AutoCloner

Multiple sequence alignment - TraesCS1D01G321600

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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	TraesCS1D01G321600	chr1D	100.000	2668	0	0	1	2668	415054528	415051861	0.000000e+00	4927.0
1	TraesCS1D01G321600	chr1D	93.234	2350	97	27	365	2668	414942151	414939818	0.000000e+00	3402.0
2	TraesCS1D01G321600	chr1D	87.873	1105	81	20	1	1075	415059624	415058543	0.000000e+00	1249.0
3	TraesCS1D01G321600	chr1D	86.239	654	58	13	1168	1817	415145634	415145009	0.000000e+00	680.0
4	TraesCS1D01G321600	chr1D	85.767	541	49	11	1262	1802	416986038	416986550	5.020000e-152	547.0
5	TraesCS1D01G321600	chr1D	91.304	368	32	0	1	368	414942655	414942288	1.100000e-138	503.0
6	TraesCS1D01G321600	chr1D	90.741	324	28	2	1	323	415039594	415039272	5.280000e-117	431.0
7	TraesCS1D01G321600	chr1D	82.561	453	47	10	641	1061	416985510	416985962	1.170000e-98	370.0
8	TraesCS1D01G321600	chr1D	85.546	339	46	3	2332	2668	272184810	272184473	4.230000e-93	351.0
9	TraesCS1D01G321600	chr1D	91.532	248	12	4	715	962	415146343	415146105	1.530000e-87	333.0
10	TraesCS1D01G321600	chr1A	89.738	2134	124	48	1	2120	511636840	511634788	0.000000e+00	2639.0
11	TraesCS1D01G321600	chr1A	89.648	1536	91	19	505	2031	512040383	512038907	0.000000e+00	1893.0
12	TraesCS1D01G321600	chr1A	84.504	897	64	15	1	846	511791253	511790381	0.000000e+00	817.0
13	TraesCS1D01G321600	chr1A	90.927	507	44	2	1	505	512040916	512040410	0.000000e+00	680.0
14	TraesCS1D01G321600	chr1A	90.722	485	45	0	779	1263	512018426	512017942	0.000000e+00	647.0
15	TraesCS1D01G321600	chr1A	86.552	580	57	12	1	560	512019105	512018527	1.050000e-173	619.0
16	TraesCS1D01G321600	chr1A	85.986	578	58	15	1247	1817	512461222	512460661	4.920000e-167	597.0
17	TraesCS1D01G321600	chr1A	85.397	541	53	11	1262	1802	514257466	514257980	3.020000e-149	538.0
18	TraesCS1D01G321600	chr1A	90.196	357	23	9	1702	2054	511784853	511784505	3.130000e-124	455.0
19	TraesCS1D01G321600	chr1A	82.540	441	48	10	641	1061	514256959	514257390	7.020000e-96	361.0
20	TraesCS1D01G321600	chr1A	91.393	244	18	1	954	1197	511789919	511789679	5.510000e-87	331.0
21	TraesCS1D01G321600	chr1A	93.258	178	12	0	2145	2322	512011609	512011432	2.040000e-66	263.0
22	TraesCS1D01G321600	chr1B	88.310	2053	149	37	1	2011	560789923	560787920	0.000000e+00	2377.0
23	TraesCS1D01G321600	chr1B	82.548	785	74	30	1168	1930	561157088	561156345	1.350000e-177	632.0
24	TraesCS1D01G321600	chr1B	86.056	502	48	13	1301	1802	563787783	563788262	1.090000e-143	520.0
