AutoCloner

Multiple sequence alignment - TraesCS7D01G293400

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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	TraesCS7D01G293400	chr7D	100.000	3591	0	0	1	3591	363052423	363048833	0.000000e+00	6632
1	TraesCS7D01G293400	chr7D	88.567	691	63	9	1	682	414494200	414493517	0.000000e+00	824
2	TraesCS7D01G293400	chr7B	96.916	2918	75	10	686	3591	322491535	322488621	0.000000e+00	4876
3	TraesCS7D01G293400	chr7B	91.884	690	47	6	3	685	322492196	322491509	0.000000e+00	955
4	TraesCS7D01G293400	chr7A	97.511	2852	62	4	748	3591	394759950	394762800	0.000000e+00	4865
5	TraesCS7D01G293400	chr5D	90.593	691	53	11	1	684	458001316	458000631	0.000000e+00	905
6	TraesCS7D01G293400	chr5D	88.567	691	68	7	1	685	56803203	56803888	0.000000e+00	828
7	TraesCS7D01G293400	chr2D	89.870	691	58	8	1	685	587269813	587269129	0.000000e+00	878
8	TraesCS7D01G293400	chr2D	89.774	665	53	8	12	668	414995604	414994947	0.000000e+00	837
9	TraesCS7D01G293400	chr2D	91.209	91	7	1	3501	3591	572692229	572692140	4.870000e-24	122
10	TraesCS7D01G293400	chr3B	89.466	693	58	11	1	685	182466520	182467205	0.000000e+00	861
11	TraesCS7D01G293400	chr6D	89.177	693	60	11	1	684	311598953	311598267	0.000000e+00	850
12	TraesCS7D01G293400	chr6D	91.304	92	8	0	3500	3591	348087599	348087690	3.760000e-25	126
13	TraesCS7D01G293400	chr5B	88.584	692	61	10	1	684	108839247	108838566	0.000000e+00	824
14	TraesCS7D01G293400	chr5B	91.304	92	8	0	3500	3591	314297469	314297378	3.760000e-25	126
15	TraesCS7D01G293400	chrUn	100.000	420	0	0	2675	3094	476912478	476912897	0.000000e+00	776
16	TraesCS7D01G293400	chr4D	91.209	91	8	0	3501	3591	9306374	9306284	1.350000e-24	124
17	TraesCS7D01G293400	chr4D	91.209	91	8	0	3501	3591	145579507	145579597	1.350000e-24	124
18	TraesCS7D01G293400	chr4A	89.796	98	8	2	3496	3591	584143269	584143172	1.350000e-24	124
19	TraesCS7D01G293400	chr1A	91.111	90	6	2	3502	3591	568073918	568073831	1.750000e-23	121

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	TraesCS7D01G293400	chr7D	363048833	363052423	3590	True	6632.0	6632	100.000	1	3591	1	chr7D.!!$R1	3590
1	TraesCS7D01G293400	chr7D	414493517	414494200	683	True	824.0	824	88.567	1	682	1	chr7D.!!$R2	681
2	TraesCS7D01G293400	chr7B	322488621	322492196	3575	True	2915.5	4876	94.400	3	3591	2	chr7B.!!$R1	3588
3	TraesCS7D01G293400	chr7A	394759950	394762800	2850	False	4865.0	4865	97.511	748	3591	1	chr7A.!!$F1	2843
4	TraesCS7D01G293400	chr5D	458000631	458001316	685	True	905.0	905	90.593	1	684	1	chr5D.!!$R1	683
