AutoCloner

Multiple sequence alignment - TraesCS1B01G163500

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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	TraesCS1B01G163500	chr1B	100.000	2318	0	0	1	2318	285997882	285995565	0.000000e+00	4281
1	TraesCS1B01G163500	chr5A	95.344	2341	86	10	1	2318	300072958	300075298	0.000000e+00	3698
2	TraesCS1B01G163500	chr5A	95.081	2338	94	9	1	2318	16602940	16600604	0.000000e+00	3661
3	TraesCS1B01G163500	chrUn	95.258	2341	88	10	1	2318	189392518	189394858	0.000000e+00	3687
4	TraesCS1B01G163500	chr2A	95.258	2341	88	13	1	2318	618279977	618277637	0.000000e+00	3687
5	TraesCS1B01G163500	chr7A	95.062	2349	81	15	1	2318	4959817	4962161	0.000000e+00	3663
6	TraesCS1B01G163500	chr7A	93.408	1244	54	12	1	1220	211246918	211248157	0.000000e+00	1818
7	TraesCS1B01G163500	chr6A	95.083	2339	94	9	1	2318	289128611	289130949	0.000000e+00	3663
8	TraesCS1B01G163500	chr7D	95.043	2340	94	10	1	2318	203556366	203554027	0.000000e+00	3659
9	TraesCS1B01G163500	chr7D	95.045	2341	93	10	1	2318	626698511	626696171	0.000000e+00	3659
10	TraesCS1B01G163500	chr7B	95.002	2341	94	11	1	2318	743086178	743088518	0.000000e+00	3653
11	TraesCS1B01G163500	chr3B	94.957	2340	94	12	1	2318	92199583	92201920	0.000000e+00	3646
12	TraesCS1B01G163500	chr1D	94.793	2343	93	13	1	2318	185769436	185771774	0.000000e+00	3624
13	TraesCS1B01G163500	chr1D	93.483	982	34	13	1	956	141321621	141320644	0.000000e+00	1432
14	TraesCS1B01G163500	chr4A	97.917	288	6	0	1	288	67587552	67587265	1.240000e-137	499

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	TraesCS1B01G163500	chr1B	285995565	285997882	2317	True	4281	4281	100.000	1	2318	1	chr1B.!!$R1	2317
1	TraesCS1B01G163500	chr5A	300072958	300075298	2340	False	3698	3698	95.344	1	2318	1	chr5A.!!$F1	2317
2	TraesCS1B01G163500	chr5A	16600604	16602940	2336	True	3661	3661	95.081	1	2318	1	chr5A.!!$R1	2317
3	TraesCS1B01G163500	chrUn	189392518	189394858	2340	False	3687	3687	95.258	1	2318	1	chrUn.!!$F1	2317
4	TraesCS1B01G163500	chr2A	618277637	618279977	2340	True	3687	3687	95.258	1	2318	1	chr2A.!!$R1	2317
5	TraesCS1B01G163500	chr7A	4959817	4962161	2344	False	3663	3663	95.062	1	2318	1	chr7A.!!$F1	2317
6	TraesCS1B01G163500	chr7A	211246918	211248157	1239	False	1818	1818	93.408	1	1220	1	chr7A.!!$F2	1219
7	TraesCS1B01G163500	chr6A	289128611	289130949	2338	False	3663	3663	95.083	1	2318	1	chr6A.!!$F1	2317
8	TraesCS1B01G163500	chr7D	203554027	203556366	2339	True	3659	3659	95.043	1	2318	1	chr7D.!!$R1	2317
9	TraesCS1B01G163500	chr7D	626696171	626698511	2340	True	3659	3659	95.045	1	2318	1	chr7D.!!$R2	2317
10	TraesCS1B01G163500	chr7B	743086178	743088518	2340	False	3653	3653	95.002	1	2318	1	chr7B.!!$F1	2317
