AutoCloner

Multiple sequence alignment - TraesCS2D01G526300

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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	TraesCS2D01G526300	chr2D	100.000	2307	0	0	1	2307	614805875	614803569	0.000000e+00	4261.0
1	TraesCS2D01G526300	chr2D	91.549	284	14	4	1420	1703	614811441	614811168	1.290000e-102	383.0
2	TraesCS2D01G526300	chr2D	83.541	401	36	11	966	1342	614819572	614819178	4.720000e-92	348.0
3	TraesCS2D01G526300	chr2D	86.598	194	8	9	729	912	614812159	614811974	5.030000e-47	198.0
4	TraesCS2D01G526300	chr2D	76.611	419	61	18	997	1385	614735170	614734759	1.810000e-46	196.0
5	TraesCS2D01G526300	chr2D	91.729	133	11	0	729	861	614819843	614819711	3.910000e-43	185.0
6	TraesCS2D01G526300	chr2D	88.732	142	11	1	962	1103	614811895	614811759	3.940000e-38	169.0
7	TraesCS2D01G526300	chr2B	92.759	1602	73	19	728	2307	749139401	749137821	0.000000e+00	2276.0
8	TraesCS2D01G526300	chr2B	92.202	731	55	1	1	729	46671197	46671927	0.000000e+00	1033.0
9	TraesCS2D01G526300	chr2B	92.213	732	53	3	1	729	704119221	704119951	0.000000e+00	1033.0
10	TraesCS2D01G526300	chr2B	82.368	777	48	30	962	1703	749148029	749147307	5.490000e-166	593.0
11	TraesCS2D01G526300	chr2B	82.701	422	47	13	975	1376	749181521	749181106	3.650000e-93	351.0
12	TraesCS2D01G526300	chr2B	90.291	206	11	3	729	926	749148309	749148105	6.320000e-66	261.0
13	TraesCS2D01G526300	chr2B	80.135	297	24	20	822	1098	749044631	749044350	3.030000e-44	189.0
14	TraesCS2D01G526300	chr2B	92.063	126	7	2	804	926	749183302	749183177	8.470000e-40	174.0
15	TraesCS2D01G526300	chr2B	96.429	56	2	0	728	783	749183348	749183293	2.440000e-15	93.5
16	TraesCS2D01G526300	chr6A	93.861	733	38	4	1	731	489861340	489860613	0.000000e+00	1098.0
17	TraesCS2D01G526300	chr5A	93.707	731	43	2	1	729	623498330	623499059	0.000000e+00	1092.0
18	TraesCS2D01G526300	chr5A	92.623	732	49	2	1	730	13422512	13423240	0.000000e+00	1048.0
19	TraesCS2D01G526300	chr4A	92.339	731	54	1	1	729	577863545	577862815	0.000000e+00	1038.0
20	TraesCS2D01G526300	chr6B	92.234	734	53	3	1	731	705916204	705916936	0.000000e+00	1037.0
21	TraesCS2D01G526300	chr6B	92.087	733	55	2	1	731	71580471	71579740	0.000000e+00	1029.0
22	TraesCS2D01G526300	chr1A	92.066	731	56	2	1	729	306145738	306146468	0.000000e+00	1027.0
23	TraesCS2D01G526300	chr2A	84.159	928	80	35	982	1877	745092840	745091948	0.000000e+00	837.0
24	TraesCS2D01G526300	chr2A	86.130	584	59	14	1290	1870	745091472	745090908	5.450000e-171	610.0
25	TraesCS2D01G526300	chr2A	95.070	284	11	1	1420	1703	745096668	745096388	5.850000e-121	444.0
26	TraesCS2D01G526300	chr2A	83.182	440	40	20	966	1376	745112194	745111760	2.800000e-99	372.0
27	TraesCS2D01G526300	chr2A	94.144	222	11	1	728	947	745093151	745092930	1.020000e-88	337.0
