AutoCloner

Multiple sequence alignment - TraesCS3B01G311400

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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	TraesCS3B01G311400	chr3B	100.000	2637	0	0	1	2637	500306707	500309343	0.000000e+00	4870.0
1	TraesCS3B01G311400	chr3B	99.883	1708	2	0	425	2132	500315678	500317385	0.000000e+00	3144.0
2	TraesCS3B01G311400	chr3B	83.854	1152	88	48	743	1825	500539532	500540654	0.000000e+00	1007.0
3	TraesCS3B01G311400	chr3B	99.537	216	1	0	2150	2365	500315462	500315677	6.840000e-106	394.0
4	TraesCS3B01G311400	chr3B	94.800	250	13	0	2153	2402	807711147	807710898	8.850000e-105	390.0
5	TraesCS3B01G311400	chr3B	95.021	241	12	0	2397	2637	807710871	807710631	1.920000e-101	379.0
6	TraesCS3B01G311400	chr3D	91.226	1550	92	22	307	1840	384654500	384656021	0.000000e+00	2069.0
7	TraesCS3B01G311400	chr3D	84.089	1169	99	46	722	1825	384659290	384660436	0.000000e+00	1048.0
8	TraesCS3B01G311400	chr3D	92.308	143	10	1	18	160	384652210	384652351	4.450000e-48	202.0
9	TraesCS3B01G311400	chr3D	92.857	126	6	2	158	281	384654212	384654336	2.090000e-41	180.0
10	TraesCS3B01G311400	chr3D	79.787	188	13	11	1843	2006	31093273	31093087	2.150000e-21	113.0
11	TraesCS3B01G311400	chr3A	85.215	1116	96	37	722	1788	507286390	507287485	0.000000e+00	1083.0
12	TraesCS3B01G311400	chr3A	87.699	878	63	23	956	1825	507273051	507273891	0.000000e+00	981.0
13	TraesCS3B01G311400	chr3A	86.175	434	25	13	507	913	507272619	507273044	1.120000e-118	436.0
14	TraesCS3B01G311400	chr3A	84.731	465	32	18	18	472	507272058	507272493	1.880000e-116	429.0
15	TraesCS3B01G311400	chr3A	79.570	186	16	8	1843	2006	647804256	647804071	2.150000e-21	113.0
16	TraesCS3B01G311400	chr6B	99.385	488	3	0	2150	2637	28493978	28493491	0.000000e+00	885.0
17	TraesCS3B01G311400	chr6B	94.862	253	13	0	2150	2402	342801181	342801433	1.900000e-106	396.0
18	TraesCS3B01G311400	chr6B	94.862	253	13	0	2150	2402	703264637	703264385	1.900000e-106	396.0
19	TraesCS3B01G311400	chr5B	96.047	253	10	0	2150	2402	316559119	316559371	1.890000e-111	412.0
20	TraesCS3B01G311400	chr5B	95.257	253	12	0	2150	2402	271162095	271161843	4.090000e-108	401.0
21	TraesCS3B01G311400	chr5B	95.851	241	10	0	2397	2637	316559398	316559638	8.850000e-105	390.0
22	TraesCS3B01G311400	chr5B	83.175	315	25	10	1846	2133	512206091	512205778	2.010000e-66	263.0
23	TraesCS3B01G311400	chr2B	95.455	242	11	0	2161	2402	626993621	626993862	1.140000e-103	387.0
24	TraesCS3B01G311400	chr2B	95.455	242	10	1	2397	2637	626993889	626994130	4.120000e-103	385.0
25	TraesCS3B01G311400	chr2B	93.061	245	13	2	2396	2637	333266054	333265811	3.230000e-94	355.0
26	TraesCS3B01G311400	chr2B	79.679	187	14	10	1843	2006	153889284	153889469	2.150000e-21	113.0
27	TraesCS3B01G311400	chr2D	89.933	298	18	5	2351	2637	620564675	620564379	8.910000e-100	374.0
28	TraesCS3B01G311400	chr2D	93.281	253	16	1	2150	2402	99202105	99201854	3.210000e-99	372.0
