AutoCloner

Multiple sequence alignment - TraesCS1D01G295600

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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	TraesCS1D01G295600	chr1D	100.000	2201	0	0	1	2201	394180077	394182277	0.000000e+00	4065.0
1	TraesCS1D01G295600	chr1D	98.913	1288	12	1	1	1288	483921798	483920513	0.000000e+00	2300.0
2	TraesCS1D01G295600	chr1D	98.717	1169	10	3	121	1288	254490942	254492106	0.000000e+00	2071.0
3	TraesCS1D01G295600	chr1D	92.537	871	48	15	1296	2154	251977740	251976875	0.000000e+00	1232.0
4	TraesCS1D01G295600	chr1D	92.683	861	54	8	1296	2154	295944836	295943983	0.000000e+00	1232.0
5	TraesCS1D01G295600	chrUn	98.991	1288	11	1	1	1288	317472026	317470741	0.000000e+00	2305.0
6	TraesCS1D01G295600	chr5D	98.680	1288	15	1	1	1288	6206663	6205378	0.000000e+00	2283.0
7	TraesCS1D01G295600	chr5D	99.210	1139	8	1	150	1288	240132461	240133598	0.000000e+00	2052.0
8	TraesCS1D01G295600	chr5D	93.271	862	52	6	1302	2161	416218840	416217983	0.000000e+00	1266.0
9	TraesCS1D01G295600	chr5D	93.256	860	54	4	1296	2154	120323929	120324785	0.000000e+00	1264.0
10	TraesCS1D01G295600	chr5D	93.031	861	54	6	1296	2154	308890069	308889213	0.000000e+00	1253.0
11	TraesCS1D01G295600	chr5D	92.691	862	49	12	1296	2154	480439548	480440398	0.000000e+00	1230.0
12	TraesCS1D01G295600	chr3B	98.525	1288	16	2	1	1288	201507738	201509022	0.000000e+00	2270.0
13	TraesCS1D01G295600	chr2D	97.902	1287	23	3	3	1288	334227078	334228361	0.000000e+00	2224.0
14	TraesCS1D01G295600	chr2D	100.000	45	0	0	1244	1288	624562247	624562291	1.400000e-12	84.2
15	TraesCS1D01G295600	chr3D	97.904	1288	7	3	1	1288	21898716	21899983	0.000000e+00	2211.0
16	TraesCS1D01G295600	chr6D	99.254	1206	7	1	1	1206	431404067	431405270	0.000000e+00	2176.0
17	TraesCS1D01G295600	chr4D	93.988	865	44	8	1296	2157	398577102	398576243	0.000000e+00	1303.0
18	TraesCS1D01G295600	chr4D	92.618	867	51	11	1296	2155	493875026	493875886	0.000000e+00	1234.0
19	TraesCS1D01G295600	chr7D	93.287	864	50	7	1296	2154	66606965	66607825	0.000000e+00	1267.0
20	TraesCS1D01G295600	chr2A	96.657	658	4	2	1	658	335827441	335828080	0.000000e+00	1077.0
21	TraesCS1D01G295600	chr2B	93.919	296	1	1	1	296	759338825	759338547	4.340000e-117	431.0
22	TraesCS1D01G295600	chr6B	98.266	173	3	0	1	173	276897521	276897349	9.870000e-79	303.0

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	TraesCS1D01G295600	chr1D	394180077	394182277	2200	False	4065	4065	100.000	1	2201	1	chr1D.!!$F2	2200
1	TraesCS1D01G295600	chr1D	483920513	483921798	1285	True	2300	2300	98.913	1	1288	1	chr1D.!!$R3	1287
