AutoCloner

Multiple sequence alignment - TraesCS2D01G327800

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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	TraesCS2D01G327800	chr2D	100.000	2523	0	0	1	2523	420992075	420989553	0.000000e+00	4660
1	TraesCS2D01G327800	chr2B	88.278	2184	143	53	1	2156	493651792	493649694	0.000000e+00	2510
2	TraesCS2D01G327800	chr2B	92.468	385	17	3	2139	2523	493648345	493647973	7.940000e-150	540
3	TraesCS2D01G327800	chr2A	83.818	2268	159	73	7	2177	566987967	566985811	0.000000e+00	1964
4	TraesCS2D01G327800	chr2A	83.712	1983	156	74	1	1905	547775200	547777093	0.000000e+00	1718
5	TraesCS2D01G327800	chr2A	84.970	499	51	14	650	1132	547271185	547271675	3.770000e-133	484
6	TraesCS2D01G327800	chr2A	85.246	305	18	10	1897	2177	547783795	547784096	3.180000e-74	289
7	TraesCS2D01G327800	chr2A	83.981	206	32	1	3	208	526312299	526312095	1.980000e-46	196
8	TraesCS2D01G327800	chr2A	90.551	127	9	2	2052	2177	547271676	547271800	5.580000e-37	165
9	TraesCS2D01G327800	chr5B	86.905	252	29	4	2273	2523	455518742	455518990	1.910000e-71	279
10	TraesCS2D01G327800	chr1A	85.657	251	31	5	2274	2523	21198747	21198501	2.490000e-65	259
11	TraesCS2D01G327800	chr1A	85.500	200	24	2	1	196	580020934	580021132	1.180000e-48	204
12	TraesCS2D01G327800	chr1A	89.032	155	15	2	1	154	518470429	518470276	9.210000e-45	191
13	TraesCS2D01G327800	chr5A	83.984	256	36	5	2270	2523	480198182	480198434	9.020000e-60	241
14	TraesCS2D01G327800	chr1D	84.878	205	30	1	3	207	291581723	291581520	3.290000e-49	206
15	TraesCS2D01G327800	chr1D	87.342	158	15	2	1	154	417951387	417951543	2.580000e-40	176
16	TraesCS2D01G327800	chr7D	83.163	196	32	1	13	208	4737259	4737065	7.170000e-41	178
17	TraesCS2D01G327800	chr7D	82.915	199	33	1	11	209	96503542	96503345	7.170000e-41	178
18	TraesCS2D01G327800	chr5D	81.193	218	33	6	1	213	510099749	510099535	4.320000e-38	169
19	TraesCS2D01G327800	chr5D	79.661	236	45	3	2273	2507	382938974	382938741	1.550000e-37	167

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	TraesCS2D01G327800	chr2D	420989553	420992075	2522	True	4660.0	4660	100.0000	1	2523	1	chr2D.!!$R1	2522
1	TraesCS2D01G327800	chr2B	493647973	493651792	3819	True	1525.0	2510	90.3730	1	2523	2	chr2B.!!$R1	2522
2	TraesCS2D01G327800	chr2A	566985811	566987967	2156	True	1964.0	1964	83.8180	7	2177	1	chr2A.!!$R2	2170
3	TraesCS2D01G327800	chr2A	547775200	547777093	1893	False	1718.0	1718	83.7120	1	1905	1	chr2A.!!$F1	1904
4	TraesCS2D01G327800	chr2A	547271185	547271800	615	False	324.5	484	87.7605	650	2177	2	chr2A.!!$F3	1527