25	TraesCS1D01G321600	chr1B	81.176	680	78	19	1247	1916	561256400	561255761	3.970000e-138	501.0
26	TraesCS1D01G321600	chr1B	83.626	342	55	1	2328	2668	175680794	175680453	1.190000e-83	320.0
27	TraesCS1D01G321600	chr1B	83.631	336	45	7	2333	2668	595541313	595540988	9.280000e-80	307.0
28	TraesCS1D01G321600	chr1B	80.482	456	39	27	641	1061	563787294	563787734	1.200000e-78	303.0
29	TraesCS1D01G321600	chr1B	79.911	448	42	16	641	1055	563847319	563847751	4.350000e-73	285.0
30	TraesCS1D01G321600	chr1B	81.518	303	28	17	2030	2321	560787699	560787414	9.610000e-55	224.0
31	TraesCS1D01G321600	chr1B	91.209	91	6	1	2029	2119	560786348	560786260	3.610000e-24	122.0
32	TraesCS1D01G321600	chr1B	90.164	61	5	1	436	495	561158142	561158082	7.920000e-11	78.7
33	TraesCS1D01G321600	chr1B	90.000	60	5	1	436	494	561257550	561257491	2.850000e-10	76.8
34	TraesCS1D01G321600	chr1B	96.970	33	1	0	530	562	563847190	563847222	3.710000e-04	56.5
35	TraesCS1D01G321600	chrUn	85.630	508	47	15	1299	1802	305658876	305659361	6.590000e-141	510.0
36	TraesCS1D01G321600	chrUn	83.871	279	28	12	235	503	305657927	305658198	1.590000e-62	250.0
37	TraesCS1D01G321600	chrUn	83.871	279	28	12	235	503	394107051	394106780	1.590000e-62	250.0
38	TraesCS1D01G321600	chr6D	88.095	336	40	0	2333	2668	392589948	392589613	1.490000e-107	399.0
39	TraesCS1D01G321600	chr7D	87.906	339	35	6	2333	2668	41749126	41748791	6.920000e-106	394.0
40	TraesCS1D01G321600	chr4D	85.163	337	48	2	2333	2668	66549137	66548802	7.070000e-91	344.0
41	TraesCS1D01G321600	chr4D	84.593	344	48	5	2326	2668	64403642	64403981	1.180000e-88	337.0
42	TraesCS1D01G321600	chr2B	84.457	341	50	3	2328	2668	545406159	545405822	1.530000e-87	333.0

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	TraesCS1D01G321600	chr1D	415051861	415054528	2667	True	4927.000000	4927	100.000000	1	2668	1	chr1D.!!$R3	2667
1	TraesCS1D01G321600	chr1D	414939818	414942655	2837	True	1952.500000	3402	92.269000	1	2668	2	chr1D.!!$R5	2667
2	TraesCS1D01G321600	chr1D	415058543	415059624	1081	True	1249.000000	1249	87.873000	1	1075	1	chr1D.!!$R4	1074
3	TraesCS1D01G321600	chr1D	415145009	415146343	1334	True	506.500000	680	88.885500	715	1817	2	chr1D.!!$R6	1102
4	TraesCS1D01G321600	chr1D	416985510	416986550	1040	False	458.500000	547	84.164000	641	1802	2	chr1D.!!$F1	1161
5	TraesCS1D01G321600	chr1A	511634788	511636840	2052	True	2639.000000	2639	89.738000	1	2120	1	chr1A.!!$R1	2119
6	TraesCS1D01G321600	chr1A	512038907	512040916	2009	True	1286.500000	1893	90.287500	1	2031	2	chr1A.!!$R7	2030