29	TraesCS3B01G311400	chr7B	93.089	246	12	3	2396	2637	259230263	259230507	3.230000e-94	355.0
30	TraesCS3B01G311400	chr7B	78.610	187	16	9	1843	2006	667793697	667793882	4.640000e-18	102.0
31	TraesCS3B01G311400	chr2A	93.089	246	12	3	2396	2637	13442536	13442780	3.230000e-94	355.0
32	TraesCS3B01G311400	chr2A	94.737	57	3	0	1950	2006	211481078	211481134	3.620000e-14	89.8
33	TraesCS3B01G311400	chr4A	92.276	246	15	2	2396	2637	703883875	703884120	1.940000e-91	346.0
34	TraesCS3B01G311400	chr4A	80.114	176	21	7	1843	2006	602719838	602719665	4.610000e-23	119.0
35	TraesCS3B01G311400	chr7D	81.212	330	23	13	1843	2134	181974868	181974540	2.040000e-56	230.0
36	TraesCS3B01G311400	chr7D	92.857	70	0	3	1721	1788	544155143	544155077	2.160000e-16	97.1
37	TraesCS3B01G311400	chr6D	81.115	323	25	6	1843	2130	263993032	263993353	2.640000e-55	226.0
38	TraesCS3B01G311400	chr4B	86.441	118	15	1	1843	1959	1737491	1737374	7.660000e-26	128.0
39	TraesCS3B01G311400	chr4B	86.047	86	10	2	1843	1927	500344449	500344533	1.010000e-14	91.6
40	TraesCS3B01G311400	chr5A	91.765	85	7	0	1843	1927	673731878	673731962	4.610000e-23	119.0
41	TraesCS3B01G311400	chr5A	94.444	54	3	0	1953	2006	328712561	328712508	1.680000e-12	84.2
42	TraesCS3B01G311400	chrUn	79.167	168	13	10	1843	1988	363732002	363731835	2.160000e-16	97.1
43	TraesCS3B01G311400	chr1B	79.167	168	13	8	1843	1988	552467619	552467452	2.160000e-16	97.1
44	TraesCS3B01G311400	chr1B	79.167	168	13	10	1843	1988	552489135	552488968	2.160000e-16	97.1
45	TraesCS3B01G311400	chr1B	91.429	70	1	3	1721	1788	659104331	659104265	1.010000e-14	91.6
46	TraesCS3B01G311400	chr7A	91.429	70	1	3	1721	1788	675749469	675749403	1.010000e-14	91.6

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	TraesCS3B01G311400	chr3B	500306707	500309343	2636	False	4870.000000	4870	100.000000	1	2637	1	chr3B.!!$F1	2636
1	TraesCS3B01G311400	chr3B	500315462	500317385	1923	False	1769.000000	3144	99.710000	425	2365	2	chr3B.!!$F3	1940
2	TraesCS3B01G311400	chr3B	500539532	500540654	1122	False	1007.000000	1007	83.854000	743	1825	1	chr3B.!!$F2	1082
3	TraesCS3B01G311400	chr3B	807710631	807711147	516	True	384.500000	390	94.910500	2153	2637	2	chr3B.!!$R1	484
4	TraesCS3B01G311400	chr3D	384652210	384660436	8226	False	874.750000	2069	90.120000	18	1840	4	chr3D.!!$F1	1822
5	TraesCS3B01G311400	chr3A	507286390	507287485	1095	False	1083.000000	1083	85.215000	722	1788	1	chr3A.!!$F1	1066
6	TraesCS3B01G311400	chr3A	507272058	507273891	1833	False	615.333333	981	86.201667	18	1825	3	chr3A.!!$F2	1807
7	TraesCS3B01G311400	chr5B	316559119	316559638	519	False	401.000000	412	95.949000	2150	2637	2	chr5B.!!$F1	487
8	TraesCS3B01G311400	chr2B	626993621	626994130	509	False	386.000000	387	95.455000	2161	2637	2	chr2B.!!$F2	476

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
