AutoCloner

Multiple sequence alignment - TraesCS5A01G413600

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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	TraesCS5A01G413600	chr5A	100.000	2684	0	0	1	2684	601722503	601719820	0.000000e+00	4957
1	TraesCS5A01G413600	chr5A	95.710	1818	72	5	114	1927	475642279	475640464	0.000000e+00	2920
2	TraesCS5A01G413600	chr5A	97.368	114	3	0	1	114	448636050	448635937	7.580000e-46	195
3	TraesCS5A01G413600	chr5A	97.368	114	3	0	1	114	539068172	539068285	7.580000e-46	195
4	TraesCS5A01G413600	chr5A	85.256	156	21	2	2418	2572	601986424	601986270	2.770000e-35	159
5	TraesCS5A01G413600	chr5A	83.871	155	18	4	2439	2587	602234551	602234398	1.000000e-29	141
6	TraesCS5A01G413600	chr7A	96.427	1819	58	5	114	1929	276126574	276124760	0.000000e+00	2992
7	TraesCS5A01G413600	chr7A	96.319	1820	59	5	114	1929	37106974	37105159	0.000000e+00	2983
8	TraesCS5A01G413600	chr7A	94.581	1827	83	11	114	1927	7870142	7868319	0.000000e+00	2811
9	TraesCS5A01G413600	chr7A	94.311	1828	89	9	114	1929	715434450	715432626	0.000000e+00	2785
10	TraesCS5A01G413600	chr7A	94.259	1829	88	10	114	1936	39414335	39412518	0.000000e+00	2780
11	TraesCS5A01G413600	chr7A	97.368	114	3	0	1	114	37107123	37107010	7.580000e-46	195
12	TraesCS5A01G413600	chr1A	95.662	1821	67	7	114	1927	575511267	575509452	0.000000e+00	2915
13	TraesCS5A01G413600	chr1A	96.491	114	4	0	1	114	286085660	286085547	3.530000e-44	189
14	TraesCS5A01G413600	chr1A	96.491	114	4	0	1	114	575511416	575511303	3.530000e-44	189
15	TraesCS5A01G413600	chr3A	95.984	1793	61	8	114	1904	676881564	676883347	0.000000e+00	2902
16	TraesCS5A01G413600	chr3A	97.321	112	3	0	1	112	640675769	640675658	9.810000e-45	191
17	TraesCS5A01G413600	chr3A	96.491	114	4	0	1	114	555333858	555333745	3.530000e-44	189
18	TraesCS5A01G413600	chr6A	94.243	1824	96	7	114	1930	562246150	562244329	0.000000e+00	2778
19	TraesCS5A01G413600	chr6A	96.491	114	4	0	1	114	91889493	91889380	3.530000e-44	189
20	TraesCS5A01G413600	chr5D	89.506	486	21	10	2224	2681	482239847	482239364	2.980000e-164	588
21	TraesCS5A01G413600	chr5D	94.079	304	13	2	1927	2229	482240172	482239873	8.760000e-125	457
22	TraesCS5A01G413600	chr5D	87.273	165	16	5	2399	2559	482272959	482272796	1.640000e-42	183
23	TraesCS5A01G413600	chr5D	88.636	88	3	3	2440	2521	482405167	482405081	1.700000e-17	100
24	TraesCS5A01G413600	chr5B	85.928	469	33	10	2238	2681	591549452	591548992	1.120000e-128	470
25	TraesCS5A01G413600	chr2A	97.368	114	3	0	1	114	565068022	565068135	7.580000e-46	195

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	TraesCS5A01G413600	chr5A	601719820	601722503	2683	True	4957.0	4957	100.0000	1	2684	1	chr5A.!!$R3	2683
1	TraesCS5A01G413600	chr5A	475640464	475642279	1815	True	2920.0	2920	95.7100	114	1927	1	chr5A.!!$R2	1813
2	TraesCS5A01G413600	chr7A	276124760	276126574	1814	True	2992.0	2992	96.4270	114	1929	1	chr7A.!!$R3	1815
