AutoCloner

Multiple sequence alignment - TraesCS5B01G546000

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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	TraesCS5B01G546000	chr5B	100.000	2498	0	0	1	2498	698069903	698067406	0.000000e+00	4614.0
1	TraesCS5B01G546000	chr5B	94.499	709	38	1	1	708	698104473	698103765	0.000000e+00	1092.0
2	TraesCS5B01G546000	chr6D	94.705	1794	82	8	715	2498	69020136	69021926	0.000000e+00	2774.0
3	TraesCS5B01G546000	chr1A	94.254	1549	80	5	917	2457	350406140	350404593	0.000000e+00	2359.0
4	TraesCS5B01G546000	chr1A	93.407	182	10	1	708	887	350406322	350406141	4.100000e-68	268.0
5	TraesCS5B01G546000	chr6B	94.190	1549	81	5	917	2457	159424104	159422557	0.000000e+00	2353.0
6	TraesCS5B01G546000	chr6B	93.653	709	44	1	1	708	689823816	689824524	0.000000e+00	1059.0
7	TraesCS5B01G546000	chr6B	93.956	182	9	1	708	887	159424286	159424105	8.800000e-70	274.0
8	TraesCS5B01G546000	chr1B	93.544	1549	90	6	917	2457	119685461	119683915	0.000000e+00	2298.0
9	TraesCS5B01G546000	chr1B	93.407	182	10	1	708	887	119685643	119685462	4.100000e-68	268.0
10	TraesCS5B01G546000	chr1B	87.302	63	8	0	2084	2146	397794180	397794118	3.450000e-09	73.1
11	TraesCS5B01G546000	chr4B	93.092	1549	97	6	917	2457	518682589	518684135	0.000000e+00	2259.0
12	TraesCS5B01G546000	chr4B	94.366	710	39	1	1	709	628915019	628915728	0.000000e+00	1088.0
13	TraesCS5B01G546000	chr4B	94.358	709	38	2	1	708	492419034	492418327	0.000000e+00	1086.0
14	TraesCS5B01G546000	chr4B	93.794	709	42	2	1	707	92407849	92407141	0.000000e+00	1064.0
15	TraesCS5B01G546000	chr4B	93.803	710	41	3	1	708	550972722	550972014	0.000000e+00	1064.0
16	TraesCS5B01G546000	chr4B	93.794	709	43	1	1	708	628901588	628902296	0.000000e+00	1064.0
17	TraesCS5B01G546000	chr4B	93.956	182	9	1	708	887	518682407	518682588	8.800000e-70	274.0
18	TraesCS5B01G546000	chr1D	90.189	1376	87	19	1150	2498	208183980	208185334	0.000000e+00	1749.0
19	TraesCS5B01G546000	chr1D	87.302	63	8	0	2084	2146	296275466	296275404	3.450000e-09	73.1
20	TraesCS5B01G546000	chr3B	94.068	708	40	2	1	707	662915560	662916266	0.000000e+00	1074.0
21	TraesCS5B01G546000	chr2B	93.653	709	43	2	1	708	223767213	223767920	0.000000e+00	1059.0
22	TraesCS5B01G546000	chr2D	88.983	354	30	2	1556	1904	301363160	301363509	1.780000e-116	429.0
23	TraesCS5B01G546000	chr2D	95.238	42	2	0	1983	2024	301363929	301363970	1.600000e-07	67.6
24	TraesCS5B01G546000	chrUn	87.461	319	27	5	1591	1904	38168896	38169206	3.060000e-94	355.0
