AutoCloner

Multiple sequence alignment - TraesCS7D01G201800

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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	TraesCS7D01G201800	chr7D	100.000	2240	0	0	1	2240	160655441	160653202	0.000000e+00	4137
1	TraesCS7D01G201800	chr7D	82.083	480	58	14	731	1182	160709160	160708681	3.490000e-103	385
2	TraesCS7D01G201800	chr7D	81.875	480	59	14	731	1182	160668495	160668016	1.620000e-101	379
3	TraesCS7D01G201800	chr7D	87.727	220	26	1	731	949	160711095	160710876	2.850000e-64	255
4	TraesCS7D01G201800	chr7A	93.627	1522	60	24	727	2239	161992287	161990794	0.000000e+00	2239
5	TraesCS7D01G201800	chr7A	82.328	481	65	14	721	1182	161996449	161995970	1.250000e-107	399
6	TraesCS7D01G201800	chr7B	92.377	1338	77	12	1	1314	122281682	122280346	0.000000e+00	1882
7	TraesCS7D01G201800	chr7B	82.341	487	55	13	723	1182	122429658	122429176	5.800000e-106	394
8	TraesCS7D01G201800	chr2D	83.265	729	99	14	1	716	102865085	102864367	0.000000e+00	649
9	TraesCS7D01G201800	chr1A	83.194	720	98	21	1	711	561622920	561622215	2.430000e-179	638
10	TraesCS7D01G201800	chr5D	83.263	711	98	14	17	713	527145101	527145804	3.140000e-178	634
11	TraesCS7D01G201800	chr5B	82.542	716	107	12	12	713	326987114	326986403	4.090000e-172	614
12	TraesCS7D01G201800	chr5A	82.555	728	97	19	4	713	673835457	673834742	4.090000e-172	614
13	TraesCS7D01G201800	chr5A	80.654	734	116	18	1	713	472991813	472992541	1.510000e-151	545
14	TraesCS7D01G201800	chr6A	81.729	717	110	19	12	713	560694651	560695361	1.490000e-161	579
15	TraesCS7D01G201800	chr4A	81.604	723	110	17	1	713	623328828	623329537	5.360000e-161	577
16	TraesCS7D01G201800	chrUn	82.083	480	58	14	731	1182	323467298	323467777	3.490000e-103	385
17	TraesCS7D01G201800	chrUn	87.727	220	26	1	731	949	301829834	301830053	2.850000e-64	255

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	TraesCS7D01G201800	chr7D	160653202	160655441	2239	True	4137	4137	100.0000	1	2240	1	chr7D.!!$R1	2239
1	TraesCS7D01G201800	chr7D	160708681	160711095	2414	True	320	385	84.9050	731	1182	2	chr7D.!!$R3	451
2	TraesCS7D01G201800	chr7A	161990794	161996449	5655	True	1319	2239	87.9775	721	2239	2	chr7A.!!$R1	1518
3	TraesCS7D01G201800	chr7B	122280346	122281682	1336	True	1882	1882	92.3770	1	1314	1	chr7B.!!$R1	1313
4	TraesCS7D01G201800	chr2D	102864367	102865085	718	True	649	649	83.2650	1	716	1	chr2D.!!$R1	715
5	TraesCS7D01G201800	chr1A	561622215	561622920	705	True	638	638	83.1940	1	711	1	chr1A.!!$R1	710
