AutoCloner

Multiple sequence alignment - TraesCS3B01G379300

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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	TraesCS3B01G379300	chr3B	100.000	2492	0	0	1	2492	597424738	597427229	0.000000e+00	4602.0
1	TraesCS3B01G379300	chr3B	89.154	544	36	11	1	533	289089146	289088615	0.000000e+00	656.0
2	TraesCS3B01G379300	chr7B	94.216	1971	79	15	534	2492	551486223	551484276	0.000000e+00	2976.0
3	TraesCS3B01G379300	chr7B	80.982	326	47	11	216	532	311405593	311405912	6.880000e-61	244.0
4	TraesCS3B01G379300	chr4D	92.912	1961	97	21	534	2492	459189866	459191786	0.000000e+00	2813.0
5	TraesCS3B01G379300	chr2D	92.817	1963	98	16	534	2492	469109414	469107491	0.000000e+00	2804.0
6	TraesCS3B01G379300	chr1A	92.300	1961	109	16	534	2492	461968265	461966345	0.000000e+00	2747.0
7	TraesCS3B01G379300	chr1A	92.198	1961	112	18	534	2492	35565481	35563560	0.000000e+00	2736.0
8	TraesCS3B01G379300	chrUn	94.350	1770	72	14	722	2485	96551768	96553515	0.000000e+00	2689.0
9	TraesCS3B01G379300	chrUn	91.328	542	33	8	1	533	239362612	239363148	0.000000e+00	728.0
10	TraesCS3B01G379300	chr7A	93.548	1550	95	3	942	2490	48780200	48781745	0.000000e+00	2303.0
11	TraesCS3B01G379300	chr2A	92.312	1626	115	10	865	2485	57824819	57826439	0.000000e+00	2302.0
12	TraesCS3B01G379300	chr2B	93.197	1514	98	3	978	2490	677290936	677292445	0.000000e+00	2220.0
13	TraesCS3B01G379300	chr2B	90.741	540	35	8	1	533	687480200	687480731	0.000000e+00	706.0
14	TraesCS3B01G379300	chr2B	90.556	540	36	8	1	533	687487611	687488142	0.000000e+00	701.0
15	TraesCS3B01G379300	chr2B	91.286	241	13	2	302	534	307354742	307354982	3.090000e-84	322.0
16	TraesCS3B01G379300	chr2B	90.417	240	15	2	302	533	368971677	368971916	2.410000e-80	309.0
17	TraesCS3B01G379300	chr2B	90.000	240	16	2	302	533	307347498	307347737	1.120000e-78	303.0
18	TraesCS3B01G379300	chr2B	92.500	40	2	1	658	696	424521892	424521853	3.460000e-04	56.5
19	TraesCS3B01G379300	chr7D	91.529	1275	61	18	534	1808	69947008	69948235	0.000000e+00	1712.0
20	TraesCS3B01G379300	chr6B	97.403	539	7	2	1	533	613405731	613405194	0.000000e+00	911.0
21	TraesCS3B01G379300	chr6B	91.328	542	33	8	1	533	325234127	325233591	0.000000e+00	728.0
22	TraesCS3B01G379300	chr6B	91.312	541	32	9	1	534	470953203	470953735	0.000000e+00	725.0
23	TraesCS3B01G379300	chr6B	91.111	540	36	7	1	533	619875519	619876053	0.000000e+00	721.0
24	TraesCS3B01G379300	chr6B	90.055	543	36	9	1	533	481524733	481525267	0.000000e+00	688.0
25	TraesCS3B01G379300	chr6B	82.921	404	30	12	534	937	658406107	658405743	6.650000e-86	327.0
