AutoCloner

Multiple sequence alignment - TraesCS7A01G479500

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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	TraesCS7A01G479500	chr7A	100.000	2309	0	0	1	2309	672009839	672007531	0.000000e+00	4265.0
1	TraesCS7A01G479500	chr7A	96.774	1178	38	0	1085	2262	501148895	501147718	0.000000e+00	1965.0
2	TraesCS7A01G479500	chr7A	93.199	941	38	4	1	915	501149835	501148895	0.000000e+00	1360.0
3	TraesCS7A01G479500	chr4A	93.413	1260	72	8	1	1255	700632653	700631400	0.000000e+00	1857.0
4	TraesCS7A01G479500	chr3B	89.701	602	52	7	1631	2230	680461352	680461945	0.000000e+00	760.0
5	TraesCS7A01G479500	chr3B	88.974	390	42	1	951	1340	498361692	498362080	4.460000e-132	481.0
6	TraesCS7A01G479500	chr3B	86.345	249	27	2	1385	1632	680461025	680461267	4.890000e-67	265.0
7	TraesCS7A01G479500	chr3B	93.421	76	5	0	1271	1346	680432228	680432303	1.870000e-21	113.0
8	TraesCS7A01G479500	chr3D	85.362	690	56	19	1	670	381998618	381999282	0.000000e+00	673.0
9	TraesCS7A01G479500	chr3D	90.201	398	38	1	951	1348	382748380	382748776	3.400000e-143	518.0
10	TraesCS7A01G479500	chr3D	100.000	51	0	0	2259	2309	202614372	202614322	6.790000e-16	95.3
11	TraesCS7A01G479500	chr5D	85.169	681	58	15	10	670	6112151	6111494	0.000000e+00	658.0
12	TraesCS7A01G479500	chr5D	89.163	203	22	0	672	874	6107927	6107725	1.060000e-63	254.0
13	TraesCS7A01G479500	chr1A	84.919	683	56	18	10	670	590842296	590841639	0.000000e+00	647.0
14	TraesCS7A01G479500	chr1A	90.148	203	20	0	672	874	590838173	590837971	4.890000e-67	265.0
15	TraesCS7A01G479500	chr5B	85.090	664	53	19	28	670	690650820	690650182	9.000000e-179	636.0
16	TraesCS7A01G479500	chr5B	86.607	448	51	7	807	1246	507064745	507064299	9.590000e-134	486.0
17	TraesCS7A01G479500	chr5B	90.845	142	13	0	1105	1246	507044459	507044318	8.420000e-45	191.0
18	TraesCS7A01G479500	chr5B	100.000	51	0	0	2259	2309	713043786	713043836	6.790000e-16	95.3
19	TraesCS7A01G479500	chr3A	91.026	390	34	1	951	1340	505717969	505718357	2.030000e-145	525.0
20	TraesCS7A01G479500	chr3A	81.934	548	50	24	1	525	736479249	736479770	3.550000e-113	418.0
21	TraesCS7A01G479500	chr6B	83.551	383	48	8	1631	2004	248299645	248299269	6.110000e-91	344.0
22	TraesCS7A01G479500	chr4D	83.242	364	49	6	1631	1985	480963560	480963920	7.960000e-85	324.0
23	TraesCS7A01G479500	chr4D	100.000	51	0	0	2259	2309	123581017	123580967	6.790000e-16	95.3
24	TraesCS7A01G479500	chr2A	86.477	281	31	6	6	279	40954888	40954608	3.730000e-78	302.0
25	TraesCS7A01G479500	chr2A	82.707	133	23	0	235	367	759029884	759030016	4.030000e-23	119.0
26	TraesCS7A01G479500	chr2A	87.500	64	5	2	2011	2071	593298437	593298500	1.140000e-08	71.3
27	TraesCS7A01G479500	chrUn	84.868	304	37	7	807	1102	302498752	302499054	4.820000e-77	298.0
