AutoCloner

Multiple sequence alignment - TraesCS3B01G348100

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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	TraesCS3B01G348100	chr3B	100.000	4028	0	0	1	4028	557086052	557090079	0.000000e+00	7439.0
1	TraesCS3B01G348100	chr3B	97.789	769	16	1	1	768	557048535	557049303	0.000000e+00	1325.0
2	TraesCS3B01G348100	chr3B	97.080	685	19	1	1	685	557057435	557058118	0.000000e+00	1153.0
3	TraesCS3B01G348100	chr3A	95.271	3214	107	17	846	4028	558893569	558890370	0.000000e+00	5051.0
4	TraesCS3B01G348100	chr3D	94.441	3274	123	31	779	4028	427445392	427448630	0.000000e+00	4983.0
5	TraesCS3B01G348100	chr6B	94.034	771	43	3	1	768	252682869	252683639	0.000000e+00	1166.0
6	TraesCS3B01G348100	chr6B	94.034	771	41	5	1	768	250996746	250997514	0.000000e+00	1164.0
7	TraesCS3B01G348100	chr6B	93.750	720	40	5	52	768	250957523	250958240	0.000000e+00	1075.0
8	TraesCS3B01G348100	chr1B	92.774	775	46	9	1	769	426588487	426587717	0.000000e+00	1112.0
9	TraesCS3B01G348100	chr5B	91.203	773	58	10	1	768	208823460	208824227	0.000000e+00	1042.0
10	TraesCS3B01G348100	chr5B	90.532	771	70	3	1	769	457250430	457251199	0.000000e+00	1016.0
11	TraesCS3B01G348100	chr5B	90.532	771	67	6	1	768	208848109	208848876	0.000000e+00	1014.0
12	TraesCS3B01G348100	chr5B	71.910	712	163	30	2129	2817	63260868	63260171	5.350000e-39	172.0
13	TraesCS3B01G348100	chr7B	71.144	402	88	21	2232	2615	683151854	683152245	1.550000e-09	75.0
14	TraesCS3B01G348100	chr7B	72.093	258	58	12	2342	2589	682843637	682843890	9.340000e-07	65.8
15	TraesCS3B01G348100	chr1D	73.822	191	47	2	2096	2286	462335956	462336143	5.580000e-09	73.1
16	TraesCS3B01G348100	chr7A	100.000	29	0	0	2561	2589	694198131	694198159	2.000000e-03	54.7

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	TraesCS3B01G348100	chr3B	557086052	557090079	4027	False	7439	7439	100.000	1	4028	1	chr3B.!!$F3	4027
1	TraesCS3B01G348100	chr3B	557048535	557049303	768	False	1325	1325	97.789	1	768	1	chr3B.!!$F1	767
2	TraesCS3B01G348100	chr3B	557057435	557058118	683	False	1153	1153	97.080	1	685	1	chr3B.!!$F2	684
3	TraesCS3B01G348100	chr3A	558890370	558893569	3199	True	5051	5051	95.271	846	4028	1	chr3A.!!$R1	3182
4	TraesCS3B01G348100	chr3D	427445392	427448630	3238	False	4983	4983	94.441	779	4028	1	chr3D.!!$F1	3249
5	TraesCS3B01G348100	chr6B	252682869	252683639	770	False	1166	1166	94.034	1	768	1	chr6B.!!$F3	767
6	TraesCS3B01G348100	chr6B	250996746	250997514	768	False	1164	1164	94.034	1	768	1	chr6B.!!$F2	767
