGGGAACT	57.565	37.500	0.00	0.00	46.44	3.01
142	147	7.549147	TTTTTAGTAGAGAAGCAGGGAACTA	57.451	36.000	0.00	0.00	40.21	2.24
143	148	6.777213	TTTAGTAGAGAAGCAGGGAACTAG	57.223	41.667	0.00	0.00	40.21	2.57
144	149	4.594675	AGTAGAGAAGCAGGGAACTAGA	57.405	45.455	0.00	0.00	40.21	2.43
145	150	4.532834	AGTAGAGAAGCAGGGAACTAGAG	58.467	47.826	0.00	0.00	40.21	2.43
146	151	3.748645	AGAGAAGCAGGGAACTAGAGA	57.251	47.619	0.00	0.00	40.21	3.10
147	152	4.264373	AGAGAAGCAGGGAACTAGAGAT	57.736	45.455	0.00	0.00	40.21	2.75
148	153	3.960102	AGAGAAGCAGGGAACTAGAGATG	59.040	47.826	0.00	0.00	40.21	2.90
317	418	0.250252	ATGTCATGTGTGTGCCGACA	60.250	50.000	0.00	0.00	40.59	4.35
321	422	0.790207	CATGTGTGTGCCGACAGTAC	59.210	55.000	0.00	0.00	30.74	2.73
353	455	0.872388	GAACGATCAAACCCAGCGTT	59.128	50.000	0.00	0.00	46.31	4.84
354	456	2.070783	GAACGATCAAACCCAGCGTTA	58.929	47.619	0.00	0.00	44.07	3.18
405	507	6.436843	AACGGAGACAAAATATTTGCCTAG	57.563	37.500	0.39	1.28	0.00	3.02
454	556	8.842358	TTGTCCAGATAGTTAACGAAAAATCT	57.158	30.769	0.00	2.91	0.00	2.40
488	590	1.879380	ACACAAATCCATCACACGTGG	59.121	47.619	21.57	9.11	38.11	4.94
494	596	1.919240	TCCATCACACGTGGACTACT	58.081	50.000	21.57	0.00	40.72	2.57
499	601	1.607148	TCACACGTGGACTACTCACAG	59.393	52.381	21.57	0.00	35.03	3.66
520	622	4.021192	CAGAACATGCAACCCCATAAAAGT	60.021	41.667	0.00	0.00	0.00	2.66
531	633	4.715297	ACCCCATAAAAGTACGATCACTCT	59.285	41.667	0.00	0.00	0.00	3.24
867	1192	5.988561	TCAGCAAACACCAACCAATTAATTC	59.011	36.000	0.00	0.00	0.00	2.17
985	1313	0.326595	ACACACAGGGACAACACACA	59.673	50.000	0.00	0.00	0.00	3.72
1034	1362	4.082190	CACCATGTCTCTTTCCTCTTCGTA	60.082	45.833	0.00	0.00	0.00	3.43
1036	1364	4.425520	CATGTCTCTTTCCTCTTCGTACC	58.574	47.826	0.00	0.00	0.00	3.34
1350	1678	2.294074	CTTGGTTGTGTCTTTCCCGAA	58.706	47.619	0.00	0.00	0.00	4.30
1662	1990	4.408821	AAGAATGGCCGCCTCGCA	62.409	61.111	11.61	0.00	0.00	5.10
1695	2023	1.042003	TTGGCTTCTTTGTGCAGGCA	61.042	50.000	0.00	0.00	41.05	4.75
1830	2158	6.149308	GGAATGATGGATGCGAATTGTATGTA	59.851	38.462	0.00	0.00	0.00	2.29
1838	2166	6.183360	GGATGCGAATTGTATGTAAGTGTCAA	60.183	38.462	0.00	0.00	0.00	3.18
1893	2221	4.454728	ACTGTGTGCAAAGACATTGTTT	57.545	36.364	0.00	0.00	41.32	2.83
1894	2222	4.819769	ACTGTGTGCAAAGACATTGTTTT	58.180	34.783	0.00	0.00	41.32	2.43
1895	2223	5.237048	ACTGTGTGCAAAGACATTGTTTTT	58.763	33.333	0.00	0.00	41.32	1.94
1915	2243	2.124529	TGCGTGGGTGCAAAGACA	60.125	55.556	0.00	0.00	43.02	3.41