11	TraesCS1B01G163500	chr3B	92199583	92201920	2337	False	3646	3646	94.957	1	2318	1	chr3B.!!$F1	2317
12	TraesCS1B01G163500	chr1D	185769436	185771774	2338	False	3624	3624	94.793	1	2318	1	chr1D.!!$F1	2317
13	TraesCS1B01G163500	chr1D	141320644	141321621	977	True	1432	1432	93.483	1	956	1	chr1D.!!$R1	955

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
304	305	0.102481	GCTGGTATTTCTCGAGGCGA	59.898	55.0	13.56	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1397	1427	0.038251	TGCCGCTATGCTCCTATTCG	60.038	55.0	0.0	0.0	0.0	3.34	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
120	121	7.149569	TCTTTGCTTCCAAGAACATAGATTG	57.850	36.000	0.00	0.00	31.52	2.67
174	175	5.648526	GGGTATCTCACTCGCATATCTAGAA	59.351	44.000	0.00	0.00	0.00	2.10
205	206	1.341531	CTCCTGAACGACACCTTCTGT	59.658	52.381	0.00	0.00	34.96	3.41
234	235	1.202099	TGGTGGTATTTCCCGAGGCA	61.202	55.000	0.00	0.00	34.77	4.75
235	236	0.182775	GGTGGTATTTCCCGAGGCAT	59.817	55.000	0.00	0.00	34.77	4.40
285	286	4.151335	CAGGAAACGACAATGACTCTTCTG	59.849	45.833	0.00	0.00	0.00	3.02
288	289	2.681706	ACGACAATGACTCTTCTGCTG	58.318	47.619	0.00	0.00	0.00	4.41
289	290	1.998315	CGACAATGACTCTTCTGCTGG	59.002	52.381	0.00	0.00	0.00	4.85
290	291	2.611473	CGACAATGACTCTTCTGCTGGT	60.611	50.000	0.00	0.00	0.00	4.00
291	292	3.367395	CGACAATGACTCTTCTGCTGGTA	60.367	47.826	0.00	0.00	0.00	3.25
292	293	4.679106	CGACAATGACTCTTCTGCTGGTAT	60.679	45.833	0.00	0.00	0.00	2.73
293	294	5.171339	ACAATGACTCTTCTGCTGGTATT	57.829	39.130	0.00	0.00	0.00	1.89
294	295	5.564550	ACAATGACTCTTCTGCTGGTATTT	58.435	37.500	0.00	0.00	0.00	1.40
295	296	5.645497	ACAATGACTCTTCTGCTGGTATTTC	59.355	40.000	0.00	0.00	0.00	2.17
296	297	5.690464	ATGACTCTTCTGCTGGTATTTCT	57.310	39.130	0.00	0.00	0.00	2.52
297	298	5.078411	TGACTCTTCTGCTGGTATTTCTC	57.922	43.478	0.00	0.00	0.00	2.87
298	299	4.109050	GACTCTTCTGCTGGTATTTCTCG	58.891	47.826	0.00	0.00	0.00	4.04
299	300	3.764434	ACTCTTCTGCTGGTATTTCTCGA	59.236	43.478	0.00	0.00	0.00	4.04
300	301	4.142271	ACTCTTCTGCTGGTATTTCTCGAG	60.142	45.833	5.93	5.93	0.00	4.04
301	302	3.131223	TCTTCTGCTGGTATTTCTCGAGG	59.869	47.826	13.56	0.00	0.00	4.63
302	303	1.137086	TCTGCTGGTATTTCTCGAGGC	59.863	52.381	13.56	5.83	0.00	4.70
304	305	0.102481	GCTGGTATTTCTCGAGGCGA	59.898	55.000	13.56	0.00	0.00	5.54
317	318	2.035449	TCGAGGCGAGGGTAAATATGTG	59.965	50.000	0.00	0.00	0.00	3.21
426	447	2.546795	CGGCTATAGACTCAAAGGGCAG	60.547	54.545	3.21	0.00	0.00	4.85
432	453	2.264455	AGACTCAAAGGGCAGAGACAT	58.736	47.619	0.00	0.00	35.83	3.06
477	503	6.485648	GCTAACTAAAGTCCAACTTCCTTTGA	59.514	38.462	0.00	0.00	37.47	2.69
568	594	6.069331	CCATCCATCTCAATCCAAAATCTCT	58.931	40.000	0.00	0.00	0.00	3.10
