AutoCloner

Multiple sequence alignment - TraesCS6A01G254400

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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	TraesCS6A01G254400	chr6A	100.000	2388	0	0	1	2388	471275617	471273230	0.000000e+00	4410
1	TraesCS6A01G254400	chr5A	95.270	2389	108	5	1	2387	539825674	539823289	0.000000e+00	3781
2	TraesCS6A01G254400	chr5A	95.065	2391	111	6	1	2388	374024445	374022059	0.000000e+00	3755
3	TraesCS6A01G254400	chr5A	93.590	78	4	1	303	379	630722938	630723015	5.390000e-22	115
4	TraesCS6A01G254400	chr7A	95.107	2391	109	8	1	2388	25224711	25222326	0.000000e+00	3760
5	TraesCS6A01G254400	chr7A	92.104	2077	148	11	1	2066	116468465	116466394	0.000000e+00	2913
6	TraesCS6A01G254400	chr3A	95.129	2094	96	6	1	2091	496386022	496388112	0.000000e+00	3297
7	TraesCS6A01G254400	chr3A	91.781	292	19	3	742	1032	603856522	603856235	3.700000e-108	401
8	TraesCS6A01G254400	chr3D	92.415	2070	145	10	1	2066	578589353	578591414	0.000000e+00	2942
9	TraesCS6A01G254400	chr4D	91.707	2074	141	16	1	2066	168888700	168890750	0.000000e+00	2848
10	TraesCS6A01G254400	chr2D	94.919	1732	82	5	659	2388	92462904	92464631	0.000000e+00	2706
11	TraesCS6A01G254400	chr2D	93.567	171	11	0	60	230	92462666	92462836	3.050000e-64	255
12	TraesCS6A01G254400	chr5B	94.629	1266	67	1	1124	2388	617730963	617729698	0.000000e+00	1960
13	TraesCS6A01G254400	chrUn	96.831	568	15	2	1822	2388	1841802	1842367	0.000000e+00	946
14	TraesCS6A01G254400	chrUn	96.655	568	17	2	1822	2388	280615524	280614958	0.000000e+00	942
15	TraesCS6A01G254400	chr2B	96.655	568	17	2	1822	2388	742333694	742334260	0.000000e+00	942
16	TraesCS6A01G254400	chr1B	96.655	568	16	3	1822	2388	563481025	563480460	0.000000e+00	941
17	TraesCS6A01G254400	chr5D	92.172	396	30	1	1	395	61858924	61859319	2.070000e-155	558
18	TraesCS6A01G254400	chr7B	96.296	81	3	0	1	81	686192715	686192795	1.490000e-27	134
19	TraesCS6A01G254400	chr4B	91.489	94	8	0	346	439	642751931	642751838	1.930000e-26	130

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	TraesCS6A01G254400	chr6A	471273230	471275617	2387	True	4410.0	4410	100.000	1	2388	1	chr6A.!!$R1	2387
1	TraesCS6A01G254400	chr5A	539823289	539825674	2385	True	3781.0	3781	95.270	1	2387	1	chr5A.!!$R2	2386
2	TraesCS6A01G254400	chr5A	374022059	374024445	2386	True	3755.0	3755	95.065	1	2388	1	chr5A.!!$R1	2387
3	TraesCS6A01G254400	chr7A	25222326	25224711	2385	True	3760.0	3760	95.107	1	2388	1	chr7A.!!$R1	2387
