AutoCloner

Multiple sequence alignment - TraesCS3A01G110500

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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	TraesCS3A01G110500	chr3A	100.000	2754	0	0	1	2754	77547371	77550124	0.000000e+00	5086.0
1	TraesCS3A01G110500	chr3A	94.685	2145	65	15	630	2754	77594540	77596655	0.000000e+00	3284.0
2	TraesCS3A01G110500	chr3A	93.377	1389	44	14	630	1998	77708094	77709454	0.000000e+00	2012.0
3	TraesCS3A01G110500	chr3A	86.923	390	26	11	2046	2424	77709455	77709830	5.490000e-112	414.0
4	TraesCS3A01G110500	chr3A	93.464	153	8	2	2413	2563	77710759	77710911	2.760000e-55	226.0
5	TraesCS3A01G110500	chr3A	80.645	155	15	6	2603	2742	77712375	77712529	3.750000e-19	106.0
6	TraesCS3A01G110500	chr3A	74.449	227	41	13	2408	2623	674991054	674991274	6.320000e-12	82.4
7	TraesCS3A01G110500	chr3D	91.061	2808	166	28	1	2747	66552354	66555137	0.000000e+00	3716.0
8	TraesCS3A01G110500	chr3D	87.758	1552	118	31	772	2295	66561416	66562923	0.000000e+00	1748.0
9	TraesCS3A01G110500	chr3D	87.838	148	8	4	630	777	66557714	66557851	6.100000e-37	165.0
10	TraesCS3A01G110500	chr3D	76.974	152	25	10	2476	2623	540111377	540111522	8.180000e-11	78.7
11	TraesCS3A01G110500	chr3B	89.646	1893	124	22	53	1920	110735027	110736872	0.000000e+00	2344.0
12	TraesCS3A01G110500	chr3B	87.968	1014	65	13	668	1665	110741440	110742412	0.000000e+00	1144.0
13	TraesCS3A01G110500	chr3B	86.643	846	73	18	1941	2754	110738010	110738847	0.000000e+00	900.0
14	TraesCS3A01G110500	chr4A	86.447	760	70	22	1041	1774	697432892	697433644	0.000000e+00	802.0
15	TraesCS3A01G110500	chr7D	85.582	756	77	23	1044	1774	31101997	31101249	0.000000e+00	763.0
16	TraesCS3A01G110500	chr7D	83.516	819	87	30	985	1774	30984575	30983776	0.000000e+00	721.0
17	TraesCS3A01G110500	chr7D	89.474	437	40	5	1354	1785	31055803	31055368	5.190000e-152	547.0
18	TraesCS3A01G110500	chr2B	84.656	756	70	17	986	1719	49886432	49887163	0.000000e+00	712.0
19	TraesCS3A01G110500	chr2B	89.510	143	11	3	1785	1925	49887407	49887547	7.840000e-41	178.0
20	TraesCS3A01G110500	chr2B	88.811	143	13	2	1785	1925	49890789	49890930	3.650000e-39	172.0
21	TraesCS3A01G110500	chr2B	88.194	144	14	2	1785	1926	49893204	49893346	4.720000e-38	169.0
22	TraesCS3A01G110500	chrUn	88.112	143	14	2	1785	1925	378540992	378541133	1.700000e-37	167.0
23	TraesCS3A01G110500	chr1A	75.082	305	69	5	21	323	26589206	26589505	4.780000e-28	135.0
24	TraesCS3A01G110500	chr4D	77.848	158	21	10	2408	2553	104633894	104634049	4.890000e-13	86.1
25	TraesCS3A01G110500	chr1D	77.465	142	20	10	2490	2623	57319518	57319381	1.060000e-09	75.0
