AutoCloner

Multiple sequence alignment - TraesCS1B01G192600

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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	TraesCS1B01G192600	chr1B	100.000	4898	0	0	1	4898	344842927	344838030	0.000000e+00	9046.0
1	TraesCS1B01G192600	chr1A	94.518	2955	124	18	1847	4775	334451724	334448782	0.000000e+00	4525.0
2	TraesCS1B01G192600	chr1A	94.050	1042	38	12	710	1733	334452842	334451807	0.000000e+00	1559.0
3	TraesCS1B01G192600	chr1A	94.173	635	31	4	4268	4896	334416718	334416084	0.000000e+00	963.0
4	TraesCS1B01G192600	chr1A	93.651	252	12	3	410	661	334453094	334452847	1.660000e-99	374.0
5	TraesCS1B01G192600	chr1A	90.435	115	6	3	1747	1856	584082913	584082799	3.950000e-31	147.0
6	TraesCS1B01G192600	chr1A	89.024	82	8	1	2519	2600	334451125	334451045	3.120000e-17	100.0
7	TraesCS1B01G192600	chr1D	93.984	2959	135	20	1845	4775	267986754	267989697	0.000000e+00	4438.0
8	TraesCS1B01G192600	chr1D	95.131	1068	31	11	681	1733	267985612	267986673	0.000000e+00	1664.0
9	TraesCS1B01G192600	chr1D	89.000	400	35	5	4219	4616	268461813	268462205	2.050000e-133	486.0
10	TraesCS1B01G192600	chr1D	94.805	231	11	1	410	640	267985368	267985597	4.660000e-95	359.0
11	TraesCS1B01G192600	chr1D	85.714	231	16	5	5	220	267984812	267985040	1.370000e-55	228.0
12	TraesCS1B01G192600	chr1D	81.145	297	29	16	4612	4883	268467360	268467654	3.840000e-51	213.0
13	TraesCS1B01G192600	chr1D	91.463	82	6	1	2519	2600	267987355	267987435	1.440000e-20	111.0
14	TraesCS1B01G192600	chr6A	98.913	92	0	1	1758	1848	503767444	503767535	3.920000e-36	163.0
15	TraesCS1B01G192600	chr4A	97.826	92	2	0	1753	1844	59254318	59254227	5.070000e-35	159.0
16	TraesCS1B01G192600	chr3B	96.842	95	2	1	1755	1849	447014633	447014540	1.830000e-34	158.0
17	TraesCS1B01G192600	chr5D	94.949	99	5	0	1744	1842	364250210	364250308	6.560000e-34	156.0
18	TraesCS1B01G192600	chr6D	95.876	97	1	3	1752	1846	79346548	79346453	2.360000e-33	154.0
19	TraesCS1B01G192600	chr6B	95.789	95	4	0	1750	1844	546656566	546656660	2.360000e-33	154.0
20	TraesCS1B01G192600	chr7B	88.793	116	11	2	1749	1864	20241016	20240903	1.840000e-29	141.0
21	TraesCS1B01G192600	chr3D	91.346	104	6	3	1744	1846	414368803	414368702	6.610000e-29	139.0
22	TraesCS1B01G192600	chr2A	85.714	84	11	1	307	389	706531654	706531571	2.430000e-13	87.9

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	TraesCS1B01G192600	chr1B	344838030	344842927	4897	True	9046.0	9046	100.00000	1	4898	1	chr1B.!!$R1	4897
1	TraesCS1B01G192600	chr1A	334448782	334453094	4312	True	1639.5	4525	92.81075	410	4775	4	chr1A.!!$R3	4365
2	TraesCS1B01G192600	chr1A	334416084	334416718	634	True	963.0	963	94.17300	4268	4896	1	chr1A.!!$R1	628
3	TraesCS1B01G192600	chr1D	267984812	267989697	4885	False	1360.0	4438	92.21940	5	4775	5	chr1D.!!$F3	4770