28	TraesCS7A01G479500	chrUn	84.868	304	37	7	807	1102	402146943	402147245	4.820000e-77	298.0
29	TraesCS7A01G479500	chr2B	85.294	136	19	1	239	373	772482198	772482333	3.090000e-29	139.0
30	TraesCS7A01G479500	chr2B	86.885	61	5	2	2014	2071	530116449	530116389	5.320000e-07	65.8
31	TraesCS7A01G479500	chr6D	100.000	51	0	0	2259	2309	83953175	83953225	6.790000e-16	95.3
32	TraesCS7A01G479500	chr6D	100.000	51	0	0	2259	2309	283169784	283169834	6.790000e-16	95.3
33	TraesCS7A01G479500	chr6A	100.000	51	0	0	2259	2309	338476892	338476842	6.790000e-16	95.3
34	TraesCS7A01G479500	chr1B	100.000	51	0	0	2259	2309	53337249	53337299	6.790000e-16	95.3
35	TraesCS7A01G479500	chr1B	100.000	51	0	0	2259	2309	338930854	338930804	6.790000e-16	95.3
36	TraesCS7A01G479500	chr1B	100.000	51	0	0	2259	2309	461454648	461454598	6.790000e-16	95.3
37	TraesCS7A01G479500	chr2D	88.525	61	4	2	2014	2071	449718444	449718384	1.140000e-08	71.3

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	TraesCS7A01G479500	chr7A	672007531	672009839	2308	True	4265.0	4265	100.0000	1	2309	1	chr7A.!!$R1	2308
1	TraesCS7A01G479500	chr7A	501147718	501149835	2117	True	1662.5	1965	94.9865	1	2262	2	chr7A.!!$R2	2261
2	TraesCS7A01G479500	chr4A	700631400	700632653	1253	True	1857.0	1857	93.4130	1	1255	1	chr4A.!!$R1	1254
3	TraesCS7A01G479500	chr3B	680461025	680461945	920	False	512.5	760	88.0230	1385	2230	2	chr3B.!!$F3	845
4	TraesCS7A01G479500	chr3D	381998618	381999282	664	False	673.0	673	85.3620	1	670	1	chr3D.!!$F1	669
5	TraesCS7A01G479500	chr5D	6107725	6112151	4426	True	456.0	658	87.1660	10	874	2	chr5D.!!$R1	864
6	TraesCS7A01G479500	chr1A	590837971	590842296	4325	True	456.0	647	87.5335	10	874	2	chr1A.!!$R1	864
7	TraesCS7A01G479500	chr5B	690650182	690650820	638	True	636.0	636	85.0900	28	670	1	chr5B.!!$R3	642
8	TraesCS7A01G479500	chr3A	736479249	736479770	521	False	418.0	418	81.9340	1	525	1	chr3A.!!$F2	524

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
88	90	0.028242	TTTTTGGTACGCACGCACTG	59.972	50.0	0.0	0.0	0.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1708	5430	1.561769	ATCTCACGTGCCCCCAATGA	61.562	55.0	11.67	0.0	0.0	2.57	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
88	90	0.028242	TTTTTGGTACGCACGCACTG	59.972	50.000	0.00	0.00	0.00	3.66
503	540	4.592942	AGTGGTACCTGAACGTCTATACA	58.407	43.478	14.36	0.00	0.00	2.29
635	672	6.528072	GCTTTTTCACTATCAAACTATGGTGC	59.472	38.462	0.00	0.00	38.01	5.01
676	4290	1.811965	CCACATGAATGAAACGGCTCA	59.188	47.619	0.00	0.00	0.00	4.26
728	4364	1.917872	TGTTAAGCACCCCAACCATC	58.082	50.000	0.00	0.00	0.00	3.51
879	4515	8.920665	GCTCATACACAGAGTAATAGCTATTTG	58.079	37.037	23.47	17.22	39.54	2.32
918	4554	3.123621	CACATTCCTGCTAACGAGTCAAC	59.876	47.826	0.00	0.00	0.00	3.18
