AutoCloner

Multiple sequence alignment - TraesCS3B01G316800

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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	TraesCS3B01G316800	chr3B	100.000	2818	0	0	1	2818	508526765	508529582	0.000000e+00	5204.0
1	TraesCS3B01G316800	chr3B	93.067	375	22	3	3	375	691446992	691447364	1.910000e-151	545.0
2	TraesCS3B01G316800	chr3B	92.267	375	24	5	3	375	504103902	504104273	6.910000e-146	527.0
3	TraesCS3B01G316800	chr3B	89.080	348	32	6	2475	2817	508554840	508555186	7.210000e-116	427.0
4	TraesCS3B01G316800	chr3B	82.682	358	47	9	2475	2817	535509051	535508694	1.270000e-78	303.0
5	TraesCS3B01G316800	chr3B	75.621	644	108	35	1046	1654	492199897	492200526	9.950000e-70	274.0
6	TraesCS3B01G316800	chr3D	96.055	1090	42	1	779	1868	391430943	391432031	0.000000e+00	1773.0
7	TraesCS3B01G316800	chr3D	80.255	314	52	9	1352	1660	377188106	377187798	7.850000e-56	228.0
8	TraesCS3B01G316800	chr3D	82.564	195	28	4	1103	1294	377188384	377188193	1.740000e-37	167.0
9	TraesCS3B01G316800	chr3A	93.861	1124	52	8	760	1868	511680518	511681639	0.000000e+00	1677.0
10	TraesCS3B01G316800	chr3A	79.012	243	44	5	1054	1293	501898146	501898384	2.910000e-35	159.0
11	TraesCS3B01G316800	chr7A	93.048	374	23	3	3	375	709393551	709393180	6.870000e-151	544.0
12	TraesCS3B01G316800	chr1B	93.011	372	22	3	3	373	3889665	3889297	8.880000e-150	540.0
13	TraesCS3B01G316800	chr1B	92.513	374	25	2	3	375	634503224	634502853	1.490000e-147	532.0
14	TraesCS3B01G316800	chr1B	92.473	372	24	3	3	373	50365802	50366170	1.920000e-146	529.0
15	TraesCS3B01G316800	chr4B	92.368	380	26	3	3	381	33174238	33173861	3.190000e-149	538.0
16	TraesCS3B01G316800	chr4B	83.662	355	46	9	2475	2817	440145782	440145428	9.740000e-85	324.0
17	TraesCS3B01G316800	chr1D	92.063	378	24	5	3	379	53166453	53166081	6.910000e-146	527.0
18	TraesCS3B01G316800	chr1D	84.651	215	27	5	2138	2347	48905457	48905244	2.840000e-50	209.0
19	TraesCS3B01G316800	chr5B	92.225	373	26	2	3	374	491624822	491624452	2.490000e-145	525.0
20	TraesCS3B01G316800	chr5B	82.913	357	47	12	2475	2817	387408598	387408242	2.730000e-80	309.0
21	TraesCS3B01G316800	chr5B	82.817	355	49	9	2475	2817	611604784	611605138	9.810000e-80	307.0
22	TraesCS3B01G316800	chr2D	85.311	354	38	10	2475	2817	450817435	450817085	1.240000e-93	353.0
23	TraesCS3B01G316800	chr2D	83.146	356	47	10	2475	2817	375741511	375741866	2.110000e-81	313.0
24	TraesCS3B01G316800	chr5D	83.616	354	47	9	2475	2817	565567760	565567407	3.500000e-84	322.0
25	TraesCS3B01G316800	chr4A	83.099	355	48	8	2475	2817	615753984	615754338	2.110000e-81	313.0
26	TraesCS3B01G316800	chr5A	81.651	109	16	4	514	619	386466990	386467097	1.390000e-13	87.9
27	TraesCS3B01G316800	chr5A	79.279	111	21	2	514	623	652057839	652057730	3.010000e-10	76.8
28	TraesCS3B01G316800	chr6B	97.143	35	1	0	514	548	578501513	578501547	3.030000e-05	60.2

