AutoCloner

Multiple sequence alignment - TraesCS2D01G501600

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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	TraesCS2D01G501600	chr2D	100.000	2487	0	0	1	2487	595722140	595719654	0.000000e+00	4593.0
1	TraesCS2D01G501600	chr7B	96.237	2498	74	8	1	2487	397829118	397831606	0.000000e+00	4074.0
2	TraesCS2D01G501600	chr3D	94.469	687	33	4	1179	1864	91313682	91314364	0.000000e+00	1053.0
3	TraesCS2D01G501600	chr3D	90.954	409	22	9	2	403	91312392	91312792	1.010000e-148	536.0
4	TraesCS2D01G501600	chr3D	84.483	58	5	4	745	798	574518168	574518111	1.000000e-03	54.7
5	TraesCS2D01G501600	chr6B	89.485	485	40	7	873	1351	712236772	712236293	9.840000e-169	603.0
6	TraesCS2D01G501600	chr6B	87.568	370	33	9	1500	1861	713262391	713262027	1.380000e-112	416.0
7	TraesCS2D01G501600	chr6B	85.086	409	49	10	1	403	59411940	59411538	8.280000e-110	407.0
8	TraesCS2D01G501600	chr3A	90.435	460	32	6	2033	2487	713316609	713316157	1.650000e-166	595.0
9	TraesCS2D01G501600	chr3A	85.714	84	8	4	67	149	682932609	682932689	4.410000e-13	86.1
10	TraesCS2D01G501600	chr1B	90.372	457	39	4	2033	2487	525798643	525799096	1.650000e-166	595.0
11	TraesCS2D01G501600	chr1B	84.878	410	48	12	1	403	650042764	650043166	3.850000e-108	401.0
12	TraesCS2D01G501600	chr1B	86.728	324	33	9	83	403	172382890	172383206	3.940000e-93	351.0
13	TraesCS2D01G501600	chr1B	85.000	140	17	1	896	1035	520820099	520819964	3.340000e-29	139.0
14	TraesCS2D01G501600	chr6A	89.765	469	39	6	889	1353	613328641	613328178	2.130000e-165	592.0
15	TraesCS2D01G501600	chr6A	87.179	234	15	9	66	297	259900059	259899839	4.110000e-63	252.0
16	TraesCS2D01G501600	chr6D	89.149	470	41	9	889	1353	467032585	467032121	5.960000e-161	577.0
17	TraesCS2D01G501600	chr4B	87.859	453	48	6	1411	1861	444593059	444592612	2.190000e-145	525.0
18	TraesCS2D01G501600	chr4B	94.286	35	2	0	745	779	190690938	190690972	1.000000e-03	54.7
19	TraesCS2D01G501600	chr4A	85.435	460	56	11	1408	1861	344038791	344039245	3.750000e-128	468.0
20	TraesCS2D01G501600	chr4A	94.595	37	2	0	745	781	548275646	548275610	9.610000e-05	58.4
21	TraesCS2D01G501600	chr1A	86.728	324	33	9	83	403	12409903	12409587	3.940000e-93	351.0
22	TraesCS2D01G501600	chr7A	85.942	313	30	9	66	378	552412023	552411725	3.090000e-84	322.0
23	TraesCS2D01G501600	chr7A	85.345	232	15	9	66	297	577495863	577496075	3.220000e-54	222.0
24	TraesCS2D01G501600	chr7A	83.190	232	16	10	66	297	577672446	577672238	9.080000e-45	191.0
25	TraesCS2D01G501600	chrUn	87.500	224	25	3	180	403	266952259	266952039	3.170000e-64	255.0
26	TraesCS2D01G501600	chrUn	87.500	224	25	3	180	403	289877896	289877676	3.170000e-64	255.0
27	TraesCS2D01G501600	chr3B	85.232	237	26	8	66	297	57284013	57283781	4.140000e-58	235.0
28	TraesCS2D01G501600	chr3B	82.530	166	20	6	66	231	57350388	57350232	1.200000e-28	137.0
29	TraesCS2D01G501600	chr2B	88.095	84	7	3	67	149	596908100	596908019	2.040000e-16	97.1