3	TraesCS5A01G413600	chr7A	7868319	7870142	1823	True	2811.0	2811	94.5810	114	1927	1	chr7A.!!$R1	1813
4	TraesCS5A01G413600	chr7A	715432626	715434450	1824	True	2785.0	2785	94.3110	114	1929	1	chr7A.!!$R4	1815
5	TraesCS5A01G413600	chr7A	39412518	39414335	1817	True	2780.0	2780	94.2590	114	1936	1	chr7A.!!$R2	1822
6	TraesCS5A01G413600	chr7A	37105159	37107123	1964	True	1589.0	2983	96.8435	1	1929	2	chr7A.!!$R5	1928
7	TraesCS5A01G413600	chr1A	575509452	575511416	1964	True	1552.0	2915	96.0765	1	1927	2	chr1A.!!$R2	1926
8	TraesCS5A01G413600	chr3A	676881564	676883347	1783	False	2902.0	2902	95.9840	114	1904	1	chr3A.!!$F1	1790
9	TraesCS5A01G413600	chr6A	562244329	562246150	1821	True	2778.0	2778	94.2430	114	1930	1	chr6A.!!$R2	1816
10	TraesCS5A01G413600	chr5D	482239364	482240172	808	True	522.5	588	91.7925	1927	2681	2	chr5D.!!$R3	754

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
797	854	1.001974	TCAAAGGCGTCTACATGCAGT	59.998	47.619	0.0	0.0	36.08	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2549	2664	0.036388	TCTTGATGAACCGCAGTCCC	60.036	55.0	0.0	0.0	0.0	4.46	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
81	82	1.958205	CGGCATCTTCCTCATCGGC	60.958	63.158	0.00	0.00	0.00	5.54
138	175	1.700042	GGCTCTCCATGGGGATCGTT	61.700	60.000	16.66	0.00	43.91	3.85
299	338	2.126071	CCTACGCGTCCACACTGG	60.126	66.667	18.63	4.04	39.43	4.00
546	594	2.254737	GAGGACGACGAGGAGGAGGA	62.255	65.000	0.00	0.00	0.00	3.71
547	595	1.820481	GGACGACGAGGAGGAGGAG	60.820	68.421	0.00	0.00	0.00	3.69
548	596	1.820481	GACGACGAGGAGGAGGAGG	60.820	68.421	0.00	0.00	0.00	4.30
564	615	4.851214	GGAGGAGGAGCCGGCTCT	62.851	72.222	45.55	34.18	43.43	4.09
696	753	3.461773	CTGCCTCGACCCGACCAT	61.462	66.667	0.00	0.00	0.00	3.55
797	854	1.001974	TCAAAGGCGTCTACATGCAGT	59.998	47.619	0.00	0.00	36.08	4.40
1297	1354	1.893544	ACGTGAAGAGAAGACCGAGA	58.106	50.000	0.00	0.00	0.00	4.04
1301	1358	0.522180	GAAGAGAAGACCGAGACGCA	59.478	55.000	0.00	0.00	0.00	5.24
1400	1457	2.358957	CGACATGGCTTTTCTGATGGA	58.641	47.619	0.00	0.00	0.00	3.41
1405	1462	0.035439	GGCTTTTCTGATGGACGGGA	60.035	55.000	0.00	0.00	0.00	5.14
1749	1809	0.179156	GCCAAACTACGTCCGATCGA	60.179	55.000	18.66	0.00	34.70	3.59
1845	1906	0.965866	CGTGACTGGGAGCTAGGTCA	60.966	60.000	22.66	8.54	36.52	4.02
1937	2003	1.972872	AGATGCCCTTATTCGCTTGG	58.027	50.000	0.00	0.00	0.00	3.61
1940	2006	2.325583	TGCCCTTATTCGCTTGGTAG	57.674	50.000	0.00	0.00	0.00	3.18
1945	2011	0.179067	TTATTCGCTTGGTAGGGCCG	60.179	55.000	0.00	0.00	41.21	6.13
1947	2013	1.696097	ATTCGCTTGGTAGGGCCGAT	61.696	55.000	0.00	0.00	41.21	4.18
1978	2044	5.129634	TGTTGAACTGTTTTCCATAGCAGA	58.870	37.500	0.00	0.00	33.57	4.26
1984	2050	3.325870	TGTTTTCCATAGCAGAGTCGTG	58.674	45.455	0.00	0.00	0.00	4.35
2006	2072	2.496817	GTGAGCTCGGCGATCCTT	59.503	61.111	11.27	0.00	0.00	3.36
2036	2102	1.016627	GAAATCATGCCGTGCTAGCA	58.983	50.000	14.93	14.93	45.94	3.49
