AutoCloner

Multiple sequence alignment - TraesCS3B01G032400

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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	TraesCS3B01G032400	chr3B	100.000	5194	0	0	1	5194	14982253	14987446	0.000000e+00	9592.0
1	TraesCS3B01G032400	chr3B	97.995	5236	45	24	1	5194	26653843	26648626	0.000000e+00	9033.0
2	TraesCS3B01G032400	chr3B	89.362	94	9	1	5098	5191	822221086	822221178	3.290000e-22	117.0
3	TraesCS3B01G032400	chr3B	89.362	94	9	1	5098	5191	822311442	822311534	3.290000e-22	117.0
4	TraesCS3B01G032400	chr3B	85.870	92	12	1	5099	5189	551052608	551052699	4.280000e-16	97.1
5	TraesCS3B01G032400	chr6D	80.626	3164	524	61	1056	4180	456424531	456427644	0.000000e+00	2364.0
6	TraesCS3B01G032400	chr6D	79.477	3177	517	86	1069	4186	456408591	456411691	0.000000e+00	2130.0
7	TraesCS3B01G032400	chr6D	77.843	3236	625	59	997	4186	17500276	17503465	0.000000e+00	1919.0
8	TraesCS3B01G032400	chr6A	80.127	3150	540	51	1068	4180	603081661	603084761	0.000000e+00	2270.0
9	TraesCS3B01G032400	chr6A	79.975	3181	521	66	1056	4180	603091783	603094903	0.000000e+00	2239.0
10	TraesCS3B01G032400	chr6A	78.186	3241	605	67	997	4186	18461143	18464332	0.000000e+00	1975.0
11	TraesCS3B01G032400	chr6A	82.232	1953	285	41	2258	4180	603101949	603103869	0.000000e+00	1628.0
12	TraesCS3B01G032400	chr6A	79.783	1845	309	38	2385	4180	603044208	603046037	0.000000e+00	1282.0
13	TraesCS3B01G032400	chr6A	79.479	307	43	8	545	833	606095906	606095602	3.170000e-47	200.0
14	TraesCS3B01G032400	chr6B	78.144	3189	601	62	1043	4186	31690355	31687218	0.000000e+00	1940.0
15	TraesCS3B01G032400	chr6B	77.884	3242	609	73	999	4186	30889721	30892908	0.000000e+00	1916.0
16	TraesCS3B01G032400	chr6B	78.169	3179	575	79	1056	4180	693927135	693930248	0.000000e+00	1916.0
17	TraesCS3B01G032400	chr6B	81.192	1845	292	37	2364	4180	693937002	693938819	0.000000e+00	1434.0
18	TraesCS3B01G032400	chr7A	78.334	2557	479	49	1679	4186	725447751	725445221	0.000000e+00	1583.0
19	TraesCS3B01G032400	chr7D	78.931	2321	428	37	1908	4186	629393865	629391564	0.000000e+00	1520.0
20	TraesCS3B01G032400	chr2B	81.686	344	42	8	499	823	415997252	415996911	3.080000e-67	267.0
21	TraesCS3B01G032400	chr2B	87.640	89	10	1	5102	5189	235858215	235858127	9.200000e-18	102.0
22	TraesCS3B01G032400	chr1B	80.826	339	36	15	516	831	662163745	662163413	6.720000e-59	239.0
23	TraesCS3B01G032400	chr1B	77.397	292	46	9	539	812	30442937	30442648	6.960000e-34	156.0
24	TraesCS3B01G032400	chr1D	79.006	362	44	19	499	833	475955248	475954892	8.760000e-53	219.0