201	2071	0.032952	TCCGAAGCATATGCCGGTAC	59.967	55.0	31.43	16.62	43.29	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2140	7565	7.723616	TCAGTCAGTTTCCTTTAATGAAATCCA	59.276	33.333	0.0	0.0	34.5	3.41	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
57	58	3.012518	CAGCTCGATCCACCAGATTTTT	58.987	45.455	0.00	0.00	34.42	1.94
100	101	4.965119	AATTTTACTTGGCGTCTCCATC	57.035	40.909	0.00	0.00	46.04	3.51
101	102	2.004583	TTTACTTGGCGTCTCCATCG	57.995	50.000	0.00	0.00	46.04	3.84
137	144	1.287730	GCAGAATAGCCTGGATCGCG	61.288	60.000	0.00	0.00	34.82	5.87
156	163	1.883275	CGGGGCATCAGTGTTTGTTTA	59.117	47.619	0.00	0.00	0.00	2.01
201	2071	0.032952	TCCGAAGCATATGCCGGTAC	59.967	55.000	31.43	16.62	43.29	3.34
206	2076	3.003275	CGAAGCATATGCCGGTACAATTT	59.997	43.478	23.96	8.35	43.38	1.82
261	2133	1.720301	GCTCCTCAAAGCGATGCAG	59.280	57.895	0.00	0.00	31.56	4.41
282	2154	5.437946	CAGTATCACCTCCTACAGTCTGTA	58.562	45.833	12.16	12.16	0.00	2.74
408	2426	1.725973	GCTGCGCTCCGTTCAAAAC	60.726	57.895	9.73	0.00	0.00	2.43
2008	7433	3.064207	CAAATACGTAGCCGGCATATGT	58.936	45.455	31.54	27.01	38.78	2.29
2136	7561	2.123077	CCTCTCCCGCCTCTGGAT	60.123	66.667	0.00	0.00	0.00	3.41
2137	7562	1.764054	CCTCTCCCGCCTCTGGATT	60.764	63.158	0.00	0.00	0.00	3.01
2138	7563	1.341156	CCTCTCCCGCCTCTGGATTT	61.341	60.000	0.00	0.00	0.00	2.17
2139	7564	0.105778	CTCTCCCGCCTCTGGATTTC	59.894	60.000	0.00	0.00	0.00	2.17
2140	7565	0.325671	TCTCCCGCCTCTGGATTTCT	60.326	55.000	0.00	0.00	0.00	2.52
2141	7566	0.179062	CTCCCGCCTCTGGATTTCTG	60.179	60.000	0.00	0.00	0.00	3.02
2142	7567	1.153086	CCCGCCTCTGGATTTCTGG	60.153	63.158	0.00	0.00	0.00	3.86
2143	7568	1.626356	CCCGCCTCTGGATTTCTGGA	61.626	60.000	0.00	0.00	0.00	3.86
2144	7569	0.471617	CCGCCTCTGGATTTCTGGAT	59.528	55.000	0.00	0.00	0.00	3.41
2145	7570	1.133976	CCGCCTCTGGATTTCTGGATT	60.134	52.381	0.00	0.00	0.00	3.01
2146	7571	2.648059	CGCCTCTGGATTTCTGGATTT	58.352	47.619	0.00	0.00	0.00	2.17
2147	7572	2.615912	CGCCTCTGGATTTCTGGATTTC	59.384	50.000	0.00	0.00	0.00	2.17
2148	7573	3.624777	GCCTCTGGATTTCTGGATTTCA	58.375	45.455	0.00	0.00	0.00	2.69
2155	7580	8.297470	TCTGGATTTCTGGATTTCATTAAAGG	57.703	34.615	0.00	0.00	0.00	3.11
2163	7588	8.110860	TCTGGATTTCATTAAAGGAAACTGAC	57.889	34.615	7.56	1.76	42.68	3.51
2254	7785	4.546829	AGGCGGTAATTACAAAGAGACA	57.453	40.909	17.16	0.00	0.00	3.41
2262	7793	5.862924	AATTACAAAGAGACATGTCCGTG	57.137	39.130	22.21	16.14	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	7.432010	GTGAGTTCCACTGAAGGTTCTTCCT	62.432	48.000	5.36	0.00	44.61	3.36
7	8	3.810386	GTGAGTTCCACTGAAGGTTCTTC	59.190	47.826	1.06	1.06	42.44	2.87
57	58	1.673920	GCACGAGGTTTGAACTTGGAA	59.326	47.619	0.00	0.00	0.00	3.53
100	101	3.096541	CAACAGTGCATTTGGAGCG	57.903	52.632	0.00	0.00	33.85	5.03
127	134	4.996434	GATGCCCCGCGATCCAGG	62.996	72.222	8.23	0.00	0.00	4.45
137	144	5.185056	AGTTATAAACAAACACTGATGCCCC	59.815	40.000	0.00	0.00	0.00	5.80
156	163	7.055378	ACCTCTATAATCGATCGGCTAGTTAT	58.945	38.462	16.41	13.44	0.00	1.89
