AutoCloner

Multiple sequence alignment - TraesCS1B01G203100

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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	TraesCS1B01G203100	chr1B	100.000	3491	0	0	1	3491	364507459	364503969	0.000000e+00	6447
1	TraesCS1B01G203100	chr1B	80.835	1461	228	39	1031	2459	522743330	522744770	0.000000e+00	1099
2	TraesCS1B01G203100	chr1B	80.459	1438	229	30	1061	2454	364424572	364423143	0.000000e+00	1051
3	TraesCS1B01G203100	chr1B	91.695	590	49	0	1025	1614	364812753	364812164	0.000000e+00	819
4	TraesCS1B01G203100	chr1B	83.887	782	109	9	1809	2573	364811951	364811170	0.000000e+00	730
5	TraesCS1B01G203100	chr1B	87.857	280	32	2	3194	3471	215820186	215820465	9.340000e-86	327
6	TraesCS1B01G203100	chr1D	94.661	2285	76	21	654	2910	250068885	250071151	0.000000e+00	3502
7	TraesCS1B01G203100	chr1D	87.612	1566	177	9	1025	2573	249754098	249755663	0.000000e+00	1801
8	TraesCS1B01G203100	chr1D	80.313	1468	238	35	1031	2468	389490741	389489295	0.000000e+00	1062
9	TraesCS1B01G203100	chr1D	80.027	1462	235	33	1046	2459	250137559	250139011	0.000000e+00	1029
10	TraesCS1B01G203100	chr1D	78.712	1475	258	33	1027	2458	467605922	467607383	0.000000e+00	933
11	TraesCS1B01G203100	chr1D	86.435	317	18	9	2911	3219	250071207	250071506	1.210000e-84	324
12	TraesCS1B01G203100	chr1A	95.088	2056	84	9	861	2910	319887704	319889748	0.000000e+00	3221
13	TraesCS1B01G203100	chr1A	87.380	1569	178	10	1025	2573	319445963	319447531	0.000000e+00	1783
14	TraesCS1B01G203100	chr1A	80.191	1469	241	39	1031	2468	488099138	488097689	0.000000e+00	1055
15	TraesCS1B01G203100	chr1A	79.041	1460	226	45	1050	2459	320154544	320155973	0.000000e+00	928
16	TraesCS1B01G203100	chr1A	86.325	234	22	5	2992	3219	319890202	319890431	2.690000e-61	246
17	TraesCS1B01G203100	chr1A	91.617	167	5	6	651	815	319887244	319887403	4.540000e-54	222
18	TraesCS1B01G203100	chr5B	88.542	288	28	5	3188	3471	288896012	288896298	9.280000e-91	344
19	TraesCS1B01G203100	chr7B	88.809	277	29	2	3197	3471	272672365	272672089	4.320000e-89	339
20	TraesCS1B01G203100	chr7B	87.676	284	33	2	3190	3471	40719178	40718895	2.600000e-86	329
21	TraesCS1B01G203100	chr7D	88.406	276	29	3	3197	3469	253029559	253029284	2.600000e-86	329
22	TraesCS1B01G203100	chr7D	87.279	283	34	2	3191	3471	102388697	102388979	4.350000e-84	322
23	TraesCS1B01G203100	chr3D	86.689	293	37	2	3181	3471	290864871	290865163	1.210000e-84	324
24	TraesCS1B01G203100	chr4B	86.897	290	35	3	3185	3471	73693999	73693710	4.350000e-84	322
25	TraesCS1B01G203100	chr6B	86.644	292	36	3	3184	3473	31436572	31436862	1.560000e-83	320
26	TraesCS1B01G203100	chr3B	74.099	583	135	13	1050	1624	11241326	11240752	3.510000e-55	226
27	TraesCS1B01G203100	chr2B	79.279	222	35	6	1	214	635202106	635201888	1.010000e-30	145

