AutoCloner

Multiple sequence alignment - TraesCS3A01G520700

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	TraesCS3A01G520700	chr3A	100.000	2867	0	0	1	2867	737479098	737476232	0.000000e+00	5295.0
1	TraesCS3A01G520700	chr3B	94.023	2794	118	17	83	2867	815357405	815360158	0.000000e+00	4189.0
2	TraesCS3A01G520700	chr3B	93.973	2356	102	17	83	2406	815275515	815273168	0.000000e+00	3528.0
3	TraesCS3A01G520700	chr3B	95.392	434	18	1	2434	2867	815273166	815272735	0.000000e+00	689.0
4	TraesCS3A01G520700	chr3D	94.973	2069	86	7	1	2068	606634163	606632112	0.000000e+00	3229.0
5	TraesCS3A01G520700	chr3D	96.650	806	20	6	2062	2867	606628285	606627487	0.000000e+00	1332.0
6	TraesCS3A01G520700	chr7D	93.878	49	3	0	1919	1967	264057421	264057373	1.100000e-09	75.0
7	TraesCS3A01G520700	chrUn	92.308	52	2	2	1910	1961	87231337	87231386	3.960000e-09	73.1
8	TraesCS3A01G520700	chr7B	97.674	43	0	1	1919	1961	585987193	585987152	3.960000e-09	73.1
9	TraesCS3A01G520700	chr6B	97.561	41	1	0	1921	1961	181126795	181126755	1.430000e-08	71.3
10	TraesCS3A01G520700	chr1A	89.286	56	2	4	1910	1964	101274487	101274435	1.840000e-07	67.6
11	TraesCS3A01G520700	chr5D	91.837	49	1	3	1913	1961	268927840	268927885	6.630000e-07	65.8

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	TraesCS3A01G520700	chr3A	737476232	737479098	2866	True	5295.0	5295	100.0000	1	2867	1	chr3A.!!$R1	2866
1	TraesCS3A01G520700	chr3B	815357405	815360158	2753	False	4189.0	4189	94.0230	83	2867	1	chr3B.!!$F1	2784
2	TraesCS3A01G520700	chr3B	815272735	815275515	2780	True	2108.5	3528	94.6825	83	2867	2	chr3B.!!$R1	2784
3	TraesCS3A01G520700	chr3D	606627487	606634163	6676	True	2280.5	3229	95.8115	1	2867	2	chr3D.!!$R1	2866

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
248	252	0.03467	GGACTTCCTGCAGCTGGAAT	60.035	55.0	28.55	19.89	39.91	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2178	6052	0.107897	GGCCACCATGTATGTCACGA	60.108	55.0	0.0	0.0	0.0	4.35	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
102	103	1.592669	CGGCGCTATGTGGGAGAAG	60.593	63.158	7.64	0.00	0.00	2.85
118	122	1.068194	AGAAGAGTTTGGCGACGAGAG	60.068	52.381	0.00	0.00	0.00	3.20
241	245	2.485124	GGATCTGATGGACTTCCTGCAG	60.485	54.545	6.78	6.78	38.40	4.41
248	252	0.034670	GGACTTCCTGCAGCTGGAAT	60.035	55.000	28.55	19.89	39.91	3.01
301	332	0.822532	AGTTGCTGCTGCTGCTTCTT	60.823	50.000	27.67	11.45	40.48	2.52
305	336	0.877071	GCTGCTGCTGCTTCTTTACA	59.123	50.000	22.10	0.00	40.48	2.41
357	391	2.095110	TCATCGTGCAATGCCAAAGAAG	60.095	45.455	1.53	0.00	0.00	2.85
383	417	1.720301	CCATCAGCAGAGAAAGCGC	59.280	57.895	0.00	0.00	37.01	5.92
453	487	0.251077	AAGAGAAGGCCAACTGCAGG	60.251	55.000	19.93	1.68	43.89	4.85
