AutoCloner

Multiple sequence alignment - TraesCS1A01G096700

Loading Multiple Alignment...

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	TraesCS1A01G096700	chr1A	100.000	2282	0	0	1	2282	92582344	92580063	0.000000e+00	4215
1	TraesCS1A01G096700	chr1A	78.320	512	92	14	797	1296	329593275	329592771	1.700000e-81	313
2	TraesCS1A01G096700	chr1D	92.298	2324	131	28	1	2282	97547915	97545598	0.000000e+00	3256
3	TraesCS1A01G096700	chr3D	87.075	588	60	10	719	1292	10825712	10825127	0.000000e+00	651
4	TraesCS1A01G096700	chr3D	90.741	108	7	2	15	122	10826100	10825996	8.500000e-30	141
5	TraesCS1A01G096700	chr3D	91.579	95	8	0	598	692	10825806	10825712	5.120000e-27	132
6	TraesCS1A01G096700	chr4B	75.841	1308	289	25	18	1308	166834201	166832904	6.870000e-180	640
7	TraesCS1A01G096700	chr1B	77.253	910	194	11	384	1284	220751208	220750303	2.600000e-144	521
8	TraesCS1A01G096700	chr1B	86.630	359	39	5	1933	2282	155730354	155730712	2.750000e-104	388
9	TraesCS1A01G096700	chr7A	77.179	780	163	13	536	1304	11072424	11073199	7.480000e-120	440
10	TraesCS1A01G096700	chrUn	74.081	1061	252	18	57	1102	27749506	27750558	4.540000e-112	414
11	TraesCS1A01G096700	chrUn	77.179	390	70	13	918	1296	407447556	407447175	2.300000e-50	209
12	TraesCS1A01G096700	chr6D	76.130	708	153	14	609	1306	55309193	55309894	7.750000e-95	357
13	TraesCS1A01G096700	chr6D	72.715	766	185	23	233	983	291226942	291226186	3.790000e-58	235
14	TraesCS1A01G096700	chr2B	83.673	294	45	3	1011	1303	128561449	128561158	8.030000e-70	274
15	TraesCS1A01G096700	chr2B	76.923	221	38	10	1666	1874	753007107	753006888	1.850000e-21	113
16	TraesCS1A01G096700	chr2D	75.499	351	60	19	1670	1998	617197394	617197048	5.080000e-32	148
17	TraesCS1A01G096700	chr2A	78.689	183	30	8	1699	1874	747306310	747306490	1.850000e-21	113

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	TraesCS1A01G096700	chr1A	92580063	92582344	2281	True	4215	4215	100.000000	1	2282	1	chr1A.!!$R1	2281
1	TraesCS1A01G096700	chr1A	329592771	329593275	504	True	313	313	78.320000	797	1296	1	chr1A.!!$R2	499
2	TraesCS1A01G096700	chr1D	97545598	97547915	2317	True	3256	3256	92.298000	1	2282	1	chr1D.!!$R1	2281
3	TraesCS1A01G096700	chr3D	10825127	10826100	973	True	308	651	89.798333	15	1292	3	chr3D.!!$R1	1277
4	TraesCS1A01G096700	chr4B	166832904	166834201	1297	True	640	640	75.841000	18	1308	1	chr4B.!!$R1	1290
5	TraesCS1A01G096700	chr1B	220750303	220751208	905	True	521	521	77.253000	384	1284	1	chr1B.!!$R1	900
6	TraesCS1A01G096700	chr7A	11072424	11073199	775	False	440	440	77.179000	536	1304	1	chr7A.!!$F1	768
7	TraesCS1A01G096700	chrUn	27749506	27750558	1052	False	414	414	74.081000	57	1102	1	chrUn.!!$F1	1045