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	TraesCS1B01G203100	chr1B	364503969	364507459	3490	True	6447.000000	6447	100.000	1	3491	1	chr1B.!!$R2	3490
1	TraesCS1B01G203100	chr1B	522743330	522744770	1440	False	1099.000000	1099	80.835	1031	2459	1	chr1B.!!$F2	1428
2	TraesCS1B01G203100	chr1B	364423143	364424572	1429	True	1051.000000	1051	80.459	1061	2454	1	chr1B.!!$R1	1393
3	TraesCS1B01G203100	chr1B	364811170	364812753	1583	True	774.500000	819	87.791	1025	2573	2	chr1B.!!$R3	1548
4	TraesCS1B01G203100	chr1D	250068885	250071506	2621	False	1913.000000	3502	90.548	654	3219	2	chr1D.!!$F4	2565
5	TraesCS1B01G203100	chr1D	249754098	249755663	1565	False	1801.000000	1801	87.612	1025	2573	1	chr1D.!!$F1	1548
6	TraesCS1B01G203100	chr1D	389489295	389490741	1446	True	1062.000000	1062	80.313	1031	2468	1	chr1D.!!$R1	1437
7	TraesCS1B01G203100	chr1D	250137559	250139011	1452	False	1029.000000	1029	80.027	1046	2459	1	chr1D.!!$F2	1413
8	TraesCS1B01G203100	chr1D	467605922	467607383	1461	False	933.000000	933	78.712	1027	2458	1	chr1D.!!$F3	1431
9	TraesCS1B01G203100	chr1A	319445963	319447531	1568	False	1783.000000	1783	87.380	1025	2573	1	chr1A.!!$F1	1548
10	TraesCS1B01G203100	chr1A	319887244	319890431	3187	False	1229.666667	3221	91.010	651	3219	3	chr1A.!!$F3	2568
11	TraesCS1B01G203100	chr1A	488097689	488099138	1449	True	1055.000000	1055	80.191	1031	2468	1	chr1A.!!$R1	1437
12	TraesCS1B01G203100	chr1A	320154544	320155973	1429	False	928.000000	928	79.041	1050	2459	1	chr1A.!!$F2	1409
13	TraesCS1B01G203100	chr3B	11240752	11241326	574	True	226.000000	226	74.099	1050	1624	1	chr3B.!!$R1	574

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
968	1265	0.100146	AACGACCGAAGCGATAGGAC	59.9	55.0	1.96	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2911	3460	0.036732	TGCTGGGGCAGTTACTTGAG	59.963	55.0	0.0	0.0	44.28	3.02	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	9.974980	GGTAAGGAATTTAATGAAAGTTTCACA	57.025	29.630	20.26	8.85	43.48	3.58
55	56	9.891828	TGAAAGTTTCACATACACACATTATTC	57.108	29.630	14.35	0.00	34.08	1.75
56	57	8.948853	AAAGTTTCACATACACACATTATTCG	57.051	30.769	0.00	0.00	0.00	3.34
57	58	7.072177	AGTTTCACATACACACATTATTCGG	57.928	36.000	0.00	0.00	0.00	4.30
58	59	5.478233	TTCACATACACACATTATTCGGC	57.522	39.130	0.00	0.00	0.00	5.54
59	60	4.765273	TCACATACACACATTATTCGGCT	58.235	39.130	0.00	0.00	0.00	5.52
60	61	5.182487	TCACATACACACATTATTCGGCTT	58.818	37.500	0.00	0.00	0.00	4.35
61	62	5.645929	TCACATACACACATTATTCGGCTTT	59.354	36.000	0.00	0.00	0.00	3.51
62	63	6.150307	TCACATACACACATTATTCGGCTTTT	59.850	34.615	0.00	0.00	0.00	2.27
63	64	6.468956	CACATACACACATTATTCGGCTTTTC	59.531	38.462	0.00	0.00	0.00	2.29
64	65	6.150307	ACATACACACATTATTCGGCTTTTCA	59.850	34.615	0.00	0.00	0.00	2.69
65	66	5.446143	ACACACATTATTCGGCTTTTCAA	57.554	34.783	0.00	0.00	0.00	2.69
66	67	5.837437	ACACACATTATTCGGCTTTTCAAA	58.163	33.333	0.00	0.00	0.00	2.69
67	68	6.454795	ACACACATTATTCGGCTTTTCAAAT	58.545	32.000	0.00	0.00	0.00	2.32
68	69	6.586082	ACACACATTATTCGGCTTTTCAAATC	59.414	34.615	0.00	0.00	0.00	2.17
69	70	5.799936	ACACATTATTCGGCTTTTCAAATCG	59.200	36.000	0.00	0.00	0.00	3.34
70	71	5.799936	CACATTATTCGGCTTTTCAAATCGT	59.200	36.000	0.00	0.00	0.00	3.73
71	72	6.307800	CACATTATTCGGCTTTTCAAATCGTT	59.692	34.615	0.00	0.00	0.00	3.85
72	73	6.866248	ACATTATTCGGCTTTTCAAATCGTTT	59.134	30.769	0.00	0.00	0.00	3.60
73	74	7.383843	ACATTATTCGGCTTTTCAAATCGTTTT	59.616	29.630	0.00	0.00	0.00	2.43
74	75	5.822584	ATTCGGCTTTTCAAATCGTTTTC	57.177	34.783	0.00	0.00	0.00	2.29
75	76	4.561735	TCGGCTTTTCAAATCGTTTTCT	57.438	36.364	0.00	0.00	0.00	2.52
76	77	4.533222	TCGGCTTTTCAAATCGTTTTCTC	58.467	39.130	0.00	0.00	0.00	2.87
77	78	4.274950	TCGGCTTTTCAAATCGTTTTCTCT	59.725	37.500	0.00	0.00	0.00	3.10
78	79	5.467399	TCGGCTTTTCAAATCGTTTTCTCTA	59.533	36.000	0.00	0.00	0.00	2.43

