AutoCloner

Multiple sequence alignment - TraesCS1B01G145700

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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	TraesCS1B01G145700	chr1B	100.000	2595	0	0	1	2595	199669051	199666457	0.000000e+00	4793.0
1	TraesCS1B01G145700	chr1B	97.895	95	2	0	783	877	667634926	667635020	5.750000e-37	165.0
2	TraesCS1B01G145700	chr1B	96.842	95	3	0	783	877	635138053	635138147	2.670000e-35	159.0
3	TraesCS1B01G145700	chr1B	90.741	54	2	3	675	726	667559714	667559766	4.630000e-08	69.4
4	TraesCS1B01G145700	chr3B	93.542	1951	99	16	1	1928	612313195	612315141	0.000000e+00	2880.0
5	TraesCS1B01G145700	chr3B	92.068	1954	99	26	1	1930	605446974	605445053	0.000000e+00	2699.0
6	TraesCS1B01G145700	chr3B	91.628	1075	82	6	874	1943	62530853	62529782	0.000000e+00	1480.0
7	TraesCS1B01G145700	chr3B	90.769	65	4	2	672	735	235986830	235986893	4.600000e-13	86.1
8	TraesCS1B01G145700	chr3B	88.333	60	4	3	675	732	770750204	770750146	4.630000e-08	69.4
9	TraesCS1B01G145700	chr1D	92.901	1789	99	18	181	1945	467476739	467474955	0.000000e+00	2575.0
10	TraesCS1B01G145700	chr1D	87.797	631	13	13	1953	2568	139142458	139143039	0.000000e+00	680.0
11	TraesCS1B01G145700	chr7A	92.460	1061	73	4	874	1931	641403709	641402653	0.000000e+00	1509.0
12	TraesCS1B01G145700	chr4B	91.894	1061	83	1	874	1931	575618123	575617063	0.000000e+00	1480.0
13	TraesCS1B01G145700	chr4D	91.698	1060	79	3	874	1930	379508030	379506977	0.000000e+00	1461.0
14	TraesCS1B01G145700	chr1A	90.943	1071	89	4	874	1941	520787835	520788900	0.000000e+00	1434.0
15	TraesCS1B01G145700	chr1A	90.605	628	28	8	1955	2568	151878086	151877476	0.000000e+00	804.0
16	TraesCS1B01G145700	chr1A	80.429	373	52	13	525	877	111797160	111796789	5.510000e-67	265.0
17	TraesCS1B01G145700	chr1A	97.872	94	2	0	783	876	543406891	543406984	2.070000e-36	163.0
18	TraesCS1B01G145700	chr1A	95.833	96	4	0	783	878	576164974	576165069	3.460000e-34	156.0
19	TraesCS1B01G145700	chr3A	91.347	1017	78	5	874	1885	170228793	170227782	0.000000e+00	1382.0
20	TraesCS1B01G145700	chr3A	92.105	76	6	0	1857	1932	203007368	203007443	9.820000e-20	108.0
21	TraesCS1B01G145700	chr2A	95.172	435	20	1	127	561	240852569	240853002	0.000000e+00	686.0
22	TraesCS1B01G145700	chr2A	93.985	133	8	0	1	133	240827543	240827675	4.380000e-48	202.0
23	TraesCS1B01G145700	chr2A	92.222	90	7	0	559	648	240853125	240853214	7.540000e-26	128.0
