AutoCloner

Multiple sequence alignment - TraesCS4B01G350800

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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	TraesCS4B01G350800	chr4B	100.000	2312	0	0	1	2312	643402122	643399811	0.000000e+00	4270.0
1	TraesCS4B01G350800	chr4B	98.119	319	5	1	993	1310	643323699	643323381	2.600000e-154	555.0
2	TraesCS4B01G350800	chrUn	94.059	1094	54	5	900	1986	264907306	264908395	0.000000e+00	1650.0
3	TraesCS4B01G350800	chr4D	92.067	416	14	2	903	1318	500036199	500035803	3.330000e-158	568.0
4	TraesCS4B01G350800	chr1A	97.134	314	9	0	997	1310	541343819	541344132	4.370000e-147	531.0
5	TraesCS4B01G350800	chr1A	96.825	315	10	0	996	1310	541460790	541460476	5.660000e-146	527.0
6	TraesCS4B01G350800	chr1A	96.825	315	10	0	996	1310	543928360	543928674	5.660000e-146	527.0
7	TraesCS4B01G350800	chr1A	95.639	321	13	1	988	1308	485011094	485010775	4.400000e-142	514.0
8	TraesCS4B01G350800	chr1A	89.320	103	10	1	385	486	258859988	258859886	6.700000e-26	128.0
9	TraesCS4B01G350800	chr1A	89.655	58	6	0	708	765	494889205	494889262	8.860000e-10	75.0
10	TraesCS4B01G350800	chr5A	97.097	310	9	0	1001	1310	556534313	556534004	7.320000e-145	523.0
11	TraesCS4B01G350800	chr5A	94.958	119	6	0	785	903	680751198	680751080	1.090000e-43	187.0
12	TraesCS4B01G350800	chr5A	93.388	121	8	0	783	903	512225987	512225867	1.830000e-41	180.0
13	TraesCS4B01G350800	chr2A	95.298	319	15	0	1001	1319	712804864	712804546	7.370000e-140	507.0
14	TraesCS4B01G350800	chr2A	94.118	119	7	0	785	903	703360116	703359998	5.070000e-42	182.0
15	TraesCS4B01G350800	chr2A	77.926	299	59	4	88	379	113384512	113384214	1.830000e-41	180.0
16	TraesCS4B01G350800	chr5D	90.265	339	14	6	1983	2312	13914721	13915049	2.120000e-115	425.0
17	TraesCS4B01G350800	chr5D	88.529	340	21	6	1982	2312	123600855	123601185	1.660000e-106	396.0
18	TraesCS4B01G350800	chr5D	83.904	292	46	1	89	379	112339501	112339792	6.290000e-71	278.0
19	TraesCS4B01G350800	chr5D	81.119	286	43	6	487	765	29644588	29644869	3.870000e-53	219.0
20	TraesCS4B01G350800	chr5D	94.118	119	7	0	785	903	22575412	22575294	5.070000e-42	182.0
21	TraesCS4B01G350800	chr5D	92.742	124	8	1	781	904	279292866	279292988	6.560000e-41	178.0
22	TraesCS4B01G350800	chr7D	89.349	338	18	7	1985	2312	576654454	576654783	2.140000e-110	409.0
23	TraesCS4B01G350800	chr7D	88.496	339	24	4	1983	2312	50515446	50515114	1.660000e-106	396.0
24	TraesCS4B01G350800	chr7D	87.683	341	20	10	1982	2312	16804216	16804544	6.030000e-101	377.0
25	TraesCS4B01G350800	chr7D	83.959	293	43	4	89	379	89291774	89292064	6.290000e-71	278.0
26	TraesCS4B01G350800	chr7D	81.034	290	32	12	481	767	617067460	617067729	2.330000e-50	209.0
27	TraesCS4B01G350800	chr7D	89.691	97	10	0	387	483	408366498	408366594	8.670000e-25	124.0
28	TraesCS4B01G350800	chr7D	75.175	286	55	11	212	482	485092664	485092948	1.120000e-23	121.0
29	TraesCS4B01G350800	chr7D	85.577	104	14	1	383	485	408366226	408366123	8.730000e-20	108.0
30	TraesCS4B01G350800	chr1D	88.539	349	18	9	1983	2312	9310002	9310347	9.950000e-109	403.0
31	TraesCS4B01G350800	chr1D	88.757	338	20	8	1985	2312	109761857	109761528	4.630000e-107	398.0
32	TraesCS4B01G350800	chr1D	87.574	338	22	5	1985	2312	486300345	486300672	7.800000e-100	374.0
33	TraesCS4B01G350800	chr1D	84.330	351	33	7	1982	2312	479438796	479439144	7.970000e-85	324.0
34	TraesCS4B01G350800	chr1D	84.694	294	42	3	88	379	403547726	403547434	8.080000e-75	291.0
35	TraesCS4B01G350800	chr1D	84.300	293	45	1	88	379	465892171	465892463	3.760000e-73	285.0
36	TraesCS4B01G350800	chr3D	87.320	347	21	5	1985	2312	615092776	615092434	2.170000e-100	375.0
37	TraesCS4B01G350800	chr3D	86.455	347	27	4	1985	2312	1085430	1085085	1.690000e-96	363.0
38	TraesCS4B01G350800	chr3D	86.644	292	38	1	89	379	485233644	485233935	2.870000e-84	322.0
39	TraesCS4B01G350800	chr3D	85.163	337	21	11	1986	2312	566060109	566060426	3.710000e-83	318.0
40	TraesCS4B01G350800	chr3D	84.642	293	42	3	89	379	397149686	397149395	2.910000e-74	289.0
41	TraesCS4B01G350800	chr7B	87.349	332	24	11	1985	2312	26875618	26875935	4.690000e-97	364.0
42	TraesCS4B01G350800	chr7B	85.345	348	26	12	1978	2312	11932595	11932260	1.020000e-88	337.0
43	TraesCS4B01G350800	chr7B	81.250	128	17	4	629	755	711204459	711204580	1.890000e-16	97.1
44	TraesCS4B01G350800	chr5B	85.251	339	32	7	1983	2312	448455290	448454961	1.320000e-87	333.0
45	TraesCS4B01G350800	chr5B	81.221	426	43	17	89	482	690595326	690595746	2.230000e-80	309.0
46	TraesCS4B01G350800	chr2D	84.300	293	43	3	89	379	447147627	447147918	1.350000e-72	283.0
47	TraesCS4B01G350800	chr2D	93.750	64	4	0	419	482	450877156	450877219	1.890000e-16	97.1
48	TraesCS4B01G350800	chr6A	84.138	290	41	5	92	379	23378722	23379008	2.260000e-70	276.0
49	TraesCS4B01G350800	chr6A	95.690	116	5	0	782	897	1971836	1971951	1.090000e-43	187.0
50	TraesCS4B01G350800	chr6A	82.895	76	13	0	403	478	522204634	522204559	4.120000e-08	69.4
51	TraesCS4B01G350800	chr7A	77.250	400	77	8	89	484	119760568	119760957	2.990000e-54	222.0
52	TraesCS4B01G350800	chr7A	93.496	123	8	0	781	903	730827248	730827126	1.410000e-42	183.0
53	TraesCS4B01G350800	chr6B	83.051	236	37	2	487	721	680078869	680079102	6.470000e-51	211.0
54	TraesCS4B01G350800	chr6B	87.097	93	10	2	387	478	666039909	666039818	1.130000e-18	104.0
55	TraesCS4B01G350800	chr3A	95.575	113	5	0	785	897	399898174	399898286	5.070000e-42	182.0
56	TraesCS4B01G350800	chr3B	88.966	145	12	4	756	897	427096776	427096919	2.360000e-40	176.0