26	TraesCS3A01G110500	chr2D	83.750	80	9	4	2476	2553	638825807	638825884	3.800000e-09	73.1

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	TraesCS3A01G110500	chr3A	77547371	77550124	2753	False	5086.000000	5086	100.000000	1	2754	1	chr3A.!!$F1	2753
1	TraesCS3A01G110500	chr3A	77594540	77596655	2115	False	3284.000000	3284	94.685000	630	2754	1	chr3A.!!$F2	2124
2	TraesCS3A01G110500	chr3A	77708094	77712529	4435	False	689.500000	2012	88.602250	630	2742	4	chr3A.!!$F4	2112
3	TraesCS3A01G110500	chr3D	66552354	66562923	10569	False	1876.333333	3716	88.885667	1	2747	3	chr3D.!!$F2	2746
4	TraesCS3A01G110500	chr3B	110735027	110742412	7385	False	1462.666667	2344	88.085667	53	2754	3	chr3B.!!$F1	2701
5	TraesCS3A01G110500	chr4A	697432892	697433644	752	False	802.000000	802	86.447000	1041	1774	1	chr4A.!!$F1	733
6	TraesCS3A01G110500	chr7D	31101249	31101997	748	True	763.000000	763	85.582000	1044	1774	1	chr7D.!!$R3	730
7	TraesCS3A01G110500	chr7D	30983776	30984575	799	True	721.000000	721	83.516000	985	1774	1	chr7D.!!$R1	789
8	TraesCS3A01G110500	chr2B	49886432	49893346	6914	False	307.750000	712	87.792750	986	1926	4	chr2B.!!$F1	940

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
654	657	0.10741	TGACGTTTCAAGCAGGGTGT	60.107	50.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2051	7350	1.732405	CGATCGCCCTTTTTCTTTGCC	60.732	52.381	0.26	0.0	0.0	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
41	42	2.299013	ACAACACTATCAGAAGGCGACA	59.701	45.455	0.00	0.00	0.00	4.35
54	55	2.103042	GCGACACAGTGGCATCCTC	61.103	63.158	7.33	0.00	37.24	3.71
107	108	4.792068	AGGAACAAACACATCCTTGAAGA	58.208	39.130	0.00	0.00	40.70	2.87
108	109	5.200483	AGGAACAAACACATCCTTGAAGAA	58.800	37.500	0.00	0.00	40.70	2.52
118	119	4.202264	ACATCCTTGAAGAAACGAGACTGT	60.202	41.667	0.00	0.00	0.00	3.55
310	313	8.595362	AAATATTTCCCCCTTCTTAGTGAAAG	57.405	34.615	0.00	0.00	33.79	2.62
429	432	1.407437	CCTCGGTTTTCCCAGATCCAG	60.407	57.143	0.00	0.00	36.42	3.86
441	444	2.158986	CCAGATCCAGGAACAGCTAGTG	60.159	54.545	0.00	0.00	0.00	2.74
573	576	5.763204	ACAGAAACCTTCGTATTCACAATGT	59.237	36.000	0.00	0.00	34.02	2.71
654	657	0.107410	TGACGTTTCAAGCAGGGTGT	60.107	50.000	0.00	0.00	0.00	4.16
751	754	2.164338	TGCATGCATATCCAATCGCAT	58.836	42.857	18.46	0.00	45.65	4.73
753	756	2.162809	GCATGCATATCCAATCGCATCA	59.837	45.455	14.21	0.00	42.99	3.07
755	758	3.130280	TGCATATCCAATCGCATCACT	57.870	42.857	0.00	0.00	0.00	3.41
789	793	4.382320	TACGTGCTTGGGCCGTCC	62.382	66.667	0.00	0.00	42.19	4.79
798	802	3.463585	GGGCCGTCCATACCGTGA	61.464	66.667	0.00	0.00	35.00	4.35
913	932	0.179037	CCCACATCGATCTGCACCAT	60.179	55.000	0.00	0.00	0.00	3.55
