AutoCloner

Multiple sequence alignment - TraesCS4A01G230900

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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	TraesCS4A01G230900	chr4A	100.000	3791	0	0	1	3791	540057987	540061777	0.000000e+00	7001.0
1	TraesCS4A01G230900	chr4A	96.385	2600	73	14	1202	3791	540415739	540418327	0.000000e+00	4261.0
2	TraesCS4A01G230900	chr4A	84.184	980	40	29	384	1326	540414842	540415743	0.000000e+00	845.0
3	TraesCS4A01G230900	chr4A	90.741	54	3	2	147	199	540414561	540414613	1.890000e-08	71.3
4	TraesCS4A01G230900	chr4D	93.428	2115	115	17	1201	3303	56744887	56742785	0.000000e+00	3114.0
5	TraesCS4A01G230900	chr4D	87.134	2495	259	26	826	3282	49938274	49935804	0.000000e+00	2772.0
6	TraesCS4A01G230900	chr4D	86.735	1078	61	34	322	1376	56745823	56744805	0.000000e+00	1123.0
7	TraesCS4A01G230900	chr4D	93.648	488	17	3	3312	3789	56742740	56742257	0.000000e+00	717.0
8	TraesCS4A01G230900	chr4D	85.640	578	75	2	1934	2508	50031868	50031296	5.420000e-168	601.0
9	TraesCS4A01G230900	chr4D	83.430	519	47	17	3283	3791	49935772	49935283	2.690000e-121	446.0
10	TraesCS4A01G230900	chr4D	87.898	314	27	5	22	326	56746165	56745854	3.600000e-95	359.0
11	TraesCS4A01G230900	chr4D	92.063	63	5	0	706	768	49938355	49938293	5.220000e-14	89.8
12	TraesCS4A01G230900	chr3A	83.851	483	60	14	3279	3750	57010850	57010375	9.660000e-121	444.0
13	TraesCS4A01G230900	chr3A	83.333	390	48	15	3367	3747	56962947	56962566	1.010000e-90	344.0
14	TraesCS4A01G230900	chr3A	93.750	48	3	0	3283	3330	56963003	56962956	5.250000e-09	73.1
15	TraesCS4A01G230900	chr4B	84.496	387	46	10	3283	3663	242924247	242923869	1.660000e-98	370.0
16	TraesCS4A01G230900	chr4B	94.972	179	9	0	3613	3791	83312376	83312198	8.020000e-72	281.0
17	TraesCS4A01G230900	chr5B	83.979	387	48	10	3283	3663	115862911	115862533	3.600000e-95	359.0
18	TraesCS4A01G230900	chr5A	83.180	327	43	7	3283	3604	600165348	600165029	4.790000e-74	289.0
19	TraesCS4A01G230900	chr6D	93.103	116	8	0	1499	1614	454585288	454585173	1.810000e-38	171.0
20	TraesCS4A01G230900	chr3D	92.241	116	9	0	1499	1614	571691624	571691509	8.420000e-37	165.0
21	TraesCS4A01G230900	chr2D	92.241	116	9	0	1499	1614	524269696	524269581	8.420000e-37	165.0
22	TraesCS4A01G230900	chr6A	91.379	116	10	0	1499	1614	521552223	521552108	3.920000e-35	159.0
23	TraesCS4A01G230900	chr6A	91.818	110	9	0	1499	1608	524317490	524317381	1.820000e-33	154.0
24	TraesCS4A01G230900	chr1D	91.379	116	10	0	1496	1611	14149004	14149119	3.920000e-35	159.0