2163	2229	2.025037	AGAGGCCATCAATTAACCAGCA	60.025	45.455	5.01	0.00	0.00	4.41
2164	2230	2.961062	GAGGCCATCAATTAACCAGCAT	59.039	45.455	5.01	0.00	0.00	3.79
2165	2231	4.141181	AGAGGCCATCAATTAACCAGCATA	60.141	41.667	5.01	0.00	0.00	3.14
2166	2232	4.744237	AGGCCATCAATTAACCAGCATAT	58.256	39.130	5.01	0.00	0.00	1.78
2193	2259	7.759489	AAGAACTACAAAATGCATAGGAACA	57.241	32.000	0.00	0.00	0.00	3.18
2251	2349	8.028938	TCATTCCTTAATAAAAAGCAGCAACTC	58.971	33.333	0.00	0.00	0.00	3.01
2286	2384	1.341156	AAGAAGAGGAGATGGCGGGG	61.341	60.000	0.00	0.00	0.00	5.73
2308	2406	3.886505	GAGGCCGTCTATATAGCTAGCAT	59.113	47.826	18.83	10.87	0.00	3.79
2331	2429	0.590195	CCGCCATTAGCTGAAGATGC	59.410	55.000	0.00	0.00	40.39	3.91
2429	2544	2.745281	TCAGGGAAATTAAAGCGAACCG	59.255	45.455	0.00	0.00	0.00	4.44
2477	2592	4.446413	GGCGTAGGACGGGTGTGG	62.446	72.222	0.70	0.00	42.82	4.17
2495	2610	2.167487	GTGGTTTTCTGTGCCTTTTCCA	59.833	45.455	0.00	0.00	0.00	3.53
2532	2647	0.549902	TTCAGGGGATCTTCTGGGCA	60.550	55.000	13.20	0.34	0.00	5.36
2536	2651	1.063417	AGGGGATCTTCTGGGCATTTG	60.063	52.381	0.00	0.00	0.00	2.32
2538	2653	1.342374	GGGATCTTCTGGGCATTTGGT	60.342	52.381	0.00	0.00	0.00	3.67
2539	2654	2.027385	GGATCTTCTGGGCATTTGGTC	58.973	52.381	0.00	0.00	0.00	4.02
2545	2660	4.415783	GGGCATTTGGTCCGACTT	57.584	55.556	0.00	0.00	0.00	3.01
2546	2661	2.653557	GGGCATTTGGTCCGACTTT	58.346	52.632	0.00	0.00	0.00	2.66
2547	2662	0.243636	GGGCATTTGGTCCGACTTTG	59.756	55.000	0.00	0.00	0.00	2.77
2548	2663	0.388520	GGCATTTGGTCCGACTTTGC	60.389	55.000	0.00	3.30	0.00	3.68
2549	2664	0.729140	GCATTTGGTCCGACTTTGCG	60.729	55.000	0.00	0.00	0.00	4.85
2581	2697	3.104512	TCATCAAGATTACCGGTGGAGT	58.895	45.455	19.93	0.00	0.00	3.85
2588	2704	1.471119	TTACCGGTGGAGTGCTAGAG	58.529	55.000	19.93	0.00	0.00	2.43
2593	2711	1.036707	GGTGGAGTGCTAGAGCTAGG	58.963	60.000	2.72	0.00	42.66	3.02
2614	2737	2.744166	GCTCCAAATTACCCTACGGACC	60.744	54.545	0.00	0.00	0.00	4.46
2634	2757	1.999735	CAACACTGAACGCGGATATGT	59.000	47.619	12.47	5.18	0.00	2.29
2666	2792	0.385598	GGAAAGCTGAACGCGGTTTC	60.386	55.000	12.47	6.80	45.59	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	1.742768	GTCGGCCGATGAGGAAGAT	59.257	57.895	33.58	0.00	45.00	2.40
384	423	2.721859	CCGCGATCGATCCTGTCA	59.278	61.111	21.57	0.00	38.10	3.58
546	594	4.851214	GAGCCGGCTCCTCCTCCT	62.851	72.222	40.99	12.50	37.11	3.69
547	595	4.851214	AGAGCCGGCTCCTCCTCC	62.851	72.222	44.91	25.00	43.70	4.30
548	596	2.762043	AAGAGCCGGCTCCTCCTC	60.762	66.667	44.91	25.89	43.70	3.71
564	615	1.376683	CGCCCCTTCATCGGAACAA	60.377	57.895	0.00	0.00	0.00	2.83
647	704	1.450312	CTTCGGCGAGGCATTCCTT	60.450	57.895	10.46	0.00	44.46	3.36
757	814	1.211190	GTACGGGTCGACGAGCTTT	59.789	57.895	24.62	14.82	37.61	3.51
830	887	4.084888	GCACGCCAACTGGTACGC	62.085	66.667	0.00	0.00	37.57	4.42
831	888	2.248135	TTGCACGCCAACTGGTACG	61.248	57.895	0.00	0.00	37.57	3.67
