AutoCloner

Multiple sequence alignment - TraesCS3B01G235700

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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	TraesCS3B01G235700	chr3B	100.000	2321	0	0	1	2321	368725297	368727617	0	4287
1	TraesCS3B01G235700	chr3B	97.313	856	22	1	1	856	368705030	368705884	0	1452
2	TraesCS3B01G235700	chr5B	95.856	1472	56	3	851	2321	679659746	679661213	0	2375
3	TraesCS3B01G235700	chr5B	89.884	860	78	9	1	856	190834613	190835467	0	1098
4	TraesCS3B01G235700	chr5B	89.779	861	77	11	1	856	190842162	190843016	0	1092
5	TraesCS3B01G235700	chrUn	95.720	1472	57	3	851	2321	189393389	189394855	0	2364
6	TraesCS3B01G235700	chrUn	85.867	842	108	11	21	856	170361883	170361047	0	885
7	TraesCS3B01G235700	chrUn	85.629	842	110	11	21	856	174107883	174108719	0	874
8	TraesCS3B01G235700	chr5A	95.720	1472	57	3	851	2321	300073829	300075295	0	2364
9	TraesCS3B01G235700	chr5A	95.380	1472	60	3	851	2321	16602071	16600607	0	2335
10	TraesCS3B01G235700	chr2A	95.652	1472	58	3	851	2321	618279106	618277640	0	2359
11	TraesCS3B01G235700	chr7D	95.448	1472	61	3	851	2321	626697640	626696174	0	2342
12	TraesCS3B01G235700	chr7D	95.380	1472	62	3	851	2321	203555496	203554030	0	2337
13	TraesCS3B01G235700	chr7B	95.451	1473	60	5	851	2321	743087048	743088515	0	2342
14	TraesCS3B01G235700	chr7B	86.429	840	106	8	21	856	301043531	301042696	0	913
15	TraesCS3B01G235700	chr6A	95.448	1472	60	3	851	2321	289129481	289130946	0	2340
16	TraesCS3B01G235700	chr6B	88.515	862	85	14	1	856	335506618	335505765	0	1031
17	TraesCS3B01G235700	chr4B	87.857	840	94	7	21	856	320836202	320837037	0	979
18	TraesCS3B01G235700	chr4B	87.247	839	101	6	21	856	320828137	320828972	0	952

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	TraesCS3B01G235700	chr3B	368725297	368727617	2320	False	4287	4287	100.000	1	2321	1	chr3B.!!$F2	2320
1	TraesCS3B01G235700	chr3B	368705030	368705884	854	False	1452	1452	97.313	1	856	1	chr3B.!!$F1	855
2	TraesCS3B01G235700	chr5B	679659746	679661213	1467	False	2375	2375	95.856	851	2321	1	chr5B.!!$F3	1470
3	TraesCS3B01G235700	chr5B	190834613	190835467	854	False	1098	1098	89.884	1	856	1	chr5B.!!$F1	855
4	TraesCS3B01G235700	chr5B	190842162	190843016	854	False	1092	1092	89.779	1	856	1	chr5B.!!$F2	855
5	TraesCS3B01G235700	chrUn	189393389	189394855	1466	False	2364	2364	95.720	851	2321	1	chrUn.!!$F2	1470
6	TraesCS3B01G235700	chrUn	170361047	170361883	836	True	885	885	85.867	21	856	1	chrUn.!!$R1	835
7	TraesCS3B01G235700	chrUn	174107883	174108719	836	False	874	874	85.629	21	856	1	chrUn.!!$F1	835
8	TraesCS3B01G235700	chr5A	300073829	300075295	1466	False	2364	2364	95.720	851	2321	1	chr5A.!!$F1	1470
9	TraesCS3B01G235700	chr5A	16600607	16602071	1464	True	2335	2335	95.380	851	2321	1	chr5A.!!$R1	1470
10	TraesCS3B01G235700	chr2A	618277640	618279106	1466	True	2359	2359	95.652	851	2321	1	chr2A.!!$R1	1470
11	TraesCS3B01G235700	chr7D	626696174	626697640	1466	True	2342	2342	95.448	851	2321	1	chr7D.!!$R2	1470