929	948	3.458189	CACCATGGCAGCTTACTACTAC	58.542	50.000	13.04	0.00	0.00	2.73
932	951	4.585162	ACCATGGCAGCTTACTACTACTAG	59.415	45.833	13.04	0.00	0.00	2.57
933	952	4.551388	CATGGCAGCTTACTACTACTAGC	58.449	47.826	0.00	0.00	0.00	3.42
934	953	3.899726	TGGCAGCTTACTACTACTAGCT	58.100	45.455	0.00	0.00	44.34	3.32
972	991	1.863454	GCTATCAGCTGATTGTGGACG	59.137	52.381	32.94	13.99	38.45	4.79
1310	1374	4.325028	AGCAGCACATTGTTGAAATTCA	57.675	36.364	0.00	0.00	29.49	2.57
1320	1386	4.517952	TGTTGAAATTCATGCGTTCCAT	57.482	36.364	0.00	0.00	33.39	3.41
1885	6067	3.571571	GAGTAGTACACGCACATGTGAA	58.428	45.455	29.80	5.66	42.55	3.18
1896	6078	1.196808	CACATGTGAACCCTAACGTGC	59.803	52.381	21.64	0.00	36.90	5.34
2027	7326	2.453983	TTCCGTTAGGGTAAACCACG	57.546	50.000	0.81	2.71	43.89	4.94
2123	7422	3.197549	GCACTTTCCTCTTCTCTCCATCT	59.802	47.826	0.00	0.00	0.00	2.90
2125	7424	3.774216	ACTTTCCTCTTCTCTCCATCTGG	59.226	47.826	0.00	0.00	0.00	3.86
2130	7429	5.533112	TCCTCTTCTCTCCATCTGGTAATT	58.467	41.667	0.00	0.00	36.34	1.40
2136	7435	5.419542	TCTCTCCATCTGGTAATTGAAACG	58.580	41.667	0.00	0.00	36.34	3.60
2137	7436	5.046591	TCTCTCCATCTGGTAATTGAAACGT	60.047	40.000	0.00	0.00	36.34	3.99
2143	7442	4.056740	TCTGGTAATTGAAACGTGCGTAA	58.943	39.130	0.00	0.00	0.00	3.18
2167	7466	7.909485	ATAATCATGCTTCTTTGATTCCCTT	57.091	32.000	1.72	0.00	40.71	3.95
2174	7473	5.363580	TGCTTCTTTGATTCCCTTTTGTCTT	59.636	36.000	0.00	0.00	0.00	3.01
2216	7515	3.769844	ACCTATCACGTGATCAAGTTCCT	59.230	43.478	33.11	10.95	36.05	3.36
2236	7535	1.867363	AGAGATGGGTAGCGGACTTT	58.133	50.000	0.00	0.00	0.00	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.368236	GCCTTCTGATAGTGTTGTCGTTC	59.632	47.826	0.00	0.00	0.00	3.95
41	42	8.166061	ACATTATATAAATGAGGATGCCACTGT	58.834	33.333	0.00	0.00	0.00	3.55
95	96	4.202264	ACAGTCTCGTTTCTTCAAGGATGT	60.202	41.667	0.00	0.00	0.00	3.06
107	108	5.171476	CCTCAATGTATGACAGTCTCGTTT	58.829	41.667	1.31	0.00	33.47	3.60
108	109	4.220821	ACCTCAATGTATGACAGTCTCGTT	59.779	41.667	1.31	0.00	33.47	3.85
118	119	1.294041	TGGGCCACCTCAATGTATGA	58.706	50.000	0.00	0.00	37.76	2.15
223	224	4.262808	CCCAAGATCTCATGTATCCCAGTC	60.263	50.000	0.00	0.00	0.00	3.51
353	356	9.971922	AGATTTGAATAAACTTGGTGAGAAAAG	57.028	29.630	0.00	0.00	0.00	2.27
364	367	7.609056	AGCTGCAATCAGATTTGAATAAACTT	58.391	30.769	1.02	0.00	42.95	2.66
477	480	2.085320	GTTTTGGTTTTGCCGGGTTTT	58.915	42.857	2.18	0.00	41.21	2.43
478	481	1.279558	AGTTTTGGTTTTGCCGGGTTT	59.720	42.857	2.18	0.00	41.21	3.27
479	482	0.906066	AGTTTTGGTTTTGCCGGGTT	59.094	45.000	2.18	0.00	41.21	4.11
480	483	0.462375	GAGTTTTGGTTTTGCCGGGT	59.538	50.000	2.18	0.00	41.21	5.28
