AutoCloner

Multiple sequence alignment - TraesCS7A01G286600

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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	TraesCS7A01G286600	chr7A	100.000	2318	0	0	1	2318	335992513	335994830	0.000000e+00	4281
1	TraesCS7A01G286600	chr7A	88.942	208	23	0	2109	2316	290840326	290840119	8.220000e-65	257
2	TraesCS7A01G286600	chr7B	92.052	1082	76	8	685	1765	339208119	339207047	0.000000e+00	1513
3	TraesCS7A01G286600	chr7B	97.004	701	17	3	1	699	339208839	339208141	0.000000e+00	1175
4	TraesCS7A01G286600	chr7B	82.660	1015	160	12	969	1980	367014793	367013792	0.000000e+00	885
5	TraesCS7A01G286600	chr7B	90.756	238	21	1	1761	1998	357910027	357910263	1.340000e-82	316
6	TraesCS7A01G286600	chr7B	89.109	202	22	0	2117	2318	357910662	357910863	3.820000e-63	252
7	TraesCS7A01G286600	chr7D	95.172	725	20	8	1	710	295312012	295311288	0.000000e+00	1131
8	TraesCS7A01G286600	chr7D	92.332	313	23	1	1802	2114	295139771	295139460	5.880000e-121	444
9	TraesCS7A01G286600	chr7D	93.301	209	14	0	2110	2318	295139437	295139229	2.240000e-80	309
10	TraesCS7A01G286600	chr5B	79.557	1355	238	26	769	2114	447128229	447126905	0.000000e+00	931
11	TraesCS7A01G286600	chr5D	78.947	1368	243	35	764	2114	266748005	266746666	0.000000e+00	889
12	TraesCS7A01G286600	chr1B	76.350	1370	271	43	772	2114	5869834	5868491	0.000000e+00	686
13	TraesCS7A01G286600	chr2B	79.123	570	90	19	770	1335	312204059	312204603	1.310000e-97	366
14	TraesCS7A01G286600	chr1A	74.894	705	175	2	1001	1704	556991249	556991952	1.030000e-83	320
15	TraesCS7A01G286600	chr6A	74.716	704	178	0	1001	1704	566599545	566600248	4.810000e-82	315
16	TraesCS7A01G286600	chrUn	73.762	747	186	8	1036	1779	253283780	253284519	3.770000e-73	285
17	TraesCS7A01G286600	chr3B	84.729	203	30	1	2117	2318	752811005	752811207	3.910000e-48	202
18	TraesCS7A01G286600	chr2A	78.010	191	39	3	2110	2299	585678676	585678488	1.460000e-22	117

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	TraesCS7A01G286600	chr7A	335992513	335994830	2317	False	4281.0	4281	100.0000	1	2318	1	chr7A.!!$F1	2317
1	TraesCS7A01G286600	chr7B	339207047	339208839	1792	True	1344.0	1513	94.5280	1	1765	2	chr7B.!!$R2	1764
2	TraesCS7A01G286600	chr7B	367013792	367014793	1001	True	885.0	885	82.6600	969	1980	1	chr7B.!!$R1	1011
3	TraesCS7A01G286600	chr7B	357910027	357910863	836	False	284.0	316	89.9325	1761	2318	2	chr7B.!!$F1	557
4	TraesCS7A01G286600	chr7D	295311288	295312012	724	True	1131.0	1131	95.1720	1	710	1	chr7D.!!$R1	709
5	TraesCS7A01G286600	chr7D	295139229	295139771	542	True	376.5	444	92.8165	1802	2318	2	chr7D.!!$R2	516
6	TraesCS7A01G286600	chr5B	447126905	447128229	1324	True	931.0	931	79.5570	769	2114	1	chr5B.!!$R1	1345
7	TraesCS7A01G286600	chr5D	266746666	266748005	1339	True	889.0	889	78.9470	764	2114	1	chr5D.!!$R1	1350