12	TraesCS3B01G235700	chr7D	203554030	203555496	1466	True	2337	2337	95.380	851	2321	1	chr7D.!!$R1	1470
13	TraesCS3B01G235700	chr7B	743087048	743088515	1467	False	2342	2342	95.451	851	2321	1	chr7B.!!$F1	1470
14	TraesCS3B01G235700	chr7B	301042696	301043531	835	True	913	913	86.429	21	856	1	chr7B.!!$R1	835
15	TraesCS3B01G235700	chr6A	289129481	289130946	1465	False	2340	2340	95.448	851	2321	1	chr6A.!!$F1	1470
16	TraesCS3B01G235700	chr6B	335505765	335506618	853	True	1031	1031	88.515	1	856	1	chr6B.!!$R1	855
17	TraesCS3B01G235700	chr4B	320836202	320837037	835	False	979	979	87.857	21	856	1	chr4B.!!$F2	835
18	TraesCS3B01G235700	chr4B	320828137	320828972	835	False	952	952	87.247	21	856	1	chr4B.!!$F1	835

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
790	799	1.082756	GTGCTTCCGCGTGTTCTTG	60.083	57.895	4.92	0.0	39.65	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1929	1940	0.976641	TACCACAAGCTCTGACCTGG	59.023	55.0	0.0	0.0	0.0	4.45	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
109	110	1.940883	TACTACCGCTGAAGCCACCG	61.941	60.000	0.00	0.00	37.91	4.94
279	281	1.134280	CATACACCTCCAGAAGCCAGG	60.134	57.143	0.00	0.00	0.00	4.45
488	491	5.042827	TCCACCTCCTCCTAGTTAGGTTTAT	60.043	44.000	5.16	0.00	44.02	1.40
790	799	1.082756	GTGCTTCCGCGTGTTCTTG	60.083	57.895	4.92	0.00	39.65	3.02
838	847	3.615614	ACGTGAAAGATCGACGCTATAC	58.384	45.455	8.80	0.00	35.15	1.47
872	881	3.160269	CATCAGAACCCTTTCCTGCTTT	58.840	45.455	0.00	0.00	31.28	3.51
888	897	3.831911	CTGCTTTCCCTTTTTACCCATCA	59.168	43.478	0.00	0.00	0.00	3.07
915	925	6.097554	ACTCGACTCACATTTTGATCTCCTAT	59.902	38.462	0.00	0.00	32.17	2.57
933	943	2.283145	ATGCTTGCTTTCACAGTCCT	57.717	45.000	0.00	0.00	0.00	3.85
966	976	3.684413	GCCCGGAATCAATGAAGGAGTTA	60.684	47.826	0.73	0.00	0.00	2.24
999	1010	1.007319	GTCGAGCGAGCGTAATTCAAC	60.007	52.381	0.00	0.00	0.00	3.18
1049	1060	3.119495	GCCTTATCACGAAAGCCACATTT	60.119	43.478	0.00	0.00	0.00	2.32
1070	1081	2.605818	TGTTTCGTTTGAGGAAGTCACG	59.394	45.455	0.00	0.00	33.71	4.35
1075	1086	0.387929	TTTGAGGAAGTCACGCGTCT	59.612	50.000	9.86	0.95	33.71	4.18
1082	1093	0.179094	AAGTCACGCGTCTTGTTCCA	60.179	50.000	9.86	0.00	0.00	3.53
1162	1173	1.281867	CCCCTATCACAAGACCAAGCA	59.718	52.381	0.00	0.00	0.00	3.91
1302	1313	6.273825	ACTACCGCTTCTACACATAAATCAG	58.726	40.000	0.00	0.00	0.00	2.90
1351	1362	8.514136	TTTCGTTAATGGCTAAAATGTTCTTG	57.486	30.769	0.00	0.00	0.00	3.02
1366	1377	0.260230	TCTTGGTGAAAGGGTTGCCA	59.740	50.000	0.00	0.00	36.46	4.92
1393	1404	0.603975	GGCAAACTCAGAGCGGTCTT	60.604	55.000	15.83	0.00	0.00	3.01
1395	1406	2.413837	GCAAACTCAGAGCGGTCTTTA	58.586	47.619	15.83	5.30	0.00	1.85
1436	1447	2.973694	GCATCATCCAAGCCAAACAT	57.026	45.000	0.00	0.00	0.00	2.71
1447	1458	1.701847	AGCCAAACATGTCTCCTCAGT	59.298	47.619	0.00	0.00	0.00	3.41
1448	1459	2.079925	GCCAAACATGTCTCCTCAGTC	58.920	52.381	0.00	0.00	0.00	3.51
1449	1460	2.341257	CCAAACATGTCTCCTCAGTCG	58.659	52.381	0.00	0.00	0.00	4.18
