AutoCloner

Multiple sequence alignment - TraesCS3A01G485600

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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	TraesCS3A01G485600	chr3A	100.000	4341	0	0	1	4341	714591684	714587344	0.000000e+00	8017
1	TraesCS3A01G485600	chr3A	89.119	2463	190	36	1633	4044	714645540	714647975	0.000000e+00	2992
2	TraesCS3A01G485600	chr3A	90.465	1248	113	5	1	1248	714643673	714644914	0.000000e+00	1640
3	TraesCS3A01G485600	chr3A	87.805	779	82	5	794	1571	714627773	714628539	0.000000e+00	900
4	TraesCS3A01G485600	chr3A	88.757	676	67	5	2717	3391	714602902	714602235	0.000000e+00	819
5	TraesCS3A01G485600	chr3A	90.811	185	15	2	1230	1414	714644930	714645112	3.350000e-61	246
6	TraesCS3A01G485600	chr3D	89.864	3374	293	23	4	3350	579423874	579420523	0.000000e+00	4290
7	TraesCS3A01G485600	chr3D	89.651	2464	185	39	1633	4045	579587107	579589551	0.000000e+00	3073
8	TraesCS3A01G485600	chr3D	94.249	1339	74	3	1	1339	579396187	579394852	0.000000e+00	2043
9	TraesCS3A01G485600	chr3D	91.960	1393	107	5	1	1393	579585292	579586679	0.000000e+00	1947
10	TraesCS3A01G485600	chr3D	91.067	1265	71	15	1364	2609	579394855	579393614	0.000000e+00	1672
11	TraesCS3A01G485600	chr3D	93.868	848	44	6	2605	3449	579383798	579382956	0.000000e+00	1271
12	TraesCS3A01G485600	chr3D	86.622	299	34	6	4046	4341	579379623	579379328	4.190000e-85	326
13	TraesCS3A01G485600	chr3D	91.703	229	7	2	3562	3779	579382959	579382732	1.520000e-79	307
14	TraesCS3A01G485600	chr3D	92.179	179	14	0	3169	3347	579367490	579367312	2.000000e-63	254
15	TraesCS3A01G485600	chr3B	88.419	3402	321	27	24	3390	773761067	773757704	0.000000e+00	4032
16	TraesCS3A01G485600	chr3B	91.165	1777	128	17	1628	3387	773900177	773901941	0.000000e+00	2385
17	TraesCS3A01G485600	chr3B	91.203	1239	106	2	8	1246	773898620	773899855	0.000000e+00	1681
18	TraesCS3A01G485600	chr3B	95.770	662	22	4	2686	3345	773743745	773743088	0.000000e+00	1062
19	TraesCS3A01G485600	chr3B	89.189	185	18	2	1230	1414	773899873	773900055	3.380000e-56	230
20	TraesCS3A01G485600	chr3B	90.722	97	8	1	3384	3479	773730251	773730155	1.270000e-25	128

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	TraesCS3A01G485600	chr3A	714587344	714591684	4340	True	8017.000000	8017	100.000000	1	4341	1	chr3A.!!$R1	4340
1	TraesCS3A01G485600	chr3A	714643673	714647975	4302	False	1626.000000	2992	90.131667	1	4044	3	chr3A.!!$F2	4043
2	TraesCS3A01G485600	chr3A	714627773	714628539	766	False	900.000000	900	87.805000	794	1571	1	chr3A.!!$F1	777
3	TraesCS3A01G485600	chr3A	714602235	714602902	667	True	819.000000	819	88.757000	2717	3391	1	chr3A.!!$R2	674
4	TraesCS3A01G485600	chr3D	579420523	579423874	3351	True	4290.000000	4290	89.864000	4	3350	1	chr3D.!!$R2	3346
5	TraesCS3A01G485600	chr3D	579585292	579589551	4259	False	2510.000000	3073	90.805500	1	4045	2	chr3D.!!$F1	4044
6	TraesCS3A01G485600	chr3D	579393614	579396187	2573	True	1857.500000	2043	92.658000	1	2609	2	chr3D.!!$R4	2608
7	TraesCS3A01G485600	chr3D	579379328	579383798	4470	True	634.666667	1271	90.731000	2605	4341	3	chr3D.!!$R3	1736
8	TraesCS3A01G485600	chr3B	773757704	773761067	3363	True	4032.000000	4032	88.419000	24	3390	1	chr3B.!!$R3	3366
9	TraesCS3A01G485600	chr3B	773898620	773901941	3321	False	1432.000000	2385	90.519000	8	3387	3	chr3B.!!$F1	3379
10	TraesCS3A01G485600	chr3B	773743088	773743745	657	True	1062.000000	1062	95.770000	2686	3345	1	chr3B.!!$R2	659