8	TraesCS1A01G096700	chr6D	55309193	55309894	701	False	357	357	76.130000	609	1306	1	chr6D.!!$F1	697
9	TraesCS1A01G096700	chr6D	291226186	291226942	756	True	235	235	72.715000	233	983	1	chr6D.!!$R1	750

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
807	888	1.203364	AGAGGGTTGGTCATGTCCTCT	60.203	52.381	10.43	11.12	46.63	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1727	1828	0.315251	GTCCTTGAGCCAAGTTTGCC	59.685	55.0	12.18	0.0	39.58	4.52	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
136	137	3.181510	GGCCAATTGATGTACAACGAGTC	60.182	47.826	7.12	0.00	41.52	3.36
277	304	4.757594	GCAAATTGCTTCATACCAATGGA	58.242	39.130	11.19	0.00	40.96	3.41
326	354	5.609533	TTAGGGTAAGATCTGGCAACTAC	57.390	43.478	0.00	0.00	37.61	2.73
333	361	3.110705	AGATCTGGCAACTACCATGTCT	58.889	45.455	0.00	0.00	39.54	3.41
344	372	3.483954	CCATGTCTGGCTAAGGTGG	57.516	57.895	0.00	0.00	35.23	4.61
469	499	6.662755	TGGTCCAGAAGATACAAAGCATATT	58.337	36.000	0.00	0.00	0.00	1.28
603	633	5.189180	ACTTCTTATGCCAGAACAGGAATC	58.811	41.667	0.00	0.00	0.00	2.52
604	634	5.045286	ACTTCTTATGCCAGAACAGGAATCT	60.045	40.000	0.00	0.00	0.00	2.40
705	785	3.355626	TCACAACGAGACAACTCAGAG	57.644	47.619	0.00	0.00	42.72	3.35
807	888	1.203364	AGAGGGTTGGTCATGTCCTCT	60.203	52.381	10.43	11.12	46.63	3.69
1333	1433	9.717942	AGAATGGTAATTATGCTCTCAATAGTC	57.282	33.333	0.00	0.00	0.00	2.59
1341	1441	1.862008	GCTCTCAATAGTCGGTGCTCG	60.862	57.143	0.00	0.00	40.90	5.03
1418	1518	4.718961	AGTAGGGATTGAAATGCGCTTAT	58.281	39.130	9.73	0.00	0.00	1.73
1419	1519	5.133221	AGTAGGGATTGAAATGCGCTTATT	58.867	37.500	9.73	0.00	0.00	1.40
1422	1522	6.463995	AGGGATTGAAATGCGCTTATTTTA	57.536	33.333	9.73	0.86	30.78	1.52
1424	1524	7.500141	AGGGATTGAAATGCGCTTATTTTAAT	58.500	30.769	17.53	17.53	38.30	1.40
1435	1535	6.034044	TGCGCTTATTTTAATAAAAACTGGCG	59.966	34.615	21.37	21.37	43.52	5.69
1439	1539	7.758076	GCTTATTTTAATAAAAACTGGCGGACT	59.242	33.333	0.00	0.00	37.41	3.85
1471	1571	6.292649	GCCAAGGTTTTAGGAATTGTTTTTCG	60.293	38.462	0.00	0.00	0.00	3.46
1490	1590	3.645884	TCGGTTTTGACGAGTTAGAAGG	58.354	45.455	0.00	0.00	35.12	3.46
1533	1633	9.549078	CTTTTTAATAGCCCCAAACAACTTTTA	57.451	29.630	0.00	0.00	0.00	1.52
1605	1706	4.895297	CCATGGGTAGCCATTACAAAGATT	59.105	41.667	23.84	0.00	33.73	2.40
1613	1714	6.272822	AGCCATTACAAAGATTGAGGAAAC	57.727	37.500	0.00	0.00	0.00	2.78
1623	1724	3.138283	AGATTGAGGAAACCCACACTTCA	59.862	43.478	0.00	0.00	0.00	3.02
1631	1732	0.629058	ACCCACACTTCACCCACTTT	59.371	50.000	0.00	0.00	0.00	2.66
1632	1733	1.032014	CCCACACTTCACCCACTTTG	58.968	55.000	0.00	0.00	0.00	2.77
1662	1763	7.290014	ACTTAGGAAACAAAAGGATGATTTGGT	59.710	33.333	4.29	0.00	41.08	3.67
1676	1777	6.146021	GGATGATTTGGTGTGACAATGAAAAC	59.854	38.462	0.00	0.00	0.00	2.43