7	TraesCS3B01G348100	chr6B	250957523	250958240	717	False	1075	1075	93.750	52	768	1	chr6B.!!$F1	716
8	TraesCS3B01G348100	chr1B	426587717	426588487	770	True	1112	1112	92.774	1	769	1	chr1B.!!$R1	768
9	TraesCS3B01G348100	chr5B	208823460	208824227	767	False	1042	1042	91.203	1	768	1	chr5B.!!$F1	767
10	TraesCS3B01G348100	chr5B	457250430	457251199	769	False	1016	1016	90.532	1	769	1	chr5B.!!$F3	768
11	TraesCS3B01G348100	chr5B	208848109	208848876	767	False	1014	1014	90.532	1	768	1	chr5B.!!$F2	767

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
788	792	1.032014	ATCCGCACCAAATACATGGC	58.968	50.0	0.0	0.0	44.75	4.40	F
1818	1832	0.472161	TGGTGCTGTGGGTGGTACTA	60.472	55.0	0.0	0.0	0.00	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2781	2795	0.030369	GTCTATGCGTGTAGTCGGGG	59.970	60.0	0.0	0.0	0.0	5.73	R
3380	3418	0.304705	GTCTGTTCAGTGCGGTTGTG	59.695	55.0	0.0	0.0	0.0	3.33	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
422	423	1.505151	TAATGCCCTTGTCCCCTGCA	61.505	55.000	0.00	0.00	36.23	4.41
494	495	1.231958	TACGTTTTTGCCCTCGCCTG	61.232	55.000	0.00	0.00	0.00	4.85
627	629	5.042593	CAGAATACAAACACAAAGCAGCAA	58.957	37.500	0.00	0.00	0.00	3.91
774	778	1.500396	GTTCCCACGACAAATCCGC	59.500	57.895	0.00	0.00	0.00	5.54
775	779	1.071642	TTCCCACGACAAATCCGCA	59.928	52.632	0.00	0.00	0.00	5.69
776	780	1.231958	TTCCCACGACAAATCCGCAC	61.232	55.000	0.00	0.00	0.00	5.34
777	781	2.686816	CCCACGACAAATCCGCACC	61.687	63.158	0.00	0.00	0.00	5.01
788	792	1.032014	ATCCGCACCAAATACATGGC	58.968	50.000	0.00	0.00	44.75	4.40
818	823	3.025262	GGGAGACGGTGACTCTATCTTT	58.975	50.000	0.00	0.00	35.10	2.52
819	824	3.181485	GGGAGACGGTGACTCTATCTTTG	60.181	52.174	0.00	0.00	35.10	2.77
835	840	4.844998	TCTTTGATTTCGCCAATGAACA	57.155	36.364	0.00	0.00	0.00	3.18
842	847	5.351740	TGATTTCGCCAATGAACAATACGTA	59.648	36.000	0.00	0.00	0.00	3.57
843	848	5.804692	TTTCGCCAATGAACAATACGTAT	57.195	34.783	1.14	1.14	0.00	3.06
844	849	6.905544	TTTCGCCAATGAACAATACGTATA	57.094	33.333	8.83	0.00	0.00	1.47
899	904	5.871396	TTTACTGGTCTCAACTCTCAAGT	57.129	39.130	0.00	0.00	37.32	3.16
1251	1265	0.978146	CCATCCCACTCTTCGACCCT	60.978	60.000	0.00	0.00	0.00	4.34
1818	1832	0.472161	TGGTGCTGTGGGTGGTACTA	60.472	55.000	0.00	0.00	0.00	1.82
1875	1889	3.067461	CAGGGATTGTTTGGTTCGTGAAA	59.933	43.478	0.00	0.00	0.00	2.69
1890	1904	3.003480	CGTGAAAGAATGGAGGAAGACC	58.997	50.000	0.00	0.00	0.00	3.85
1945	1959	1.030457	AATGGGGTACGACGAGCTAG	58.970	55.000	0.00	0.00	0.00	3.42
