AutoCloner

Multiple sequence alignment - TraesCS4A01G476600

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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	TraesCS4A01G476600	chr4A	100.000	5090	0	0	1	5090	735003171	735008260	0.000000e+00	9400.0
1	TraesCS4A01G476600	chr4A	95.031	4186	173	22	126	4293	735488074	735483906	0.000000e+00	6545.0
2	TraesCS4A01G476600	chr4A	99.876	2426	3	0	126	2551	734582507	734584932	0.000000e+00	4464.0
3	TraesCS4A01G476600	chr4A	85.755	4205	537	31	1	4166	736147040	736151221	0.000000e+00	4390.0
4	TraesCS4A01G476600	chr4A	85.293	3971	527	36	233	4157	735316290	735320249	0.000000e+00	4045.0
5	TraesCS4A01G476600	chr4A	82.931	4224	639	46	137	4314	735818599	735822786	0.000000e+00	3731.0
6	TraesCS4A01G476600	chr4A	83.831	3915	570	37	300	4166	735747182	735751081	0.000000e+00	3664.0
7	TraesCS4A01G476600	chr4A	85.554	2762	358	26	138	2889	734917362	734920092	0.000000e+00	2852.0
8	TraesCS4A01G476600	chr4A	88.939	2206	229	8	56	2255	734584941	734587137	0.000000e+00	2708.0
9	TraesCS4A01G476600	chr4A	87.215	1971	237	8	297	2254	734480184	734482152	0.000000e+00	2230.0
10	TraesCS4A01G476600	chr4A	83.693	1901	277	26	2272	4159	736758370	736760250	0.000000e+00	1762.0
11	TraesCS4A01G476600	chr4A	82.867	1932	297	27	2272	4188	736411244	736409332	0.000000e+00	1703.0
12	TraesCS4A01G476600	chr4A	82.802	1913	311	16	2272	4175	735691110	735693013	0.000000e+00	1694.0
13	TraesCS4A01G476600	chr4A	91.848	368	23	3	123	490	736823959	736824319	1.640000e-139	507.0
14	TraesCS4A01G476600	chr4A	94.167	120	4	2	4	121	736823790	736823908	4.050000e-41	180.0
15	TraesCS4A01G476600	chr4A	97.500	40	0	1	129	167	736823903	736823942	3.290000e-07	67.6
16	TraesCS4A01G476600	chr7D	95.241	3005	126	13	1389	4382	5459031	5456033	0.000000e+00	4741.0
17	TraesCS4A01G476600	chr7D	84.708	4061	561	33	126	4141	5649508	5645463	0.000000e+00	4004.0
18	TraesCS4A01G476600	chr7D	82.872	2890	418	46	1513	4364	5665585	5662735	0.000000e+00	2523.0
19	TraesCS4A01G476600	chr7D	86.624	2041	238	17	238	2254	5638106	5636077	0.000000e+00	2224.0
20	TraesCS4A01G476600	chr7D	96.490	1282	39	2	126	1407	5464379	5463104	0.000000e+00	2113.0
21	TraesCS4A01G476600	chr7D	81.827	2113	337	35	2272	4349	5636017	5633917	0.000000e+00	1731.0
22	TraesCS4A01G476600	chr7D	96.062	711	17	4	4382	5090	5456002	5455301	0.000000e+00	1147.0
23	TraesCS4A01G476600	chr7D	92.148	433	26	4	4	436	5778026	5777602	5.640000e-169	604.0
24	TraesCS4A01G476600	chr7A	82.263	2086	319	29	2272	4318	6926596	6924523	0.000000e+00	1755.0
25	TraesCS4A01G476600	chr7A	82.096	2061	325	35	2272	4318	7320287	7318257	0.000000e+00	1722.0
26	TraesCS4A01G476600	chr7A	85.217	115	16	1	4511	4625	6968711	6968598	3.220000e-22	117.0
27	TraesCS4A01G476600	chrUn	87.879	99	6	2	4379	4477	182415797	182415889	1.500000e-20	111.0