30	TraesCS2D01G501600	chr2B	94.444	36	1	1	744	779	637106639	637106605	1.000000e-03	54.7
31	TraesCS2D01G501600	chr7D	94.286	35	2	0	745	779	278231040	278231074	1.000000e-03	54.7
32	TraesCS2D01G501600	chr7D	94.286	35	2	0	745	779	579762548	579762514	1.000000e-03	54.7
33	TraesCS2D01G501600	chr2A	85.455	55	4	3	745	795	423069784	423069838	1.000000e-03	54.7
34	TraesCS2D01G501600	chr1D	88.636	44	5	0	745	788	210925684	210925641	1.000000e-03	54.7

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	TraesCS2D01G501600	chr2D	595719654	595722140	2486	True	4593.0	4593	100.0000	1	2487	1	chr2D.!!$R1	2486
1	TraesCS2D01G501600	chr7B	397829118	397831606	2488	False	4074.0	4074	96.2370	1	2487	1	chr7B.!!$F1	2486
2	TraesCS2D01G501600	chr3D	91312392	91314364	1972	False	794.5	1053	92.7115	2	1864	2	chr3D.!!$F1	1862

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
472	484	0.172803	ACGACAGGGCGATGTACTTC	59.827	55.0	0.00	0.0	32.25	3.01	F
507	519	0.603975	GTGTGGGTCTGGACTTGCTC	60.604	60.0	0.67	0.0	0.00	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1343	1945	0.183971	CCAATGGGCGGGGTAACATA	59.816	55.0	0.0	0.0	39.74	2.29	R
2118	2721	0.462759	GCAGGTGGCATCAGTAGGTC	60.463	60.0	0.0	0.0	43.97	3.85	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
35	36	4.783621	TGATGCAGAGCGGCCACC	62.784	66.667	2.24	0.00	0.00	4.61
36	37	4.783621	GATGCAGAGCGGCCACCA	62.784	66.667	2.24	0.00	0.00	4.17
50	51	1.285078	GCCACCATAAGTTTCTCCCCT	59.715	52.381	0.00	0.00	0.00	4.79
51	52	2.508300	GCCACCATAAGTTTCTCCCCTA	59.492	50.000	0.00	0.00	0.00	3.53
52	53	3.684697	GCCACCATAAGTTTCTCCCCTAC	60.685	52.174	0.00	0.00	0.00	3.18
139	146	1.691196	CAGCCACCAAAAGTTCCTCA	58.309	50.000	0.00	0.00	0.00	3.86
216	223	3.005554	AGCTACAGAATGATGTGTGTGC	58.994	45.455	0.00	0.00	39.69	4.57
414	426	2.792947	TTGATCTAGGCCGGTCCGC	61.793	63.158	0.08	1.02	40.77	5.54
472	484	0.172803	ACGACAGGGCGATGTACTTC	59.827	55.000	0.00	0.00	32.25	3.01
507	519	0.603975	GTGTGGGTCTGGACTTGCTC	60.604	60.000	0.67	0.00	0.00	4.26
572	584	1.134401	TGCCCGAGTTGAAGATGGATC	60.134	52.381	0.00	0.00	0.00	3.36
585	597	6.227522	TGAAGATGGATCGTTGTTTCTACAA	58.772	36.000	0.00	0.00	41.82	2.41
599	611	4.346734	TTCTACAATAGACGACGTGGAC	57.653	45.455	4.58	0.00	33.84	4.02
620	632	4.594970	ACGGTTGGGATTGATCACATTTA	58.405	39.130	0.00	0.00	40.43	1.40
622	634	5.299279	ACGGTTGGGATTGATCACATTTATC	59.701	40.000	0.00	0.00	40.43	1.75
639	651	8.495949	CACATTTATCGTGAATAGGTGGATAAC	58.504	37.037	0.00	0.00	36.43	1.89
648	660	0.696501	AGGTGGATAACTTGGCCGTT	59.303	50.000	0.00	0.00	0.00	4.44
655	667	2.772077	TAACTTGGCCGTTATCAGCA	57.228	45.000	0.00	0.00	0.00	4.41
665	677	5.411361	TGGCCGTTATCAGCAATTATATGAC	59.589	40.000	0.00	0.00	0.00	3.06
715	727	2.943033	GTGCCTAATGCGTGTAAGGAAT	59.057	45.455	6.44	0.00	45.60	3.01
800	812	5.290493	TGTCTGTCCTTATCACACTTTGT	57.710	39.130	0.00	0.00	0.00	2.83