1533	1544	1.153449	CCGCCCGCTCTCAATACAA	60.153	57.895	0.00	0.00	0.00	2.41
1590	1601	5.937975	ACCGATTCATCCAATCCAATTTT	57.062	34.783	0.00	0.00	38.17	1.82
1591	1602	5.906073	ACCGATTCATCCAATCCAATTTTC	58.094	37.500	0.00	0.00	38.17	2.29
1601	1612	5.047802	TCCAATCCAATTTTCTCAGAAGTGC	60.048	40.000	0.00	0.00	0.00	4.40
1602	1613	5.279106	CCAATCCAATTTTCTCAGAAGTGCA	60.279	40.000	0.00	0.00	0.00	4.57
1753	1764	5.127194	TGCGATTAGAAACCAGTGACTCTAT	59.873	40.000	0.00	0.00	0.00	1.98
1762	1773	2.424957	CCAGTGACTCTATAGCCAGGGA	60.425	54.545	0.00	0.00	0.00	4.20
1802	1813	7.321530	AGATATAAAGAATGGGGAGTTAGGGA	58.678	38.462	0.00	0.00	0.00	4.20
1814	1825	3.054582	GGAGTTAGGGATTCGGTTTCCTT	60.055	47.826	0.00	0.00	33.53	3.36
1929	1940	3.568007	TGGGTGAATCAAGTACAACAAGC	59.432	43.478	0.00	0.00	0.00	4.01
1962	1973	1.559682	TGTGGTAGAAGATTGGGCTCC	59.440	52.381	0.00	0.00	0.00	4.70
2009	2020	3.868757	AGAAGTACGCATTGCTGACTA	57.131	42.857	7.12	0.00	0.00	2.59
2021	2032	5.733091	GCATTGCTGACTAACTGTTTGAACA	60.733	40.000	8.91	7.46	37.37	3.18
2027	2038	6.566753	GCTGACTAACTGTTTGAACAATCCTC	60.567	42.308	8.91	0.00	38.66	3.71
2101	2112	1.300853	CCCCCAAAAGCAAAGCACG	60.301	57.895	0.00	0.00	0.00	5.34
2120	2131	1.676916	CGGACTCTACTCACCCACGTA	60.677	57.143	0.00	0.00	0.00	3.57
2134	2145	2.094078	CCCACGTATTTTCCACCTACGA	60.094	50.000	8.17	0.00	40.38	3.43
2211	2222	3.546417	CGAGAGTGGATAGCGTGACTAAC	60.546	52.174	0.00	0.00	33.57	2.34
2212	2223	3.353557	AGAGTGGATAGCGTGACTAACA	58.646	45.455	0.00	0.00	33.57	2.41
2217	2228	2.159085	GGATAGCGTGACTAACAAGGCT	60.159	50.000	0.00	0.00	41.31	4.58
2221	2232	1.993370	GCGTGACTAACAAGGCTGTAG	59.007	52.381	0.00	0.00	33.45	2.74
2224	2235	3.921021	CGTGACTAACAAGGCTGTAGAAG	59.079	47.826	7.03	0.00	33.45	2.85
2285	2296	5.075670	CGAGAGCAGCATAATTGTTAGTG	57.924	43.478	0.00	0.00	0.00	2.74
2289	2300	4.848357	AGCAGCATAATTGTTAGTGAGGT	58.152	39.130	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
260	262	1.207791	CCTGGCTTCTGGAGGTGTAT	58.792	55.000	0.00	0.00	0.00	2.29
282	284	1.537814	TAGTTCCGCTCGAAGCCCAA	61.538	55.000	0.00	0.00	38.18	4.12
488	491	7.774625	TCACACAAATATGAGCTAATCCAATGA	59.225	33.333	0.00	0.00	0.00	2.57
809	818	2.069273	CGATCTTTCACGTTTGGAGCT	58.931	47.619	0.00	0.00	0.00	4.09
838	847	3.458189	GTTCTGATGTAGGATGGAACCG	58.542	50.000	0.00	0.00	34.73	4.44
846	855	3.519510	CAGGAAAGGGTTCTGATGTAGGA	59.480	47.826	0.00	0.00	33.92	2.94
872	881	3.055385	CGAGTCTGATGGGTAAAAAGGGA	60.055	47.826	0.00	0.00	0.00	4.20
888	897	5.398603	AGATCAAAATGTGAGTCGAGTCT	57.601	39.130	20.51	0.00	40.43	3.24
915	925	1.597742	GAGGACTGTGAAAGCAAGCA	58.402	50.000	0.00	0.00	0.00	3.91
933	943	3.949885	TTCCGGGCTGCTCGTAGGA	62.950	63.158	21.69	8.27	0.00	2.94
966	976	0.737715	GCTCGACTCGGTGCTGAATT	60.738	55.000	0.00	0.00	0.00	2.17
999	1010	5.408299	TCCTTCGTTCAGTACAATCAACATG	59.592	40.000	0.00	0.00	0.00	3.21
1049	1060	2.605818	CGTGACTTCCTCAAACGAAACA	59.394	45.455	0.00	0.00	0.00	2.83
