AutoCloner

Multiple sequence alignment - TraesCS6D01G074400

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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	TraesCS6D01G074400	chr6D	100.000	2303	0	0	1	2303	37933108	37935410	0.000000e+00	4253.0
1	TraesCS6D01G074400	chr6D	82.535	1838	184	67	1	1766	37926858	37928630	0.000000e+00	1489.0
2	TraesCS6D01G074400	chr6D	89.491	923	61	18	828	1729	38119724	38120631	0.000000e+00	1134.0
3	TraesCS6D01G074400	chr6D	87.081	805	44	22	1	792	38118963	38119720	0.000000e+00	856.0
4	TraesCS6D01G074400	chr6D	83.641	758	91	21	1540	2272	37923622	37924371	0.000000e+00	682.0
5	TraesCS6D01G074400	chr6A	89.354	1672	117	33	657	2300	49550574	49552212	0.000000e+00	2045.0
6	TraesCS6D01G074400	chr6A	89.931	1162	84	13	828	1976	49196665	49197806	0.000000e+00	1467.0
7	TraesCS6D01G074400	chr6A	88.025	1286	81	25	711	1969	49499535	49500774	0.000000e+00	1454.0
8	TraesCS6D01G074400	chr6A	84.426	1464	148	35	828	2245	49483666	49485095	0.000000e+00	1367.0
9	TraesCS6D01G074400	chr6A	93.452	504	22	2	1797	2300	49202918	49203410	0.000000e+00	737.0
10	TraesCS6D01G074400	chr6A	88.525	610	42	15	868	1459	49201968	49202567	0.000000e+00	713.0
11	TraesCS6D01G074400	chr6A	82.811	797	91	31	1540	2300	49192800	49193586	0.000000e+00	671.0
12	TraesCS6D01G074400	chr6A	89.362	329	17	7	1485	1804	49202561	49202880	4.610000e-107	398.0
13	TraesCS6D01G074400	chr6A	79.572	607	70	33	1	581	49195908	49196486	3.590000e-103	385.0
14	TraesCS6D01G074400	chr6A	87.973	291	20	8	1962	2245	49197832	49198114	1.710000e-86	329.0
15	TraesCS6D01G074400	chr6A	91.515	165	13	1	628	792	49483499	49483662	2.300000e-55	226.0
16	TraesCS6D01G074400	chr6A	96.032	126	5	0	1	126	49483103	49483228	3.000000e-49	206.0
17	TraesCS6D01G074400	chr6A	91.818	110	9	0	683	792	49196552	49196661	1.100000e-33	154.0
18	TraesCS6D01G074400	chr6A	89.157	83	6	2	282	363	49201311	49201391	1.460000e-17	100.0
19	TraesCS6D01G074400	chr6B	92.102	937	45	11	1372	2299	88816852	88817768	0.000000e+00	1293.0
20	TraesCS6D01G074400	chr6B	87.587	1144	93	18	764	1881	88717282	88718402	0.000000e+00	1280.0
21	TraesCS6D01G074400	chr6B	86.997	1069	71	29	639	1681	88735818	88736844	0.000000e+00	1142.0
22	TraesCS6D01G074400	chr6B	83.721	774	91	22	1540	2292	88714139	88714898	0.000000e+00	699.0
23	TraesCS6D01G074400	chr6B	89.369	555	48	5	828	1376	88781212	88781761	0.000000e+00	688.0
24	TraesCS6D01G074400	chr6B	80.987	547	65	21	1	518	88778809	88779345	4.610000e-107	398.0
25	TraesCS6D01G074400	chr6B	81.818	495	40	19	279	744	88716820	88717293	1.010000e-98	370.0
26	TraesCS6D01G074400	chr6B	76.728	593	79	27	1	540	88735237	88735823	2.250000e-70	276.0
27	TraesCS6D01G074400	chr6B	87.500	168	20	1	625	792	88781042	88781208	2.330000e-45	193.0