24	TraesCS1B01G145700	chr4A	97.895	95	2	0	783	877	738535100	738535006	5.750000e-37	165.0
25	TraesCS1B01G145700	chr4A	88.333	60	4	3	675	732	662769477	662769419	4.630000e-08	69.4
26	TraesCS1B01G145700	chr7B	88.333	60	4	3	675	732	558985610	558985552	4.630000e-08	69.4

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	TraesCS1B01G145700	chr1B	199666457	199669051	2594	True	4793	4793	100.000	1	2595	1	chr1B.!!$R1	2594
1	TraesCS1B01G145700	chr3B	612313195	612315141	1946	False	2880	2880	93.542	1	1928	1	chr3B.!!$F2	1927
2	TraesCS1B01G145700	chr3B	605445053	605446974	1921	True	2699	2699	92.068	1	1930	1	chr3B.!!$R2	1929
3	TraesCS1B01G145700	chr3B	62529782	62530853	1071	True	1480	1480	91.628	874	1943	1	chr3B.!!$R1	1069
4	TraesCS1B01G145700	chr1D	467474955	467476739	1784	True	2575	2575	92.901	181	1945	1	chr1D.!!$R1	1764
5	TraesCS1B01G145700	chr1D	139142458	139143039	581	False	680	680	87.797	1953	2568	1	chr1D.!!$F1	615
6	TraesCS1B01G145700	chr7A	641402653	641403709	1056	True	1509	1509	92.460	874	1931	1	chr7A.!!$R1	1057
7	TraesCS1B01G145700	chr4B	575617063	575618123	1060	True	1480	1480	91.894	874	1931	1	chr4B.!!$R1	1057
8	TraesCS1B01G145700	chr4D	379506977	379508030	1053	True	1461	1461	91.698	874	1930	1	chr4D.!!$R1	1056
9	TraesCS1B01G145700	chr1A	520787835	520788900	1065	False	1434	1434	90.943	874	1941	1	chr1A.!!$F1	1067
10	TraesCS1B01G145700	chr1A	151877476	151878086	610	True	804	804	90.605	1955	2568	1	chr1A.!!$R2	613
11	TraesCS1B01G145700	chr3A	170227782	170228793	1011	True	1382	1382	91.347	874	1885	1	chr3A.!!$R1	1011
12	TraesCS1B01G145700	chr2A	240852569	240853214	645	False	407	686	93.697	127	648	2	chr2A.!!$F2	521

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
299	300	2.110006	TTGTGTGTAGGCAGCGCA	59.89	55.556	11.47	0.0	0.0	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	2424	0.87909	ACGAAACGGAGGCATTTTCC	59.121	50.0	0.0	0.0	0.0	3.13	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
65	66	7.113965	CGATTTATCTTGCTAATGACCATTTGC	59.886	37.037	17.77	17.77	45.34	3.68
185	186	6.674694	AGACAAAGCTTATGAATGTAGCAG	57.325	37.500	0.00	0.00	37.37	4.24
191	192	4.079787	AGCTTATGAATGTAGCAGGGGAAA	60.080	41.667	0.00	0.00	37.37	3.13
202	203	4.322057	AGCAGGGGAAAACATAGTTGAT	57.678	40.909	0.00	0.00	0.00	2.57
299	300	2.110006	TTGTGTGTAGGCAGCGCA	59.890	55.556	11.47	0.00	0.00	6.09