1996	2010	1.392510	GACGGTTCCGTTATGCTGAAC	59.607	52.381	17.90	0.00	43.08	3.18
2004	2018	1.533625	GTTATGCTGAACTGGTGGCA	58.466	50.000	0.00	0.00	39.06	4.92
2013	2027	0.975040	AACTGGTGGCAGCAACCAAA	60.975	50.000	22.80	0.53	46.85	3.28
2085	2099	1.474143	CGGGGATTCTTGAAGGAGCTC	60.474	57.143	4.71	4.71	0.00	4.09
2613	2627	0.958091	TGGAAATTGCTTGTGGACGG	59.042	50.000	0.00	0.00	0.00	4.79
2688	2702	3.788142	TCTGGGAGCTTTATGGGAAGAAT	59.212	43.478	0.00	0.00	0.00	2.40
2703	2717	2.592102	AGAATGCCCTTCTTGAAGCA	57.408	45.000	4.94	2.79	41.60	3.91
2730	2744	0.778083	GGAGGTTGAAGGGGGAGTTT	59.222	55.000	0.00	0.00	0.00	2.66
2750	2764	1.202498	TGATGAGAAGCAGATGGAGCG	60.202	52.381	0.00	0.00	37.01	5.03
2763	2777	1.153549	GGAGCGTCTGATGGTGGTC	60.154	63.158	6.27	0.19	0.00	4.02
2766	2780	2.184322	CGTCTGATGGTGGTCGGG	59.816	66.667	0.00	0.00	0.00	5.14
2781	2795	2.897350	GGGCTATGGTGCGCTCAC	60.897	66.667	9.73	0.00	41.74	3.51
2799	2813	0.394762	ACCCCGACTACACGCATAGA	60.395	55.000	0.78	0.00	0.00	1.98
2857	2871	3.057548	CGCCATTGCCTGTGCTGA	61.058	61.111	0.00	0.00	38.71	4.26
2919	2933	1.798626	TGGCTGCTCTGGTATCATCT	58.201	50.000	0.00	0.00	0.00	2.90
2958	2975	0.953960	CACAGAACCCAGGCGTTACC	60.954	60.000	0.00	0.00	39.61	2.85
2997	3014	1.106285	CTAATGCTGGCAAAGGGTCC	58.894	55.000	0.00	0.00	0.00	4.46
3067	3084	4.510038	AGCTGCTTTCACGATGATTTTT	57.490	36.364	0.00	0.00	0.00	1.94
3104	3124	2.557924	GCAACATGGAGGTGTGATTGAA	59.442	45.455	0.00	0.00	37.23	2.69
3162	3182	6.832520	TGTATAGCATGAAAATGTGTTGGT	57.167	33.333	0.00	0.00	0.00	3.67
3177	3197	6.243811	TGTGTTGGTTTATATCGGTCAAAC	57.756	37.500	0.00	0.00	0.00	2.93
3229	3252	5.122396	GCAGTTTGAGGTATTAGGTTGAGTG	59.878	44.000	0.00	0.00	0.00	3.51
3252	3275	5.129320	TGAGGTGATAAAGCTGCTAGATTGA	59.871	40.000	0.90	0.00	36.52	2.57
3283	3318	3.871006	GTGTGAGATGATTTGCCGATACA	59.129	43.478	0.00	0.00	0.00	2.29
3296	3334	2.418197	GCCGATACAAGCCAACTAGTCA	60.418	50.000	0.00	0.00	0.00	3.41
3354	3392	3.009301	ACCAACAACGAGACTAGAACG	57.991	47.619	0.00	1.51	0.00	3.95
3380	3418	6.021596	CGCTCAAACTTTCACATGGTTATAC	58.978	40.000	0.00	0.00	0.00	1.47
3826	3870	4.711355	CCAGATTTATCTTCCCCAAAAGCA	59.289	41.667	0.00	0.00	34.22	3.91
3882	3927	5.413213	ACAAATTATACACCTTAGCACGCAA	59.587	36.000	0.00	0.00	0.00	4.85
3897	3942	2.532723	CACGCAATGCATGAAATAGTGC	59.467	45.455	5.91	3.27	41.61	4.40
3926	3971	8.364129	TCTAAAAATTCATTGCCAAACAGAAC	57.636	30.769	0.00	0.00	0.00	3.01
4013	4062	2.611518	CGAGCAGTAGGAACTCAAAGG	58.388	52.381	0.00	0.00	41.75	3.11
