AutoCloner

Multiple sequence alignment - TraesCS3D01G427600

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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	TraesCS3D01G427600	chr3D	100.000	2414	0	0	1	2414	541034903	541032490	0.000000e+00	4458.0
1	TraesCS3D01G427600	chr3D	93.737	2347	115	12	1	2340	397849382	397851703	0.000000e+00	3491.0
2	TraesCS3D01G427600	chr2D	94.770	2352	102	12	1	2344	450557237	450554899	0.000000e+00	3642.0
3	TraesCS3D01G427600	chr2D	94.433	2353	118	10	1	2347	167550650	167548305	0.000000e+00	3607.0
4	TraesCS3D01G427600	chr2D	94.343	2351	100	15	1	2346	260388083	260385761	0.000000e+00	3574.0
5	TraesCS3D01G427600	chr2D	90.541	74	7	0	2341	2414	202622663	202622590	5.490000e-17	99.0
6	TraesCS3D01G427600	chr2D	85.294	68	9	1	2346	2413	245691263	245691329	4.310000e-08	69.4
7	TraesCS3D01G427600	chr4D	94.401	2322	104	16	32	2341	476807252	476809559	0.000000e+00	3544.0
8	TraesCS3D01G427600	chr4D	94.721	2292	87	13	53	2337	65499330	65497066	0.000000e+00	3531.0
9	TraesCS3D01G427600	chr7D	94.037	2348	121	14	1	2340	188532558	188534894	0.000000e+00	3542.0
10	TraesCS3D01G427600	chr1D	93.968	2354	123	14	1	2342	349280154	349277808	0.000000e+00	3542.0
11	TraesCS3D01G427600	chr5D	93.583	2353	114	14	1	2346	249656391	249654069	0.000000e+00	3474.0
12	TraesCS3D01G427600	chr2B	90.767	1722	118	13	635	2341	650548386	650546691	0.000000e+00	2261.0
13	TraesCS3D01G427600	chr5A	90.798	1717	114	22	635	2341	593807636	593809318	0.000000e+00	2255.0
14	TraesCS3D01G427600	chr3A	89.753	1054	69	11	1299	2340	477692012	477690986	0.000000e+00	1312.0
15	TraesCS3D01G427600	chr7B	89.205	704	58	9	1649	2341	526008788	526009484	0.000000e+00	863.0

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	TraesCS3D01G427600	chr3D	541032490	541034903	2413	True	4458	4458	100.000	1	2414	1	chr3D.!!$R1	2413
1	TraesCS3D01G427600	chr3D	397849382	397851703	2321	False	3491	3491	93.737	1	2340	1	chr3D.!!$F1	2339
2	TraesCS3D01G427600	chr2D	450554899	450557237	2338	True	3642	3642	94.770	1	2344	1	chr2D.!!$R4	2343
3	TraesCS3D01G427600	chr2D	167548305	167550650	2345	True	3607	3607	94.433	1	2347	1	chr2D.!!$R1	2346
4	TraesCS3D01G427600	chr2D	260385761	260388083	2322	True	3574	3574	94.343	1	2346	1	chr2D.!!$R3	2345
5	TraesCS3D01G427600	chr4D	476807252	476809559	2307	False	3544	3544	94.401	32	2341	1	chr4D.!!$F1	2309
6	TraesCS3D01G427600	chr4D	65497066	65499330	2264	True	3531	3531	94.721	53	2337	1	chr4D.!!$R1	2284