8	TraesCS7A01G286600	chr1B	5868491	5869834	1343	True	686.0	686	76.3500	772	2114	1	chr1B.!!$R1	1342
9	TraesCS7A01G286600	chr2B	312204059	312204603	544	False	366.0	366	79.1230	770	1335	1	chr2B.!!$F1	565
10	TraesCS7A01G286600	chr1A	556991249	556991952	703	False	320.0	320	74.8940	1001	1704	1	chr1A.!!$F1	703
11	TraesCS7A01G286600	chr6A	566599545	566600248	703	False	315.0	315	74.7160	1001	1704	1	chr6A.!!$F1	703
12	TraesCS7A01G286600	chrUn	253283780	253284519	739	False	285.0	285	73.7620	1036	1779	1	chrUn.!!$F1	743

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
752	804	0.103755	GTAACCCTAGCGCACCTACC	59.896	60.0	11.47	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	2038	0.036875	GCACCCCTGCTTGTCTTAGT	59.963	55.0	0.0	0.0	40.63	2.24	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
67	68	0.395311	TCCTCTACGGCGAACCAGAT	60.395	55.000	16.62	0.00	34.57	2.90
214	215	1.530655	CCCTTCTTGCCACCCGTTT	60.531	57.895	0.00	0.00	0.00	3.60
235	236	6.183360	CGTTTTCATTGCAAGGTAGCAGTATA	60.183	38.462	11.36	0.00	46.54	1.47
322	325	2.789092	GCAGAATCCGATTCGCAACAAG	60.789	50.000	22.19	9.21	43.92	3.16
354	357	1.968493	GAATCGTATAGCCCCAGACCA	59.032	52.381	0.00	0.00	0.00	4.02
373	376	4.101448	GCTGCGGTGACCAGGGAT	62.101	66.667	1.11	0.00	31.62	3.85
516	519	1.334869	CAACGCCAATATGCTCCTTCC	59.665	52.381	0.00	0.00	0.00	3.46
520	523	1.071699	GCCAATATGCTCCTTCCCGTA	59.928	52.381	0.00	0.00	0.00	4.02
524	527	4.058817	CAATATGCTCCTTCCCGTAGTTC	58.941	47.826	0.00	0.00	0.00	3.01
669	686	1.821216	CCCGACCAGCATTAGTTTGT	58.179	50.000	0.00	0.00	0.00	2.83
680	697	6.127925	CCAGCATTAGTTTGTAGCAAATCTGA	60.128	38.462	0.00	0.00	0.00	3.27
710	762	1.153745	GCAATCTCCGTGTCGAGCT	60.154	57.895	0.00	0.00	0.00	4.09
716	768	3.190849	CCGTGTCGAGCTGCCATG	61.191	66.667	0.00	0.00	0.00	3.66
731	783	4.747810	CTGCCATGTAAATTGACTTTCCC	58.252	43.478	0.00	0.00	0.00	3.97
748	800	1.153429	CCTGTAACCCTAGCGCACC	60.153	63.158	11.47	0.00	0.00	5.01
750	802	1.108776	CTGTAACCCTAGCGCACCTA	58.891	55.000	11.47	0.00	0.00	3.08
751	803	0.819582	TGTAACCCTAGCGCACCTAC	59.180	55.000	11.47	2.71	0.00	3.18
752	804	0.103755	GTAACCCTAGCGCACCTACC	59.896	60.000	11.47	0.00	0.00	3.18
761	813	0.240145	GCGCACCTACCACTTTTTCC	59.760	55.000	0.30	0.00	0.00	3.13
765	817	2.148768	CACCTACCACTTTTTCCCGTC	58.851	52.381	0.00	0.00	0.00	4.79
809	863	4.099170	CGTTCCTCTCGTCGCCGT	62.099	66.667	0.00	0.00	35.01	5.68
842	896	0.533032	GACCCGTCTTCCTTCTCCTG	59.467	60.000	0.00	0.00	0.00	3.86
860	914	1.220749	GCGCTGGGTTGAGTATCCA	59.779	57.895	0.00	0.00	0.00	3.41
863	917	2.643551	CGCTGGGTTGAGTATCCATTT	58.356	47.619	0.00	0.00	0.00	2.32
922	977	1.550976	GTCTTGGTTCGGTCTCCTCAT	59.449	52.381	0.00	0.00	0.00	2.90
929	986	1.075970	CGGTCTCCTCATCCTGGGA	60.076	63.158	0.00	0.00	0.00	4.37
965	1023	0.389948	CTTCGCTGGTCGCTAAACCT	60.390	55.000	2.10	0.00	40.20	3.50