583	609	5.850557	AAATCTCTGATCGTCTGTGATCT	57.149	39.130	11.74	0.00	44.12	2.75
584	610	4.834357	ATCTCTGATCGTCTGTGATCTG	57.166	45.455	11.74	11.21	44.12	2.90
675	701	4.722361	AGTTCCTATCGAGAACAAGACC	57.278	45.455	15.79	0.00	44.91	3.85
679	705	3.830178	TCCTATCGAGAACAAGACCACAA	59.170	43.478	0.00	0.00	0.00	3.33
691	717	7.667219	AGAACAAGACCACAAATCAATATGACT	59.333	33.333	0.00	0.00	0.00	3.41
729	755	4.128643	TCGGGTGAATACGTGAAAAAGTT	58.871	39.130	0.00	0.00	0.00	2.66
732	758	6.259608	TCGGGTGAATACGTGAAAAAGTTTTA	59.740	34.615	0.24	0.00	0.00	1.52
748	774	9.569167	AAAAAGTTTTACTTAGCTCAGTGAAAC	57.431	29.630	28.05	28.05	46.31	2.78
762	788	6.049955	TCAGTGAAACGGAATAAGGAAGAT	57.950	37.500	0.00	0.00	45.86	2.40
805	831	4.184079	AGATGCAAGTCAATTTTGAGGC	57.816	40.909	0.00	0.00	37.98	4.70
892	918	2.291346	CCCCTTTTTACCCATCGGACTT	60.291	50.000	0.00	0.00	0.00	3.01
937	964	3.181439	GCTTGCTTTCATAGTCCCCCTAT	60.181	47.826	0.00	0.00	36.79	2.57
1049	1076	3.119495	GCCTTATCACGAAAGCCACATTT	60.119	43.478	0.00	0.00	0.00	2.32
1093	1120	7.709182	CACACGTCATGTTCCCTATAAATAAGA	59.291	37.037	0.00	0.00	40.64	2.10
1094	1121	8.429641	ACACGTCATGTTCCCTATAAATAAGAT	58.570	33.333	0.00	0.00	38.98	2.40
1148	1178	1.009552	TCCTCCTCAAGCCCCTATCAA	59.990	52.381	0.00	0.00	0.00	2.57
1183	1213	5.009610	GGATCTCATCCTGTAGAAGACTCAC	59.990	48.000	0.00	0.00	46.19	3.51
1208	1238	3.369787	CGGATCTATCTAATGGCATGGCA	60.370	47.826	25.52	25.52	0.00	4.92
1289	1319	3.944015	TCTTCACTACTACCGCTTCTACC	59.056	47.826	0.00	0.00	0.00	3.18
1327	1357	4.381825	GCATTGTGGAATAGTGGCATTTCA	60.382	41.667	0.00	0.00	0.00	2.69
1361	1391	7.418337	AAAATGTTCTTAGTGAAAGGGTTGT	57.582	32.000	0.00	0.00	36.30	3.32
1385	1415	0.820871	AAACCGGCAAACTCAAAGCA	59.179	45.000	0.00	0.00	0.00	3.91
1397	1427	3.137533	ACTCAAAGCAGTCTCTGAAAGC	58.862	45.455	0.66	0.00	32.44	3.51
1427	1457	0.952497	ATAGCGGCATCATCCAAGCG	60.952	55.000	1.45	0.00	0.00	4.68
1471	1501	4.049186	GGTCTTCTCGCGCAAATAAGATA	58.951	43.478	8.75	0.00	0.00	1.98
1515	1545	1.920734	TAATGCATGTCACCCGCCCT	61.921	55.000	0.00	0.00	0.00	5.19
1565	1595	6.267699	TCTCACAAGACAGAGAAAGATTACCA	59.732	38.462	0.00	0.00	37.91	3.25
1596	1631	6.893554	TCCAATCCAATTTGATCAGAAGTGAT	59.106	34.615	15.09	6.51	46.75	3.06
1747	1782	6.711277	TGCAATTAGAAACCAGTGACTCTAT	58.289	36.000	0.00	0.00	0.00	1.98
1859	1894	1.132453	CGACATGCGGACTCACTTCTA	59.868	52.381	0.00	0.00	36.03	2.10
1873	1908	7.993183	GGACTCACTTCTATTTTATGGGATGAA	59.007	37.037	0.00	0.00	0.00	2.57
1915	1950	4.062293	TCTTTACGTGGGTGAATCAAGTG	58.938	43.478	0.00	0.00	0.00	3.16
1958	1993	2.237392	GTGGTAGAAGATTGGGCTCTGT	59.763	50.000	0.00	0.00	0.00	3.41
1961	1996	4.721776	TGGTAGAAGATTGGGCTCTGTTAT	59.278	41.667	0.00	0.00	0.00	1.89