919	4555	3.244078	ACATTCCTGCTAACGAGTCAACA	60.244	43.478	0.00	0.00	0.00	3.33
957	4593	6.381481	TCCATCGCTAATAGTAAGAAACGA	57.619	37.500	0.00	0.00	0.00	3.85
984	4620	4.640647	GTCCAACAATATGAAGAGGTTCCC	59.359	45.833	0.00	0.00	0.00	3.97
991	4627	3.659183	ATGAAGAGGTTCCCATTCCAG	57.341	47.619	0.00	0.00	0.00	3.86
995	4631	4.352595	TGAAGAGGTTCCCATTCCAGTTTA	59.647	41.667	0.00	0.00	0.00	2.01
1016	4652	7.390718	AGTTTATCTAATGGTTGTGACTTCCAC	59.609	37.037	2.00	0.00	45.88	4.02
1022	4658	3.804036	TGGTTGTGACTTCCACTGTTAG	58.196	45.455	0.00	0.00	45.86	2.34
1225	4861	4.077108	GGGTTTCACCTTTCCTTTCGTAT	58.923	43.478	0.00	0.00	38.64	3.06
1255	4891	1.138859	CCTTGATATCGTCAGGCACCA	59.861	52.381	0.00	0.00	38.29	4.17
1438	5074	9.645128	ATGTGTCATTGATTTATTCTCCCATTA	57.355	29.630	0.00	0.00	0.00	1.90
1480	5116	4.901868	TGTTATCCAAGACCAGTGGTTAC	58.098	43.478	17.93	4.34	35.25	2.50
1514	5150	9.739276	GGTCAATATTCAGGATAATCACCATTA	57.261	33.333	0.00	0.00	0.00	1.90
1525	5161	8.860088	AGGATAATCACCATTAATTAAGCAACC	58.140	33.333	3.94	0.00	0.00	3.77
1720	5442	4.751767	TTATGAAAATCATTGGGGGCAC	57.248	40.909	0.00	0.00	38.26	5.01
1793	5515	8.458573	TTTAATCTTCTGGTCTGTTGCTTTTA	57.541	30.769	0.00	0.00	0.00	1.52
1961	5683	2.360350	CAGCCCCTCACAACGCAT	60.360	61.111	0.00	0.00	0.00	4.73
2012	5734	0.037326	TCACACTTCTGCCCGTCATC	60.037	55.000	0.00	0.00	0.00	2.92
2092	5815	8.459911	TCATATCAGGTTTCTCGTCTACATTA	57.540	34.615	0.00	0.00	0.00	1.90
2169	5892	5.463724	GTCCATGCAGTTATAGCTCTGTTAC	59.536	44.000	0.00	0.00	34.57	2.50
2238	5961	0.595095	GTCTTGCTGAAAGGGCAGTG	59.405	55.000	0.00	0.00	40.90	3.66
2256	5979	4.437239	CAGTGAGTCAGTGACAGTTTCTT	58.563	43.478	24.73	2.17	36.99	2.52
2262	5985	2.938451	TCAGTGACAGTTTCTTGCAGTG	59.062	45.455	0.00	0.00	32.10	3.66
2263	5986	2.032550	CAGTGACAGTTTCTTGCAGTGG	59.967	50.000	0.00	0.00	0.00	4.00
2264	5987	1.334869	GTGACAGTTTCTTGCAGTGGG	59.665	52.381	0.00	0.00	0.00	4.61
2265	5988	1.064758	TGACAGTTTCTTGCAGTGGGT	60.065	47.619	0.00	0.00	0.00	4.51
2266	5989	2.171659	TGACAGTTTCTTGCAGTGGGTA	59.828	45.455	0.00	0.00	0.00	3.69
2267	5990	2.808543	GACAGTTTCTTGCAGTGGGTAG	59.191	50.000	0.00	0.00	0.00	3.18
2268	5991	1.537202	CAGTTTCTTGCAGTGGGTAGC	59.463	52.381	0.00	0.00	0.00	3.58
2269	5992	0.881796	GTTTCTTGCAGTGGGTAGCC	59.118	55.000	3.29	3.29	0.00	3.93
2270	5993	0.476338	TTTCTTGCAGTGGGTAGCCA	59.524	50.000	10.27	10.27	0.00	4.75
2271	5994	0.250727	TTCTTGCAGTGGGTAGCCAC	60.251	55.000	32.31	32.31	40.64	5.01
2273	5996	0.674895	CTTGCAGTGGGTAGCCACTC	60.675	60.000	37.62	30.08	46.65	3.51
2274	5997	2.124507	TTGCAGTGGGTAGCCACTCC	62.125	60.000	37.62	31.57	46.65	3.85
2275	5998	2.990479	CAGTGGGTAGCCACTCCC	59.010	66.667	37.62	16.54	46.65	4.30
2276	5999	1.613630	CAGTGGGTAGCCACTCCCT	60.614	63.158	37.62	19.25	46.65	4.20
2277	6000	1.161113	AGTGGGTAGCCACTCCCTT	59.839	57.895	35.50	17.66	46.65	3.95
