AutoCloner

Multiple sequence alignment - TraesCS5A01G422900

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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	TraesCS5A01G422900	chr5A	100.000	2368	0	0	1	2368	608949488	608951855	0.000000e+00	4373.0
1	TraesCS5A01G422900	chr5B	93.684	2375	128	12	1	2368	600727200	600729559	0.000000e+00	3535.0
2	TraesCS5A01G422900	chr5D	96.238	1462	45	5	199	1655	488203202	488204658	0.000000e+00	2386.0
3	TraesCS5A01G422900	chr5D	94.482	598	27	4	1651	2246	488205713	488206306	0.000000e+00	917.0
4	TraesCS5A01G422900	chr5D	96.970	132	4	0	2237	2368	488214901	488215032	3.060000e-54	222.0
5	TraesCS5A01G422900	chr5D	86.170	94	7	4	34	126	230015985	230016073	1.940000e-16	97.1
6	TraesCS5A01G422900	chr1B	79.478	1686	244	64	312	1936	63201664	63203308	0.000000e+00	1103.0
7	TraesCS5A01G422900	chr1B	78.923	1319	188	50	312	1579	63888743	63890022	0.000000e+00	813.0
8	TraesCS5A01G422900	chr1A	79.392	1679	258	53	312	1935	42670184	42671829	0.000000e+00	1103.0
9	TraesCS5A01G422900	chr1A	80.519	1309	199	35	665	1929	42685948	42687244	0.000000e+00	953.0
10	TraesCS5A01G422900	chr1A	80.091	1316	204	38	665	1935	42721111	42722413	0.000000e+00	926.0
11	TraesCS5A01G422900	chr1A	78.571	462	77	12	1456	1899	42696080	42696537	3.850000e-73	285.0
12	TraesCS5A01G422900	chr1A	76.305	249	46	11	312	549	42692914	42693160	1.150000e-23	121.0
13	TraesCS5A01G422900	chr1A	89.189	74	5	3	56	126	316902874	316902801	3.240000e-14	89.8
14	TraesCS5A01G422900	chr1D	79.345	1680	256	56	312	1935	43305634	43307278	0.000000e+00	1096.0
15	TraesCS5A01G422900	chr1D	81.286	1042	143	31	570	1579	44628959	44629980	0.000000e+00	797.0
16	TraesCS5A01G422900	chr1D	81.214	1038	145	28	573	1579	43823166	43824184	0.000000e+00	791.0
17	TraesCS5A01G422900	chr2D	82.353	136	22	2	1	135	636649140	636649006	1.490000e-22	117.0

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	TraesCS5A01G422900	chr5A	608949488	608951855	2367	False	4373.0	4373	100.000	1	2368	1	chr5A.!!$F1	2367
1	TraesCS5A01G422900	chr5B	600727200	600729559	2359	False	3535.0	3535	93.684	1	2368	1	chr5B.!!$F1	2367
2	TraesCS5A01G422900	chr5D	488203202	488206306	3104	False	1651.5	2386	95.360	199	2246	2	chr5D.!!$F3	2047
3	TraesCS5A01G422900	chr1B	63201664	63203308	1644	False	1103.0	1103	79.478	312	1936	1	chr1B.!!$F1	1624
4	TraesCS5A01G422900	chr1B	63888743	63890022	1279	False	813.0	813	78.923	312	1579	1	chr1B.!!$F2	1267
5	TraesCS5A01G422900	chr1A	42670184	42671829	1645	False	1103.0	1103	79.392	312	1935	1	chr1A.!!$F1	1623
