AutoCloner

Multiple sequence alignment - TraesCS7D01G466300

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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	TraesCS7D01G466300	chr7D	100.000	2270	0	0	1	2270	580112441	580110172	0.000000e+00	4193
1	TraesCS7D01G466300	chr1A	89.672	2285	205	16	1	2270	94243758	94241490	0.000000e+00	2883
2	TraesCS7D01G466300	chr5B	87.195	2296	257	23	1	2270	239324187	239321903	0.000000e+00	2577
3	TraesCS7D01G466300	chr4B	87.168	2299	253	25	1	2270	92551144	92553429	0.000000e+00	2573
4	TraesCS7D01G466300	chr6B	87.059	2295	261	20	1	2270	346415421	346413138	0.000000e+00	2560
5	TraesCS7D01G466300	chr5A	87.021	2296	261	23	1	2270	320270628	320272912	0.000000e+00	2555
6	TraesCS7D01G466300	chr6D	89.266	1947	182	12	35	1957	87669178	87667235	0.000000e+00	2412
7	TraesCS7D01G466300	chr1B	87.686	1819	192	20	471	2270	269072705	269070900	0.000000e+00	2089
8	TraesCS7D01G466300	chr1B	91.736	121	10	0	344	464	269072710	269072830	3.880000e-38	169
9	TraesCS7D01G466300	chr3A	88.171	1564	171	10	719	2270	711443773	711442212	0.000000e+00	1851
10	TraesCS7D01G466300	chr7B	86.558	1354	166	10	925	2270	27982672	27984017	0.000000e+00	1478
11	TraesCS7D01G466300	chr7B	86.330	1346	158	16	1	1326	516451624	516452963	0.000000e+00	1443
12	TraesCS7D01G466300	chr7B	88.353	953	100	7	1324	2270	516455488	516456435	0.000000e+00	1134
13	TraesCS7D01G466300	chr2A	86.784	1135	114	19	346	1456	608935380	608934258	0.000000e+00	1232
14	TraesCS7D01G466300	chr2A	85.130	269	32	3	281	541	608936157	608935889	3.720000e-68	268

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	TraesCS7D01G466300	chr7D	580110172	580112441	2269	True	4193.0	4193	100.0000	1	2270	1	chr7D.!!$R1	2269
1	TraesCS7D01G466300	chr1A	94241490	94243758	2268	True	2883.0	2883	89.6720	1	2270	1	chr1A.!!$R1	2269
2	TraesCS7D01G466300	chr5B	239321903	239324187	2284	True	2577.0	2577	87.1950	1	2270	1	chr5B.!!$R1	2269
3	TraesCS7D01G466300	chr4B	92551144	92553429	2285	False	2573.0	2573	87.1680	1	2270	1	chr4B.!!$F1	2269
4	TraesCS7D01G466300	chr6B	346413138	346415421	2283	True	2560.0	2560	87.0590	1	2270	1	chr6B.!!$R1	2269
5	TraesCS7D01G466300	chr5A	320270628	320272912	2284	False	2555.0	2555	87.0210	1	2270	1	chr5A.!!$F1	2269
6	TraesCS7D01G466300	chr6D	87667235	87669178	1943	True	2412.0	2412	89.2660	35	1957	1	chr6D.!!$R1	1922
7	TraesCS7D01G466300	chr1B	269070900	269072705	1805	True	2089.0	2089	87.6860	471	2270	1	chr1B.!!$R1	1799
8	TraesCS7D01G466300	chr3A	711442212	711443773	1561	True	1851.0	1851	88.1710	719	2270	1	chr3A.!!$R1	1551
9	TraesCS7D01G466300	chr7B	27982672	27984017	1345	False	1478.0	1478	86.5580	925	2270	1	chr7B.!!$F1	1345
