AutoCloner

Multiple sequence alignment - TraesCS3B01G306000

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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	TraesCS3B01G306000	chr3B	100.000	3801	0	0	1	3801	491522219	491518419	0.000000e+00	7020
1	TraesCS3B01G306000	chr3B	94.737	171	9	0	3631	3801	582034916	582034746	2.250000e-67	267
2	TraesCS3B01G306000	chr3D	92.945	1701	46	23	1411	3062	376920420	376918745	0.000000e+00	2409
3	TraesCS3B01G306000	chr3D	94.131	443	22	3	960	1401	376920914	376920475	0.000000e+00	671
4	TraesCS3B01G306000	chr3D	93.478	138	8	1	3443	3580	5619085	5619221	1.790000e-48	204
5	TraesCS3B01G306000	chr3A	92.836	1005	27	8	2070	3041	501650524	501649532	0.000000e+00	1415
6	TraesCS3B01G306000	chr3A	94.609	575	22	7	830	1401	501651890	501651322	0.000000e+00	881
7	TraesCS3B01G306000	chr3A	93.493	584	14	7	1509	2069	501651190	501650608	0.000000e+00	846
8	TraesCS3B01G306000	chr5B	98.555	761	11	0	1	761	672844191	672844951	0.000000e+00	1345
9	TraesCS3B01G306000	chr1B	98.292	761	13	0	1	761	7970783	7971543	0.000000e+00	1334
10	TraesCS3B01G306000	chr1B	78.162	751	136	13	1	749	645333716	645332992	1.610000e-123	453
11	TraesCS3B01G306000	chr7B	97.900	762	15	1	1	761	678854403	678855164	0.000000e+00	1317
12	TraesCS3B01G306000	chr4D	84.265	769	110	4	1	758	51905946	51906714	0.000000e+00	739
13	TraesCS3B01G306000	chr2B	90.602	532	32	11	3117	3633	30486629	30486101	0.000000e+00	689
14	TraesCS3B01G306000	chr2B	75.469	693	152	16	16	699	534230476	534229793	4.740000e-84	322
15	TraesCS3B01G306000	chr5D	90.057	523	36	9	3072	3580	344876840	344876320	0.000000e+00	664
16	TraesCS3B01G306000	chr5D	94.152	171	10	0	3631	3801	458866846	458866676	1.050000e-65	261
17	TraesCS3B01G306000	chr7A	76.340	765	162	16	6	761	711299280	711298526	3.560000e-105	392
18	TraesCS3B01G306000	chr1A	75.617	689	156	11	16	698	369370535	369369853	7.870000e-87	331
19	TraesCS3B01G306000	chr1A	91.228	171	15	0	3631	3801	522149310	522149140	2.280000e-57	233
20	TraesCS3B01G306000	chr1A	91.228	171	15	0	3631	3801	577605750	577605580	2.280000e-57	233
21	TraesCS3B01G306000	chr5A	74.459	693	159	17	16	699	473609495	473608812	2.240000e-72	283
22	TraesCS3B01G306000	chr2D	94.767	172	9	0	3630	3801	629979964	629980135	6.260000e-68	268
23	TraesCS3B01G306000	chr6B	94.737	171	9	0	3631	3801	132934083	132933913	2.250000e-67	267
24	TraesCS3B01G306000	chr6B	95.092	163	8	0	3639	3801	34805208	34805046	1.350000e-64	257
25	TraesCS3B01G306000	chr2A	94.152	171	10	0	3631	3801	11995116	11995286	1.050000e-65	261
26	TraesCS3B01G306000	chr2A	93.023	172	12	0	3630	3801	766643699	766643870	6.300000e-63	252

