AutoCloner

Multiple sequence alignment - TraesCS5D01G526300

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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	TraesCS5D01G526300	chr5D	100.000	3293	0	0	1	3293	544230470	544233762	0.000000e+00	6082.0
1	TraesCS5D01G526300	chr5D	85.206	2109	239	35	408	2496	544148404	544150459	0.000000e+00	2098.0
2	TraesCS5D01G526300	chr5D	78.405	1329	252	18	999	2320	544481609	544482909	0.000000e+00	832.0
3	TraesCS5D01G526300	chr5D	77.646	1266	273	10	999	2259	544459877	544461137	0.000000e+00	761.0
4	TraesCS5D01G526300	chr5D	76.843	1153	248	13	999	2139	544532515	544533660	1.670000e-177	632.0
5	TraesCS5D01G526300	chr5D	81.368	424	27	13	179	574	544213705	544214104	6.910000e-77	298.0
6	TraesCS5D01G526300	chr5D	87.952	83	7	2	9	90	544147953	544148033	9.730000e-16	95.3
7	TraesCS5D01G526300	chr4A	93.701	3318	146	20	1	3293	625078604	625075325	0.000000e+00	4911.0
8	TraesCS5D01G526300	chr4A	84.275	1946	246	38	587	2508	625166651	625164742	0.000000e+00	1844.0
9	TraesCS5D01G526300	chr4A	78.751	1073	202	21	999	2055	624992940	624991878	0.000000e+00	695.0
10	TraesCS5D01G526300	chr4A	82.072	251	25	11	106	348	625167332	625167094	2.590000e-46	196.0
11	TraesCS5D01G526300	chr4A	97.753	89	2	0	534	622	625091899	625091811	1.580000e-33	154.0
12	TraesCS5D01G526300	chr5B	93.029	2367	124	23	932	3285	686432169	686434507	0.000000e+00	3419.0
13	TraesCS5D01G526300	chr5B	84.025	1953	251	44	578	2508	686200687	686202600	0.000000e+00	1821.0
14	TraesCS5D01G526300	chr5B	85.387	1355	113	39	317	1599	686333231	686334572	0.000000e+00	1327.0
15	TraesCS5D01G526300	chr5B	88.087	915	86	17	1597	2508	686342920	686343814	0.000000e+00	1064.0
16	TraesCS5D01G526300	chr5B	78.641	515	62	22	317	789	686430414	686430922	6.910000e-77	298.0
17	TraesCS5D01G526300	chr5B	78.144	334	41	13	170	474	686410676	686411006	2.020000e-42	183.0

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	TraesCS5D01G526300	chr5D	544230470	544233762	3292	False	6082.00	6082	100.0000	1	3293	1	chr5D.!!$F2	3292
1	TraesCS5D01G526300	chr5D	544147953	544150459	2506	False	1096.65	2098	86.5790	9	2496	2	chr5D.!!$F6	2487
2	TraesCS5D01G526300	chr5D	544481609	544482909	1300	False	832.00	832	78.4050	999	2320	1	chr5D.!!$F4	1321
3	TraesCS5D01G526300	chr5D	544459877	544461137	1260	False	761.00	761	77.6460	999	2259	1	chr5D.!!$F3	1260
4	TraesCS5D01G526300	chr5D	544532515	544533660	1145	False	632.00	632	76.8430	999	2139	1	chr5D.!!$F5	1140
5	TraesCS5D01G526300	chr4A	625075325	625078604	3279	True	4911.00	4911	93.7010	1	3293	1	chr4A.!!$R2	3292
6	TraesCS5D01G526300	chr4A	625164742	625167332	2590	True	1020.00	1844	83.1735	106	2508	2	chr4A.!!$R4	2402
7	TraesCS5D01G526300	chr4A	624991878	624992940	1062	True	695.00	695	78.7510	999	2055	1	chr4A.!!$R1	1056
8	TraesCS5D01G526300	chr5B	686430414	686434507	4093	False	1858.50	3419	85.8350	317	3285	2	chr5B.!!$F5	2968
