AutoCloner

Multiple sequence alignment - TraesCS4B01G109000

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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	TraesCS4B01G109000	chr4B	100.000	3939	0	0	1	3939	120262497	120258559	0.000000e+00	7275
1	TraesCS4B01G109000	chr4B	97.139	3845	99	7	1	3838	222595108	222598948	0.000000e+00	6481
2	TraesCS4B01G109000	chr4B	96.981	3577	88	10	270	3836	40493151	40496717	0.000000e+00	5989
3	TraesCS4B01G109000	chr3A	97.373	3844	83	9	1	3837	91838455	91842287	0.000000e+00	6523
4	TraesCS4B01G109000	chr6B	97.343	3839	91	8	4	3836	706416545	706412712	0.000000e+00	6514
5	TraesCS4B01G109000	chr4A	97.146	3819	93	8	1	3813	531952595	531956403	0.000000e+00	6434
6	TraesCS4B01G109000	chr4A	97.087	103	3	0	3837	3939	688183949	688183847	1.450000e-39	174
7	TraesCS4B01G109000	chr2D	95.792	3850	139	13	4	3840	340331807	340327968	0.000000e+00	6191
8	TraesCS4B01G109000	chr5B	97.560	3401	73	7	445	3836	10418338	10414939	0.000000e+00	5812
9	TraesCS4B01G109000	chr5B	98.039	408	8	0	4	411	10418738	10418331	0.000000e+00	710
10	TraesCS4B01G109000	chr7A	97.612	3183	69	5	4	3180	492427303	492424122	0.000000e+00	5450
11	TraesCS4B01G109000	chr7A	88.532	1805	174	16	2052	3836	36253195	36251404	0.000000e+00	2156
12	TraesCS4B01G109000	chr7A	99.029	103	1	0	3837	3939	482428601	482428499	6.720000e-43	185
13	TraesCS4B01G109000	chr5A	93.606	3300	194	10	549	3836	220265040	220268334	0.000000e+00	4909
14	TraesCS4B01G109000	chr5A	99.029	103	1	0	3837	3939	488189355	488189457	6.720000e-43	185
15	TraesCS4B01G109000	chr5A	99.029	103	1	0	3837	3939	659579916	659580018	6.720000e-43	185
16	TraesCS4B01G109000	chr2B	97.553	899	17	3	4	898	758243817	758242920	0.000000e+00	1533
17	TraesCS4B01G109000	chr4D	99.029	103	1	0	3837	3939	51681711	51681609	6.720000e-43	185
18	TraesCS4B01G109000	chr4D	98.058	103	2	0	3837	3939	424561056	424561158	3.130000e-41	180
19	TraesCS4B01G109000	chr4D	98.058	103	2	0	3837	3939	458441117	458441015	3.130000e-41	180
20	TraesCS4B01G109000	chr3D	99.029	103	1	0	3837	3939	539656456	539656558	6.720000e-43	185
21	TraesCS4B01G109000	chr1D	99.029	103	1	0	3837	3939	124138200	124138302	6.720000e-43	185

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	TraesCS4B01G109000	chr4B	120258559	120262497	3938	True	7275	7275	100.0000	1	3939	1	chr4B.!!$R1	3938
1	TraesCS4B01G109000	chr4B	222595108	222598948	3840	False	6481	6481	97.1390	1	3838	1	chr4B.!!$F2	3837
2	TraesCS4B01G109000	chr4B	40493151	40496717	3566	False	5989	5989	96.9810	270	3836	1	chr4B.!!$F1	3566