28	TraesCS2D01G526300	chr2A	80.739	379	31	23	997	1340	745097083	745096712	8.180000e-65	257.0
29	TraesCS2D01G526300	chr2A	91.975	162	9	1	729	890	745112474	745112317	8.290000e-55	224.0
30	TraesCS2D01G526300	chr2A	75.495	555	66	35	822	1323	745067125	745066588	8.350000e-50	207.0
31	TraesCS2D01G526300	chr2A	93.056	72	4	1	841	911	745097279	745097208	1.130000e-18	104.0
32	TraesCS2D01G526300	chr3B	87.850	107	11	2	2199	2304	492205413	492205308	8.650000e-25	124.0
33	TraesCS2D01G526300	chr3A	87.850	107	11	2	2199	2304	501930903	501930798	8.650000e-25	124.0

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	TraesCS2D01G526300	chr2D	614803569	614805875	2306	True	4261.000000	4261	100.000000	1	2307	1	chr2D.!!$R2	2306
1	TraesCS2D01G526300	chr2D	614819178	614819843	665	True	266.500000	348	87.635000	729	1342	2	chr2D.!!$R4	613
2	TraesCS2D01G526300	chr2D	614811168	614812159	991	True	250.000000	383	88.959667	729	1703	3	chr2D.!!$R3	974
3	TraesCS2D01G526300	chr2B	749137821	749139401	1580	True	2276.000000	2276	92.759000	728	2307	1	chr2B.!!$R2	1579
4	TraesCS2D01G526300	chr2B	46671197	46671927	730	False	1033.000000	1033	92.202000	1	729	1	chr2B.!!$F1	728
5	TraesCS2D01G526300	chr2B	704119221	704119951	730	False	1033.000000	1033	92.213000	1	729	1	chr2B.!!$F2	728
6	TraesCS2D01G526300	chr2B	749147307	749148309	1002	True	427.000000	593	86.329500	729	1703	2	chr2B.!!$R3	974
7	TraesCS2D01G526300	chr2B	749181106	749183348	2242	True	206.166667	351	90.397667	728	1376	3	chr2B.!!$R4	648
8	TraesCS2D01G526300	chr6A	489860613	489861340	727	True	1098.000000	1098	93.861000	1	731	1	chr6A.!!$R1	730
9	TraesCS2D01G526300	chr5A	623498330	623499059	729	False	1092.000000	1092	93.707000	1	729	1	chr5A.!!$F2	728
10	TraesCS2D01G526300	chr5A	13422512	13423240	728	False	1048.000000	1048	92.623000	1	730	1	chr5A.!!$F1	729
11	TraesCS2D01G526300	chr4A	577862815	577863545	730	True	1038.000000	1038	92.339000	1	729	1	chr4A.!!$R1	728
12	TraesCS2D01G526300	chr6B	705916204	705916936	732	False	1037.000000	1037	92.234000	1	731	1	chr6B.!!$F1	730
13	TraesCS2D01G526300	chr6B	71579740	71580471	731	True	1029.000000	1029	92.087000	1	731	1	chr6B.!!$R1	730
14	TraesCS2D01G526300	chr1A	306145738	306146468	730	False	1027.000000	1027	92.066000	1	729	1	chr1A.!!$F1	728
15	TraesCS2D01G526300	chr2A	745090908	745097279	6371	True	431.500000	837	88.883000	728	1877	6	chr2A.!!$R2	1149
16	TraesCS2D01G526300	chr2A	745111760	745112474	714	True	298.000000	372	87.578500	729	1376	2	chr2A.!!$R3	647
17	TraesCS2D01G526300	chr2A	745066588	745067125	537	True	207.000000	207	75.495000	822	1323	1	chr2A.!!$R1	501

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
