AutoCloner

Multiple sequence alignment - TraesCS1D01G351500

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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	TraesCS1D01G351500	chr1D	100.000	3197	0	0	1	3197	436655274	436652078	0.000000e+00	5904
1	TraesCS1D01G351500	chr1A	93.527	2750	83	21	482	3197	533734291	533731603	0.000000e+00	4004
2	TraesCS1D01G351500	chr1A	97.508	321	7	1	482	801	30919388	30919708	6.030000e-152	547
3	TraesCS1D01G351500	chr1A	81.031	485	25	18	1	464	533734775	533734337	1.110000e-84	324
4	TraesCS1D01G351500	chr1B	90.283	2542	118	50	579	3059	591452287	591449814	0.000000e+00	3206
5	TraesCS1D01G351500	chr1B	81.048	496	36	25	7	468	591452916	591452445	3.050000e-90	342
6	TraesCS1D01G351500	chr1B	97.902	143	2	1	3055	3197	591449748	591449607	2.460000e-61	246
7	TraesCS1D01G351500	chr7D	89.430	1457	124	16	969	2422	496785497	496786926	0.000000e+00	1810
8	TraesCS1D01G351500	chr7B	87.984	1548	144	15	963	2495	524919263	524920783	0.000000e+00	1790
9	TraesCS1D01G351500	chr7B	81.446	733	115	16	572	1298	194924975	194925692	5.940000e-162	580
10	TraesCS1D01G351500	chr7A	89.156	1457	128	13	969	2422	562215664	562217093	0.000000e+00	1788
11	TraesCS1D01G351500	chr2A	98.131	321	5	1	482	801	643979474	643979794	2.790000e-155	558
12	TraesCS1D01G351500	chr2A	78.829	444	33	17	39	464	643979028	643979428	3.190000e-60	243
13	TraesCS1D01G351500	chr6A	96.573	321	8	2	482	801	30404127	30403809	2.180000e-146	529
14	TraesCS1D01G351500	chr6A	77.405	447	34	18	39	464	30404573	30404173	1.500000e-48	204
15	TraesCS1D01G351500	chr4A	96.262	321	11	1	482	801	119349080	119348760	2.830000e-145	525
16	TraesCS1D01G351500	chr4A	78.747	447	28	20	39	464	119349526	119349126	1.480000e-58	237
17	TraesCS1D01G351500	chr5A	96.333	300	9	2	482	780	555366899	555366601	2.870000e-135	492
18	TraesCS1D01G351500	chr5A	78.202	445	34	15	39	464	555367344	555366944	3.210000e-55	226

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	TraesCS1D01G351500	chr1D	436652078	436655274	3196	True	5904.000000	5904	100.000000	1	3197	1	chr1D.!!$R1	3196
1	TraesCS1D01G351500	chr1A	533731603	533734775	3172	True	2164.000000	4004	87.279000	1	3197	2	chr1A.!!$R1	3196
2	TraesCS1D01G351500	chr1B	591449607	591452916	3309	True	1264.666667	3206	89.744333	7	3197	3	chr1B.!!$R1	3190
3	TraesCS1D01G351500	chr7D	496785497	496786926	1429	False	1810.000000	1810	89.430000	969	2422	1	chr7D.!!$F1	1453
4	TraesCS1D01G351500	chr7B	524919263	524920783	1520	False	1790.000000	1790	87.984000	963	2495	1	chr7B.!!$F2	1532