3	TraesCS4B01G109000	chr3A	91838455	91842287	3832	False	6523	6523	97.3730	1	3837	1	chr3A.!!$F1	3836
4	TraesCS4B01G109000	chr6B	706412712	706416545	3833	True	6514	6514	97.3430	4	3836	1	chr6B.!!$R1	3832
5	TraesCS4B01G109000	chr4A	531952595	531956403	3808	False	6434	6434	97.1460	1	3813	1	chr4A.!!$F1	3812
6	TraesCS4B01G109000	chr2D	340327968	340331807	3839	True	6191	6191	95.7920	4	3840	1	chr2D.!!$R1	3836
7	TraesCS4B01G109000	chr5B	10414939	10418738	3799	True	3261	5812	97.7995	4	3836	2	chr5B.!!$R1	3832
8	TraesCS4B01G109000	chr7A	492424122	492427303	3181	True	5450	5450	97.6120	4	3180	1	chr7A.!!$R3	3176
9	TraesCS4B01G109000	chr7A	36251404	36253195	1791	True	2156	2156	88.5320	2052	3836	1	chr7A.!!$R1	1784
10	TraesCS4B01G109000	chr5A	220265040	220268334	3294	False	4909	4909	93.6060	549	3836	1	chr5A.!!$F1	3287
11	TraesCS4B01G109000	chr2B	758242920	758243817	897	True	1533	1533	97.5530	4	898	1	chr2B.!!$R1	894

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	Hairpin	End Stability	Orientation
365	368	0.486879	TTGGGGAAGTTTCTGGGCAT	59.513	50.000	0.00	4.40	F
1241	1250	4.122776	CTCGGGATCAAGTTATGGTTCAG	58.877	47.826	0.00	3.02	F
1642	1651	5.105853	AGGACTTCTTTATCCCACCCTTTA	58.894	41.667	35.38	1.85	F
2466	2491	0.373716	GGGCATTAGACTTCGTTGCG	59.626	55.000	34.17	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2213	2227	0.182775	AGTCCTTTGCTGGTTCGGTT	59.817	50.000	0.00	4.44	R
2435	2457	1.281867	CTAATGCCCAAGGTCACCTCA	59.718	52.381	30.89	3.86	R
2839	2875	4.848357	TCAGAATGTGGAAGGGAAGATTC	58.152	43.478	37.40	2.52	R
3867	3916	0.179161	GTGGTCTGGATGACGACGAG	60.179	60.000	46.24	4.18	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
121	124	7.390718	AGTTCACAATCAAGGTAACAACCTATC	59.609	37.037	0.00	0.00	39.65	2.08
284	287	1.144708	TGTCTGGAACATGCCAAAGGA	59.855	47.619	0.00	0.00	38.20	3.36
285	288	2.238521	GTCTGGAACATGCCAAAGGAA	58.761	47.619	0.00	0.00	38.20	3.36
365	368	0.486879	TTGGGGAAGTTTCTGGGCAT	59.513	50.000	0.00	0.00	0.00	4.40
798	807	5.449999	GGGCTTGTTAAATATTGGAAGTCCG	60.450	44.000	0.00	0.00	39.43	4.79
833	842	8.643324	AGGGTAATGAATGAGATACTGTACTTC	58.357	37.037	0.00	0.00	0.00	3.01
886	895	5.743872	CGGGCTTATCTTAAAAGTTGCATTC	59.256	40.000	0.00	0.00	0.00	2.67
1071	1080	6.007076	TCATATGGGTGCTGTTTCTGTTTTA	58.993	36.000	2.13	0.00	0.00	1.52
1241	1250	4.122776	CTCGGGATCAAGTTATGGTTCAG	58.877	47.826	0.00	0.00	0.00	3.02
1490	1499	5.946942	ATGACTACAACTGATGGATCACT	57.053	39.130	0.00	0.00	32.50	3.41
1642	1651	5.105853	AGGACTTCTTTATCCCACCCTTTA	58.894	41.667	0.00	0.00	35.38	1.85
1950	1963	8.354711	ACTCTTACTCATGTCACAAAGATAGA	57.645	34.615	0.00	0.44	0.00	1.98