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	TraesCS3B01G306000	chr3B	491518419	491522219	3800	True	7020.000000	7020	100.000	1	3801	1	chr3B.!!$R1	3800
1	TraesCS3B01G306000	chr3D	376918745	376920914	2169	True	1540.000000	2409	93.538	960	3062	2	chr3D.!!$R1	2102
2	TraesCS3B01G306000	chr3A	501649532	501651890	2358	True	1047.333333	1415	93.646	830	3041	3	chr3A.!!$R1	2211
3	TraesCS3B01G306000	chr5B	672844191	672844951	760	False	1345.000000	1345	98.555	1	761	1	chr5B.!!$F1	760
4	TraesCS3B01G306000	chr1B	7970783	7971543	760	False	1334.000000	1334	98.292	1	761	1	chr1B.!!$F1	760
5	TraesCS3B01G306000	chr1B	645332992	645333716	724	True	453.000000	453	78.162	1	749	1	chr1B.!!$R1	748
6	TraesCS3B01G306000	chr7B	678854403	678855164	761	False	1317.000000	1317	97.900	1	761	1	chr7B.!!$F1	760
7	TraesCS3B01G306000	chr4D	51905946	51906714	768	False	739.000000	739	84.265	1	758	1	chr4D.!!$F1	757
8	TraesCS3B01G306000	chr2B	30486101	30486629	528	True	689.000000	689	90.602	3117	3633	1	chr2B.!!$R1	516
9	TraesCS3B01G306000	chr2B	534229793	534230476	683	True	322.000000	322	75.469	16	699	1	chr2B.!!$R2	683
10	TraesCS3B01G306000	chr5D	344876320	344876840	520	True	664.000000	664	90.057	3072	3580	1	chr5D.!!$R1	508
11	TraesCS3B01G306000	chr7A	711298526	711299280	754	True	392.000000	392	76.340	6	761	1	chr7A.!!$R1	755
12	TraesCS3B01G306000	chr1A	369369853	369370535	682	True	331.000000	331	75.617	16	698	1	chr1A.!!$R1	682
13	TraesCS3B01G306000	chr5A	473608812	473609495	683	True	283.000000	283	74.459	16	699	1	chr5A.!!$R1	683

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
889	906	0.256464	TTCCGTCCCTCTCTCTCCTC	59.744	60.0	0.00	0.0	0.00	3.71	F
1787	1873	0.839946	CATGGTACCCTAAGGCTGCT	59.160	55.0	10.07	0.0	36.11	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2526	2709	0.252197	ACTTGTTAGCCGGGTCATCC	59.748	55.0	10.79	0.0	0.0	3.51	R
3637	3859	0.107606	AGTGTGGTACCAACGTGCAA	60.108	50.0	18.31	0.0	0.0	4.08	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	Hairpin	End Stability
45	46	9.482627	TCAACGAGGTTGCATTAATTAAATTTT	57.517	25.926	1.21	42.55	1.82
85	86	5.237779	GGGAATCATCGGCGAAAAGTAAATA	59.762	40.000	15.93	0.00	1.40
251	252	8.648557	TTGTAGGAATAAATTCATCAGTCTCG	57.351	34.615	5.15	38.53	4.04
801	816	9.216117	TCGATGACGATGAGAAAATATAGTAGA	57.784	33.333	0.00	43.81	2.59
802	817	9.827411	CGATGACGATGAGAAAATATAGTAGAA	57.173	33.333	0.00	42.66	2.10
805	820	9.745880	TGACGATGAGAAAATATAGTAGAAACC	57.254	33.333	0.00	0.00	3.27
806	821	9.968870	GACGATGAGAAAATATAGTAGAAACCT	57.031	33.333	0.00	0.00	3.50
807	822	9.968870	ACGATGAGAAAATATAGTAGAAACCTC	57.031	33.333	0.00	0.00	3.85
808	823	9.413048	CGATGAGAAAATATAGTAGAAACCTCC	57.587	37.037	0.00	0.00	4.30
822	837	8.101419	AGTAGAAACCTCCTTATTTAACACTGG	58.899	37.037	0.00	0.00	4.00
823	838	5.710567	AGAAACCTCCTTATTTAACACTGGC	59.289	40.000	0.00	0.00	4.85
824	839	4.650972	ACCTCCTTATTTAACACTGGCA	57.349	40.909	0.00	0.00	4.92
825	840	4.993028	ACCTCCTTATTTAACACTGGCAA	58.007	39.130	0.00	0.00	4.52
826	841	5.390387	ACCTCCTTATTTAACACTGGCAAA	58.610	37.500	0.00	0.00	3.68
827	842	6.016555	ACCTCCTTATTTAACACTGGCAAAT	58.983	36.000	0.00	0.00	2.32
828	843	6.152831	ACCTCCTTATTTAACACTGGCAAATC	59.847	38.462	0.00	0.00	2.17
833	848	9.271828	CCTTATTTAACACTGGCAAATCTTTTT	57.728	29.630	0.00	0.00	1.94
874	891	0.755686	CCCATCTCCTCCTCTTTCCG	59.244	60.000	0.00	0.00	4.30
885	902	1.341581	CCTCTTTCCGTCCCTCTCTCT	60.342	57.143	0.00	0.00	3.10
886	903	2.021457	CTCTTTCCGTCCCTCTCTCTC	58.979	57.143	0.00	0.00	3.20
887	904	1.107945	CTTTCCGTCCCTCTCTCTCC	58.892	60.000	0.00	0.00	3.71
888	905	0.705253	TTTCCGTCCCTCTCTCTCCT	59.295	55.000	0.00	0.00	3.69
889	906	0.256464	TTCCGTCCCTCTCTCTCCTC	59.744	60.000	0.00	0.00	3.71
907	924	3.100671	CCTCCTATCCCCTTCTTATCCG	58.899	54.545	0.00	0.00	4.18
1137	1155	2.028925	TGCGAGCAGAGCGACAAA	59.971	55.556	0.00	37.44	2.83