4014	4063	2.028930	CGAGCAGTAGGAACTCAAAGGT	60.029	50.000	0.00	0.00	41.75	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	3.444818	TTGCCGGGGCCTTGTCTTT	62.445	57.895	2.18	0.00	41.09	2.52
422	423	4.290196	AGTGTCCTCTACCTAACTCTGACT	59.710	45.833	0.00	0.00	0.00	3.41
769	773	1.032014	GCCATGTATTTGGTGCGGAT	58.968	50.000	0.00	0.00	39.11	4.18
770	774	1.034838	GGCCATGTATTTGGTGCGGA	61.035	55.000	0.00	0.00	39.11	5.54
771	775	1.437160	GGCCATGTATTTGGTGCGG	59.563	57.895	0.00	0.00	39.11	5.69
772	776	1.437160	GGGCCATGTATTTGGTGCG	59.563	57.895	4.39	0.00	39.11	5.34
773	777	1.437160	CGGGCCATGTATTTGGTGC	59.563	57.895	4.39	0.00	39.11	5.01
774	778	1.437160	GCGGGCCATGTATTTGGTG	59.563	57.895	4.39	0.00	39.11	4.17
775	779	2.118404	CGCGGGCCATGTATTTGGT	61.118	57.895	4.39	0.00	39.11	3.67
776	780	1.662438	AACGCGGGCCATGTATTTGG	61.662	55.000	12.47	0.00	39.94	3.28
777	781	0.525242	CAACGCGGGCCATGTATTTG	60.525	55.000	12.47	0.00	0.00	2.32
798	802	3.695060	TCAAAGATAGAGTCACCGTCTCC	59.305	47.826	0.00	0.00	32.93	3.71
818	823	4.155099	ACGTATTGTTCATTGGCGAAATCA	59.845	37.500	0.00	0.00	0.00	2.57
819	824	4.658071	ACGTATTGTTCATTGGCGAAATC	58.342	39.130	0.00	0.00	0.00	2.17
842	847	8.576442	GCTGGCATTAGTGGTTTGTATTATTAT	58.424	33.333	0.00	0.00	0.00	1.28
843	848	7.777910	AGCTGGCATTAGTGGTTTGTATTATTA	59.222	33.333	0.00	0.00	0.00	0.98
844	849	6.607198	AGCTGGCATTAGTGGTTTGTATTATT	59.393	34.615	0.00	0.00	0.00	1.40
854	859	1.191535	TACGAGCTGGCATTAGTGGT	58.808	50.000	0.00	0.00	0.00	4.16
1369	1383	1.153289	CAGCGGATCTGTTGGGGAG	60.153	63.158	10.38	0.00	38.02	4.30
1398	1412	1.604915	GGAGGAGTTGAAGAGCCCC	59.395	63.158	0.00	0.00	0.00	5.80
1463	1477	1.559065	GGGGTCCCAATCGTTCCTGA	61.559	60.000	10.98	0.00	35.81	3.86
1818	1832	1.004745	ACAAGGAATCCGCACAATCCT	59.995	47.619	0.00	0.00	44.08	3.24
1875	1889	1.007238	TCTCCGGTCTTCCTCCATTCT	59.993	52.381	0.00	0.00	0.00	2.40
1890	1904	1.654954	CGTAGGGGACACACTCTCCG	61.655	65.000	0.00	0.00	45.86	4.63
1996	2010	0.177604	TTTTTGGTTGCTGCCACCAG	59.822	50.000	22.66	0.00	42.13	4.00
2004	2018	3.552890	GCTCGGAGAAATTTTTGGTTGCT	60.553	43.478	9.69	0.00	34.09	3.91
2013	2027	3.604582	CTTCCTCTGCTCGGAGAAATTT	58.395	45.455	9.69	0.00	34.09	1.82
2085	2099	3.391665	GATGGCCACCTCCTGACCG	62.392	68.421	8.16	0.00	0.00	4.79
2346	2360	1.388065	CCTCGTGGAGGTAGAGCAGG	61.388	65.000	0.00	0.00	44.25	4.85
2347	2361	2.111162	CCTCGTGGAGGTAGAGCAG	58.889	63.158	0.00	0.00	44.25	4.24
2688	2702	1.968017	CGCTGCTTCAAGAAGGGCA	60.968	57.895	11.44	4.56	38.80	5.36
2697	2711	2.659016	CTCCAGTCCGCTGCTTCA	59.341	61.111	0.00	0.00	41.26	3.02