488	493	6.261381	GCTTGGATTATCGTATGGGTTGTAAA	59.739	38.462	0.00	0.00	0.00	2.01
619	749	9.265901	CACCTGATCTCCTAAAAGTATTATGTG	57.734	37.037	0.00	0.00	0.00	3.21
627	757	6.538742	TCCTAAAAGTATTATGTGCTGCAGAC	59.461	38.462	20.43	13.30	0.00	3.51
639	769	5.229423	TGTGCTGCAGACATTTTTATTTCC	58.771	37.500	20.43	0.00	0.00	3.13
854	1004	7.175641	CAGTGGAGATCCTTGTTTTCAAATAGT	59.824	37.037	0.00	0.00	39.47	2.12
986	1136	5.630415	TGAACATAATCTAACCCCTCTGG	57.370	43.478	0.00	0.00	41.37	3.86
987	1137	5.285401	TGAACATAATCTAACCCCTCTGGA	58.715	41.667	0.00	0.00	38.00	3.86
1022	1172	4.665833	TGATTGTACACCTCCTATTCCG	57.334	45.455	0.00	0.00	0.00	4.30
1029	1179	2.169978	ACACCTCCTATTCCGGCTTAAC	59.830	50.000	0.00	0.00	0.00	2.01
1080	1230	4.853468	TCTGATTTTATGGCTGGGTACA	57.147	40.909	0.00	0.00	0.00	2.90
1085	1235	5.593909	TGATTTTATGGCTGGGTACATTGAG	59.406	40.000	0.00	0.00	0.00	3.02
1157	1308	7.370383	CAATCTTTGTTACTTGCCTACACATT	58.630	34.615	0.00	0.00	0.00	2.71
1266	1423	2.034376	ACTCTCGACGCCCTCTGT	59.966	61.111	0.00	0.00	0.00	3.41
1382	1541	0.249911	GTGGTTCTTCTGCACCTCGT	60.250	55.000	0.00	0.00	33.76	4.18
1514	1673	9.705290	GTGGATTTAGGTGTTGAAAAATTATGT	57.295	29.630	0.00	0.00	0.00	2.29
1685	1844	8.617290	TCTTAGACCTTTAGATTTCCAAACAC	57.383	34.615	0.00	0.00	0.00	3.32
1896	2060	1.066143	CAATACTTGGCTCCCACTCGT	60.066	52.381	0.00	0.00	30.78	4.18
1897	2061	1.276622	ATACTTGGCTCCCACTCGTT	58.723	50.000	0.00	0.00	30.78	3.85
1931	2095	2.287668	GGCGCAACGAGTCATCTAGTAT	60.288	50.000	10.83	0.00	0.00	2.12
1932	2096	2.974536	GCGCAACGAGTCATCTAGTATC	59.025	50.000	0.30	0.00	0.00	2.24
1936	2100	5.375717	GCAACGAGTCATCTAGTATCGTAG	58.624	45.833	0.00	0.00	45.08	3.51
1942	2106	8.121708	ACGAGTCATCTAGTATCGTAGAAAAAC	58.878	37.037	0.00	0.00	44.11	2.43
1943	2107	7.318439	CGAGTCATCTAGTATCGTAGAAAAACG	59.682	40.741	0.00	0.00	43.58	3.60
1979	2143	2.872245	TGTCCTTTGAAGAAAGTGCTCG	59.128	45.455	0.00	0.00	37.47	5.03
2120	2289	2.024868	TTCGTTCGGTCCGTGCATG	61.025	57.895	11.88	0.00	0.00	4.06
2121	2290	2.702751	TTCGTTCGGTCCGTGCATGT	62.703	55.000	11.88	0.00	0.00	3.21
2122	2291	1.444724	CGTTCGGTCCGTGCATGTA	60.445	57.895	11.88	0.00	0.00	2.29
2123	2292	1.680105	CGTTCGGTCCGTGCATGTAC	61.680	60.000	11.88	3.51	0.00	2.90
2180	2359	1.535028	CACAATCTGCCGTGTAAAGCA	59.465	47.619	0.00	0.00	37.46	3.91
