AutoCloner

Multiple sequence alignment - TraesCS5B01G409000

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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	TraesCS5B01G409000	chr5B	100.000	2516	0	0	1	2516	584291044	584293559	0.000000e+00	4647.0
1	TraesCS5B01G409000	chr5B	86.328	1024	76	20	735	1706	584245498	584246509	0.000000e+00	1057.0
2	TraesCS5B01G409000	chr5B	84.080	848	74	29	759	1565	584142353	584143180	0.000000e+00	761.0
3	TraesCS5B01G409000	chr5B	80.705	964	92	39	734	1627	584126541	584127480	0.000000e+00	664.0
4	TraesCS5B01G409000	chr5B	93.114	334	21	2	2179	2511	584252842	584253174	2.910000e-134	488.0
5	TraesCS5B01G409000	chr5B	89.888	267	3	3	1704	1946	584250130	584250396	3.120000e-84	322.0
6	TraesCS5B01G409000	chr5D	88.913	1840	126	42	735	2512	476749558	476751381	0.000000e+00	2196.0
7	TraesCS5B01G409000	chr5D	87.177	1279	99	31	546	1782	476784617	476785872	0.000000e+00	1393.0
8	TraesCS5B01G409000	chr5D	84.918	915	79	31	759	1627	476724986	476725887	0.000000e+00	870.0
9	TraesCS5B01G409000	chr5D	81.400	957	106	31	732	1627	476708262	476709207	0.000000e+00	715.0
10	TraesCS5B01G409000	chr5D	87.451	510	46	11	1	508	476782773	476783266	2.810000e-159	571.0
11	TraesCS5B01G409000	chr5A	82.654	1816	188	67	754	2511	596054645	596056391	0.000000e+00	1491.0
12	TraesCS5B01G409000	chr5A	87.797	926	73	14	738	1627	596086523	596087444	0.000000e+00	1048.0
13	TraesCS5B01G409000	chr5A	82.435	928	98	25	738	1627	596044237	596045137	0.000000e+00	750.0
14	TraesCS5B01G409000	chr5A	86.771	446	37	16	64	508	596082658	596083082	6.300000e-131	477.0
15	TraesCS5B01G409000	chr5A	83.505	194	18	9	508	698	596084321	596084503	4.300000e-38	169.0
16	TraesCS5B01G409000	chr5A	83.117	77	13	0	2305	2381	419056547	419056623	1.250000e-08	71.3

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	TraesCS5B01G409000	chr5B	584291044	584293559	2515	False	4647.000000	4647	100.000000	1	2516	1	chr5B.!!$F3	2515
1	TraesCS5B01G409000	chr5B	584142353	584143180	827	False	761.000000	761	84.080000	759	1565	1	chr5B.!!$F2	806
2	TraesCS5B01G409000	chr5B	584126541	584127480	939	False	664.000000	664	80.705000	734	1627	1	chr5B.!!$F1	893
3	TraesCS5B01G409000	chr5B	584245498	584253174	7676	False	622.333333	1057	89.776667	735	2511	3	chr5B.!!$F4	1776
4	TraesCS5B01G409000	chr5D	476749558	476751381	1823	False	2196.000000	2196	88.913000	735	2512	1	chr5D.!!$F3	1777
5	TraesCS5B01G409000	chr5D	476782773	476785872	3099	False	982.000000	1393	87.314000	1	1782	2	chr5D.!!$F4	1781
6	TraesCS5B01G409000	chr5D	476724986	476725887	901	False	870.000000	870	84.918000	759	1627	1	chr5D.!!$F2	868
