AutoCloner

Multiple sequence alignment - TraesCS4B01G263600

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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	TraesCS4B01G263600	chr4B	100.000	2437	0	0	1	2437	534709524	534711960	0.000000e+00	4501
1	TraesCS4B01G263600	chr2B	93.152	1913	119	9	5	1911	159215123	159213217	0.000000e+00	2796
2	TraesCS4B01G263600	chr2B	83.166	1693	267	17	32	1715	441899135	441897452	0.000000e+00	1531
3	TraesCS4B01G263600	chr2B	95.745	470	16	4	1901	2368	412698949	412699416	0.000000e+00	754
4	TraesCS4B01G263600	chr2B	95.329	471	18	4	1901	2368	412636565	412637034	0.000000e+00	745
5	TraesCS4B01G263600	chr2B	90.789	532	38	10	1911	2437	136263694	136263169	0.000000e+00	701
6	TraesCS4B01G263600	chr2B	97.368	114	3	0	2324	2437	412706629	412706742	6.880000e-46	195
7	TraesCS4B01G263600	chr2B	94.355	124	7	0	2314	2437	412637368	412637491	8.890000e-45	191
8	TraesCS4B01G263600	chr7B	93.182	1892	116	10	4	1890	45045419	45043536	0.000000e+00	2767
9	TraesCS4B01G263600	chr2A	89.775	1907	179	15	8	1907	672641164	672639267	0.000000e+00	2427
10	TraesCS4B01G263600	chr2A	88.860	1912	194	12	6	1907	596371856	596373758	0.000000e+00	2333
11	TraesCS4B01G263600	chr5D	89.310	1899	186	12	15	1905	484147928	484146039	0.000000e+00	2366
12	TraesCS4B01G263600	chr4D	88.837	1917	180	20	4	1907	360457162	360459057	0.000000e+00	2324
13	TraesCS4B01G263600	chr4D	91.887	530	38	5	1911	2437	389569125	389569652	0.000000e+00	736
14	TraesCS4B01G263600	chr7D	87.893	1908	200	20	5	1904	203026883	203024999	0.000000e+00	2215
15	TraesCS4B01G263600	chr1D	85.084	1609	232	8	113	1717	379793062	379791458	0.000000e+00	1635
16	TraesCS4B01G263600	chr1B	96.205	527	17	3	1913	2437	316808188	316808713	0.000000e+00	859
17	TraesCS4B01G263600	chr1B	95.094	530	23	3	1910	2437	63880339	63879811	0.000000e+00	832
18	TraesCS4B01G263600	chr3B	94.528	530	27	2	1910	2437	26447504	26448033	0.000000e+00	817
19	TraesCS4B01G263600	chr6D	93.797	532	29	4	1909	2437	359247218	359247748	0.000000e+00	797
20	TraesCS4B01G263600	chr5B	94.670	469	20	5	1904	2368	371685987	371686454	0.000000e+00	723
21	TraesCS4B01G263600	chr3A	89.516	248	20	4	1661	1905	737814663	737814907	2.350000e-80	309

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	TraesCS4B01G263600	chr4B	534709524	534711960	2436	False	4501	4501	100.000	1	2437	1	chr4B.!!$F1	2436
1	TraesCS4B01G263600	chr2B	159213217	159215123	1906	True	2796	2796	93.152	5	1911	1	chr2B.!!$R2	1906