9	TraesCS5D01G526300	chr5B	686200687	686202600	1913	False	1821.00	1821	84.0250	578	2508	1	chr5B.!!$F1	1930
10	TraesCS5D01G526300	chr5B	686333231	686334572	1341	False	1327.00	1327	85.3870	317	1599	1	chr5B.!!$F2	1282
11	TraesCS5D01G526300	chr5B	686342920	686343814	894	False	1064.00	1064	88.0870	1597	2508	1	chr5B.!!$F3	911

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
684	1104	0.037605	ACTAGTGCCGAACCTTTCCG	60.038	55.0	0.0	0.0	0.0	4.3	F
1451	3070	0.178975	TTGGATTTGTCCGCCAACCT	60.179	50.0	0.0	0.0	36.8	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1567	3192	0.389166	CTGAGGTTGAGCTCACGGAC	60.389	60.0	18.03	12.39	0.00	4.79	R
3107	4774	0.178767	CATGGAGCCATCTCGGTTGA	59.821	55.0	0.00	0.00	40.26	3.18	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
132	134	7.986562	ACTTAGAAAGAGTTGAGTTTTTGACC	58.013	34.615	0.00	0.00	0.00	4.02
208	321	5.469760	GCTACAGCATTTTCCCACAATTTTT	59.530	36.000	0.00	0.00	41.59	1.94
254	371	3.084039	TGGGTAAGAACAGTCGACGTAT	58.916	45.455	10.46	0.00	0.00	3.06
393	535	6.374333	GCATAAGTATTCTTTGTGTTCTCCCA	59.626	38.462	0.00	0.00	35.36	4.37
435	589	2.202797	CCGCACGGGATCACTGAG	60.203	66.667	0.00	0.00	38.47	3.35
485	639	1.562942	TGCTTGCATGAGGGAATCTCT	59.437	47.619	3.33	0.00	42.86	3.10
490	644	3.273434	TGCATGAGGGAATCTCTTTTCG	58.727	45.455	0.00	0.00	42.86	3.46
499	653	4.568760	GGGAATCTCTTTTCGCTTACTCAG	59.431	45.833	0.00	0.00	36.09	3.35
506	674	4.992951	TCTTTTCGCTTACTCAGTTTACCC	59.007	41.667	0.00	0.00	0.00	3.69
574	757	4.547532	CTGTTCACGTCTAGTTGCTACTT	58.452	43.478	6.03	0.00	35.78	2.24
684	1104	0.037605	ACTAGTGCCGAACCTTTCCG	60.038	55.000	0.00	0.00	0.00	4.30
799	2352	1.681327	GGAGTCAGTCGTGGGCCTA	60.681	63.158	4.53	0.00	0.00	3.93
801	2354	0.966370	GAGTCAGTCGTGGGCCTAGT	60.966	60.000	4.53	0.00	0.00	2.57
804	2357	1.741770	CAGTCGTGGGCCTAGTTGC	60.742	63.158	4.53	0.00	0.00	4.17
853	2453	3.177600	CAAGCATGCTTACGGCGT	58.822	55.556	31.48	19.64	45.43	5.68
858	2458	2.358125	ATGCTTACGGCGTGCACA	60.358	55.556	24.41	18.01	45.43	4.57
862	2462	1.954146	CTTACGGCGTGCACACACT	60.954	57.895	24.86	0.00	45.10	3.55
875	2475	2.797156	GCACACACTCGCTATAAGATGG	59.203	50.000	0.00	0.00	0.00	3.51
876	2476	2.797156	CACACACTCGCTATAAGATGGC	59.203	50.000	0.00	0.00	0.00	4.40
884	2484	2.507484	GCTATAAGATGGCATGCACCA	58.493	47.619	21.36	9.76	45.82	4.17
902	2502	0.667184	CACCCAGCAATTTTCGCCAC	60.667	55.000	0.00	0.00	0.00	5.01
929	2530	0.447406	TGCGAATCACTTGCATTCCG	59.553	50.000	0.00	0.00	32.86	4.30
1451	3070	0.178975	TTGGATTTGTCCGCCAACCT	60.179	50.000	0.00	0.00	36.80	3.50
1567	3192	5.976534	CCGTCTCTTTCATCACTATCTTCTG	59.023	44.000	0.00	0.00	0.00	3.02
1632	3257	1.202313	GCTCGTGTTAGCTTCTCCGAT	60.202	52.381	0.00	0.00	39.50	4.18
1640	3265	1.123077	AGCTTCTCCGATATGCCACA	58.877	50.000	0.00	0.00	0.00	4.17
1799	3424	5.357032	AGTTTGACAACCTTTGGTACTTGAG	59.643	40.000	0.00	0.00	33.12	3.02
1830	3455	3.302365	AATTCATTTGTTGGCGAGGTG	57.698	42.857	0.00	0.00	0.00	4.00
