AutoCloner

Multiple sequence alignment - TraesCS2D01G075900

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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	TraesCS2D01G075900	chr2D	100.000	2893	0	0	1	2893	32504587	32501695	0.000000e+00	5343
1	TraesCS2D01G075900	chr2A	96.009	2130	67	12	7	2128	35528611	35526492	0.000000e+00	3446
2	TraesCS2D01G075900	chr2A	87.306	1095	105	13	716	1793	35589513	35588436	0.000000e+00	1221
3	TraesCS2D01G075900	chr2A	95.226	775	30	4	2123	2893	35526154	35525383	0.000000e+00	1219
4	TraesCS2D01G075900	chr2A	84.354	147	16	4	1842	1982	35586607	35586462	1.400000e-28	137
5	TraesCS2D01G075900	chr2A	94.444	72	4	0	1776	1847	35588418	35588347	8.470000e-21	111
6	TraesCS2D01G075900	chr2B	94.964	1549	54	9	740	2277	53512229	53510694	0.000000e+00	2407
7	TraesCS2D01G075900	chr2B	86.126	1283	135	19	716	1969	53525114	53523846	0.000000e+00	1343
8	TraesCS2D01G075900	chr2B	92.051	629	33	11	2280	2893	53504281	53503655	0.000000e+00	869
9	TraesCS2D01G075900	chr2B	84.712	556	41	20	1981	2518	53523364	53522835	1.540000e-142	516

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	TraesCS2D01G075900	chr2D	32501695	32504587	2892	True	5343.000000	5343	100.000000	1	2893	1	chr2D.!!$R1	2892
1	TraesCS2D01G075900	chr2A	35525383	35528611	3228	True	2332.500000	3446	95.617500	7	2893	2	chr2A.!!$R1	2886
2	TraesCS2D01G075900	chr2A	35586462	35589513	3051	True	489.666667	1221	88.701333	716	1982	3	chr2A.!!$R2	1266
3	TraesCS2D01G075900	chr2B	53510694	53512229	1535	True	2407.000000	2407	94.964000	740	2277	1	chr2B.!!$R2	1537
4	TraesCS2D01G075900	chr2B	53522835	53525114	2279	True	929.500000	1343	85.419000	716	2518	2	chr2B.!!$R3	1802
5	TraesCS2D01G075900	chr2B	53503655	53504281	626	True	869.000000	869	92.051000	2280	2893	1	chr2B.!!$R1	613

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
913	923	1.144057	CTCCATCGGCCACTGTACC	59.856	63.158	2.24	0.0	0.0	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2592	5253	0.439985	CCTCATGTCGTGACTTTGCG	59.56	55.0	1.23	0.0	32.22	4.85	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
33	34	4.263572	CTTCGTGCCACCCCCACA	62.264	66.667	0.00	0.00	32.85	4.17
79	80	4.441495	CGAGCTGTATACTGATTGGGTTCA	60.441	45.833	13.44	0.00	0.00	3.18
159	160	4.941263	TCCGATCCAAAATAAGTGTCTTGG	59.059	41.667	0.00	0.00	39.80	3.61
213	214	8.036575	ACATAGTGAACCCAATGAATTCAATTG	58.963	33.333	13.09	15.65	34.28	2.32
216	217	6.041865	AGTGAACCCAATGAATTCAATTGTGA	59.958	34.615	13.09	0.00	34.28	3.58
217	218	6.875195	GTGAACCCAATGAATTCAATTGTGAT	59.125	34.615	13.09	4.31	34.28	3.06
281	285	1.164411	CAAGGTGCCAATTACAGCGA	58.836	50.000	0.00	0.00	40.41	4.93
474	479	4.097286	TGTTTGTGGAAAAACTAGCCAGTC	59.903	41.667	0.00	0.00	40.11	3.51
601	606	1.957765	GCAAGTACTCCCTCCGTCCC	61.958	65.000	0.00	0.00	0.00	4.46