2	TraesCS4B01G263600	chr2B	441897452	441899135	1683	True	1531	1531	83.166	32	1715	1	chr2B.!!$R3	1683
3	TraesCS4B01G263600	chr2B	136263169	136263694	525	True	701	701	90.789	1911	2437	1	chr2B.!!$R1	526
4	TraesCS4B01G263600	chr2B	412636565	412637491	926	False	468	745	94.842	1901	2437	2	chr2B.!!$F3	536
5	TraesCS4B01G263600	chr7B	45043536	45045419	1883	True	2767	2767	93.182	4	1890	1	chr7B.!!$R1	1886
6	TraesCS4B01G263600	chr2A	672639267	672641164	1897	True	2427	2427	89.775	8	1907	1	chr2A.!!$R1	1899
7	TraesCS4B01G263600	chr2A	596371856	596373758	1902	False	2333	2333	88.860	6	1907	1	chr2A.!!$F1	1901
8	TraesCS4B01G263600	chr5D	484146039	484147928	1889	True	2366	2366	89.310	15	1905	1	chr5D.!!$R1	1890
9	TraesCS4B01G263600	chr4D	360457162	360459057	1895	False	2324	2324	88.837	4	1907	1	chr4D.!!$F1	1903
10	TraesCS4B01G263600	chr4D	389569125	389569652	527	False	736	736	91.887	1911	2437	1	chr4D.!!$F2	526
11	TraesCS4B01G263600	chr7D	203024999	203026883	1884	True	2215	2215	87.893	5	1904	1	chr7D.!!$R1	1899
12	TraesCS4B01G263600	chr1D	379791458	379793062	1604	True	1635	1635	85.084	113	1717	1	chr1D.!!$R1	1604
13	TraesCS4B01G263600	chr1B	316808188	316808713	525	False	859	859	96.205	1913	2437	1	chr1B.!!$F1	524
14	TraesCS4B01G263600	chr1B	63879811	63880339	528	True	832	832	95.094	1910	2437	1	chr1B.!!$R1	527
15	TraesCS4B01G263600	chr3B	26447504	26448033	529	False	817	817	94.528	1910	2437	1	chr3B.!!$F1	527
16	TraesCS4B01G263600	chr6D	359247218	359247748	530	False	797	797	93.797	1909	2437	1	chr6D.!!$F1	528

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
562	563	0.106015	GCAAGGGGATATGTGGGCTT	60.106	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2322	2345	0.250513	GGCGGATCTCTTCACAAGGT	59.749	55.0	0.0	0.0	0.0	3.5	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
34	35	5.815581	AGCTAACCAACTTCATGAATACCA	58.184	37.500	8.96	0.00	0.00	3.25
177	178	3.252351	GAGGGGGAAGCTATTGTCCTAT	58.748	50.000	2.26	0.00	34.10	2.57
225	226	5.377478	GCTTGTTTAGCTAGTATCCCCATT	58.623	41.667	0.00	0.00	46.77	3.16
429	430	1.382420	TTTGCTGGGCAGTTGGGTT	60.382	52.632	0.00	0.00	40.61	4.11
431	432	0.539438	TTGCTGGGCAGTTGGGTTAG	60.539	55.000	0.00	0.00	40.61	2.34
466	467	6.608808	CCAAGATGAGGGTAAAATCTGGAAAT	59.391	38.462	0.00	0.00	31.11	2.17
551	552	2.371510	CCTCAAATTTTTGGCAAGGGGA	59.628	45.455	0.00	0.00	38.66	4.81
562	563	0.106015	GCAAGGGGATATGTGGGCTT	60.106	55.000	0.00	0.00	0.00	4.35
567	568	1.479389	GGGGATATGTGGGCTTCCAAG	60.479	57.143	0.00	0.00	43.12	3.61