435	441	0.555769	TGCTCCTTGGTCTTTTGGGT	59.444	50.0	0.0	0.0	0.0	4.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1368	6523	0.036732	TGAGGCACCACCATCTTGAC	59.963	55.0	0.0	0.0	43.14	3.18	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
139	142	4.160635	GTTTGGATGCCGCGGTCG	62.161	66.667	28.70	0.72	0.00	4.79
302	308	1.079681	CTGGTAAGGCGGTTGCGTA	60.080	57.895	0.00	0.00	44.10	4.42
413	419	1.151777	GCGTCTGCGGCTGCTTAATA	61.152	55.000	20.27	0.00	43.34	0.98
435	441	0.555769	TGCTCCTTGGTCTTTTGGGT	59.444	50.000	0.00	0.00	0.00	4.51
468	474	6.408035	TGGTTTAGCTTATCATCGTGGTTTA	58.592	36.000	0.00	0.00	0.00	2.01
502	509	2.295349	TGTCTACTTCCGTGGTGTTCTC	59.705	50.000	0.00	0.00	0.00	2.87
557	565	1.336240	GCTTGGGTCTGTTGCATGTTC	60.336	52.381	0.00	0.00	0.00	3.18
570	578	5.008118	TGTTGCATGTTCGAAATGTCTGTAA	59.992	36.000	0.00	0.00	0.00	2.41
574	582	5.334879	GCATGTTCGAAATGTCTGTAAGGTT	60.335	40.000	0.00	0.00	0.00	3.50
590	598	0.733566	GGTTGACGGTGCGATTACGA	60.734	55.000	0.00	0.00	42.66	3.43
600	608	4.117685	GGTGCGATTACGAGGTTTTAGAT	58.882	43.478	0.00	0.00	42.66	1.98
915	4382	1.301244	CACTCACTCAACAGCCGCT	60.301	57.895	0.00	0.00	0.00	5.52
1039	6136	0.108756	GCTCCTGGACGTGTTCTACC	60.109	60.000	0.00	0.00	0.00	3.18
1047	6144	1.000938	GACGTGTTCTACCACCTCGTT	60.001	52.381	0.00	0.00	31.47	3.85
1093	6190	3.057337	CCGAGGACGACAAGGGTT	58.943	61.111	0.00	0.00	42.66	4.11
1108	6229	3.662247	AGGGTTCGTAAACACTCTGAG	57.338	47.619	2.45	2.45	46.39	3.35
1122	6243	2.031012	TGAGAACGCCACAGCTGG	59.969	61.111	19.93	2.55	41.13	4.85
1182	6327	1.623811	TCTTCCTGTTGCAGACCTACC	59.376	52.381	0.00	0.00	32.44	3.18
1315	6470	3.072038	TGGACGGTATGTAGAGCTAGCTA	59.928	47.826	19.38	1.43	0.00	3.32
1334	6489	1.664321	AAGCCTCTACGTACGGCAGG	61.664	60.000	25.02	20.24	46.14	4.85
1368	6523	0.999406	CCGTGTGGTTTCTCATAGCG	59.001	55.000	0.00	0.00	0.00	4.26
1380	6535	2.101415	TCTCATAGCGTCAAGATGGTGG	59.899	50.000	4.36	0.00	0.00	4.61
1384	6539	2.690778	GCGTCAAGATGGTGGTGCC	61.691	63.158	0.00	0.00	37.90	5.01
1385	6540	1.003355	CGTCAAGATGGTGGTGCCT	60.003	57.895	0.00	0.00	38.35	4.75
1387	6542	0.036732	GTCAAGATGGTGGTGCCTCA	59.963	55.000	0.00	0.00	38.35	3.86
1389	6544	1.065199	TCAAGATGGTGGTGCCTCATC	60.065	52.381	13.23	13.23	37.97	2.92
1423	7633	3.432252	GTGTGTGTGTGTCCTAGTAATGC	59.568	47.826	0.00	0.00	0.00	3.56
1538	7748	8.196771	ACTTGATGAACTTGCTTGTTAATTTCA	58.803	29.630	0.00	0.00	33.28	2.69
1580	7790	7.506328	TTTTTCTCCAAGCTTACTTTCTACC	57.494	36.000	0.00	0.00	32.29	3.18
1764	7974	1.153978	ATTGCGATGCACAAAGCCG	60.154	52.632	0.00	0.00	44.83	5.52
1821	8032	8.446273	CAAAGTCATCAACAAGTGGAGTATAAG	58.554	37.037	0.00	0.00	0.00	1.73
1853	8064	7.116662	GGCGACAACGATATAACCATTACAATA	59.883	37.037	0.00	0.00	42.66	1.90
1901	8112	5.585047	AGACAACCTTTTCTACAATATCGCC	59.415	40.000	0.00	0.00	0.00	5.54