201	2071	2.126914	TCAAACGTGCCGGAAAATTG	57.873	45.000	5.05	0.44	0.00	2.32
206	2076	2.289195	ACTCTTATCAAACGTGCCGGAA	60.289	45.455	5.05	0.00	0.00	4.30
212	2082	6.480524	TCCAAATGACTCTTATCAAACGTG	57.519	37.500	0.00	0.00	30.82	4.49
261	2133	5.191426	TGTACAGACTGTAGGAGGTGATAC	58.809	45.833	15.69	3.44	32.84	2.24
294	2312	7.405292	TGCTAAAACCTACTCCTACTGTACTA	58.595	38.462	0.00	0.00	0.00	1.82
295	2313	6.251471	TGCTAAAACCTACTCCTACTGTACT	58.749	40.000	0.00	0.00	0.00	2.73
296	2314	6.405619	CCTGCTAAAACCTACTCCTACTGTAC	60.406	46.154	0.00	0.00	0.00	2.90
297	2315	5.655532	CCTGCTAAAACCTACTCCTACTGTA	59.344	44.000	0.00	0.00	0.00	2.74
298	2316	4.466726	CCTGCTAAAACCTACTCCTACTGT	59.533	45.833	0.00	0.00	0.00	3.55
299	2317	4.141914	CCCTGCTAAAACCTACTCCTACTG	60.142	50.000	0.00	0.00	0.00	2.74
300	2318	4.031611	CCCTGCTAAAACCTACTCCTACT	58.968	47.826	0.00	0.00	0.00	2.57
301	2319	3.431905	GCCCTGCTAAAACCTACTCCTAC	60.432	52.174	0.00	0.00	0.00	3.18
302	2320	2.770232	GCCCTGCTAAAACCTACTCCTA	59.230	50.000	0.00	0.00	0.00	2.94
303	2321	1.560146	GCCCTGCTAAAACCTACTCCT	59.440	52.381	0.00	0.00	0.00	3.69
304	2322	1.408405	GGCCCTGCTAAAACCTACTCC	60.408	57.143	0.00	0.00	0.00	3.85
305	2323	1.280998	TGGCCCTGCTAAAACCTACTC	59.719	52.381	0.00	0.00	0.00	2.59
408	2426	2.188524	CAAGTCACCATGTCGATCTCG	58.811	52.381	0.00	0.00	41.45	4.04
1854	4082	8.299570	CAGACAAAATGGGTATAGATTTATGGC	58.700	37.037	0.00	0.00	0.00	4.40
2132	7557	8.663209	TTCCTTTAATGAAATCCAGAAATCCA	57.337	30.769	0.00	0.00	0.00	3.41
2133	7558	9.371136	GTTTCCTTTAATGAAATCCAGAAATCC	57.629	33.333	0.00	0.00	34.50	3.01
2135	7560	9.933723	CAGTTTCCTTTAATGAAATCCAGAAAT	57.066	29.630	0.00	0.00	34.50	2.17
2136	7561	9.142014	TCAGTTTCCTTTAATGAAATCCAGAAA	57.858	29.630	0.00	0.00	34.50	2.52
2137	7562	8.576442	GTCAGTTTCCTTTAATGAAATCCAGAA	58.424	33.333	0.00	0.00	34.50	3.02
2138	7563	7.944554	AGTCAGTTTCCTTTAATGAAATCCAGA	59.055	33.333	0.00	0.00	34.50	3.86
2139	7564	8.025445	CAGTCAGTTTCCTTTAATGAAATCCAG	58.975	37.037	0.00	0.00	34.50	3.86
2140	7565	7.723616	TCAGTCAGTTTCCTTTAATGAAATCCA	59.276	33.333	0.00	0.00	34.50	3.41
2141	7566	8.110860	TCAGTCAGTTTCCTTTAATGAAATCC	57.889	34.615	0.00	0.00	34.50	3.01
2142	7567	9.003658	TCTCAGTCAGTTTCCTTTAATGAAATC	57.996	33.333	0.00	0.00	34.50	2.17
2143	7568	8.924511	TCTCAGTCAGTTTCCTTTAATGAAAT	57.075	30.769	0.00	0.00	34.50	2.17
2144	7569	8.746052	TTCTCAGTCAGTTTCCTTTAATGAAA	57.254	30.769	0.00	0.00	0.00	2.69
2145	7570	8.786898	CATTCTCAGTCAGTTTCCTTTAATGAA	58.213	33.333	0.00	0.00	0.00	2.57
2146	7571	8.156820	TCATTCTCAGTCAGTTTCCTTTAATGA	58.843	33.333	0.00	0.00	0.00	2.57
2147	7572	8.327941	TCATTCTCAGTCAGTTTCCTTTAATG	57.672	34.615	0.00	0.00	0.00	1.90
2148	7573	8.924511	TTCATTCTCAGTCAGTTTCCTTTAAT	57.075	30.769	0.00	0.00	0.00	1.40
2432	8151	1.227249	TCCCACAGGGTTTTTGGAGA	58.773	50.000	1.36	0.00	44.74	3.71
2546	8266	9.978044	TCTCATATGAGTTATCAAGAGACAATG	57.022	33.333	27.80	1.70	42.60	2.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.