594	595	3.525800	AAGTTTGGCTACAGATGGGTT	57.474	42.857	0.00	0.00	0.00	4.11
654	655	3.842069	GTTTGGAACCTCCCCACTT	57.158	52.632	0.00	0.00	35.03	3.16
817	818	7.223584	TGAACAAATCATAAAGGAGACTGTGA	58.776	34.615	0.00	0.00	34.67	3.58
826	827	3.777106	AGGAGACTGTGATCAAAGCAA	57.223	42.857	13.13	0.00	41.13	3.91
862	863	3.370953	GGTCTGGCAGTATGAATCCAAGT	60.371	47.826	15.27	0.00	39.69	3.16
870	871	5.455326	GCAGTATGAATCCAAGTGGGTCTAT	60.455	44.000	0.00	0.00	39.69	1.98
954	955	0.755686	TTTGGTCCATTGTTGTGCCC	59.244	50.000	0.00	0.00	0.00	5.36
1109	1110	2.937469	TTTGACTGTGTGGTTGCAAG	57.063	45.000	0.00	0.00	0.00	4.01
1159	1160	7.650104	CGTTTCTTTCCATAGAAGTAGGATCTC	59.350	40.741	0.00	0.00	35.69	2.75
1164	1165	8.707796	TTTCCATAGAAGTAGGATCTCGTTAT	57.292	34.615	0.00	0.00	32.35	1.89
1240	1241	1.832883	TTGTGCTTGTGTCTTGTGGT	58.167	45.000	0.00	0.00	0.00	4.16
1243	1244	1.360192	GCTTGTGTCTTGTGGTGCC	59.640	57.895	0.00	0.00	0.00	5.01
1324	1326	0.326904	TGGTGGCTGATCTGGAGGAT	60.327	55.000	1.46	0.00	37.37	3.24
1353	1355	2.550978	GGTGGATGATTCTGTACACCG	58.449	52.381	7.86	0.00	38.96	4.94
1438	1440	3.230134	TCCAATTGACTTTGGGGTGAAG	58.770	45.455	7.12	0.00	45.21	3.02
1480	1482	0.321919	GTGCCACTCATGCCTCTTCA	60.322	55.000	0.00	0.00	0.00	3.02
1512	1514	3.085952	TGATTCTGGGGCTTGTAAAGG	57.914	47.619	0.00	0.00	46.35	3.11
1528	1530	0.104409	AAGGTGGGTTCCAGAGTCCT	60.104	55.000	0.00	0.00	32.34	3.85
1543	1545	0.687354	GTCCTGACTCTTCAAGGCCA	59.313	55.000	5.01	0.00	28.35	5.36
1643	1645	5.060427	TCAACCCCTCAAGAAGATGAAAA	57.940	39.130	0.00	0.00	0.00	2.29
1675	1677	1.689273	GAGCATATCAAGGAGGTCCGT	59.311	52.381	0.00	0.00	42.08	4.69
1676	1678	1.414181	AGCATATCAAGGAGGTCCGTG	59.586	52.381	5.65	5.65	45.13	4.94
1707	1709	3.730061	GCTGCAAAAGACATGAGGATTCG	60.730	47.826	0.00	0.00	0.00	3.34
1761	1766	4.435651	GCTGTAGTGTTTCATCGGTTTAGC	60.436	45.833	0.00	0.00	0.00	3.09
1773	1783	1.668919	CGGTTTAGCTCAGCGTCAAGA	60.669	52.381	8.82	0.00	0.00	3.02
1779	1789	2.139118	AGCTCAGCGTCAAGAAAAGTC	58.861	47.619	0.00	0.00	0.00	3.01
1786	1796	2.931320	GCGTCAAGAAAAGTCGGATCCT	60.931	50.000	10.75	0.00	0.00	3.24
1787	1797	2.924290	CGTCAAGAAAAGTCGGATCCTC	59.076	50.000	10.75	2.85	0.00	3.71
1836	1846	9.673454	CTTATTTTTGTTACCCTGTACTGTTTC	57.327	33.333	0.00	0.00	0.00	2.78
1838	1848	7.463961	TTTTTGTTACCCTGTACTGTTTCAA	57.536	32.000	0.00	0.00	0.00	2.69
1850	1863	7.043192	CCTGTACTGTTTCAATTTTGCTCTTTG	60.043	37.037	0.00	0.00	0.00	2.77