1965	2000	3.589951	AGATTGGGCTCTGTTATGCAT	57.410	42.857	3.79	3.79	0.00	3.96
2003	2038	3.045601	AGAAGTACGCATTGCTGACTT	57.954	42.857	19.18	19.18	33.14	3.01
2004	2039	3.403038	AGAAGTACGCATTGCTGACTTT	58.597	40.909	19.75	11.13	30.66	2.66
2011	2046	3.563808	ACGCATTGCTGACTTTCTGTTTA	59.436	39.130	7.12	0.00	0.00	2.01
2056	2091	2.992847	TCAAGTCAGAGTAGGGTGGA	57.007	50.000	0.00	0.00	0.00	4.02
2159	2194	6.378661	AATCATCGAAATATCCTCATCCCA	57.621	37.500	0.00	0.00	0.00	4.37
2218	2253	3.323751	TGACTAAGGAGGCCGTAAAAC	57.676	47.619	0.00	0.00	0.00	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
120	121	1.815003	CATGACCTGGGTTGAAGAAGC	59.185	52.381	0.00	0.00	0.00	3.86
174	175	0.908198	GTTCAGGAGAGATGCTGGGT	59.092	55.000	0.00	0.00	0.00	4.51
205	206	5.206587	GGGAAATACCACCAGTAGAGTCTA	58.793	45.833	0.00	0.00	41.20	2.59
234	235	7.067372	CCGATATGAATGCACATATTTACCCAT	59.933	37.037	10.27	0.00	41.60	4.00
235	236	6.374053	CCGATATGAATGCACATATTTACCCA	59.626	38.462	10.27	0.00	41.60	4.51
285	286	0.102481	TCGCCTCGAGAAATACCAGC	59.898	55.000	15.71	4.91	0.00	4.85
296	297	2.035449	CACATATTTACCCTCGCCTCGA	59.965	50.000	0.00	0.00	0.00	4.04
297	298	2.223971	ACACATATTTACCCTCGCCTCG	60.224	50.000	0.00	0.00	0.00	4.63
298	299	3.131396	CACACATATTTACCCTCGCCTC	58.869	50.000	0.00	0.00	0.00	4.70
299	300	2.769663	TCACACATATTTACCCTCGCCT	59.230	45.455	0.00	0.00	0.00	5.52
300	301	3.188159	TCACACATATTTACCCTCGCC	57.812	47.619	0.00	0.00	0.00	5.54
301	302	3.936453	TGTTCACACATATTTACCCTCGC	59.064	43.478	0.00	0.00	0.00	5.03
302	303	6.509517	CGAATGTTCACACATATTTACCCTCG	60.510	42.308	0.00	0.00	43.34	4.63
304	305	6.177610	ACGAATGTTCACACATATTTACCCT	58.822	36.000	0.00	0.00	43.34	4.34
305	306	6.431198	ACGAATGTTCACACATATTTACCC	57.569	37.500	0.00	0.00	43.34	3.69
306	307	7.123830	GCTACGAATGTTCACACATATTTACC	58.876	38.462	0.00	0.00	43.34	2.85
307	308	7.680982	TGCTACGAATGTTCACACATATTTAC	58.319	34.615	0.00	0.00	43.34	2.01
308	309	7.835634	TGCTACGAATGTTCACACATATTTA	57.164	32.000	0.00	0.00	43.34	1.40
309	310	6.735678	TGCTACGAATGTTCACACATATTT	57.264	33.333	0.00	0.00	43.34	1.40
312	313	5.872070	TGAATGCTACGAATGTTCACACATA	59.128	36.000	0.00	0.00	43.34	2.29
314	315	4.061596	TGAATGCTACGAATGTTCACACA	58.938	39.130	0.00	0.00	37.31	3.72
315	316	4.661993	TGAATGCTACGAATGTTCACAC	57.338	40.909	0.00	0.00	0.00	3.82
317	318	5.631026	ACAATGAATGCTACGAATGTTCAC	58.369	37.500	0.00	0.00	32.30	3.18
426	447	2.393271	AAGTACCAGCAGCATGTCTC	57.607	50.000	0.00	0.00	39.31	3.36
477	503	3.056107	TGATCCGTTTCATCCTCTTTCGT	60.056	43.478	0.00	0.00	0.00	3.85
510	536	4.158394	AGTTACGAGTCGGGTAATGCTAAA	59.842	41.667	18.30	0.00	32.94	1.85
568	594	2.166459	GGGTTCAGATCACAGACGATCA	59.834	50.000	0.00	0.00	43.61	2.92