7	TraesCS3D01G427600	chr7D	188532558	188534894	2336	False	3542	3542	94.037	1	2340	1	chr7D.!!$F1	2339
8	TraesCS3D01G427600	chr1D	349277808	349280154	2346	True	3542	3542	93.968	1	2342	1	chr1D.!!$R1	2341
9	TraesCS3D01G427600	chr5D	249654069	249656391	2322	True	3474	3474	93.583	1	2346	1	chr5D.!!$R1	2345
10	TraesCS3D01G427600	chr2B	650546691	650548386	1695	True	2261	2261	90.767	635	2341	1	chr2B.!!$R1	1706
11	TraesCS3D01G427600	chr5A	593807636	593809318	1682	False	2255	2255	90.798	635	2341	1	chr5A.!!$F1	1706
12	TraesCS3D01G427600	chr3A	477690986	477692012	1026	True	1312	1312	89.753	1299	2340	1	chr3A.!!$R1	1041
13	TraesCS3D01G427600	chr7B	526008788	526009484	696	False	863	863	89.205	1649	2341	1	chr7B.!!$F1	692

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
399	411	0.037697	CCGTTGGATCACAAGGACGA	60.038	55.0	14.38	0.0	45.38	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1436	1461	0.322277	TAGACGACGCCTTCTCCACT	60.322	55.0	0.0	0.0	0.0	4.0	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
19	20	2.525750	ATAAGACAACATTGTGCGCG	57.474	45.000	0.00	0.00	42.43	6.86
24	25	1.167155	ACAACATTGTGCGCGGGTTA	61.167	50.000	8.83	0.00	40.49	2.85
30	31	4.823157	ACATTGTGCGCGGGTTATATATA	58.177	39.130	8.83	0.00	0.00	0.86
91	95	0.328258	ATCGTGCCAGCTAGGGTTTT	59.672	50.000	4.65	0.00	38.09	2.43
172	176	0.515564	CGACGAATGGCGAAGGTTTT	59.484	50.000	0.00	0.00	44.57	2.43
182	188	7.305190	CGAATGGCGAAGGTTTTATATTTTTCG	60.305	37.037	0.00	0.55	44.57	3.46
288	298	0.544595	AACCCTAGCTCCCAACGTCT	60.545	55.000	0.00	0.00	0.00	4.18
310	320	0.586802	CGTCCGATCATACTCTCGCA	59.413	55.000	0.00	0.00	33.63	5.10
399	411	0.037697	CCGTTGGATCACAAGGACGA	60.038	55.000	14.38	0.00	45.38	4.20
401	413	1.068474	GTTGGATCACAAGGACGACG	58.932	55.000	0.00	0.00	40.38	5.12
417	429	2.823593	CGCCGCACCATTGGATCA	60.824	61.111	10.37	0.00	0.00	2.92
424	436	0.397394	CACCATTGGATCATGGGGCA	60.397	55.000	10.37	0.00	42.10	5.36
426	438	1.045407	CCATTGGATCATGGGGCAAG	58.955	55.000	0.00	0.00	34.39	4.01
464	476	2.047274	GGTTGTGCTCGGCTGCTA	60.047	61.111	0.00	0.00	0.00	3.49
475	487	2.352805	GCTGCTAGCCCACCACTT	59.647	61.111	13.29	0.00	34.48	3.16
594	608	2.928801	TTGTGAACTTGCTGGCTCTA	57.071	45.000	0.00	0.00	0.00	2.43
859	880	4.830600	ACTTCACATTTGACCCCGTTATTT	59.169	37.500	0.00	0.00	0.00	1.40
1168	1192	3.001406	GCTACCACCACCTCCCGT	61.001	66.667	0.00	0.00	0.00	5.28
1420	1445	2.925170	AGGAGCAGTGAAGGGCGT	60.925	61.111	0.00	0.00	34.54	5.68