5	TraesCS7D01G293400	chr5D	56803203	56803888	685	False	828.0	828	88.567	1	685	1	chr5D.!!$F1	684
6	TraesCS7D01G293400	chr2D	587269129	587269813	684	True	878.0	878	89.870	1	685	1	chr2D.!!$R3	684
7	TraesCS7D01G293400	chr2D	414994947	414995604	657	True	837.0	837	89.774	12	668	1	chr2D.!!$R1	656
8	TraesCS7D01G293400	chr3B	182466520	182467205	685	False	861.0	861	89.466	1	685	1	chr3B.!!$F1	684
9	TraesCS7D01G293400	chr6D	311598267	311598953	686	True	850.0	850	89.177	1	684	1	chr6D.!!$R1	683
10	TraesCS7D01G293400	chr5B	108838566	108839247	681	True	824.0	824	88.584	1	684	1	chr5B.!!$R1	683

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
824	844	0.252197	ACGGGTTAGGTTGGAGATGC	59.748	55.0	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2673	2701	0.111061	ACTGAGCAATGGAGCCAACA	59.889	50.0	0.0	0.0	34.23	3.33	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
19	22	0.525761	GGCACGCTTTCTTTGGCATA	59.474	50.000	0.00	0.00	35.91	3.14
20	23	1.134946	GGCACGCTTTCTTTGGCATAT	59.865	47.619	0.00	0.00	35.91	1.78
283	287	2.376518	AGGGCATTTGGAGTTCTTCAGA	59.623	45.455	0.00	0.00	0.00	3.27
354	362	4.080582	CCTTGTGGGAGGTATGACATGTTA	60.081	45.833	0.00	0.00	37.23	2.41
390	401	1.882623	CATGATCGTCGAGGATGAGGA	59.117	52.381	24.24	6.74	37.20	3.71
432	443	3.843422	TGGAATTTGAGAACATGGGTGT	58.157	40.909	0.00	0.00	41.28	4.16
443	454	4.608170	AACATGGGTGTTCCTATCCAAT	57.392	40.909	0.00	0.00	45.14	3.16
499	514	7.837202	ATTCAAATGCATCAACAAATTCGAT	57.163	28.000	0.00	0.00	0.00	3.59
549	567	5.221481	GGAAGATCTGATTGAGCATCTCTGA	60.221	44.000	0.00	0.00	34.92	3.27
560	578	1.404717	GCATCTCTGAGCGGTGAAAGA	60.405	52.381	0.00	0.00	0.00	2.52
673	693	0.457853	GCTACTTGATCGTGCGGACA	60.458	55.000	8.11	0.00	0.00	4.02
677	697	2.540515	ACTTGATCGTGCGGACATTAG	58.459	47.619	8.11	4.89	0.00	1.73
678	698	2.165641	ACTTGATCGTGCGGACATTAGA	59.834	45.455	8.11	0.00	0.00	2.10
679	699	2.951457	TGATCGTGCGGACATTAGAA	57.049	45.000	8.11	0.00	0.00	2.10
680	700	3.239587	TGATCGTGCGGACATTAGAAA	57.760	42.857	8.11	0.00	0.00	2.52
681	701	3.591023	TGATCGTGCGGACATTAGAAAA	58.409	40.909	8.11	0.00	0.00	2.29
682	702	3.997681	TGATCGTGCGGACATTAGAAAAA	59.002	39.130	8.11	0.00	0.00	1.94
701	721	4.336532	AAAAATACTTGATCGTGCGGAC	57.663	40.909	0.00	0.00	0.00	4.79
702	722	2.961526	AATACTTGATCGTGCGGACT	57.038	45.000	5.27	0.00	0.00	3.85
703	723	4.380841	AAATACTTGATCGTGCGGACTA	57.619	40.909	5.27	0.00	0.00	2.59
731	751	4.755266	ACTAAAAGACCGGATGTATGCT	57.245	40.909	9.46	0.00	0.00	3.79
736	756	2.251818	AGACCGGATGTATGCTGCTAT	58.748	47.619	9.46	0.00	0.00	2.97