25	TraesCS4A01G230900	chr7A	91.304	115	10	0	1500	1614	422485332	422485218	1.410000e-34	158.0
26	TraesCS4A01G230900	chr2A	91.525	59	4	1	3593	3651	172527390	172527333	3.140000e-11	80.5

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	TraesCS4A01G230900	chr4A	540057987	540061777	3790	False	7001.000000	7001	100.000000	1	3791	1	chr4A.!!$F1	3790
1	TraesCS4A01G230900	chr4A	540414561	540418327	3766	False	1725.766667	4261	90.436667	147	3791	3	chr4A.!!$F2	3644
2	TraesCS4A01G230900	chr4D	56742257	56746165	3908	True	1328.250000	3114	90.427250	22	3789	4	chr4D.!!$R3	3767
3	TraesCS4A01G230900	chr4D	49935283	49938355	3072	True	1102.600000	2772	87.542333	706	3791	3	chr4D.!!$R2	3085
4	TraesCS4A01G230900	chr4D	50031296	50031868	572	True	601.000000	601	85.640000	1934	2508	1	chr4D.!!$R1	574

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
782	928	0.625316	TCGGTAGCCTGTACACCCTA	59.375	55.0	0.00	0.0	0.00	3.53	F
1669	2056	1.150567	GATCGCGTTCAGCTCTGCAT	61.151	55.0	12.18	0.0	45.59	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1921	2314	0.183492	AAGCCACTTTCACTCTGCCA	59.817	50.000	0.00	0.00	0.0	4.92	R
3110	3508	1.005748	CTTGTCAGCGCTGGACAGA	60.006	57.895	35.36	22.86	45.2	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
46	47	3.834799	CGCGGACCTCCTACACCC	61.835	72.222	0.00	0.00	0.00	4.61
110	111	1.672356	CCACGACCTCCCTTGCTTG	60.672	63.158	0.00	0.00	0.00	4.01
113	114	2.436109	GACCTCCCTTGCTTGCCA	59.564	61.111	0.00	0.00	0.00	4.92
119	129	3.726517	CCTTGCTTGCCACCGACG	61.727	66.667	0.00	0.00	0.00	5.12
181	191	1.673808	GAAGGTACCTGATCGGCCGT	61.674	60.000	27.15	12.96	35.61	5.68
287	297	1.599047	CTGGTCCTGCTCCAACGAT	59.401	57.895	0.00	0.00	34.35	3.73
292	302	0.965866	TCCTGCTCCAACGATCGAGT	60.966	55.000	24.34	6.14	0.00	4.18
316	326	2.264794	GGTACTGTCACGCCCCTG	59.735	66.667	0.00	0.00	0.00	4.45
317	327	2.580601	GGTACTGTCACGCCCCTGT	61.581	63.158	0.00	0.00	0.00	4.00
406	493	6.978659	CCTTCATCAGATTTCATCACCAATTG	59.021	38.462	0.00	0.00	0.00	2.32
483	576	5.181622	GTGTATCCCTGTACCTATCTCTTCG	59.818	48.000	0.00	0.00	0.00	3.79
535	633	0.975887	AAATTGGGGCGAAACATGCT	59.024	45.000	0.00	0.00	0.00	3.79
579	677	2.742053	TCTACCGTATACGTATTCGGGC	59.258	50.000	39.19	16.56	46.66	6.13
669	795	0.864455	GCCTGATCTTGATAGCGTGC	59.136	55.000	0.00	0.00	0.00	5.34
777	923	1.002257	TCGGTCGGTAGCCTGTACA	60.002	57.895	0.00	0.00	0.00	2.90
778	924	1.138247	CGGTCGGTAGCCTGTACAC	59.862	63.158	0.00	0.00	0.00	2.90