25	TraesCS3B01G032400	chr5D	79.725	291	40	6	539	812	383074482	383074770	5.310000e-45	193.0
26	TraesCS3B01G032400	chr5D	85.542	83	11	1	559	641	236944389	236944470	9.270000e-13	86.1
27	TraesCS3B01G032400	chr5D	80.612	98	18	1	545	641	281011383	281011286	2.010000e-09	75.0
28	TraesCS3B01G032400	chrUn	79.322	295	41	8	535	812	108880276	108879985	6.870000e-44	189.0
29	TraesCS3B01G032400	chr2D	79.725	291	35	9	539	812	514252901	514252618	6.870000e-44	189.0
30	TraesCS3B01G032400	chr2D	78.305	295	42	10	536	812	525514858	525515148	2.490000e-38	171.0
31	TraesCS3B01G032400	chr7B	79.433	282	38	10	545	808	589393127	589393406	1.150000e-41	182.0
32	TraesCS3B01G032400	chr7B	84.694	98	14	1	545	641	384192410	384192313	4.280000e-16	97.1
33	TraesCS3B01G032400	chr4B	87.778	90	10	1	5099	5187	391554412	391554323	2.560000e-18	104.0
34	TraesCS3B01G032400	chr4B	86.813	91	11	1	5101	5191	130615645	130615556	3.310000e-17	100.0
35	TraesCS3B01G032400	chr3D	87.778	90	8	3	5101	5189	534687134	534687047	9.200000e-18	102.0
36	TraesCS3B01G032400	chr3A	87.952	83	10	0	5101	5183	501650525	501650607	1.190000e-16	99.0
37	TraesCS3B01G032400	chr5B	85.542	83	11	1	559	641	268293980	268293899	9.270000e-13	86.1
38	TraesCS3B01G032400	chr5A	87.500	64	7	1	578	641	40157045	40157107	7.210000e-09	73.1

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	TraesCS3B01G032400	chr3B	14982253	14987446	5193	False	9592	9592	100.000	1	5194	1	chr3B.!!$F1	5193
1	TraesCS3B01G032400	chr3B	26648626	26653843	5217	True	9033	9033	97.995	1	5194	1	chr3B.!!$R1	5193
2	TraesCS3B01G032400	chr6D	456424531	456427644	3113	False	2364	2364	80.626	1056	4180	1	chr6D.!!$F3	3124
3	TraesCS3B01G032400	chr6D	456408591	456411691	3100	False	2130	2130	79.477	1069	4186	1	chr6D.!!$F2	3117
4	TraesCS3B01G032400	chr6D	17500276	17503465	3189	False	1919	1919	77.843	997	4186	1	chr6D.!!$F1	3189
5	TraesCS3B01G032400	chr6A	603081661	603084761	3100	False	2270	2270	80.127	1068	4180	1	chr6A.!!$F3	3112
6	TraesCS3B01G032400	chr6A	603091783	603094903	3120	False	2239	2239	79.975	1056	4180	1	chr6A.!!$F4	3124
7	TraesCS3B01G032400	chr6A	18461143	18464332	3189	False	1975	1975	78.186	997	4186	1	chr6A.!!$F1	3189
8	TraesCS3B01G032400	chr6A	603101949	603103869	1920	False	1628	1628	82.232	2258	4180	1	chr6A.!!$F5	1922
9	TraesCS3B01G032400	chr6A	603044208	603046037	1829	False	1282	1282	79.783	2385	4180	1	chr6A.!!$F2	1795
10	TraesCS3B01G032400	chr6B	31687218	31690355	3137	True	1940	1940	78.144	1043	4186	1	chr6B.!!$R1	3143