7	TraesCS5B01G409000	chr5D	476708262	476709207	945	False	715.000000	715	81.400000	732	1627	1	chr5D.!!$F1	895
8	TraesCS5B01G409000	chr5A	596054645	596056391	1746	False	1491.000000	1491	82.654000	754	2511	1	chr5A.!!$F3	1757
9	TraesCS5B01G409000	chr5A	596044237	596045137	900	False	750.000000	750	82.435000	738	1627	1	chr5A.!!$F2	889
10	TraesCS5B01G409000	chr5A	596082658	596087444	4786	False	564.666667	1048	86.024333	64	1627	3	chr5A.!!$F4	1563

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
615	2011	0.179225	GCCGCATTTGACTGTACGTG	60.179	55.0	0.0	0.0	0.0	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1635	5177	0.523125	CACATACCATTTGCCGCGTG	60.523	55.0	4.92	0.0	0.0	5.34	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
21	22	4.224715	GAACTAACCCAAAGAGTTGCAC	57.775	45.455	0.00	0.00	33.61	4.57
32	33	1.207089	AGAGTTGCACGCAAGCCTATA	59.793	47.619	4.35	0.00	45.62	1.31
34	35	2.418628	GAGTTGCACGCAAGCCTATAAA	59.581	45.455	4.35	0.00	45.62	1.40
57	58	5.343307	AAAAGCTCAAAAGTCACCAATGT	57.657	34.783	0.00	0.00	0.00	2.71
60	61	4.460263	AGCTCAAAAGTCACCAATGTGTA	58.540	39.130	0.00	0.00	43.26	2.90
62	63	5.536161	AGCTCAAAAGTCACCAATGTGTATT	59.464	36.000	0.00	0.00	43.26	1.89
88	89	3.215568	CGCGCATGGCCCCATAAA	61.216	61.111	8.75	0.00	38.94	1.40
106	107	7.391148	CCATAAAAGATGGGTTAATATCCGG	57.609	40.000	0.00	0.00	35.58	5.14
133	135	7.382218	CCAATTCTCATTGTCTTGGTTTTACAC	59.618	37.037	0.00	0.00	38.58	2.90
174	176	5.811399	ACAAACTCGAATGAAACTTGTCA	57.189	34.783	0.08	0.00	0.00	3.58
175	177	5.810525	ACAAACTCGAATGAAACTTGTCAG	58.189	37.500	0.08	0.00	0.00	3.51
176	178	5.207768	CAAACTCGAATGAAACTTGTCAGG	58.792	41.667	0.00	0.00	0.00	3.86
189	191	7.437862	TGAAACTTGTCAGGCAATAATTCAAAC	59.562	33.333	7.27	0.00	36.36	2.93
192	194	7.593825	ACTTGTCAGGCAATAATTCAAACTAC	58.406	34.615	0.00	0.00	36.36	2.73
359	362	3.356290	GGGTTTGATTAGCAGGTGATGT	58.644	45.455	0.00	0.00	0.00	3.06
381	384	6.305693	GTGATTTTCACACTCTTTGTAGCT	57.694	37.500	2.85	0.00	46.22	3.32
394	397	6.260271	ACTCTTTGTAGCTCAACCAGTAAAAC	59.740	38.462	0.00	0.00	35.61	2.43
395	398	6.116806	TCTTTGTAGCTCAACCAGTAAAACA	58.883	36.000	0.00	0.00	35.61	2.83
396	399	6.260050	TCTTTGTAGCTCAACCAGTAAAACAG	59.740	38.462	0.00	0.00	35.61	3.16
397	400	5.284861	TGTAGCTCAACCAGTAAAACAGA	57.715	39.130	0.00	0.00	0.00	3.41
398	401	5.865085	TGTAGCTCAACCAGTAAAACAGAT	58.135	37.500	0.00	0.00	0.00	2.90
399	402	6.296026	TGTAGCTCAACCAGTAAAACAGATT	58.704	36.000	0.00	0.00	0.00	2.40
402	405	7.817418	AGCTCAACCAGTAAAACAGATTAAA	57.183	32.000	0.00	0.00	0.00	1.52