2228	2407	1.539827	CAAACATGTCCTCCGTTTCCC	59.460	52.381	0.00	0.00	30.66	3.97
2233	2412	0.761323	TGTCCTCCGTTTCCCACTCA	60.761	55.000	0.00	0.00	0.00	3.41
2245	2424	5.405571	CGTTTCCCACTCATAATTATCTCCG	59.594	44.000	0.00	0.00	0.00	4.63
2249	2428	5.605069	TCCCACTCATAATTATCTCCGGAAA	59.395	40.000	5.23	0.00	0.00	3.13
2289	2468	1.215014	TGCGCGCCGAGATTCTAATG	61.215	55.000	30.77	0.00	0.00	1.90
2297	2476	1.524355	CGAGATTCTAATGTGGCAGCG	59.476	52.381	0.00	0.00	0.00	5.18
2314	2493	2.315176	AGCGCAGATGAATCTACTCCT	58.685	47.619	11.47	0.00	34.85	3.69
2315	2494	3.491342	AGCGCAGATGAATCTACTCCTA	58.509	45.455	11.47	0.00	34.85	2.94
2366	2545	7.776107	TGAGAATATAAGATGAATCTAGCCGG	58.224	38.462	0.00	0.00	35.76	6.13
2458	2642	7.226441	CCTGTCATGATTGAGACCCATTAATA	58.774	38.462	0.00	0.00	33.89	0.98
2568	2752	2.184322	CCGCTGATACACGCACCT	59.816	61.111	0.00	0.00	0.00	4.00
2569	2753	1.878522	CCGCTGATACACGCACCTC	60.879	63.158	0.00	0.00	0.00	3.85
2570	2754	1.139734	CGCTGATACACGCACCTCT	59.860	57.895	0.00	0.00	0.00	3.69
2571	2755	1.142185	CGCTGATACACGCACCTCTG	61.142	60.000	0.00	0.00	0.00	3.35
2572	2756	1.424493	GCTGATACACGCACCTCTGC	61.424	60.000	0.00	0.00	40.38	4.26
2573	2757	0.174389	CTGATACACGCACCTCTGCT	59.826	55.000	0.00	0.00	41.77	4.24
2574	2758	0.173481	TGATACACGCACCTCTGCTC	59.827	55.000	0.00	0.00	41.77	4.26
2575	2759	0.457851	GATACACGCACCTCTGCTCT	59.542	55.000	0.00	0.00	41.77	4.09
2576	2760	0.174389	ATACACGCACCTCTGCTCTG	59.826	55.000	0.00	0.00	41.77	3.35
2577	2761	0.893727	TACACGCACCTCTGCTCTGA	60.894	55.000	0.00	0.00	41.77	3.27
2578	2762	1.735920	CACGCACCTCTGCTCTGAC	60.736	63.158	0.00	0.00	41.77	3.51
2579	2763	2.125753	CGCACCTCTGCTCTGACC	60.126	66.667	0.00	0.00	41.77	4.02
2580	2764	2.644212	CGCACCTCTGCTCTGACCT	61.644	63.158	0.00	0.00	41.77	3.85
2581	2765	1.217779	GCACCTCTGCTCTGACCTC	59.782	63.158	0.00	0.00	40.63	3.85
2582	2766	1.257055	GCACCTCTGCTCTGACCTCT	61.257	60.000	0.00	0.00	40.63	3.69
2583	2767	0.817013	CACCTCTGCTCTGACCTCTC	59.183	60.000	0.00	0.00	0.00	3.20
2584	2768	0.324275	ACCTCTGCTCTGACCTCTCC	60.324	60.000	0.00	0.00	0.00	3.71
2585	2769	1.042559	CCTCTGCTCTGACCTCTCCC	61.043	65.000	0.00	0.00	0.00	4.30
2586	2770	1.000993	TCTGCTCTGACCTCTCCCC	59.999	63.158	0.00	0.00	0.00	4.81
2587	2771	2.039624	TGCTCTGACCTCTCCCCC	59.960	66.667	0.00	0.00	0.00	5.40
2588	2772	2.039624	GCTCTGACCTCTCCCCCA	59.960	66.667	0.00	0.00	0.00	4.96