1846	3471	2.814336	GAGGTGCCCAAGAGTTTGTTAG	59.186	50.000	0.00	0.00	32.21	2.34
1851	3476	2.876581	CCCAAGAGTTTGTTAGGGCTT	58.123	47.619	0.00	0.00	32.21	4.35
2034	3668	4.914983	ACAACATTGTCATGTCTGGAGAT	58.085	39.130	0.00	0.00	43.34	2.75
2202	3836	2.364324	GAGCAACCATACTGTATCCGGA	59.636	50.000	6.61	6.61	0.00	5.14
2325	3959	5.064452	CAGTGGACTGATTTCATCTACAAGC	59.936	44.000	0.04	0.00	46.59	4.01
2326	3960	5.046014	AGTGGACTGATTTCATCTACAAGCT	60.046	40.000	0.00	0.00	0.00	3.74
2327	3961	6.155221	AGTGGACTGATTTCATCTACAAGCTA	59.845	38.462	0.00	0.00	0.00	3.32
2328	3962	6.818644	GTGGACTGATTTCATCTACAAGCTAA	59.181	38.462	0.00	0.00	0.00	3.09
2329	3963	7.010923	GTGGACTGATTTCATCTACAAGCTAAG	59.989	40.741	0.00	0.00	0.00	2.18
2338	3972	7.661536	TCATCTACAAGCTAAGTATGAGGTT	57.338	36.000	0.00	0.00	37.93	3.50
2360	3994	4.914983	TCCAAAGCACATCAAAGAGAGAT	58.085	39.130	0.00	0.00	0.00	2.75
2361	3995	4.940046	TCCAAAGCACATCAAAGAGAGATC	59.060	41.667	0.00	0.00	0.00	2.75
2692	4339	5.654650	ACTTTTTAATTGGTCATGGCCGATA	59.345	36.000	19.72	5.50	32.48	2.92
2798	4445	4.074259	TGCATGGTTCATATACAGATGGC	58.926	43.478	0.00	0.00	0.00	4.40
2821	4483	1.648504	GACGTTAGCATGTACCCACC	58.351	55.000	0.00	0.00	0.00	4.61
2856	4518	1.813337	CCGGACGTACATGCATGCA	60.813	57.895	26.53	25.04	0.00	3.96
2971	4633	5.710984	CTGCAGAGAATCATTGCTTCTTTT	58.289	37.500	8.42	0.00	37.82	2.27
3022	4684	2.750166	CTCCTCGTGCTTTCTCTCTGTA	59.250	50.000	0.00	0.00	0.00	2.74
3034	4698	6.369890	GCTTTCTCTCTGTATGTGACATGAAA	59.630	38.462	8.61	6.58	37.45	2.69
3092	4759	3.730761	CTCAGTTGGTGCCGCTGC	61.731	66.667	0.00	0.00	38.26	5.25
3107	4774	1.437160	CTGCCAAACAAACACGCCT	59.563	52.632	0.00	0.00	0.00	5.52
3157	4824	2.125832	CCCGCGAACGTATGTGGT	60.126	61.111	8.23	0.00	37.70	4.16
3166	4833	3.737047	CGAACGTATGTGGTATCAGGCTT	60.737	47.826	0.00	0.00	0.00	4.35
3202	4869	0.969149	CACTATGGCGAGCATAGGGA	59.031	55.000	11.62	0.00	38.07	4.20
3287	4955	1.317613	AGCGAGGTTGACAATGCAAA	58.682	45.000	0.00	0.00	0.00	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	9.961265	CGTTTCTAAGTTGACCACATATATAGA	57.039	33.333	0.00	0.00	0.00	1.98
66	67	9.193133	CCGTTTCTAAGTTGACCACATATATAG	57.807	37.037	0.00	0.00	0.00	1.31
132	134	7.116662	CCAATTTGATGATGGCGTATAAAATGG	59.883	37.037	0.00	0.00	0.00	3.16
299	422	0.392998	ACCAACCGAGATGATGTGCC	60.393	55.000	0.00	0.00	0.00	5.01
393	535	3.319972	ACAGTTGCATTGCACAGAGAAAT	59.680	39.130	11.66	0.00	38.71	2.17
435	589	2.805099	GCTCTTGTCACATATGCCTAGC	59.195	50.000	1.58	0.00	0.00	3.42
485	639	4.067192	GGGGTAAACTGAGTAAGCGAAAA	58.933	43.478	0.00	0.00	0.00	2.29
490	644	2.570302	TGGAGGGGTAAACTGAGTAAGC	59.430	50.000	0.00	0.00	0.00	3.09
499	653	0.919710	AGGATGCTGGAGGGGTAAAC	59.080	55.000	0.00	0.00	0.00	2.01
506	674	0.742281	CGTTGACAGGATGCTGGAGG	60.742	60.000	19.22	6.07	42.53	4.30
574	757	2.093658	GGCTAAAGCTGGTGTAGTAGCA	60.094	50.000	5.99	0.00	42.29	3.49
799	2352	0.034896	CTGTTAGTCCGTGGGCAACT	59.965	55.000	0.00	0.00	0.00	3.16