26	TraesCS3B01G379300	chr1B	87.485	807	45	9	534	1329	470719577	470720338	0.000000e+00	880.0
27	TraesCS3B01G379300	chr3D	80.909	330	45	14	215	533	381835361	381835039	6.880000e-61	244.0
28	TraesCS3B01G379300	chr5D	90.476	147	9	3	695	838	437458853	437458997	3.270000e-44	189.0

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	TraesCS3B01G379300	chr3B	597424738	597427229	2491	False	4602	4602	100.000	1	2492	1	chr3B.!!$F1	2491
1	TraesCS3B01G379300	chr3B	289088615	289089146	531	True	656	656	89.154	1	533	1	chr3B.!!$R1	532
2	TraesCS3B01G379300	chr7B	551484276	551486223	1947	True	2976	2976	94.216	534	2492	1	chr7B.!!$R1	1958
3	TraesCS3B01G379300	chr4D	459189866	459191786	1920	False	2813	2813	92.912	534	2492	1	chr4D.!!$F1	1958
4	TraesCS3B01G379300	chr2D	469107491	469109414	1923	True	2804	2804	92.817	534	2492	1	chr2D.!!$R1	1958
5	TraesCS3B01G379300	chr1A	461966345	461968265	1920	True	2747	2747	92.300	534	2492	1	chr1A.!!$R2	1958
6	TraesCS3B01G379300	chr1A	35563560	35565481	1921	True	2736	2736	92.198	534	2492	1	chr1A.!!$R1	1958
7	TraesCS3B01G379300	chrUn	96551768	96553515	1747	False	2689	2689	94.350	722	2485	1	chrUn.!!$F1	1763
8	TraesCS3B01G379300	chrUn	239362612	239363148	536	False	728	728	91.328	1	533	1	chrUn.!!$F2	532
9	TraesCS3B01G379300	chr7A	48780200	48781745	1545	False	2303	2303	93.548	942	2490	1	chr7A.!!$F1	1548
10	TraesCS3B01G379300	chr2A	57824819	57826439	1620	False	2302	2302	92.312	865	2485	1	chr2A.!!$F1	1620
11	TraesCS3B01G379300	chr2B	677290936	677292445	1509	False	2220	2220	93.197	978	2490	1	chr2B.!!$F4	1512
12	TraesCS3B01G379300	chr2B	687480200	687480731	531	False	706	706	90.741	1	533	1	chr2B.!!$F5	532
13	TraesCS3B01G379300	chr2B	687487611	687488142	531	False	701	701	90.556	1	533	1	chr2B.!!$F6	532
14	TraesCS3B01G379300	chr7D	69947008	69948235	1227	False	1712	1712	91.529	534	1808	1	chr7D.!!$F1	1274
15	TraesCS3B01G379300	chr6B	613405194	613405731	537	True	911	911	97.403	1	533	1	chr6B.!!$R2	532
16	TraesCS3B01G379300	chr6B	325233591	325234127	536	True	728	728	91.328	1	533	1	chr6B.!!$R1	532
17	TraesCS3B01G379300	chr6B	470953203	470953735	532	False	725	725	91.312	1	534	1	chr6B.!!$F1	533
18	TraesCS3B01G379300	chr6B	619875519	619876053	534	False	721	721	91.111	1	533	1	chr6B.!!$F3	532
19	TraesCS3B01G379300	chr6B	481524733	481525267	534	False	688	688	90.055	1	533	1	chr6B.!!$F2	532
20	TraesCS3B01G379300	chr1B	470719577	470720338	761	False	880	880	87.485	534	1329	1	chr1B.!!$F1	795

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
