AutoCloner

Multiple sequence alignment - TraesCS1D01G026800

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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	TraesCS1D01G026800	chr1D	100.000	4091	0	0	1	4091	10807283	10811373	0.000000e+00	7555
1	TraesCS1D01G026800	chr1B	95.442	3203	134	8	847	4040	16260927	16257728	0.000000e+00	5096
2	TraesCS1D01G026800	chr1B	95.411	3203	135	8	847	4040	16296746	16293547	0.000000e+00	5090
3	TraesCS1D01G026800	chr1B	95.348	3203	135	9	847	4040	16256031	16252834	0.000000e+00	5077
4	TraesCS1D01G026800	chr1B	95.317	3203	136	9	847	4040	16251138	16247941	0.000000e+00	5072
5	TraesCS1D01G026800	chr1B	95.220	3201	140	9	847	4038	16273627	16270431	0.000000e+00	5051
6	TraesCS1D01G026800	chr1B	95.064	3201	146	8	847	4040	16246244	16243049	0.000000e+00	5025
7	TraesCS1D01G026800	chr1B	97.079	856	20	4	1	851	16274593	16273738	0.000000e+00	1437
8	TraesCS1D01G026800	chr1B	96.948	852	23	3	1	850	16261889	16261039	0.000000e+00	1426
9	TraesCS1D01G026800	chr1B	96.725	855	23	4	1	850	16297712	16296858	0.000000e+00	1419
10	TraesCS1D01G026800	chr1B	97.282	699	17	2	154	850	16247054	16246356	0.000000e+00	1184
11	TraesCS1D01G026800	chr1B	97.143	700	17	1	154	850	16256842	16256143	0.000000e+00	1179
12	TraesCS1D01G026800	chr1B	97.135	698	19	1	154	850	16251947	16251250	0.000000e+00	1177
13	TraesCS1D01G026800	chr1A	92.453	3326	234	12	622	3937	13082719	13086037	0.000000e+00	4735
14	TraesCS1D01G026800	chrUn	91.286	2892	233	13	1040	3921	2571536	2568654	0.000000e+00	3927
15	TraesCS1D01G026800	chrUn	94.814	1639	77	4	2409	4040	337751964	337750327	0.000000e+00	2549
16	TraesCS1D01G026800	chrUn	97.079	856	20	4	1	851	393576715	393577570	0.000000e+00	1437
17	TraesCS1D01G026800	chrUn	97.363	493	11	1	847	1337	393577681	393578173	0.000000e+00	837
18	TraesCS1D01G026800	chrUn	88.780	205	18	4	3876	4078	2568655	2568454	3.160000e-61	246
19	TraesCS1D01G026800	chr4A	75.639	1917	391	58	633	2520	636680088	636678219	0.000000e+00	883

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	TraesCS1D01G026800	chr1D	10807283	10811373	4090	False	7555.0	7555	100.000000	1	4091	1	chr1D.!!$F1	4090
1	TraesCS1D01G026800	chr1B	16293547	16297712	4165	True	3254.5	5090	96.068000	1	4040	2	chr1B.!!$R3	4039
2	TraesCS1D01G026800	chr1B	16270431	16274593	4162	True	3244.0	5051	96.149500	1	4038	2	chr1B.!!$R2	4037
3	TraesCS1D01G026800	chr1B	16243049	16261889	18840	True	3154.5	5096	96.209875	1	4040	8	chr1B.!!$R1	4039