6	TraesCS5A01G422900	chr1A	42685948	42687244	1296	False	953.0	953	80.519	665	1929	1	chr1A.!!$F2	1264
7	TraesCS5A01G422900	chr1A	42721111	42722413	1302	False	926.0	926	80.091	665	1935	1	chr1A.!!$F3	1270
8	TraesCS5A01G422900	chr1A	42692914	42696537	3623	False	203.0	285	77.438	312	1899	2	chr1A.!!$F4	1587
9	TraesCS5A01G422900	chr1D	43305634	43307278	1644	False	1096.0	1096	79.345	312	1935	1	chr1D.!!$F1	1623
10	TraesCS5A01G422900	chr1D	44628959	44629980	1021	False	797.0	797	81.286	570	1579	1	chr1D.!!$F3	1009
11	TraesCS5A01G422900	chr1D	43823166	43824184	1018	False	791.0	791	81.214	573	1579	1	chr1D.!!$F2	1006

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
159	160	0.108774	TGGTTCCGGCACAATGTGTA	59.891	50.000	15.36	0.0	35.75	2.90	F
986	3024	1.911357	AGGACATGATCAAGGAGTGCA	59.089	47.619	0.00	0.0	0.00	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1163	3202	0.602905	ACTTCCGCACTTGTAGCCAC	60.603	55.0	0.00	0.0	0.00	5.01	R
2248	5412	0.398664	CCCGAGGATCCCACCTAGTT	60.399	60.0	8.55	0.0	40.73	2.24	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
53	54	5.528043	TGTTGTCACATAATTTGCAGGTT	57.472	34.783	0.00	0.00	0.00	3.50
55	56	6.344500	TGTTGTCACATAATTTGCAGGTTTT	58.656	32.000	0.00	0.00	0.00	2.43
148	149	3.692101	TGCTTTATGTAACATGGTTCCGG	59.308	43.478	0.00	0.00	0.00	5.14
159	160	0.108774	TGGTTCCGGCACAATGTGTA	59.891	50.000	15.36	0.00	35.75	2.90
172	173	4.753610	CACAATGTGTAGGGCATCATCTAG	59.246	45.833	5.00	0.00	0.00	2.43
178	179	5.414765	TGTGTAGGGCATCATCTAGTATACG	59.585	44.000	0.00	0.00	0.00	3.06
182	183	4.283467	AGGGCATCATCTAGTATACGCAAA	59.717	41.667	0.00	0.00	0.00	3.68
189	190	9.809096	CATCATCTAGTATACGCAAATAGGAAT	57.191	33.333	0.00	0.00	0.00	3.01
202	203	2.623878	TAGGAATGCCGGCGATTTTA	57.376	45.000	23.90	14.74	39.96	1.52
241	242	4.213270	ACAATGTACGTGTCCAATGTCTTG	59.787	41.667	0.00	0.00	0.00	3.02
564	591	8.917415	TGCATATCTTCGAGATATACACAATC	57.083	34.615	13.53	0.00	43.95	2.67
628	655	9.537192	ACATTCATTATTTAATGCAATGTCCTG	57.463	29.630	20.60	6.46	42.43	3.86
727	2745	8.728833	ACGGTACTATAGCTTCAAGATATACAC	58.271	37.037	0.00	0.84	28.68	2.90
986	3024	1.911357	AGGACATGATCAAGGAGTGCA	59.089	47.619	0.00	0.00	0.00	4.57
1163	3202	1.243342	TGCAAGAAGCCATTCCCACG	61.243	55.000	0.00	0.00	44.83	4.94
1282	3321	9.667989	ATTCACACGGTTTTGTTATTAGTTAAC	57.332	29.630	0.00	0.00	40.59	2.01
1355	3397	2.107378	TGATGCAGGTTACACTTTCCCA	59.893	45.455	0.00	0.00	0.00	4.37
1359	3401	2.039348	GCAGGTTACACTTTCCCACCTA	59.961	50.000	0.00	0.00	35.57	3.08