497	500	4.980339	AGCCAAACCAGGAATTTGAAAT	57.020	36.364	4.42	0.00	39.01	2.17
544	1935	3.429141	CGGCAAGGAGCTGCACTG	61.429	66.667	8.35	5.44	43.88	3.66
545	1936	2.033141	GGCAAGGAGCTGCACTGA	59.967	61.111	8.35	0.00	44.52	3.41
546	1937	2.039405	GGCAAGGAGCTGCACTGAG	61.039	63.158	8.35	0.00	44.52	3.35
547	1938	2.039405	GCAAGGAGCTGCACTGAGG	61.039	63.158	8.35	0.00	42.17	3.86
548	1939	1.675801	CAAGGAGCTGCACTGAGGA	59.324	57.895	8.35	0.00	0.00	3.71
549	1940	0.673022	CAAGGAGCTGCACTGAGGAC	60.673	60.000	8.35	0.00	0.00	3.85
550	1941	1.835927	AAGGAGCTGCACTGAGGACC	61.836	60.000	8.35	0.00	0.00	4.46
551	1942	2.289532	GGAGCTGCACTGAGGACCT	61.290	63.158	0.00	0.00	0.00	3.85
552	1943	1.079266	GAGCTGCACTGAGGACCTG	60.079	63.158	0.00	0.00	0.00	4.00
553	1944	2.745492	GCTGCACTGAGGACCTGC	60.745	66.667	0.00	0.00	0.00	4.85
554	1945	2.745698	CTGCACTGAGGACCTGCA	59.254	61.111	0.00	1.71	38.60	4.41
579	1975	7.517614	TGTTAGATTGTTTGCTGGATGTTTA	57.482	32.000	0.00	0.00	0.00	2.01
600	1996	1.135699	CATGAAGAACGCATTGCCGC	61.136	55.000	2.41	0.00	0.00	6.53
601	1997	1.585267	ATGAAGAACGCATTGCCGCA	61.585	50.000	2.41	0.00	0.00	5.69
615	2011	0.179225	GCCGCATTTGACTGTACGTG	60.179	55.000	0.00	0.00	0.00	4.49
629	2025	9.866936	TTGACTGTACGTGTAATGAAATAAAAC	57.133	29.630	0.00	0.00	0.00	2.43
636	2032	6.364261	CGTGTAATGAAATAAAACCACGTCA	58.636	36.000	0.00	0.00	39.47	4.35
653	2049	2.733026	CGTCAAAGTATTTCCGAACGGT	59.267	45.455	12.93	0.00	35.03	4.83
686	2084	4.017877	GTGCCTCGCTGTGTGTGC	62.018	66.667	0.00	0.00	0.00	4.57
722	4029	1.535462	CGTGAGGTTTTGCTAGTTGGG	59.465	52.381	0.00	0.00	0.00	4.12
833	4217	2.716828	CGGCTACACGACAACGCTG	61.717	63.158	0.00	0.00	43.96	5.18
881	4285	5.432390	TCCGCTATATATACCTCTTCCTCCT	59.568	44.000	0.00	0.00	0.00	3.69
908	4315	2.360350	CTCCGGCAGCAACCACAT	60.360	61.111	0.00	0.00	0.00	3.21
909	4316	1.973281	CTCCGGCAGCAACCACATT	60.973	57.895	0.00	0.00	0.00	2.71
941	4379	1.003972	CAACAGCGCGAACAAGAGAAA	60.004	47.619	12.10	0.00	0.00	2.52
990	4443	3.326981	CAGCACACACGCGACGAA	61.327	61.111	15.93	0.00	36.85	3.85
1077	4567	2.124236	CTCCGGGAGTACTCGCCT	60.124	66.667	28.36	0.00	38.86	5.52
1628	5162	2.481449	GCTGATGTTAGATCGGACGGTT	60.481	50.000	2.12	0.00	0.00	4.44
1631	5165	3.193903	TGATGTTAGATCGGACGGTTGAA	59.806	43.478	0.00	0.00	0.00	2.69
1635	5177	5.104374	TGTTAGATCGGACGGTTGAAATAC	58.896	41.667	0.00	0.00	0.00	1.89
1648	5190	1.135546	TGAAATACACGCGGCAAATGG	60.136	47.619	12.47	0.00	0.00	3.16
2085	9301	2.607892	GCGCCGTGAGCAAAACTCT	61.608	57.895	0.00	0.00	46.41	3.24
2151	9922	6.496144	AACCCAAGAACTTGTAGAAGTAGT	57.504	37.500	5.58	0.00	41.87	2.73
2153	9924	6.990798	ACCCAAGAACTTGTAGAAGTAGTAC	58.009	40.000	5.58	0.00	41.87	2.73