6	TraesCS7D01G201800	chr5D	527145101	527145804	703	False	634	634	83.2630	17	713	1	chr5D.!!$F1	696
7	TraesCS7D01G201800	chr5B	326986403	326987114	711	True	614	614	82.5420	12	713	1	chr5B.!!$R1	701
8	TraesCS7D01G201800	chr5A	673834742	673835457	715	True	614	614	82.5550	4	713	1	chr5A.!!$R1	709
9	TraesCS7D01G201800	chr5A	472991813	472992541	728	False	545	545	80.6540	1	713	1	chr5A.!!$F1	712
10	TraesCS7D01G201800	chr6A	560694651	560695361	710	False	579	579	81.7290	12	713	1	chr6A.!!$F1	701
11	TraesCS7D01G201800	chr4A	623328828	623329537	709	False	577	577	81.6040	1	713	1	chr4A.!!$F1	712

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
826	4993	0.541392	TTATCTGCCCAGTCGCACAT	59.459	50.0	0.0	0.0	34.35	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2199	6414	0.036952	CGTGTGGAAGATGGCAGAGT	60.037	55.0	0.0	0.0	0.0	3.24	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
218	233	2.439880	TGGTGTGGTTCTGTGTTATCCA	59.560	45.455	0.00	0.00	0.00	3.41
347	366	2.351726	GGTGCACGAGATTGGTATGTTC	59.648	50.000	11.45	0.00	0.00	3.18
386	408	7.591057	TGATGTCGATTGATTTGAAAAACTGTC	59.409	33.333	0.00	0.00	0.00	3.51
671	708	6.609616	ACCCAACTTCAATTAAAGACCTCAAA	59.390	34.615	0.00	0.00	0.00	2.69
728	765	7.938715	AGTGTTATAGTGTTACGGAGGATTAG	58.061	38.462	0.00	0.00	0.00	1.73
730	767	8.840321	GTGTTATAGTGTTACGGAGGATTAGTA	58.160	37.037	0.00	0.00	0.00	1.82
731	768	9.407380	TGTTATAGTGTTACGGAGGATTAGTAA	57.593	33.333	0.00	0.00	0.00	2.24
732	769	9.890352	GTTATAGTGTTACGGAGGATTAGTAAG	57.110	37.037	0.00	0.00	31.91	2.34
734	771	4.708421	AGTGTTACGGAGGATTAGTAAGCA	59.292	41.667	0.00	0.00	31.91	3.91
735	772	5.041940	GTGTTACGGAGGATTAGTAAGCAG	58.958	45.833	0.00	0.00	31.91	4.24
736	773	4.708421	TGTTACGGAGGATTAGTAAGCAGT	59.292	41.667	0.00	0.00	31.91	4.40
771	4938	2.111999	TAGGTGCGGATAGGCATGCC	62.112	60.000	30.12	30.12	45.99	4.40
785	4952	1.745087	GCATGCCGAAAGAATTCTCCA	59.255	47.619	8.78	2.22	33.17	3.86
826	4993	0.541392	TTATCTGCCCAGTCGCACAT	59.459	50.000	0.00	0.00	34.35	3.21
902	5069	5.854010	AAATAGTGCGATACCTGAAGAGA	57.146	39.130	0.00	0.00	0.00	3.10
955	5138	2.174210	AGCACAATCCAGCTATCCACAT	59.826	45.455	0.00	0.00	39.78	3.21
964	5147	3.681897	CCAGCTATCCACATCGCTATTTC	59.318	47.826	0.00	0.00	29.98	2.17
990	5173	3.739300	AGTTAGTTTGTGTGAACCGATCG	59.261	43.478	8.51	8.51	0.00	3.69
994	5177	2.242047	TTGTGTGAACCGATCGGAAA	57.758	45.000	39.55	21.01	38.96	3.13
1183	5392	0.254178	TCTGCAGAATCTTCAGGGGC	59.746	55.000	15.67	0.00	0.00	5.80