2116	2130	6.329496	CCTTTTGAGTTTTGAAGTTGTAGCA	58.671	36.000	0.00	0.00	0.00	3.49
2117	2131	6.811170	CCTTTTGAGTTTTGAAGTTGTAGCAA	59.189	34.615	0.00	0.00	0.00	3.91
2213	2227	7.931578	ATATTACGGGTGAATCTGTTTCAAA	57.068	32.000	2.90	0.00	45.71	2.69
2466	2491	0.373716	GGGCATTAGACTTCGTTGCG	59.626	55.000	0.00	0.00	34.17	4.85
2839	2875	4.518970	TGGCCTTCAGCTTTTGTAAGTTAG	59.481	41.667	3.32	0.00	43.05	2.34
3218	3258	6.649141	ACGAATTTCTGTATGTGTTCTGCTTA	59.351	34.615	0.00	0.00	0.00	3.09
3628	3674	1.483415	AGTGTGTTACCGGTGTGTTCT	59.517	47.619	19.93	5.78	0.00	3.01
3824	3873	2.940410	ACGGTGTTACAAAAGGTCTGTG	59.060	45.455	0.00	0.00	0.00	3.66
3841	3890	0.389948	GTGCTCTTGTAGTGTCCCCG	60.390	60.000	0.00	0.00	0.00	5.73
3842	3891	1.218316	GCTCTTGTAGTGTCCCCGG	59.782	63.158	0.00	0.00	0.00	5.73
3843	3892	1.218316	CTCTTGTAGTGTCCCCGGC	59.782	63.158	0.00	0.00	0.00	6.13
3844	3893	1.229082	TCTTGTAGTGTCCCCGGCT	60.229	57.895	0.00	0.00	0.00	5.52
3845	3894	1.218316	CTTGTAGTGTCCCCGGCTC	59.782	63.158	0.00	0.00	0.00	4.70
3846	3895	2.240162	CTTGTAGTGTCCCCGGCTCC	62.240	65.000	0.00	0.00	0.00	4.70
3847	3896	3.834799	GTAGTGTCCCCGGCTCCG	61.835	72.222	0.00	0.48	39.44	4.63
3860	3909	4.493747	CTCCGCGTCGTCCCCTTC	62.494	72.222	4.92	0.00	0.00	3.46
3863	3912	3.136123	CGCGTCGTCCCCTTCCTA	61.136	66.667	0.00	0.00	0.00	2.94
3864	3913	2.806237	GCGTCGTCCCCTTCCTAG	59.194	66.667	0.00	0.00	0.00	3.02
3865	3914	2.783288	GCGTCGTCCCCTTCCTAGG	61.783	68.421	0.82	0.82	41.60	3.02
3866	3915	2.783288	CGTCGTCCCCTTCCTAGGC	61.783	68.421	2.96	0.00	40.50	3.93
3867	3916	2.042230	TCGTCCCCTTCCTAGGCC	60.042	66.667	2.96	0.00	40.50	5.19
3868	3917	2.041819	CGTCCCCTTCCTAGGCCT	60.042	66.667	11.78	11.78	40.50	5.19
3869	3918	2.134933	CGTCCCCTTCCTAGGCCTC	61.135	68.421	9.68	0.00	40.50	4.70
3870	3919	2.134933	GTCCCCTTCCTAGGCCTCG	61.135	68.421	9.68	1.43	40.50	4.63
3871	3920	2.041819	CCCCTTCCTAGGCCTCGT	60.042	66.667	9.68	0.00	40.50	4.18
3872	3921	2.134933	CCCCTTCCTAGGCCTCGTC	61.135	68.421	9.68	0.00	40.50	4.20
3873	3922	2.491022	CCCTTCCTAGGCCTCGTCG	61.491	68.421	9.68	0.00	40.50	5.12
3874	3923	1.753463	CCTTCCTAGGCCTCGTCGT	60.753	63.158	9.68	0.00	33.99	4.34
3875	3924	1.726533	CCTTCCTAGGCCTCGTCGTC	61.727	65.000	9.68	0.00	33.99	4.20
3876	3925	1.001764	TTCCTAGGCCTCGTCGTCA	60.002	57.895	9.68	0.00	0.00	4.35
3877	3926	0.395311	TTCCTAGGCCTCGTCGTCAT	60.395	55.000	9.68	0.00	0.00	3.06
3878	3927	0.818445	TCCTAGGCCTCGTCGTCATC	60.818	60.000	9.68	0.00	0.00	2.92
3879	3928	1.655329	CTAGGCCTCGTCGTCATCC	59.345	63.158	9.68	0.00	0.00	3.51
3880	3929	1.077285	TAGGCCTCGTCGTCATCCA	60.077	57.895	9.68	0.00	0.00	3.41