4	TraesCS1D01G026800	chr1A	13082719	13086037	3318	False	4735.0	4735	92.453000	622	3937	1	chr1A.!!$F1	3315
5	TraesCS1D01G026800	chrUn	337750327	337751964	1637	True	2549.0	2549	94.814000	2409	4040	1	chrUn.!!$R1	1631
6	TraesCS1D01G026800	chrUn	2568454	2571536	3082	True	2086.5	3927	90.033000	1040	4078	2	chrUn.!!$R2	3038
7	TraesCS1D01G026800	chrUn	393576715	393578173	1458	False	1137.0	1437	97.221000	1	1337	2	chrUn.!!$F1	1336
8	TraesCS1D01G026800	chr4A	636678219	636680088	1869	True	883.0	883	75.639000	633	2520	1	chr4A.!!$R1	1887

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
659	5563	0.178995	TCATTGCAGGCAAGTCCACA	60.179	50.000	12.66	0.0	39.47	4.17	F
1185	6327	1.409427	GGAGATGTCCAGTTCTACCCG	59.591	57.143	3.49	0.0	43.31	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1846	11881	1.367840	GCTGGACAGACTCCACGTT	59.632	57.895	3.0	0.0	44.99	3.99	R
3092	13136	0.886563	CTGAAGCAAGGAAAGCCAGG	59.113	55.000	0.0	0.0	36.29	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
45	46	7.899178	AATAACATTCGTAACATGTCTGTGA	57.101	32.000	0.00	0.00	33.54	3.58
96	97	5.914635	GCATACCGATGTTTTGATTATGTGG	59.085	40.000	0.00	0.00	35.30	4.17
131	132	9.764363	TCTATAGCTTGTCCATACTTTATGTTG	57.236	33.333	0.00	0.00	34.36	3.33
202	5101	3.129287	GCAGCATAGCATGTTTACACCTT	59.871	43.478	0.00	0.00	0.00	3.50
206	5106	6.308766	CAGCATAGCATGTTTACACCTTTTTC	59.691	38.462	0.00	0.00	0.00	2.29
219	5121	9.744468	TTTACACCTTTTTCTTTTTGCTAGATC	57.256	29.630	0.00	0.00	0.00	2.75
364	5266	5.417580	ACTTGTTTGTTCCTTTCAGTTAGCA	59.582	36.000	0.00	0.00	0.00	3.49
369	5271	3.135712	TGTTCCTTTCAGTTAGCAGGTCA	59.864	43.478	0.00	0.00	0.00	4.02
409	5311	7.032580	TCAAAATGTACTTGGTTGTTGTTCTG	58.967	34.615	0.00	0.00	0.00	3.02
458	5361	9.498307	CAATAATCAATACGTCACCTTTTTACC	57.502	33.333	0.00	0.00	0.00	2.85
573	5476	9.096823	TGTTACTCCCTGAAAGTTTCTAAGATA	57.903	33.333	16.33	0.70	0.00	1.98
577	5480	9.268282	ACTCCCTGAAAGTTTCTAAGATATGTA	57.732	33.333	16.33	0.00	0.00	2.29
597	5500	4.754618	TGTATGCTGTCTTTTCGAATGTGT	59.245	37.500	0.00	0.00	0.00	3.72
626	5529	5.700722	ATTGTGCAATATATGACCTGCTG	57.299	39.130	8.24	0.00	35.78	4.41
659	5563	0.178995	TCATTGCAGGCAAGTCCACA	60.179	50.000	12.66	0.00	39.47	4.17
1017	6159	2.766263	TGAGATGGTTAGGCCTGTACTG	59.234	50.000	17.99	0.00	38.35	2.74
1035	6177	7.418368	CCTGTACTGTGTCTGAATAAGATGGAT	60.418	40.741	0.00	0.00	37.23	3.41
1136	6278	2.166870	TCATTCAGAATGCCAATGCCAC	59.833	45.455	17.26	0.00	38.77	5.01