1306	5519	4.010667	TGAACTTGGTTTATACACCGCT	57.989	40.909	3.65	0.00	40.09	5.52
1307	5520	3.749088	TGAACTTGGTTTATACACCGCTG	59.251	43.478	3.65	0.00	40.09	5.18
1308	5521	2.706890	ACTTGGTTTATACACCGCTGG	58.293	47.619	3.65	0.00	40.09	4.85
1309	5522	2.039348	ACTTGGTTTATACACCGCTGGT	59.961	45.455	3.65	0.00	40.09	4.00
1354	5567	6.321945	TCGTTGGTGCTTCATACTATAGGTTA	59.678	38.462	4.43	0.00	0.00	2.85
1480	5694	5.867716	CAGTAGTTACTGTCGGCTTTTGTAT	59.132	40.000	10.45	0.00	46.51	2.29
1502	5716	7.693120	TGTATTTTTGTTAACCGCGATATGTTC	59.307	33.333	8.23	0.00	0.00	3.18
1685	5900	0.385473	GCCCACACGTTTGATGTTCG	60.385	55.000	2.58	0.00	0.00	3.95
1690	5905	3.424302	CCACACGTTTGATGTTCGGTATG	60.424	47.826	2.58	0.00	0.00	2.39
1764	5979	5.765182	CCCTCTCGTTCAATTAAGGCATATT	59.235	40.000	0.00	0.00	0.00	1.28
1796	6011	3.333029	TTGGCTCATGATTTCGACAGA	57.667	42.857	0.00	0.00	0.00	3.41
1797	6012	2.897436	TGGCTCATGATTTCGACAGAG	58.103	47.619	0.00	0.00	0.00	3.35
1809	6024	7.132213	TGATTTCGACAGAGTCAACAATTTTC	58.868	34.615	0.00	0.00	32.09	2.29
2000	6215	4.203226	TCAAATATATCGGCAGCAACCAA	58.797	39.130	0.00	0.00	0.00	3.67
2010	6225	3.057174	CGGCAGCAACCAACCTATAAAAA	60.057	43.478	0.00	0.00	0.00	1.94
2018	6233	6.568844	GCAACCAACCTATAAAAACACATCGA	60.569	38.462	0.00	0.00	0.00	3.59
2025	6240	4.875544	ATAAAAACACATCGATCCCACG	57.124	40.909	0.00	0.00	0.00	4.94
2037	6252	1.137872	GATCCCACGCACTCTCTCATT	59.862	52.381	0.00	0.00	0.00	2.57
2070	6285	0.606130	AGTGCCAACATGCGACATCA	60.606	50.000	0.00	0.00	0.00	3.07
2084	6299	5.769367	TGCGACATCATAGGACTAATGTAC	58.231	41.667	0.00	0.00	32.70	2.90
2116	6331	3.565482	TCATCAGCGCAAGAAAATATCCC	59.435	43.478	11.47	0.00	43.02	3.85
2147	6362	8.083462	TGTGTGACTTGATTAACAGATAACAC	57.917	34.615	0.00	0.00	34.95	3.32
2177	6392	0.897863	CTCCCGAAATGGCCCAACAA	60.898	55.000	0.00	0.00	35.87	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
347	366	2.035449	TCGACATCAACCGGCCTATAAG	59.965	50.000	0.00	0.00	0.00	1.73
386	408	4.457603	TGGTTTATGATTTTGACCAGGTCG	59.542	41.667	15.24	0.00	35.58	4.79
652	689	8.076178	ACGTTCATTTGAGGTCTTTAATTGAAG	58.924	33.333	3.62	3.62	29.61	3.02
689	726	7.550551	ACACTATAACACTACGCTCACTAGTTA	59.449	37.037	0.00	0.00	0.00	2.24
728	765	1.725164	GGACGTTGCACTACTGCTTAC	59.275	52.381	0.00	0.00	44.57	2.34
730	767	0.944311	CGGACGTTGCACTACTGCTT	60.944	55.000	0.00	0.00	44.57	3.91
731	768	1.372997	CGGACGTTGCACTACTGCT	60.373	57.895	0.00	0.00	44.57	4.24
732	769	2.380410	CCGGACGTTGCACTACTGC	61.380	63.158	0.00	0.00	44.52	4.40