4	TraesCS6A01G254400	chr7A	116466394	116468465	2071	True	2913.0	2913	92.104	1	2066	1	chr7A.!!$R2	2065
5	TraesCS6A01G254400	chr3A	496386022	496388112	2090	False	3297.0	3297	95.129	1	2091	1	chr3A.!!$F1	2090
6	TraesCS6A01G254400	chr3D	578589353	578591414	2061	False	2942.0	2942	92.415	1	2066	1	chr3D.!!$F1	2065
7	TraesCS6A01G254400	chr4D	168888700	168890750	2050	False	2848.0	2848	91.707	1	2066	1	chr4D.!!$F1	2065
8	TraesCS6A01G254400	chr2D	92462666	92464631	1965	False	1480.5	2706	94.243	60	2388	2	chr2D.!!$F1	2328
9	TraesCS6A01G254400	chr5B	617729698	617730963	1265	True	1960.0	1960	94.629	1124	2388	1	chr5B.!!$R1	1264
10	TraesCS6A01G254400	chrUn	1841802	1842367	565	False	946.0	946	96.831	1822	2388	1	chrUn.!!$F1	566
11	TraesCS6A01G254400	chrUn	280614958	280615524	566	True	942.0	942	96.655	1822	2388	1	chrUn.!!$R1	566
12	TraesCS6A01G254400	chr2B	742333694	742334260	566	False	942.0	942	96.655	1822	2388	1	chr2B.!!$F1	566
13	TraesCS6A01G254400	chr1B	563480460	563481025	565	True	941.0	941	96.655	1822	2388	1	chr1B.!!$R1	566

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
572	580	0.767375	AGGACTTGGTCAGTGCATGT	59.233	50.0	0.0	0.0	46.3	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1681	1710	1.143684	AGTGGAAGTTGATGGTGCTGT	59.856	47.619	0.0	0.0	0.0	4.4	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
288	290	1.648720	CACGCCAACCTGTGACTTG	59.351	57.895	0.00	0.00	38.36	3.16
364	368	9.571810	TTTTTCTAGACGAACTAAATATACGCA	57.428	29.630	0.00	0.00	0.00	5.24
429	433	4.876679	CACTCTCAGTGCATCAGATGAAAT	59.123	41.667	15.12	0.00	39.62	2.17
471	477	7.201723	GCCCTGCAAAATATTTATTTTTCCCAG	60.202	37.037	0.01	10.85	42.26	4.45
572	580	0.767375	AGGACTTGGTCAGTGCATGT	59.233	50.000	0.00	0.00	46.30	3.21
727	738	3.181455	ACATACAAAGGATCCTGCGCATA	60.181	43.478	17.02	1.91	0.00	3.14
738	749	1.446907	CTGCGCATAGAATGGATCCC	58.553	55.000	12.24	0.00	0.00	3.85
921	941	6.462073	TGTGTTTTCAGTTCGCTATCTTAC	57.538	37.500	0.00	0.00	0.00	2.34
974	995	2.358737	CAGCCCACAACTCCGACC	60.359	66.667	0.00	0.00	0.00	4.79
998	1019	1.211457	GACTCCAGATGAAGGCACCAT	59.789	52.381	0.00	0.00	0.00	3.55
1065	1086	0.109272	CGAAGGCAGTGAACGAGCTA	60.109	55.000	0.00	0.00	0.00	3.32
1071	1092	1.335964	GCAGTGAACGAGCTACTGTCA	60.336	52.381	13.66	0.88	42.79	3.58
1130	1151	0.534203	GCCGACAAGGTCAGGTTCAA	60.534	55.000	0.00	0.00	43.70	2.69
1145	1166	4.699257	CAGGTTCAAGTACTACTAGTCGGT	59.301	45.833	0.00	2.45	0.00	4.69