976	1034	0.106894	GCTAAACCTGGGGAGATCGG	59.893	60.000	0.00	0.00	0.00	4.18
996	1058	4.925054	TCGGTCTATTTTTCGTTCGACAAT	59.075	37.500	0.00	0.03	0.00	2.71
1205	1272	4.967084	TTAGCACCTACTGGTTCTTTCA	57.033	40.909	0.00	0.00	46.05	2.69
1294	1362	5.011586	TCCAGATGCAATTCAATTGTCTGA	58.988	37.500	23.22	12.20	41.88	3.27
1315	1383	1.757699	GCGATTGGGAGAGAGTTACCT	59.242	52.381	0.00	0.00	0.00	3.08
1424	1493	6.924111	ACAAATTTGAGATATGGGTTCACAC	58.076	36.000	24.64	0.00	0.00	3.82
1447	1516	4.262420	CCATCGACCTTCCAATTGGTTTTT	60.262	41.667	23.76	7.67	36.59	1.94
1465	1534	2.871096	TTATGGGAAAGTGAAGGCGT	57.129	45.000	0.00	0.00	0.00	5.68
1513	1582	2.933260	GACTCGGAGCCATCTTCTTTTC	59.067	50.000	4.58	0.00	0.00	2.29
1598	1671	0.965866	AACTCGCTGATCCGTGGAGA	60.966	55.000	12.02	0.00	0.00	3.71
1600	1673	0.173481	CTCGCTGATCCGTGGAGAAA	59.827	55.000	0.00	0.00	0.00	2.52
1615	1688	4.223923	GTGGAGAAAAGAGGGAGATCTTCA	59.776	45.833	2.72	0.00	38.59	3.02
1887	1961	0.617413	ATGGAGGTGTCTGAAGCCAG	59.383	55.000	0.00	0.00	41.74	4.85
1913	1987	0.319900	GCGCTCTTCAGAACAGTCCA	60.320	55.000	0.00	0.00	0.00	4.02
1932	2006	2.517959	CATGGATCCCATTACCGCAAT	58.482	47.619	9.90	0.00	42.23	3.56
1964	2038	1.210478	GGATGGAGCTGGTCTTAGCAA	59.790	52.381	6.83	0.00	46.07	3.91
2051	2378	0.251653	TACCCAGCAGACCGAGAAGT	60.252	55.000	0.00	0.00	0.00	3.01
2109	2437	5.560567	CGGGGAAAAACAATGAAGCAAAATG	60.561	40.000	0.00	0.00	0.00	2.32
2114	2442	0.722848	CAATGAAGCAAAATGGGCGC	59.277	50.000	0.00	0.00	36.08	6.53
2129	2484	0.598065	GGCGCCATGAGTCTTTTGTT	59.402	50.000	24.80	0.00	0.00	2.83
2130	2485	1.000274	GGCGCCATGAGTCTTTTGTTT	60.000	47.619	24.80	0.00	0.00	2.83
2203	2558	1.143277	TCGCACAAAAGTTTCCCCCTA	59.857	47.619	0.00	0.00	0.00	3.53
2278	2633	8.990163	TTTAAAGAGTACTCTGGGTTTTGATT	57.010	30.769	25.83	14.63	40.36	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
214	215	5.584649	GTGTATACTGCTACCTTGCAATGAA	59.415	40.000	8.84	0.00	42.83	2.57
235	236	6.697019	CGAAAATTCTTGGTTTCTTGATGTGT	59.303	34.615	0.00	0.00	32.63	3.72
322	325	0.747255	TACGATTCTCTGGCTCCTGC	59.253	55.000	0.00	0.00	38.76	4.85
373	376	0.913924	TCCCAGCAAGAGCATCATCA	59.086	50.000	0.00	0.00	45.49	3.07
570	587	1.050204	AAGCAGCAAATCAAAGCCCA	58.950	45.000	0.00	0.00	0.00	5.36
669	686	3.603532	CTCAGGTGCTTCAGATTTGCTA	58.396	45.455	0.00	0.00	0.00	3.49
710	762	4.220382	CAGGGAAAGTCAATTTACATGGCA	59.780	41.667	0.00	0.00	39.39	4.92
716	768	6.008331	AGGGTTACAGGGAAAGTCAATTTAC	58.992	40.000	0.00	0.00	0.00	2.01
731	783	1.108776	TAGGTGCGCTAGGGTTACAG	58.891	55.000	9.73	0.00	0.00	2.74
748	800	5.671493	AGATATGACGGGAAAAAGTGGTAG	58.329	41.667	0.00	0.00	0.00	3.18
750	802	4.569719	AGATATGACGGGAAAAAGTGGT	57.430	40.909	0.00	0.00	0.00	4.16
751	803	5.163652	GGAAAGATATGACGGGAAAAAGTGG	60.164	44.000	0.00	0.00	0.00	4.00
752	804	5.163652	GGGAAAGATATGACGGGAAAAAGTG	60.164	44.000	0.00	0.00	0.00	3.16