28	TraesCS6D01G074400	chr6B	91.803	61	4	1	2185	2245	88754962	88755021	1.470000e-12	84.2
29	TraesCS6D01G074400	chr7A	80.877	1072	124	42	925	1941	679004351	679003306	0.000000e+00	769.0
30	TraesCS6D01G074400	chr7A	82.869	718	76	29	683	1372	511011968	511012666	3.270000e-168	601.0
31	TraesCS6D01G074400	chr7D	84.927	617	70	8	683	1295	587150435	587149838	9.100000e-169	603.0
32	TraesCS6D01G074400	chr7D	80.381	734	65	36	687	1376	422152791	422152093	3.440000e-133	484.0
33	TraesCS6D01G074400	chr7D	97.297	37	1	0	286	322	133398234	133398270	1.910000e-06	63.9
34	TraesCS6D01G074400	chr5D	97.436	39	0	1	284	322	454396968	454397005	5.310000e-07	65.8
35	TraesCS6D01G074400	chr7B	91.667	48	1	3	286	330	94750195	94750242	1.910000e-06	63.9

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	TraesCS6D01G074400	chr6D	37933108	37935410	2302	False	4253.000000	4253	100.000000	1	2303	1	chr6D.!!$F1	2302
1	TraesCS6D01G074400	chr6D	37923622	37928630	5008	False	1085.500000	1489	83.088000	1	2272	2	chr6D.!!$F2	2271
2	TraesCS6D01G074400	chr6D	38118963	38120631	1668	False	995.000000	1134	88.286000	1	1729	2	chr6D.!!$F3	1728
3	TraesCS6D01G074400	chr6A	49550574	49552212	1638	False	2045.000000	2045	89.354000	657	2300	1	chr6A.!!$F2	1643
4	TraesCS6D01G074400	chr6A	49499535	49500774	1239	False	1454.000000	1454	88.025000	711	1969	1	chr6A.!!$F1	1258
5	TraesCS6D01G074400	chr6A	49483103	49485095	1992	False	599.666667	1367	90.657667	1	2245	3	chr6A.!!$F4	2244
6	TraesCS6D01G074400	chr6A	49192800	49203410	10610	False	550.444444	1467	88.066778	1	2300	9	chr6A.!!$F3	2299
7	TraesCS6D01G074400	chr6B	88816852	88817768	916	False	1293.000000	1293	92.102000	1372	2299	1	chr6B.!!$F2	927
8	TraesCS6D01G074400	chr6B	88714139	88718402	4263	False	783.000000	1280	84.375333	279	2292	3	chr6B.!!$F3	2013
9	TraesCS6D01G074400	chr6B	88735237	88736844	1607	False	709.000000	1142	81.862500	1	1681	2	chr6B.!!$F4	1680
10	TraesCS6D01G074400	chr6B	88778809	88781761	2952	False	426.333333	688	85.952000	1	1376	3	chr6B.!!$F5	1375
11	TraesCS6D01G074400	chr7A	679003306	679004351	1045	True	769.000000	769	80.877000	925	1941	1	chr7A.!!$R1	1016
12	TraesCS6D01G074400	chr7A	511011968	511012666	698	False	601.000000	601	82.869000	683	1372	1	chr7A.!!$F1	689
13	TraesCS6D01G074400	chr7D	587149838	587150435	597	True	603.000000	603	84.927000	683	1295	1	chr7D.!!$R2	612
14	TraesCS6D01G074400	chr7D	422152093	422152791	698	True	484.000000	484	80.381000	687	1376	1	chr7D.!!$R1	689

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
817	6035	0.401738	CACTCCTCTCCAGCCCAAAA	59.598	55.0	0.0	0.0	0.0	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1991	12712	3.054802	CCTCTGACCCAAGCTAAGAACAT	60.055	47.826	0.0	0.0	0.0	2.71	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