555	569	1.69415	CACCTTCCTCCTGTTGTCTCA	59.306	52.381	0.0	0.0	0.0	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2460	2524	0.461339	CTGCCCAGCCATCAAAATGC	60.461	55.0	0.0	0.0	0.0	3.56	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
130	135	4.509230	CCTTTTCTTTTCCAGCAGCTTTTC	59.491	41.667	0.00	0.00	0.00	2.29
288	293	8.776061	AGGGCATTTAATTTATTGCTTAGGTA	57.224	30.769	10.18	0.00	35.46	3.08
418	432	9.414295	TGAGCAATTTTGAAATTTCACTCATAG	57.586	29.630	22.94	13.53	36.43	2.23
555	569	1.694150	CACCTTCCTCCTGTTGTCTCA	59.306	52.381	0.00	0.00	0.00	3.27
573	587	2.415512	CTCATCTATGATGGTGCGCATG	59.584	50.000	15.91	3.21	36.02	4.06
625	639	1.963338	GCATAGCAGATCGGCCACC	60.963	63.158	14.56	0.00	0.00	4.61
638	652	3.114616	CCACCGTCGAAGCAGCTG	61.115	66.667	10.11	10.11	0.00	4.24
649	701	2.669569	GCAGCTGCTTCGACCCAA	60.670	61.111	31.33	0.00	38.21	4.12
807	859	5.033589	TGTTCATGTTTGGGCAGATTTTT	57.966	34.783	0.00	0.00	0.00	1.94
838	890	4.018870	TGTGTGCCATGTTCCTCCTTAATA	60.019	41.667	0.00	0.00	0.00	0.98
839	891	4.576463	GTGTGCCATGTTCCTCCTTAATAG	59.424	45.833	0.00	0.00	0.00	1.73
840	892	4.473196	TGTGCCATGTTCCTCCTTAATAGA	59.527	41.667	0.00	0.00	0.00	1.98
841	893	5.045213	TGTGCCATGTTCCTCCTTAATAGAA	60.045	40.000	0.00	0.00	0.00	2.10
842	894	5.529060	GTGCCATGTTCCTCCTTAATAGAAG	59.471	44.000	0.00	0.00	0.00	2.85
843	895	4.517075	GCCATGTTCCTCCTTAATAGAAGC	59.483	45.833	0.00	0.00	0.00	3.86
844	896	5.684704	CCATGTTCCTCCTTAATAGAAGCA	58.315	41.667	0.00	0.00	0.00	3.91
845	897	5.529060	CCATGTTCCTCCTTAATAGAAGCAC	59.471	44.000	0.00	0.00	0.00	4.40
846	898	5.755409	TGTTCCTCCTTAATAGAAGCACA	57.245	39.130	0.00	0.00	0.00	4.57
847	899	6.313519	TGTTCCTCCTTAATAGAAGCACAT	57.686	37.500	0.00	0.00	0.00	3.21
848	900	7.432148	TGTTCCTCCTTAATAGAAGCACATA	57.568	36.000	0.00	0.00	0.00	2.29
849	901	8.034313	TGTTCCTCCTTAATAGAAGCACATAT	57.966	34.615	0.00	0.00	0.00	1.78
850	902	9.154632	TGTTCCTCCTTAATAGAAGCACATATA	57.845	33.333	0.00	0.00	0.00	0.86
898	950	5.866633	GCTTCTATGTAGTATGCAGATCCAC	59.133	44.000	0.00	0.00	31.11	4.02
979	1032	8.292444	ACAAGTCATTGCTAGCCATATTTTTA	57.708	30.769	13.29	0.00	40.27	1.52
1022	1077	7.472334	AGATGGTAAGCAAGATGAACAAAAT	57.528	32.000	0.00	0.00	0.00	1.82
1149	1204	5.221185	CCCAATGCATGAAAGAGATCGAATT	60.221	40.000	0.00	0.00	0.00	2.17
1234	1289	5.052481	GGTTTGAAAGAGCTGCATTCTTTT	58.948	37.500	20.74	6.86	43.07	2.27
1259	1314	1.486310	GTGTGGCATACTGAGGGATCA	59.514	52.381	7.17	0.00	0.00	2.92
1361	1417	4.104102	TCGGAATAGGGTTATTTCAGCCAT	59.896	41.667	0.00	0.00	36.72	4.40