1877	1894	1.865788	GCGTTTGAGGCATGCTTGGA	61.866	55.000	18.92	0.00	0.00	3.53
1890	1908	3.998913	TGCTTGGATGTTGGACTGATA	57.001	42.857	0.00	0.00	0.00	2.15
2081	2099	0.903942	TTACGGGGCGTTTACTGGAT	59.096	50.000	0.00	0.00	41.54	3.41
2091	2110	2.669950	CGTTTACTGGATTTTTGCCCCG	60.670	50.000	0.00	0.00	0.00	5.73
2254	2275	2.136878	CCGATGCTAGCTCCCCACT	61.137	63.158	17.23	0.00	0.00	4.00
2257	2278	1.381872	ATGCTAGCTCCCCACTCGT	60.382	57.895	17.23	0.00	0.00	4.18
2322	2345	0.550147	CTCCCTTTCCCTTCCTCCCA	60.550	60.000	0.00	0.00	0.00	4.37
2330	2741	1.133809	CCCTTCCTCCCACCTTGTGA	61.134	60.000	0.00	0.00	35.23	3.58
2345	2756	3.074369	TGAAGAGATCCGCCGCCA	61.074	61.111	0.00	0.00	0.00	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.909610	TGGTTAGCTCTCCCCCTGTG	60.910	60.000	0.00	0.00	0.00	3.66
2	3	0.253327	GTTGGTTAGCTCTCCCCCTG	59.747	60.000	0.00	0.00	0.00	4.45
3	4	0.119358	AGTTGGTTAGCTCTCCCCCT	59.881	55.000	0.00	0.00	0.00	4.79
6	7	3.055094	TCATGAAGTTGGTTAGCTCTCCC	60.055	47.826	0.00	0.00	0.00	4.30
7	8	4.207891	TCATGAAGTTGGTTAGCTCTCC	57.792	45.455	0.00	0.00	0.00	3.71
11	12	5.815581	TGGTATTCATGAAGTTGGTTAGCT	58.184	37.500	14.54	0.00	0.00	3.32
12	13	6.699575	ATGGTATTCATGAAGTTGGTTAGC	57.300	37.500	14.54	9.97	34.22	3.09
135	136	2.423947	CCAGCCAGCCATCCTCTTTAAT	60.424	50.000	0.00	0.00	0.00	1.40
177	178	7.976734	GCTTTAATGAGAGTTAGTCTAGCAGAA	59.023	37.037	3.25	0.00	34.71	3.02
225	226	6.879458	GGAACTTAAAGAAGGACAGCAGATAA	59.121	38.462	0.00	0.00	36.95	1.75
429	430	4.099633	CCTCATCTTGGGCATATCTCCTA	58.900	47.826	0.00	0.00	0.00	2.94
431	432	2.026449	CCCTCATCTTGGGCATATCTCC	60.026	54.545	0.00	0.00	37.99	3.71
497	498	6.040391	TGGCCTACATGCAAAAATATTAGGAC	59.960	38.462	3.32	2.57	34.31	3.85
529	530	2.552809	CCCCTTGCCAAAAATTTGAGGG	60.553	50.000	17.93	17.93	43.91	4.30
551	552	0.929244	AGCCTTGGAAGCCCACATAT	59.071	50.000	0.00	0.00	43.41	1.78
562	563	2.108250	AGCCAAACTTAAGAGCCTTGGA	59.892	45.455	22.78	0.00	39.70	3.53
567	568	3.939066	TCTGTAGCCAAACTTAAGAGCC	58.061	45.455	10.09	0.00	0.00	4.70
654	655	3.513515	ACAAAGGCCAAAACTGAACAGAA	59.486	39.130	5.01	0.00	0.00	3.02
759	760	1.152819	CTCCATCATGGCAGGGGTG	60.153	63.158	0.00	0.00	37.47	4.61
817	818	6.041637	ACCATAGCATCATCATTTGCTTTGAT	59.958	34.615	14.23	0.00	46.71	2.57
826	827	3.181437	TGCCAGACCATAGCATCATCATT	60.181	43.478	0.00	0.00	0.00	2.57
862	863	4.873010	AGTGAGCTAGAAGAATAGACCCA	58.127	43.478	0.00	0.00	0.00	4.51
870	871	5.420725	TGGCATAAAGTGAGCTAGAAGAA	57.579	39.130	0.00	0.00	0.00	2.52