1184	1205	2.047274	CCCCGACAACGTCTGCAT	60.047	61.111	0.00	0.00	37.88	3.96
1197	1218	6.127703	ACAACGTCTGCATCTACTACTACAAT	60.128	38.462	0.00	0.00	0.00	2.71
1247	1268	6.909550	ATGTTGTTGGGCTGAAATTAACTA	57.090	33.333	0.00	0.00	0.00	2.24
1356	1377	2.284921	CCTCCCAGCTCCTCACCA	60.285	66.667	0.00	0.00	0.00	4.17
1369	1396	3.125656	TCCTCACCAAGGGATCATCATT	58.874	45.455	0.00	0.00	46.23	2.57
1381	1408	4.338012	GGATCATCATTGCCATCACCATA	58.662	43.478	0.00	0.00	0.00	2.74
1446	1473	4.212004	CGAACTTCAGCACATCTCTTTTGA	59.788	41.667	0.00	0.00	0.00	2.69
1452	1479	4.456911	TCAGCACATCTCTTTTGATTGACC	59.543	41.667	0.00	0.00	0.00	4.02
1599	1628	4.414337	AGTGCCCAAATTTTTGCAAGTA	57.586	36.364	11.79	0.00	36.86	2.24
1681	1710	4.202535	GGGGTCCTCCTTTGTAAAAGAAGA	60.203	45.833	1.31	0.00	35.33	2.87
1682	1711	4.760715	GGGTCCTCCTTTGTAAAAGAAGAC	59.239	45.833	1.31	5.20	0.00	3.01
1684	1713	5.470437	GGTCCTCCTTTGTAAAAGAAGACAG	59.530	44.000	1.31	0.00	0.00	3.51
1695	1724	3.498774	AAGAAGACAGCACCATCAACT	57.501	42.857	0.00	0.00	0.00	3.16
1743	1772	5.256806	ACTCCACCATTTAAGGCTAGTTT	57.743	39.130	0.00	0.00	0.00	2.66
1776	1805	4.618693	GCTGAACCCTTCTCTGTGTAGTAC	60.619	50.000	0.00	0.00	0.00	2.73
1824	1853	9.777297	AATAATGCTAAAACTTTTCACATTGGT	57.223	25.926	17.20	8.81	0.00	3.67
1927	1958	6.851330	GTGTGATGAGTTTAGTTTTGTACTGC	59.149	38.462	0.00	0.00	37.73	4.40
1930	1961	6.765989	TGATGAGTTTAGTTTTGTACTGCAGT	59.234	34.615	25.12	25.12	37.73	4.40
2054	2151	9.739276	ACTTCTTTGAGATACAAATTCCACATA	57.261	29.630	0.00	0.00	45.63	2.29
2133	2230	6.778834	ATTCCACATTGCATGTTTATGAGA	57.221	33.333	2.39	0.00	42.70	3.27
2183	2280	3.391506	TGTGTCAACATGTCTCTCCTG	57.608	47.619	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	9.334947	CACATTCACATGTATAAAGAAGAGGAT	57.665	33.333	0.00	0.00	42.14	3.24
87	89	6.072119	GGGGAGATAAAAACTCGTTTGTGAAT	60.072	38.462	0.00	0.00	35.49	2.57
91	93	4.721132	TGGGGAGATAAAAACTCGTTTGT	58.279	39.130	0.00	0.00	35.49	2.83
207	209	7.963532	ACCTTCAGTTCACTATTTCAGTTCTA	58.036	34.615	0.00	0.00	34.26	2.10
249	251	3.774766	TGGTGTGAGAAGTATGCTATGGT	59.225	43.478	0.00	0.00	0.00	3.55
288	290	2.165845	AGTACCTCGCCACTATGTTGTC	59.834	50.000	0.00	0.00	0.00	3.18
364	368	8.517878	CATTTTCAGACATGTCCTTGAACTAAT	58.482	33.333	23.08	18.83	0.00	1.73
421	425	6.597280	GCCACTTCTTAACTCTCATTTCATCT	59.403	38.462	0.00	0.00	0.00	2.90
429	433	2.303022	CAGGGCCACTTCTTAACTCTCA	59.697	50.000	6.18	0.00	0.00	3.27