801	2354	0.250124	CACTGTTAGTCCGTGGGCAA	60.250	55.000	0.00	0.00	0.00	4.52
804	2357	1.375523	GGCACTGTTAGTCCGTGGG	60.376	63.158	0.00	0.00	33.02	4.61
853	2453	3.447742	CATCTTATAGCGAGTGTGTGCA	58.552	45.455	0.00	0.00	0.00	4.57
856	2456	2.430694	TGCCATCTTATAGCGAGTGTGT	59.569	45.455	0.00	0.00	0.00	3.72
858	2458	3.657634	CATGCCATCTTATAGCGAGTGT	58.342	45.455	0.00	0.00	0.00	3.55
862	2462	2.416747	GTGCATGCCATCTTATAGCGA	58.583	47.619	16.68	0.00	0.00	4.93
875	2475	2.175035	AATTGCTGGGTGGTGCATGC	62.175	55.000	11.82	11.82	39.07	4.06
876	2476	0.322322	AAATTGCTGGGTGGTGCATG	59.678	50.000	0.00	0.00	39.07	4.06
884	2484	1.665442	GTGGCGAAAATTGCTGGGT	59.335	52.632	0.00	0.00	0.00	4.51
902	2502	2.563976	CAAGTGATTCGCAAGTGTTCG	58.436	47.619	0.00	0.00	39.48	3.95
1027	2635	0.749454	GGCAAGAGGAACGCCATGAT	60.749	55.000	0.00	0.00	45.52	2.45
1451	3070	2.687566	GGAGGGGGCCGAAGAAGA	60.688	66.667	0.00	0.00	0.00	2.87
1567	3192	0.389166	CTGAGGTTGAGCTCACGGAC	60.389	60.000	18.03	12.39	0.00	4.79
1873	3504	4.295141	TGAAAACCATACCCGATGAACT	57.705	40.909	0.00	0.00	37.82	3.01
2034	3668	1.078497	CCCGGACACAGCATTGCTA	60.078	57.895	11.55	0.00	36.40	3.49
2202	3836	3.078837	CCCAGTTACGGTATTGTTGCTT	58.921	45.455	0.00	0.00	0.00	3.91
2325	3959	5.245531	TGTGCTTTGGAACCTCATACTTAG	58.754	41.667	0.00	0.00	0.00	2.18
2326	3960	5.235850	TGTGCTTTGGAACCTCATACTTA	57.764	39.130	0.00	0.00	0.00	2.24
2327	3961	4.098914	TGTGCTTTGGAACCTCATACTT	57.901	40.909	0.00	0.00	0.00	2.24
2328	3962	3.788227	TGTGCTTTGGAACCTCATACT	57.212	42.857	0.00	0.00	0.00	2.12
2329	3963	4.009675	TGATGTGCTTTGGAACCTCATAC	58.990	43.478	0.00	0.00	0.00	2.39
2338	3972	4.356405	TCTCTCTTTGATGTGCTTTGGA	57.644	40.909	0.00	0.00	0.00	3.53
2360	3994	7.401493	AGAACCTCTTATTCTTCTCTTCATGGA	59.599	37.037	0.00	0.00	32.32	3.41
2361	3995	7.563906	AGAACCTCTTATTCTTCTCTTCATGG	58.436	38.462	0.00	0.00	32.32	3.66
2442	4083	2.432510	AGAAGGTCTTTATGGAGCCTCG	59.567	50.000	0.00	0.00	34.64	4.63
2599	4246	8.142994	ACCATAAGCTGTAATAAAGACATTCG	57.857	34.615	0.00	0.00	0.00	3.34
2636	4283	2.388310	TTCAACCGGATTCGCACATA	57.612	45.000	9.46	0.00	34.56	2.29
2692	4339	2.173519	CCCACCTCACAATTTGCATCT	58.826	47.619	0.00	0.00	0.00	2.90
2798	4445	2.277084	GGGTACATGCTAACGTCCAAG	58.723	52.381	0.00	0.00	0.00	3.61
2856	4518	4.833478	AGCCTGTCAAGTCATATGAGTT	57.167	40.909	18.30	18.30	38.16	3.01
2994	4656	1.893919	AAAGCACGAGGAGGAGGAGC	61.894	60.000	0.00	0.00	0.00	4.70
3022	4684	4.002982	ACATACGTGCTTTCATGTCACAT	58.997	39.130	0.00	0.00	41.28	3.21
3092	4759	1.555477	GTTGAGGCGTGTTTGTTTGG	58.445	50.000	0.00	0.00	0.00	3.28
3107	4774	0.178767	CATGGAGCCATCTCGGTTGA	59.821	55.000	0.00	0.00	40.26	3.18
3157	4824	8.243426	GTGTGTTGAATTATTGAAAGCCTGATA	58.757	33.333	0.00	0.00	0.00	2.15
3166	4833	7.312154	GCCATAGTGTGTGTTGAATTATTGAA	58.688	34.615	0.00	0.00	0.00	2.69
3202	4869	1.442773	ATCTGTGCTGGGAGCCATAT	58.557	50.000	0.00	0.00	41.51	1.78

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.