AutoCloner

Multiple sequence alignment - TraesCS4B01G299200

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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	TraesCS4B01G299200	chr4B	100.000	5003	0	0	1	5003	585469993	585464991	0.000000e+00	9239
1	TraesCS4B01G299200	chr4B	96.830	757	24	0	3	759	434847182	434847938	0.000000e+00	1266
2	TraesCS4B01G299200	chr4B	93.617	94	4	2	751	843	666599934	666599842	6.750000e-29	139
3	TraesCS4B01G299200	chr4D	92.364	2737	147	32	1632	4324	467441422	467438704	0.000000e+00	3840
4	TraesCS4B01G299200	chr4D	89.925	804	57	14	841	1634	467442239	467441450	0.000000e+00	1014
5	TraesCS4B01G299200	chr4D	94.236	399	11	3	4615	5003	467438211	467437815	2.580000e-167	599
6	TraesCS4B01G299200	chr4A	92.389	2641	141	26	1632	4237	3442844	3445459	0.000000e+00	3709
7	TraesCS4B01G299200	chr4A	91.650	503	26	6	4516	5003	3445815	3446316	0.000000e+00	682
8	TraesCS4B01G299200	chr4A	92.708	384	20	4	841	1220	3442017	3442396	9.470000e-152	547
9	TraesCS4B01G299200	chr4A	92.308	234	14	1	1221	1450	3442429	3442662	3.730000e-86	329
10	TraesCS4B01G299200	chr4A	93.421	152	6	2	1485	1634	3442665	3442814	6.520000e-54	222
11	TraesCS4B01G299200	chr1B	97.124	765	17	5	1	763	372696286	372695525	0.000000e+00	1286
12	TraesCS4B01G299200	chr3A	96.706	759	25	0	1	759	281431556	281430798	0.000000e+00	1264
13	TraesCS4B01G299200	chr3A	93.617	94	4	2	751	843	728326312	728326220	6.750000e-29	139
14	TraesCS4B01G299200	chr2A	96.697	757	23	2	1	757	438818784	438819538	0.000000e+00	1258
15	TraesCS4B01G299200	chr2A	96.574	759	24	2	1	759	245805403	245804647	0.000000e+00	1256
16	TraesCS4B01G299200	chr2A	96.570	758	24	2	1	757	769854850	769855606	0.000000e+00	1254
17	TraesCS4B01G299200	chr2A	92.903	155	11	0	4849	5003	231290835	231290989	5.040000e-55	226
18	TraesCS4B01G299200	chr2A	94.068	118	7	0	4886	5003	121215763	121215880	3.980000e-41	180
19	TraesCS4B01G299200	chr2B	96.570	758	25	1	1	757	265337904	265337147	0.000000e+00	1254
20	TraesCS4B01G299200	chr2B	96.204	764	26	2	1	762	575301849	575301087	0.000000e+00	1247
21	TraesCS4B01G299200	chr2B	94.068	118	7	0	4886	5003	171453266	171453383	3.980000e-41	180
22	TraesCS4B01G299200	chr5B	96.073	764	27	3	1	763	674036737	674035976	0.000000e+00	1242
23	TraesCS4B01G299200	chr5B	93.548	93	5	1	751	843	874157	874066	2.430000e-28	137
24	TraesCS4B01G299200	chr5B	92.708	96	5	2	751	846	508800900	508800807	2.430000e-28	137
25	TraesCS4B01G299200	chr6D	96.129	155	6	0	4849	5003	450739114	450739268	2.310000e-63	254
26	TraesCS4B01G299200	chr7A	95.484	155	7	0	4849	5003	641827478	641827324	1.080000e-61	248
27	TraesCS4B01G299200	chr7B	93.464	153	10	0	4849	5001	707684876	707684724	1.400000e-55	228
28	TraesCS4B01G299200	chr2D	94.068	118	7	0	4886	5003	119263196	119263313	3.980000e-41	180
29	TraesCS4B01G299200	chr2D	91.919	99	7	1	751	848	14756697	14756599	2.430000e-28	137
30	TraesCS4B01G299200	chr2D	92.632	95	7	0	751	845	558189855	558189949	2.430000e-28	137
31	TraesCS4B01G299200	chrUn	94.565	92	4	1	751	842	15545192	15545282	1.880000e-29	141
32	TraesCS4B01G299200	chr3D	94.505	91	4	1	751	841	43660517	43660606	6.750000e-29	139
33	TraesCS4B01G299200	chr1A	93.617	94	5	1	751	844	561376672	561376580	6.750000e-29	139