37	3364	6.040166	CACATTCAGAAAAGGGGGAGAATATG	59.960	42.308	0.00	0.00	0.00	1.78
43	3370	1.522900	AGGGGGAGAATATGTGGTGG	58.477	55.000	0.00	0.00	0.00	4.61
64	3391	2.946762	GTTGCACTGAACTCCGGC	59.053	61.111	0.00	0.00	0.00	6.13
435	3907	6.350110	CGGAAAAGGAGCCAAATCAGAAAATA	60.350	38.462	0.00	0.00	0.00	1.40
469	3945	6.659242	CCAGAACCATATACCACTGAAAAACT	59.341	38.462	0.00	0.00	0.00	2.66
498	3974	3.409851	AAAACCACGGAAGAAACGAAC	57.590	42.857	0.00	0.00	34.93	3.95
599	5711	3.734463	TGAACGTAGCCATTCACAAAGA	58.266	40.909	0.00	0.00	29.89	2.52
600	5712	4.130857	TGAACGTAGCCATTCACAAAGAA	58.869	39.130	0.00	0.00	41.28	2.52
602	5714	4.749245	ACGTAGCCATTCACAAAGAAAG	57.251	40.909	0.00	0.00	40.22	2.62
603	5715	4.385825	ACGTAGCCATTCACAAAGAAAGA	58.614	39.130	0.00	0.00	40.22	2.52
604	5716	4.819630	ACGTAGCCATTCACAAAGAAAGAA	59.180	37.500	0.00	0.00	40.22	2.52
605	5717	5.298276	ACGTAGCCATTCACAAAGAAAGAAA	59.702	36.000	0.00	0.00	40.22	2.52
606	5718	6.183360	ACGTAGCCATTCACAAAGAAAGAAAA	60.183	34.615	0.00	0.00	40.22	2.29
607	5719	6.695278	CGTAGCCATTCACAAAGAAAGAAAAA	59.305	34.615	0.00	0.00	40.22	1.94
652	5807	3.783082	AGAAAATTCGAATCTCCCTCCCT	59.217	43.478	11.83	0.00	0.00	4.20
730	5911	5.388371	CCTCCAAACATTTCGCGAAATTTTC	60.388	40.000	37.26	0.00	38.84	2.29
809	6027	1.700368	CTCCCTCCACTCCTCTCCA	59.300	63.158	0.00	0.00	0.00	3.86
813	6031	2.039624	TCCACTCCTCTCCAGCCC	59.960	66.667	0.00	0.00	0.00	5.19
814	6032	2.284921	CCACTCCTCTCCAGCCCA	60.285	66.667	0.00	0.00	0.00	5.36
815	6033	1.920325	CCACTCCTCTCCAGCCCAA	60.920	63.158	0.00	0.00	0.00	4.12
816	6034	1.492133	CCACTCCTCTCCAGCCCAAA	61.492	60.000	0.00	0.00	0.00	3.28
817	6035	0.401738	CACTCCTCTCCAGCCCAAAA	59.598	55.000	0.00	0.00	0.00	2.44
818	6036	1.005215	CACTCCTCTCCAGCCCAAAAT	59.995	52.381	0.00	0.00	0.00	1.82
819	6037	1.713078	ACTCCTCTCCAGCCCAAAATT	59.287	47.619	0.00	0.00	0.00	1.82
820	6038	2.110721	ACTCCTCTCCAGCCCAAAATTT	59.889	45.455	0.00	0.00	0.00	1.82
821	6039	2.757314	CTCCTCTCCAGCCCAAAATTTC	59.243	50.000	0.00	0.00	0.00	2.17
822	6040	1.827344	CCTCTCCAGCCCAAAATTTCC	59.173	52.381	0.00	0.00	0.00	3.13
823	6041	1.827344	CTCTCCAGCCCAAAATTTCCC	59.173	52.381	0.00	0.00	0.00	3.97
824	6042	0.904649	CTCCAGCCCAAAATTTCCCC	59.095	55.000	0.00	0.00	0.00	4.81
825	6043	0.491371	TCCAGCCCAAAATTTCCCCT	59.509	50.000	0.00	0.00	0.00	4.79
999	6266	2.431782	GGCAGCTCTTCTCTTCTCTGAT	59.568	50.000	0.00	0.00	0.00	2.90
1160	6451	0.106149	AACCTCTTCGTTGCCGAGTT	59.894	50.000	0.00	0.00	45.24	3.01
1526	6921	5.690464	ATACTTGGACTTGAGATCTGCTT	57.310	39.130	0.00	0.00	0.00	3.91
1527	6922	3.936564	ACTTGGACTTGAGATCTGCTTC	58.063	45.455	0.00	0.00	0.00	3.86
1528	6923	3.582208	ACTTGGACTTGAGATCTGCTTCT	59.418	43.478	0.00	0.00	0.00	2.85
1529	6924	3.883830	TGGACTTGAGATCTGCTTCTC	57.116	47.619	0.00	5.32	42.10	2.87