1449	1474	2.048127	GCGAAGTGGAGAAGGCGT	60.048	61.111	0.00	0.00	0.00	5.68
2156	2271	2.359478	GGCCCAACGGTCGAACAT	60.359	61.111	0.00	0.00	0.00	2.71
2170	2293	1.734163	GAACATCTACACCCCCAACG	58.266	55.000	0.00	0.00	0.00	4.10
2356	2480	5.892160	AAACCCTAATTTCTAACCTTCGC	57.108	39.130	0.00	0.00	0.00	4.70
2357	2481	4.563140	ACCCTAATTTCTAACCTTCGCA	57.437	40.909	0.00	0.00	0.00	5.10
2358	2482	5.112129	ACCCTAATTTCTAACCTTCGCAT	57.888	39.130	0.00	0.00	0.00	4.73
2359	2483	6.243216	ACCCTAATTTCTAACCTTCGCATA	57.757	37.500	0.00	0.00	0.00	3.14
2360	2484	6.655930	ACCCTAATTTCTAACCTTCGCATAA	58.344	36.000	0.00	0.00	0.00	1.90
2361	2485	7.287810	ACCCTAATTTCTAACCTTCGCATAAT	58.712	34.615	0.00	0.00	0.00	1.28
2362	2486	8.434392	ACCCTAATTTCTAACCTTCGCATAATA	58.566	33.333	0.00	0.00	0.00	0.98
2363	2487	9.449719	CCCTAATTTCTAACCTTCGCATAATAT	57.550	33.333	0.00	0.00	0.00	1.28
2368	2492	7.724305	TTCTAACCTTCGCATAATATGTTCC	57.276	36.000	1.92	0.00	0.00	3.62
2369	2493	6.822442	TCTAACCTTCGCATAATATGTTCCA	58.178	36.000	1.92	0.00	0.00	3.53
2370	2494	7.276658	TCTAACCTTCGCATAATATGTTCCAA	58.723	34.615	1.92	0.00	0.00	3.53
2371	2495	6.767524	AACCTTCGCATAATATGTTCCAAA	57.232	33.333	1.92	0.00	0.00	3.28
2372	2496	6.377327	ACCTTCGCATAATATGTTCCAAAG	57.623	37.500	1.92	0.33	0.00	2.77
2373	2497	5.885912	ACCTTCGCATAATATGTTCCAAAGT	59.114	36.000	1.92	0.00	0.00	2.66
2374	2498	6.038271	ACCTTCGCATAATATGTTCCAAAGTC	59.962	38.462	1.92	0.00	0.00	3.01
2375	2499	6.038161	CCTTCGCATAATATGTTCCAAAGTCA	59.962	38.462	1.92	0.00	0.00	3.41
2376	2500	6.993786	TCGCATAATATGTTCCAAAGTCAA	57.006	33.333	1.92	0.00	0.00	3.18
2377	2501	7.566760	TCGCATAATATGTTCCAAAGTCAAT	57.433	32.000	1.92	0.00	0.00	2.57
2378	2502	7.416817	TCGCATAATATGTTCCAAAGTCAATG	58.583	34.615	1.92	0.00	0.00	2.82
2379	2503	7.066887	TCGCATAATATGTTCCAAAGTCAATGT	59.933	33.333	1.92	0.00	0.00	2.71
2380	2504	7.376866	CGCATAATATGTTCCAAAGTCAATGTC	59.623	37.037	1.92	0.00	0.00	3.06
2381	2505	7.376866	GCATAATATGTTCCAAAGTCAATGTCG	59.623	37.037	1.92	0.00	0.00	4.35
2382	2506	8.611757	CATAATATGTTCCAAAGTCAATGTCGA	58.388	33.333	0.00	0.00	0.00	4.20
2383	2507	7.630242	AATATGTTCCAAAGTCAATGTCGAT	57.370	32.000	0.00	0.00	0.00	3.59
2384	2508	5.964958	ATGTTCCAAAGTCAATGTCGATT	57.035	34.783	0.00	0.00	0.00	3.34
2385	2509	5.356882	TGTTCCAAAGTCAATGTCGATTC	57.643	39.130	0.00	0.00	0.00	2.52
2386	2510	4.819088	TGTTCCAAAGTCAATGTCGATTCA	59.181	37.500	0.00	0.00	0.00	2.57
2387	2511	5.473162	TGTTCCAAAGTCAATGTCGATTCAT	59.527	36.000	0.00	0.00	0.00	2.57