1682	1783	7.867305	TTGGTGTGACAATGAAAACTTACTA	57.133	32.000	0.00	0.00	0.00	1.82
1692	1793	9.220767	ACAATGAAAACTTACTAGGAATGACTC	57.779	33.333	0.00	0.00	0.00	3.36
1784	1885	4.026228	CAGAATGCATGCTTAGTGTAGACG	60.026	45.833	20.33	0.00	0.00	4.18
2045	2157	8.924303	AGTATTCAAGATAGCACATAAGGTACA	58.076	33.333	0.00	0.00	0.00	2.90
2067	2179	7.661536	ACACCTAGATGATTAAGACTTAGCA	57.338	36.000	0.00	0.00	0.00	3.49
2106	2218	7.822161	TCACCAAGCTTATATTATGCACAAT	57.178	32.000	0.00	0.00	0.00	2.71
2195	2307	1.537202	GATCGTGCCAGCTTTCTTTGT	59.463	47.619	0.00	0.00	0.00	2.83
2199	2311	0.662619	TGCCAGCTTTCTTTGTCACG	59.337	50.000	0.00	0.00	0.00	4.35
2208	2320	2.971660	TCTTTGTCACGGTCACTTCA	57.028	45.000	0.00	0.00	0.00	3.02
2219	2331	2.743664	CGGTCACTTCATCAAGCAATCA	59.256	45.455	0.00	0.00	32.09	2.57
2222	2334	4.495349	GGTCACTTCATCAAGCAATCATCG	60.495	45.833	0.00	0.00	32.09	3.84
2225	2337	4.791676	CACTTCATCAAGCAATCATCGTTG	59.208	41.667	0.00	0.00	32.09	4.10
2233	2345	6.215121	TCAAGCAATCATCGTTGTTGATTTT	58.785	32.000	10.83	1.36	40.84	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	7.016072	CCTCTGGGAGTAATGACAATTCTATCT	59.984	40.741	0.00	0.00	33.58	1.98
136	137	1.227089	CGAGATTGGGACTGCGAGG	60.227	63.158	0.00	0.00	0.00	4.63
207	234	6.599356	AAAAATAGGCGGACCAAACTAAAT	57.401	33.333	0.00	0.00	39.06	1.40
277	304	3.495434	TTAACTGTGGTTCGTCCCATT	57.505	42.857	0.00	0.00	36.74	3.16
326	354	6.631620	AAAGTCCACCTTAGCCAGACATGG	62.632	50.000	0.00	0.00	40.34	3.66
469	499	6.599244	CCCTTGCTTTGTGACATAGAAATAGA	59.401	38.462	7.23	0.00	0.00	1.98
603	633	9.155975	GCACATTCTGGTTACCTATAATATGAG	57.844	37.037	2.07	0.00	0.00	2.90
604	634	7.817478	CGCACATTCTGGTTACCTATAATATGA	59.183	37.037	2.07	0.00	0.00	2.15
705	785	3.201290	CCCATAGAGATCTGTTGTGCAC	58.799	50.000	10.75	10.75	0.00	4.57
807	888	7.648039	ACATTGAGTTTAACAAAACCTACCA	57.352	32.000	0.00	0.00	33.28	3.25
994	1085	5.823861	TTAATGACTAGCTGCATCCCATA	57.176	39.130	1.02	0.00	0.00	2.74
1075	1170	1.169661	TCATCAAAAACCGCCGCAGT	61.170	50.000	0.00	0.00	0.00	4.40
1215	1311	4.225042	ACAATTTCATTTAAAGGCCCCTCC	59.775	41.667	0.00	0.00	0.00	4.30
1316	1416	4.039730	AGCACCGACTATTGAGAGCATAAT	59.960	41.667	0.00	0.00	0.00	1.28
1333	1433	0.108615	ATCACTTTCCTCGAGCACCG	60.109	55.000	6.99	0.00	40.25	4.94
1341	1441	6.801539	TTATGTTGTGTCATCACTTTCCTC	57.198	37.500	0.00	0.00	44.14	3.71
1368	1468	7.147549	CCCTCTGTGATGGTCCTATACTTTTAA	60.148	40.741	0.00	0.00	0.00	1.52
1376	1476	3.310954	ACTTCCCTCTGTGATGGTCCTAT	60.311	47.826	0.00	0.00	0.00	2.57
1387	1487	3.491766	TCAATCCCTACTTCCCTCTGT	57.508	47.619	0.00	0.00	0.00	3.41
1418	1518	8.794553	TCATAAGTCCGCCAGTTTTTATTAAAA	58.205	29.630	0.00	0.00	0.00	1.52
1419	1519	8.338072	TCATAAGTCCGCCAGTTTTTATTAAA	57.662	30.769	0.00	0.00	0.00	1.52