1530	6925	2.499289	TGGACTTGAGATCTGCTTCTCC	59.501	50.000	0.00	0.00	41.24	3.71
1531	6926	2.158971	GGACTTGAGATCTGCTTCTCCC	60.159	54.545	0.00	0.00	41.24	4.30
1532	6927	1.836802	ACTTGAGATCTGCTTCTCCCC	59.163	52.381	0.00	0.00	41.24	4.81
1533	6928	1.836166	CTTGAGATCTGCTTCTCCCCA	59.164	52.381	0.00	0.00	41.24	4.96
1548	6945	2.562298	CTCCCCATCTCTAGCTGACATC	59.438	54.545	0.00	0.00	0.00	3.06
1597	6994	6.898041	TCATGTCTTCTGTACGAAAATTTGG	58.102	36.000	0.00	0.00	0.00	3.28
1600	6998	7.789273	TGTCTTCTGTACGAAAATTTGGTTA	57.211	32.000	0.00	0.00	0.00	2.85
1601	6999	8.385898	TGTCTTCTGTACGAAAATTTGGTTAT	57.614	30.769	0.00	0.00	0.00	1.89
1814	7242	9.444600	GGTTTGTTAACATATTCCACTCTTCTA	57.555	33.333	9.56	0.00	35.92	2.10
1818	7246	9.431887	TGTTAACATATTCCACTCTTCTACAAC	57.568	33.333	3.59	0.00	0.00	3.32
1932	7369	4.713553	TGCAAAGATGTCAAGACTAACCA	58.286	39.130	1.53	0.00	0.00	3.67
2008	12729	4.379918	GCAAAGATGTTCTTAGCTTGGGTC	60.380	45.833	0.00	0.00	35.27	4.46
2094	12818	2.736400	GCATTTTGGCATACACTGAGGC	60.736	50.000	0.00	0.00	0.00	4.70
2234	12966	8.611654	TGTTAAAATAGGAAGTGTTGTAGGTC	57.388	34.615	0.00	0.00	0.00	3.85
2251	12983	7.859325	TGTAGGTCTTTTGTAATTAGGCATC	57.141	36.000	0.00	0.00	0.00	3.91
2300	13032	3.812053	CAGCACTAATGAATGGGCTAGTC	59.188	47.826	0.00	0.00	0.00	2.59
2301	13033	3.713764	AGCACTAATGAATGGGCTAGTCT	59.286	43.478	0.00	0.00	0.00	3.24
2302	13034	4.164988	AGCACTAATGAATGGGCTAGTCTT	59.835	41.667	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	3364	3.209097	AGTGCAACGTGCCACCAC	61.209	61.111	13.37	5.90	44.23	4.16
43	3370	1.279840	GGAGTTCAGTGCAACGTGC	59.720	57.895	0.00	0.00	45.86	5.34
54	3381	0.537143	AAATGTGCTGCCGGAGTTCA	60.537	50.000	5.05	4.36	0.00	3.18
374	3824	8.813643	TCGTTTCTTTTTGTGTTTCCTTTTTA	57.186	26.923	0.00	0.00	0.00	1.52
379	3829	7.716768	TTTTTCGTTTCTTTTTGTGTTTCCT	57.283	28.000	0.00	0.00	0.00	3.36
498	3974	5.335949	CGTTACTGTTTCTTGCGTTTATGTG	59.664	40.000	0.00	0.00	0.00	3.21
562	5674	0.916086	TTCACACGGGCCAATCCTAT	59.084	50.000	4.39	0.00	34.39	2.57
618	5730	9.801873	AGATTCGAATTTTCTTTTTCTTTGTGA	57.198	25.926	12.81	0.00	0.00	3.58
620	5732	9.249457	GGAGATTCGAATTTTCTTTTTCTTTGT	57.751	29.630	12.81	0.00	0.00	2.83
621	5733	8.703336	GGGAGATTCGAATTTTCTTTTTCTTTG	58.297	33.333	12.81	0.00	0.00	2.77
622	5734	8.642432	AGGGAGATTCGAATTTTCTTTTTCTTT	58.358	29.630	12.81	0.00	0.00	2.52
623	5735	8.183104	AGGGAGATTCGAATTTTCTTTTTCTT	57.817	30.769	12.81	0.00	0.00	2.52
626	5738	6.071334	GGGAGGGAGATTCGAATTTTCTTTTT	60.071	38.462	12.81	1.97	0.00	1.94
631	5747	4.157849	AGGGAGGGAGATTCGAATTTTC	57.842	45.455	12.81	12.69	0.00	2.29
652	5807	3.853698	AACTTTGGCGCGGGGCTAA	62.854	57.895	26.00	22.62	40.70	3.09
694	5859	4.577988	TGTTTGGAGGAAATCGGGATTA	57.422	40.909	0.00	0.00	0.00	1.75