2163	9934	2.732763	AGAAGTAGTACCCGGGAAGTC	58.267	52.381	32.02	13.95	0.00	3.01
2164	9935	2.311243	AGAAGTAGTACCCGGGAAGTCT	59.689	50.000	32.02	20.25	0.00	3.24
2169	9940	2.547990	AGTACCCGGGAAGTCTTTGAT	58.452	47.619	32.02	1.99	0.00	2.57
2188	11615	9.413734	TCTTTGATGTAGATCAGAAGACTCATA	57.586	33.333	16.41	2.85	39.81	2.15
2205	11632	7.777095	AGACTCATAAGAACTGGTGAAGTATC	58.223	38.462	0.00	0.00	38.56	2.24
2338	11768	1.944709	ACGACAATATTTTAGCGGGGC	59.055	47.619	0.00	0.00	0.00	5.80
2349	11779	2.018355	TAGCGGGGCCAATATACTCA	57.982	50.000	4.39	0.00	0.00	3.41
2392	11827	6.377712	CGTATCCTCCTCTAAACTATAAGGGG	59.622	46.154	0.00	0.00	34.36	4.79
2417	11852	0.730494	GCACATGCGCTTGGTTTCTC	60.730	55.000	24.99	5.79	0.00	2.87
2512	11948	4.358851	CGAAAACAAGAGGAAATGCACAA	58.641	39.130	0.00	0.00	0.00	3.33
2513	11949	4.984161	CGAAAACAAGAGGAAATGCACAAT	59.016	37.500	0.00	0.00	0.00	2.71
2514	11950	5.107760	CGAAAACAAGAGGAAATGCACAATG	60.108	40.000	0.00	0.00	0.00	2.82
2515	11951	4.942761	AACAAGAGGAAATGCACAATGT	57.057	36.364	0.00	0.00	0.00	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	1.034838	TTGCGTGCAACTCTTTGGGT	61.035	50.000	2.58	0.00	32.81	4.51
34	35	5.733676	ACATTGGTGACTTTTGAGCTTTTT	58.266	33.333	0.00	0.00	0.00	1.94
40	41	7.167968	CACAAATACACATTGGTGACTTTTGAG	59.832	37.037	18.64	12.26	45.52	3.02
57	58	2.172179	CGCGCGCACACAAATACA	59.828	55.556	32.61	0.00	0.00	2.29
84	85	5.949952	GGCCGGATATTAACCCATCTTTTAT	59.050	40.000	5.05	0.00	0.00	1.40
85	86	5.163077	TGGCCGGATATTAACCCATCTTTTA	60.163	40.000	5.05	0.00	0.00	1.52
88	89	2.714250	TGGCCGGATATTAACCCATCTT	59.286	45.455	5.05	0.00	0.00	2.40
106	107	4.525912	AACCAAGACAATGAGAATTGGC	57.474	40.909	2.28	0.00	43.40	4.52
150	152	6.027131	TGACAAGTTTCATTCGAGTTTGTTG	58.973	36.000	0.00	0.00	0.00	3.33
359	362	6.054941	TGAGCTACAAAGAGTGTGAAAATCA	58.945	36.000	0.00	0.00	41.89	2.57
461	464	4.576053	GGTTTGGCTTCAAGCTTTCATTTT	59.424	37.500	9.83	0.00	41.99	1.82
497	500	4.950475	TGGCATCCAACGGTTTCAATAATA	59.050	37.500	0.00	0.00	0.00	0.98
542	1933	3.834489	ATCTAACATGCAGGTCCTCAG	57.166	47.619	3.65	0.15	0.00	3.35
543	1934	3.264193	ACAATCTAACATGCAGGTCCTCA	59.736	43.478	3.65	0.00	0.00	3.86
544	1935	3.878778	ACAATCTAACATGCAGGTCCTC	58.121	45.455	3.65	0.00	0.00	3.71
545	1936	4.307032	AACAATCTAACATGCAGGTCCT	57.693	40.909	3.65	0.00	0.00	3.85
546	1937	4.737054	CAAACAATCTAACATGCAGGTCC	58.263	43.478	3.65	0.00	0.00	4.46
547	1938	4.082571	AGCAAACAATCTAACATGCAGGTC	60.083	41.667	3.65	0.00	36.30	3.85
548	1939	3.828451	AGCAAACAATCTAACATGCAGGT	59.172	39.130	0.00	0.00	36.30	4.00