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	TraesCS4B01G350800	chr4B	643399811	643402122	2311	True	4270	4270	100.000	1	2312	1	chr4B.!!$R2	2311
1	TraesCS4B01G350800	chrUn	264907306	264908395	1089	False	1650	1650	94.059	900	1986	1	chrUn.!!$F1	1086

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
244	245	0.034863	TTGGCGGTAGGAAACATCCC	60.035	55.0	0.0	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1366	1367	0.027979	CACACGCAAGACACCAACAG	59.972	55.0	0.0	0.0	43.62	3.16	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
23	24	6.579491	GATCAATCAACAAATTAAGCTGCC	57.421	37.500	0.00	0.00	0.00	4.85
24	25	4.819769	TCAATCAACAAATTAAGCTGCCC	58.180	39.130	0.00	0.00	0.00	5.36
25	26	4.527816	TCAATCAACAAATTAAGCTGCCCT	59.472	37.500	0.00	0.00	0.00	5.19
26	27	5.011943	TCAATCAACAAATTAAGCTGCCCTT	59.988	36.000	0.00	0.00	37.57	3.95
27	28	4.953940	TCAACAAATTAAGCTGCCCTTT	57.046	36.364	0.00	0.00	34.95	3.11
28	29	4.630111	TCAACAAATTAAGCTGCCCTTTG	58.370	39.130	0.00	4.35	34.95	2.77
29	30	4.100808	TCAACAAATTAAGCTGCCCTTTGT	59.899	37.500	11.31	11.31	40.65	2.83
30	31	3.993920	ACAAATTAAGCTGCCCTTTGTG	58.006	40.909	14.51	3.51	38.30	3.33
31	32	3.244181	ACAAATTAAGCTGCCCTTTGTGG	60.244	43.478	14.51	0.00	38.30	4.17
32	33	2.603075	ATTAAGCTGCCCTTTGTGGA	57.397	45.000	0.00	0.00	38.35	4.02
33	34	2.603075	TTAAGCTGCCCTTTGTGGAT	57.397	45.000	0.00	0.00	38.35	3.41
34	35	1.838112	TAAGCTGCCCTTTGTGGATG	58.162	50.000	0.00	0.00	38.35	3.51
35	36	0.112995	AAGCTGCCCTTTGTGGATGA	59.887	50.000	0.00	0.00	38.35	2.92
36	37	0.333993	AGCTGCCCTTTGTGGATGAT	59.666	50.000	0.00	0.00	38.35	2.45
37	38	0.458669	GCTGCCCTTTGTGGATGATG	59.541	55.000	0.00	0.00	38.35	3.07
38	39	0.458669	CTGCCCTTTGTGGATGATGC	59.541	55.000	0.00	0.00	38.35	3.91
39	40	0.040058	TGCCCTTTGTGGATGATGCT	59.960	50.000	0.00	0.00	38.35	3.79
40	41	0.743097	GCCCTTTGTGGATGATGCTC	59.257	55.000	0.00	0.00	38.35	4.26
41	42	1.396653	CCCTTTGTGGATGATGCTCC	58.603	55.000	0.00	0.00	38.35	4.70
42	43	1.341285	CCCTTTGTGGATGATGCTCCA	60.341	52.381	0.00	0.00	43.09	3.86
43	44	2.022195	CCTTTGTGGATGATGCTCCAG	58.978	52.381	0.00	0.00	45.87	3.86
44	45	1.404391	CTTTGTGGATGATGCTCCAGC	59.596	52.381	0.00	0.00	45.87	4.85
45	46	0.622136	TTGTGGATGATGCTCCAGCT	59.378	50.000	0.00	0.00	45.87	4.24
46	47	0.622136	TGTGGATGATGCTCCAGCTT	59.378	50.000	0.00	0.00	45.87	3.74
47	48	1.307097	GTGGATGATGCTCCAGCTTC	58.693	55.000	7.37	7.37	45.87	3.86