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	TraesCS4B01G299200	chr4B	585464991	585469993	5002	True	9239.000000	9239	100.0000	1	5003	1	chr4B.!!$R1	5002
1	TraesCS4B01G299200	chr4B	434847182	434847938	756	False	1266.000000	1266	96.8300	3	759	1	chr4B.!!$F1	756
2	TraesCS4B01G299200	chr4D	467437815	467442239	4424	True	1817.666667	3840	92.1750	841	5003	3	chr4D.!!$R1	4162
3	TraesCS4B01G299200	chr4A	3442017	3446316	4299	False	1097.800000	3709	92.4952	841	5003	5	chr4A.!!$F1	4162
4	TraesCS4B01G299200	chr1B	372695525	372696286	761	True	1286.000000	1286	97.1240	1	763	1	chr1B.!!$R1	762
5	TraesCS4B01G299200	chr3A	281430798	281431556	758	True	1264.000000	1264	96.7060	1	759	1	chr3A.!!$R1	758
6	TraesCS4B01G299200	chr2A	438818784	438819538	754	False	1258.000000	1258	96.6970	1	757	1	chr2A.!!$F3	756
7	TraesCS4B01G299200	chr2A	245804647	245805403	756	True	1256.000000	1256	96.5740	1	759	1	chr2A.!!$R1	758
8	TraesCS4B01G299200	chr2A	769854850	769855606	756	False	1254.000000	1254	96.5700	1	757	1	chr2A.!!$F4	756
9	TraesCS4B01G299200	chr2B	265337147	265337904	757	True	1254.000000	1254	96.5700	1	757	1	chr2B.!!$R1	756
10	TraesCS4B01G299200	chr2B	575301087	575301849	762	True	1247.000000	1247	96.2040	1	762	1	chr2B.!!$R2	761
11	TraesCS4B01G299200	chr5B	674035976	674036737	761	True	1242.000000	1242	96.0730	1	763	1	chr5B.!!$R3	762

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
794	802	0.106149	GTACCCTAGCCGGTTGATGG	59.894	60.000	1.90	1.87	37.34	3.51	F
1265	1311	0.533308	TCCGTGGTTGGTTGTGCTAC	60.533	55.000	0.00	0.00	0.00	3.58	F
1452	1502	0.899720	TGCCCGGAGTAGTAAACCTG	59.100	55.000	0.73	0.00	0.00	4.00	F
2022	2109	1.616865	TCGCTAGCCGTATTATGCCTT	59.383	47.619	9.66	0.00	38.35	4.35	F
3835	3971	1.523758	GCAACGAGTTCAATCACCCT	58.476	50.000	0.00	0.00	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2703	2821	0.104487	TCCACGTAACGGCAGAACAA	59.896	50.000	0.00	2.83	R
2983	3101	0.037326	TACTGCCAACGAAGCTCCAG	60.037	55.000	0.00	3.86	R
3023	3141	2.093500	TCACCAGCACTTATACTGCCAG	60.093	50.000	35.01	4.85	R
3856	3992	0.033504	GCTCGAAGGGAACTGTGTCA	59.966	55.000	42.68	3.58	R
4660	5205	2.582978	GACCGGCCCAGGTTACTC	59.417	66.667	46.09	2.59	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
172	173	7.790823	TTAAACTACCCGAGGTAATTAATGC	57.209	36.000	4.63	37.76	3.56
529	537	4.942761	ACAATGCTTTTGTCCTGAATGT	57.057	36.364	0.47	0.00	2.71
707	715	5.357257	ACTGAGCAAGTTCGAAAAGTAAGA	58.643	37.500	0.00	34.57	2.10
763	771	7.606073	GGTAAAAATGCAATTGTCCCTTGTAAT	59.394	33.333	7.40	36.10	1.89
764	772	8.998377	GTAAAAATGCAATTGTCCCTTGTAATT	58.002	29.630	7.40	36.10	1.40
765	773	8.462589	AAAAATGCAATTGTCCCTTGTAATTT	57.537	26.923	7.40	36.10	1.82
766	774	9.566432	AAAAATGCAATTGTCCCTTGTAATTTA	57.434	25.926	7.40	36.10	1.40
767	775	8.776376	AAATGCAATTGTCCCTTGTAATTTAG	57.224	30.769	7.40	36.10	1.85
768	776	5.719173	TGCAATTGTCCCTTGTAATTTAGC	58.281	37.500	7.40	0.00	3.09
769	777	5.244851	TGCAATTGTCCCTTGTAATTTAGCA	59.755	36.000	7.40	0.00	3.49
770	778	5.576774	GCAATTGTCCCTTGTAATTTAGCAC	59.423	40.000	7.40	0.00	4.40
771	779	5.914898	ATTGTCCCTTGTAATTTAGCACC	57.085	39.130	0.00	0.00	5.01
772	780	4.374689	TGTCCCTTGTAATTTAGCACCA	57.625	40.909	0.00	0.00	4.17
773	781	4.929479	TGTCCCTTGTAATTTAGCACCAT	58.071	39.130	0.00	0.00	3.55
774	782	5.329399	TGTCCCTTGTAATTTAGCACCATT	58.671	37.500	0.00	0.00	3.16
775	783	5.184864	TGTCCCTTGTAATTTAGCACCATTG	59.815	40.000	0.00	0.00	2.82
776	784	5.185056	GTCCCTTGTAATTTAGCACCATTGT	59.815	40.000	0.00	0.00	2.71
777	785	6.376018	GTCCCTTGTAATTTAGCACCATTGTA	59.624	38.462	0.00	0.00	2.41
778	786	6.376018	TCCCTTGTAATTTAGCACCATTGTAC	59.624	38.462	0.00	0.00	2.90
779	787	6.405397	CCCTTGTAATTTAGCACCATTGTACC	60.405	42.308	0.00	0.00	3.34
780	788	6.405397	CCTTGTAATTTAGCACCATTGTACCC	60.405	42.308	0.00	0.00	3.69
781	789	5.822204	TGTAATTTAGCACCATTGTACCCT	58.178	37.500	0.00	0.00	4.34
782	790	6.959904	TGTAATTTAGCACCATTGTACCCTA	58.040	36.000	0.00	0.00	3.53
783	791	7.051623	TGTAATTTAGCACCATTGTACCCTAG	58.948	38.462	0.00	0.00	3.02
784	792	3.553828	TTAGCACCATTGTACCCTAGC	57.446	47.619	0.00	0.00	3.42