Showing 1 to 25 of 641 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
15	16	9.974980	TGTGAAACTTTCATTAAATTCCTTACC	57.025	29.630	7.47	42.47	2.85
29	30	9.891828	GAATAATGTGTGTATGTGAAACTTTCA	57.108	29.630	0.00	38.04	2.69
30	31	9.051027	CGAATAATGTGTGTATGTGAAACTTTC	57.949	33.333	0.00	38.04	2.62
31	32	8.020819	CCGAATAATGTGTGTATGTGAAACTTT	58.979	33.333	0.00	38.04	2.66
32	33	7.526608	CCGAATAATGTGTGTATGTGAAACTT	58.473	34.615	0.00	38.04	2.66
33	34	6.403200	GCCGAATAATGTGTGTATGTGAAACT	60.403	38.462	0.00	38.04	2.66
34	35	5.737290	GCCGAATAATGTGTGTATGTGAAAC	59.263	40.000	0.00	37.35	2.78
35	36	5.645929	AGCCGAATAATGTGTGTATGTGAAA	59.354	36.000	0.00	0.00	2.69
36	37	5.182487	AGCCGAATAATGTGTGTATGTGAA	58.818	37.500	0.00	0.00	3.18
37	38	4.765273	AGCCGAATAATGTGTGTATGTGA	58.235	39.130	0.00	0.00	3.58
38	39	5.484173	AAGCCGAATAATGTGTGTATGTG	57.516	39.130	0.00	0.00	3.21
39	40	6.150307	TGAAAAGCCGAATAATGTGTGTATGT	59.850	34.615	0.00	0.00	2.29
40	41	6.550843	TGAAAAGCCGAATAATGTGTGTATG	58.449	36.000	0.00	0.00	2.39
41	42	6.751514	TGAAAAGCCGAATAATGTGTGTAT	57.248	33.333	0.00	0.00	2.29
42	43	6.561737	TTGAAAAGCCGAATAATGTGTGTA	57.438	33.333	0.00	0.00	2.90
43	44	5.446143	TTGAAAAGCCGAATAATGTGTGT	57.554	34.783	0.00	0.00	3.72
44	45	6.237279	CGATTTGAAAAGCCGAATAATGTGTG	60.237	38.462	0.00	0.00	3.82
45	46	5.799936	CGATTTGAAAAGCCGAATAATGTGT	59.200	36.000	0.00	0.00	3.72
46	47	5.799936	ACGATTTGAAAAGCCGAATAATGTG	59.200	36.000	0.00	0.00	3.21
47	48	5.949735	ACGATTTGAAAAGCCGAATAATGT	58.050	33.333	0.00	0.00	2.71
48	49	6.869421	AACGATTTGAAAAGCCGAATAATG	57.131	33.333	0.00	0.00	1.90
49	50	7.812669	AGAAAACGATTTGAAAAGCCGAATAAT	59.187	29.630	0.00	0.00	1.28
50	51	7.142680	AGAAAACGATTTGAAAAGCCGAATAA	58.857	30.769	0.00	0.00	1.40
51	52	6.674066	AGAAAACGATTTGAAAAGCCGAATA	58.326	32.000	0.00	0.00	1.75
52	53	5.528870	AGAAAACGATTTGAAAAGCCGAAT	58.471	33.333	0.00	0.00	3.34

Showing 1 to 25 of 612 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.