3881	3930	1.101635	TAGGCCTCGTCGTCATCCAG	61.102	60.000	9.68	0.00	0.00	3.86
3882	3931	2.415608	GGCCTCGTCGTCATCCAGA	61.416	63.158	0.00	0.00	0.00	3.86
3883	3932	1.226717	GCCTCGTCGTCATCCAGAC	60.227	63.158	0.00	0.00	44.02	3.51
3884	3933	1.433879	CCTCGTCGTCATCCAGACC	59.566	63.158	0.00	0.00	44.66	3.85
3885	3934	1.313091	CCTCGTCGTCATCCAGACCA	61.313	60.000	0.00	0.00	44.66	4.02
3886	3935	0.179161	CTCGTCGTCATCCAGACCAC	60.179	60.000	0.00	0.00	44.66	4.16
3887	3936	1.153823	CGTCGTCATCCAGACCACC	60.154	63.158	0.00	0.00	44.66	4.61
3888	3937	1.153823	GTCGTCATCCAGACCACCG	60.154	63.158	0.00	0.00	44.66	4.94
3889	3938	2.509336	CGTCATCCAGACCACCGC	60.509	66.667	0.00	0.00	44.66	5.68
3890	3939	2.125106	GTCATCCAGACCACCGCC	60.125	66.667	0.00	0.00	41.56	6.13
3891	3940	3.399181	TCATCCAGACCACCGCCC	61.399	66.667	0.00	0.00	0.00	6.13
3892	3941	3.402681	CATCCAGACCACCGCCCT	61.403	66.667	0.00	0.00	0.00	5.19
3893	3942	3.402681	ATCCAGACCACCGCCCTG	61.403	66.667	0.00	0.00	0.00	4.45
3938	3987	4.256813	GGTCAACGACCGACTTCC	57.743	61.111	0.00	0.00	43.14	3.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	3.961480	TCTTCATCATCACGTTGGTCT	57.039	42.857	0.00	0.00	0.00	3.85
284	287	6.882610	TGCATTTCACAACTATTCTCTGTT	57.117	33.333	0.00	0.00	0.00	3.16
285	288	6.882610	TTGCATTTCACAACTATTCTCTGT	57.117	33.333	0.00	0.00	0.00	3.41
365	368	4.591321	AATCCTCCATTTCTAGCAACCA	57.409	40.909	0.00	0.00	0.00	3.67
798	807	7.703058	TCTCATTCATTACCCTTCCTTTTTC	57.297	36.000	0.00	0.00	0.00	2.29
833	842	7.209475	ACTCACATTTAAATGTCAAAACAGGG	58.791	34.615	27.12	17.62	46.10	4.45
912	921	7.489435	CGACTAATTATGTTCTTCTCAGCAAGA	59.511	37.037	0.00	0.00	0.00	3.02
1071	1080	2.687297	TCAGGATCAGCTTGCCTCTAT	58.313	47.619	0.00	0.00	0.00	1.98
1211	1220	6.095440	CCATAACTTGATCCCGAGAACAATTT	59.905	38.462	0.00	0.00	34.65	1.82
1241	1250	8.879342	AAGAATCATGCATACACTAGTTAGAC	57.121	34.615	0.00	0.00	0.00	2.59
1357	1366	3.137544	TCTTTCCCTAACACTTCCTGCAA	59.862	43.478	0.00	0.00	0.00	4.08
1490	1499	8.685427	CCCAAACATCATGTTCAACTTCATATA	58.315	33.333	2.74	0.00	40.14	0.86
1839	1848	3.891586	GACGAGCGTGCCTCAACGA	62.892	63.158	0.00	0.00	46.49	3.85
2213	2227	0.182775	AGTCCTTTGCTGGTTCGGTT	59.817	50.000	0.00	0.00	0.00	4.44
2314	2334	2.777459	TGGGTTGGTAATTTGGGTGT	57.223	45.000	0.00	0.00	0.00	4.16
2435	2457	1.281867	CTAATGCCCAAGGTCACCTCA	59.718	52.381	0.00	0.00	30.89	3.86
2466	2491	7.338703	CCTAAGAAACTAAATAAACTGGACCCC	59.661	40.741	0.00	0.00	0.00	4.95
2839	2875	4.848357	TCAGAATGTGGAAGGGAAGATTC	58.152	43.478	0.00	0.00	37.40	2.52
3824	3873	1.218316	CCGGGGACACTACAAGAGC	59.782	63.158	0.00	0.00	0.00	4.09