734	771	0.895100	TACCCGGACGTTGCACTACT	60.895	55.000	0.73	0.00	0.00	2.57
735	772	0.457337	CTACCCGGACGTTGCACTAC	60.457	60.000	0.73	0.00	0.00	2.73
736	773	1.597797	CCTACCCGGACGTTGCACTA	61.598	60.000	0.73	0.00	33.16	2.74
771	4938	4.310769	ACAGTGAGTGGAGAATTCTTTCG	58.689	43.478	9.87	0.00	36.93	3.46
785	4952	9.088512	GATAATTTGACGAGATAAACAGTGAGT	57.911	33.333	0.00	0.00	0.00	3.41
902	5069	4.147321	AGCACTGTGAGATGGTTGAAATT	58.853	39.130	12.86	0.00	0.00	1.82
955	5138	6.261381	ACACAAACTAACTTTGGAAATAGCGA	59.739	34.615	0.00	0.00	43.32	4.93
964	5147	4.095185	TCGGTTCACACAAACTAACTTTGG	59.905	41.667	0.00	0.00	43.32	3.28
990	5173	8.255905	ACAAAGGATTTCATCATTCTGATTTCC	58.744	33.333	0.00	0.00	35.03	3.13
994	5177	8.033038	CACAACAAAGGATTTCATCATTCTGAT	58.967	33.333	0.00	0.00	35.03	2.90
1007	5195	0.673437	CACCGGCACAACAAAGGATT	59.327	50.000	0.00	0.00	0.00	3.01
1008	5196	0.179004	TCACCGGCACAACAAAGGAT	60.179	50.000	0.00	0.00	0.00	3.24
1009	5197	0.179004	ATCACCGGCACAACAAAGGA	60.179	50.000	0.00	0.00	0.00	3.36
1010	5198	0.240945	GATCACCGGCACAACAAAGG	59.759	55.000	0.00	0.00	0.00	3.11
1011	5199	0.240945	GGATCACCGGCACAACAAAG	59.759	55.000	0.00	0.00	0.00	2.77
1079	5273	4.740431	GCACATTGCCGCCCAACC	62.740	66.667	0.00	0.00	37.42	3.77
1264	5473	0.955919	GTGTAGGCCTGCCAGTTCAC	60.956	60.000	17.99	2.79	38.92	3.18
1265	5474	1.374947	GTGTAGGCCTGCCAGTTCA	59.625	57.895	17.99	0.00	38.92	3.18
1315	5528	2.890311	ACCAACGATGATCCTGCAAAAA	59.110	40.909	0.00	0.00	0.00	1.94
1316	5529	2.228582	CACCAACGATGATCCTGCAAAA	59.771	45.455	0.00	0.00	0.00	2.44
1317	5530	1.811965	CACCAACGATGATCCTGCAAA	59.188	47.619	0.00	0.00	0.00	3.68
1318	5531	1.452110	CACCAACGATGATCCTGCAA	58.548	50.000	0.00	0.00	0.00	4.08
1319	5532	1.026182	GCACCAACGATGATCCTGCA	61.026	55.000	0.00	0.00	0.00	4.41
1320	5533	0.745845	AGCACCAACGATGATCCTGC	60.746	55.000	0.00	0.00	0.00	4.85
1321	5534	1.667724	GAAGCACCAACGATGATCCTG	59.332	52.381	0.00	0.00	0.00	3.86
1322	5535	1.278985	TGAAGCACCAACGATGATCCT	59.721	47.619	0.00	0.00	0.00	3.24
1323	5536	1.737838	TGAAGCACCAACGATGATCC	58.262	50.000	0.00	0.00	0.00	3.36
1324	5537	4.122776	AGTATGAAGCACCAACGATGATC	58.877	43.478	0.00	0.00	0.00	2.92
1325	5538	4.142609	AGTATGAAGCACCAACGATGAT	57.857	40.909	0.00	0.00	0.00	2.45
1326	5539	3.610040	AGTATGAAGCACCAACGATGA	57.390	42.857	0.00	0.00	0.00	2.92
1327	5540	5.635280	CCTATAGTATGAAGCACCAACGATG	59.365	44.000	0.00	0.00	0.00	3.84
1328	5541	5.304614	ACCTATAGTATGAAGCACCAACGAT	59.695	40.000	0.00	0.00	0.00	3.73