954	955	3.092301	GAGAAAAACCTGGATTCTGGGG	58.908	50.000	15.24	0.00	33.73	4.96
1028	1029	4.884961	ACAGTCAGGGTTCCTATCTATGT	58.115	43.478	0.00	0.00	29.64	2.29
1109	1110	2.941720	GAGACTGCATCCCAGATGTTTC	59.058	50.000	6.46	1.55	44.64	2.78
1159	1160	8.977505	CCAAAATTTGGCTATGGAATAATAACG	58.022	33.333	12.23	0.00	45.17	3.18
1189	1190	6.699575	AAGCACTTCATGTTTCTTGTTAGT	57.300	33.333	0.00	0.00	0.00	2.24
1240	1241	6.065374	TGTTATTTCTAGTTTTCCACAGGCA	58.935	36.000	0.00	0.00	0.00	4.75
1243	1244	9.965824	AAACATGTTATTTCTAGTTTTCCACAG	57.034	29.630	12.39	0.00	0.00	3.66
1324	1326	3.453717	CAGAATCATCCACCTCTTGAGGA	59.546	47.826	22.10	1.79	35.59	3.71
1353	1355	2.095053	GCATTTTCTCAAGCGAGTCCTC	59.905	50.000	0.00	0.00	40.44	3.71
1438	1440	0.393537	CAGTGCCCATCAGGTTCCTC	60.394	60.000	0.00	0.00	38.26	3.71
1480	1482	3.117738	CCCCAGAATCAAGCTTGGAGTAT	60.118	47.826	25.73	9.49	0.00	2.12
1512	1514	0.321996	GTCAGGACTCTGGAACCCAC	59.678	60.000	0.00	0.00	41.23	4.61
1528	1530	1.768275	TCACTTGGCCTTGAAGAGTCA	59.232	47.619	3.32	0.00	0.00	3.41
1567	1569	4.823276	CTCGAAATCGCCTGAGCT	57.177	55.556	0.00	0.00	39.60	4.09
1569	1571	1.884926	GGGCTCGAAATCGCCTGAG	60.885	63.158	12.59	0.00	45.57	3.35
1691	1693	3.529533	CAGCTCGAATCCTCATGTCTTT	58.470	45.455	0.00	0.00	0.00	2.52
1707	1709	0.747283	CATTCCTCCTGCACCAGCTC	60.747	60.000	0.00	0.00	42.74	4.09
1761	1766	1.457303	CCGACTTTTCTTGACGCTGAG	59.543	52.381	0.00	0.00	0.00	3.35
1813	1823	7.648039	TGAAACAGTACAGGGTAACAAAAAT	57.352	32.000	0.00	0.00	39.74	1.82
1815	1825	7.648039	ATTGAAACAGTACAGGGTAACAAAA	57.352	32.000	0.00	0.00	39.74	2.44
1819	1829	6.419710	GCAAAATTGAAACAGTACAGGGTAAC	59.580	38.462	0.00	0.00	0.00	2.50
1836	1846	5.388061	CGCATGTTCTCAAAGAGCAAAATTG	60.388	40.000	0.00	0.00	38.90	2.32
1838	1848	4.232221	CGCATGTTCTCAAAGAGCAAAAT	58.768	39.130	0.00	0.00	38.90	1.82
1850	1863	0.874390	TGCCTCAAACGCATGTTCTC	59.126	50.000	0.00	0.00	37.31	2.87
1877	1894	4.927267	TGAAACCCTATCAGTCCAACAT	57.073	40.909	0.00	0.00	0.00	2.71
2060	2078	1.278699	TCCAGTAAACGCCCCGTAAAT	59.721	47.619	0.00	0.00	39.99	1.40
2081	2099	0.753479	TGTGAAGCTCGGGGCAAAAA	60.753	50.000	1.17	0.00	44.79	1.94
2254	2275	3.749064	GAGACAGGGCAGCGACGA	61.749	66.667	0.00	0.00	0.00	4.20
2322	2345	0.250513	GGCGGATCTCTTCACAAGGT	59.749	55.000	0.00	0.00	0.00	3.50
2330	2741	3.077556	AGTGGCGGCGGATCTCTT	61.078	61.111	9.78	0.00	0.00	2.85
2345	2756	3.223661	CTGCGAAGAAGAAGGCAGT	57.776	52.632	3.84	0.00	45.84	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.