28	TraesCS4A01G476600	chrUn	87.879	99	6	2	4379	4477	237258616	237258708	1.500000e-20	111.0
29	TraesCS4A01G476600	chr4D	87.879	99	6	2	4379	4477	123521620	123521712	1.500000e-20	111.0
30	TraesCS4A01G476600	chr4D	87.879	99	6	2	4379	4477	135007005	135007097	1.500000e-20	111.0
31	TraesCS4A01G476600	chr4D	87.879	99	6	2	4379	4477	241144028	241144120	1.500000e-20	111.0
32	TraesCS4A01G476600	chr3D	88.542	96	5	2	4382	4477	281314579	281314490	1.500000e-20	111.0
33	TraesCS4A01G476600	chr1D	88.542	96	5	2	4382	4477	185761367	185761278	1.500000e-20	111.0
34	TraesCS4A01G476600	chr1D	87.879	99	6	2	4379	4477	351043608	351043700	1.500000e-20	111.0

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	TraesCS4A01G476600	chr4A	735003171	735008260	5089	False	9400.000000	9400	100.0000	1	5090	1	chr4A.!!$F3	5089
1	TraesCS4A01G476600	chr4A	735483906	735488074	4168	True	6545.000000	6545	95.0310	126	4293	1	chr4A.!!$R1	4167
2	TraesCS4A01G476600	chr4A	736147040	736151221	4181	False	4390.000000	4390	85.7550	1	4166	1	chr4A.!!$F8	4165
3	TraesCS4A01G476600	chr4A	735316290	735320249	3959	False	4045.000000	4045	85.2930	233	4157	1	chr4A.!!$F4	3924
4	TraesCS4A01G476600	chr4A	735818599	735822786	4187	False	3731.000000	3731	82.9310	137	4314	1	chr4A.!!$F7	4177
5	TraesCS4A01G476600	chr4A	735747182	735751081	3899	False	3664.000000	3664	83.8310	300	4166	1	chr4A.!!$F6	3866
6	TraesCS4A01G476600	chr4A	734582507	734587137	4630	False	3586.000000	4464	94.4075	56	2551	2	chr4A.!!$F10	2495
7	TraesCS4A01G476600	chr4A	734917362	734920092	2730	False	2852.000000	2852	85.5540	138	2889	1	chr4A.!!$F2	2751
8	TraesCS4A01G476600	chr4A	734480184	734482152	1968	False	2230.000000	2230	87.2150	297	2254	1	chr4A.!!$F1	1957
9	TraesCS4A01G476600	chr4A	736758370	736760250	1880	False	1762.000000	1762	83.6930	2272	4159	1	chr4A.!!$F9	1887
10	TraesCS4A01G476600	chr4A	736409332	736411244	1912	True	1703.000000	1703	82.8670	2272	4188	1	chr4A.!!$R2	1916
11	TraesCS4A01G476600	chr4A	735691110	735693013	1903	False	1694.000000	1694	82.8020	2272	4175	1	chr4A.!!$F5	1903
12	TraesCS4A01G476600	chr4A	736823790	736824319	529	False	251.533333	507	94.5050	4	490	3	chr4A.!!$F11	486
13	TraesCS4A01G476600	chr7D	5645463	5649508	4045	True	4004.000000	4004	84.7080	126	4141	1	chr7D.!!$R2	4015
14	TraesCS4A01G476600	chr7D	5455301	5459031	3730	True	2944.000000	4741	95.6515	1389	5090	2	chr7D.!!$R5	3701
15	TraesCS4A01G476600	chr7D	5662735	5665585	2850	True	2523.000000	2523	82.8720	1513	4364	1	chr7D.!!$R3	2851
16	TraesCS4A01G476600	chr7D	5463104	5464379	1275	True	2113.000000	2113	96.4900	126	1407	1	chr7D.!!$R1	1281
17	TraesCS4A01G476600	chr7D	5633917	5638106	4189	True	1977.500000	2224	84.2255	238	4349	2	chr7D.!!$R6	4111
18	TraesCS4A01G476600	chr7A	6924523	6926596	2073	True	1755.000000	1755	82.2630	2272	4318	1	chr7A.!!$R1	2046