10	TraesCS7D01G466300	chr7B	516451624	516456435	4811	False	1288.5	1443	87.3415	1	2270	2	chr7B.!!$F2	2269
11	TraesCS7D01G466300	chr2A	608934258	608936157	1899	True	750.0	1232	85.9570	281	1456	2	chr2A.!!$R1	1175

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
778	1502	0.247736	TCCTTCCTTCGAAGCTGAGC	59.752	55.0	19.99	0.0	43.66	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1735	5017	0.03467	GAGAAGCAAGATGCCACCCT	60.035	55.0	0.0	0.0	46.52	4.34	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
17	20	3.862991	TTCACCCCACGCCAACGA	61.863	61.111	0.00	0.00	43.93	3.85
19	22	4.619227	CACCCCACGCCAACGACT	62.619	66.667	0.00	0.00	43.93	4.18
30	33	1.143183	CAACGACTACATCCCCCGG	59.857	63.158	0.00	0.00	0.00	5.73
49	52	3.606662	GGCCTCGCTCCTCGCATA	61.607	66.667	0.00	0.00	39.08	3.14
95	98	1.888436	GACGGTGAGTCCAGGATGCA	61.888	60.000	0.00	0.00	43.95	3.96
99	102	0.835941	GTGAGTCCAGGATGCAGGAT	59.164	55.000	0.69	0.00	36.11	3.24
140	143	2.107343	CCACAACGACCACGACCA	59.893	61.111	0.00	0.00	42.66	4.02
152	155	0.598942	CACGACCATGACCACGACAA	60.599	55.000	0.00	0.00	0.00	3.18
259	262	1.581447	CACTTTTTCCGGAGCAGGC	59.419	57.895	3.34	0.00	0.00	4.85
261	264	2.282887	TTTTTCCGGAGCAGGCCC	60.283	61.111	3.34	0.00	0.00	5.80
317	320	3.764466	CGGCAGAGAAGACCGCCT	61.764	66.667	0.00	0.00	42.59	5.52
426	1141	4.554036	GCCGTCATCCCAGCCTCC	62.554	72.222	0.00	0.00	0.00	4.30
464	1179	1.078848	GCCCTGTTGACTGCTCGAT	60.079	57.895	0.00	0.00	0.00	3.59
465	1180	1.364626	GCCCTGTTGACTGCTCGATG	61.365	60.000	0.00	0.00	0.00	3.84
492	1213	4.106925	CACTCTGGAGGGGCTGCC	62.107	72.222	11.05	11.05	0.00	4.85
504	1225	4.410400	GCTGCCAGCCCGGTAAGT	62.410	66.667	5.06	0.00	34.48	2.24
546	1267	1.667154	CTCCTTCCTCGCCACGATCA	61.667	60.000	0.00	0.00	34.61	2.92
566	1287	2.674852	CAACCTCCTGTGATGTGATTCG	59.325	50.000	0.00	0.00	0.00	3.34
624	1345	1.477685	GGATCGCCCCCTATTTCGGA	61.478	60.000	0.00	0.00	0.00	4.55
631	1352	0.837272	CCCCTATTTCGGAGCCAAGA	59.163	55.000	0.00	0.00	0.00	3.02
635	1356	3.343617	CCTATTTCGGAGCCAAGAAACA	58.656	45.455	1.04	0.00	38.90	2.83
678	1399	3.050275	GCTCCACAGGCGTCAACC	61.050	66.667	0.00	0.00	0.00	3.77
708	1432	2.540516	CACGACTCTAGACGTCATCGAT	59.459	50.000	19.50	0.00	43.67	3.59
767	1491	1.988107	TGTTGCTCCATCTCCTTCCTT	59.012	47.619	0.00	0.00	0.00	3.36
778	1502	0.247736	TCCTTCCTTCGAAGCTGAGC	59.752	55.000	19.99	0.00	43.66	4.26
779	1509	1.080995	CCTTCCTTCGAAGCTGAGCG	61.081	60.000	19.99	5.11	43.66	5.03
798	1528	0.906775	GGGTCACCCCGATCTTTGTA	59.093	55.000	0.00	0.00	42.41	2.41
988	1718	4.473520	CCAGCCCGCGTCTCCAAT	62.474	66.667	4.92	0.00	0.00	3.16
1011	1747	0.179034	AGAGGAAGATGCCGATTGCC	60.179	55.000	0.00	0.00	40.16	4.52
1057	1793	2.800736	GCATGGGCGTTGTGGATC	59.199	61.111	0.00	0.00	0.00	3.36