5	TraesCS1D01G351500	chr7B	194924975	194925692	717	False	580.000000	580	81.446000	572	1298	1	chr7B.!!$F1	726
6	TraesCS1D01G351500	chr7A	562215664	562217093	1429	False	1788.000000	1788	89.156000	969	2422	1	chr7A.!!$F1	1453
7	TraesCS1D01G351500	chr2A	643979028	643979794	766	False	400.500000	558	88.480000	39	801	2	chr2A.!!$F1	762
8	TraesCS1D01G351500	chr6A	30403809	30404573	764	True	366.500000	529	86.989000	39	801	2	chr6A.!!$R1	762
9	TraesCS1D01G351500	chr4A	119348760	119349526	766	True	381.000000	525	87.504500	39	801	2	chr4A.!!$R1	762
10	TraesCS1D01G351500	chr5A	555366601	555367344	743	True	359.000000	492	87.267500	39	780	2	chr5A.!!$R1	741

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
273	302	0.246635	AGGTTGGTTCGTCTCATCCG	59.753	55.0	0.00	0.0	0.00	4.18	F
1003	1128	0.242017	GTTCCTGCAGTTGGACATGC	59.758	55.0	13.81	0.0	42.86	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1353	1478	0.671472	TGTTGCAGTGGCTGAGATCG	60.671	55.0	0.0	0.0	41.91	3.69	R
2665	2825	0.658244	CACACGCACAGACACATTGC	60.658	55.0	0.0	0.0	0.00	3.56	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
66	68	1.474320	GCCCCCAACCAAGAAAAACAC	60.474	52.381	0.00	0.00	0.00	3.32
175	190	1.364171	CTCCCCTACTTCATCGGCG	59.636	63.158	0.00	0.00	0.00	6.46
176	191	2.280186	CCCCTACTTCATCGGCGC	60.280	66.667	0.00	0.00	0.00	6.53
190	219	4.457496	GCGCCCTGCTGCTGTCTA	62.457	66.667	0.00	0.00	41.73	2.59
192	221	2.510238	GCCCTGCTGCTGTCTACG	60.510	66.667	0.00	0.00	0.00	3.51
267	296	2.166664	GAGCAGATAGGTTGGTTCGTCT	59.833	50.000	0.00	0.00	0.00	4.18
268	297	2.166664	AGCAGATAGGTTGGTTCGTCTC	59.833	50.000	0.00	0.00	0.00	3.36
269	298	2.094182	GCAGATAGGTTGGTTCGTCTCA	60.094	50.000	0.00	0.00	0.00	3.27
270	299	3.430929	GCAGATAGGTTGGTTCGTCTCAT	60.431	47.826	0.00	0.00	0.00	2.90
271	300	4.363999	CAGATAGGTTGGTTCGTCTCATC	58.636	47.826	0.00	0.00	0.00	2.92
272	301	3.385111	AGATAGGTTGGTTCGTCTCATCC	59.615	47.826	0.00	0.00	0.00	3.51
273	302	0.246635	AGGTTGGTTCGTCTCATCCG	59.753	55.000	0.00	0.00	0.00	4.18
274	303	0.739813	GGTTGGTTCGTCTCATCCGG	60.740	60.000	0.00	0.00	0.00	5.14
275	304	1.079405	TTGGTTCGTCTCATCCGGC	60.079	57.895	0.00	0.00	0.00	6.13
276	305	2.582498	GGTTCGTCTCATCCGGCG	60.582	66.667	0.00	0.00	0.00	6.46
277	306	3.255379	GTTCGTCTCATCCGGCGC	61.255	66.667	0.00	0.00	0.00	6.53
278	307	3.754530	TTCGTCTCATCCGGCGCA	61.755	61.111	10.83	0.00	0.00	6.09
279	308	3.699955	TTCGTCTCATCCGGCGCAG	62.700	63.158	10.83	4.65	0.00	5.18
338	367	4.902258	GGGTAGGGAGGGGAGGGC	62.902	77.778	0.00	0.00	0.00	5.19
353	382	4.002797	GGCACCTCCGCAATTTCT	57.997	55.556	0.00	0.00	0.00	2.52