2278	6001	0.910088	AGTGGGTAGCCACTCCCTTC	60.910	60.000	35.50	13.47	46.65	3.46
2279	6002	0.910088	GTGGGTAGCCACTCCCTTCT	60.910	60.000	32.12	0.00	43.74	2.85
2280	6003	0.617820	TGGGTAGCCACTCCCTTCTC	60.618	60.000	10.27	0.00	43.74	2.87
2281	6004	0.617820	GGGTAGCCACTCCCTTCTCA	60.618	60.000	5.96	0.00	40.48	3.27
2282	6005	0.827368	GGTAGCCACTCCCTTCTCAG	59.173	60.000	0.00	0.00	0.00	3.35
2283	6006	0.827368	GTAGCCACTCCCTTCTCAGG	59.173	60.000	0.00	0.00	40.45	3.86
2299	6022	4.876652	GGGAACCGTACGTGAGAC	57.123	61.111	15.21	0.17	40.86	3.36
2300	6023	2.261215	GGGAACCGTACGTGAGACT	58.739	57.895	15.21	0.00	40.86	3.24
2301	6024	0.600057	GGGAACCGTACGTGAGACTT	59.400	55.000	15.21	0.00	40.86	3.01
2302	6025	1.402062	GGGAACCGTACGTGAGACTTC	60.402	57.143	15.21	5.61	40.86	3.01
2303	6026	1.402062	GGAACCGTACGTGAGACTTCC	60.402	57.143	15.21	10.37	0.00	3.46
2304	6027	0.239347	AACCGTACGTGAGACTTCCG	59.761	55.000	15.21	0.00	0.00	4.30
2305	6028	1.513586	CCGTACGTGAGACTTCCGC	60.514	63.158	15.21	0.00	0.00	5.54
2306	6029	1.208358	CGTACGTGAGACTTCCGCA	59.792	57.895	7.22	0.00	0.00	5.69
2307	6030	0.179171	CGTACGTGAGACTTCCGCAT	60.179	55.000	7.22	0.00	0.00	4.73
2308	6031	1.546834	GTACGTGAGACTTCCGCATC	58.453	55.000	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.185315	TGAGCGTGATGATGTCCTCA	58.815	50.000	0.00	0.00	38.53	3.86
85	87	2.610859	AAGGGTGATCGGGGCAGT	60.611	61.111	0.00	0.00	0.00	4.40
88	90	4.191015	GGGAAGGGTGATCGGGGC	62.191	72.222	0.00	0.00	0.00	5.80
271	278	2.125952	CAGTCGCAGTCCGCATCA	60.126	61.111	0.00	0.00	42.60	3.07
635	672	6.920758	TGTGGGACGAAACAAAATAAAGATTG	59.079	34.615	0.00	0.00	0.00	2.67
700	4314	0.109132	GGTGCTTAACATGCCTGTGC	60.109	55.000	0.00	0.00	35.22	4.57
774	4410	3.930336	TCACTGAATAACTGAGTGCAGG	58.070	45.455	8.96	1.25	46.60	4.85
918	4554	4.142945	GCGATGGAGCTAAATATCTGCTTG	60.143	45.833	0.00	0.00	37.16	4.01
919	4555	3.999663	GCGATGGAGCTAAATATCTGCTT	59.000	43.478	0.00	0.00	37.16	3.91
946	4582	4.761975	TGTTGGACAACTCGTTTCTTACT	58.238	39.130	15.37	0.00	41.67	2.24
957	4593	5.880901	ACCTCTTCATATTGTTGGACAACT	58.119	37.500	15.37	0.13	41.40	3.16
984	4620	8.184192	GTCACAACCATTAGATAAACTGGAATG	58.816	37.037	0.00	0.00	32.92	2.67
991	4627	7.527457	GTGGAAGTCACAACCATTAGATAAAC	58.473	38.462	0.00	0.00	45.39	2.01
1096	4732	9.793252	ATCAAATAGTTCATGTATTTGTGCTTC	57.207	29.630	19.07	0.00	43.70	3.86
1225	4861	5.795972	TGACGATATCAAGGTTTGGTGTAA	58.204	37.500	3.12	0.00	33.02	2.41
1255	4891	6.911250	AAATCCCTTTTTCCACTTAACGAT	57.089	33.333	0.00	0.00	0.00	3.73
1383	5019	4.324267	ACAAGAAAGGATAAGAACCACCG	58.676	43.478	0.00	0.00	0.00	4.94
1438	5074	5.041191	ACAAAGTCAGTGTTTCTCTGGAT	57.959	39.130	0.00	0.00	34.15	3.41
1480	5116	2.874701	CCTGAATATTGACCCAAGAGCG	59.125	50.000	0.00	0.00	0.00	5.03