665	670	5.755861	ACCACAACAATAATTTTGAAACGGG	59.244	36.000	7.18	0.00	0.00	5.28
693	698	8.999431	TGAGTAATTAAGTTAACTGCTCTTTGG	58.001	33.333	18.65	0.00	0.00	3.28
698	703	5.668558	AAGTTAACTGCTCTTTGGTTACG	57.331	39.130	9.34	0.00	0.00	3.18
828	833	3.210227	GGCATCTAAAGAGGAAGGAAGC	58.790	50.000	0.00	0.00	0.00	3.86
913	923	1.144057	CTCCATCGGCCACTGTACC	59.856	63.158	2.24	0.00	0.00	3.34
1009	1028	5.163478	ACACGGCCTTAACCACTATAAGTAG	60.163	44.000	0.00	0.00	0.00	2.57
1180	1203	3.493303	GCATGGGAGGGGAGGGAC	61.493	72.222	0.00	0.00	0.00	4.46
1250	1273	1.679305	GGTCTGCCGAGAGTGGAGA	60.679	63.158	0.00	0.00	0.00	3.71
1416	1439	3.309436	TAGCAGTGCCGCGAATGGT	62.309	57.895	12.58	6.41	36.85	3.55
1446	1469	2.224159	TGGGGGACAAGCTGGAGAC	61.224	63.158	0.00	0.00	0.00	3.36
1536	1559	7.229907	GGAGTTTCTAGAGGACCTAGTTATCTG	59.770	44.444	0.00	0.00	44.15	2.90
1758	1788	6.954684	TGTTTCATGTATTAAGGGGCCTAAAA	59.045	34.615	0.84	0.00	0.00	1.52
2076	4369	1.091771	CCCATGCAGCTTGTCTACCG	61.092	60.000	7.47	0.00	0.00	4.02
2144	4786	4.829872	ATATCAACTGGTTCCCGTGTAA	57.170	40.909	0.00	0.00	0.00	2.41
2156	4799	1.202245	CCCGTGTAAAATCAATGGGCG	60.202	52.381	0.00	0.00	31.62	6.13
2201	4844	6.597832	TCTGTAAATTTGTAACCCCCATTG	57.402	37.500	0.00	0.00	0.00	2.82
2214	4857	3.843619	ACCCCCATTGTCCCATTTAAAAG	59.156	43.478	0.00	0.00	0.00	2.27
2226	4869	4.081198	CCCATTTAAAAGCCTGCCACATTA	60.081	41.667	0.00	0.00	0.00	1.90
2425	5074	4.992688	TGTTCACCAAGATTTGACACAAC	58.007	39.130	0.00	0.00	0.00	3.32
2461	5121	6.949463	TGACATGATATGCCACCAATGAATAT	59.051	34.615	0.00	0.00	0.00	1.28
2469	5129	4.639755	TGCCACCAATGAATATGTGTACTG	59.360	41.667	0.00	0.00	0.00	2.74
2592	5253	7.975616	TGGCAAGCTAAATGATGTAAGAAAATC	59.024	33.333	0.00	0.00	0.00	2.17
2631	5294	6.406370	TGAGGGCAAATATGGAATATACTCG	58.594	40.000	0.00	0.00	38.94	4.18
2713	5382	6.570672	TTGTTTTACCCGCATATGTAAACA	57.429	33.333	4.29	8.76	36.84	2.83
2714	5383	6.570672	TGTTTTACCCGCATATGTAAACAA	57.429	33.333	4.29	0.00	36.84	2.83
2752	5423	7.686438	AGTGTTTATATGAACATGCACTTCA	57.314	32.000	15.28	10.33	41.18	3.02
2858	5530	3.894759	AGCATGTTTCTGCAGGATACAT	58.105	40.909	15.13	16.80	43.76	2.29
2865	5537	6.346096	TGTTTCTGCAGGATACATAGTTACC	58.654	40.000	15.13	0.00	41.41	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	4.995058	TCCCTTCGCCTTGGGGGT	62.995	66.667	3.89	0.00	43.51	4.95
37	38	1.866853	GCTTTGTCCCTTCGCCTTGG	61.867	60.000	0.00	0.00	0.00	3.61
38	39	1.581447	GCTTTGTCCCTTCGCCTTG	59.419	57.895	0.00	0.00	0.00	3.61
130	131	5.123979	ACACTTATTTTGGATCGGAAAGAGC	59.876	40.000	0.00	0.00	33.78	4.09
192	193	6.222389	TCACAATTGAATTCATTGGGTTCAC	58.778	36.000	21.70	0.00	32.10	3.18
413	418	6.154534	TCAACTATAGTAGGCACACATTGAGT	59.845	38.462	5.65	0.00	0.00	3.41
414	419	6.573434	TCAACTATAGTAGGCACACATTGAG	58.427	40.000	5.65	0.00	0.00	3.02