1422	1522	6.680378	GCATCATAAGTCCGCCAGTTTTTATT	60.680	38.462	0.00	0.00	0.00	1.40
1424	1524	4.095782	GCATCATAAGTCCGCCAGTTTTTA	59.904	41.667	0.00	0.00	0.00	1.52
1435	1535	5.067805	CCTAAAACCTTGGCATCATAAGTCC	59.932	44.000	0.00	0.00	0.00	3.85
1439	1539	7.180051	ACAATTCCTAAAACCTTGGCATCATAA	59.820	33.333	0.00	0.00	0.00	1.90
1471	1571	3.736720	ACCCTTCTAACTCGTCAAAACC	58.263	45.455	0.00	0.00	0.00	3.27
1533	1633	8.758829	ACAAAGGAACTCCAAAACTAAAGAAAT	58.241	29.630	0.00	0.00	38.49	2.17
1589	1690	6.377146	GGTTTCCTCAATCTTTGTAATGGCTA	59.623	38.462	0.00	0.00	0.00	3.93
1605	1706	1.133915	GGTGAAGTGTGGGTTTCCTCA	60.134	52.381	0.00	0.00	34.50	3.86
1613	1714	1.032014	CAAAGTGGGTGAAGTGTGGG	58.968	55.000	0.00	0.00	0.00	4.61
1623	1724	5.717654	TGTTTCCTAAGTTTTCAAAGTGGGT	59.282	36.000	0.00	0.00	0.00	4.51
1631	1732	8.299990	TCATCCTTTTGTTTCCTAAGTTTTCA	57.700	30.769	0.00	0.00	0.00	2.69
1632	1733	9.764363	AATCATCCTTTTGTTTCCTAAGTTTTC	57.236	29.630	0.00	0.00	0.00	2.29
1662	1763	8.783093	CATTCCTAGTAAGTTTTCATTGTCACA	58.217	33.333	0.00	0.00	0.00	3.58
1682	1783	8.733092	TCCTATCATGAATAAGAGTCATTCCT	57.267	34.615	0.00	0.00	33.37	3.36
1705	1806	6.174049	GCCATAAGAGTCCATTATACCTTCC	58.826	44.000	0.00	0.00	0.00	3.46
1718	1819	3.084786	AGCCAAGTTTGCCATAAGAGTC	58.915	45.455	0.00	0.00	0.00	3.36
1727	1828	0.315251	GTCCTTGAGCCAAGTTTGCC	59.685	55.000	12.18	0.00	39.58	4.52
1767	1868	2.860735	CCTTCGTCTACACTAAGCATGC	59.139	50.000	10.51	10.51	0.00	4.06
1784	1885	5.303333	ACTTCCTAGTCTATTGCTAGCCTTC	59.697	44.000	13.29	0.00	35.75	3.46
1865	1967	9.933240	AGTGTTAGTATCCTACTTATGTTACCT	57.067	33.333	0.00	0.00	40.14	3.08
1906	2008	4.492494	AATTCCAATTCATCCCCAAAGC	57.508	40.909	0.00	0.00	0.00	3.51
2019	2131	8.924303	TGTACCTTATGTGCTATCTTGAATACT	58.076	33.333	0.00	0.00	0.00	2.12
2020	2132	8.979574	GTGTACCTTATGTGCTATCTTGAATAC	58.020	37.037	0.00	0.00	0.00	1.89
2045	2157	6.546403	TCGTGCTAAGTCTTAATCATCTAGGT	59.454	38.462	0.00	0.00	0.00	3.08
2067	2179	3.057969	TGGTGATTCATGCTTTCTCGT	57.942	42.857	0.00	0.00	0.00	4.18
2171	2283	1.065926	AGAAAGCTGGCACGATCATCA	60.066	47.619	0.00	0.00	0.00	3.07
2173	2285	2.119801	AAGAAAGCTGGCACGATCAT	57.880	45.000	0.00	0.00	0.00	2.45
2195	2307	1.069978	TGCTTGATGAAGTGACCGTGA	59.930	47.619	0.00	0.00	0.00	4.35
2199	2311	4.495349	CGATGATTGCTTGATGAAGTGACC	60.495	45.833	0.00	0.00	0.00	4.02
2208	2320	5.571784	ATCAACAACGATGATTGCTTGAT	57.428	34.783	0.00	1.31	36.54	2.57
2219	2331	5.347342	TGCAAGTGAAAAATCAACAACGAT	58.653	33.333	0.00	0.00	0.00	3.73
2222	2334	6.586868	TCATGCAAGTGAAAAATCAACAAC	57.413	33.333	0.00	0.00	0.00	3.32
2225	2337	7.410800	TCAATCATGCAAGTGAAAAATCAAC	57.589	32.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.