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	Hairpin	End Stability	Orientation
448	449	0.106918	GACCCACAAGACACACCCAA	60.107	55.0	0.00	0.00	4.12	F
1331	1400	0.316204	GCATGACAACTTGCTGCCTT	59.684	50.0	0.00	41.77	4.35	F
1778	2272	0.451783	CCTTGTATGGTTCCGCAAGC	59.548	55.0	11.92	37.56	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1483	1581	0.034574	AACAACATGGGGATAGCGCA	60.035	50.000	11.47	0.0	0.00	6.09	R
2495	3018	2.047274	AATCGTGTCGGCCAGTGG	60.047	61.111	4.20	4.2	0.00	4.00	R
3559	4112	0.034896	AGTGATCACGGGGACACAAC	59.965	55.000	19.85	0.0	35.97	3.32	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
22	23	1.070275	CTCTGCACACCTGACAGCA	59.930	57.895	0.00	0.00	35.43	4.41
65	66	4.594920	TCTCACTCCTGGAAAAACTCTCAT	59.405	41.667	0.00	0.00	0.00	2.90
72	73	4.563580	CCTGGAAAAACTCTCATCTCGGAA	60.564	45.833	0.00	0.00	0.00	4.30
84	85	2.607631	TCTCGGAACAAGGTTCGTTT	57.392	45.000	3.30	0.00	0.00	3.60
286	287	2.620367	GGCCACCACATACTTTGGATGA	60.620	50.000	0.00	0.00	37.58	2.92
321	322	1.871772	CAGCAACTCTTCGGCCAAG	59.128	57.895	2.24	6.06	0.00	3.61
355	356	7.066284	ACAATGGCAATCTTGTAGTCTTATCAC	59.934	37.037	3.24	0.00	33.96	3.06
396	397	2.101415	GCAGAGCTTTGAAAACCCAAGT	59.899	45.455	8.73	0.00	0.00	3.16
448	449	0.106918	GACCCACAAGACACACCCAA	60.107	55.000	0.00	0.00	0.00	4.12
474	475	1.765314	CGGATGATCTCTTGGAAGGGT	59.235	52.381	0.00	0.00	0.00	4.34
524	525	1.073763	TGGTGGGAATGACCTTGACAG	59.926	52.381	0.00	0.00	38.98	3.51
609	610	1.580059	ATGTATCCTCCAACGTGGGT	58.420	50.000	9.33	0.00	38.32	4.51
648	649	7.604164	AGTCCACTCATGTATTTGACAGTTTAG	59.396	37.037	0.00	0.00	42.79	1.85
655	656	5.876357	TGTATTTGACAGTTTAGAAGGGCT	58.124	37.500	0.00	0.00	32.86	5.19
656	657	6.303839	TGTATTTGACAGTTTAGAAGGGCTT	58.696	36.000	0.00	0.00	32.86	4.35
858	859	1.497991	GCTACTGCGACAACACAGAA	58.502	50.000	0.00	0.00	37.35	3.02
873	874	2.559668	CACAGAAGCAATTCCCACATGT	59.440	45.455	0.00	0.00	0.00	3.21
901	902	4.202441	CCTTGATGGATTTGACCCTAGTG	58.798	47.826	0.00	0.00	38.35	2.74
910	911	5.300792	GGATTTGACCCTAGTGACAAAACAA	59.699	40.000	6.89	0.00	36.19	2.83
918	919	4.036380	CCTAGTGACAAAACAAAGTGGGTC	59.964	45.833	0.00	0.00	0.00	4.46
946	947	1.988293	TTTTTCTCATGGTTGCCGGA	58.012	45.000	5.05	0.00	0.00	5.14
1054	1055	4.439289	GGAACAAAAGCTATGATGACTGCC	60.439	45.833	6.45	0.00	0.00	4.85
1067	1068	0.819259	GACTGCCAAGTGGAGTGCAA	60.819	55.000	0.18	0.00	36.52	4.08
1183	1184	3.539604	CTGATTGATGTGGAGAAGGGTC	58.460	50.000	0.00	0.00	0.00	4.46
1215	1216	3.612955	GCTATGAGAACCTGTATCTCCGC	60.613	52.174	1.45	0.00	42.14	5.54