1114	1125	4.719273	AGGAGGAAGAAGAGGGTATTTCTG	59.281	45.833	0.00	0.00	34.09	3.02
1121	1132	2.545810	CTTGAGGAGGAAGAAGAGGGT	58.454	52.381	0.00	0.00	0.00	4.34
1162	1173	3.638160	GAGTCTTCTGCAGGATGAGATCT	59.362	47.826	15.13	0.00	39.69	2.75
1216	1227	2.887783	ACGAGAATAGATCACATCCGCT	59.112	45.455	0.00	0.00	0.00	5.52
1302	1313	3.065925	GCCACTATTCCACAATGCTTCTC	59.934	47.826	0.00	0.00	0.00	2.87
1351	1362	0.827368	TTTGTGGCAACCCTTTCACC	59.173	50.000	0.00	0.00	0.00	4.02
1366	1377	1.676006	CTCTGAGTTTGCCGGTTTTGT	59.324	47.619	1.90	0.00	0.00	2.83
1393	1404	5.758296	CCGCTATGCTCCTATTCACTTTTAA	59.242	40.000	0.00	0.00	0.00	1.52
1395	1406	4.130118	CCGCTATGCTCCTATTCACTTTT	58.870	43.478	0.00	0.00	0.00	2.27
1436	1447	1.248486	CCTTGACGACTGAGGAGACA	58.752	55.000	0.00	0.00	32.11	3.41
1447	1458	1.585006	GCGAGAAGACCCTTGACGA	59.415	57.895	0.00	0.00	0.00	4.20
1448	1459	1.801913	CGCGAGAAGACCCTTGACG	60.802	63.158	0.00	0.00	0.00	4.35
1449	1460	2.095252	GCGCGAGAAGACCCTTGAC	61.095	63.158	12.10	0.00	0.00	3.18
1533	1544	4.037446	GTCTTGTGAGAGAGAGTCACTTGT	59.963	45.833	4.96	0.00	44.02	3.16
1590	1601	4.823442	ACAACAATGAATGCACTTCTGAGA	59.177	37.500	0.00	0.00	34.75	3.27
1591	1602	5.117355	ACAACAATGAATGCACTTCTGAG	57.883	39.130	0.00	0.00	34.75	3.35
1601	1612	7.008266	GGTTTCGCTATACAACAACAATGAATG	59.992	37.037	0.00	0.00	0.00	2.67
1602	1613	7.027161	GGTTTCGCTATACAACAACAATGAAT	58.973	34.615	0.00	0.00	0.00	2.57
1663	1674	4.045207	ACCCTGATCTGGATAGATAGCTCA	59.955	45.833	19.59	0.00	43.63	4.26
1782	1793	5.163237	CGAATCCCTAACTCCCCATTCTTTA	60.163	44.000	0.00	0.00	0.00	1.85
1802	1813	3.081804	CTGGCTACAAAGGAAACCGAAT	58.918	45.455	0.00	0.00	0.00	3.34
1814	1825	5.860941	TTTGGAATTGAAACTGGCTACAA	57.139	34.783	0.00	0.00	0.00	2.41
1929	1940	0.976641	TACCACAAGCTCTGACCTGG	59.023	55.000	0.00	0.00	0.00	4.45
2009	2020	5.820947	AGTAACGAGGATTGTTCAAACAGTT	59.179	36.000	0.00	0.00	38.69	3.16
2021	2032	8.461249	TTGATTAGCTACTAGTAACGAGGATT	57.539	34.615	3.76	0.00	0.00	3.01
2027	2038	7.917597	TCTGACTTGATTAGCTACTAGTAACG	58.082	38.462	3.76	0.00	0.00	3.18
2101	2112	2.119801	TACGTGGGTGAGTAGAGTCC	57.880	55.000	0.00	0.00	0.00	3.85
2120	2131	3.178865	TCTCCCTTCGTAGGTGGAAAAT	58.821	45.455	7.37	0.00	40.19	1.82
2134	2145	7.084268	AGGATATTTCGATGATTTCTCCCTT	57.916	36.000	0.00	0.00	0.00	3.95
2184	2195	1.140452	ACGCTATCCACTCTCGTCCTA	59.860	52.381	0.00	0.00	0.00	2.94
2202	2213	3.570926	TCTACAGCCTTGTTAGTCACG	57.429	47.619	0.00	0.00	38.76	4.35
2211	2222	4.865365	GCACTACTAACTTCTACAGCCTTG	59.135	45.833	0.00	0.00	0.00	3.61
2212	2223	4.527038	TGCACTACTAACTTCTACAGCCTT	59.473	41.667	0.00	0.00	0.00	4.35
2217	2228	8.896320	TCAAAAATGCACTACTAACTTCTACA	57.104	30.769	0.00	0.00	0.00	2.74
2221	2232	9.899226	ATCTTTCAAAAATGCACTACTAACTTC	57.101	29.630	0.00	0.00	0.00	3.01
2285	2296	1.328430	CCCGTCCCCTCTTACACCTC	61.328	65.000	0.00	0.00	0.00	3.85
2289	2300	2.686106	GGCCCGTCCCCTCTTACA	60.686	66.667	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.