761	813	1.000955	CGAGGGGGAAAGATATGACGG	59.999	57.143	0.00	0.00	0.00	4.79
765	817	2.234908	CCTAGCGAGGGGGAAAGATATG	59.765	54.545	4.68	0.00	39.48	1.78
809	863	2.488355	GGTCTCAACGATCGCCGA	59.512	61.111	16.60	10.96	41.76	5.54
842	896	0.179045	ATGGATACTCAACCCAGCGC	60.179	55.000	0.00	0.00	32.90	5.92
860	914	4.540153	CGTGATCGGCCCAGAAAT	57.460	55.556	0.00	0.00	0.00	2.17
922	977	3.508952	AAGAACCCTAATCTCCCAGGA	57.491	47.619	0.00	0.00	33.42	3.86
929	986	6.284459	CAGCGAAGATAAAGAACCCTAATCT	58.716	40.000	0.00	0.00	30.74	2.40
931	988	5.104485	ACCAGCGAAGATAAAGAACCCTAAT	60.104	40.000	0.00	0.00	0.00	1.73
965	1023	3.181469	CGAAAAATAGACCGATCTCCCCA	60.181	47.826	0.00	0.00	36.29	4.96
976	1034	9.409949	CATAAGATTGTCGAACGAAAAATAGAC	57.590	33.333	3.97	0.00	0.00	2.59
1205	1272	0.469917	CCAGGCCGTCCTCATATTGT	59.530	55.000	0.00	0.00	41.93	2.71
1227	1294	1.241315	TTTTGACCGGCCTAGCAAGC	61.241	55.000	0.00	0.00	0.00	4.01
1294	1362	1.757699	GGTAACTCTCTCCCAATCGCT	59.242	52.381	0.00	0.00	0.00	4.93
1424	1493	2.128771	ACCAATTGGAAGGTCGATGG	57.871	50.000	31.22	0.16	38.94	3.51
1447	1516	2.432444	CAACGCCTTCACTTTCCCATA	58.568	47.619	0.00	0.00	0.00	2.74
1465	1534	0.035534	TCGCCAATCTTAGCAGCCAA	60.036	50.000	0.00	0.00	0.00	4.52
1580	1653	0.965866	TTCTCCACGGATCAGCGAGT	60.966	55.000	9.38	0.00	0.00	4.18
1615	1688	4.338682	GGGTAGACACTCATACTTGATCGT	59.661	45.833	0.00	0.00	0.00	3.73
1648	1721	1.133294	TCCCATCATACCGCAGACCTA	60.133	52.381	0.00	0.00	0.00	3.08
1672	1745	3.009033	CCATCCCTGTGTTCCTTGAACTA	59.991	47.826	8.30	0.00	42.39	2.24
1711	1785	6.253512	GCAAGTTTTTGAAGGTCAACACTAAG	59.746	38.462	3.55	2.32	35.89	2.18
1712	1786	6.096695	GCAAGTTTTTGAAGGTCAACACTAA	58.903	36.000	3.55	0.00	35.89	2.24
1713	1787	5.646606	GCAAGTTTTTGAAGGTCAACACTA	58.353	37.500	3.55	0.00	35.89	2.74
1714	1788	4.494484	GCAAGTTTTTGAAGGTCAACACT	58.506	39.130	0.00	0.00	35.89	3.55
1772	1846	3.662759	AGGGTTCTGGTTTCTGTTTCA	57.337	42.857	0.00	0.00	0.00	2.69
1887	1961	4.157958	CTGAAGAGCGCTTGCGGC	62.158	66.667	13.26	0.00	45.69	6.53
1932	2006	1.151921	TCCATCCCAGTGGTGACCA	60.152	57.895	8.74	0.00	40.27	4.02
1964	2038	0.036875	GCACCCCTGCTTGTCTTAGT	59.963	55.000	0.00	0.00	40.63	2.24
2051	2378	3.178046	TCCTCAACACTGTATTGCCCTA	58.822	45.455	0.00	0.00	0.00	3.53
2109	2437	1.244019	ACAAAAGACTCATGGCGCCC	61.244	55.000	26.77	7.06	0.00	6.13
2114	2442	6.762661	ACAATTCCAAAACAAAAGACTCATGG	59.237	34.615	0.00	0.00	0.00	3.66
2129	2484	2.289320	CCAATCCCGCAACAATTCCAAA	60.289	45.455	0.00	0.00	0.00	3.28
2130	2485	1.274728	CCAATCCCGCAACAATTCCAA	59.725	47.619	0.00	0.00	0.00	3.53
2197	2552	5.952347	ACAATACAAAGTACTCTAGGGGG	57.048	43.478	0.00	0.00	0.00	5.40
2203	2558	7.970102	TGGGTTTCTACAATACAAAGTACTCT	58.030	34.615	0.00	0.00	0.00	3.24
2278	2633	6.049149	CGGAGGAGTCAATAGCAAAAGAATA	58.951	40.000	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.