25	TraesCS5B01G546000	chrUn	95.238	42	2	0	1983	2024	38169623	38169664	1.600000e-07	67.6
26	TraesCS5B01G546000	chr5D	91.429	245	17	3	708	948	553279603	553279847	1.430000e-87	333.0
27	TraesCS5B01G546000	chr7D	82.736	307	43	9	951	1255	581430090	581430388	5.300000e-67	265.0
28	TraesCS5B01G546000	chr7A	82.353	306	48	4	951	1255	673132382	673132682	6.850000e-66	261.0
29	TraesCS5B01G546000	chr7B	78.818	203	42	1	1060	1261	24152614	24152412	4.330000e-28	135.0
30	TraesCS5B01G546000	chr4D	93.023	86	5	1	862	946	109358810	109358725	9.380000e-25	124.0
31	TraesCS5B01G546000	chr4A	93.023	86	5	1	862	946	467147090	467147175	9.380000e-25	124.0

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	TraesCS5B01G546000	chr5B	698067406	698069903	2497	True	4614.0	4614	100.0000	1	2498	1	chr5B.!!$R1	2497
1	TraesCS5B01G546000	chr5B	698103765	698104473	708	True	1092.0	1092	94.4990	1	708	1	chr5B.!!$R2	707
2	TraesCS5B01G546000	chr6D	69020136	69021926	1790	False	2774.0	2774	94.7050	715	2498	1	chr6D.!!$F1	1783
3	TraesCS5B01G546000	chr1A	350404593	350406322	1729	True	1313.5	2359	93.8305	708	2457	2	chr1A.!!$R1	1749
4	TraesCS5B01G546000	chr6B	159422557	159424286	1729	True	1313.5	2353	94.0730	708	2457	2	chr6B.!!$R1	1749
5	TraesCS5B01G546000	chr6B	689823816	689824524	708	False	1059.0	1059	93.6530	1	708	1	chr6B.!!$F1	707
6	TraesCS5B01G546000	chr1B	119683915	119685643	1728	True	1283.0	2298	93.4755	708	2457	2	chr1B.!!$R2	1749
7	TraesCS5B01G546000	chr4B	518682407	518684135	1728	False	1266.5	2259	93.5240	708	2457	2	chr4B.!!$F3	1749
8	TraesCS5B01G546000	chr4B	628915019	628915728	709	False	1088.0	1088	94.3660	1	709	1	chr4B.!!$F2	708
9	TraesCS5B01G546000	chr4B	492418327	492419034	707	True	1086.0	1086	94.3580	1	708	1	chr4B.!!$R2	707
10	TraesCS5B01G546000	chr4B	92407141	92407849	708	True	1064.0	1064	93.7940	1	707	1	chr4B.!!$R1	706
11	TraesCS5B01G546000	chr4B	550972014	550972722	708	True	1064.0	1064	93.8030	1	708	1	chr4B.!!$R3	707
12	TraesCS5B01G546000	chr4B	628901588	628902296	708	False	1064.0	1064	93.7940	1	708	1	chr4B.!!$F1	707
13	TraesCS5B01G546000	chr1D	208183980	208185334	1354	False	1749.0	1749	90.1890	1150	2498	1	chr1D.!!$F1	1348
14	TraesCS5B01G546000	chr3B	662915560	662916266	706	False	1074.0	1074	94.0680	1	707	1	chr3B.!!$F1	706
15	TraesCS5B01G546000	chr2B	223767213	223767920	707	False	1059.0	1059	93.6530	1	708	1	chr2B.!!$F1	707
16	TraesCS5B01G546000	chr2D	301363160	301363970	810	False	248.3	429	92.1105	1556	2024	2	chr2D.!!$F1	468
17	TraesCS5B01G546000	chrUn	38168896	38169664	768	False	211.3	355	91.3495	1591	2024	2	chrUn.!!$F1	433