481	484	0.461961	TGAGTTTTGGTTTTGCCGGG	59.538	50.000	2.18	0.00	41.21	5.73
482	485	2.524569	ATGAGTTTTGGTTTTGCCGG	57.475	45.000	0.00	0.00	41.21	6.13
546	549	5.547465	TGTGAATACGAAGGTTTCTGTCAT	58.453	37.500	0.00	0.00	0.00	3.06
547	550	4.951254	TGTGAATACGAAGGTTTCTGTCA	58.049	39.130	0.00	0.00	0.00	3.58
573	576	7.868775	ACATTCTTGCGTCGTAGTTCTATATA	58.131	34.615	0.00	0.00	0.00	0.86
654	657	2.123251	TGGAAAGCGGGGCCAAAA	60.123	55.556	4.39	0.00	0.00	2.44
751	754	2.223548	ACGTACGTAGTTGCACAAGTGA	60.224	45.455	21.41	0.00	37.78	3.41
753	756	2.497107	ACGTACGTAGTTGCACAAGT	57.503	45.000	21.41	0.00	37.78	3.16
755	758	2.306169	CGTACGTACGTAGTTGCACAA	58.694	47.619	33.95	2.77	37.78	3.33
789	793	0.248054	GCATTGCGGTTCACGGTATG	60.248	55.000	0.00	0.00	44.51	2.39
798	802	1.596752	TCTGACGTGCATTGCGGTT	60.597	52.632	3.84	0.00	0.00	4.44
913	932	3.899726	AGCTAGTAGTAGTAAGCTGCCA	58.100	45.455	6.47	0.00	43.46	4.92
953	972	1.863454	GCGTCCACAATCAGCTGATAG	59.137	52.381	28.92	20.20	33.73	2.08
956	975	1.375908	GGCGTCCACAATCAGCTGA	60.376	57.895	20.79	20.79	0.00	4.26
991	1023	3.005155	GTGAGAGAAGCCATTTTGCAACT	59.995	43.478	0.00	0.00	0.00	3.16
1310	1374	0.036732	ATGGCCGATATGGAACGCAT	59.963	50.000	0.00	0.00	42.00	4.73
1320	1386	2.038814	ATGTGACGCCATGGCCGATA	62.039	55.000	30.79	13.17	37.98	2.92
1378	1468	1.002134	CTCGAATTGCCACACCCCT	60.002	57.895	0.00	0.00	0.00	4.79
1896	6078	3.955650	TCTAAGAAAGAAGTCACGGGG	57.044	47.619	0.00	0.00	0.00	5.73
2027	7326	2.182030	CTCGAGCGGGAGTGTTCC	59.818	66.667	0.00	0.00	43.23	3.62
2051	7350	1.732405	CGATCGCCCTTTTTCTTTGCC	60.732	52.381	0.26	0.00	0.00	4.52
2123	7422	6.477669	TTATTACGCACGTTTCAATTACCA	57.522	33.333	0.00	0.00	0.00	3.25
2125	7424	8.669801	CATGATTATTACGCACGTTTCAATTAC	58.330	33.333	0.00	0.00	0.00	1.89
2130	7429	4.331443	AGCATGATTATTACGCACGTTTCA	59.669	37.500	0.00	0.00	0.00	2.69
2136	7435	6.486248	TCAAAGAAGCATGATTATTACGCAC	58.514	36.000	3.71	0.00	0.00	5.34
2137	7436	6.676237	TCAAAGAAGCATGATTATTACGCA	57.324	33.333	3.71	0.00	0.00	5.24
2143	7442	7.909485	AAGGGAATCAAAGAAGCATGATTAT	57.091	32.000	0.00	0.00	44.15	1.28
2167	7466	9.029243	CAACACATTATAGTTTTGCAAGACAAA	57.971	29.630	20.91	12.45	46.51	2.83
2174	7473	6.892658	AGGTCAACACATTATAGTTTTGCA	57.107	33.333	0.00	0.00	31.13	4.08
2186	7485	3.953712	TCACGTGATAGGTCAACACAT	57.046	42.857	15.76	0.00	35.80	3.21
2216	7515	2.750141	AAGTCCGCTACCCATCTCTA	57.250	50.000	0.00	0.00	0.00	2.43
2446	8695	3.323403	CCAACAACTTTTCTGGCCCATTA	59.677	43.478	0.00	0.00	0.00	1.90
2525	8774	7.630242	AAACTAATATGTGTGCAGTAATGCT	57.370	32.000	17.03	0.00	35.49	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.