1419	3463	6.287525	ACCATTGGTTTTTACTTTCATGTGG	58.712	36.000	1.37	0.00	27.29	4.17
1422	3466	4.942852	TGGTTTTTACTTTCATGTGGCTG	58.057	39.130	0.00	0.00	0.00	4.85
1423	3467	4.202202	TGGTTTTTACTTTCATGTGGCTGG	60.202	41.667	0.00	0.00	0.00	4.85
1424	3468	3.658757	TTTTACTTTCATGTGGCTGGC	57.341	42.857	0.00	0.00	0.00	4.85
1642	3723	5.897050	AGAAATCGGTGTTGTTAAAGCAAA	58.103	33.333	0.00	0.00	0.00	3.68
1645	3726	7.494298	AGAAATCGGTGTTGTTAAAGCAAAAAT	59.506	29.630	0.00	0.00	0.00	1.82
1694	4835	7.463431	AGTTAATGGGTGTAGTTATGGTTGAA	58.537	34.615	0.00	0.00	0.00	2.69
1738	4886	6.313519	TGTAACCTGAATTCCTAGCTGATT	57.686	37.500	2.27	0.00	0.00	2.57
1842	4995	5.979993	TCAGTTAGTTGTATTAATCCGCCA	58.020	37.500	0.00	0.00	0.00	5.69
1874	5027	6.199154	CCGATATAGTTCGATTGTGCCATATC	59.801	42.308	0.00	0.00	41.62	1.63
1902	5055	7.668525	TTGATTTTGTGATGCATGCAATTTA	57.331	28.000	26.68	9.22	0.00	1.40
1903	5056	7.062906	TGATTTTGTGATGCATGCAATTTAC	57.937	32.000	26.68	19.78	0.00	2.01
2014	5174	8.428063	TGAAAAAGGATACAACCATCACAAAAT	58.572	29.630	0.00	0.00	41.41	1.82
2018	5178	8.831715	AAGGATACAACCATCACAAAATTTTC	57.168	30.769	0.00	0.00	41.41	2.29
2082	5242	6.645790	ATCCTATTTTGAGATCACAATGGC	57.354	37.500	6.40	0.00	29.99	4.40
2246	5410	4.294347	TGATGTCCATGTAGACCCATGTA	58.706	43.478	0.00	0.00	40.50	2.29
2248	5412	5.190726	TGATGTCCATGTAGACCCATGTAAA	59.809	40.000	0.00	0.00	40.50	2.01
2254	5418	6.055588	CCATGTAGACCCATGTAAAACTAGG	58.944	44.000	0.00	0.00	40.50	3.02
2266	5430	1.497161	AAACTAGGTGGGATCCTCGG	58.503	55.000	12.58	3.84	38.86	4.63
2292	5456	8.952278	GGTAGGACTTCTCTATGATGTGTATAG	58.048	40.741	0.00	0.00	33.86	1.31
2296	5460	8.961634	GGACTTCTCTATGATGTGTATAGCATA	58.038	37.037	0.00	0.00	33.86	3.14
2338	5502	3.421844	AGTCCTTGTCCAAAAGGTATGC	58.578	45.455	3.06	0.00	45.94	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	6.843069	AAAACCTGCAAATTATGTGACAAC	57.157	33.333	0.00	0.00	0.00	3.32
99	100	9.738832	GTGCTTAAAACAACTAAAACTAATGGA	57.261	29.630	0.00	0.00	0.00	3.41
148	149	1.462616	TGATGCCCTACACATTGTGC	58.537	50.000	16.62	2.98	36.98	4.57
159	160	3.431415	TGCGTATACTAGATGATGCCCT	58.569	45.455	0.00	0.00	0.00	5.19
172	173	3.124636	CCGGCATTCCTATTTGCGTATAC	59.875	47.826	0.00	0.00	39.78	1.47
178	179	1.008538	CGCCGGCATTCCTATTTGC	60.009	57.895	28.98	0.00	38.14	3.68
182	183	1.981256	AAAATCGCCGGCATTCCTAT	58.019	45.000	28.98	6.41	0.00	2.57
189	190	1.735571	GAAGAACTAAAATCGCCGGCA	59.264	47.619	28.98	14.46	0.00	5.69
202	203	7.225931	ACGTACATTGTGTGTATTTGAAGAACT	59.774	33.333	0.00	0.00	44.65	3.01