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
690	694	1.133294	CCAAAACCAACTAGGGGTGGT	60.133	52.381	8.9	8.81	43.89	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2138	2493	1.201647	CCATTCTGCAAGTTCAGCTGG	59.798	52.381	15.13	0.0	33.48	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
132	135	2.359531	AGCCGTATCTAACTCTGAGCAC	59.640	50.000	4.19	0.00	0.00	4.40
196	200	1.890876	CAACCCGACCTGATTTGTCA	58.109	50.000	0.00	0.00	32.91	3.58
208	212	5.014123	ACCTGATTTGTCAGAAATGACCCTA	59.986	40.000	6.99	0.00	39.99	3.53
259	263	2.286833	CGGTCAGATTTCAAACACACGT	59.713	45.455	0.00	0.00	0.00	4.49
321	325	7.061054	TCCGACTCTGGATAAGATTTTCTCTA	58.939	38.462	0.00	0.00	33.29	2.43
359	363	6.073548	CGAAGATATAGGATTTGGTTGAGCAC	60.074	42.308	0.00	0.00	0.00	4.40
563	567	8.196771	AGCTTCAATGTCTTCACACATTTTTAA	58.803	29.630	0.00	0.00	43.17	1.52
593	597	4.826274	TCTGGTAGGGAAACTGAATCAG	57.174	45.455	8.98	8.98	37.52	2.90
621	625	4.954826	GGACTACTACCTGTGTTATCCTGT	59.045	45.833	0.00	0.00	0.00	4.00
646	650	4.015872	TCTCACAAACACATTAGTCCCC	57.984	45.455	0.00	0.00	0.00	4.81
658	662	2.436964	TAGTCCCCCAACCAGGTTTA	57.563	50.000	0.44	0.00	34.66	2.01
690	694	1.133294	CCAAAACCAACTAGGGGTGGT	60.133	52.381	8.90	8.81	43.89	4.16
713	717	5.483685	ACTAGATGCACTTACAAGGTTGA	57.516	39.130	0.00	0.00	0.00	3.18
767	773	3.733337	ACTTGTTGGTTCAGTAGAGCTG	58.267	45.455	0.00	0.00	46.34	4.24
807	813	1.620822	GGGGGATATCAATGTGGCAC	58.379	55.000	11.55	11.55	0.00	5.01
873	879	7.225931	ACTTCGCTTTTCTGAAAGTATGTTACA	59.774	33.333	2.75	0.00	43.36	2.41
888	894	2.375174	TGTTACAATCCTGCTCTTGGGT	59.625	45.455	0.00	0.00	0.00	4.51
1046	1052	4.002906	TCTGCCAACGACTTGACTATTT	57.997	40.909	0.00	0.00	0.00	1.40
1047	1053	3.745975	TCTGCCAACGACTTGACTATTTG	59.254	43.478	0.00	0.00	0.00	2.32
1148	1154	4.722700	GCGGCAAGGAGAAGGGCA	62.723	66.667	0.00	0.00	0.00	5.36
1157	1163	2.852130	AGGAGAAGGGCACTTAGGATT	58.148	47.619	0.00	0.00	36.97	3.01
1234	1240	9.050601	GTTTCTCTATTTTCCTCATATCACCAG	57.949	37.037	0.00	0.00	0.00	4.00
1239	1245	5.779241	TTTTCCTCATATCACCAGGTTCT	57.221	39.130	0.00	0.00	0.00	3.01
1240	1246	4.760530	TTCCTCATATCACCAGGTTCTG	57.239	45.455	0.00	0.00	0.00	3.02
1258	1264	7.591426	CAGGTTCTGAATTTTACAAACTGCTAC	59.409	37.037	0.00	0.00	32.44	3.58
1276	1282	3.349006	GTGACGCACAGTGGCCAG	61.349	66.667	5.11	0.00	34.08	4.85
1298	1304	2.651455	CCATGCACTGGTGAGATTCAT	58.349	47.619	4.79	0.00	40.49	2.57
1305	1311	2.224843	ACTGGTGAGATTCATGGTGCAA	60.225	45.455	0.00	0.00	0.00	4.08