779	925	1.514553	GGTCGGTAGCCTGTACACC	59.485	63.158	0.00	0.00	0.00	4.16
780	926	1.514553	GTCGGTAGCCTGTACACCC	59.485	63.158	0.00	0.00	0.00	4.61
781	927	0.969409	GTCGGTAGCCTGTACACCCT	60.969	60.000	0.00	0.00	0.00	4.34
782	928	0.625316	TCGGTAGCCTGTACACCCTA	59.375	55.000	0.00	0.00	0.00	3.53
783	929	1.216175	TCGGTAGCCTGTACACCCTAT	59.784	52.381	0.00	0.00	0.00	2.57
784	930	2.442878	TCGGTAGCCTGTACACCCTATA	59.557	50.000	0.00	0.00	0.00	1.31
785	931	2.555757	CGGTAGCCTGTACACCCTATAC	59.444	54.545	0.00	0.00	0.00	1.47
786	932	2.555757	GGTAGCCTGTACACCCTATACG	59.444	54.545	0.00	0.00	0.00	3.06
787	933	2.449137	AGCCTGTACACCCTATACGT	57.551	50.000	0.00	0.00	0.00	3.57
788	934	3.582998	AGCCTGTACACCCTATACGTA	57.417	47.619	0.00	0.00	0.00	3.57
789	935	3.484407	AGCCTGTACACCCTATACGTAG	58.516	50.000	0.08	0.00	0.00	3.51
790	936	3.137176	AGCCTGTACACCCTATACGTAGA	59.863	47.826	0.08	0.00	0.00	2.59
791	937	3.885297	GCCTGTACACCCTATACGTAGAA	59.115	47.826	0.08	0.00	0.00	2.10
792	938	4.339247	GCCTGTACACCCTATACGTAGAAA	59.661	45.833	0.08	0.00	0.00	2.52
793	939	5.163519	GCCTGTACACCCTATACGTAGAAAA	60.164	44.000	0.08	0.00	0.00	2.29
794	940	6.462067	GCCTGTACACCCTATACGTAGAAAAT	60.462	42.308	0.08	0.00	0.00	1.82
795	941	7.255590	GCCTGTACACCCTATACGTAGAAAATA	60.256	40.741	0.08	0.00	0.00	1.40
796	942	8.632679	CCTGTACACCCTATACGTAGAAAATAA	58.367	37.037	0.08	0.00	0.00	1.40
797	943	9.674824	CTGTACACCCTATACGTAGAAAATAAG	57.325	37.037	0.08	0.00	0.00	1.73
798	944	8.137437	TGTACACCCTATACGTAGAAAATAAGC	58.863	37.037	0.08	0.00	0.00	3.09
799	945	7.357429	ACACCCTATACGTAGAAAATAAGCT	57.643	36.000	0.08	0.00	0.00	3.74
807	953	8.961294	ATACGTAGAAAATAAGCTACCGTATG	57.039	34.615	0.08	0.00	36.77	2.39
1669	2056	1.150567	GATCGCGTTCAGCTCTGCAT	61.151	55.000	12.18	0.00	45.59	3.96
1684	2071	1.520342	GCATCTCTCGACAGTGGCC	60.520	63.158	0.00	0.00	0.00	5.36
1752	2139	2.483714	CCAATGCCTGTATCGCTACTGT	60.484	50.000	0.00	0.00	0.00	3.55
1785	2178	2.936032	GTGGTGGCCTCCTTCCCT	60.936	66.667	23.90	0.00	0.00	4.20
1921	2314	2.753452	ACACTCGTGACTTATCGTCCAT	59.247	45.455	3.74	0.00	42.13	3.41
2130	2526	0.883814	CAGCCGGAATCAGCATCTCC	60.884	60.000	5.05	0.00	0.00	3.71
2184	2580	2.409870	CGGCTTCTCCCATTGTGCC	61.410	63.158	0.00	0.00	37.24	5.01
2271	2667	3.257393	CAACTGGGAACGATCTGAGAAG	58.743	50.000	0.00	0.00	0.00	2.85
2425	2821	1.000955	GCCGTCTGAAGAGGTTTCTGA	59.999	52.381	0.00	0.00	32.79	3.27
2598	2994	2.865343	AGTTCAAACGACGAGTGTCT	57.135	45.000	0.00	0.42	43.21	3.41