Showing 1 to 25 of 191 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
104	105	5.221481	TGCAAATGATATGCCCATAAAGGTG	60.221	40.000	0.00	0.00	43.16	4.00
497	505	6.981559	GGACAAAAGCATTGTTTAAACTACCA	59.018	34.615	18.72	1.82	31.96	3.25
529	537	9.821240	ACATTACCTTTATGGGCATATCATTTA	57.179	29.630	0.00	0.00	41.11	1.40
615	623	7.097834	ACCGTTTGACCAAAACTTTGAAAATA	58.902	30.769	3.72	0.00	45.10	1.40
763	771	3.371166	GGCTAGGGTACAATGGTGCTAAA	60.371	47.826	0.00	0.00	0.00	1.85
764	772	2.171870	GGCTAGGGTACAATGGTGCTAA	59.828	50.000	0.00	0.00	0.00	3.09
765	773	1.766496	GGCTAGGGTACAATGGTGCTA	59.234	52.381	0.00	0.00	0.00	3.49
766	774	0.546598	GGCTAGGGTACAATGGTGCT	59.453	55.000	0.00	0.00	0.00	4.40
767	775	0.814010	CGGCTAGGGTACAATGGTGC	60.814	60.000	0.00	0.00	0.00	5.01
768	776	0.179056	CCGGCTAGGGTACAATGGTG	60.179	60.000	0.00	0.00	35.97	4.17
769	777	0.619543	ACCGGCTAGGGTACAATGGT	60.620	55.000	0.00	0.00	46.96	3.55
770	778	0.544697	AACCGGCTAGGGTACAATGG	59.455	55.000	0.00	0.00	46.96	3.16
771	779	1.208535	TCAACCGGCTAGGGTACAATG	59.791	52.381	0.00	0.00	46.96	2.82
772	780	1.575419	TCAACCGGCTAGGGTACAAT	58.425	50.000	0.00	0.00	46.96	2.71
773	781	1.208535	CATCAACCGGCTAGGGTACAA	59.791	52.381	0.00	0.00	46.96	2.41
774	782	0.828022	CATCAACCGGCTAGGGTACA	59.172	55.000	0.00	0.00	46.96	2.90
775	783	0.106149	CCATCAACCGGCTAGGGTAC	59.894	60.000	0.00	0.00	46.96	3.34
776	784	1.692173	GCCATCAACCGGCTAGGGTA	61.692	60.000	0.00	0.00	46.56	3.69
777	785	3.043999	GCCATCAACCGGCTAGGGT	62.044	63.158	0.00	0.00	46.56	4.34
778	786	2.203209	GCCATCAACCGGCTAGGG	60.203	66.667	0.00	0.00	46.56	3.53
784	792	4.654091	AATTAATGAAGCCATCAACCGG	57.346	40.909	0.00	0.00	42.54	5.28
785	793	5.649557	TCAAATTAATGAAGCCATCAACCG	58.350	37.500	0.00	0.00	42.54	4.44
786	794	7.529880	CTTCAAATTAATGAAGCCATCAACC	57.470	36.000	6.89	0.00	46.88	3.77
796	804	6.128391	CGAAGGTCCGACTTCAAATTAATGAA	60.128	38.462	12.63	0.00	45.54	2.57
797	805	5.350365	CGAAGGTCCGACTTCAAATTAATGA	59.650	40.000	12.63	0.00	45.54	2.57

Showing 1 to 25 of 166 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.