Showing 1 to 25 of 139 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	0.179009	ACAAGCATGCTGTCAGGTGT	60.179	50.000	23.48	17.63	0.00	4.16
65	66	2.206750	CAAACGAACCTTGTTCCGAGA	58.793	47.619	0.00	0.00	0.00	4.04
100	101	3.893753	TTCAGTTGAATTTGAGGGGGA	57.106	42.857	0.00	0.00	0.00	4.81
188	189	4.371786	TGAAGCATCAGTGATCGGATTAC	58.628	43.478	1.56	4.84	0.00	1.89
286	287	1.067516	GCTGCCAGTGATTGTGTTTGT	59.932	47.619	0.00	0.00	0.00	2.83
321	322	3.863142	AGATTGCCATTGTTGAGAAGC	57.137	42.857	0.00	0.00	0.00	3.86
355	356	1.958579	CCATAACATGGCACCATCTGG	59.041	52.381	0.00	1.48	44.70	3.86
396	397	2.879233	GCCAGGAAGGACGGTGTCA	61.879	63.158	0.00	0.00	41.22	3.58
448	449	1.202734	CCAAGAGATCATCCGCCATGT	60.203	52.381	0.00	0.00	33.66	3.21
474	475	3.508845	CCTTTTGAAGGGTCTTCAGGA	57.491	47.619	9.81	2.26	45.27	3.86
524	525	2.094649	CAGACGAAGAACTGTAGGGGAC	60.095	54.545	0.00	0.00	33.13	4.46
609	610	1.075050	AGTGGACTAACGGTCTGGAGA	59.925	52.381	0.00	0.00	43.97	3.71
648	649	0.462759	CCTCACCATCGAAGCCCTTC	60.463	60.000	0.00	0.00	36.29	3.46
655	656	0.106708	GCATAGGCCTCACCATCGAA	59.893	55.000	9.68	0.00	43.14	3.71
656	657	1.048160	TGCATAGGCCTCACCATCGA	61.048	55.000	9.68	0.00	43.14	3.59
739	740	2.028112	TGGTATTCCATCTCCATAGCGC	60.028	50.000	0.00	0.00	39.03	5.92
807	808	6.016693	CACCACAGTATCCATAGAGACTACAG	60.017	46.154	0.00	0.00	42.67	2.74
858	859	2.493278	GCACTTACATGTGGGAATTGCT	59.507	45.455	9.11	0.00	38.31	3.91
901	902	3.066760	CCTCTGACCCACTTTGTTTTGTC	59.933	47.826	0.00	0.00	0.00	3.18
910	911	2.683211	AAATTGCCTCTGACCCACTT	57.317	45.000	0.00	0.00	0.00	3.16
918	919	4.796038	ACCATGAGAAAAATTGCCTCTG	57.204	40.909	0.00	0.00	0.00	3.35
946	947	3.209410	CACACTGCAGTTCTTCCTTTCT	58.791	45.455	18.94	0.00	0.00	2.52
1054	1055	5.146482	CAATTTTTGTTGCACTCCACTTG	57.854	39.130	0.00	0.00	0.00	3.16
1067	1068	5.199024	TGCTACACATGAGCAATTTTTGT	57.801	34.783	5.17	0.00	46.71	2.83
1183	1184	0.249447	TTCTCATAGCCGATGGTGCG	60.249	55.000	0.00	0.00	36.08	5.34

Showing 1 to 25 of 150 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.