1067	1803	1.304381	TTGTGGATCAAGGCCAGCC	60.304	57.895	5.01	0.00	35.77	4.85
1223	1959	4.954118	TGGTGGTGAGGCGGGACT	62.954	66.667	0.00	0.00	0.00	3.85
1226	1962	4.954118	TGGTGAGGCGGGACTGGT	62.954	66.667	0.00	0.00	0.00	4.00
1284	2020	2.059541	GAGTGACTGGAGCGTTTGTAC	58.940	52.381	0.00	0.00	0.00	2.90
1385	4653	1.142748	GGCGTCTGCTATCTGCTGT	59.857	57.895	0.00	0.00	43.37	4.40
1435	4704	1.040646	GGTCATCTCGCTCCACCATA	58.959	55.000	0.00	0.00	0.00	2.74
1518	4788	4.278310	ACTTCTGCTGTACCCAAAGTTTT	58.722	39.130	0.00	0.00	0.00	2.43
1585	4855	3.195661	GCTTAAATTGTCCCGATCGTCT	58.804	45.455	15.09	0.00	0.00	4.18
1602	4884	3.130516	TCGTCTAGCAACAATCCGAGAAT	59.869	43.478	0.00	0.00	0.00	2.40
1626	4908	1.153568	ATCGCCACTCCATGTCACG	60.154	57.895	0.00	0.00	0.00	4.35
1637	4919	0.246360	CATGTCACGTGGTCTGCCTA	59.754	55.000	17.00	0.00	35.27	3.93
1638	4920	1.134699	CATGTCACGTGGTCTGCCTAT	60.135	52.381	17.00	0.00	35.27	2.57
1764	5046	2.259917	TCTTGCTTCTCTGGGATGACA	58.740	47.619	0.00	0.00	0.00	3.58
1820	5102	2.775911	TCTTCCTCTCCTGCAATGTG	57.224	50.000	0.00	0.00	0.00	3.21
1879	5161	3.068560	CGGTTTATGGACCAACGAGAAA	58.931	45.455	0.00	0.00	39.78	2.52
1935	5217	1.452108	GAGAAACCTCCCCATGGCG	60.452	63.158	6.09	0.00	0.00	5.69
1940	5222	2.679642	CCTCCCCATGGCGCAAAA	60.680	61.111	10.83	0.00	0.00	2.44
1944	5226	2.658064	CCCCATGGCGCAAAATGGT	61.658	57.895	25.36	0.00	41.59	3.55
1980	5262	6.018588	TGACTTTAATCAAATATACCGTGCCG	60.019	38.462	0.00	0.00	0.00	5.69
2011	5293	1.662446	GAGCAAACGTCGACCGGAA	60.662	57.895	9.46	0.00	42.24	4.30
2028	5310	0.319641	GAACCGACTTGTCCGCTTCT	60.320	55.000	0.00	0.00	0.00	2.85
2058	5340	5.909610	GCACTGAATACTTGTGAACTCAAAC	59.090	40.000	0.00	0.00	33.95	2.93
2075	5357	8.441312	AACTCAAACAGATTCATTTGCAAAAT	57.559	26.923	17.19	5.16	36.06	1.82
2124	5407	1.892209	CGACCCAACCTTAAGCAAGT	58.108	50.000	0.00	0.00	0.00	3.16
2229	5514	4.168291	GCCCCTCCTCCTCGCAAG	62.168	72.222	0.00	0.00	0.00	4.01
2242	5527	2.904866	GCAAGTGACAACGGCCCA	60.905	61.111	0.00	0.00	0.00	5.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	52	1.080974	CGTAGCGGAAGGTGAACGT	60.081	57.895	0.00	0.00	44.53	3.99
95	98	1.834822	GCCACCTCCGCTCTATCCT	60.835	63.158	0.00	0.00	0.00	3.24
99	102	2.759973	CCAGCCACCTCCGCTCTA	60.760	66.667	0.00	0.00	33.17	2.43
140	143	0.460284	GCGATCCTTGTCGTGGTCAT	60.460	55.000	0.00	0.00	43.27	3.06
152	155	3.823330	GGTCGTGGTCGCGATCCT	61.823	66.667	18.31	0.00	43.07	3.24
452	1167	1.807165	GAGCGCATCGAGCAGTCAA	60.807	57.895	11.47	0.00	46.13	3.18
476	1191	4.664267	TGGCAGCCCCTCCAGAGT	62.664	66.667	9.64	0.00	0.00	3.24
492	1213	0.320374	TGTCTTCACTTACCGGGCTG	59.680	55.000	6.32	0.00	0.00	4.85
504	1225	2.338620	CGGCCACGAGTGTCTTCA	59.661	61.111	2.24	0.00	44.60	3.02