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
894	963	0.472161	TGTTTAAACCCTTGGCCCCC	60.472	55.0	15.59	0.0	0.0	5.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1894	1995	0.032912	AGATGGTTCATGGCATGGCA	60.033	50.0	25.52	25.52	0.0	4.92	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	4.008933	GGCCTCCGTGTGCTCTGT	62.009	66.667	0.00	0.00	0.00	3.41
77	78	2.341543	CTCCGTGTGCTCTGTGCT	59.658	61.111	3.20	0.00	43.37	4.40
124	125	1.803289	GTGCATCGGAAGGAAAGCC	59.197	57.895	0.00	0.00	0.00	4.35
133	134	2.216782	GAAGGAAAGCCTGGGAGGGG	62.217	65.000	0.00	0.00	46.28	4.79
152	153	1.716826	GGCGGGTGACGTGTTTTTGA	61.717	55.000	0.00	0.00	46.52	2.69
157	158	3.304391	CGGGTGACGTGTTTTTGATTGAT	60.304	43.478	0.00	0.00	37.93	2.57
175	177	6.650390	TGATTGATCAAAACAGTCAGAATCGA	59.350	34.615	13.09	0.00	33.08	3.59
176	178	7.335171	TGATTGATCAAAACAGTCAGAATCGAT	59.665	33.333	13.09	0.00	33.08	3.59
178	180	6.165577	TGATCAAAACAGTCAGAATCGATCA	58.834	36.000	0.00	0.00	35.59	2.92
208	210	2.029560	GTCCGGACTTTCGTAAACCTCT	60.030	50.000	27.64	0.00	0.00	3.69
210	212	2.991866	CCGGACTTTCGTAAACCTCTTC	59.008	50.000	0.00	0.00	0.00	2.87
211	213	3.553508	CCGGACTTTCGTAAACCTCTTCA	60.554	47.826	0.00	0.00	0.00	3.02
212	214	3.427863	CGGACTTTCGTAAACCTCTTCAC	59.572	47.826	0.00	0.00	0.00	3.18
216	234	3.713858	TTCGTAAACCTCTTCACGTGA	57.286	42.857	15.76	15.76	35.91	4.35
225	243	4.703897	ACCTCTTCACGTGAAAGAAATCA	58.296	39.130	29.32	7.27	33.07	2.57
229	247	6.293626	CCTCTTCACGTGAAAGAAATCATGTT	60.294	38.462	29.32	0.00	45.00	2.71
242	260	2.226602	TCATGTTCGAACCGTGTTGA	57.773	45.000	24.78	15.82	0.00	3.18
256	274	5.702865	ACCGTGTTGAATGATTTTCATGAG	58.297	37.500	0.00	0.00	37.15	2.90
257	275	4.560035	CCGTGTTGAATGATTTTCATGAGC	59.440	41.667	0.00	0.00	37.15	4.26
293	316	1.144057	GGATCGGCGTTGGAGATGT	59.856	57.895	6.85	0.00	0.00	3.06
294	317	1.154205	GGATCGGCGTTGGAGATGTG	61.154	60.000	6.85	0.00	0.00	3.21
295	318	1.766143	GATCGGCGTTGGAGATGTGC	61.766	60.000	6.85	0.00	0.00	4.57
296	319	2.244117	ATCGGCGTTGGAGATGTGCT	62.244	55.000	6.85	0.00	0.00	4.40
304	327	4.142600	GCGTTGGAGATGTGCTAAAAGATT	60.143	41.667	0.00	0.00	0.00	2.40
513	540	1.048724	TCTGCTCCCCCGTCCTATTG	61.049	60.000	0.00	0.00	0.00	1.90

Showing 1 to 25 of 123 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
133	134	1.298788	CAAAAACACGTCACCCGCC	60.299	57.895	0.00	0.00	41.42	6.13
152	153	7.335171	TGATCGATTCTGACTGTTTTGATCAAT	59.665	33.333	9.40	0.00	37.38	2.57
157	158	8.034804	TCTTATGATCGATTCTGACTGTTTTGA	58.965	33.333	0.00	0.00	0.00	2.69
175	177	2.877866	AGTCCGGACCGATCTTATGAT	58.122	47.619	30.82	4.74	35.26	2.45
176	178	2.359981	AGTCCGGACCGATCTTATGA	57.640	50.000	30.82	0.00	0.00	2.15
178	180	2.034305	CGAAAGTCCGGACCGATCTTAT	59.966	50.000	30.82	6.96	0.00	1.73
208	210	5.235401	TCGAACATGATTTCTTTCACGTGAA	59.765	36.000	26.53	26.53	0.00	3.18
210	212	5.017484	TCGAACATGATTTCTTTCACGTG	57.983	39.130	9.94	9.94	0.00	4.49
211	213	5.440685	GTTCGAACATGATTTCTTTCACGT	58.559	37.500	23.12	0.00	0.00	4.49
212	214	4.846137	GGTTCGAACATGATTTCTTTCACG	59.154	41.667	28.24	0.00	0.00	4.35
216	234	4.274950	ACACGGTTCGAACATGATTTCTTT	59.725	37.500	28.52	9.73	0.00	2.52
225	243	3.135225	TCATTCAACACGGTTCGAACAT	58.865	40.909	28.24	14.01	0.00	2.71
228	246	4.822036	AAATCATTCAACACGGTTCGAA	57.178	36.364	0.00	0.00	0.00	3.71
229	247	4.273724	TGAAAATCATTCAACACGGTTCGA	59.726	37.500	0.00	0.00	0.00	3.71
242	260	2.355756	CGTCCGGCTCATGAAAATCATT	59.644	45.455	0.00	0.00	34.28	2.57
257	275	4.215742	TTATCCGCAGCCGTCCGG	62.216	66.667	0.24	0.24	45.64	5.14
265	283	1.734477	CGCCGATCCTTATCCGCAG	60.734	63.158	0.00	0.00	36.49	5.18
272	290	1.068588	CATCTCCAACGCCGATCCTTA	59.931	52.381	0.00	0.00	0.00	2.69
273	291	0.179073	CATCTCCAACGCCGATCCTT	60.179	55.000	0.00	0.00	0.00	3.36
294	317	9.295214	GCTCAAATTCTCCTAAAATCTTTTAGC	57.705	33.333	14.29	1.37	45.11	3.09
304	327	7.094205	GGATTTGTCTGCTCAAATTCTCCTAAA	60.094	37.037	13.16	0.00	44.62	1.85
308	331	4.704057	AGGATTTGTCTGCTCAAATTCTCC	59.296	41.667	13.55	11.72	45.19	3.71
319	342	0.255890	TGCCCCTAGGATTTGTCTGC	59.744	55.000	11.48	0.29	33.47	4.26
485	512	2.125188	GGGAGCAGAGCAGAGTGC	60.125	66.667	0.00	0.00	45.46	4.40
513	540	2.811317	CGGTGAGCGAGACAAGGC	60.811	66.667	0.00	0.00	0.00	4.35

Showing 1 to 25 of 112 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.