2589	2773	1.383803	GCTCTGACCTCTCCCCCAT	60.384	63.158	0.00	0.00	0.00	4.00
2590	2774	1.694133	GCTCTGACCTCTCCCCCATG	61.694	65.000	0.00	0.00	0.00	3.66
2591	2775	1.690633	TCTGACCTCTCCCCCATGC	60.691	63.158	0.00	0.00	0.00	4.06
2592	2776	2.692368	TGACCTCTCCCCCATGCC	60.692	66.667	0.00	0.00	0.00	4.40
2593	2777	2.367512	GACCTCTCCCCCATGCCT	60.368	66.667	0.00	0.00	0.00	4.75
2594	2778	1.074471	GACCTCTCCCCCATGCCTA	60.074	63.158	0.00	0.00	0.00	3.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	8.749841	TTAGCAAGATAAATCGAGAATAGCTC	57.250	34.615	0.00	0.00	40.38	4.09
218	219	8.353423	ACAAAAGATGGTTCATATAAGCAAGT	57.647	30.769	0.00	0.00	0.00	3.16
299	300	5.889289	ACAACCTTGTAACATTGGTACAGTT	59.111	36.000	13.90	12.63	38.91	3.16
619	749	6.646240	TCAAAGGAAATAAAAATGTCTGCAGC	59.354	34.615	9.47	4.92	0.00	5.25
639	769	9.770097	TCTACATGAAGCTATAGGAAATCAAAG	57.230	33.333	0.00	0.00	0.00	2.77
670	820	3.096092	GGTGCCTGAAATACAATCCCAA	58.904	45.455	0.00	0.00	0.00	4.12
755	905	8.733857	AAGATTTGAAAAATAAGAACAGAGCG	57.266	30.769	0.00	0.00	0.00	5.03
888	1038	6.963242	CACTGATTAATGTTACAGCACACATC	59.037	38.462	0.00	0.00	32.21	3.06
1022	1172	5.348164	ACAAAATGAACACACAGTTAAGCC	58.652	37.500	0.00	0.00	41.51	4.35
1050	1200	6.406624	CCAGCCATAAAATCAGATGCTTCTTT	60.407	38.462	0.00	0.00	0.00	2.52
1113	1263	6.290605	AGATTGGTCAAAGGGAAACAAATTG	58.709	36.000	0.00	0.00	31.14	2.32
1185	1342	1.771073	CGAGGCAACACACAAAGCGA	61.771	55.000	0.00	0.00	41.41	4.93
1191	1348	1.299850	CGACTCGAGGCAACACACA	60.300	57.895	20.47	0.00	41.41	3.72
1382	1541	3.500448	TGGACACAACAATCCTTGCTA	57.500	42.857	0.00	0.00	35.86	3.49
1452	1611	5.231702	AGGAAATCATGGCAAAAACATGT	57.768	34.783	0.00	0.00	44.57	3.21
1514	1673	3.010027	TCCTTAATCCTGCATCCACAACA	59.990	43.478	0.00	0.00	0.00	3.33
1685	1844	7.939039	ACCATACCACCATATCTTCATTTAGTG	59.061	37.037	0.00	0.00	0.00	2.74
1731	1892	9.034800	TCAAAGAAAATATAAAGCATGGAAGGT	57.965	29.630	0.00	0.00	0.00	3.50
1932	2096	7.169308	AGGATATACATGCTTCGTTTTTCTACG	59.831	37.037	0.00	0.00	42.68	3.51
1936	2100	7.016361	ACAGGATATACATGCTTCGTTTTTC	57.984	36.000	0.00	0.00	33.22	2.29
1942	2106	4.527509	AGGACAGGATATACATGCTTCG	57.472	45.455	0.00	0.00	33.22	3.79
1943	2107	6.291377	TCAAAGGACAGGATATACATGCTTC	58.709	40.000	0.00	0.00	33.22	3.86
1944	2108	6.252599	TCAAAGGACAGGATATACATGCTT	57.747	37.500	0.00	0.00	33.22	3.91