2	TraesCS1D01G295600	chr1D	254490942	254492106	1164	False	2071	2071	98.717	121	1288	1	chr1D.!!$F1	1167
3	TraesCS1D01G295600	chr1D	251976875	251977740	865	True	1232	1232	92.537	1296	2154	1	chr1D.!!$R1	858
4	TraesCS1D01G295600	chr1D	295943983	295944836	853	True	1232	1232	92.683	1296	2154	1	chr1D.!!$R2	858
5	TraesCS1D01G295600	chrUn	317470741	317472026	1285	True	2305	2305	98.991	1	1288	1	chrUn.!!$R1	1287
6	TraesCS1D01G295600	chr5D	6205378	6206663	1285	True	2283	2283	98.680	1	1288	1	chr5D.!!$R1	1287
7	TraesCS1D01G295600	chr5D	240132461	240133598	1137	False	2052	2052	99.210	150	1288	1	chr5D.!!$F2	1138
8	TraesCS1D01G295600	chr5D	416217983	416218840	857	True	1266	1266	93.271	1302	2161	1	chr5D.!!$R3	859
9	TraesCS1D01G295600	chr5D	120323929	120324785	856	False	1264	1264	93.256	1296	2154	1	chr5D.!!$F1	858
10	TraesCS1D01G295600	chr5D	308889213	308890069	856	True	1253	1253	93.031	1296	2154	1	chr5D.!!$R2	858
11	TraesCS1D01G295600	chr5D	480439548	480440398	850	False	1230	1230	92.691	1296	2154	1	chr5D.!!$F3	858
12	TraesCS1D01G295600	chr3B	201507738	201509022	1284	False	2270	2270	98.525	1	1288	1	chr3B.!!$F1	1287
13	TraesCS1D01G295600	chr2D	334227078	334228361	1283	False	2224	2224	97.902	3	1288	1	chr2D.!!$F1	1285
14	TraesCS1D01G295600	chr3D	21898716	21899983	1267	False	2211	2211	97.904	1	1288	1	chr3D.!!$F1	1287
15	TraesCS1D01G295600	chr6D	431404067	431405270	1203	False	2176	2176	99.254	1	1206	1	chr6D.!!$F1	1205
16	TraesCS1D01G295600	chr4D	398576243	398577102	859	True	1303	1303	93.988	1296	2157	1	chr4D.!!$R1	861
17	TraesCS1D01G295600	chr4D	493875026	493875886	860	False	1234	1234	92.618	1296	2155	1	chr4D.!!$F1	859
18	TraesCS1D01G295600	chr7D	66606965	66607825	860	False	1267	1267	93.287	1296	2154	1	chr7D.!!$F1	858
19	TraesCS1D01G295600	chr2A	335827441	335828080	639	False	1077	1077	96.657	1	658	1	chr2A.!!$F1	657

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
1308	1314	5.593909	ACAACAGAAAGATGTGGTTTGATGA	59.406	36.0	0.0	0.0	33.37	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2177	2209	1.07597	TCCCTCCTCCTCCGTCATG	60.076	63.158	0.0	0.0	0.0	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
1300	1306	9.823647	AGTATAGAATACAACAGAAAGATGTGG	57.176	33.333	0.33	0.00	34.76	4.17
1308	1314	5.593909	ACAACAGAAAGATGTGGTTTGATGA	59.406	36.000	0.00	0.00	33.37	2.92
1311	1317	5.593909	ACAGAAAGATGTGGTTTGATGAACA	59.406	36.000	0.00	0.00	40.13	3.18
1739	1763	2.495952	CCCCTCCTTTATATACGGGGGT	60.496	54.545	12.94	0.00	46.07	4.95
1798	1830	3.636231	CGGTGCCCTCCTCCACAA	61.636	66.667	0.00	0.00	33.72	3.33
1875	1907	3.001902	ATCATCACCGTCGCCACGT	62.002	57.895	2.55	0.00	45.17	4.49