746	766	2.742428	ATGCTGCTATGGTTGGATGT	57.258	45.000	0.00	0.00	0.00	3.06
753	773	4.454678	TGCTATGGTTGGATGTCATTCTC	58.545	43.478	0.00	0.00	0.00	2.87
773	793	2.174639	TCCCGCATCCTTGTTTATGGAT	59.825	45.455	0.00	0.00	40.45	3.41
793	813	2.471815	TGGTCCCTCTATTCGTGGAT	57.528	50.000	0.00	0.00	0.00	3.41
796	816	1.344763	GTCCCTCTATTCGTGGATGGG	59.655	57.143	0.00	0.00	34.76	4.00
805	825	6.664714	TCTATTCGTGGATGGGGAAAATTTA	58.335	36.000	0.00	0.00	0.00	1.40
812	832	4.264262	TGGATGGGGAAAATTTACGGGTTA	60.264	41.667	0.00	0.00	0.00	2.85
813	833	4.340097	GGATGGGGAAAATTTACGGGTTAG	59.660	45.833	0.00	0.00	0.00	2.34
815	835	3.075732	TGGGGAAAATTTACGGGTTAGGT	59.924	43.478	0.00	0.00	0.00	3.08
824	844	0.252197	ACGGGTTAGGTTGGAGATGC	59.748	55.000	0.00	0.00	0.00	3.91
828	848	2.124411	GGTTAGGTTGGAGATGCCCTA	58.876	52.381	0.00	0.00	34.97	3.53
898	926	8.879759	CCGATTTTGAGTTTTAGCTACTGATTA	58.120	33.333	0.00	0.00	0.00	1.75
1525	1553	1.812922	CAGCGCCATCGAGCTCTTT	60.813	57.895	12.85	0.00	44.07	2.52
1635	1663	0.538584	TTCGAGCAGATGCCTGTCAT	59.461	50.000	0.14	0.00	42.35	3.06
2226	2254	2.125461	GCTCGAGCTTGTTTTGCTTT	57.875	45.000	29.88	0.00	41.30	3.51
2447	2475	0.381801	CAAGTGCTTTGAACAGGCGT	59.618	50.000	0.00	0.00	39.21	5.68
3359	3396	4.395854	TGGCAAGTACATTGTTAGAGCATG	59.604	41.667	0.00	0.00	41.29	4.06
3386	3423	7.961326	ACTGCTTTGGTCTAATATTTCCATT	57.039	32.000	0.00	0.00	0.00	3.16
3509	3546	4.345854	CACTGAGTTAAGGTACTCCCTCT	58.654	47.826	0.00	0.00	45.47	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	22	2.291089	TGTCATTGTGAGACCCATGCAT	60.291	45.455	0.00	0.00	35.15	3.96
20	23	1.073603	TGTCATTGTGAGACCCATGCA	59.926	47.619	0.00	0.00	35.15	3.96
80	83	3.366781	GCAAGGATGAGCTTTTCCTTCAC	60.367	47.826	21.93	15.63	47.00	3.18
233	237	5.537674	ACATCCTTTCTTGTTGCTTCTTGAT	59.462	36.000	0.00	0.00	0.00	2.57
283	287	0.099791	CGAACAACTGCAAAACGGGT	59.900	50.000	0.00	0.00	0.00	5.28
354	362	5.297527	ACGATCATGTTGTGCATAATCACAT	59.702	36.000	0.00	0.00	45.26	3.21
390	401	0.955428	AGTTGCGGCAACATCGTCAT	60.955	50.000	38.11	19.39	45.66	3.06
432	443	4.226394	TCTGGTCCGAAAATTGGATAGGAA	59.774	41.667	0.00	0.00	37.93	3.36
443	454	2.940994	TGTGGATTCTGGTCCGAAAA	57.059	45.000	1.19	0.00	41.35	2.29
499	514	1.132453	CTGCTCGTGAGTTGGTCGATA	59.868	52.381	0.00	0.00	33.26	2.92
549	567	0.468226	TGTTGTCCTCTTTCACCGCT	59.532	50.000	0.00	0.00	0.00	5.52
560	578	3.243359	ACATCCCAACATTGTTGTCCT	57.757	42.857	24.01	8.48	34.06	3.85
680	700	4.000988	AGTCCGCACGATCAAGTATTTTT	58.999	39.130	0.00	0.00	0.00	1.94