Showing 1 to 25 of 302 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.692625	CCTCGTTGAGACATGTTCTTGATT	59.307	41.667	0.00	0.00	33.22	2.57
85	86	3.057315	CAGAAATGCACCATCGGTTTCTT	60.057	43.478	6.49	0.00	37.10	2.52
251	252	9.730420	AAATATAAGGTGCGTTTTAATGATCAC	57.270	29.630	0.00	0.00	0.00	3.06
379	380	5.218885	CGGTGAAACTTGACATGCATAAAA	58.781	37.500	0.00	0.00	36.74	1.52
439	442	5.702670	GTGGCTTATGAGTGTATGCATATGT	59.297	40.000	10.16	0.00	0.00	2.29
776	791	9.827411	TTCTACTATATTTTCTCATCGTCATCG	57.173	33.333	0.00	0.00	38.55	3.84
779	794	9.745880	GGTTTCTACTATATTTTCTCATCGTCA	57.254	33.333	0.00	0.00	0.00	4.35
780	795	9.968870	AGGTTTCTACTATATTTTCTCATCGTC	57.031	33.333	0.00	0.00	0.00	4.20
781	796	9.968870	GAGGTTTCTACTATATTTTCTCATCGT	57.031	33.333	0.00	0.00	0.00	3.73
782	797	9.413048	GGAGGTTTCTACTATATTTTCTCATCG	57.587	37.037	0.00	0.00	0.00	3.84
796	811	8.101419	CCAGTGTTAAATAAGGAGGTTTCTACT	58.899	37.037	0.00	0.00	35.15	2.57
797	812	7.148289	GCCAGTGTTAAATAAGGAGGTTTCTAC	60.148	40.741	0.00	0.00	0.00	2.59
798	813	6.882678	GCCAGTGTTAAATAAGGAGGTTTCTA	59.117	38.462	0.00	0.00	0.00	2.10
799	814	5.710567	GCCAGTGTTAAATAAGGAGGTTTCT	59.289	40.000	0.00	0.00	0.00	2.52
800	815	5.475564	TGCCAGTGTTAAATAAGGAGGTTTC	59.524	40.000	0.00	0.00	0.00	2.78
801	816	5.390387	TGCCAGTGTTAAATAAGGAGGTTT	58.610	37.500	0.00	0.00	0.00	3.27
802	817	4.993028	TGCCAGTGTTAAATAAGGAGGTT	58.007	39.130	0.00	0.00	0.00	3.50
803	818	4.650972	TGCCAGTGTTAAATAAGGAGGT	57.349	40.909	0.00	0.00	0.00	3.85
804	819	5.975693	TTTGCCAGTGTTAAATAAGGAGG	57.024	39.130	0.00	0.00	0.00	4.30
805	820	7.396540	AGATTTGCCAGTGTTAAATAAGGAG	57.603	36.000	2.82	0.00	0.00	3.69
806	821	7.775053	AAGATTTGCCAGTGTTAAATAAGGA	57.225	32.000	2.82	0.00	0.00	3.36
807	822	8.831715	AAAAGATTTGCCAGTGTTAAATAAGG	57.168	30.769	2.82	0.00	0.00	2.69
811	826	8.829612	CAAGAAAAAGATTTGCCAGTGTTAAAT	58.170	29.630	2.51	2.51	0.00	1.40
812	827	7.279758	CCAAGAAAAAGATTTGCCAGTGTTAAA	59.720	33.333	0.00	0.00	0.00	1.52
813	828	6.760770	CCAAGAAAAAGATTTGCCAGTGTTAA	59.239	34.615	0.00	0.00	0.00	2.01

Showing 1 to 25 of 288 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.