Showing 1 to 25 of 686 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.521372	GGGCAGCTTAATTTGTTGATTGATC	59.479	40.000	0.00	0.00	0.00	2.92
1	2	5.188359	AGGGCAGCTTAATTTGTTGATTGAT	59.812	36.000	0.00	0.00	0.00	2.57
2	3	4.527816	AGGGCAGCTTAATTTGTTGATTGA	59.472	37.500	0.00	0.00	0.00	2.57
3	4	4.824289	AGGGCAGCTTAATTTGTTGATTG	58.176	39.130	0.00	0.00	0.00	2.67
4	5	5.488262	AAGGGCAGCTTAATTTGTTGATT	57.512	34.783	0.00	0.00	0.00	2.57
5	6	5.221702	ACAAAGGGCAGCTTAATTTGTTGAT	60.222	36.000	9.24	0.00	40.22	2.57
6	7	4.100808	ACAAAGGGCAGCTTAATTTGTTGA	59.899	37.500	9.24	0.00	40.22	3.18
7	8	4.211794	CACAAAGGGCAGCTTAATTTGTTG	59.788	41.667	11.43	1.98	40.95	3.33
8	9	4.379652	CACAAAGGGCAGCTTAATTTGTT	58.620	39.130	11.43	0.00	40.95	2.83
9	10	3.244181	CCACAAAGGGCAGCTTAATTTGT	60.244	43.478	9.24	9.24	42.99	2.83
10	11	3.006752	TCCACAAAGGGCAGCTTAATTTG	59.993	43.478	8.25	8.25	38.24	2.32
11	12	3.238597	TCCACAAAGGGCAGCTTAATTT	58.761	40.909	0.00	0.00	38.24	1.82
12	13	2.888212	TCCACAAAGGGCAGCTTAATT	58.112	42.857	0.00	0.00	38.24	1.40
13	14	2.603075	TCCACAAAGGGCAGCTTAAT	57.397	45.000	0.00	0.00	38.24	1.40
14	15	2.170166	CATCCACAAAGGGCAGCTTAA	58.830	47.619	0.00	0.00	38.24	1.85
15	16	1.354031	TCATCCACAAAGGGCAGCTTA	59.646	47.619	0.00	0.00	38.24	3.09
16	17	0.112995	TCATCCACAAAGGGCAGCTT	59.887	50.000	0.00	0.00	38.24	3.74
17	18	0.333993	ATCATCCACAAAGGGCAGCT	59.666	50.000	0.00	0.00	38.24	4.24
18	19	0.458669	CATCATCCACAAAGGGCAGC	59.541	55.000	0.00	0.00	38.24	5.25
19	20	0.458669	GCATCATCCACAAAGGGCAG	59.541	55.000	0.00	0.00	38.24	4.85
20	21	0.040058	AGCATCATCCACAAAGGGCA	59.960	50.000	0.00	0.00	38.24	5.36
21	22	0.743097	GAGCATCATCCACAAAGGGC	59.257	55.000	0.00	0.00	34.04	5.19
22	23	1.341285	TGGAGCATCATCCACAAAGGG	60.341	52.381	0.00	0.00	44.56	3.95
23	24	2.022195	CTGGAGCATCATCCACAAAGG	58.978	52.381	0.00	0.00	44.56	3.11
24	25	1.404391	GCTGGAGCATCATCCACAAAG	59.596	52.381	0.00	0.00	44.56	2.77

Showing 1 to 25 of 716 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.