1319	1325	2.741930	TGCAATCGAGCAAGAGTCG	58.258	52.632	0.00	0.00	42.46	4.18
1343	1349	0.104304	GAGGTGAGGTGTGTCACGTT	59.896	55.000	0.00	0.00	46.72	3.99
1372	1378	4.828925	GCTCACCAGCGAGGCTCC	62.829	72.222	9.32	1.69	43.14	4.70
1373	1379	3.385384	CTCACCAGCGAGGCTCCA	61.385	66.667	9.32	0.00	43.14	3.86
1471	1477	9.570488	CTACAACTACTATGTCTTTGTACCTTC	57.430	37.037	0.00	0.00	32.73	3.46
1533	1539	6.715280	ACTCAGTTTGATAATGGAGTCACAT	58.285	36.000	0.00	0.00	30.27	3.21
1679	1686	6.138263	TCCTATGCCAATTGATTTTCTCCAT	58.862	36.000	7.12	0.00	0.00	3.41
1883	1896	5.580297	CAGCCATCTACTTTCAGAGAGTTTC	59.420	44.000	0.00	0.00	0.00	2.78
1969	2179	8.706936	CCGATCTACAGAATTACAATTGAGATG	58.293	37.037	13.59	4.61	0.00	2.90
2058	2413	6.801862	GGCTATTCAATTATAAACGTCATGCC	59.198	38.462	0.00	0.00	0.00	4.40
2077	2432	3.932710	TGCCGCAGTGATTACTTTCTTAG	59.067	43.478	0.00	0.00	34.07	2.18
2090	2445	5.216614	ACTTTCTTAGTCCCTTCAGACAC	57.783	43.478	0.00	0.00	39.34	3.67
2138	2493	6.968131	TGAACTGACACTAGCAATATTGAC	57.032	37.500	19.73	10.26	0.00	3.18
2156	2511	2.157738	GACCAGCTGAACTTGCAGAAT	58.842	47.619	17.39	0.00	38.14	2.40
2196	2551	8.877864	AGGAACATCTTACATATTTTTGGTCA	57.122	30.769	0.00	0.00	0.00	4.02
2381	2758	1.944024	TCAGTGCCTGTGTTTAAACCG	59.056	47.619	15.59	4.44	32.61	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	2.422803	CCCAGACCCAAAGAGTGTTTGA	60.423	50.000	14.01	0.00	0.00	2.69
259	263	1.055849	TAGCCCAAGTCAAGCTGTCA	58.944	50.000	0.00	0.00	37.45	3.58
408	412	4.974645	TTGTTGAGTCATAGGAACCACT	57.025	40.909	0.00	0.00	0.00	4.00
563	567	3.974642	GTTTCCCTACCAGATATGACCCT	59.025	47.826	0.00	0.00	0.00	4.34
593	597	2.805194	ACACAGGTAGTAGTCCCTCAC	58.195	52.381	0.00	0.00	0.00	3.51
621	625	6.657541	GGGGACTAATGTGTTTGTGAGAATTA	59.342	38.462	0.00	0.00	0.00	1.40
646	650	5.183228	AGTATTGACGATAAACCTGGTTGG	58.817	41.667	13.79	5.81	42.93	3.77
658	662	5.313712	AGTTGGTTTTGGAGTATTGACGAT	58.686	37.500	0.00	0.00	0.00	3.73
690	694	6.599356	TCAACCTTGTAAGTGCATCTAGTA	57.401	37.500	0.00	0.00	0.00	1.82
736	740	4.460263	TGAACCAACAAGTTAGCATGTCT	58.540	39.130	0.00	0.00	0.00	3.41
773	779	4.129148	CCCCTACTGCAAGCCCCC	62.129	72.222	0.00	0.00	37.60	5.40
799	805	3.795877	CTTTGGTTTTCAAGTGCCACAT	58.204	40.909	0.00	0.00	36.62	3.21
807	813	7.656948	TCATGAATAAAGGCTTTGGTTTTCAAG	59.343	33.333	22.32	18.75	36.62	3.02
873	879	4.530875	CTTAATCACCCAAGAGCAGGATT	58.469	43.478	0.00	0.00	0.00	3.01
888	894	4.099266	AGCAAAACCACAACAGCTTAATCA	59.901	37.500	0.00	0.00	0.00	2.57
1024	1030	3.895232	ATAGTCAAGTCGTTGGCAGAT	57.105	42.857	0.00	0.00	41.08	2.90