11	TraesCS3B01G032400	chr6B	30889721	30892908	3187	False	1916	1916	77.884	999	4186	1	chr6B.!!$F1	3187
12	TraesCS3B01G032400	chr6B	693927135	693930248	3113	False	1916	1916	78.169	1056	4180	1	chr6B.!!$F2	3124
13	TraesCS3B01G032400	chr6B	693937002	693938819	1817	False	1434	1434	81.192	2364	4180	1	chr6B.!!$F3	1816
14	TraesCS3B01G032400	chr7A	725445221	725447751	2530	True	1583	1583	78.334	1679	4186	1	chr7A.!!$R1	2507
15	TraesCS3B01G032400	chr7D	629391564	629393865	2301	True	1520	1520	78.931	1908	4186	1	chr7D.!!$R1	2278

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
119	120	0.471780	TGCTGACCCTCTTGACCAGA	60.472	55.000	0.00	0.00	3.86	F
512	528	1.340568	GGGAGTTCCACGCCTCTATAC	59.659	57.143	0.00	38.21	1.47	F
1066	1090	0.319813	GGCAACAACATTCAGCCACC	60.320	55.000	0.00	44.59	4.61	F
1903	1933	1.953686	CATCCAACAACTTCACCGGTT	59.046	47.619	2.97	0.00	4.44	F
3582	3619	1.893808	AACAGCTGCGAACCACCAG	60.894	57.895	15.27	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1066	1090	0.107508	AAGGCATCCACATCAGTCCG	60.108	55.000	0.00	0.00	4.79	R
1903	1933	2.110578	TCCAATCTCTCGAGGCAATCA	58.889	47.619	13.56	0.00	2.57	R
3039	3073	0.233332	GCGAAACTCACACACAGAGC	59.767	55.000	0.00	36.58	4.09	R
3700	3737	0.951040	CCCAACCGAGCTCTGTGAAC	60.951	60.000	11.85	0.00	3.18	R
4938	5067	0.378610	GAAGAAAGCAGGCGTATGGC	59.621	55.000	0.00	42.51	4.40	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
91	92	1.164041	GCTAACCAACAGCACACGGT	61.164	55.000	0.00	0.00	38.93	4.83
117	118	1.483595	CCTGCTGACCCTCTTGACCA	61.484	60.000	0.00	0.00	0.00	4.02
119	120	0.471780	TGCTGACCCTCTTGACCAGA	60.472	55.000	0.00	0.00	0.00	3.86
159	165	2.284625	TCATGGTGGAGGGAGCGT	60.285	61.111	0.00	0.00	0.00	5.07
354	370	6.268617	TGTCACTTAGCCATATGAGCTCTTAT	59.731	38.462	16.19	15.34	41.83	1.73
503	519	2.088950	AAATACACGGGAGTTCCACG	57.911	50.000	0.00	4.28	44.67	4.94
512	528	1.340568	GGGAGTTCCACGCCTCTATAC	59.659	57.143	0.00	0.00	38.21	1.47
656	672	2.492088	GGCAAAGGAAATACTGTCCCAC	59.508	50.000	0.00	0.00	35.59	4.61
973	991	6.095021	ACAGGAAAAGCTTACGTTTCTTCTTT	59.905	34.615	0.00	0.00	42.01	2.52
1066	1090	0.319813	GGCAACAACATTCAGCCACC	60.320	55.000	0.00	0.00	44.59	4.61
1424	1454	2.863704	GCTTGAACAATTGCACCAGTCC	60.864	50.000	5.05	0.00	0.00	3.85
1903	1933	1.953686	CATCCAACAACTTCACCGGTT	59.046	47.619	2.97	0.00	0.00	4.44
3039	3073	6.435277	AGTTATCCCAATTATTGCTGGCATAG	59.565	38.462	0.00	0.00	0.00	2.23
3582	3619	1.893808	AACAGCTGCGAACCACCAG	60.894	57.895	15.27	0.00	0.00	4.00
3719	3756	0.951040	GTTCACAGAGCTCGGTTGGG	60.951	60.000	17.36	7.09	0.00	4.12