832	889	3.739167	TTGCACGCCAACTGGTAC	58.261	55.556	0.00	0.00	37.57	3.34
1301	1358	0.109086	CTTCATCAGCGACGACCACT	60.109	55.000	0.00	0.00	0.00	4.00
1400	1457	3.771160	GGAGCATGTCCGTCCCGT	61.771	66.667	0.00	0.00	34.84	5.28
1749	1809	1.001815	CAAAAGACGCCACAAATCCGT	60.002	47.619	0.00	0.00	37.99	4.69
1783	1843	5.245075	AGGATGCGGGAAATTTAAAACTTGA	59.755	36.000	0.00	0.00	0.00	3.02
1845	1906	2.121228	TAGTTTGGCCCCTGGGGT	60.121	61.111	31.95	14.37	46.51	4.95
1917	1983	2.301346	CCAAGCGAATAAGGGCATCTT	58.699	47.619	0.00	0.00	39.40	2.40
1937	2003	1.141053	ACAATCTGGAATCGGCCCTAC	59.859	52.381	0.00	0.00	0.00	3.18
1940	2006	0.740737	CAACAATCTGGAATCGGCCC	59.259	55.000	0.00	0.00	0.00	5.80
1945	2011	6.642540	GGAAAACAGTTCAACAATCTGGAATC	59.357	38.462	0.00	0.00	34.02	2.52
1947	2013	5.420421	TGGAAAACAGTTCAACAATCTGGAA	59.580	36.000	0.00	0.00	34.02	3.53
1978	2044	1.870383	GAGCTCACGACTCACGACT	59.130	57.895	9.40	0.00	45.77	4.18
1984	2050	2.975167	GATCGCCGAGCTCACGACTC	62.975	65.000	25.72	19.88	38.85	3.36
2006	2072	3.119743	CGGCATGATTTCTCTCAAGCAAA	60.120	43.478	0.00	0.00	40.64	3.68
2036	2102	4.279169	CAGGGTTGATCATGACAAGTTGTT	59.721	41.667	10.45	0.00	0.00	2.83
2142	2208	2.025037	TGCTGGTTAATTGATGGCCTCT	60.025	45.455	3.32	0.00	0.00	3.69
2193	2259	7.120726	GCATTTTGTAGGTGGTTACTTCTGTAT	59.879	37.037	0.00	0.00	0.00	2.29
2233	2331	4.472286	GTGCGAGTTGCTGCTTTTTATTA	58.528	39.130	3.50	0.00	46.63	0.98
2236	2334	1.333702	CGTGCGAGTTGCTGCTTTTTA	60.334	47.619	3.50	0.00	46.63	1.52
2286	2384	3.280295	TGCTAGCTATATAGACGGCCTC	58.720	50.000	17.23	0.00	0.00	4.70
2331	2429	1.372582	CCTCCATCGTTCACACATGG	58.627	55.000	0.00	0.00	38.83	3.66
2371	2486	3.223661	GGAGCATCGCAGGGATTAG	57.776	57.895	0.00	0.00	34.37	1.73
2473	2588	2.167487	GGAAAAGGCACAGAAAACCACA	59.833	45.455	0.00	0.00	0.00	4.17
2477	2592	3.069443	TGGATGGAAAAGGCACAGAAAAC	59.931	43.478	0.00	0.00	0.00	2.43
2495	2610	2.176045	GAAACCCCACGGAAAATGGAT	58.824	47.619	0.00	0.00	39.87	3.41
2541	2656	3.423154	CCGCAGTCCCGCAAAGTC	61.423	66.667	0.00	0.00	0.00	3.01
2542	2657	3.767630	AACCGCAGTCCCGCAAAGT	62.768	57.895	0.00	0.00	0.00	2.66
2543	2658	2.966309	GAACCGCAGTCCCGCAAAG	61.966	63.158	0.00	0.00	0.00	2.77
2544	2659	2.975799	GAACCGCAGTCCCGCAAA	60.976	61.111	0.00	0.00	0.00	3.68
2545	2660	3.545124	ATGAACCGCAGTCCCGCAA	62.545	57.895	0.00	0.00	0.00	4.85
2546	2661	3.950794	GATGAACCGCAGTCCCGCA	62.951	63.158	0.00	0.00	0.00	5.69
2547	2662	3.195698	GATGAACCGCAGTCCCGC	61.196	66.667	0.00	0.00	0.00	6.13
2548	2663	1.361668	CTTGATGAACCGCAGTCCCG	61.362	60.000	0.00	0.00	0.00	5.14
2549	2664	0.036388	TCTTGATGAACCGCAGTCCC	60.036	55.000	0.00	0.00	0.00	4.46
2588	2704	3.741249	GTAGGGTAATTTGGAGCCTAGC	58.259	50.000	5.14	0.00	45.37	3.42
2614	2737	1.999735	ACATATCCGCGTTCAGTGTTG	59.000	47.619	4.92	0.00	0.00	3.33
2634	2757	4.160329	TCAGCTTTCCAGGAAGAAGAGTA	58.840	43.478	1.07	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.