1185	6327	1.409427	GGAGATGTCCAGTTCTACCCG	59.591	57.143	3.49	0.00	43.31	5.28
1390	6532	7.978975	CCAAAACTTGTAAAAGAGGATTTGTCA	59.021	33.333	0.00	0.00	0.00	3.58
1413	6555	8.768019	GTCATGTTCATCTATGATCAAATCGAA	58.232	33.333	0.00	0.00	39.23	3.71
1456	6598	4.460382	TGGAGAACCAGAAAGATGAATTGC	59.540	41.667	0.00	0.00	41.77	3.56
1490	6632	2.447047	AGAAGGTTGGGGTGAACTTGAT	59.553	45.455	0.00	0.00	0.00	2.57
1540	6682	3.133691	GCTCTTGTGAAGTGTGTCATGA	58.866	45.455	0.00	0.00	0.00	3.07
1846	11881	1.462616	CGGCATGGGAACTGATTTGA	58.537	50.000	0.00	0.00	0.00	2.69
1953	11988	2.812836	TGATTGGTCTGGATGCATGT	57.187	45.000	2.46	0.00	0.00	3.21
1958	11993	6.545567	TGATTGGTCTGGATGCATGTATAAT	58.454	36.000	2.46	0.00	0.00	1.28
1983	12018	0.320421	GTGCTACCCTGACAAGCGAA	60.320	55.000	0.00	0.00	39.14	4.70
2771	12815	1.672145	GCTTCTCGAACCCACCTACAC	60.672	57.143	0.00	0.00	0.00	2.90
3052	13096	2.169832	AATGGTCTTGGATATCCGCG	57.830	50.000	17.04	10.16	39.43	6.46
3092	13136	1.407575	GCCCTCTTTCCAGAAGTAGCC	60.408	57.143	0.00	0.00	0.00	3.93
3275	13319	6.424812	AGGTTTAGCAACATTCTGAAATTTGC	59.575	34.615	22.24	22.24	38.16	3.68
3291	13335	1.159285	TTGCATCTTCAGGTCAAGCG	58.841	50.000	0.00	0.00	0.00	4.68
3337	13381	4.265073	CCTGCCTAGCTTAGATTTTGTGT	58.735	43.478	0.00	0.00	0.00	3.72
3372	13416	7.620880	ACACATAATCCTAGTTAGCTTTGTCA	58.379	34.615	0.00	0.00	0.00	3.58
3413	13459	2.814805	ATCTCCTGATTTGGTGGTGG	57.185	50.000	0.00	0.00	0.00	4.61
3428	13474	2.368548	GTGGTGGCTTCAAGGGATTTTT	59.631	45.455	0.00	0.00	0.00	1.94
3437	13483	5.466728	GCTTCAAGGGATTTTTCAGGTTTTC	59.533	40.000	0.00	0.00	0.00	2.29
3447	13493	7.657354	GGATTTTTCAGGTTTTCTATGCAAAGT	59.343	33.333	0.00	0.00	0.00	2.66
3462	13508	5.450818	TGCAAAGTAGGGGAATCAATAGT	57.549	39.130	0.00	0.00	0.00	2.12
3518	13567	7.162082	ACTTCATACTCTGTTAGGAACTTTGG	58.838	38.462	0.00	0.00	41.75	3.28
3527	13576	8.350852	TCTGTTAGGAACTTTGGTTGTTTTTA	57.649	30.769	0.00	0.00	41.75	1.52
3556	13607	5.066505	ACCGAACCAAATAGAGAAATGCATC	59.933	40.000	0.00	0.00	0.00	3.91
3557	13608	5.297776	CCGAACCAAATAGAGAAATGCATCT	59.702	40.000	0.00	0.00	0.00	2.90
3695	13746	7.065324	CCTTTGGACATTTGATTGATGAAATGG	59.935	37.037	16.50	3.65	42.92	3.16
3713	13764	0.390209	GGTGTTGATGCCACAATGCC	60.390	55.000	0.00	0.00	34.46	4.40
3715	13766	0.542467	TGTTGATGCCACAATGCCCT	60.542	50.000	0.00	0.00	32.36	5.19
3725	13776	0.040058	ACAATGCCCTCATGCCTTGA	59.960	50.000	7.80	0.00	38.62	3.02