1934	8145	7.266922	TCCATAAAATTCCTTATTACCGCAC	57.733	36.000	0.00	0.00	0.00	5.34
1938	8149	8.832521	CATAAAATTCCTTATTACCGCACTGTA	58.167	33.333	0.00	0.00	0.00	2.74
1939	8150	6.673154	AAATTCCTTATTACCGCACTGTAC	57.327	37.500	0.00	0.00	0.00	2.90
1942	8153	3.510753	TCCTTATTACCGCACTGTACACA	59.489	43.478	0.00	0.00	0.00	3.72
2028	8239	1.135689	GCACATCAAAAAGCGACGGAT	60.136	47.619	0.00	0.00	0.00	4.18
2066	8277	6.491745	TGAGCCAAACAAATAATTAGGTGTCA	59.508	34.615	4.72	0.00	0.00	3.58
2125	8336	0.029834	CTGTGTGCTTGCAGGTGTTC	59.970	55.000	0.00	0.00	0.00	3.18
2126	8337	0.679321	TGTGTGCTTGCAGGTGTTCA	60.679	50.000	0.00	0.00	0.00	3.18
2136	8347	2.224843	TGCAGGTGTTCATTGAGGATGT	60.225	45.455	0.00	0.00	37.06	3.06
2159	8370	5.982516	GTCATGGATCTTGTAGAGCTTACAG	59.017	44.000	8.21	4.96	30.02	2.74
2164	8375	5.236047	GGATCTTGTAGAGCTTACAGCATTG	59.764	44.000	0.00	0.00	45.56	2.82
2178	8389	0.244721	GCATTGAGGGGTGAACTTGC	59.755	55.000	0.00	0.00	0.00	4.01
2230	8441	0.675633	ATTGTTGTGGAGCTGGTTGC	59.324	50.000	0.00	0.00	43.29	4.17
2257	8468	7.976414	ACCCTTCAATCATTTTTATGGATGA	57.024	32.000	0.00	0.00	36.77	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	1.925255	AGCCCATCTCCTTTGGAATCA	59.075	47.619	0.00	0.00	36.26	2.57
103	106	0.817013	CCTGCACACACCACAAAGTT	59.183	50.000	0.00	0.00	0.00	2.66
139	142	2.355244	GGTCATAGGCGAGCGAGC	60.355	66.667	0.00	0.00	0.00	5.03
151	154	0.114954	ACCACTTGCCCAATGGTCAT	59.885	50.000	0.00	0.00	43.40	3.06
413	419	2.310538	CCAAAAGACCAAGGAGCAACT	58.689	47.619	0.00	0.00	0.00	3.16
435	441	4.404394	TGATAAGCTAAACCATGAGGACGA	59.596	41.667	0.00	0.00	38.69	4.20
502	509	1.544724	TCGCAAAGGAATCCCCAAAG	58.455	50.000	0.00	0.00	37.41	2.77
557	565	3.122948	CCGTCAACCTTACAGACATTTCG	59.877	47.826	0.00	0.00	32.68	3.46
570	578	0.734942	CGTAATCGCACCGTCAACCT	60.735	55.000	0.00	0.00	0.00	3.50
574	582	1.138036	CCTCGTAATCGCACCGTCA	59.862	57.895	0.00	0.00	36.96	4.35
590	598	6.482524	GGACTACTCCCAAAATCTAAAACCT	58.517	40.000	0.00	0.00	0.00	3.50
600	608	1.349688	ACATGCGGACTACTCCCAAAA	59.650	47.619	0.00	0.00	31.93	2.44
895	4312	1.560860	GCGGCTGTTGAGTGAGTGTC	61.561	60.000	0.00	0.00	0.00	3.67
896	4313	1.595382	GCGGCTGTTGAGTGAGTGT	60.595	57.895	0.00	0.00	0.00	3.55
897	4314	0.038251	TAGCGGCTGTTGAGTGAGTG	60.038	55.000	13.86	0.00	0.00	3.51
915	4382	2.146342	GCTTGCTTTGAGCTGTGAGTA	58.854	47.619	0.00	0.00	42.97	2.59
960	4477	2.032178	GGGTAATTCAAGCTGCTTAGCG	59.968	50.000	15.51	3.09	40.27	4.26
992	6089	2.329539	GAAGCTGGCCATGGGATCGA	62.330	60.000	15.13	0.00	0.00	3.59
1039	6136	3.470567	GACGCGCTCAACGAGGTG	61.471	66.667	5.73	0.00	46.87	4.00
1093	6190	2.606308	GGCGTTCTCAGAGTGTTTACGA	60.606	50.000	0.00	0.00	0.00	3.43
1108	6229	0.108138	ATACTCCAGCTGTGGCGTTC	60.108	55.000	13.81	0.00	38.76	3.95