801	813	6.413783	TGTCTGTCCTTATCACACTTTGTA	57.586	37.500	0.00	0.00	0.00	2.41
802	814	7.004555	TGTCTGTCCTTATCACACTTTGTAT	57.995	36.000	0.00	0.00	0.00	2.29
803	815	6.873605	TGTCTGTCCTTATCACACTTTGTATG	59.126	38.462	0.00	0.00	0.00	2.39
804	816	7.097192	GTCTGTCCTTATCACACTTTGTATGA	58.903	38.462	0.00	0.00	0.00	2.15
805	817	7.766278	GTCTGTCCTTATCACACTTTGTATGAT	59.234	37.037	0.00	0.00	36.95	2.45
945	957	3.181467	CCTTGGCATCTCCTACTCTTGAG	60.181	52.174	0.00	0.00	35.26	3.02
946	958	1.759445	TGGCATCTCCTACTCTTGAGC	59.241	52.381	0.00	0.00	35.26	4.26
976	988	2.420022	AGCAGCAATATTTCGTGGTGAC	59.580	45.455	8.20	1.28	44.17	3.67
980	992	4.034048	CAGCAATATTTCGTGGTGACTACC	59.966	45.833	0.00	0.00	44.17	3.18
1599	2201	3.423539	TTCTCCCCATGTTTCACTCAG	57.576	47.619	0.00	0.00	0.00	3.35
1615	2217	4.473196	TCACTCAGCCCCTACAATATTTCA	59.527	41.667	0.00	0.00	0.00	2.69
1645	2247	2.419324	GTGAGCTTTCTTCTGCATCCAG	59.581	50.000	0.00	0.00	40.54	3.86
1659	2261	1.955778	CATCCAGTTGCAGGTCAAACA	59.044	47.619	0.00	0.00	36.26	2.83
1730	2332	9.290988	TCAGGTATTGTAGCTTATTTTCACAAA	57.709	29.630	0.00	0.00	33.57	2.83
2052	2655	6.266103	TGTTCTTTCTTTTCTCAATGCAGGAT	59.734	34.615	0.00	0.00	0.00	3.24
2053	2656	6.263516	TCTTTCTTTTCTCAATGCAGGATG	57.736	37.500	0.00	0.00	40.87	3.51
2118	2721	5.528870	TGTATACCTCACATATTGCACGAG	58.471	41.667	0.00	0.00	0.00	4.18
2128	2731	4.342378	ACATATTGCACGAGACCTACTGAT	59.658	41.667	0.00	0.00	0.00	2.90
2162	2765	7.643569	TGTTGCCACATCAATTTCATATAGT	57.356	32.000	0.00	0.00	0.00	2.12
2215	2818	4.935702	TGGTGAAAAGCAATGACAGAAAG	58.064	39.130	0.00	0.00	0.00	2.62
2226	2829	2.378038	TGACAGAAAGCAGCACCTTTT	58.622	42.857	0.00	0.00	35.31	2.27
2286	2889	2.612972	GCTTGATTCGGTGTCTCCTTCA	60.613	50.000	0.00	0.00	0.00	3.02
2304	2907	3.213206	TCATGTTCTGCCAACAAGACT	57.787	42.857	2.68	0.00	33.42	3.24
2328	2931	9.899226	ACTTCTTGCACTAAAATTAACTGATTC	57.101	29.630	0.00	0.00	0.00	2.52
2348	2951	6.489700	TGATTCTGTGAAACCATTGTGTACAT	59.510	34.615	0.00	0.00	34.36	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	9.984190	GAATACTAAGTAGGGGAGAAACTTATG	57.016	37.037	0.00	0.00	35.70	1.90
36	37	9.725206	TGAATACTAAGTAGGGGAGAAACTTAT	57.275	33.333	0.00	0.00	35.70	1.73
50	51	7.827787	AGGGAGAGGAATCTGAATACTAAGTA	58.172	38.462	0.00	0.00	0.00	2.24
51	52	6.688554	AGGGAGAGGAATCTGAATACTAAGT	58.311	40.000	0.00	0.00	0.00	2.24
52	53	7.508977	AGAAGGGAGAGGAATCTGAATACTAAG	59.491	40.741	0.00	0.00	0.00	2.18
139	146	1.978080	TGGCCGCTGTGCATCAAAT	60.978	52.632	0.00	0.00	0.00	2.32
216	223	4.983215	TCACATTAGCAAGTAACACACG	57.017	40.909	0.00	0.00	0.00	4.49
370	381	8.755028	ACCGTATTGGGCTTTTCTATTTAAAAT	58.245	29.630	0.00	0.00	44.64	1.82
387	399	2.767505	GGCCTAGATCAACCGTATTGG	58.232	52.381	0.00	0.00	46.41	3.16
472	484	0.035881	ACACACAGGCATCACCAGAG	59.964	55.000	0.00	0.00	43.14	3.35
585	597	0.169672	CAACCGTCCACGTCGTCTAT	59.830	55.000	0.00	0.00	37.74	1.98
599	611	5.560760	CGATAAATGTGATCAATCCCAACCG	60.561	44.000	0.00	0.00	0.00	4.44