354	383	1.803289	GGCACCTCCGCAATTTCTC	59.197	57.895	0.00	0.00	0.00	2.87
424	462	9.464714	CATATTATGCGGAGTCATATAGGTTAC	57.535	37.037	0.00	0.00	0.00	2.50
425	463	7.719871	ATTATGCGGAGTCATATAGGTTACT	57.280	36.000	0.00	0.00	0.00	2.24
426	464	8.818622	ATTATGCGGAGTCATATAGGTTACTA	57.181	34.615	0.00	0.00	0.00	1.82
427	465	8.640063	TTATGCGGAGTCATATAGGTTACTAA	57.360	34.615	0.00	0.00	31.86	2.24
464	507	4.339872	TGAGCCATTGTGCAAGATTTTT	57.660	36.364	0.00	0.00	0.00	1.94
468	511	3.808726	GCCATTGTGCAAGATTTTTGTGA	59.191	39.130	0.00	0.00	0.00	3.58
469	512	4.084223	GCCATTGTGCAAGATTTTTGTGAG	60.084	41.667	0.00	0.00	0.00	3.51
473	516	5.771153	TGTGCAAGATTTTTGTGAGATGA	57.229	34.783	0.00	0.00	0.00	2.92
474	517	5.765176	TGTGCAAGATTTTTGTGAGATGAG	58.235	37.500	0.00	0.00	0.00	2.90
475	518	5.300034	TGTGCAAGATTTTTGTGAGATGAGT	59.700	36.000	0.00	0.00	0.00	3.41
476	519	5.855395	GTGCAAGATTTTTGTGAGATGAGTC	59.145	40.000	0.00	0.00	0.00	3.36
479	522	7.391275	TGCAAGATTTTTGTGAGATGAGTCATA	59.609	33.333	5.38	0.00	0.00	2.15
480	523	8.404000	GCAAGATTTTTGTGAGATGAGTCATAT	58.596	33.333	5.38	1.88	0.00	1.78
842	964	6.837992	TCTAATTACCATTTGTTTCGAGTGC	58.162	36.000	0.00	0.00	0.00	4.40
851	973	4.794278	TTGTTTCGAGTGCTCCTACATA	57.206	40.909	0.00	0.00	0.00	2.29
857	979	4.969484	TCGAGTGCTCCTACATATACTCA	58.031	43.478	0.00	0.00	35.49	3.41
917	1041	8.491134	TGTATTGGGCTATTAGTGTAGTTCAAT	58.509	33.333	0.00	0.00	34.35	2.57
1003	1128	0.242017	GTTCCTGCAGTTGGACATGC	59.758	55.000	13.81	0.00	42.86	4.06
1029	1154	3.681897	CAGCTGTTACCATGACTTCAGTC	59.318	47.826	5.25	0.00	44.97	3.51
1088	1213	1.202710	TGGCATCACAAGTTACGGTGT	60.203	47.619	9.30	0.41	36.43	4.16
1104	1229	1.336609	GGTGTCTTAAAGGCGTCGTCT	60.337	52.381	0.00	0.00	0.00	4.18
1353	1478	2.435059	GTCAAGGGAGTCGCTGCC	60.435	66.667	10.92	8.90	42.52	4.85
2217	2345	5.962433	TGAGGTAAAGGAGAACGATAACTG	58.038	41.667	0.00	0.00	0.00	3.16
2283	2412	3.555966	AGTTTTGCAGCCTAGAGTGTTT	58.444	40.909	0.00	0.00	0.00	2.83
2340	2474	5.810587	GCTATATTTCTCAGTTGTCGGTCAA	59.189	40.000	0.00	0.00	0.00	3.18
2433	2585	1.522668	TGACACATTACACCTGCTGC	58.477	50.000	0.00	0.00	0.00	5.25
2478	2630	8.679100	TGACAAACCGTGGAATAATAATAAAGG	58.321	33.333	0.00	0.00	0.00	3.11
2548	2702	2.205022	ATGTTGTGGTCACCATCAGG	57.795	50.000	0.00	0.00	35.28	3.86
2631	2791	2.422597	TGATTGGCGAGTTTACACAGG	58.577	47.619	0.00	0.00	0.00	4.00
2665	2825	7.702348	TGTCAGTCTTGTTATTATCGATGTGAG	59.298	37.037	8.54	0.00	0.00	3.51
2974	3165	1.246737	GGAGGCCTTTGCTGGTCAAG	61.247	60.000	6.77	0.00	35.84	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	68	1.607467	CCCTTGGCTCACCCTTTGG	60.607	63.158	0.00	0.00	33.59	3.28