1514	5150	7.768807	TTATTGTAGGTGTGGTTGCTTAATT	57.231	32.000	0.00	0.00	0.00	1.40
1525	5161	4.511454	CCGGATGACATTATTGTAGGTGTG	59.489	45.833	0.00	0.00	35.79	3.82
1708	5430	1.561769	ATCTCACGTGCCCCCAATGA	61.562	55.000	11.67	0.00	0.00	2.57
1720	5442	2.886862	ATGCTCCAAGAGATCTCACG	57.113	50.000	24.39	14.03	0.00	4.35
1793	5515	8.582437	CATGCCTTAAATGTCCATCATCTATTT	58.418	33.333	0.00	0.00	35.48	1.40
1961	5683	7.705325	GTCGTCTTAGATCCTGCAAATACTAAA	59.295	37.037	0.00	0.00	0.00	1.85
2032	5754	1.852157	TGCCCAATCCCACACCTCT	60.852	57.895	0.00	0.00	0.00	3.69
2075	5797	8.543774	CATCAAGATTAATGTAGACGAGAAACC	58.456	37.037	0.00	0.00	0.00	3.27
2076	5798	9.088512	ACATCAAGATTAATGTAGACGAGAAAC	57.911	33.333	0.00	0.00	34.42	2.78
2141	5864	5.636965	CAGAGCTATAACTGCATGGACATAC	59.363	44.000	0.00	0.00	0.00	2.39
2169	5892	7.229506	ACAAAGAAACCACATAGAGAAGGAAAG	59.770	37.037	0.00	0.00	0.00	2.62
2219	5942	0.595095	CACTGCCCTTTCAGCAAGAC	59.405	55.000	0.00	0.00	40.35	3.01
2238	5961	3.198068	TGCAAGAAACTGTCACTGACTC	58.802	45.455	10.54	0.00	33.15	3.36
2262	5985	0.617820	TGAGAAGGGAGTGGCTACCC	60.618	60.000	0.00	0.00	45.88	3.69
2263	5986	0.827368	CTGAGAAGGGAGTGGCTACC	59.173	60.000	0.00	0.00	33.84	3.18
2264	5987	0.827368	CCTGAGAAGGGAGTGGCTAC	59.173	60.000	0.00	0.00	0.00	3.58
2265	5988	3.306902	CCTGAGAAGGGAGTGGCTA	57.693	57.895	0.00	0.00	0.00	3.93
2266	5989	4.143740	CCTGAGAAGGGAGTGGCT	57.856	61.111	0.00	0.00	0.00	4.75
2274	5997	0.172803	CGTACGGTTCCCTGAGAAGG	59.827	60.000	7.57	0.00	34.29	3.46
2275	5998	0.886563	ACGTACGGTTCCCTGAGAAG	59.113	55.000	21.06	0.00	34.29	2.85
2276	5999	0.599558	CACGTACGGTTCCCTGAGAA	59.400	55.000	21.06	0.00	0.00	2.87
2277	6000	0.250858	TCACGTACGGTTCCCTGAGA	60.251	55.000	21.06	0.41	0.00	3.27
2278	6001	0.170561	CTCACGTACGGTTCCCTGAG	59.829	60.000	21.06	17.18	0.00	3.35
2279	6002	0.250858	TCTCACGTACGGTTCCCTGA	60.251	55.000	21.06	11.69	0.00	3.86
2280	6003	0.109412	GTCTCACGTACGGTTCCCTG	60.109	60.000	21.06	7.60	0.00	4.45
2281	6004	0.251077	AGTCTCACGTACGGTTCCCT	60.251	55.000	21.06	6.71	0.00	4.20
2282	6005	0.600057	AAGTCTCACGTACGGTTCCC	59.400	55.000	21.06	4.34	0.00	3.97
2283	6006	1.402062	GGAAGTCTCACGTACGGTTCC	60.402	57.143	21.06	15.85	0.00	3.62
2284	6007	1.727213	CGGAAGTCTCACGTACGGTTC	60.727	57.143	21.06	11.25	30.21	3.62
2285	6008	0.239347	CGGAAGTCTCACGTACGGTT	59.761	55.000	21.06	0.00	30.21	4.44
2286	6009	1.871772	CGGAAGTCTCACGTACGGT	59.128	57.895	21.06	2.13	30.21	4.83
2287	6010	1.513586	GCGGAAGTCTCACGTACGG	60.514	63.158	21.06	8.79	34.48	4.02
2288	6011	0.179171	ATGCGGAAGTCTCACGTACG	60.179	55.000	15.01	15.01	36.99	3.67
2289	6012	1.546834	GATGCGGAAGTCTCACGTAC	58.453	55.000	0.00	0.00	0.00	3.67
2291	6014	4.891566	GATGCGGAAGTCTCACGT	57.108	55.556	0.00	0.00	0.00	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.