7	TraesCS1D01G321600	chr1A	512017942	512019105	1163	True	633.000000	647	88.637000	1	1263	2	chr1A.!!$R6	1262
8	TraesCS1D01G321600	chr1A	512460661	512461222	561	True	597.000000	597	85.986000	1247	1817	1	chr1A.!!$R4	570
9	TraesCS1D01G321600	chr1A	511789679	511791253	1574	True	574.000000	817	87.948500	1	1197	2	chr1A.!!$R5	1196
10	TraesCS1D01G321600	chr1A	514256959	514257980	1021	False	449.500000	538	83.968500	641	1802	2	chr1A.!!$F1	1161
11	TraesCS1D01G321600	chr1B	560786260	560789923	3663	True	907.666667	2377	87.012333	1	2321	3	chr1B.!!$R3	2320
12	TraesCS1D01G321600	chr1B	563787294	563788262	968	False	411.500000	520	83.269000	641	1802	2	chr1B.!!$F1	1161
13	TraesCS1D01G321600	chr1B	561156345	561158142	1797	True	355.350000	632	86.356000	436	1930	2	chr1B.!!$R4	1494
14	TraesCS1D01G321600	chr1B	561255761	561257550	1789	True	288.900000	501	85.588000	436	1916	2	chr1B.!!$R5	1480
15	TraesCS1D01G321600	chrUn	305657927	305659361	1434	False	380.000000	510	84.750500	235	1802	2	chrUn.!!$F1	1567

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
760	1072	0.321671	CAACTTCCTCTTCGGCTCCA	59.678	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2120	3657	0.040157	TGCAGCGAAGTTCATGCAAC	60.04	50.0	23.42	8.5	45.09	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
406	574	7.259882	TCTGTTTCTTGCCTAAATATTGCATG	58.740	34.615	0.29	3.54	34.51	4.06
442	622	5.537300	TGAGAAGATAGAATGGCTACACC	57.463	43.478	0.00	0.00	39.84	4.16
662	958	1.533033	TCCCGCCTCAGTTCTCACA	60.533	57.895	0.00	0.00	0.00	3.58
760	1072	0.321671	CAACTTCCTCTTCGGCTCCA	59.678	55.000	0.00	0.00	0.00	3.86
1175	2437	8.872845	CAGTTAACCAAGGCAAATATTCATTTC	58.127	33.333	0.88	0.00	31.82	2.17
1205	2471	6.095377	GCCAATTAACCAATCTTGTCTTCTG	58.905	40.000	0.00	0.00	0.00	3.02
1212	2478	2.746362	CAATCTTGTCTTCTGTCCTGCC	59.254	50.000	0.00	0.00	0.00	4.85
1235	2501	2.196749	CCCGTGTTGATCTTCTCGATG	58.803	52.381	11.45	0.00	30.84	3.84
1383	2661	4.828291	CGTAAGGTACGTGTATTGGTTG	57.172	45.455	0.00	0.00	46.41	3.77
1523	2810	2.446802	GCGGAGGGGAGGAAGGAT	60.447	66.667	0.00	0.00	0.00	3.24
1536	2823	0.250081	GAAGGATGTGCGGGAGATCC	60.250	60.000	16.52	16.52	36.63	3.36
1714	3016	1.269621	CCGGTCGTAGATCCATGAACC	60.270	57.143	0.00	0.00	40.67	3.62
2120	3657	2.644555	ATTTGCTCGTCGATCCGGGG	62.645	60.000	0.00	0.00	0.00	5.73
2122	3659	3.834799	GCTCGTCGATCCGGGGTT	61.835	66.667	0.00	0.00	0.00	4.11
2123	3660	2.104331	CTCGTCGATCCGGGGTTG	59.896	66.667	0.00	0.00	0.00	3.77