1916	2244	1.528076	TGCGTGGGTGCAAAGACAT	60.528	52.632	0.00	0.00	43.02	3.06
1917	2245	1.106351	TGCGTGGGTGCAAAGACATT	61.106	50.000	0.00	0.00	43.02	2.71
1918	2246	0.664166	GCGTGGGTGCAAAGACATTG	60.664	55.000	0.00	0.00	42.21	2.82
1919	2247	0.667993	CGTGGGTGCAAAGACATTGT	59.332	50.000	0.00	0.00	41.32	2.71
1920	2248	1.066908	CGTGGGTGCAAAGACATTGTT	59.933	47.619	0.00	0.00	41.32	2.83
1923	2251	2.158986	TGGGTGCAAAGACATTGTTTGG	60.159	45.455	0.00	0.00	41.32	3.28
1955	2283	3.177884	AAGTGCCACTGCTCCCCA	61.178	61.111	0.00	0.00	38.71	4.96
2028	2356	8.771766	CAGAATATCCATAACTTGTGATGACAG	58.228	37.037	0.00	0.00	32.26	3.51
2127	2456	5.642919	GTGATGTGATTGCTCTTCTTCTCTT	59.357	40.000	0.00	0.00	0.00	2.85
2177	2506	0.472471	TGCCGGAGTTTTCCTTCTGT	59.528	50.000	5.05	0.00	41.67	3.41
2184	2513	4.994852	CGGAGTTTTCCTTCTGTGATTACA	59.005	41.667	0.00	0.00	41.67	2.41
2213	2542	1.818674	TGAGCACAGTGAAGCGATCTA	59.181	47.619	4.15	0.00	35.48	1.98
2347	2677	1.139058	CCTTCGGCTACACCAATAGCT	59.861	52.381	4.89	0.00	45.81	3.32
2360	2690	3.635373	ACCAATAGCTTTGAGGCATCATG	59.365	43.478	0.03	0.00	34.73	3.07
2371	2701	0.604780	GGCATCATGGATGGTCTCGG	60.605	60.000	8.18	0.00	40.10	4.63
2392	2751	3.055094	GGTTGATTGGAGCTCTTGGTCTA	60.055	47.826	14.64	1.83	40.29	2.59
2395	2754	3.582647	TGATTGGAGCTCTTGGTCTACAA	59.417	43.478	14.64	6.95	40.29	2.41
2433	2792	2.567049	CTTCCGTTCGCGAGGACT	59.433	61.111	16.00	0.00	44.71	3.85
2556	2925	2.985896	TGCCGGTTCCTTCTTAATGAG	58.014	47.619	1.90	0.00	0.00	2.90
2576	2945	4.100344	TGAGTGAAAAGTAGTGCTGGTACA	59.900	41.667	0.00	0.00	0.00	2.90
2588	2957	4.024048	AGTGCTGGTACATTTCGTCAAAAG	60.024	41.667	0.00	0.00	38.20	2.27
2593	2962	6.142320	GCTGGTACATTTCGTCAAAAGAAAAG	59.858	38.462	0.00	0.00	40.44	2.27
2639	3015	3.996363	GGATCCAATTCACCTGCAAAAAC	59.004	43.478	6.95	0.00	0.00	2.43
2640	3016	4.502950	GGATCCAATTCACCTGCAAAAACA	60.503	41.667	6.95	0.00	0.00	2.83
2734	3111	1.980765	TGTCAGCCTCAGAATCAACCT	59.019	47.619	0.00	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	1.675483	GCTCATCAAACACCACACACA	59.325	47.619	0.00	0.00	0.00	3.72
96	97	7.840342	AAATAAAGACTAGACTCATGCACAG	57.160	36.000	0.00	0.00	0.00	3.66
137	142	9.213799	CCAATTAATTAGCTCCATCTCTAGTTC	57.786	37.037	0.00	0.00	0.00	3.01
138	143	8.718656	ACCAATTAATTAGCTCCATCTCTAGTT	58.281	33.333	0.00	0.00	0.00	2.24
139	144	8.153550	CACCAATTAATTAGCTCCATCTCTAGT	58.846	37.037	0.00	0.00	0.00	2.57
140	145	7.605691	CCACCAATTAATTAGCTCCATCTCTAG	59.394	40.741	0.00	0.00	0.00	2.43