175	190	2.510238	CGTAGACAGCAGCAGGGC	60.510	66.667	0.00	0.00	0.00	5.19
176	191	2.510238	GCGTAGACAGCAGCAGGG	60.510	66.667	0.00	0.00	34.19	4.45
186	215	4.139234	GTGGGACGGGGCGTAGAC	62.139	72.222	0.00	0.00	41.37	2.59
267	296	4.159901	TGATGCTGCGCCGGATGA	62.160	61.111	11.11	0.00	0.00	2.92
268	297	3.646976	CTGATGCTGCGCCGGATG	61.647	66.667	11.11	0.00	0.00	3.51
269	298	3.687321	AACTGATGCTGCGCCGGAT	62.687	57.895	5.05	5.33	0.00	4.18
270	299	3.899981	AAACTGATGCTGCGCCGGA	62.900	57.895	5.05	0.00	0.00	5.14
271	300	3.386867	GAAACTGATGCTGCGCCGG	62.387	63.158	4.18	0.00	0.00	6.13
272	301	2.099062	GAAACTGATGCTGCGCCG	59.901	61.111	4.18	0.00	0.00	6.46
273	302	1.023513	AGAGAAACTGATGCTGCGCC	61.024	55.000	4.18	0.00	0.00	6.53
274	303	0.373024	GAGAGAAACTGATGCTGCGC	59.627	55.000	0.00	0.00	0.00	6.09
275	304	1.659601	CAGAGAGAAACTGATGCTGCG	59.340	52.381	0.00	0.00	37.54	5.18
276	305	2.697654	ACAGAGAGAAACTGATGCTGC	58.302	47.619	0.00	0.00	38.55	5.25
277	306	4.063689	ACAACAGAGAGAAACTGATGCTG	58.936	43.478	0.00	0.00	40.23	4.41
278	307	4.348863	ACAACAGAGAGAAACTGATGCT	57.651	40.909	0.00	0.00	40.23	3.79
279	308	6.545504	TTAACAACAGAGAGAAACTGATGC	57.454	37.500	0.00	0.00	40.23	3.91
280	309	9.604626	GATTTTAACAACAGAGAGAAACTGATG	57.395	33.333	0.00	0.00	41.58	3.07
281	310	9.342308	TGATTTTAACAACAGAGAGAAACTGAT	57.658	29.630	0.00	0.00	38.55	2.90
282	311	8.731275	TGATTTTAACAACAGAGAGAAACTGA	57.269	30.769	0.00	0.00	38.55	3.41
283	312	9.956720	ATTGATTTTAACAACAGAGAGAAACTG	57.043	29.630	0.00	0.00	40.68	3.16
399	437	9.422681	AGTAACCTATATGACTCCGCATAATAT	57.577	33.333	0.00	0.00	34.67	1.28
407	445	8.088981	AGCAATTTAGTAACCTATATGACTCCG	58.911	37.037	0.00	0.00	0.00	4.63
418	456	9.113838	CATCTCACAATAGCAATTTAGTAACCT	57.886	33.333	0.00	0.00	0.00	3.50
419	457	9.109393	TCATCTCACAATAGCAATTTAGTAACC	57.891	33.333	0.00	0.00	0.00	2.85
421	459	8.830580	GCTCATCTCACAATAGCAATTTAGTAA	58.169	33.333	0.00	0.00	33.38	2.24
422	460	7.442364	GGCTCATCTCACAATAGCAATTTAGTA	59.558	37.037	0.00	0.00	34.85	1.82
423	461	6.261826	GGCTCATCTCACAATAGCAATTTAGT	59.738	38.462	0.00	0.00	34.85	2.24
424	462	6.261603	TGGCTCATCTCACAATAGCAATTTAG	59.738	38.462	0.00	0.00	34.85	1.85
425	463	6.121590	TGGCTCATCTCACAATAGCAATTTA	58.878	36.000	0.00	0.00	34.85	1.40
426	464	4.951715	TGGCTCATCTCACAATAGCAATTT	59.048	37.500	0.00	0.00	34.85	1.82
427	465	4.529897	TGGCTCATCTCACAATAGCAATT	58.470	39.130	0.00	0.00	34.85	2.32
434	472	2.426024	GCACAATGGCTCATCTCACAAT	59.574	45.455	0.00	0.00	0.00	2.71