3843	3892	4.493747	GAAGGGGACGACGCGGAG	62.494	72.222	12.47	6.26	37.07	4.63
3846	3895	3.122250	CTAGGAAGGGGACGACGCG	62.122	68.421	3.53	3.53	37.07	6.01
3847	3896	2.783288	CCTAGGAAGGGGACGACGC	61.783	68.421	1.05	0.00	39.48	5.19
3848	3897	2.783288	GCCTAGGAAGGGGACGACG	61.783	68.421	14.75	0.00	43.87	5.12
3849	3898	2.433146	GGCCTAGGAAGGGGACGAC	61.433	68.421	14.75	0.00	43.87	4.34
3850	3899	2.042230	GGCCTAGGAAGGGGACGA	60.042	66.667	14.75	0.00	43.87	4.20
3851	3900	2.041819	AGGCCTAGGAAGGGGACG	60.042	66.667	14.75	0.00	43.87	4.79
3852	3901	2.134933	CGAGGCCTAGGAAGGGGAC	61.135	68.421	14.75	0.00	43.87	4.46
3853	3902	2.282446	CGAGGCCTAGGAAGGGGA	59.718	66.667	14.75	0.00	43.87	4.81
3854	3903	2.041819	ACGAGGCCTAGGAAGGGG	60.042	66.667	17.90	0.00	43.87	4.79
3855	3904	2.491022	CGACGAGGCCTAGGAAGGG	61.491	68.421	17.90	0.45	43.87	3.95
3856	3905	1.726533	GACGACGAGGCCTAGGAAGG	61.727	65.000	17.90	5.61	46.76	3.46
3857	3906	1.030488	TGACGACGAGGCCTAGGAAG	61.030	60.000	17.90	9.98	0.00	3.46
3858	3907	0.395311	ATGACGACGAGGCCTAGGAA	60.395	55.000	17.90	0.00	0.00	3.36
3859	3908	0.818445	GATGACGACGAGGCCTAGGA	60.818	60.000	17.90	0.00	0.00	2.94
3860	3909	1.655329	GATGACGACGAGGCCTAGG	59.345	63.158	17.90	3.67	0.00	3.02
3861	3910	1.101635	TGGATGACGACGAGGCCTAG	61.102	60.000	4.42	8.81	0.00	3.02
3862	3911	1.077285	TGGATGACGACGAGGCCTA	60.077	57.895	4.42	0.00	0.00	3.93
3863	3912	2.362503	TGGATGACGACGAGGCCT	60.363	61.111	3.86	3.86	0.00	5.19
3864	3913	2.105128	CTGGATGACGACGAGGCC	59.895	66.667	0.00	0.00	0.00	5.19
3865	3914	1.226717	GTCTGGATGACGACGAGGC	60.227	63.158	0.00	0.00	35.81	4.70
3866	3915	1.313091	TGGTCTGGATGACGACGAGG	61.313	60.000	0.00	0.00	46.24	4.63
3867	3916	0.179161	GTGGTCTGGATGACGACGAG	60.179	60.000	0.00	0.00	46.24	4.18
3868	3917	1.880894	GTGGTCTGGATGACGACGA	59.119	57.895	0.00	0.00	46.24	4.20
3869	3918	4.478195	GTGGTCTGGATGACGACG	57.522	61.111	0.00	0.00	46.24	5.12
3871	3920	3.001902	GCGGTGGTCTGGATGACGA	62.002	63.158	0.00	0.00	46.24	4.20
3872	3921	2.509336	GCGGTGGTCTGGATGACG	60.509	66.667	0.00	0.00	46.24	4.35
3873	3922	2.125106	GGCGGTGGTCTGGATGAC	60.125	66.667	0.00	0.00	44.63	3.06
3874	3923	3.399181	GGGCGGTGGTCTGGATGA	61.399	66.667	0.00	0.00	0.00	2.92
3875	3924	3.402681	AGGGCGGTGGTCTGGATG	61.403	66.667	0.00	0.00	0.00	3.51
3876	3925	3.402681	CAGGGCGGTGGTCTGGAT	61.403	66.667	0.00	0.00	0.00	3.41
3910	3959	1.639534	CGTTGACCACGTTGACCAC	59.360	57.895	0.00	0.00	44.49	4.16
3911	3960	4.112086	CGTTGACCACGTTGACCA	57.888	55.556	0.00	0.00	44.49	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.