462	496	1.000938	GCCAACTGCAGGAAACAAGAG	60.001	52.381	19.93	0.00	40.77	2.85
503	537	2.957474	AGTCTTCAGGGAGAGGCTATC	58.043	52.381	0.00	0.00	0.00	2.08
600	635	2.618709	CGAGCTTTTCCTTGTTGGTCTT	59.381	45.455	0.00	0.00	37.07	3.01
653	688	3.411517	CCAGAACGGGGGCAGGAT	61.412	66.667	0.00	0.00	0.00	3.24
655	690	1.447643	CAGAACGGGGGCAGGATAG	59.552	63.158	0.00	0.00	0.00	2.08
982	1017	3.674138	GCAACCGAGCATCAACATTCAAT	60.674	43.478	0.00	0.00	33.17	2.57
1068	1103	6.154363	CAGGTCTTGAGAAGATCCCTATATCC	59.846	46.154	0.00	0.00	39.53	2.59
1107	1142	3.140814	GAGGCCCCGGCAACATTC	61.141	66.667	8.23	0.00	44.11	2.67
1159	1194	4.219725	GGAAGTATCAGCTAGATCCTCCAC	59.780	50.000	0.00	0.00	38.19	4.02
1170	1205	1.838073	ATCCTCCACCGGGTTGTGAC	61.838	60.000	6.32	0.00	38.55	3.67
1258	1293	2.525368	TCAGAAAGATCGGTGGTCTCA	58.475	47.619	0.00	0.00	0.00	3.27
1317	1352	1.662044	CAAGTGCCCTCCAACTTGC	59.338	57.895	2.90	0.00	34.15	4.01
1419	1454	4.070009	GCCTTGATTTTATACCTACGGGG	58.930	47.826	0.00	0.00	41.89	5.73
1685	1720	7.363205	ACCTTTTCACACAAAATGTTCTTTG	57.637	32.000	0.00	0.00	40.64	2.77
1726	1761	2.362736	TGCCTCACATCATGCTCTTTC	58.637	47.619	0.00	0.00	0.00	2.62
1759	1794	3.685139	TTCAGCCTCTTGAACCACTAG	57.315	47.619	0.00	0.00	32.39	2.57
1842	1877	1.863454	CGATGCTTATGTGGCTCTGTC	59.137	52.381	0.00	0.00	0.00	3.51
1850	1885	1.735920	GTGGCTCTGTCGAGTGCAG	60.736	63.158	0.00	0.00	39.95	4.41
2091	5965	5.010922	TCTGGCATACAAAATTCTTGCACTT	59.989	36.000	0.00	0.00	35.04	3.16
2152	6026	9.909043	ATTTACACAATTTTTGTTTCTTAACGC	57.091	25.926	0.00	0.00	43.23	4.84
2262	6137	6.550938	TGACCATCTATCATCTTTCTGTGT	57.449	37.500	0.00	0.00	0.00	3.72
2268	6143	9.987272	CCATCTATCATCTTTCTGTGTATTGTA	57.013	33.333	0.00	0.00	0.00	2.41
2281	6156	7.489160	TCTGTGTATTGTATACATGAGTGTCC	58.511	38.462	6.36	0.00	39.77	4.02
2302	6177	7.970614	GTGTCCAATCTCAGGTTTTCATTAATC	59.029	37.037	0.00	0.00	0.00	1.75
2596	6471	5.163754	ACAGAACTTTCGTTTGGACAAGAAG	60.164	40.000	0.00	0.00	32.39	2.85
2652	6527	5.869344	TGAACCGACTATGAATTCTGAACAG	59.131	40.000	7.05	0.00	0.00	3.16
2767	6642	7.833682	TCAGCCTGATCAAAATAGGAATTAACA	59.166	33.333	0.00	0.00	33.33	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	3.305881	CCATAGAGAGCATCATCGAAGCA	60.306	47.826	0.00	0.00	37.82	3.91
20	21	3.252400	CCATAGAGAGCATCATCGAAGC	58.748	50.000	0.00	0.00	37.82	3.86
102	103	2.726887	GACTCTCGTCGCCAAACTC	58.273	57.895	0.00	0.00	0.00	3.01
118	122	3.116531	GCAACCACCCGTAGCGAC	61.117	66.667	0.00	0.00	0.00	5.19
301	332	5.048921	TGTCAACCTTCGTTTTGTTGTGTAA	60.049	36.000	0.00	0.00	40.13	2.41
305	336	4.481463	CTTGTCAACCTTCGTTTTGTTGT	58.519	39.130	0.00	0.00	40.13	3.32
357	391	0.248990	CTCTGCTGATGGCGACTCTC	60.249	60.000	0.00	0.00	45.43	3.20