583	609	0.685097	CGGAGGAGAGTTTGGGTTCA	59.315	55.000	0.00	0.00	0.00	3.18
584	610	3.534721	CGGAGGAGAGTTTGGGTTC	57.465	57.895	0.00	0.00	0.00	3.62
729	755	5.204409	TCCGTTTCACTGAGCTAAGTAAA	57.796	39.130	2.48	0.00	0.00	2.01
732	758	3.746045	TTCCGTTTCACTGAGCTAAGT	57.254	42.857	0.00	0.00	0.00	2.24
748	774	7.980099	ACACTACACTTTATCTTCCTTATTCCG	59.020	37.037	0.00	0.00	0.00	4.30
762	788	7.786046	TCTTCCCTTATCACACTACACTTTA	57.214	36.000	0.00	0.00	0.00	1.85
892	918	5.410924	CGTAGGAGATCAAAATGTGAGTCA	58.589	41.667	0.00	0.00	40.43	3.41
937	964	0.749091	CATTGATTCCGGGCTGCTCA	60.749	55.000	0.00	0.00	0.00	4.26
1049	1076	3.372822	GTGTGACTTCCTCAAACGAAACA	59.627	43.478	0.00	0.00	26.84	2.83
1107	1134	5.075067	AGGAAGAAGAGGGGATTTCTGAAAA	59.925	40.000	6.95	0.00	34.09	2.29
1148	1178	2.420687	GGATGAGATCCGCTTGGTCTTT	60.421	50.000	0.00	0.00	40.13	2.52
1172	1202	3.006112	AGATCCGCTGTGAGTCTTCTA	57.994	47.619	0.00	0.00	0.00	2.10
1183	1213	3.599730	TGCCATTAGATAGATCCGCTG	57.400	47.619	0.00	0.00	0.00	5.18
1208	1238	2.073252	TAGATCACATCCGACAGCCT	57.927	50.000	0.00	0.00	0.00	4.58
1289	1319	6.632909	TCCACAATGCTTCTTTGATTTATGG	58.367	36.000	0.00	0.00	0.00	2.74
1361	1391	1.357334	GAGTTTGCCGGTTTTGCGA	59.643	52.632	1.90	0.00	0.00	5.10
1385	1415	3.181480	GCTCCTATTCGCTTTCAGAGACT	60.181	47.826	0.00	0.00	0.00	3.24
1397	1427	0.038251	TGCCGCTATGCTCCTATTCG	60.038	55.000	0.00	0.00	0.00	3.34
1427	1457	2.795175	TGACTGAGGAGACGTGTTTC	57.205	50.000	0.00	0.00	0.00	2.78
1515	1545	4.769488	AGAGTCACTTGCTGTATTGAGAGA	59.231	41.667	0.00	0.00	0.00	3.10
1565	1595	8.313944	TCTGATCAAATTGGATTGGATGAATT	57.686	30.769	0.00	0.00	33.11	2.17
1596	1631	8.908903	AGGTTTCACTATACAACAACAATGAAA	58.091	29.630	0.00	0.00	33.62	2.69
1762	1797	5.991606	CCCATTCTTTCTATCTTACATCGCA	59.008	40.000	0.00	0.00	0.00	5.10
1890	1925	4.610605	TGATTCACCCACGTAAAGAGAA	57.389	40.909	0.00	0.00	0.00	2.87
1894	1929	3.364964	GCACTTGATTCACCCACGTAAAG	60.365	47.826	0.00	0.00	0.00	1.85
1915	1950	2.772287	AGCTCTGACCTAACTTGTTGC	58.228	47.619	0.00	0.00	0.00	4.17
1958	1993	6.994421	TCCTAGTTGAGTGGATATGCATAA	57.006	37.500	11.13	0.00	0.00	1.90
1961	1996	5.425217	TCTTTCCTAGTTGAGTGGATATGCA	59.575	40.000	0.00	0.00	0.00	3.96
1965	2000	7.148120	CGTACTTCTTTCCTAGTTGAGTGGATA	60.148	40.741	0.00	0.00	0.00	2.59
2004	2039	9.236006	ACTAGTAACTAGGATCGTTTAAACAGA	57.764	33.333	18.07	15.15	38.30	3.41
2011	2046	8.970859	TTAGCTACTAGTAACTAGGATCGTTT	57.029	34.615	11.78	0.00	38.30	3.60
2056	2091	0.674534	ACCGACAAGAAGCTTCTCGT	59.325	50.000	28.58	24.32	36.28	4.18
2159	2194	2.890945	CTGTTTTCGGGTTCCCTTTCAT	59.109	45.455	6.31	0.00	0.00	2.57
2197	2232	3.518303	AGTTTTACGGCCTCCTTAGTCAT	59.482	43.478	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.