2703	2717	1.674057	CTTCAACCTCCAGTCCGCT	59.326	57.895	0.00	0.00	0.00	5.52
2730	2744	1.202498	CGCTCCATCTGCTTCTCATCA	60.202	52.381	0.00	0.00	0.00	3.07
2750	2764	1.327690	TAGCCCGACCACCATCAGAC	61.328	60.000	0.00	0.00	0.00	3.51
2763	2777	4.529219	TGAGCGCACCATAGCCCG	62.529	66.667	11.47	0.00	0.00	6.13
2781	2795	0.030369	GTCTATGCGTGTAGTCGGGG	59.970	60.000	0.00	0.00	0.00	5.73
2784	2798	2.451132	CTTGGTCTATGCGTGTAGTCG	58.549	52.381	0.00	0.00	0.00	4.18
2799	2813	2.362120	GCCTGCCTGATGCTTGGT	60.362	61.111	0.00	0.00	42.00	3.67
2919	2933	2.911928	TTGGACGCACCTCCAACA	59.088	55.556	1.29	0.00	44.05	3.33
2958	2975	1.226802	CCCTGATGACTCGCACTCG	60.227	63.158	0.00	0.00	0.00	4.18
2997	3014	0.528470	GAAGTCTGTCCCTCACCGAG	59.472	60.000	0.00	0.00	0.00	4.63
3009	3026	0.318441	TTCACGGCTCCAGAAGTCTG	59.682	55.000	1.05	1.05	43.40	3.51
3067	3084	7.157347	TCCATGTTGCAGCACAATAATAAAAA	58.843	30.769	5.00	0.00	41.27	1.94
3071	3088	4.338964	CCTCCATGTTGCAGCACAATAATA	59.661	41.667	5.00	0.00	41.27	0.98
3072	3089	3.131577	CCTCCATGTTGCAGCACAATAAT	59.868	43.478	5.00	0.00	41.27	1.28
3075	3092	0.892755	CCTCCATGTTGCAGCACAAT	59.107	50.000	5.00	0.00	41.27	2.71
3177	3197	5.109903	AGATATTTCTTCTTGTTCGGTCCG	58.890	41.667	4.39	4.39	0.00	4.79
3229	3252	5.605534	TCAATCTAGCAGCTTTATCACCTC	58.394	41.667	0.00	0.00	0.00	3.85
3252	3275	7.254898	CGGCAAATCATCTCACACAGTTATAAT	60.255	37.037	0.00	0.00	0.00	1.28
3273	3308	2.027561	ACTAGTTGGCTTGTATCGGCAA	60.028	45.455	0.00	0.00	43.45	4.52
3274	3309	1.553248	ACTAGTTGGCTTGTATCGGCA	59.447	47.619	0.00	0.00	34.94	5.69
3283	3318	1.768870	ACTGTGGTGACTAGTTGGCTT	59.231	47.619	0.00	0.00	0.00	4.35
3313	3351	1.881252	GACGTTGCGTGTGACCTGT	60.881	57.895	0.00	0.00	41.37	4.00
3354	3392	1.666888	CCATGTGAAAGTTTGAGCGGC	60.667	52.381	0.00	0.00	0.00	6.53
3380	3418	0.304705	GTCTGTTCAGTGCGGTTGTG	59.695	55.000	0.00	0.00	0.00	3.33
3484	3528	8.397906	CAATGGTGTCGTTTGACTATTATGAAT	58.602	33.333	0.00	0.00	45.70	2.57
3726	3770	1.186200	TCACCTCCTGAGATGGAACG	58.814	55.000	0.00	0.00	35.43	3.95
3826	3870	1.078143	GCGGGAGATGGTTGCTTCT	60.078	57.895	0.00	0.00	0.00	2.85
3892	3937	7.035004	GGCAATGAATTTTTAGATGTGCACTA	58.965	34.615	19.41	4.84	0.00	2.74
3897	3942	8.085720	TGTTTGGCAATGAATTTTTAGATGTG	57.914	30.769	0.00	0.00	0.00	3.21
3898	3943	8.149647	TCTGTTTGGCAATGAATTTTTAGATGT	58.850	29.630	0.00	0.00	0.00	3.06
3926	3971	6.072618	ACGAGAGGGTACTATTTATCGATGTG	60.073	42.308	8.54	0.00	33.43	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.