1468	1524	2.557229	CCACCATCATTGGAAACTCCCA	60.557	50.000	0.00	0.00	46.92	4.37
1689	1745	2.559668	CCACTCAAAATGTGATGGCAGT	59.440	45.455	0.00	0.00	37.60	4.40
2016	2076	8.854117	GTCCAAAATGATAAGGAGCTATTCAAT	58.146	33.333	0.00	0.00	0.00	2.57
2068	2128	1.484240	AGAGGGCTTTTGGATCTCTCG	59.516	52.381	0.00	0.00	29.81	4.04
2076	2136	1.729470	TTGGATCTCTCGAGAGGCGC	61.729	60.000	35.70	25.26	41.33	6.53
2103	2163	6.878389	TCAAAATTTTAGATGATGCCAAACCC	59.122	34.615	2.44	0.00	0.00	4.11
2117	2177	2.293399	CCAAACCCTTCTTCACTTTCCG	59.707	50.000	0.00	0.00	0.00	4.30
2288	2349	5.190925	TGGTAGACCATAGGCTACAAATTGT	59.809	40.000	6.49	3.43	42.01	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
130	135	6.930722	AGTCAATTGTGGCTAAAAGAAAATGG	59.069	34.615	5.13	0.00	38.16	3.16
288	293	7.058525	AGTGGCCTAAACTACTTAAAACAGTT	58.941	34.615	3.32	0.00	34.03	3.16
555	569	2.148768	CACATGCGCACCATCATAGAT	58.851	47.619	14.90	0.00	29.71	1.98
603	617	2.740055	CCGATCTGCTATGCCGCC	60.740	66.667	0.00	0.00	0.00	6.13
633	647	0.449388	GATTTGGGTCGAAGCAGCTG	59.551	55.000	10.11	10.11	0.00	4.24
638	652	0.811281	CCTTGGATTTGGGTCGAAGC	59.189	55.000	0.00	0.00	33.99	3.86
648	700	1.021390	CGTCGCTGCTCCTTGGATTT	61.021	55.000	0.00	0.00	0.00	2.17
649	701	1.448540	CGTCGCTGCTCCTTGGATT	60.449	57.895	0.00	0.00	0.00	3.01
711	763	1.759445	GCTGCTGATCCAGACCTTCTA	59.241	52.381	3.41	0.00	34.77	2.10
739	791	0.323957	GGAAACCGTACCTTGCCTCT	59.676	55.000	0.00	0.00	0.00	3.69
1022	1077	2.174854	GCTCCCCTAGCCATCCTTTTTA	59.825	50.000	0.00	0.00	46.25	1.52
1234	1289	1.611410	CCTCAGTATGCCACACAAGCA	60.611	52.381	0.00	0.00	45.94	3.91
1259	1314	6.711277	TGTGGACTATCTTCTAGCAAATTGT	58.289	36.000	0.00	0.00	0.00	2.71
1310	1366	4.348863	TGCCCAATTGTATGCAAAAACT	57.651	36.364	10.90	0.00	38.21	2.66
1893	1953	7.418597	CCATAACCAGCATCAACTAGGTAGTAA	60.419	40.741	0.00	0.00	34.99	2.24
1954	2014	5.195940	CCACTCATTCAAATGGTACCTCAT	58.804	41.667	14.36	0.00	37.03	2.90
2016	2076	3.215151	CCGTAGAGATGAGTGCCTAAGA	58.785	50.000	0.00	0.00	0.00	2.10
2068	2128	5.296813	TCTAAAATTTTGAAGCGCCTCTC	57.703	39.130	13.76	0.00	0.00	3.20
2076	2136	8.445493	GGTTTGGCATCATCTAAAATTTTGAAG	58.555	33.333	13.76	4.13	0.00	3.02
2103	2163	3.386768	TGGACTCGGAAAGTGAAGAAG	57.613	47.619	0.00	0.00	38.74	2.85
2117	2177	5.232414	GCTATAACAATGTCGACTTGGACTC	59.768	44.000	22.82	9.81	37.81	3.36
2373	2434	5.187381	TCCAGCCATCAAATAAATGCAAAGA	59.813	36.000	0.00	0.00	0.00	2.52
2457	2521	1.606885	CCCAGCCATCAAAATGCCGT	61.607	55.000	0.00	0.00	0.00	5.68
2460	2524	0.461339	CTGCCCAGCCATCAAAATGC	60.461	55.000	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.