1892	1924	1.954146	GTCGTCGTGCTGGCAGAAA	60.954	57.895	20.86	1.81	0.00	2.52
1977	2009	2.562912	GAGGTGCCGTACGTTCGA	59.437	61.111	16.59	0.00	0.00	3.71
2026	2058	1.085893	TCGACTACATCAACCGCGTA	58.914	50.000	4.92	0.00	0.00	4.42
2044	2076	2.916716	CGTAACTAAACGCTTCCGCTTA	59.083	45.455	0.00	0.00	38.22	3.09
2159	2191	0.033781	TACGTTCCCCAACACGAAGG	59.966	55.000	0.00	0.00	39.76	3.46
2160	2192	1.227734	CGTTCCCCAACACGAAGGT	60.228	57.895	0.00	0.00	38.76	3.50
2169	2201	2.347490	CACGAAGGTGTGGGGGAG	59.653	66.667	0.00	0.00	39.38	4.30
2170	2202	2.928396	ACGAAGGTGTGGGGGAGG	60.928	66.667	0.00	0.00	0.00	4.30
2171	2203	4.410400	CGAAGGTGTGGGGGAGGC	62.410	72.222	0.00	0.00	0.00	4.70
2172	2204	3.256960	GAAGGTGTGGGGGAGGCA	61.257	66.667	0.00	0.00	0.00	4.75
2173	2205	3.569200	GAAGGTGTGGGGGAGGCAC	62.569	68.421	0.00	0.00	0.00	5.01
2174	2206	4.918360	AGGTGTGGGGGAGGCACA	62.918	66.667	0.00	0.00	35.05	4.57
2175	2207	3.661648	GGTGTGGGGGAGGCACAT	61.662	66.667	0.00	0.00	35.05	3.21
2176	2208	2.044946	GTGTGGGGGAGGCACATC	60.045	66.667	0.00	0.00	33.70	3.06
2177	2209	3.338250	TGTGGGGGAGGCACATCC	61.338	66.667	0.00	0.00	38.76	3.51
2178	2210	3.338250	GTGGGGGAGGCACATCCA	61.338	66.667	3.47	0.00	41.52	3.41
2179	2211	2.287117	TGGGGGAGGCACATCCAT	60.287	61.111	3.47	0.00	41.52	3.41
2180	2212	2.196776	GGGGGAGGCACATCCATG	59.803	66.667	3.47	0.00	41.52	3.66
2181	2213	2.386100	GGGGGAGGCACATCCATGA	61.386	63.158	3.47	0.00	41.52	3.07
2182	2214	1.152881	GGGGAGGCACATCCATGAC	60.153	63.158	3.47	0.00	41.52	3.06
2183	2215	1.524621	GGGAGGCACATCCATGACG	60.525	63.158	3.47	0.00	41.52	4.35
2184	2216	1.524621	GGAGGCACATCCATGACGG	60.525	63.158	0.00	0.00	39.34	4.79
2192	2224	4.686695	TCCATGACGGAGGAGGAG	57.313	61.111	0.00	0.00	39.64	3.69
2193	2225	1.075970	TCCATGACGGAGGAGGAGG	60.076	63.158	0.00	0.00	39.64	4.30
2194	2226	2.136878	CCATGACGGAGGAGGAGGG	61.137	68.421	0.00	0.00	36.56	4.30
2195	2227	1.075970	CATGACGGAGGAGGAGGGA	60.076	63.158	0.00	0.00	0.00	4.20
2196	2228	1.112315	CATGACGGAGGAGGAGGGAG	61.112	65.000	0.00	0.00	0.00	4.30
2197	2229	2.123640	GACGGAGGAGGAGGGAGG	60.124	72.222	0.00	0.00	0.00	4.30
2198	2230	4.467107	ACGGAGGAGGAGGGAGGC	62.467	72.222	0.00	0.00	0.00	4.70
2200	2232	4.890306	GGAGGAGGAGGGAGGCCC	62.890	77.778	0.00	0.00	45.90	5.80

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
362	363	3.444742	TCTTGCCCAAGATTGTTATGCTG	59.555	43.478	6.62	0.00	42.06	4.41
1288	1294	6.075762	TGTTCATCAAACCACATCTTTCTG	57.924	37.500	0.00	0.00	37.03	3.02
1289	1295	6.713762	TTGTTCATCAAACCACATCTTTCT	57.286	33.333	0.00	0.00	37.03	2.52
1290	1296	7.492344	ACTTTTGTTCATCAAACCACATCTTTC	59.508	33.333	0.00	0.00	44.39	2.62