416	421	6.986231	TGATCAACTATAGTAGGCACACATTG	59.014	38.462	5.65	0.00	0.00	2.82
458	463	4.023963	GTCAACTGACTGGCTAGTTTTTCC	60.024	45.833	3.47	0.00	41.65	3.13
474	479	6.192234	ACAAGTATAGTACGAGGTCAACTG	57.808	41.667	0.00	0.00	0.00	3.16
551	556	7.147897	ACGTATTCATGATTTCTCTGACACCTA	60.148	37.037	0.00	0.00	0.00	3.08
624	629	8.327941	TGTTGTGGTTTCATTTCAAATTTGAA	57.672	26.923	26.01	26.01	44.78	2.69
646	651	6.163135	TCACCCCGTTTCAAAATTATTGTT	57.837	33.333	0.00	0.00	0.00	2.83
659	664	7.173735	CAGTTAACTTAATTACTCACCCCGTTT	59.826	37.037	5.07	0.00	0.00	3.60
665	670	8.549338	AAGAGCAGTTAACTTAATTACTCACC	57.451	34.615	5.07	0.00	0.00	4.02
698	703	2.301902	CTGGATCGCGCTTCACTTGC	62.302	60.000	5.56	0.00	0.00	4.01
703	708	0.528466	GTCATCTGGATCGCGCTTCA	60.528	55.000	5.56	0.00	0.00	3.02
828	833	3.862267	CGATCTGCAACTTCTAAGTCCTG	59.138	47.826	0.00	0.00	38.57	3.86
913	923	5.459536	AGCAAGGAGAAGGCTTTAAAAAG	57.540	39.130	0.00	0.00	39.03	2.27
1009	1028	5.047731	AGTTTTAAGAGAAGGATTGCAAGGC	60.048	40.000	4.94	0.00	0.00	4.35
1180	1203	4.849310	CACATACCCACCGCCCCG	62.849	72.222	0.00	0.00	0.00	5.73
1218	1241	2.281970	GACCCAACACCGTTCCCC	60.282	66.667	0.00	0.00	0.00	4.81
1250	1273	1.003355	CTTGCACGGACTCCACCAT	60.003	57.895	0.00	0.00	0.00	3.55
1536	1559	5.010012	ACCATTTCCATCGGATTTAGCATTC	59.990	40.000	0.00	0.00	0.00	2.67
1657	1684	3.983344	GCTGCAAACCATCTTTGTACTTG	59.017	43.478	0.00	0.00	0.00	3.16
1664	1691	2.299326	AGAGGCTGCAAACCATCTTT	57.701	45.000	8.09	0.00	0.00	2.52
1731	1761	5.337788	AGGCCCCTTAATACATGAAACAAA	58.662	37.500	0.00	0.00	0.00	2.83
1758	1788	3.775261	AATCCAAGCAATGTGCCTTTT	57.225	38.095	0.00	0.00	46.52	2.27
1929	3750	4.562082	TGTCTTAACAGTTACCCATCACG	58.438	43.478	0.00	0.00	0.00	4.35
2144	4786	5.596836	AAATGATGTACGCCCATTGATTT	57.403	34.783	7.61	0.00	31.62	2.17
2156	4799	8.157476	ACAGATATGGGGTAGAAAATGATGTAC	58.843	37.037	0.00	0.00	0.00	2.90
2201	4844	1.899142	TGGCAGGCTTTTAAATGGGAC	59.101	47.619	0.00	0.00	0.00	4.46
2214	4857	7.636150	AATTATGAGATATAATGTGGCAGGC	57.364	36.000	0.00	0.00	0.00	4.85
2251	4894	6.698008	TGTATTGATAAAAGCCATGGTCAG	57.302	37.500	14.67	0.00	0.00	3.51
2425	5074	6.932960	TGGCATATCATGTCAAAGTCTATGAG	59.067	38.462	0.00	0.00	42.78	2.90
2461	5121	0.531090	GGTTGACGTGGCAGTACACA	60.531	55.000	0.00	0.00	41.38	3.72
2469	5129	1.265905	CCACTTTTAGGTTGACGTGGC	59.734	52.381	0.00	0.00	35.96	5.01
2556	5216	6.642430	TCATTTAGCTTGCCATATTTTGCTT	58.358	32.000	0.00	0.00	32.72	3.91
2592	5253	0.439985	CCTCATGTCGTGACTTTGCG	59.560	55.000	1.23	0.00	32.22	4.85
2631	5294	8.630917	TCTTGGCAGTTAATAGTACTATCTCAC	58.369	37.037	15.72	12.04	0.00	3.51
2783	5454	5.505173	GCTCATGCAACATGTATTACCTT	57.495	39.130	0.00	0.00	39.41	3.50
2865	5537	3.607741	ACATCTCCAAGCTCATGTTGAG	58.392	45.455	0.08	0.08	46.90	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.