546	1267	2.355108	CCGAATCACATCACAGGAGGTT	60.355	50.000	0.00	0.00	35.53	3.50
612	1333	0.837272	TCTTGGCTCCGAAATAGGGG	59.163	55.000	0.00	0.00	34.01	4.79
617	1338	2.955660	TGTTGTTTCTTGGCTCCGAAAT	59.044	40.909	0.00	0.00	32.43	2.17
624	1345	1.035139	CTGCCTGTTGTTTCTTGGCT	58.965	50.000	0.00	0.00	43.57	4.75
683	1407	2.614779	TGACGTCTAGAGTCGTGGTAG	58.385	52.381	17.92	0.00	39.64	3.18
693	1417	4.876679	GGGATGATATCGATGACGTCTAGA	59.123	45.833	17.92	13.19	40.69	2.43
708	1432	1.823648	GCAGGAGAGGACGGGATGATA	60.824	57.143	0.00	0.00	0.00	2.15
767	1491	2.989253	TGACCCGCTCAGCTTCGA	60.989	61.111	0.00	0.00	0.00	3.71
988	1718	1.500474	ATCGGCATCTTCCTCTTGGA	58.500	50.000	0.00	0.00	41.36	3.53
1011	1747	0.809241	GCAGTCTCTCCGCCATCTTG	60.809	60.000	0.00	0.00	0.00	3.02
1057	1793	1.970114	CTGTGACTGGCTGGCCTTG	60.970	63.158	13.05	8.16	36.94	3.61
1067	1803	2.082231	CAATGGCTTCCTCTGTGACTG	58.918	52.381	0.00	0.00	0.00	3.51
1182	1918	1.379916	CACCAGGGCATCCTCAACA	59.620	57.895	0.00	0.00	42.67	3.33
1203	1939	4.802051	CCCGCCTCACCACCATGG	62.802	72.222	11.19	11.19	45.02	3.66
1261	1997	2.436087	AAACGCTCCAGTCACTCCGG	62.436	60.000	0.00	0.00	0.00	5.14
1284	2020	3.030291	AGAGCACATCTTCTACAGGAGG	58.970	50.000	0.00	0.00	32.99	4.30
1385	4653	1.600636	CACAAAAGCCTCGCCAGGA	60.601	57.895	0.00	0.00	43.65	3.86
1435	4704	4.763279	TGACATTCAACATTCAGCTCACAT	59.237	37.500	0.00	0.00	0.00	3.21
1495	4764	4.699925	AACTTTGGGTACAGCAGAAGTA	57.300	40.909	0.00	0.00	0.00	2.24
1585	4855	5.427378	TGATTGATTCTCGGATTGTTGCTA	58.573	37.500	0.00	0.00	0.00	3.49
1602	4884	1.210234	ACATGGAGTGGCGATGATTGA	59.790	47.619	0.00	0.00	36.35	2.57
1637	4919	2.998316	GCTCAAGCTTGGTCTCCTAT	57.002	50.000	25.73	0.00	38.21	2.57
1733	5015	0.322816	GAAGCAAGATGCCACCCTGA	60.323	55.000	0.00	0.00	46.52	3.86
1735	5017	0.034670	GAGAAGCAAGATGCCACCCT	60.035	55.000	0.00	0.00	46.52	4.34
1764	5046	3.260884	ACATCCTTCACGTCCACAGTATT	59.739	43.478	0.00	0.00	0.00	1.89
1820	5102	5.334414	GGTTCTATTGGATGCATTGATCGTC	60.334	44.000	0.00	0.00	0.00	4.20
1879	5161	3.515602	AGAAAGCATCCTTCAGGTTGT	57.484	42.857	5.92	0.00	37.26	3.32
1980	5262	4.246458	ACGTTTGCTCTATTCTTGTCTCC	58.754	43.478	0.00	0.00	0.00	3.71
2011	5293	1.006102	CAGAAGCGGACAAGTCGGT	60.006	57.895	9.12	1.38	40.18	4.69
2028	5310	6.710295	AGTTCACAAGTATTCAGTGCATTACA	59.290	34.615	0.00	0.00	33.44	2.41
2075	5357	7.064609	CGCTCATTACTCCAAGTGAATTTTCTA	59.935	37.037	0.00	0.00	0.00	2.10
2124	5407	8.657074	TCTTCATTACAAAAGAAAGAGTCGAA	57.343	30.769	0.00	0.00	0.00	3.71
2229	5514	0.534203	TCTCTTTGGGCCGTTGTCAC	60.534	55.000	0.00	0.00	0.00	3.67
2242	5527	3.008485	AGCGGAAGGACTTTGATCTCTTT	59.992	43.478	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.