141	146	7.072454	ACCACCAATTAATTAGCTCCATCTCTA	59.928	37.037	0.00	0.00	0.00	2.43
142	147	6.126361	ACCACCAATTAATTAGCTCCATCTCT	60.126	38.462	0.00	0.00	0.00	3.10
143	148	6.064717	ACCACCAATTAATTAGCTCCATCTC	58.935	40.000	0.00	0.00	0.00	2.75
144	149	6.018433	ACCACCAATTAATTAGCTCCATCT	57.982	37.500	0.00	0.00	0.00	2.90
145	150	5.827797	TGACCACCAATTAATTAGCTCCATC	59.172	40.000	0.00	0.00	0.00	3.51
146	151	5.594317	GTGACCACCAATTAATTAGCTCCAT	59.406	40.000	0.00	0.00	0.00	3.41
147	152	4.947388	GTGACCACCAATTAATTAGCTCCA	59.053	41.667	0.00	0.00	0.00	3.86
148	153	4.035208	CGTGACCACCAATTAATTAGCTCC	59.965	45.833	0.00	0.00	0.00	4.70
295	396	1.089112	CGGCACACACATGACATGAT	58.911	50.000	22.19	6.78	0.00	2.45
317	418	6.425721	TGATCGTTCCAGAAAATTTTCGTACT	59.574	34.615	21.98	5.10	41.92	2.73
321	422	6.129194	GGTTTGATCGTTCCAGAAAATTTTCG	60.129	38.462	21.98	16.89	41.92	3.46
475	577	1.816835	GAGTAGTCCACGTGTGATGGA	59.183	52.381	15.65	0.42	44.20	3.41
488	590	3.433615	GGTTGCATGTTCTGTGAGTAGTC	59.566	47.826	0.00	0.00	0.00	2.59
494	596	0.184692	TGGGGTTGCATGTTCTGTGA	59.815	50.000	0.00	0.00	0.00	3.58
499	601	4.535526	ACTTTTATGGGGTTGCATGTTC	57.464	40.909	0.00	0.00	0.00	3.18
520	622	5.168569	GGTTTGATTGTCAGAGTGATCGTA	58.831	41.667	0.00	0.00	0.00	3.43
531	633	1.066303	GCGTGTTGGGTTTGATTGTCA	59.934	47.619	0.00	0.00	0.00	3.58
615	920	4.603989	TTTCCCAACGTACATCACACTA	57.396	40.909	0.00	0.00	0.00	2.74
867	1192	6.529220	CCTTGAGGGAACAAGAATATAGAGG	58.471	44.000	9.55	0.00	46.85	3.69
985	1313	0.179129	GCCATTGCGCTGCACTTATT	60.179	50.000	9.73	0.00	38.71	1.40
1122	1450	2.220133	GCTGCTCGACGAAACTTGTTTA	59.780	45.455	0.00	0.00	0.00	2.01
1623	1951	3.131223	TGATCTCCTTAACCTTGAGCTCG	59.869	47.826	9.64	0.00	0.00	5.03
1662	1990	4.154942	AGAAGCCAAACATGGAGAACATT	58.845	39.130	0.00	0.00	37.84	2.71
1695	2023	2.275380	GCCCTTGCCGGTGACAATT	61.275	57.895	1.90	0.00	0.00	2.32
1830	2158	9.248291	GTTGATGTTACAATTCAATTGACACTT	57.752	29.630	17.30	10.02	42.83	3.16
1852	2180	9.283768	ACACAGTTCTCATAATTTACATGTTGA	57.716	29.630	2.30	0.00	0.00	3.18
1864	2192	5.122519	TGTCTTTGCACACAGTTCTCATAA	58.877	37.500	0.00	0.00	0.00	1.90
1873	2201	5.783100	AAAAACAATGTCTTTGCACACAG	57.217	34.783	0.00	0.00	39.03	3.66
1898	2226	1.106351	AATGTCTTTGCACCCACGCA	61.106	50.000	0.00	0.00	41.03	5.24
1899	2227	0.664166	CAATGTCTTTGCACCCACGC	60.664	55.000	0.00	0.00	0.00	5.34
1900	2228	0.667993	ACAATGTCTTTGCACCCACG	59.332	50.000	0.00	0.00	39.03	4.94