3829	13880	1.080995	GTGCTACTGCTCGAAGCCAG	61.081	60.000	3.71	4.97	41.51	4.85
3848	13899	0.670162	GCTTTGCTGGCAGAACAAGA	59.330	50.000	20.86	4.52	0.00	3.02
3880	13931	2.803155	TTAGTGAGGCCGGCAGCTTG	62.803	60.000	30.85	0.00	43.05	4.01
3939	14034	2.216331	TGTCCAGCCTGCTGTGCTA	61.216	57.895	17.23	0.00	42.15	3.49
3978	18967	2.926250	TGCCAGAAAGTGCAGGGT	59.074	55.556	0.00	0.00	32.77	4.34
4020	19009	8.576442	TGTGGTATATGTATGTATCTCTGTGTG	58.424	37.037	0.00	0.00	0.00	3.82
4071	19062	4.445453	TGCAATTATGTTTTGTGGTGCAA	58.555	34.783	0.00	0.00	37.78	4.08
4072	19063	4.272018	TGCAATTATGTTTTGTGGTGCAAC	59.728	37.500	0.00	0.00	37.78	4.17
4073	19064	4.511082	GCAATTATGTTTTGTGGTGCAACT	59.489	37.500	2.04	0.00	36.72	3.16
4074	19065	5.558653	GCAATTATGTTTTGTGGTGCAACTG	60.559	40.000	2.04	0.00	36.72	3.16
4075	19066	1.938625	ATGTTTTGTGGTGCAACTGC	58.061	45.000	2.04	0.00	36.72	4.40
4089	19080	4.697300	GCAACTGCAGTTATGTTTTGTG	57.303	40.909	30.67	17.21	41.59	3.33
4090	19081	3.490526	GCAACTGCAGTTATGTTTTGTGG	59.509	43.478	30.67	15.56	41.59	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	87	3.104512	AGAAGACCGGACCACATAATCA	58.895	45.455	9.46	0.00	0.00	2.57
96	97	3.243468	GGACAAGCTATAGAAGACCGGAC	60.243	52.174	9.46	0.10	0.00	4.79
394	5296	6.697019	CCATTTACTTCAGAACAACAACCAAG	59.303	38.462	0.00	0.00	0.00	3.61
409	5311	6.791303	TGAAATAATCGCACCCATTTACTTC	58.209	36.000	0.00	0.00	0.00	3.01
493	5396	9.787435	TGAACATACATAAACAGGAACTAAACT	57.213	29.630	0.00	0.00	36.02	2.66
573	5476	5.412594	ACACATTCGAAAAGACAGCATACAT	59.587	36.000	0.00	0.00	0.00	2.29
577	5480	4.516698	AGAACACATTCGAAAAGACAGCAT	59.483	37.500	0.00	0.00	40.04	3.79
597	5500	9.276590	CAGGTCATATATTGCACAATTAGAGAA	57.723	33.333	0.47	0.00	32.50	2.87
1035	6177	4.711355	CCTTGAAGCCCAGGAAATAATTCA	59.289	41.667	0.00	0.00	37.29	2.57
1136	6278	2.292569	GCATCTCCATGTGTTGCCATAG	59.707	50.000	7.40	0.00	31.86	2.23
1185	6327	2.149973	ATGCCACATTTCCCTTCTCC	57.850	50.000	0.00	0.00	0.00	3.71
1390	6532	9.551734	TCTTTCGATTTGATCATAGATGAACAT	57.448	29.630	0.00	0.00	38.98	2.71
1413	6555	0.694771	TGCAGGCTTGGATCACTCTT	59.305	50.000	0.00	0.00	0.00	2.85
1456	6598	1.813513	ACCTTCTGCAACATTCTCCG	58.186	50.000	0.00	0.00	0.00	4.63
1490	6632	5.104776	CCTGTTAGGTTCTTCTCATCATCCA	60.105	44.000	0.00	0.00	0.00	3.41
1835	11870	4.058817	AGACTCCACGTTCAAATCAGTTC	58.941	43.478	0.00	0.00	0.00	3.01
1846	11881	1.367840	GCTGGACAGACTCCACGTT	59.632	57.895	3.00	0.00	44.99	3.99