1945	2109	5.894298	TCAAAGGACAGGATATACATGCT	57.106	39.130	0.00	0.00	33.22	3.79
1946	2110	6.291377	TCTTCAAAGGACAGGATATACATGC	58.709	40.000	0.00	0.00	33.22	4.06
1947	2111	8.737168	TTTCTTCAAAGGACAGGATATACATG	57.263	34.615	0.00	0.00	36.29	3.21
1948	2112	8.552296	ACTTTCTTCAAAGGACAGGATATACAT	58.448	33.333	0.00	0.00	43.12	2.29
1949	2113	7.824289	CACTTTCTTCAAAGGACAGGATATACA	59.176	37.037	0.00	0.00	43.12	2.29
1950	2114	7.201652	GCACTTTCTTCAAAGGACAGGATATAC	60.202	40.741	0.00	0.00	43.12	1.47
1951	2115	6.823689	GCACTTTCTTCAAAGGACAGGATATA	59.176	38.462	0.00	0.00	43.12	0.86
1979	2143	2.352617	GCTCGGATCTCTCATCATGGAC	60.353	54.545	0.00	0.00	0.00	4.02
2120	2289	9.617975	GGAATACCACTACTAATTCATACGTAC	57.382	37.037	0.00	0.00	35.97	3.67
2121	2290	9.353431	TGGAATACCACTACTAATTCATACGTA	57.647	33.333	0.00	0.00	41.77	3.57
2122	2291	8.241497	TGGAATACCACTACTAATTCATACGT	57.759	34.615	0.00	0.00	41.77	3.57
2123	2292	8.573885	TCTGGAATACCACTACTAATTCATACG	58.426	37.037	0.00	0.00	41.77	3.06
2180	2359	4.387026	TCTTCTGGATCAACAACCCATT	57.613	40.909	0.00	0.00	0.00	3.16
2228	2407	7.301054	GCATTTTCCGGAGATAATTATGAGTG	58.699	38.462	3.34	0.00	0.00	3.51
2233	2412	5.946377	GGAGGCATTTTCCGGAGATAATTAT	59.054	40.000	3.34	0.00	0.00	1.28
2245	2424	0.879090	ACGAAACGGAGGCATTTTCC	59.121	50.000	0.00	0.00	0.00	3.13
2249	2428	1.439679	GAAGACGAAACGGAGGCATT	58.560	50.000	0.00	0.00	0.00	3.56
2289	2468	1.094073	AGATTCATCTGCGCTGCCAC	61.094	55.000	9.73	0.00	35.42	5.01
2366	2545	4.378563	GCTATGCATCTCATCTCATGTTGC	60.379	45.833	0.19	0.00	36.63	4.17
2458	2642	2.533266	AGCGATATCCTGCAAATCGT	57.467	45.000	16.74	6.20	43.33	3.73
2568	2752	1.000993	GGGGAGAGGTCAGAGCAGA	59.999	63.158	1.66	0.00	0.00	4.26
2569	2753	2.063378	GGGGGAGAGGTCAGAGCAG	61.063	68.421	1.66	0.00	0.00	4.24
2570	2754	2.039624	GGGGGAGAGGTCAGAGCA	59.960	66.667	1.66	0.00	0.00	4.26
2571	2755	1.383803	ATGGGGGAGAGGTCAGAGC	60.384	63.158	0.00	0.00	0.00	4.09
2572	2756	1.694133	GCATGGGGGAGAGGTCAGAG	61.694	65.000	0.00	0.00	0.00	3.35
2573	2757	1.690633	GCATGGGGGAGAGGTCAGA	60.691	63.158	0.00	0.00	0.00	3.27
2574	2758	2.750657	GGCATGGGGGAGAGGTCAG	61.751	68.421	0.00	0.00	0.00	3.51
2575	2759	1.897037	TAGGCATGGGGGAGAGGTCA	61.897	60.000	0.00	0.00	0.00	4.02
2576	2760	1.074471	TAGGCATGGGGGAGAGGTC	60.074	63.158	0.00	0.00	0.00	3.85
2577	2761	3.128991	TAGGCATGGGGGAGAGGT	58.871	61.111	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.