2837	3233	3.270960	ACTGTCTAGAAGGATCCAGAGGT	59.729	47.826	15.82	6.98	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	2.439701	TGTAGGAGGTCCGCGGAG	60.440	66.667	31.97	0.72	42.08	4.63
27	28	2.753043	GTGTAGGAGGTCCGCGGA	60.753	66.667	27.28	27.28	42.08	5.54
28	29	3.834799	GGTGTAGGAGGTCCGCGG	61.835	72.222	22.12	22.12	42.08	6.46
29	30	3.834799	GGGTGTAGGAGGTCCGCG	61.835	72.222	0.00	0.00	42.08	6.46
30	31	2.682494	TGGGTGTAGGAGGTCCGC	60.682	66.667	0.00	0.00	42.08	5.54
31	32	2.356780	GGTGGGTGTAGGAGGTCCG	61.357	68.421	0.00	0.00	42.08	4.79
32	33	1.993948	GGGTGGGTGTAGGAGGTCC	60.994	68.421	0.00	0.00	0.00	4.46
33	34	1.993948	GGGGTGGGTGTAGGAGGTC	60.994	68.421	0.00	0.00	0.00	3.85
34	35	2.124312	GGGGTGGGTGTAGGAGGT	59.876	66.667	0.00	0.00	0.00	3.85
123	133	4.416738	GGGAGTGGGGTGAGCAGC	62.417	72.222	0.00	0.00	0.00	5.25
135	145	2.444895	GAGCCGATCCAGGGGAGT	60.445	66.667	0.00	0.00	34.05	3.85
204	214	2.125350	CGAGTCAGGCAAGGGAGC	60.125	66.667	0.00	0.00	0.00	4.70
205	215	2.581354	CCGAGTCAGGCAAGGGAG	59.419	66.667	0.00	0.00	0.00	4.30
267	277	2.360475	GTTGGAGCAGGACCAGCC	60.360	66.667	5.06	0.00	38.70	4.85
268	278	2.527951	ATCGTTGGAGCAGGACCAGC	62.528	60.000	0.00	0.00	38.70	4.85
273	283	0.965866	ACTCGATCGTTGGAGCAGGA	60.966	55.000	15.94	0.00	31.34	3.86
287	297	2.359107	AGTACCGGCGTGACTCGA	60.359	61.111	6.01	0.00	42.86	4.04
292	302	2.646719	GTGACAGTACCGGCGTGA	59.353	61.111	6.01	0.00	0.00	4.35
316	326	1.656441	CAACACAAGCAGCAGGGAC	59.344	57.895	0.00	0.00	0.00	4.46
317	327	2.195567	GCAACACAAGCAGCAGGGA	61.196	57.895	0.00	0.00	0.00	4.20
353	399	0.790207	GAATCACGCAGCGACTTCAA	59.210	50.000	24.65	0.00	0.00	2.69
354	400	0.319469	TGAATCACGCAGCGACTTCA	60.319	50.000	24.65	21.58	0.00	3.02
355	401	0.368227	CTGAATCACGCAGCGACTTC	59.632	55.000	24.65	19.39	0.00	3.01
356	402	0.319900	ACTGAATCACGCAGCGACTT	60.320	50.000	24.65	11.33	36.86	3.01
357	403	0.734253	GACTGAATCACGCAGCGACT	60.734	55.000	24.65	1.81	36.86	4.18
359	405	0.319469	TTGACTGAATCACGCAGCGA	60.319	50.000	24.65	0.00	36.92	4.93
360	406	0.723414	ATTGACTGAATCACGCAGCG	59.277	50.000	14.82	14.82	36.92	5.18
361	407	2.476854	GGAATTGACTGAATCACGCAGC	60.477	50.000	0.00	0.00	36.92	5.25
362	408	3.005554	AGGAATTGACTGAATCACGCAG	58.994	45.455	0.00	0.00	36.92	5.18
406	493	2.740447	GCCGATATAACCAAATCCGTCC	59.260	50.000	0.00	0.00	0.00	4.79
535	633	2.006169	TCAGTACGTATACGGCGTTCA	58.994	47.619	27.62	0.00	44.95	3.18
712	840	1.674057	CAGCTGTTCCTTCGGGTCT	59.326	57.895	5.25	0.00	36.28	3.85