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	Hairpin	End Stability	Orientation
267	413	0.893270	CACCGGGCATGGAAAAGACA	60.893	55.0	6.32	0.00	3.41	F
268	414	0.893727	ACCGGGCATGGAAAAGACAC	60.894	55.0	6.32	0.00	3.67	F
269	415	0.893270	CCGGGCATGGAAAAGACACA	60.893	55.0	0.00	0.00	3.72	F
2003	2203	0.530744	GTCATAGGGTCGAGTGTGCA	59.469	55.0	0.00	0.00	4.57	F
2139	2339	0.257328	TGGGCTTTGTTGTCCACTCA	59.743	50.0	0.00	36.71	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1858	2058	0.184451	CTGGGTAGGGCCGTACTCTA	59.816	60.000	30.30	18.84	38.44	2.43	R
1944	2144	5.011533	TCCCTATGCTTCTAGATGCTTCTTC	59.988	44.000	25.75	2.78	33.17	2.87	R
2139	2339	5.247110	AGGAATGACTGACAGTGTGAGTATT	59.753	40.000	15.74	14.20	28.74	1.89	R
3774	3996	1.228124	CGGGCAAGTGGGTTCTTCA	60.228	57.895	0.00	0.00	0.00	3.02	R
4093	4318	4.165372	GGTCCAGGTAGATATTTGGTTCCA	59.835	45.833	0.00	0.00	32.51	3.53	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
41	42	4.673441	ACATGTGTATGAAGTCGCTACTC	58.327	43.478	0.00	0.00	37.73	2.59
56	57	3.066760	CGCTACTCCATCAGTGATACACA	59.933	47.826	5.03	0.00	36.74	3.72
87	89	2.286184	CCGTTATGAAGTATTGCGGTGC	60.286	50.000	0.00	0.00	33.23	5.01
98	114	3.423154	GCGGTGCGAAGAAGGTGG	61.423	66.667	0.00	0.00	0.00	4.61
100	116	2.032681	GGTGCGAAGAAGGTGGCT	59.967	61.111	0.00	0.00	0.00	4.75
122	138	3.719144	GGCGCGCGTTTAGGTGTT	61.719	61.111	32.35	0.00	0.00	3.32
177	193	4.097741	TGCAACTATGTTAACCCATCATGC	59.902	41.667	2.48	7.63	32.69	4.06
207	223	3.900966	TGAGAGAAGACCCATCACATG	57.099	47.619	0.00	0.00	0.00	3.21
220	236	4.400251	CCCATCACATGCAATTCTTGTACT	59.600	41.667	0.00	0.00	32.52	2.73
221	237	5.589855	CCCATCACATGCAATTCTTGTACTA	59.410	40.000	0.00	0.00	32.52	1.82
222	238	6.095300	CCCATCACATGCAATTCTTGTACTAA	59.905	38.462	0.00	0.00	32.52	2.24
223	239	6.968904	CCATCACATGCAATTCTTGTACTAAC	59.031	38.462	0.00	0.00	32.52	2.34
224	240	7.361971	CCATCACATGCAATTCTTGTACTAACA	60.362	37.037	0.00	0.00	32.52	2.41
225	241	7.686438	TCACATGCAATTCTTGTACTAACAT	57.314	32.000	0.00	0.00	34.97	2.71
226	242	7.529158	TCACATGCAATTCTTGTACTAACATG	58.471	34.615	0.00	0.00	38.59	3.21
253	399	2.912771	TGTAATTCACTATGCCACCGG	58.087	47.619	0.00	0.00	0.00	5.28
264	410	3.287445	CCACCGGGCATGGAAAAG	58.713	61.111	6.32	0.00	39.87	2.27
265	411	1.304052	CCACCGGGCATGGAAAAGA	60.304	57.895	6.32	0.00	39.87	2.52
266	412	1.595093	CCACCGGGCATGGAAAAGAC	61.595	60.000	6.32	0.00	39.87	3.01
267	413	0.893270	CACCGGGCATGGAAAAGACA	60.893	55.000	6.32	0.00	0.00	3.41
268	414	0.893727	ACCGGGCATGGAAAAGACAC	60.894	55.000	6.32	0.00	0.00	3.67
269	415	0.893270	CCGGGCATGGAAAAGACACA	60.893	55.000	0.00	0.00	0.00	3.72
270	416	1.176527	CGGGCATGGAAAAGACACAT	58.823	50.000	0.00	0.00	0.00	3.21
271	417	1.133025	CGGGCATGGAAAAGACACATC	59.867	52.381	0.00	0.00	0.00	3.06
272	418	2.450476	GGGCATGGAAAAGACACATCT	58.550	47.619	0.00	0.00	36.42	2.90