19	TraesCS4A01G476600	chr7A	7318257	7320287	2030	True	1722.000000	1722	82.0960	2272	4318	1	chr7A.!!$R3	2046

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
3422	5315	2.787473	TTAGAGTTGGCATGTGGAGG	57.213	50.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
5056	7026	0.109913	GGAGCTGCCATCATCCATCA	59.89	55.0	0.0	0.0	36.34	3.07	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
3422	5315	2.787473	TTAGAGTTGGCATGTGGAGG	57.213	50.000	0.00	0.00	0.00	4.30
3437	5330	2.424956	GTGGAGGAGAATGTTTGCCATC	59.575	50.000	0.00	0.00	31.75	3.51
3498	5391	3.446873	CAGCTGACTTCCTCTGTACTGAT	59.553	47.826	8.42	0.00	0.00	2.90
3517	5410	3.131400	TGATTGGCCACACATGAATCATG	59.869	43.478	20.58	20.58	46.18	3.07
3539	5432	4.943705	TGTTCTCATAGGGAATTGCAGAAC	59.056	41.667	15.71	15.71	39.05	3.01
3589	5485	5.238432	ACATCTGTTAAATGTTTGTCGCTGA	59.762	36.000	0.00	0.00	33.62	4.26
3871	5769	2.069273	GTCTGACGTTCTGGGATTGTG	58.931	52.381	0.00	0.00	0.00	3.33
3926	5824	4.662468	TCTCCAATCTGAAGAATCTCGG	57.338	45.455	0.00	0.00	0.00	4.63
3927	5825	4.026744	TCTCCAATCTGAAGAATCTCGGT	58.973	43.478	0.00	0.00	0.00	4.69
4314	6252	2.486907	GCTTCAGGCTGGCTCATCTTAT	60.487	50.000	15.73	0.00	38.06	1.73
4399	6368	3.140895	ACTCCCAATCCCAATATTCCCAG	59.859	47.826	0.00	0.00	0.00	4.45
4404	6373	5.012354	CCCAATCCCAATATTCCCAGATTTG	59.988	44.000	0.00	0.00	0.00	2.32
4452	6421	8.174733	TGAATGAAAGAAATGAGCTTTTCTCT	57.825	30.769	12.65	0.60	43.42	3.10
4454	6423	5.766222	TGAAAGAAATGAGCTTTTCTCTGC	58.234	37.500	12.65	7.07	43.42	4.26
4466	6436	2.492449	TTCTCTGCGCCCTTCACTCG	62.492	60.000	4.18	0.00	0.00	4.18
4479	6449	3.320626	CTTCACTCGCTTCTGAATGTGA	58.679	45.455	9.78	9.78	33.41	3.58
4502	6472	8.180267	GTGAATGTTGGATATCTGTTTCTTCAG	58.820	37.037	2.05	0.00	36.85	3.02
4649	6619	5.040635	GCTCTCTCTTGTATGCTCTTACAC	58.959	45.833	0.00	0.00	31.98	2.90
4656	6626	4.551702	TGTATGCTCTTACACACCATGT	57.448	40.909	0.00	0.00	46.06	3.21
4686	6656	5.368989	AGGTCTCATTTATCGTTCATTCCC	58.631	41.667	0.00	0.00	0.00	3.97
4790	6760	3.314357	CAGGCATTGTCATCACATACAGG	59.686	47.826	0.00	0.00	30.55	4.00
4887	6857	5.466728	TCTGACTGAGCACTTTTGATTGTAC	59.533	40.000	0.00	0.00	0.00	2.90
4889	6859	5.764686	TGACTGAGCACTTTTGATTGTACAT	59.235	36.000	0.00	0.00	0.00	2.29
4948	6918	5.208463	TGTGATATGAGCGCCAGTTTATA	57.792	39.130	2.29	0.00	0.00	0.98
4998	6968	4.652421	TTATTTGCCATGTGGTATGCTG	57.348	40.909	0.35	0.00	37.57	4.41
5001	6971	4.662023	CCATGTGGTATGCTGGCA	57.338	55.556	0.00	0.00	0.00	4.92
5002	6972	3.120796	CCATGTGGTATGCTGGCAT	57.879	52.632	12.76	12.76	40.19	4.40
5051	7021	3.031013	ACTGGGAAACAAACTGGGAAAG	58.969	45.455	0.00	0.00	0.00	2.62
5052	7022	3.295973	CTGGGAAACAAACTGGGAAAGA	58.704	45.455	0.00	0.00	0.00	2.52
5053	7023	3.028130	TGGGAAACAAACTGGGAAAGAC	58.972	45.455	0.00	0.00	0.00	3.01
