AutoCloner

Multiple sequence alignment - TraesCS4A01G055200

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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	TraesCS4A01G055200	chr4A	100.000	2366	0	0	1	2366	46214300	46216665	0.000000e+00	4370.0
1	TraesCS4A01G055200	chr4B	87.167	1278	108	30	777	2026	515066601	515065352	0.000000e+00	1400.0
2	TraesCS4A01G055200	chr5B	98.579	774	11	0	1	774	662060600	662059827	0.000000e+00	1369.0
3	TraesCS4A01G055200	chr2A	98.579	774	11	0	1	774	672822065	672822838	0.000000e+00	1369.0
4	TraesCS4A01G055200	chr2A	98.065	775	13	2	1	774	675483466	675482693	0.000000e+00	1347.0
5	TraesCS4A01G055200	chr6B	97.933	774	11	3	1	774	299093233	299092465	0.000000e+00	1336.0
6	TraesCS4A01G055200	chr6B	97.545	774	17	2	1	774	370666116	370665345	0.000000e+00	1323.0
7	TraesCS4A01G055200	chr2B	97.806	775	15	2	1	774	587101454	587102227	0.000000e+00	1336.0
8	TraesCS4A01G055200	chr1A	97.806	775	16	1	1	774	57690737	57689963	0.000000e+00	1336.0
9	TraesCS4A01G055200	chr1A	96.377	138	5	0	2226	2363	263857111	263857248	6.580000e-56	228.0
10	TraesCS4A01G055200	chr1A	96.992	133	3	1	2235	2366	404855109	404854977	3.060000e-54	222.0
11	TraesCS4A01G055200	chr3B	97.419	775	18	2	1	774	737775891	737775118	0.000000e+00	1319.0
12	TraesCS4A01G055200	chr3A	97.419	775	18	2	1	774	521945316	521946089	0.000000e+00	1319.0
13	TraesCS4A01G055200	chr3A	97.761	134	3	0	2233	2366	61406110	61405977	5.090000e-57	231.0
14	TraesCS4A01G055200	chr3A	97.727	132	3	0	2235	2366	535564865	535564734	6.580000e-56	228.0
15	TraesCS4A01G055200	chr3A	96.970	132	4	0	2235	2366	621957559	621957428	3.060000e-54	222.0
16	TraesCS4A01G055200	chr4D	90.416	793	52	11	896	1673	418850702	418851485	0.000000e+00	1022.0
17	TraesCS4A01G055200	chr4D	93.220	59	4	0	800	858	418850642	418850700	1.160000e-13	87.9
18	TraesCS4A01G055200	chr6A	97.122	139	3	1	2225	2363	457033845	457033982	1.410000e-57	233.0
19	TraesCS4A01G055200	chr7A	97.744	133	3	0	2231	2363	121308668	121308800	1.830000e-56	230.0
20	TraesCS4A01G055200	chr7A	97.744	133	3	0	2234	2366	667600672	667600540	1.830000e-56	230.0
21	TraesCS4A01G055200	chr5A	95.172	145	5	2	2223	2366	298567977	298567834	6.580000e-56	228.0

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	TraesCS4A01G055200	chr4A	46214300	46216665	2365	False	4370.00	4370	100.000	1	2366	1	chr4A.!!$F1	2365
1	TraesCS4A01G055200	chr4B	515065352	515066601	1249	True	1400.00	1400	87.167	777	2026	1	chr4B.!!$R1	1249
2	TraesCS4A01G055200	chr5B	662059827	662060600	773	True	1369.00	1369	98.579	1	774	1	chr5B.!!$R1	773
3	TraesCS4A01G055200	chr2A	672822065	672822838	773	False	1369.00	1369	98.579	1	774	1	chr2A.!!$F1	773
4	TraesCS4A01G055200	chr2A	675482693	675483466	773	True	1347.00	1347	98.065	1	774	1	chr2A.!!$R1	773
5	TraesCS4A01G055200	chr6B	299092465	299093233	768	True	1336.00	1336	97.933	1	774	1	chr6B.!!$R1	773
6	TraesCS4A01G055200	chr6B	370665345	370666116	771	True	1323.00	1323	97.545	1	774	1	chr6B.!!$R2	773
7	TraesCS4A01G055200	chr2B	587101454	587102227	773	False	1336.00	1336	97.806	1	774	1	chr2B.!!$F1	773
8	TraesCS4A01G055200	chr1A	57689963	57690737	774	True	1336.00	1336	97.806	1	774	1	chr1A.!!$R1	773
9	TraesCS4A01G055200	chr3B	737775118	737775891	773	True	1319.00	1319	97.419	1	774	1	chr3B.!!$R1	773
10	TraesCS4A01G055200	chr3A	521945316	521946089	773	False	1319.00	1319	97.419	1	774	1	chr3A.!!$F1	773
11	TraesCS4A01G055200	chr4D	418850642	418851485	843	False	554.95	1022	91.818	800	1673	2	chr4D.!!$F1	873