3765	3802	3.723260	GCTCCAGGTATAGCTTGACTTC	58.277	50.000	0.55	0.00	35.80	3.01
4374	4503	0.108662	GCCCTGTTTGGTTAGCATGC	60.109	55.000	10.51	10.51	0.00	4.06
4530	4659	4.824479	AAAGCCAGGAAATTAATGGTGG	57.176	40.909	0.00	0.00	36.43	4.61
4564	4693	7.887996	CATGTAAAAGGCAACATGTGTAAAT	57.112	32.000	0.00	0.00	45.08	1.40
4706	4835	8.905702	GCAAGTAAAGTTGATCAACATAAACAG	58.094	33.333	33.92	21.14	43.47	3.16
4879	5008	2.345876	GACTCTGAGCTCTGCCTTTTC	58.654	52.381	16.19	3.61	0.00	2.29
4881	5010	2.371510	ACTCTGAGCTCTGCCTTTTCTT	59.628	45.455	16.19	0.00	0.00	2.52
4882	5011	3.181446	ACTCTGAGCTCTGCCTTTTCTTT	60.181	43.478	16.19	0.00	0.00	2.52
4922	5051	4.810191	AAGGAAGACTTGCTGGTAGTAG	57.190	45.455	10.27	0.00	38.21	2.57
4938	5067	1.277557	AGTAGTTGAGCCCTCTTGCAG	59.722	52.381	0.00	0.00	0.00	4.41
4999	5128	7.483307	TGAATTCTTTCACTGAAAACCTCTTG	58.517	34.615	7.05	0.00	36.94	3.02
5000	5129	7.122650	TGAATTCTTTCACTGAAAACCTCTTGT	59.877	33.333	7.05	0.00	36.94	3.16
5001	5130	8.519799	AATTCTTTCACTGAAAACCTCTTGTA	57.480	30.769	5.72	0.00	30.84	2.41
5031	5160	0.449388	GAAAACCTGCAGCTCGGATG	59.551	55.000	8.66	0.00	0.00	3.51
5041	5170	0.034186	AGCTCGGATGGGATGCAAAA	60.034	50.000	0.00	0.00	0.00	2.44
5042	5171	0.101219	GCTCGGATGGGATGCAAAAC	59.899	55.000	0.00	0.00	0.00	2.43
5043	5172	1.462616	CTCGGATGGGATGCAAAACA	58.537	50.000	0.00	0.00	0.00	2.83
5044	5173	2.026641	CTCGGATGGGATGCAAAACAT	58.973	47.619	0.00	0.00	43.54	2.71
5045	5174	1.750206	TCGGATGGGATGCAAAACATG	59.250	47.619	5.28	0.00	39.84	3.21
5123	5275	0.774908	TCCCTCCGTCCCAAAATGTT	59.225	50.000	0.00	0.00	0.00	2.71
5124	5276	1.146152	TCCCTCCGTCCCAAAATGTTT	59.854	47.619	0.00	0.00	0.00	2.83
5125	5277	1.967779	CCCTCCGTCCCAAAATGTTTT	59.032	47.619	0.00	0.00	0.00	2.43
5157	5309	5.297547	TGACTCTAGTGTAGTGCCAAAAAG	58.702	41.667	0.00	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	92	3.371063	GGGTCAGCAGGTCGTCGA	61.371	66.667	0.00	0.00	0.00	4.20
117	118	5.227569	TGACATGACATTACACCTTGTCT	57.772	39.130	0.00	0.00	42.17	3.41
119	120	5.316167	ACATGACATGACATTACACCTTGT	58.684	37.500	22.19	0.00	0.00	3.16
159	165	2.986019	TGGAGGTCTTGAGGAATTTCCA	59.014	45.455	17.57	0.00	39.61	3.53
354	370	4.429108	GCTTGTTCCAAACAACTGCTAAA	58.571	39.130	1.27	0.00	45.79	1.85
471	487	7.093201	ACTCCCGTGTATTTTCCTTAGACATAA	60.093	37.037	0.00	0.00	0.00	1.90
811	829	5.110814	CCCCCTATGTGAACATGAAGTTA	57.889	43.478	0.00	0.00	41.51	2.24
837	855	3.005367	AGTTGCCATCGAAAACGGAAATT	59.995	39.130	0.00	0.00	0.00	1.82
838	856	2.556622	AGTTGCCATCGAAAACGGAAAT	59.443	40.909	0.00	0.00	0.00	2.17
839	857	1.950909	AGTTGCCATCGAAAACGGAAA	59.049	42.857	0.00	0.00	0.00	3.13