1901	2229	2.865551	CAAACAATGTCTTTGCACCCAC	59.134	45.455	0.00	0.00	39.03	4.61
1902	2230	2.158986	CCAAACAATGTCTTTGCACCCA	60.159	45.455	0.00	0.00	39.03	4.51
1903	2231	2.158971	ACCAAACAATGTCTTTGCACCC	60.159	45.455	0.00	0.00	39.03	4.61
1904	2232	3.177997	ACCAAACAATGTCTTTGCACC	57.822	42.857	0.00	0.00	39.03	5.01
1905	2233	3.309410	CCAACCAAACAATGTCTTTGCAC	59.691	43.478	0.00	0.00	39.03	4.57
1906	2234	3.055530	ACCAACCAAACAATGTCTTTGCA	60.056	39.130	0.00	0.00	39.03	4.08
1907	2235	3.530535	ACCAACCAAACAATGTCTTTGC	58.469	40.909	0.00	0.00	39.03	3.68
1908	2236	4.119136	GGACCAACCAAACAATGTCTTTG	58.881	43.478	0.00	0.00	38.78	2.77
1909	2237	3.772025	TGGACCAACCAAACAATGTCTTT	59.228	39.130	0.00	0.00	46.75	2.52
1910	2238	3.370104	TGGACCAACCAAACAATGTCTT	58.630	40.909	0.00	0.00	46.75	3.01
1911	2239	3.025322	TGGACCAACCAAACAATGTCT	57.975	42.857	0.00	0.00	46.75	3.41
1945	2273	2.158475	TGAAAACAAGATGGGGAGCAGT	60.158	45.455	0.00	0.00	0.00	4.40
1955	2283	7.649306	GTGCTTAGTGATTTGTGAAAACAAGAT	59.351	33.333	0.00	0.00	0.00	2.40
2028	2356	2.548480	GCTCCCCAACGCTAATTGTATC	59.452	50.000	0.00	0.00	0.00	2.24
2058	2387	0.109272	CAATGTCAGCAAGCAGGCAG	60.109	55.000	0.00	0.00	35.83	4.85
2127	2456	0.105964	CACCCGAAGAAGACACCACA	59.894	55.000	0.00	0.00	0.00	4.17
2177	2506	1.067142	GCTCACCGACCACTGTAATCA	60.067	52.381	0.00	0.00	0.00	2.57
2184	2513	2.134287	ACTGTGCTCACCGACCACT	61.134	57.895	0.00	0.00	0.00	4.00
2213	2542	0.542232	AAGGAGCCGAGTGTACACCT	60.542	55.000	22.28	12.03	0.00	4.00
2347	2677	2.242965	AGACCATCCATGATGCCTCAAA	59.757	45.455	0.00	0.00	38.59	2.69
2360	2690	1.209504	TCCAATCAACCGAGACCATCC	59.790	52.381	0.00	0.00	0.00	3.51
2371	2701	3.064900	AGACCAAGAGCTCCAATCAAC	57.935	47.619	10.93	0.00	0.00	3.18
2392	2751	1.888512	GCATGAGAACACCACCATTGT	59.111	47.619	0.00	0.00	0.00	2.71
2395	2754	1.830279	CTGCATGAGAACACCACCAT	58.170	50.000	0.00	0.00	0.00	3.55
2433	2792	3.559811	CCGGAATGCCATCATCTTCCATA	60.560	47.826	0.00	0.00	31.84	2.74
2556	2925	5.941948	AATGTACCAGCACTACTTTTCAC	57.058	39.130	0.00	0.00	0.00	3.18
2603	2979	9.453572	GTGAATTGGATCCATATAGCTAATTGA	57.546	33.333	17.06	0.68	0.00	2.57
2639	3015	7.148507	GGCTCATTGGATCGATATAACTCTTTG	60.149	40.741	0.00	0.00	0.00	2.77
2640	3016	6.876257	GGCTCATTGGATCGATATAACTCTTT	59.124	38.462	0.00	0.00	0.00	2.52
2661	3038	6.835819	AAATTAGAGGTTTAAACTGGGCTC	57.164	37.500	17.50	14.39	0.00	4.70
2734	3111	4.016444	GGGTGTATGAATGGAAAGCTTGA	58.984	43.478	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.