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
862	869	0.249741	ACGTGGGACTCCAACGAAAG	60.25	55.0	28.55	3.08	46.04	2.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2048	2096	0.036875	CCCCGAGCTCTCCTTTTGTT	59.963	55.0	12.85	0.0	0.0	2.83	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	Self end TH	Hairpin	End Stability
683	690	8.816894	TCACTAATTATCAAGAAGTGTTCTCCT	58.183	33.333	0.00	0.00	39.61	3.69
746	753	2.628178	ACGTGATGATCGGGTGTGATAT	59.372	45.455	0.00	0.00	0.00	1.63
774	781	2.657184	GTTCAAATACAACGGGTGCAC	58.343	47.619	8.80	8.80	0.00	4.57
775	782	0.869068	TCAAATACAACGGGTGCACG	59.131	50.000	11.45	2.44	40.31	5.34
788	795	2.550606	GGGTGCACGACAAATTCTGTTA	59.449	45.455	11.45	0.00	38.84	2.41
791	798	4.083537	GGTGCACGACAAATTCTGTTATCA	60.084	41.667	11.45	0.00	38.84	2.15
795	802	6.636447	TGCACGACAAATTCTGTTATCAAAAG	59.364	34.615	0.00	0.00	38.84	2.27
841	848	4.142902	CGTACATGACATCCAAGTTTCCAC	60.143	45.833	0.00	0.00	0.00	4.02
846	853	3.070446	TGACATCCAAGTTTCCACTACGT	59.930	43.478	0.00	0.00	30.68	3.57
859	866	0.538057	ACTACGTGGGACTCCAACGA	60.538	55.000	28.55	12.93	46.04	3.85
862	869	0.249741	ACGTGGGACTCCAACGAAAG	60.250	55.000	28.55	3.08	46.04	2.62
863	870	1.566018	CGTGGGACTCCAACGAAAGC	61.566	60.000	19.00	0.00	46.04	3.51
864	871	0.534203	GTGGGACTCCAACGAAAGCA	60.534	55.000	0.00	0.00	46.04	3.91
918	935	5.860941	TTATCGCTCTTCCTTTCTCTCAT	57.139	39.130	0.00	0.00	0.00	2.90
919	936	3.791973	TCGCTCTTCCTTTCTCTCATC	57.208	47.619	0.00	0.00	0.00	2.92
920	937	3.360867	TCGCTCTTCCTTTCTCTCATCT	58.639	45.455	0.00	0.00	0.00	2.90
921	938	3.380004	TCGCTCTTCCTTTCTCTCATCTC	59.620	47.826	0.00	0.00	0.00	2.75
922	939	3.130164	CGCTCTTCCTTTCTCTCATCTCA	59.870	47.826	0.00	0.00	0.00	3.27
974	997	1.185315	CCAACAACACCCCATCCATC	58.815	55.000	0.00	0.00	0.00	3.51
975	998	1.272648	CCAACAACACCCCATCCATCT	60.273	52.381	0.00	0.00	0.00	2.90
976	999	2.025416	CCAACAACACCCCATCCATCTA	60.025	50.000	0.00	0.00	0.00	1.98
977	1000	3.016736	CAACAACACCCCATCCATCTAC	58.983	50.000	0.00	0.00	0.00	2.59
1003	1026	9.615067	CTTGAAAAGGACGAGAGTTGAGAATGC	62.615	44.444	0.00	0.00	40.81	3.56
1126	1149	0.248784	ATACGAGTCGCTTAACGCCC	60.249	55.000	13.59	0.00	43.23	6.13
1257	1280	2.541120	GCTGCGCATCCTCATGGAC	61.541	63.158	12.24	0.00	46.51	4.02