2124	3661	4.137872	TCGTCGATCCGGGGTTGC	62.138	66.667	0.00	0.00	0.00	4.17
2126	3663	2.189521	GTCGATCCGGGGTTGCAT	59.810	61.111	0.00	0.00	0.00	3.96
2127	3664	2.180204	GTCGATCCGGGGTTGCATG	61.180	63.158	0.00	0.00	0.00	4.06
2128	3665	2.189257	CGATCCGGGGTTGCATGA	59.811	61.111	0.00	0.00	0.00	3.07
2129	3666	1.451207	CGATCCGGGGTTGCATGAA	60.451	57.895	0.00	0.00	0.00	2.57
2130	3667	1.714899	CGATCCGGGGTTGCATGAAC	61.715	60.000	0.00	0.00	0.00	3.18
2132	3669	0.039618	ATCCGGGGTTGCATGAACTT	59.960	50.000	0.00	0.00	34.66	2.66
2135	3672	1.212751	GGGGTTGCATGAACTTCGC	59.787	57.895	0.00	0.00	34.66	4.70
2136	3673	1.244019	GGGGTTGCATGAACTTCGCT	61.244	55.000	0.00	0.00	34.66	4.93
2137	3674	0.109597	GGGTTGCATGAACTTCGCTG	60.110	55.000	0.00	0.00	34.66	5.18
2138	3675	0.730494	GGTTGCATGAACTTCGCTGC	60.730	55.000	0.00	8.51	34.66	5.25
2140	3677	0.883153	TTGCATGAACTTCGCTGCAT	59.117	45.000	15.67	0.00	43.51	3.96
2141	3678	0.169451	TGCATGAACTTCGCTGCATG	59.831	50.000	12.48	0.00	39.54	4.06
2142	3679	2.939782	CATGAACTTCGCTGCATGC	58.060	52.632	11.82	11.82	32.73	4.06
2143	3680	0.169451	CATGAACTTCGCTGCATGCA	59.831	50.000	21.29	21.29	43.06	3.96
2214	3767	2.999331	TGACTAATAAAGTGCCAGCCC	58.001	47.619	0.00	0.00	39.07	5.19
2256	3815	3.546724	TCCGATCCAAACAAGTGAACAA	58.453	40.909	0.00	0.00	0.00	2.83
2299	3858	0.108138	GTGCGTGATAAGTGAGGGCT	60.108	55.000	0.00	0.00	0.00	5.19
2331	3890	8.015658	ACACTAGACGCATACATTTTTCTTTTC	58.984	33.333	0.00	0.00	0.00	2.29
2359	3918	3.244044	TGAAAAAGAAGGCAAAATCCCCG	60.244	43.478	0.00	0.00	0.00	5.73
2366	3925	1.032114	GGCAAAATCCCCGACCTCTG	61.032	60.000	0.00	0.00	0.00	3.35
2396	3955	5.062528	TCGATGCATGCAACCATCTTATTA	58.937	37.500	26.68	0.00	36.55	0.98
2399	3958	6.142798	CGATGCATGCAACCATCTTATTAAAC	59.857	38.462	26.68	0.00	36.55	2.01
2451	4086	3.005791	GGGCCCATAATCATAGTGCAAAC	59.994	47.826	19.95	0.00	0.00	2.93
2452	4087	3.636300	GGCCCATAATCATAGTGCAAACA	59.364	43.478	0.00	0.00	0.00	2.83
2453	4088	4.281688	GGCCCATAATCATAGTGCAAACAT	59.718	41.667	0.00	0.00	0.00	2.71
2506	4141	1.284657	CAACAGAGCAGGCTACGATG	58.715	55.000	0.00	0.00	0.00	3.84
2529	4164	6.499436	TGCCTATACACCTAGCCTATTATCA	58.501	40.000	0.00	0.00	0.00	2.15
2532	4167	3.944055	ACACCTAGCCTATTATCAGCG	57.056	47.619	0.00	0.00	0.00	5.18
2624	4620	3.994317	TCCTGGAGTCCATATGAGTGAA	58.006	45.455	13.56	0.00	30.82	3.18
2630	4626	6.772605	TGGAGTCCATATGAGTGAATAATGG	58.227	40.000	8.12	0.00	0.00	3.16
2640	4636	4.141824	TGAGTGAATAATGGCCACATACGA	60.142	41.667	8.16	0.00	35.94	3.43
2653	4649	3.927758	CCACATACGAATCCACGTTGTAA	59.072	43.478	0.00	0.00	44.14	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