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	TraesCS3B01G316800	chr3B	508526765	508529582	2817	False	5204	5204	100.000	1	2818	1	chr3B.!!$F3	2817
1	TraesCS3B01G316800	chr3B	492199897	492200526	629	False	274	274	75.621	1046	1654	1	chr3B.!!$F1	608
2	TraesCS3B01G316800	chr3D	391430943	391432031	1088	False	1773	1773	96.055	779	1868	1	chr3D.!!$F1	1089
3	TraesCS3B01G316800	chr3A	511680518	511681639	1121	False	1677	1677	93.861	760	1868	1	chr3A.!!$F2	1108

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
525	526	0.03213	TTGAGTCACTGAGCCGACAC	59.968	55.0	0.0	0.3	34.48	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2346	2388	0.027979	CAACGGCGATTAGTGCATGG	59.972	55.0	16.62	0.0	0.0	3.66	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
29	30	3.694889	CGGAAGGGACATTTTTCGC	57.305	52.632	0.00	0.00	0.00	4.70
30	31	0.179200	CGGAAGGGACATTTTTCGCG	60.179	55.000	0.00	0.00	33.74	5.87
31	32	0.170339	GGAAGGGACATTTTTCGCGG	59.830	55.000	6.13	0.00	33.74	6.46
32	33	0.879090	GAAGGGACATTTTTCGCGGT	59.121	50.000	6.13	0.00	33.74	5.68
33	34	2.078392	GAAGGGACATTTTTCGCGGTA	58.922	47.619	6.13	0.00	33.74	4.02
34	35	1.445871	AGGGACATTTTTCGCGGTAC	58.554	50.000	6.13	0.00	33.74	3.34
35	36	1.002773	AGGGACATTTTTCGCGGTACT	59.997	47.619	6.13	0.00	33.74	2.73
36	37	1.395954	GGGACATTTTTCGCGGTACTC	59.604	52.381	6.13	0.00	0.00	2.59
37	38	2.070783	GGACATTTTTCGCGGTACTCA	58.929	47.619	6.13	0.00	0.00	3.41
38	39	2.481185	GGACATTTTTCGCGGTACTCAA	59.519	45.455	6.13	0.00	0.00	3.02
39	40	3.058777	GGACATTTTTCGCGGTACTCAAA	60.059	43.478	6.13	0.00	0.00	2.69
40	41	4.141855	ACATTTTTCGCGGTACTCAAAG	57.858	40.909	6.13	0.00	0.00	2.77
41	42	2.673976	TTTTTCGCGGTACTCAAAGC	57.326	45.000	6.13	0.00	0.00	3.51
42	43	0.869730	TTTTCGCGGTACTCAAAGCC	59.130	50.000	6.13	0.00	0.00	4.35
43	44	0.249953	TTTCGCGGTACTCAAAGCCA	60.250	50.000	6.13	0.00	0.00	4.75
44	45	0.249953	TTCGCGGTACTCAAAGCCAA	60.250	50.000	6.13	0.00	0.00	4.52
45	46	0.249953	TCGCGGTACTCAAAGCCAAA	60.250	50.000	6.13	0.00	0.00	3.28
46	47	0.165944	CGCGGTACTCAAAGCCAAAG	59.834	55.000	0.00	0.00	0.00	2.77
47	48	1.519408	GCGGTACTCAAAGCCAAAGA	58.481	50.000	0.00	0.00	0.00	2.52
48	49	2.084546	GCGGTACTCAAAGCCAAAGAT	58.915	47.619	0.00	0.00	0.00	2.40
49	50	2.159517	GCGGTACTCAAAGCCAAAGATG	60.160	50.000	0.00	0.00	0.00	2.90
58	59	2.436646	CCAAAGATGGCGACGGCT	60.437	61.111	22.70	7.99	40.58	5.52
59	60	2.753966	CCAAAGATGGCGACGGCTG	61.754	63.158	22.70	11.47	40.58	4.85
60	61	2.034879	CAAAGATGGCGACGGCTGT	61.035	57.895	22.70	11.12	39.81	4.40
61	62	1.302511	AAAGATGGCGACGGCTGTT	60.303	52.632	22.70	9.96	39.81	3.16