777	923	7.308830	CGGTAGCTTATTTTCTACGTATAGGGT	60.309	40.741	0.00	0.00	36.82	4.34
778	924	7.025963	CGGTAGCTTATTTTCTACGTATAGGG	58.974	42.308	0.00	0.00	36.82	3.53
779	925	7.588512	ACGGTAGCTTATTTTCTACGTATAGG	58.411	38.462	0.00	0.00	36.82	2.57
782	928	7.540055	GCATACGGTAGCTTATTTTCTACGTAT	59.460	37.037	0.00	0.00	36.78	3.06
783	929	6.857964	GCATACGGTAGCTTATTTTCTACGTA	59.142	38.462	0.00	0.00	36.82	3.57
784	930	5.689068	GCATACGGTAGCTTATTTTCTACGT	59.311	40.000	0.00	0.00	36.82	3.57
785	931	5.164215	CGCATACGGTAGCTTATTTTCTACG	60.164	44.000	0.00	0.00	36.82	3.51
786	932	5.689068	ACGCATACGGTAGCTTATTTTCTAC	59.311	40.000	0.00	0.00	46.04	2.59
787	933	5.835257	ACGCATACGGTAGCTTATTTTCTA	58.165	37.500	0.00	0.00	46.04	2.10
788	934	4.690122	ACGCATACGGTAGCTTATTTTCT	58.310	39.130	0.00	0.00	46.04	2.52
789	935	5.916883	TCTACGCATACGGTAGCTTATTTTC	59.083	40.000	0.00	0.00	46.04	2.29
790	936	5.835257	TCTACGCATACGGTAGCTTATTTT	58.165	37.500	0.00	0.00	46.04	1.82
791	937	5.443185	TCTACGCATACGGTAGCTTATTT	57.557	39.130	0.00	0.00	46.04	1.40
792	938	5.443185	TTCTACGCATACGGTAGCTTATT	57.557	39.130	0.00	0.00	46.04	1.40
793	939	5.443185	TTTCTACGCATACGGTAGCTTAT	57.557	39.130	0.00	0.00	46.04	1.73
794	940	4.898829	TTTCTACGCATACGGTAGCTTA	57.101	40.909	0.00	0.00	46.04	3.09
795	941	3.788333	TTTCTACGCATACGGTAGCTT	57.212	42.857	0.00	0.00	46.04	3.74
796	942	3.788333	TTTTCTACGCATACGGTAGCT	57.212	42.857	0.00	0.00	46.04	3.32
797	943	4.087648	CGTATTTTCTACGCATACGGTAGC	59.912	45.833	3.54	0.00	46.04	3.58
798	944	5.720156	CGTATTTTCTACGCATACGGTAG	57.280	43.478	3.54	0.00	46.04	3.18
1230	1383	1.085715	AGTCTGACAGGAGGTAGGGT	58.914	55.000	10.88	0.00	0.00	4.34
1669	2056	0.900182	ACATGGCCACTGTCGAGAGA	60.900	55.000	17.61	0.00	38.16	3.10
1684	2071	4.053295	CCCTTTGCAAAGACAAGAACATG	58.947	43.478	35.25	16.84	38.28	3.21
1785	2178	1.214325	CTGTACGGACGTGATGGCA	59.786	57.895	7.73	0.00	0.00	4.92
1921	2314	0.183492	AAGCCACTTTCACTCTGCCA	59.817	50.000	0.00	0.00	0.00	4.92
2184	2580	3.782244	GAGCTCTGGTGCGTTGCG	61.782	66.667	6.43	0.00	38.13	4.85
2271	2667	1.130373	TCAAGCATCGATTTTGACGGC	59.870	47.619	14.87	5.90	0.00	5.68
2385	2781	2.545526	GCATGTGTATCCTTGGATGACG	59.454	50.000	12.08	0.00	0.00	4.35
2425	2821	0.250901	AGAACCAGCGATTTGTGCCT	60.251	50.000	0.00	0.00	0.00	4.75
2664	3060	1.076533	CCGGTTCGACTCCATCAACG	61.077	60.000	0.00	0.00	0.00	4.10
3110	3508	1.005748	CTTGTCAGCGCTGGACAGA	60.006	57.895	35.36	22.86	45.20	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.