549	1940	4.171005	CAGCAAACAATCTAACATGCAGG	58.829	43.478	0.00	0.00	36.30	4.85
550	1941	4.082625	TCCAGCAAACAATCTAACATGCAG	60.083	41.667	0.00	0.00	36.30	4.41
551	1942	3.825585	TCCAGCAAACAATCTAACATGCA	59.174	39.130	0.00	0.00	36.30	3.96
552	1943	4.439305	TCCAGCAAACAATCTAACATGC	57.561	40.909	0.00	0.00	0.00	4.06
553	1944	5.957798	ACATCCAGCAAACAATCTAACATG	58.042	37.500	0.00	0.00	0.00	3.21
554	1945	6.594788	AACATCCAGCAAACAATCTAACAT	57.405	33.333	0.00	0.00	0.00	2.71
579	1975	1.064505	CGGCAATGCGTTCTTCATGAT	59.935	47.619	0.00	0.00	0.00	2.45
615	2011	8.791355	ACTTTGACGTGGTTTTATTTCATTAC	57.209	30.769	0.00	0.00	0.00	1.89
629	2025	3.422603	CGTTCGGAAATACTTTGACGTGG	60.423	47.826	0.00	0.00	0.00	4.94
636	2032	5.727434	ACTATCACCGTTCGGAAATACTTT	58.273	37.500	18.28	0.00	0.00	2.66
653	2049	4.441495	CGAGGCACAGTCCAAATACTATCA	60.441	45.833	0.00	0.00	0.00	2.15
686	2084	2.476619	CTCACGAGGTTAAGTTGCACAG	59.523	50.000	0.00	0.00	0.00	3.66
729	4044	1.664649	GGGCTTTTCTTTGCGGTGC	60.665	57.895	0.00	0.00	0.00	5.01
908	4315	2.226912	GCGCTGTTGTGGTGGTAATTAA	59.773	45.455	0.00	0.00	0.00	1.40
909	4316	1.807742	GCGCTGTTGTGGTGGTAATTA	59.192	47.619	0.00	0.00	0.00	1.40
941	4379	1.694150	TGCTTGCTACTGTCTGGTTCT	59.306	47.619	0.00	0.00	0.00	3.01
964	4417	1.962822	GTGTGTGCTGCTGCTGCTA	60.963	57.895	27.67	16.36	40.48	3.49
990	4443	1.002134	CAGGCCCATTCCGTCTTGT	60.002	57.895	0.00	0.00	0.00	3.16
1389	4879	1.219522	ACTTCGCCAAGGTTTCGTCG	61.220	55.000	0.00	0.00	33.37	5.12
1547	5075	1.207811	GCTATGTGCAAAAATGCCCCT	59.792	47.619	0.00	0.00	42.31	4.79
1628	5162	1.135546	CCATTTGCCGCGTGTATTTCA	60.136	47.619	4.92	0.00	0.00	2.69
1631	5165	1.740297	TACCATTTGCCGCGTGTATT	58.260	45.000	4.92	0.00	0.00	1.89
1635	5177	0.523125	CACATACCATTTGCCGCGTG	60.523	55.000	4.92	0.00	0.00	5.34
1648	5190	7.305474	CCAACTTGACAAACTAATCCACATAC	58.695	38.462	0.00	0.00	0.00	2.39
2113	9330	6.043854	TCTTGGGTTTAAACAAGTTTGCTT	57.956	33.333	19.57	0.00	43.40	3.91
2151	9922	2.262637	ACATCAAAGACTTCCCGGGTA	58.737	47.619	22.86	10.78	0.00	3.69
2153	9924	2.500098	TCTACATCAAAGACTTCCCGGG	59.500	50.000	16.85	16.85	0.00	5.73
2169	9940	8.681806	CAGTTCTTATGAGTCTTCTGATCTACA	58.318	37.037	0.00	0.00	0.00	2.74
2188	11615	4.593206	TGGTCAGATACTTCACCAGTTCTT	59.407	41.667	0.00	0.00	36.88	2.52
2245	11674	2.723273	CTTTGGGCCTCCGAGTTAAAT	58.277	47.619	4.53	0.00	35.24	1.40
2349	11779	6.518208	GATACGGCTGAGTATCCTTTAGAT	57.482	41.667	0.00	0.00	44.28	1.98
2392	11827	2.076628	CAAGCGCATGTGCAACGAC	61.077	57.895	31.29	2.55	42.39	4.34
2417	11852	4.320456	ACCGCACCCAGCACTCTG	62.320	66.667	0.00	0.00	46.13	3.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.