383	417	1.259609	TTCCTGCAAAGAAGCCATGG	58.740	50.000	7.63	7.63	0.00	3.66
462	496	3.226346	TGAAAAGCTGCAAGATCATGC	57.774	42.857	15.84	15.84	46.58	4.06
503	537	7.042456	CGTACCTCCTATCATCAAATTCAACAG	60.042	40.741	0.00	0.00	0.00	3.16
600	635	1.008875	GCGACTGCTGTGAACGATGA	61.009	55.000	0.00	0.00	38.39	2.92
653	688	1.878088	CGATGCTAACGGCTAGACCTA	59.122	52.381	0.00	0.00	42.39	3.08
655	690	0.384669	ACGATGCTAACGGCTAGACC	59.615	55.000	0.00	0.00	42.39	3.85
677	712	0.878523	GGCAGACTGTTGCACGTACA	60.879	55.000	3.99	0.00	45.86	2.90
683	718	1.412079	ATTTTGGGCAGACTGTTGCA	58.588	45.000	3.99	0.00	45.86	4.08
1068	1103	4.033932	TCGTTTGATATGGAGTTGATTGCG	59.966	41.667	0.00	0.00	0.00	4.85
1101	1136	9.283768	TGTATGTGTGAAATGTAGAAGAATGTT	57.716	29.630	0.00	0.00	0.00	2.71
1102	1137	8.846943	TGTATGTGTGAAATGTAGAAGAATGT	57.153	30.769	0.00	0.00	0.00	2.71
1107	1142	9.383519	AGGTATTGTATGTGTGAAATGTAGAAG	57.616	33.333	0.00	0.00	0.00	2.85
1159	1194	1.444119	CCAACACAGTCACAACCCGG	61.444	60.000	0.00	0.00	0.00	5.73
1170	1205	0.874390	CCGAACATGGACCAACACAG	59.126	55.000	0.00	0.00	0.00	3.66
1247	1282	2.820728	TTCCTCTATGAGACCACCGA	57.179	50.000	0.00	0.00	0.00	4.69
1317	1352	1.077787	TTGGCCCACTCTATTGCGG	60.078	57.895	0.00	0.00	0.00	5.69
1419	1454	6.427150	CCCTATATATTCACACACAAAACGC	58.573	40.000	0.00	0.00	0.00	4.84
1641	1676	2.171870	GTTAGGGGTGCAGCTATGGTTA	59.828	50.000	16.65	0.00	0.00	2.85
1685	1720	1.981256	ACCCTTGTTGTCATGGTCAC	58.019	50.000	0.00	0.00	37.23	3.67
1726	1761	3.737850	GAGGCTGAATATCCTCACAAGG	58.262	50.000	0.00	0.00	46.24	3.61
1842	1877	0.603707	ACAACCATCCACTGCACTCG	60.604	55.000	0.00	0.00	0.00	4.18
1850	1885	7.923414	AAGAAAATCTAGTACAACCATCCAC	57.077	36.000	0.00	0.00	0.00	4.02
1893	1928	3.181469	GGCCGAACTGATACAAGGTGATA	60.181	47.826	0.00	0.00	0.00	2.15
1907	1942	0.533308	TAAAGCAACACGGCCGAACT	60.533	50.000	35.90	17.70	0.00	3.01
2091	5965	9.725206	AAGGTACTCCTCACTCCTTATATTTTA	57.275	33.333	0.00	0.00	44.35	1.52
2152	6026	4.614555	TCAAATCCGATTTTGATCCACG	57.385	40.909	3.48	0.00	39.91	4.94
2178	6052	0.107897	GGCCACCATGTATGTCACGA	60.108	55.000	0.00	0.00	0.00	4.35
2262	6137	8.923270	TGAGATTGGACACTCATGTATACAATA	58.077	33.333	10.14	0.00	39.95	1.90
2268	6143	4.718774	ACCTGAGATTGGACACTCATGTAT	59.281	41.667	0.00	0.00	39.95	2.29
2330	6205	3.255642	GCCTGGTCACTTTTCTGCATTTA	59.744	43.478	0.00	0.00	0.00	1.40
2331	6206	2.036346	GCCTGGTCACTTTTCTGCATTT	59.964	45.455	0.00	0.00	0.00	2.32
2347	6222	1.974236	CTAGGTATTCTGGGAGCCTGG	59.026	57.143	0.00	0.00	0.00	4.45
2596	6471	3.829886	TGTTGATGATCGGAAGTTTGC	57.170	42.857	0.00	0.00	0.00	3.68
2652	6527	6.258947	GTGTTTCCCTCTCAATAATCTGCTAC	59.741	42.308	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.