2388	2512	6.016360	TGTTCCAAAGTCAATGTCGATTCATT	60.016	34.615	0.00	0.00	38.38	2.57
2389	2513	7.174080	TGTTCCAAAGTCAATGTCGATTCATTA	59.826	33.333	1.35	0.00	36.44	1.90
2390	2514	7.680442	TCCAAAGTCAATGTCGATTCATTAA	57.320	32.000	1.35	0.00	36.44	1.40
2391	2515	8.279970	TCCAAAGTCAATGTCGATTCATTAAT	57.720	30.769	1.35	0.00	36.44	1.40
2392	2516	9.389755	TCCAAAGTCAATGTCGATTCATTAATA	57.610	29.630	1.35	0.00	36.44	0.98
2393	2517	9.655769	CCAAAGTCAATGTCGATTCATTAATAG	57.344	33.333	1.35	0.00	36.44	1.73
2396	2520	9.599866	AAGTCAATGTCGATTCATTAATAGTGA	57.400	29.630	1.35	0.00	36.44	3.41
2397	2521	9.770097	AGTCAATGTCGATTCATTAATAGTGAT	57.230	29.630	1.35	0.00	36.44	3.06
2410	2534	9.256228	TCATTAATAGTGATAGGTAGTGATCCC	57.744	37.037	0.00	0.00	0.00	3.85
2411	2535	9.035890	CATTAATAGTGATAGGTAGTGATCCCA	57.964	37.037	0.00	0.00	0.00	4.37
2412	2536	6.919775	AATAGTGATAGGTAGTGATCCCAC	57.080	41.667	0.00	0.00	43.50	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	53	2.096496	CGAGGTCAAATGAGCACCATTC	59.904	50.000	14.36	2.77	44.28	2.67
91	95	7.773489	TGGTCTATGGTCATTTTCATGAAAA	57.227	32.000	30.27	30.27	41.30	2.29
190	199	5.579511	GGCTTTGACTGAGCGTAACTAATTA	59.420	40.000	0.00	0.00	41.03	1.40
200	209	0.667487	TCGAAGGCTTTGACTGAGCG	60.667	55.000	13.24	3.80	41.03	5.03
288	298	0.952280	GAGAGTATGATCGGACGGCA	59.048	55.000	0.00	0.00	0.00	5.69
310	320	3.241530	TGAGGGCTGTCGCTTGGT	61.242	61.111	0.00	0.00	35.44	3.67
399	411	2.824041	GATCCAATGGTGCGGCGT	60.824	61.111	9.37	0.00	0.00	5.68
401	413	1.361271	CATGATCCAATGGTGCGGC	59.639	57.895	0.00	0.00	0.00	6.53
407	419	1.045407	CTTGCCCCATGATCCAATGG	58.955	55.000	5.28	5.28	45.82	3.16
464	476	1.258445	CGAGGAGTAAGTGGTGGGCT	61.258	60.000	0.00	0.00	0.00	5.19
491	505	2.370189	CCTTTTGGGCCCAATAACAACA	59.630	45.455	37.41	18.52	35.70	3.33
583	597	5.360429	TGATGCAAAAATATAGAGCCAGCAA	59.640	36.000	0.00	0.00	32.83	3.91
859	880	0.250381	ACGTGTTATTTGGCCGTGGA	60.250	50.000	0.00	0.00	0.00	4.02
1053	1077	0.104304	CGTACATGCCAGGAGGGTAC	59.896	60.000	0.00	0.00	39.65	3.34
1168	1192	1.846439	GAACATCCTTGGAGATCCCCA	59.154	52.381	0.00	0.00	34.29	4.96
1420	1445	2.440430	CTTCGCTCCTCCTCCGGA	60.440	66.667	2.93	2.93	0.00	5.14
1436	1461	0.322277	TAGACGACGCCTTCTCCACT	60.322	55.000	0.00	0.00	0.00	4.00
1597	1636	9.273016	CATAGTTGAAACTAGGAAGAACTTCAA	57.727	33.333	15.02	3.55	43.81	2.69
1925	1984	4.794439	CCACGGATGCAGCGACGA	62.794	66.667	7.61	0.00	0.00	4.20
2079	2194	2.202878	GCCGCCACGATAGAAGCA	60.203	61.111	0.00	0.00	37.47	3.91