464	507	6.662663	CAGATCCCTATATGACTCATCTCACA	59.337	42.308	0.00	0.00	0.00	3.58
468	511	7.900246	ACAATCAGATCCCTATATGACTCATCT	59.100	37.037	0.00	0.00	36.22	2.90
469	512	8.076910	ACAATCAGATCCCTATATGACTCATC	57.923	38.462	0.00	0.00	36.22	2.92
473	516	6.070881	GCAGACAATCAGATCCCTATATGACT	60.071	42.308	0.00	0.00	36.22	3.41
474	517	6.105333	GCAGACAATCAGATCCCTATATGAC	58.895	44.000	0.00	0.00	36.22	3.06
475	518	5.105595	CGCAGACAATCAGATCCCTATATGA	60.106	44.000	0.00	0.00	37.71	2.15
476	519	5.107824	CGCAGACAATCAGATCCCTATATG	58.892	45.833	0.00	0.00	0.00	1.78
479	522	2.968574	ACGCAGACAATCAGATCCCTAT	59.031	45.455	0.00	0.00	0.00	2.57
480	523	2.101415	CACGCAGACAATCAGATCCCTA	59.899	50.000	0.00	0.00	0.00	3.53
821	943	5.335661	GGAGCACTCGAAACAAATGGTAATT	60.336	40.000	0.00	0.00	0.00	1.40
842	964	7.038729	ACACCATCCATTGAGTATATGTAGGAG	60.039	40.741	0.00	0.00	0.00	3.69
857	979	7.062322	TGCAGATTCTAATTACACCATCCATT	58.938	34.615	0.00	0.00	0.00	3.16
1029	1154	2.670934	AAAGCGGCCTGAGCACTG	60.671	61.111	0.00	0.00	42.56	3.66
1088	1213	3.057104	TGATGAAGACGACGCCTTTAAGA	60.057	43.478	0.00	0.00	0.00	2.10
1104	1229	6.234920	TCCCAATTCGAAGTTAACTGATGAA	58.765	36.000	9.34	13.32	0.00	2.57
1353	1478	0.671472	TGTTGCAGTGGCTGAGATCG	60.671	55.000	0.00	0.00	41.91	3.69
2217	2345	5.461078	TGCCTTTATTATTCTCTTCGTACGC	59.539	40.000	11.24	0.00	0.00	4.42
2283	2412	5.246203	GGCATACTCCTTCCTACATGATGTA	59.754	44.000	5.05	5.05	0.00	2.29
2433	2585	3.675698	GTCAACTTCGGAAGCTACAAGAG	59.324	47.826	17.37	0.00	0.00	2.85
2478	2630	4.094887	TCCGAGCAACTATCAAAGAAATGC	59.905	41.667	0.00	0.00	34.93	3.56
2631	2791	6.481954	AATAACAAGACTGACAACGGAATC	57.518	37.500	0.00	0.00	0.00	2.52
2665	2825	0.658244	CACACGCACAGACACATTGC	60.658	55.000	0.00	0.00	0.00	3.56
2709	2869	6.088883	CGCCAAAATTGTACCAAAATACTCAC	59.911	38.462	0.00	0.00	0.00	3.51
2734	2894	1.661112	AGAGCAGCGCGAGATAAAAAC	59.339	47.619	12.10	0.00	0.00	2.43
2976	3167	4.436998	CTCCACGACACTCCCCGC	62.437	72.222	0.00	0.00	0.00	6.13
2977	3168	3.760035	CCTCCACGACACTCCCCG	61.760	72.222	0.00	0.00	0.00	5.73
2979	3170	2.997897	AGCCTCCACGACACTCCC	60.998	66.667	0.00	0.00	0.00	4.30
2980	3171	2.262915	CAGCCTCCACGACACTCC	59.737	66.667	0.00	0.00	0.00	3.85
2981	3172	2.262915	CCAGCCTCCACGACACTC	59.737	66.667	0.00	0.00	0.00	3.51
2982	3173	3.314331	CCCAGCCTCCACGACACT	61.314	66.667	0.00	0.00	0.00	3.55
3113	3373	5.132502	CCTGCCATACAACTCCATATTTGA	58.867	41.667	0.00	0.00	0.00	2.69
3144	3404	1.021390	GTGCAATCCACGGACTCAGG	61.021	60.000	0.00	0.00	34.22	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.