1953	11988	7.907841	TGTCAGGGTAGCACTCTTTATTATA	57.092	36.000	0.00	0.00	0.00	0.98
1958	11993	3.306780	GCTTGTCAGGGTAGCACTCTTTA	60.307	47.826	0.00	0.00	35.05	1.85
1983	12018	1.733526	GCGTGCAACAACCTCCTTT	59.266	52.632	0.00	0.00	35.74	3.11
2839	12883	3.664107	TCACAAACTCCTCATACACAGC	58.336	45.455	0.00	0.00	0.00	4.40
3052	13096	1.140652	CCTGCCCATCTTCTTCCTCTC	59.859	57.143	0.00	0.00	0.00	3.20
3092	13136	0.886563	CTGAAGCAAGGAAAGCCAGG	59.113	55.000	0.00	0.00	36.29	4.45
3264	13308	5.072055	TGACCTGAAGATGCAAATTTCAGA	58.928	37.500	26.67	13.15	46.71	3.27
3275	13319	1.372087	GCCCGCTTGACCTGAAGATG	61.372	60.000	0.00	0.00	0.00	2.90
3291	13335	5.979517	GCATATCTACAAGAAAATTGTGCCC	59.020	40.000	3.58	0.00	34.11	5.36
3337	13381	8.630054	AACTAGGATTATGTGTTTACTTGCAA	57.370	30.769	0.00	0.00	0.00	4.08
3372	13416	7.177878	AGATATGTCTCCCAAACAAATTCTGT	58.822	34.615	0.00	0.00	41.27	3.41
3413	13459	4.607293	AACCTGAAAAATCCCTTGAAGC	57.393	40.909	0.00	0.00	0.00	3.86
3428	13474	5.253330	CCCTACTTTGCATAGAAAACCTGA	58.747	41.667	11.39	0.00	0.00	3.86
3437	13483	7.227156	ACTATTGATTCCCCTACTTTGCATAG	58.773	38.462	2.27	2.27	0.00	2.23
3447	13493	5.782331	CCAGATCTGACTATTGATTCCCCTA	59.218	44.000	24.62	0.00	0.00	3.53
3518	13567	4.113354	TGGTTCGGTGCAATAAAAACAAC	58.887	39.130	0.00	0.00	0.00	3.32
3527	13576	3.950397	TCTCTATTTGGTTCGGTGCAAT	58.050	40.909	0.00	0.00	0.00	3.56
3556	13607	7.206981	TCTGAAGCTAAATCAGGACAAAAAG	57.793	36.000	12.80	0.00	43.58	2.27
3557	13608	7.765695	ATCTGAAGCTAAATCAGGACAAAAA	57.234	32.000	12.80	0.00	43.58	1.94
3695	13746	0.390209	GGGCATTGTGGCATCAACAC	60.390	55.000	5.86	0.00	45.76	3.32
3715	13766	1.885887	CGGGAAAAACTCAAGGCATGA	59.114	47.619	0.00	0.00	36.38	3.07
3725	13776	0.831711	ATGCTTGGGCGGGAAAAACT	60.832	50.000	0.00	0.00	42.25	2.66
3731	13782	3.961225	ATTGCATGCTTGGGCGGGA	62.961	57.895	20.33	0.00	42.25	5.14
3829	13880	0.670162	TCTTGTTCTGCCAGCAAAGC	59.330	50.000	0.00	0.00	0.00	3.51
3839	13890	1.528586	CAACCGAGCTGTCTTGTTCTG	59.471	52.381	0.00	0.00	0.00	3.02
3848	13899	2.093973	CCTCACTAATCAACCGAGCTGT	60.094	50.000	0.00	0.00	0.00	4.40
3880	13931	6.095720	ACCTCTAGTACTAGATGAACAACAGC	59.904	42.308	30.54	0.00	40.97	4.40
3939	14034	3.070018	GCGATGTTATTATGCTCCTGCT	58.930	45.455	0.00	0.00	40.48	4.24
4042	19033	6.183360	ACCACAAAACATAATTGCAGTGAGAA	60.183	34.615	0.00	0.00	0.00	2.87
4053	19044	4.057432	GCAGTTGCACCACAAAACATAAT	58.943	39.130	0.00	0.00	40.82	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.