620	632	5.611374	CCAAGTTATCCACCTATTCACGAT	58.389	41.667	0.00	0.00	0.00	3.73
622	634	3.560068	GCCAAGTTATCCACCTATTCACG	59.440	47.826	0.00	0.00	0.00	4.35
639	651	4.836125	ATAATTGCTGATAACGGCCAAG	57.164	40.909	2.24	0.00	46.76	3.61
648	660	8.669946	TGGTTTTCGTCATATAATTGCTGATA	57.330	30.769	0.00	0.00	0.00	2.15
655	667	7.415206	GCCACTTCTGGTTTTCGTCATATAATT	60.415	37.037	0.00	0.00	40.17	1.40
665	677	1.596954	CGTTGCCACTTCTGGTTTTCG	60.597	52.381	0.00	0.00	40.17	3.46
681	693	4.591202	CATTAGGCACTCTATTTGCGTTG	58.409	43.478	0.00	0.00	41.18	4.10
685	697	2.614057	ACGCATTAGGCACTCTATTTGC	59.386	45.455	0.00	0.00	45.17	3.68
772	784	3.201290	GTGATAAGGACAGACATGGCAG	58.799	50.000	0.00	0.00	35.42	4.85
800	812	6.430925	GGGCTGCTTGTGTTATCATAATCATA	59.569	38.462	0.00	0.00	0.00	2.15
801	813	5.242393	GGGCTGCTTGTGTTATCATAATCAT	59.758	40.000	0.00	0.00	0.00	2.45
802	814	4.580167	GGGCTGCTTGTGTTATCATAATCA	59.420	41.667	0.00	0.00	0.00	2.57
803	815	4.823989	AGGGCTGCTTGTGTTATCATAATC	59.176	41.667	0.00	0.00	0.00	1.75
804	816	4.796606	AGGGCTGCTTGTGTTATCATAAT	58.203	39.130	0.00	0.00	0.00	1.28
805	817	4.235079	AGGGCTGCTTGTGTTATCATAA	57.765	40.909	0.00	0.00	0.00	1.90
904	916	6.691491	GCCAAGGGATCAATATTCTACCTGAA	60.691	42.308	0.00	0.00	39.24	3.02
976	988	8.820933	CATATGAAAGTGTAGTTCATGTGGTAG	58.179	37.037	13.13	0.00	44.46	3.18
980	992	7.615582	ACCATATGAAAGTGTAGTTCATGTG	57.384	36.000	3.65	13.71	46.19	3.21
1343	1945	0.183971	CCAATGGGCGGGGTAACATA	59.816	55.000	0.00	0.00	39.74	2.29
1599	2201	6.670695	AATTCCATGAAATATTGTAGGGGC	57.329	37.500	0.00	0.00	0.00	5.80
1615	2217	5.566230	GCAGAAGAAAGCTCACAAATTCCAT	60.566	40.000	0.00	0.00	0.00	3.41
1645	2247	2.859538	CACACAATGTTTGACCTGCAAC	59.140	45.455	0.00	0.00	35.91	4.17
1730	2332	5.757320	TCAACAAAATCACGCCATTTCAAAT	59.243	32.000	0.00	0.00	0.00	2.32
1940	2543	9.918630	AAATCCAGAACAATGTAAAAATCTCTG	57.081	29.630	2.87	2.87	0.00	3.35
2052	2655	1.304381	GCCCAATCCAACTCAGGCA	60.304	57.895	0.00	0.00	40.20	4.75
2053	2656	1.000396	AGCCCAATCCAACTCAGGC	60.000	57.895	0.00	0.00	40.79	4.85
2118	2721	0.462759	GCAGGTGGCATCAGTAGGTC	60.463	60.000	0.00	0.00	43.97	3.85
2162	2765	6.946340	TGTTATTCAGGATAAGCTTGTCAGA	58.054	36.000	22.69	16.81	31.01	3.27
2215	2818	3.163630	TGAGAAACAAAAAGGTGCTGC	57.836	42.857	0.00	0.00	0.00	5.25
2226	2829	4.572389	GTCTTCTGTGAGCTTGAGAAACAA	59.428	41.667	0.00	0.00	36.97	2.83
2286	2889	3.825328	AGAAGTCTTGTTGGCAGAACAT	58.175	40.909	1.72	0.00	0.00	2.71
2304	2907	9.897744	CAGAATCAGTTAATTTTAGTGCAAGAA	57.102	29.630	0.00	0.00	0.00	2.52
2328	2931	5.687770	TGATGTACACAATGGTTTCACAG	57.312	39.130	0.00	0.00	0.00	3.66
2336	2939	7.541783	CCAGTTTACAAATGATGTACACAATGG	59.458	37.037	0.00	4.19	44.21	3.16
2348	2951	4.212425	CACTACGCACCAGTTTACAAATGA	59.788	41.667	0.00	0.00	0.00	2.57
2460	3063	6.657966	GGTGGCTGGTATATTAAATAGGGAAC	59.342	42.308	0.00	0.00	0.00	3.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.