495	503	8.360390	GTGTCCAAAGAAGTCCTAAATCATTTT	58.640	33.333	0.00	0.00	0.00	1.82
546	554	0.888619	CTGACCAAGTCCTACAGCGA	59.111	55.000	0.00	0.00	0.00	4.93
662	672	8.072567	GCTTTATCACATATTCTGGCAGTAAAG	58.927	37.037	15.27	16.60	0.00	1.85
738	749	6.920569	AATAACTAGAATTAGCACCCAACG	57.079	37.500	0.00	0.00	0.00	4.10
921	941	3.384668	CATATAGCACACCAGGTTCTCG	58.615	50.000	0.00	0.00	0.00	4.04
974	995	0.809241	GCCTTCATCTGGAGTCGCAG	60.809	60.000	3.04	3.04	0.00	5.18
1130	1151	1.661341	CGGCACCGACTAGTAGTACT	58.339	55.000	8.14	8.14	42.83	2.73
1226	1247	6.972901	GCTATAGTTAATTTCAGCCCAACAAC	59.027	38.462	0.84	0.00	0.00	3.32
1247	1268	6.434028	AGACAACACACAAACCATTATGCTAT	59.566	34.615	0.00	0.00	0.00	2.97
1356	1377	3.228453	GTGATGGCAATGATGATCCCTT	58.772	45.455	0.00	0.00	0.00	3.95
1369	1396	7.041167	CGAAAGATTTAGAATATGGTGATGGCA	60.041	37.037	0.00	0.00	0.00	4.92
1381	1408	4.007659	ACGTTGGCCGAAAGATTTAGAAT	58.992	39.130	0.00	0.00	40.70	2.40
1446	1473	6.480320	GCATCTTCAGTACTAATTCGGTCAAT	59.520	38.462	0.00	0.00	0.00	2.57
1452	1479	5.755375	ACATGGCATCTTCAGTACTAATTCG	59.245	40.000	0.00	0.00	0.00	3.34
1599	1628	7.577616	GCTTAAGTTGCAACCAGGAATAGAAAT	60.578	37.037	25.62	0.00	0.00	2.17
1681	1710	1.143684	AGTGGAAGTTGATGGTGCTGT	59.856	47.619	0.00	0.00	0.00	4.40
1682	1711	1.901591	AGTGGAAGTTGATGGTGCTG	58.098	50.000	0.00	0.00	0.00	4.41
1684	1713	3.059352	ACTAGTGGAAGTTGATGGTGC	57.941	47.619	0.00	0.00	0.00	5.01
1695	1724	6.936279	CAGATTTCCTTCTGTACTAGTGGAA	58.064	40.000	5.39	5.82	38.64	3.53
1743	1772	4.426704	AGAAGGGTTCAGCCTTAAGTCTA	58.573	43.478	10.30	0.00	37.43	2.59
1776	1805	3.631686	TGCCATATGTTTCCTTGGAATCG	59.368	43.478	2.65	0.00	0.00	3.34
1807	1836	5.244755	AGCAACACCAATGTGAAAAGTTTT	58.755	33.333	0.00	0.00	45.76	2.43
1824	1853	3.758023	CCACCAGATCAAACATAGCAACA	59.242	43.478	0.00	0.00	0.00	3.33
1912	1943	5.433526	AGGTGACTGCAGTACAAAACTAAA	58.566	37.500	21.73	0.00	41.13	1.85
1927	1958	6.093495	TCAACAAGTAAACAAGAAGGTGACTG	59.907	38.462	0.00	0.00	42.68	3.51
1930	1961	7.201785	GGATTCAACAAGTAAACAAGAAGGTGA	60.202	37.037	0.00	0.00	0.00	4.02
2054	2151	7.975616	CAGGTTTAATTAGCACATAAACATGCT	59.024	33.333	12.61	3.95	41.39	3.79
2147	2244	5.366460	TTGACACATTCATTTGGCAACATT	58.634	33.333	0.00	0.00	39.82	2.71
2183	2280	1.682323	TGCGGTTTAAAACAACCCCTC	59.318	47.619	3.76	0.00	43.12	4.30
2248	2345	9.563748	ACATTTTGATCTTTGAAAATGAACCAT	57.436	25.926	24.62	8.55	45.98	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.