254	255	3.002656	GGAAATATGCACCAGATCGTGTG	59.997	47.826	11.85	11.85	36.08	3.82
256	257	3.205338	TGGAAATATGCACCAGATCGTG	58.795	45.455	0.00	0.00	36.80	4.35
263	264	4.075682	TCGTTCTTTGGAAATATGCACCA	58.924	39.130	0.00	0.00	32.81	4.17
480	507	7.412237	CCACATCTACATGTTATGCATACATCG	60.412	40.741	5.74	10.16	40.66	3.84
943	2981	0.815615	GGTCACCCTCGCATTCATCC	60.816	60.000	0.00	0.00	0.00	3.51
1163	3202	0.602905	ACTTCCGCACTTGTAGCCAC	60.603	55.000	0.00	0.00	0.00	5.01
1355	3397	1.414158	AGCATCACTACGCCATAGGT	58.586	50.000	0.00	0.00	34.89	3.08
1359	3401	5.611374	ACTAAAATAGCATCACTACGCCAT	58.389	37.500	0.00	0.00	32.32	4.40
1422	3466	2.130073	GAAGTTGTTGTGAGGCCGCC	62.130	60.000	3.22	0.00	0.00	6.13
1423	3467	1.166531	AGAAGTTGTTGTGAGGCCGC	61.167	55.000	0.00	0.00	0.00	6.53
1424	3468	0.868406	GAGAAGTTGTTGTGAGGCCG	59.132	55.000	0.00	0.00	0.00	6.13
1625	3706	5.710613	ACATTTTTGCTTTAACAACACCG	57.289	34.783	0.00	0.00	0.00	4.94
1642	3723	7.118723	TGGAGGTAAGAAGCATATGAACATTT	58.881	34.615	6.97	0.00	0.00	2.32
1645	3726	5.692115	TGGAGGTAAGAAGCATATGAACA	57.308	39.130	6.97	0.00	0.00	3.18
1694	4835	5.140454	ACAAAGGCTAGAAATTGGTTGAGT	58.860	37.500	0.00	0.00	0.00	3.41
1709	4850	4.388577	AGGAATTCAGGTTACAAAGGCT	57.611	40.909	7.93	0.00	0.00	4.58
1770	4918	2.104170	CCCCTCTGTCTCTTCACTACC	58.896	57.143	0.00	0.00	0.00	3.18
1771	4919	2.104170	CCCCCTCTGTCTCTTCACTAC	58.896	57.143	0.00	0.00	0.00	2.73
1772	4920	2.000803	TCCCCCTCTGTCTCTTCACTA	58.999	52.381	0.00	0.00	0.00	2.74
1842	4995	7.518370	GCACAATCGAACTATATCGGATTTGTT	60.518	37.037	0.00	0.00	42.92	2.83
1874	5027	4.449405	TGCATGCATCACAAAATCAAAGTG	59.551	37.500	18.46	0.00	34.67	3.16
1902	5055	7.147863	TGGTAGTGTATATAATGGACAACACGT	60.148	37.037	0.00	0.00	41.51	4.49
1903	5056	7.204604	TGGTAGTGTATATAATGGACAACACG	58.795	38.462	0.00	0.00	41.51	4.49
1995	5155	9.921637	TTAGAAAATTTTGTGATGGTTGTATCC	57.078	29.630	8.47	0.00	0.00	2.59
2195	5359	3.826157	CCAAGCCAATGAAAGTCCAAGTA	59.174	43.478	0.00	0.00	0.00	2.24
2246	5410	1.838077	CCGAGGATCCCACCTAGTTTT	59.162	52.381	8.55	0.00	40.73	2.43
2248	5412	0.398664	CCCGAGGATCCCACCTAGTT	60.399	60.000	8.55	0.00	40.73	2.24
2266	5430	7.768807	ATACACATCATAGAGAAGTCCTACC	57.231	40.000	0.00	0.00	0.00	3.18
2292	5456	7.105241	AGATCCTTGTTTTCCAAATCTATGC	57.895	36.000	0.00	0.00	31.71	3.14
2296	5460	6.887002	GGACTAGATCCTTGTTTTCCAAATCT	59.113	38.462	0.00	0.00	45.22	2.40
2338	5502	1.086696	ATCAATGCCCAAGAACGACG	58.913	50.000	0.00	0.00	0.00	5.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.