730	5911	0.169672	CAACAGCCTGCGAATCTTGG	59.830	55.000	0.00	0.00	0.00	3.61
809	6027	2.371841	GTTTCAGGGGAAATTTTGGGCT	59.628	45.455	0.00	0.00	44.32	5.19
813	6031	7.219322	AGATTTGAGTTTCAGGGGAAATTTTG	58.781	34.615	0.00	0.00	44.32	2.44
814	6032	7.379059	AGATTTGAGTTTCAGGGGAAATTTT	57.621	32.000	0.00	0.00	44.32	1.82
815	6033	7.379059	AAGATTTGAGTTTCAGGGGAAATTT	57.621	32.000	0.00	0.00	44.32	1.82
816	6034	7.379059	AAAGATTTGAGTTTCAGGGGAAATT	57.621	32.000	0.00	0.00	44.32	1.82
817	6035	7.071071	TGAAAAGATTTGAGTTTCAGGGGAAAT	59.929	33.333	0.00	0.00	44.32	2.17
818	6036	6.382570	TGAAAAGATTTGAGTTTCAGGGGAAA	59.617	34.615	0.00	0.00	40.60	3.13
819	6037	5.896678	TGAAAAGATTTGAGTTTCAGGGGAA	59.103	36.000	0.00	0.00	36.58	3.97
820	6038	5.301805	GTGAAAAGATTTGAGTTTCAGGGGA	59.698	40.000	0.00	0.00	40.82	4.81
821	6039	5.509670	GGTGAAAAGATTTGAGTTTCAGGGG	60.510	44.000	0.00	0.00	40.82	4.79
822	6040	5.509670	GGGTGAAAAGATTTGAGTTTCAGGG	60.510	44.000	0.00	0.00	40.82	4.45
823	6041	5.509670	GGGGTGAAAAGATTTGAGTTTCAGG	60.510	44.000	0.00	0.00	40.82	3.86
824	6042	5.509670	GGGGGTGAAAAGATTTGAGTTTCAG	60.510	44.000	0.00	0.00	40.82	3.02
825	6043	4.343814	GGGGGTGAAAAGATTTGAGTTTCA	59.656	41.667	0.00	0.00	38.57	2.69
856	6085	2.610873	GAGGTAGGTAGGAGGGAATGG	58.389	57.143	0.00	0.00	0.00	3.16
999	6266	2.817834	GCGCGGTCAACTGCCATA	60.818	61.111	8.83	0.00	45.16	2.74
1260	6581	1.871418	AGTATCTGCCAGGCTTCAGA	58.129	50.000	14.15	15.87	42.72	3.27
1526	6921	1.570979	TGTCAGCTAGAGATGGGGAGA	59.429	52.381	0.00	0.00	31.33	3.71
1527	6922	2.079170	TGTCAGCTAGAGATGGGGAG	57.921	55.000	0.00	0.00	31.33	4.30
1528	6923	2.603021	GATGTCAGCTAGAGATGGGGA	58.397	52.381	0.00	0.00	28.94	4.81
1529	6924	1.622811	GGATGTCAGCTAGAGATGGGG	59.377	57.143	0.00	0.00	28.94	4.96
1530	6925	2.036992	GTGGATGTCAGCTAGAGATGGG	59.963	54.545	0.00	0.00	28.94	4.00
1531	6926	2.697229	TGTGGATGTCAGCTAGAGATGG	59.303	50.000	0.00	0.00	28.94	3.51
1532	6927	4.397481	TTGTGGATGTCAGCTAGAGATG	57.603	45.455	0.00	0.00	28.94	2.90
1533	6928	5.426689	TTTTGTGGATGTCAGCTAGAGAT	57.573	39.130	0.00	0.00	31.99	2.75
1716	7119	9.788960	AGTAAAATCTGAAAACAGAAAGTCAAC	57.211	29.630	4.09	0.25	34.56	3.18
1850	7286	5.221185	GCTGCACATTCATGGAGATTACATT	60.221	40.000	0.00	0.00	40.28	2.71
1907	7344	6.939730	TGGTTAGTCTTGACATCTTTGCATTA	59.060	34.615	3.49	0.00	0.00	1.90
1932	7369	5.882557	CCAGTGCAAGAACCAATATAGACTT	59.117	40.000	0.00	0.00	0.00	3.01
1991	12712	3.054802	CCTCTGACCCAAGCTAAGAACAT	60.055	47.826	0.00	0.00	0.00	2.71
2008	12729	4.774124	TGATGATAGGTTTGAAGCCTCTG	58.226	43.478	3.12	0.00	37.54	3.35
2094	12818	9.853555	TGTAAGTTTCAAAATACATAGCCAATG	57.146	29.630	0.00	0.00	41.74	2.82
2234	12966	7.682021	GCCCACTAAGATGCCTAATTACAAAAG	60.682	40.741	0.00	0.00	0.00	2.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.