1122	6243	7.921214	TCATTAGCAACTAGTAGTGCAATACTC	59.079	37.037	28.44	14.80	40.89	2.59
1182	6327	1.370900	GCCAACTTGCTGTGCTTCG	60.371	57.895	0.00	0.00	0.00	3.79
1334	6489	1.214367	CACGGCCGTTATGTATGTCC	58.786	55.000	32.11	0.00	0.00	4.02
1368	6523	0.036732	TGAGGCACCACCATCTTGAC	59.963	55.000	0.00	0.00	43.14	3.18
1380	6535	0.957395	CACACACCAGGATGAGGCAC	60.957	60.000	0.00	0.00	39.69	5.01
1384	6539	1.202687	ACACACACACACCAGGATGAG	60.203	52.381	0.00	0.00	39.69	2.90
1385	6540	0.836606	ACACACACACACCAGGATGA	59.163	50.000	0.00	0.00	39.69	2.92
1387	6542	0.546122	ACACACACACACACCAGGAT	59.454	50.000	0.00	0.00	0.00	3.24
1389	6544	0.676466	ACACACACACACACACCAGG	60.676	55.000	0.00	0.00	0.00	4.45
1423	7633	8.495949	ACGATAGAACATTGTAACAAACTGAAG	58.504	33.333	0.00	0.00	41.38	3.02
1595	7805	7.398618	TCTTCCCTTTCACCATGCATTTAATAA	59.601	33.333	0.00	0.00	0.00	1.40
1596	7806	6.894654	TCTTCCCTTTCACCATGCATTTAATA	59.105	34.615	0.00	0.00	0.00	0.98
1597	7807	5.721000	TCTTCCCTTTCACCATGCATTTAAT	59.279	36.000	0.00	0.00	0.00	1.40
1764	7974	6.972328	TGCCTAGCATCGATTTCAATAAAAAC	59.028	34.615	0.00	0.00	31.71	2.43
1821	8032	4.620184	GGTTATATCGTTGTCGCCTATGTC	59.380	45.833	0.00	0.00	36.96	3.06
1874	8085	8.328864	GCGATATTGTAGAAAAGGTTGTCTTAG	58.671	37.037	0.00	0.00	34.78	2.18
1875	8086	7.279313	GGCGATATTGTAGAAAAGGTTGTCTTA	59.721	37.037	0.00	0.00	34.78	2.10
1931	8142	2.672961	TAGCCAGATGTGTACAGTGC	57.327	50.000	0.00	0.00	0.00	4.40
1934	8145	4.327357	CGTCTTTTAGCCAGATGTGTACAG	59.673	45.833	0.00	0.00	0.00	2.74
1938	8149	2.699954	CCGTCTTTTAGCCAGATGTGT	58.300	47.619	0.00	0.00	0.00	3.72
1939	8150	1.398390	GCCGTCTTTTAGCCAGATGTG	59.602	52.381	0.00	0.00	0.00	3.21
1942	8153	3.478540	GGCCGTCTTTTAGCCAGAT	57.521	52.632	0.00	0.00	46.34	2.90
2006	8217	1.059657	CGTCGCTTTTTGATGTGCCG	61.060	55.000	0.00	0.00	0.00	5.69
2028	8239	1.742880	GGCTCAGCTGCGATGAACA	60.743	57.895	9.47	0.00	0.00	3.18
2066	8277	7.548196	TTACAATCAGTCGAGAACAAACTTT	57.452	32.000	0.00	0.00	0.00	2.66
2075	8286	8.239038	AGGATAAGATTTACAATCAGTCGAGA	57.761	34.615	0.00	0.00	0.00	4.04
2125	8336	5.131067	ACAAGATCCATGACATCCTCAATG	58.869	41.667	0.00	0.00	41.48	2.82
2126	8337	5.384145	ACAAGATCCATGACATCCTCAAT	57.616	39.130	0.00	0.00	30.60	2.57
2136	8347	6.154203	CTGTAAGCTCTACAAGATCCATGA	57.846	41.667	0.00	0.00	0.00	3.07
2159	8370	0.244721	GCAAGTTCACCCCTCAATGC	59.755	55.000	0.00	0.00	0.00	3.56
2164	8375	1.303643	CCCAGCAAGTTCACCCCTC	60.304	63.158	0.00	0.00	0.00	4.30
2178	8389	5.128827	TCTTGGCTAGTGAATAGTTACCCAG	59.871	44.000	0.00	0.00	33.65	4.45
2230	8441	9.754382	CATCCATAAAAATGATTGAAGGGTTAG	57.246	33.333	0.00	0.00	0.00	2.34
2266	8477	3.050619	GTTGTCTACACGTCAAGACCAG	58.949	50.000	19.18	0.00	41.19	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.