2156	2271	3.697747	CCGCGTTGGGGGTGTAGA	61.698	66.667	4.92	0.00	41.19	2.59
2347	2471	7.554835	ACTTTGGAACATATTATGCGAAGGTTA	59.445	33.333	3.52	0.00	39.30	2.85
2348	2472	6.377146	ACTTTGGAACATATTATGCGAAGGTT	59.623	34.615	3.52	0.00	39.30	3.50
2349	2473	5.885912	ACTTTGGAACATATTATGCGAAGGT	59.114	36.000	3.52	0.00	39.30	3.50
2350	2474	6.038161	TGACTTTGGAACATATTATGCGAAGG	59.962	38.462	3.52	0.00	39.30	3.46
2351	2475	7.015226	TGACTTTGGAACATATTATGCGAAG	57.985	36.000	3.52	6.06	39.30	3.79
2352	2476	6.993786	TGACTTTGGAACATATTATGCGAA	57.006	33.333	3.52	0.00	39.30	4.70
2353	2477	6.993786	TTGACTTTGGAACATATTATGCGA	57.006	33.333	3.52	0.00	39.30	5.10
2354	2478	7.195646	ACATTGACTTTGGAACATATTATGCG	58.804	34.615	3.52	0.00	39.30	4.73
2355	2479	7.376866	CGACATTGACTTTGGAACATATTATGC	59.623	37.037	3.52	0.00	39.30	3.14
2356	2480	8.611757	TCGACATTGACTTTGGAACATATTATG	58.388	33.333	2.03	2.03	39.30	1.90
2357	2481	8.731275	TCGACATTGACTTTGGAACATATTAT	57.269	30.769	0.00	0.00	39.30	1.28
2358	2482	8.731275	ATCGACATTGACTTTGGAACATATTA	57.269	30.769	0.00	0.00	39.30	0.98
2359	2483	7.630242	ATCGACATTGACTTTGGAACATATT	57.370	32.000	0.00	0.00	39.30	1.28
2360	2484	7.336679	TGAATCGACATTGACTTTGGAACATAT	59.663	33.333	0.00	0.00	39.30	1.78
2361	2485	6.652900	TGAATCGACATTGACTTTGGAACATA	59.347	34.615	0.00	0.00	39.30	2.29
2362	2486	5.473162	TGAATCGACATTGACTTTGGAACAT	59.527	36.000	0.00	0.00	39.30	2.71
2363	2487	4.819088	TGAATCGACATTGACTTTGGAACA	59.181	37.500	0.00	0.00	0.00	3.18
2364	2488	5.356882	TGAATCGACATTGACTTTGGAAC	57.643	39.130	0.00	0.00	0.00	3.62
2365	2489	6.573664	AATGAATCGACATTGACTTTGGAA	57.426	33.333	0.80	0.00	38.76	3.53
2366	2490	7.680442	TTAATGAATCGACATTGACTTTGGA	57.320	32.000	10.61	0.00	40.15	3.53
2367	2491	9.655769	CTATTAATGAATCGACATTGACTTTGG	57.344	33.333	10.61	0.00	40.15	3.28
2370	2494	9.599866	TCACTATTAATGAATCGACATTGACTT	57.400	29.630	10.61	0.00	40.15	3.01
2371	2495	9.770097	ATCACTATTAATGAATCGACATTGACT	57.230	29.630	10.61	0.32	40.15	3.41
2384	2508	9.256228	GGGATCACTACCTATCACTATTAATGA	57.744	37.037	0.00	0.00	0.00	2.57
2385	2509	9.035890	TGGGATCACTACCTATCACTATTAATG	57.964	37.037	0.00	0.00	0.00	1.90
2386	2510	9.036980	GTGGGATCACTACCTATCACTATTAAT	57.963	37.037	0.00	0.00	40.58	1.40
2387	2511	8.418597	GTGGGATCACTACCTATCACTATTAA	57.581	38.462	0.00	0.00	40.58	1.40
2389	2513	6.919775	GTGGGATCACTACCTATCACTATT	57.080	41.667	0.00	0.00	40.58	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.