840	858	1.600023	AGTTGCCATCGAAAACGGAA	58.400	45.000	0.00	0.00	0.00	4.30
1066	1090	0.107508	AAGGCATCCACATCAGTCCG	60.108	55.000	0.00	0.00	0.00	4.79
1424	1454	3.318839	TGCTCCAAGGTTGATGTTTTCAG	59.681	43.478	0.00	0.00	35.27	3.02
1903	1933	2.110578	TCCAATCTCTCGAGGCAATCA	58.889	47.619	13.56	0.00	0.00	2.57
2341	2371	2.282462	AAGCGGCCCCTCAAACTG	60.282	61.111	0.00	0.00	0.00	3.16
2970	3004	1.477553	CTCAAACCATGTCCCATGGG	58.522	55.000	26.30	26.30	43.32	4.00
3039	3073	0.233332	GCGAAACTCACACACAGAGC	59.767	55.000	0.00	0.00	36.58	4.09
3582	3619	4.377431	CGGCTTCAAGTCACAGTGAATTAC	60.377	45.833	15.63	6.36	31.77	1.89
3624	3661	2.159366	CGACGTGAGCAACTAGATCCTT	60.159	50.000	0.00	0.00	0.00	3.36
3700	3737	0.951040	CCCAACCGAGCTCTGTGAAC	60.951	60.000	11.85	0.00	0.00	3.18
3719	3756	5.287226	ACGTATCCAATTGTTCCTCGTATC	58.713	41.667	4.43	0.00	0.00	2.24
3765	3802	8.469125	GCAAAATTGTTGTTTAACGTTAGAGAG	58.531	33.333	8.23	0.00	39.71	3.20
4374	4503	3.058432	CACAACTGCAAAGGACAGATCAG	60.058	47.826	0.00	0.00	38.55	2.90
4637	4766	6.935208	GGTTTTACTGTCAGGTCTTATCTTGT	59.065	38.462	4.53	0.00	0.00	3.16
4638	4767	6.090898	CGGTTTTACTGTCAGGTCTTATCTTG	59.909	42.308	4.53	0.00	0.00	3.02
4706	4835	2.095364	CACTCTGCATCTTTCAACTGCC	60.095	50.000	0.00	0.00	35.02	4.85
4900	5029	4.593634	ACTACTACCAGCAAGTCTTCCTTT	59.406	41.667	0.00	0.00	0.00	3.11
4922	5051	2.338785	GGCTGCAAGAGGGCTCAAC	61.339	63.158	0.50	0.00	34.07	3.18
4938	5067	0.378610	GAAGAAAGCAGGCGTATGGC	59.621	55.000	0.00	0.00	42.51	4.40
5041	5170	7.227512	GGTAGCACATCTTTTAGAATAGCATGT	59.772	37.037	0.00	0.00	0.00	3.21
5042	5171	7.227314	TGGTAGCACATCTTTTAGAATAGCATG	59.773	37.037	0.00	0.00	0.00	4.06
5043	5172	7.282585	TGGTAGCACATCTTTTAGAATAGCAT	58.717	34.615	0.00	0.00	0.00	3.79
5044	5173	6.649155	TGGTAGCACATCTTTTAGAATAGCA	58.351	36.000	0.00	0.00	0.00	3.49
5045	5174	7.308229	CCATGGTAGCACATCTTTTAGAATAGC	60.308	40.741	2.57	0.00	0.00	2.97
5046	5175	7.716998	ACCATGGTAGCACATCTTTTAGAATAG	59.283	37.037	18.10	0.00	0.00	1.73
5047	5176	7.498900	CACCATGGTAGCACATCTTTTAGAATA	59.501	37.037	19.28	0.00	0.00	1.75
5048	5177	6.319658	CACCATGGTAGCACATCTTTTAGAAT	59.680	38.462	19.28	0.00	0.00	2.40
5050	5179	5.045942	TCACCATGGTAGCACATCTTTTAGA	60.046	40.000	19.28	2.08	0.00	2.10
5051	5180	5.185454	TCACCATGGTAGCACATCTTTTAG	58.815	41.667	19.28	0.00	0.00	1.85
5052	5181	5.172687	TCACCATGGTAGCACATCTTTTA	57.827	39.130	19.28	0.00	0.00	1.52
5157	5309	4.171754	GTCCGTCCCATAATATAAGACGC	58.828	47.826	14.86	3.73	46.66	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.