Showing 1 to 25 of 367 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
357	361	0.833287	AGCGACAACCATATGGCTCT	59.167	50.000	22.18	3.63	39.32	4.09
746	753	3.676172	CCGTTGTATTTGAACGTAGAGCA	59.324	43.478	0.00	0.00	43.70	4.26
774	781	8.970691	AATCCTTTTGATAACAGAATTTGTCG	57.029	30.769	0.00	0.00	33.34	4.35
841	848	0.599558	TTCGTTGGAGTCCCACGTAG	59.400	55.000	28.95	7.84	43.41	3.51
846	853	0.181587	TTGCTTTCGTTGGAGTCCCA	59.818	50.000	6.74	0.00	41.64	4.37
875	883	1.871039	TCTTTGCGTAGTTGTGCCTTC	59.129	47.619	0.00	0.00	0.00	3.46
879	887	4.263800	CGATAATCTTTGCGTAGTTGTGC	58.736	43.478	0.00	0.00	0.00	4.57
888	905	3.126831	AGGAAGAGCGATAATCTTTGCG	58.873	45.455	0.00	0.00	37.14	4.85
940	957	0.743097	GTTGGATCTTGGCTGGATGC	59.257	55.000	0.00	5.26	41.94	3.91
974	997	5.529791	TCAACTCTCGTCCTTTTCAAGTAG	58.470	41.667	0.00	0.00	0.00	2.57
975	998	5.301045	TCTCAACTCTCGTCCTTTTCAAGTA	59.699	40.000	0.00	0.00	0.00	2.24
976	999	4.099573	TCTCAACTCTCGTCCTTTTCAAGT	59.900	41.667	0.00	0.00	0.00	3.16
977	1000	4.621991	TCTCAACTCTCGTCCTTTTCAAG	58.378	43.478	0.00	0.00	0.00	3.02
989	1012	2.688507	TGAACGGCATTCTCAACTCTC	58.311	47.619	0.00	0.00	38.25	3.20
990	1013	2.839486	TGAACGGCATTCTCAACTCT	57.161	45.000	0.00	0.00	38.25	3.24
1021	1044	3.878519	GACGGCGGTCGAGAGGAG	61.879	72.222	9.82	0.00	42.43	3.69
1059	1082	3.710722	CTGAAGCTGGCCGACCCT	61.711	66.667	0.00	0.00	33.59	4.34
1061	1084	4.785453	CCCTGAAGCTGGCCGACC	62.785	72.222	0.00	0.00	0.00	4.79
1203	1226	3.316573	CTCCGGGACCTTGGACAGC	62.317	68.421	0.00	0.00	0.00	4.40
1257	1280	2.383855	CCCTCCTTAGTCACTCTCCTG	58.616	57.143	0.00	0.00	0.00	3.86
1258	1281	1.342574	GCCCTCCTTAGTCACTCTCCT	60.343	57.143	0.00	0.00	0.00	3.69
1278	1301	4.335647	AGGCTGCCCTTGACCACG	62.336	66.667	16.57	0.00	38.74	4.94
1284	1307	1.378250	CTGAAGGAGGCTGCCCTTG	60.378	63.158	16.57	0.00	43.59	3.61
1312	1335	1.808945	CCTCGTCAGCTTTTTGCATCT	59.191	47.619	0.00	0.00	45.94	2.90
1324	1347	0.526524	GCGATGAACTCCCTCGTCAG	60.527	60.000	0.00	0.00	34.96	3.51

Showing 1 to 25 of 365 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.