1046	1052	3.239587	TCCGCGTCATAAAAGATGACA	57.760	42.857	15.80	0.00	46.38	3.58
1047	1053	3.184581	GGATCCGCGTCATAAAAGATGAC	59.815	47.826	4.92	7.48	43.55	3.06
1100	1106	4.320456	CTGGTGGTGAGGCGCTGT	62.320	66.667	7.64	0.00	0.00	4.40
1148	1154	2.226437	CACAACGCAGCAAATCCTAAGT	59.774	45.455	0.00	0.00	0.00	2.24
1177	1183	1.825090	TGGCGATGCTGAACTTCAAT	58.175	45.000	0.00	0.00	0.00	2.57
1230	1236	6.682861	GCAGTTTGTAAAATTCAGAACCTGGT	60.683	38.462	0.00	0.00	31.51	4.00
1234	1240	6.577427	CGTAGCAGTTTGTAAAATTCAGAACC	59.423	38.462	0.00	0.00	0.00	3.62
1239	1245	6.423862	GTCACGTAGCAGTTTGTAAAATTCA	58.576	36.000	0.00	0.00	0.00	2.57
1240	1246	5.558888	CGTCACGTAGCAGTTTGTAAAATTC	59.441	40.000	0.00	0.00	0.00	2.17
1281	1287	1.352017	ACCATGAATCTCACCAGTGCA	59.648	47.619	0.00	0.00	0.00	4.57
1298	1304	0.035317	ACTCTTGCTCGATTGCACCA	59.965	50.000	0.00	0.00	43.20	4.17
1305	1311	0.179161	CGAACCGACTCTTGCTCGAT	60.179	55.000	0.00	0.00	32.65	3.59
1319	1325	0.319641	GACACACCTCACCTCGAACC	60.320	60.000	0.00	0.00	0.00	3.62
1343	1349	0.906282	TGGTGAGCAGCAGGAGATCA	60.906	55.000	0.00	0.00	34.41	2.92
1372	1378	1.953138	GATCTGGCCGCTCGTCATG	60.953	63.158	0.00	0.00	0.00	3.07
1373	1379	2.419198	GATCTGGCCGCTCGTCAT	59.581	61.111	0.00	0.00	0.00	3.06
1471	1477	7.446319	TCACCATGGATGAAAGAGCAATATAAG	59.554	37.037	21.47	0.00	0.00	1.73
1649	1656	5.393068	AATCAATTGGCATAGGAGGAGAA	57.607	39.130	5.42	0.00	0.00	2.87
1778	1786	7.558444	TGTCACCTCCATAAACAGTAAAACTTT	59.442	33.333	0.00	0.00	0.00	2.66
1856	1864	1.210478	TCTGAAAGTAGATGGCTGCCC	59.790	52.381	17.53	0.80	33.76	5.36
1883	1896	5.570206	TGAGTTAGCGTGATAGTACGTTTTG	59.430	40.000	0.00	0.00	45.36	2.44
1969	2179	6.070136	ACAAAAGGGAAATAGAGGAGGTAGAC	60.070	42.308	0.00	0.00	0.00	2.59
2034	2389	6.519761	CGGCATGACGTTTATAATTGAATAGC	59.480	38.462	14.35	0.00	0.00	2.97
2058	2413	4.567159	GGGACTAAGAAAGTAATCACTGCG	59.433	45.833	0.00	0.00	39.07	5.18
2077	2432	2.347731	GGAAATCGTGTCTGAAGGGAC	58.652	52.381	0.00	0.00	36.81	4.46
2090	2445	3.505680	TGAATGTTTGGACAGGGAAATCG	59.494	43.478	0.00	0.00	39.58	3.34
2138	2493	1.201647	CCATTCTGCAAGTTCAGCTGG	59.798	52.381	15.13	0.00	33.48	4.85
2156	2511	4.136341	TGTTCCTTTAGTACCTCTCCCA	57.864	45.455	0.00	0.00	0.00	4.37
2311	2666	9.374838	ACTATACCTTTCATTTTTACACGGTAG	57.625	33.333	0.00	0.00	0.00	3.18
2381	2758	3.034635	ACCTGACCATCTCTACATCCAC	58.965	50.000	0.00	0.00	0.00	4.02
2451	2829	9.220767	CTACTTACTTCCTTTTATGTGCTTCTT	57.779	33.333	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.