1291	1297	7.330262	ACTTTTGTTCATCAAACCACATCTTT	58.670	30.769	0.00	0.00	44.39	2.52
1292	1298	6.877236	ACTTTTGTTCATCAAACCACATCTT	58.123	32.000	0.00	0.00	44.39	2.40
1293	1299	6.469782	ACTTTTGTTCATCAAACCACATCT	57.530	33.333	0.00	0.00	44.39	2.90
1294	1300	7.401080	CAAACTTTTGTTCATCAAACCACATC	58.599	34.615	0.00	0.00	44.39	3.06
1328	1334	0.395173	TGTCCGTGATCTCATCCGGA	60.395	55.000	6.61	6.61	44.26	5.14
1474	1483	0.853586	TAAGGCCCATTGGTTCCCCT	60.854	55.000	0.00	0.00	0.00	4.79
1493	1503	0.631212	CTCCCCACTTAAGGCCCATT	59.369	55.000	7.53	0.00	0.00	3.16
1503	1513	0.252927	CCCTTCCTCTCTCCCCACTT	60.253	60.000	0.00	0.00	0.00	3.16
1547	1559	0.842905	TCCAATTCGGACCCAAGGGA	60.843	55.000	13.15	0.00	39.64	4.20
1753	1781	5.413523	ACGGTTAAGAGAAACTTGTGTGTTT	59.586	36.000	0.00	0.00	42.11	2.83
1798	1830	3.635373	ACGATATGACCGAGGTGTGTAAT	59.365	43.478	0.00	0.00	0.00	1.89
1875	1907	1.005037	ATTTCTGCCAGCACGACGA	60.005	52.632	0.00	0.00	0.00	4.20
1886	1918	1.524849	GGCCGAGGGAGATTTCTGC	60.525	63.158	0.00	0.00	0.00	4.26
1892	1924	1.002274	AGTTGAGGCCGAGGGAGAT	59.998	57.895	0.00	0.00	0.00	2.75
1977	2009	1.811558	CGATCCAACCGATCCAAGCAT	60.812	52.381	0.00	0.00	44.07	3.79
2044	2076	0.321653	AACGTACCCTCGTAGACCGT	60.322	55.000	0.00	0.00	43.38	4.83
2063	2095	2.203640	AGCGGGGAGAGTGTGTCA	60.204	61.111	0.00	0.00	0.00	3.58
2159	2191	2.044946	GATGTGCCTCCCCCACAC	60.045	66.667	0.00	0.00	45.00	3.82
2160	2192	3.338250	GGATGTGCCTCCCCCACA	61.338	66.667	0.00	0.00	46.10	4.17
2161	2193	2.693871	ATGGATGTGCCTCCCCCAC	61.694	63.158	0.00	0.00	37.63	4.61
2162	2194	2.287117	ATGGATGTGCCTCCCCCA	60.287	61.111	0.00	0.00	37.63	4.96
2163	2195	2.196776	CATGGATGTGCCTCCCCC	59.803	66.667	0.00	0.00	37.63	5.40
2164	2196	1.152881	GTCATGGATGTGCCTCCCC	60.153	63.158	0.00	0.00	37.63	4.81
2165	2197	1.524621	CGTCATGGATGTGCCTCCC	60.525	63.158	0.00	0.00	37.63	4.30
2166	2198	1.524621	CCGTCATGGATGTGCCTCC	60.525	63.158	0.00	0.00	42.00	4.30
2167	2199	1.522092	TCCGTCATGGATGTGCCTC	59.478	57.895	0.00	0.00	43.74	4.70
2168	2200	3.726004	TCCGTCATGGATGTGCCT	58.274	55.556	0.00	0.00	43.74	4.75
2176	2208	2.136878	CCCTCCTCCTCCGTCATGG	61.137	68.421	0.00	0.00	40.09	3.66
2177	2209	1.075970	TCCCTCCTCCTCCGTCATG	60.076	63.158	0.00	0.00	0.00	3.07
2178	2210	1.231641	CTCCCTCCTCCTCCGTCAT	59.768	63.158	0.00	0.00	0.00	3.06
2179	2211	2.684104	CTCCCTCCTCCTCCGTCA	59.316	66.667	0.00	0.00	0.00	4.35
2180	2212	2.123640	CCTCCCTCCTCCTCCGTC	60.124	72.222	0.00	0.00	0.00	4.79
2181	2213	4.467107	GCCTCCCTCCTCCTCCGT	62.467	72.222	0.00	0.00	0.00	4.69
2183	2215	4.890306	GGGCCTCCCTCCTCCTCC	62.890	77.778	0.84	0.00	41.34	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.