5054	7024	3.028130	GGGAAACAAACTGGGAAAGACA	58.972	45.455	0.00	0.00	0.00	3.41
5055	7025	3.068165	GGGAAACAAACTGGGAAAGACAG	59.932	47.826	0.00	0.00	41.64	3.51
5086	7056	0.463474	GGCAGCTCCAGGACTCATTC	60.463	60.000	0.00	0.00	34.01	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	6.518493	ACCTGTTGAAGTAGTAAATCACGAA	58.482	36.000	0.00	0.00	0.00	3.85
75	78	5.387113	AGTGTGGAATGGCCTGAATATAA	57.613	39.130	3.32	0.00	37.63	0.98
3422	5315	4.978083	AGTGATGATGGCAAACATTCTC	57.022	40.909	10.84	2.40	40.72	2.87
3437	5330	7.013750	TCTGTATACTAAGCCTCTCAAGTGATG	59.986	40.741	4.17	0.00	0.00	3.07
3517	5410	4.336713	GGTTCTGCAATTCCCTATGAGAAC	59.663	45.833	0.00	0.00	35.43	3.01
3589	5485	3.828451	ACACATAAATCTGGCAAGCACTT	59.172	39.130	0.00	0.00	0.00	3.16
3871	5769	3.959535	TGTTGGCAGGGAAATCATTTC	57.040	42.857	0.97	0.97	38.94	2.17
3926	5824	8.023021	TGATATGTTGGGGCATCTATAGATAC	57.977	38.462	14.92	9.56	32.63	2.24
3927	5825	8.803600	ATGATATGTTGGGGCATCTATAGATA	57.196	34.615	14.92	0.00	32.63	1.98
4214	6132	8.710835	TTGAAGTAAACAAATGAAGGGAAAAC	57.289	30.769	0.00	0.00	0.00	2.43
4399	6368	4.761739	TGGACACTGAACCAGAATCAAATC	59.238	41.667	0.45	0.00	35.18	2.17
4404	6373	3.691609	GGAATGGACACTGAACCAGAATC	59.308	47.826	0.45	0.00	39.62	2.52
4413	6382	4.639078	TTCATTCAGGAATGGACACTGA	57.361	40.909	18.94	0.00	46.08	3.41
4454	6423	2.097038	CAGAAGCGAGTGAAGGGCG	61.097	63.158	0.00	0.00	0.00	6.13
4466	6436	4.771590	TCCAACATTCACATTCAGAAGC	57.228	40.909	0.00	0.00	0.00	3.86
4479	6449	7.177878	ACCTGAAGAAACAGATATCCAACATT	58.822	34.615	0.00	0.00	39.94	2.71
4502	6472	4.331968	TGTCCAGTGGATGAATAACAACC	58.668	43.478	16.67	0.00	41.08	3.77
4649	6619	4.271696	TGAGACCTTCAGTTACATGGTG	57.728	45.455	0.00	0.00	0.00	4.17
4656	6626	7.608153	TGAACGATAAATGAGACCTTCAGTTA	58.392	34.615	0.00	0.41	46.64	2.24
4686	6656	5.457799	CCCAAGTATCACATAACTCGTTACG	59.542	44.000	0.00	0.00	0.00	3.18
4790	6760	9.362539	TGTCTCTACGATATTCAAGGTTAAAAC	57.637	33.333	0.00	0.00	0.00	2.43
4998	6968	2.540265	ATGTGCTAGCTAGACATGCC	57.460	50.000	25.15	10.24	0.00	4.40
5001	6971	5.860941	ACAGTTATGTGCTAGCTAGACAT	57.139	39.130	27.16	27.16	38.57	3.06
5002	6972	5.661056	AACAGTTATGTGCTAGCTAGACA	57.339	39.130	25.15	22.52	40.39	3.41
5051	7021	2.219458	CTGCCATCATCCATCACTGTC	58.781	52.381	0.00	0.00	0.00	3.51
5052	7022	1.749635	GCTGCCATCATCCATCACTGT	60.750	52.381	0.00	0.00	0.00	3.55
5053	7023	0.952280	GCTGCCATCATCCATCACTG	59.048	55.000	0.00	0.00	0.00	3.66
5054	7024	0.844660	AGCTGCCATCATCCATCACT	59.155	50.000	0.00	0.00	0.00	3.41
5055	7025	1.236628	GAGCTGCCATCATCCATCAC	58.763	55.000	0.00	0.00	0.00	3.06
5056	7026	0.109913	GGAGCTGCCATCATCCATCA	59.890	55.000	0.00	0.00	36.34	3.07
5057	7027	0.109913	TGGAGCTGCCATCATCCATC	59.890	55.000	1.53	0.00	43.33	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.