1329	5542	4.647853	ACCTATAGTATGAAGCACCAACGA	59.352	41.667	0.00	0.00	0.00	3.85
1330	5543	4.945246	ACCTATAGTATGAAGCACCAACG	58.055	43.478	0.00	0.00	0.00	4.10
1331	5544	8.904099	AATAACCTATAGTATGAAGCACCAAC	57.096	34.615	0.00	0.00	0.00	3.77
1332	5545	9.337396	CAAATAACCTATAGTATGAAGCACCAA	57.663	33.333	0.00	0.00	0.00	3.67
1368	5581	5.976458	ACCATGCAATACCCAAGTTAAATG	58.024	37.500	0.00	0.00	0.00	2.32
1414	5628	5.875910	CACCACCATACACTACGGAAAATTA	59.124	40.000	0.00	0.00	0.00	1.40
1415	5629	4.698304	CACCACCATACACTACGGAAAATT	59.302	41.667	0.00	0.00	0.00	1.82
1464	5678	5.257082	ACAAAAATACAAAAGCCGACAGT	57.743	34.783	0.00	0.00	0.00	3.55
1480	5694	5.080731	CGAACATATCGCGGTTAACAAAAA	58.919	37.500	6.13	0.00	45.89	1.94
1502	5716	5.862924	ATGATTCTTTGTAGTTCACCACG	57.137	39.130	0.00	0.00	0.00	4.94
1577	5791	7.659290	ACTAAATTTTGAAAAAGACGTGACG	57.341	32.000	2.24	2.24	0.00	4.35
1796	6011	5.941788	AGGTCACCTAGAAAATTGTTGACT	58.058	37.500	0.00	0.00	28.47	3.41
1797	6012	7.923414	ATAGGTCACCTAGAAAATTGTTGAC	57.077	36.000	10.07	0.00	39.70	3.18
1809	6024	7.309194	CCAAAACAAAGGAAATAGGTCACCTAG	60.309	40.741	10.07	0.00	39.70	3.02
1889	6104	7.836842	ACTCAGTCAAAACTACAAACCAAATT	58.163	30.769	0.00	0.00	33.25	1.82
1972	6187	7.485913	GGTTGCTGCCGATATATTTGATAAATG	59.514	37.037	0.00	0.00	32.38	2.32
2000	6215	5.820947	GTGGGATCGATGTGTTTTTATAGGT	59.179	40.000	0.54	0.00	0.00	3.08
2010	6225	1.447838	GTGCGTGGGATCGATGTGT	60.448	57.895	0.54	0.00	0.00	3.72
2018	6233	1.198713	AATGAGAGAGTGCGTGGGAT	58.801	50.000	0.00	0.00	0.00	3.85
2025	6240	1.208052	TGCCAGGTAATGAGAGAGTGC	59.792	52.381	0.00	0.00	0.00	4.40
2052	6267	0.452987	ATGATGTCGCATGTTGGCAC	59.547	50.000	0.00	0.00	0.00	5.01
2070	6285	7.783119	TGACCACATGTAGTACATTAGTCCTAT	59.217	37.037	22.43	5.18	36.53	2.57
2084	6299	0.933097	GCGCTGATGACCACATGTAG	59.067	55.000	0.00	0.00	36.82	2.74
2147	6362	4.394300	GCCATTTCGGGAGATATGATTCTG	59.606	45.833	1.52	0.00	46.84	3.02
2157	6372	1.001393	GTTGGGCCATTTCGGGAGA	60.001	57.895	7.26	0.00	34.06	3.71
2197	6412	2.159043	CGTGTGGAAGATGGCAGAGTAT	60.159	50.000	0.00	0.00	0.00	2.12
2198	6413	1.204704	CGTGTGGAAGATGGCAGAGTA	59.795	52.381	0.00	0.00	0.00	2.59
2199	6414	0.036952	CGTGTGGAAGATGGCAGAGT	60.037	55.000	0.00	0.00	0.00	3.24
2200	6415	0.742281	CCGTGTGGAAGATGGCAGAG	60.742	60.000	0.00	0.00	37.49	3.35
2201	6416	1.296392	CCGTGTGGAAGATGGCAGA	59.704	57.895	0.00	0.00	37.49	4.26
2203	6418	2.350895	CCCGTGTGGAAGATGGCA	59.649	61.111	0.00	0.00	34.29	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.