681	701	3.596214	AGTCCGCACGATCAAGTATTTT	58.404	40.909	0.00	0.00	0.00	1.82
682	702	3.247006	AGTCCGCACGATCAAGTATTT	57.753	42.857	0.00	0.00	0.00	1.40
683	703	2.961526	AGTCCGCACGATCAAGTATT	57.038	45.000	0.00	0.00	0.00	1.89
684	704	4.380841	TTTAGTCCGCACGATCAAGTAT	57.619	40.909	0.00	0.00	0.00	2.12
685	705	3.853831	TTTAGTCCGCACGATCAAGTA	57.146	42.857	0.00	0.00	0.00	2.24
686	706	2.736144	TTTAGTCCGCACGATCAAGT	57.264	45.000	0.00	0.00	0.00	3.16
711	731	3.248602	GCAGCATACATCCGGTCTTTTAG	59.751	47.826	0.00	0.00	0.00	1.85
718	738	1.002430	CCATAGCAGCATACATCCGGT	59.998	52.381	0.00	0.00	0.00	5.28
719	739	1.002430	ACCATAGCAGCATACATCCGG	59.998	52.381	0.00	0.00	0.00	5.14
731	751	4.454678	GAGAATGACATCCAACCATAGCA	58.545	43.478	0.00	0.00	0.00	3.49
736	756	1.065491	CGGGAGAATGACATCCAACCA	60.065	52.381	0.00	0.00	37.33	3.67
746	766	0.911769	ACAAGGATGCGGGAGAATGA	59.088	50.000	0.00	0.00	0.00	2.57
753	773	2.051334	TCCATAAACAAGGATGCGGG	57.949	50.000	0.00	0.00	0.00	6.13
773	793	2.241281	TCCACGAATAGAGGGACCAA	57.759	50.000	0.00	0.00	0.00	3.67
793	813	3.075732	ACCTAACCCGTAAATTTTCCCCA	59.924	43.478	0.00	0.00	0.00	4.96
796	816	4.766373	TCCAACCTAACCCGTAAATTTTCC	59.234	41.667	0.00	0.00	0.00	3.13
805	825	0.252197	GCATCTCCAACCTAACCCGT	59.748	55.000	0.00	0.00	0.00	5.28
812	832	2.091665	CCAATTAGGGCATCTCCAACCT	60.092	50.000	0.00	0.00	36.21	3.50
813	833	2.310538	CCAATTAGGGCATCTCCAACC	58.689	52.381	0.00	0.00	36.21	3.77
815	835	3.756082	AACCAATTAGGGCATCTCCAA	57.244	42.857	0.00	0.00	43.89	3.53
869	897	7.606456	TCAGTAGCTAAAACTCAAAATCGGAAT	59.394	33.333	0.00	0.00	0.00	3.01
898	926	4.236527	GGGGGTTTCATGTAACAGAGAT	57.763	45.455	15.91	0.00	0.00	2.75
1153	1181	1.228490	AGACGGACTTGAGGACGGT	60.228	57.895	0.00	0.00	0.00	4.83
1278	1306	1.831286	GGGGTCGCGGGAATAGAGA	60.831	63.158	6.13	0.00	0.00	3.10
1506	1534	4.887987	AGAGCTCGATGGCGCTGC	62.888	66.667	7.64	2.66	40.58	5.25
1525	1553	2.580815	CGCTCAGGCATCTGGTCA	59.419	61.111	0.00	0.00	41.23	4.02
1635	1663	2.093288	GTGATCCAGGAGATGTTGCTCA	60.093	50.000	0.00	0.00	34.42	4.26
1870	1898	2.037620	CTAGCTGGGAGCAAGCGGAT	62.038	60.000	0.00	0.00	45.56	4.18
2405	2433	1.073199	CAACGACCTCCCCAAGCTT	59.927	57.895	0.00	0.00	0.00	3.74
2447	2475	7.667635	CAGTATGTAATATCCACTCTCTCCAGA	59.332	40.741	0.00	0.00	0.00	3.86
2673	2701	0.111061	ACTGAGCAATGGAGCCAACA	59.889	50.000	0.00	0.00	34.23	3.33
3359	3396	8.276252	TGGAAATATTAGACCAAAGCAGTAAC	57.724	34.615	6.51	0.00	0.00	2.50
3509	3546	7.175293	ACCTAATATGCGGAGTAAACAAAAACA	59.825	33.333	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.