179	201	1.658114	CCTGTGACGGACGTCTTCA	59.342	57.895	23.18	19.49	44.80	3.02
368	534	9.584008	AGGCAAGAAACAGATCATATATGAAAT	57.416	29.630	19.03	8.19	40.69	2.17
406	574	5.549742	ATCTTCTCATGATCTTCACCTCC	57.450	43.478	0.00	0.00	0.00	4.30
442	622	4.457496	ACCCGCTCCGCTCATGTG	62.457	66.667	0.00	0.00	0.00	3.21
655	942	2.280524	CGGGTGGCGTTGTGAGAA	60.281	61.111	0.00	0.00	0.00	2.87
699	995	0.399091	AGAGGGGAAGATGGCGATCA	60.399	55.000	11.55	0.00	0.00	2.92
889	1216	4.020617	CTTCCTGAGCGGCACCCA	62.021	66.667	1.45	0.00	0.00	4.51
1212	2478	1.079127	AGAAGATCAACACGGGCGG	60.079	57.895	0.00	0.00	0.00	6.13
1383	2661	1.081175	GAGCTTTGCAAACGCCTCC	60.081	57.895	21.98	12.67	0.00	4.30
1523	2810	0.904865	AGAACTGGATCTCCCGCACA	60.905	55.000	0.00	0.00	37.93	4.57
1536	2823	0.818296	ATCCTCGTCGGGAAGAACTG	59.182	55.000	0.00	0.00	39.02	3.16
1732	3038	6.815142	GCTCCAGAAATGACAAGCATTAATTT	59.185	34.615	0.00	0.00	46.25	1.82
2120	3657	0.040157	TGCAGCGAAGTTCATGCAAC	60.040	50.000	23.42	8.50	45.09	4.17
2121	3658	2.329244	TGCAGCGAAGTTCATGCAA	58.671	47.368	23.42	11.81	45.09	4.08
2122	3659	4.061949	TGCAGCGAAGTTCATGCA	57.938	50.000	22.37	22.37	45.82	3.96
2123	3660	2.939782	CATGCAGCGAAGTTCATGC	58.060	52.632	18.60	18.60	39.14	4.06
2124	3661	2.939782	GCATGCAGCGAAGTTCATG	58.060	52.632	14.21	2.32	39.29	3.07
2135	3672	6.312672	TCATTGATTTCAGAAATTGCATGCAG	59.687	34.615	21.50	8.30	0.00	4.41
2136	3673	6.166982	TCATTGATTTCAGAAATTGCATGCA	58.833	32.000	18.46	18.46	0.00	3.96
2137	3674	6.656314	TCATTGATTTCAGAAATTGCATGC	57.344	33.333	11.82	11.82	0.00	4.06
2138	3675	8.878769	TCATTCATTGATTTCAGAAATTGCATG	58.121	29.630	9.84	10.09	0.00	4.06
2140	3677	8.714179	GTTCATTCATTGATTTCAGAAATTGCA	58.286	29.630	9.84	1.84	33.34	4.08
2141	3678	8.932791	AGTTCATTCATTGATTTCAGAAATTGC	58.067	29.630	9.84	0.00	33.34	3.56
2214	3767	1.670406	GGACAGAGCAGCAGTGGTG	60.670	63.158	18.01	18.01	33.41	4.17
2354	3913	0.982852	ATTGATGCAGAGGTCGGGGA	60.983	55.000	0.00	0.00	0.00	4.81
2506	4141	6.461788	GCTGATAATAGGCTAGGTGTATAGGC	60.462	46.154	0.00	0.00	46.02	3.93
2529	4164	2.404789	CGATTTGAATGGCGCGCT	59.595	55.556	32.29	11.92	0.00	5.92
2603	4599	3.688049	TCACTCATATGGACTCCAGGA	57.312	47.619	3.62	0.83	36.75	3.86
2624	4620	4.072131	GTGGATTCGTATGTGGCCATTAT	58.928	43.478	9.72	9.88	32.29	1.28
2630	4626	1.062002	CAACGTGGATTCGTATGTGGC	59.938	52.381	0.00	0.00	43.38	5.01
2640	4636	5.717078	TCTACAGAGTTACAACGTGGATT	57.283	39.130	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.