Showing 1 to 25 of 1,040 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.161609	CGAAAAATGTCCCTTCCGGAAG	59.838	50.000	33.29	33.29	44.47	3.46
8	9	2.156098	CGAAAAATGTCCCTTCCGGAA	58.844	47.619	17.73	17.73	44.47	4.30
9	10	1.816074	CGAAAAATGTCCCTTCCGGA	58.184	50.000	0.00	0.00	38.83	5.14
10	11	0.170339	GCGAAAAATGTCCCTTCCGG	59.830	55.000	0.00	0.00	0.00	5.14
11	12	0.179200	CGCGAAAAATGTCCCTTCCG	60.179	55.000	0.00	0.00	0.00	4.30
12	13	0.170339	CCGCGAAAAATGTCCCTTCC	59.830	55.000	8.23	0.00	0.00	3.46
13	14	0.879090	ACCGCGAAAAATGTCCCTTC	59.121	50.000	8.23	0.00	0.00	3.46
14	15	1.808343	GTACCGCGAAAAATGTCCCTT	59.192	47.619	8.23	0.00	0.00	3.95
15	16	1.002773	AGTACCGCGAAAAATGTCCCT	59.997	47.619	8.23	0.00	0.00	4.20
16	17	1.395954	GAGTACCGCGAAAAATGTCCC	59.604	52.381	8.23	0.00	0.00	4.46
17	18	2.070783	TGAGTACCGCGAAAAATGTCC	58.929	47.619	8.23	0.00	0.00	4.02
18	19	3.799137	TTGAGTACCGCGAAAAATGTC	57.201	42.857	8.23	0.00	0.00	3.06
19	20	3.608474	GCTTTGAGTACCGCGAAAAATGT	60.608	43.478	8.23	0.00	0.00	2.71
20	21	2.908626	GCTTTGAGTACCGCGAAAAATG	59.091	45.455	8.23	0.00	0.00	2.32
21	22	2.095415	GGCTTTGAGTACCGCGAAAAAT	60.095	45.455	8.23	0.00	0.00	1.82
22	23	1.264826	GGCTTTGAGTACCGCGAAAAA	59.735	47.619	8.23	0.00	0.00	1.94
23	24	0.869730	GGCTTTGAGTACCGCGAAAA	59.130	50.000	8.23	0.00	0.00	2.29
24	25	0.249953	TGGCTTTGAGTACCGCGAAA	60.250	50.000	8.23	0.00	0.00	3.46
25	26	0.249953	TTGGCTTTGAGTACCGCGAA	60.250	50.000	8.23	0.00	0.00	4.70
26	27	0.249953	TTTGGCTTTGAGTACCGCGA	60.250	50.000	8.23	0.00	0.00	5.87
27	28	0.165944	CTTTGGCTTTGAGTACCGCG	59.834	55.000	0.00	0.00	0.00	6.46
28	29	1.519408	TCTTTGGCTTTGAGTACCGC	58.481	50.000	0.00	0.00	0.00	5.68
29	30	2.420022	CCATCTTTGGCTTTGAGTACCG	59.580	50.000	0.00	0.00	35.85	4.02
41	42	2.436646	AGCCGTCGCCATCTTTGG	60.437	61.111	0.00	0.00	46.66	3.28
42	43	1.577328	AACAGCCGTCGCCATCTTTG	61.577	55.000	0.00	0.00	34.57	2.77

Showing 1 to 25 of 1,006 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.