Showing 1 to 25 of 164 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	7.944002	GAGTAGCGACTTCATACACATGTATGT	60.944	40.741	24.42	11.19	45.21	2.29
16	17	6.360947	GAGTAGCGACTTCATACACATGTATG	59.639	42.308	21.17	21.17	45.71	2.39
41	42	7.754924	GGTGTTTAAATTGTGTATCACTGATGG	59.245	37.037	1.42	0.00	35.11	3.51
56	57	9.349145	GCAATACTTCATAACGGTGTTTAAATT	57.651	29.630	0.00	0.00	0.00	1.82
87	89	1.153628	CCGGTAGCCACCTTCTTCG	60.154	63.158	0.00	0.00	43.33	3.79
106	122	0.585519	CATAACACCTAAACGCGCGC	60.586	55.000	32.58	23.91	0.00	6.86
107	123	0.993532	TCATAACACCTAAACGCGCG	59.006	50.000	30.96	30.96	0.00	6.86
144	160	7.094549	GGGTTAACATAGTTGCATGTTACAAGA	60.095	37.037	9.57	0.00	46.10	3.02
147	163	6.004574	TGGGTTAACATAGTTGCATGTTACA	58.995	36.000	9.57	3.72	46.10	2.41
177	193	3.139850	GGTCTTCTCTCATGCATGATGG	58.860	50.000	28.81	22.30	36.02	3.51
190	206	2.408271	TGCATGTGATGGGTCTTCTC	57.592	50.000	0.00	0.00	0.00	2.87
220	236	6.832520	AGTGAATTACATGGTTGCATGTTA	57.167	33.333	0.00	0.00	42.56	2.41
221	237	5.726980	AGTGAATTACATGGTTGCATGTT	57.273	34.783	0.00	0.00	42.56	2.71
222	238	6.681120	GCATAGTGAATTACATGGTTGCATGT	60.681	38.462	0.00	0.00	46.35	3.21
223	239	5.688621	GCATAGTGAATTACATGGTTGCATG	59.311	40.000	0.00	0.00	38.46	4.06
224	240	5.221303	GGCATAGTGAATTACATGGTTGCAT	60.221	40.000	0.00	0.00	0.00	3.96
225	241	4.097741	GGCATAGTGAATTACATGGTTGCA	59.902	41.667	0.00	0.00	0.00	4.08
226	242	4.097741	TGGCATAGTGAATTACATGGTTGC	59.902	41.667	0.00	0.00	0.00	4.17
253	399	2.821969	ACAGATGTGTCTTTTCCATGCC	59.178	45.455	0.00	0.00	30.42	4.40
278	424	9.243637	GCAAACAAAGATGTGTCTATGTTAAAA	57.756	29.630	0.00	0.00	40.46	1.52
279	425	7.589587	CGCAAACAAAGATGTGTCTATGTTAAA	59.410	33.333	0.00	0.00	40.46	1.52
280	426	7.075121	CGCAAACAAAGATGTGTCTATGTTAA	58.925	34.615	0.00	0.00	40.46	2.01
281	427	6.598525	CGCAAACAAAGATGTGTCTATGTTA	58.401	36.000	0.00	0.00	40.46	2.41
282	428	5.451908	CGCAAACAAAGATGTGTCTATGTT	58.548	37.500	0.00	0.00	40.46	2.71
283	429	4.613622	GCGCAAACAAAGATGTGTCTATGT	60.614	41.667	0.30	0.00	40.46	2.29

Showing 1 to 25 of 149 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.