AutoCloner

Multiple sequence alignment - TraesCS4D01G021400

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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	TraesCS4D01G021400	chr4D	100.000	5632	0	0	1	5632	9212407	9218038	0.000000e+00	10401.0
1	TraesCS4D01G021400	chr4D	88.785	107	12	0	528	634	11114307	11114201	1.270000e-26	132.0
2	TraesCS4D01G021400	chr4D	88.785	107	12	0	528	634	11130921	11130815	1.270000e-26	132.0
3	TraesCS4D01G021400	chr4A	95.061	2288	97	10	3356	5631	594214792	594212509	0.000000e+00	3585.0
4	TraesCS4D01G021400	chr4A	93.714	1050	55	5	2317	3358	594215804	594214758	0.000000e+00	1563.0
5	TraesCS4D01G021400	chr4A	95.007	721	35	1	966	1685	594217157	594216437	0.000000e+00	1131.0
6	TraesCS4D01G021400	chr4A	86.219	283	18	11	1683	1963	594216334	594216071	2.570000e-73	287.0
7	TraesCS4D01G021400	chr4A	96.429	112	3	1	396	506	594217524	594217413	3.470000e-42	183.0
8	TraesCS4D01G021400	chr4A	86.916	107	14	0	528	634	591929019	591928913	2.760000e-23	121.0
9	TraesCS4D01G021400	chr4A	87.000	100	3	1	157	246	594217764	594217665	2.780000e-18	104.0
10	TraesCS4D01G021400	chr4A	90.000	70	3	3	103	171	594217850	594217784	2.800000e-13	87.9
11	TraesCS4D01G021400	chr4A	97.917	48	0	1	563	609	594217419	594217372	1.300000e-11	82.4
12	TraesCS4D01G021400	chr4A	100.000	42	0	0	369	410	594217577	594217536	1.680000e-10	78.7
13	TraesCS4D01G021400	chr4B	92.353	1713	95	12	3427	5106	17093983	17095692	0.000000e+00	2405.0
14	TraesCS4D01G021400	chr4B	93.582	1044	57	5	2314	3350	17092915	17093955	0.000000e+00	1548.0
15	TraesCS4D01G021400	chr4B	90.201	1194	71	22	779	1963	17091494	17092650	0.000000e+00	1515.0
16	TraesCS4D01G021400	chr4B	97.668	386	9	0	5246	5631	17095705	17096090	0.000000e+00	664.0
17	TraesCS4D01G021400	chr4B	87.963	108	12	1	528	634	21149725	21149618	5.920000e-25	126.0
18	TraesCS4D01G021400	chrUn	100.000	416	0	0	5216	5631	477166291	477166706	0.000000e+00	769.0

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	TraesCS4D01G021400	chr4D	9212407	9218038	5631	False	10401.000000	10401	100.000	1	5632	1	chr4D.!!$F1	5631
1	TraesCS4D01G021400	chr4A	594212509	594217850	5341	True	789.111111	3585	93.483	103	5631	9	chr4A.!!$R2	5528
2	TraesCS4D01G021400	chr4B	17091494	17096090	4596	False	1533.000000	2405	93.451	779	5631	4	chr4B.!!$F1	4852

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
72	73	0.036010	CTCCCTGTTGCATCGAGGTT	60.036	55.000	0.00	0.0	0.00	3.50	F
521	608	0.171007	CCATTGCCAAGCCAAGTACG	59.829	55.000	0.00	0.0	0.00	3.67	F
525	612	0.179043	TGCCAAGCCAAGTACGTTCA	60.179	50.000	0.00	0.0	0.00	3.18	F
1272	1364	0.449388	CGCTCCCAGCATTTGAAGAC	59.551	55.000	0.00	0.0	42.58	3.01	F
1821	2020	1.133482	CCTGGTTTTGGAGTTGAGGGT	60.133	52.381	0.00	0.0	0.00	4.34	F
2179	2381	0.389025	GCACAAGGTTTTGGTCCAGG	59.611	55.000	0.00	0.0	38.66	4.45	F
2184	2386	0.396811	AGGTTTTGGTCCAGGACTCG	59.603	55.000	19.57	0.0	32.47	4.18	F
2185	2387	0.605589	GGTTTTGGTCCAGGACTCGG	60.606	60.000	19.57	0.0	32.47	4.63	F
2204	2406	0.615850	GGTTCTCCCCACTCCTTCAG	59.384	60.000	0.00	0.0	0.00	3.02	F
2428	2741	1.167851	TGGGTAGTCCTCGTTACACG	58.832	55.000	0.00	0.0	44.19	4.49	F
4139	4489	1.304713	CATTGGGGCTCTTGGCACT	60.305	57.895	0.00	0.0	45.22	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1665	1759	0.320050	TACGTGGTTGCATGAGAGCA	59.680	50.000	0.00	0.00	43.99	4.26	R
2160	2362	0.389025	CCTGGACCAAAACCTTGTGC	59.611	55.000	0.00	0.00	0.00	4.57	R
2165	2367	0.396811	CGAGTCCTGGACCAAAACCT	59.603	55.000	22.81	2.52	32.18	3.50	R
2166	2368	0.605589	CCGAGTCCTGGACCAAAACC	60.606	60.000	22.81	5.28	32.18	3.27	R
2632	2945	1.202794	TCAATGGAGCTCACAACAGCA	60.203	47.619	17.19	2.25	42.40	4.41	R
3511	3837	1.268079	TCTGTCGATCTGGCGATCATC	59.732	52.381	15.84	10.02	45.11	2.92	R
4022	4372	1.891919	TGCTTCGTTGCACCACTCC	60.892	57.895	0.00	0.00	38.12	3.85	R
4067	4417	5.125356	TCATAACCAGGTGCAATATCAGTG	58.875	41.667	0.00	0.00	0.00	3.66	R
4139	4489	5.590663	TGGTGTTACATAACAAAGAAGTGCA	59.409	36.000	6.05	0.00	46.54	4.57	R
4382	4732	1.009829	CTACTTTGGCGCCATCAGAC	58.990	55.000	32.56	6.87	0.00	3.51	R
5045	5410	4.405548	TGGATCATTCAACCACATTGTCA	58.594	39.130	0.00	0.00	39.54	3.58	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
23	24	6.089249	AGGGTTCAACATTCATCTTTTCAC	57.911	37.500	0.00	0.00	0.00	3.18
24	25	5.598005	AGGGTTCAACATTCATCTTTTCACA	59.402	36.000	0.00	0.00	0.00	3.58
25	26	5.922544	GGGTTCAACATTCATCTTTTCACAG	59.077	40.000	0.00	0.00	0.00	3.66
26	27	5.922544	GGTTCAACATTCATCTTTTCACAGG	59.077	40.000	0.00	0.00	0.00	4.00
27	28	6.239008	GGTTCAACATTCATCTTTTCACAGGA	60.239	38.462	0.00	0.00	0.00	3.86
28	29	6.957920	TCAACATTCATCTTTTCACAGGAA	57.042	33.333	0.00	0.00	0.00	3.36
29	30	7.528996	TCAACATTCATCTTTTCACAGGAAT	57.471	32.000	0.00	0.00	31.93	3.01
30	31	7.954835	TCAACATTCATCTTTTCACAGGAATT	58.045	30.769	0.00	0.00	31.93	2.17
31	32	9.076781	TCAACATTCATCTTTTCACAGGAATTA	57.923	29.630	0.00	0.00	31.93	1.40
32	33	9.132521	CAACATTCATCTTTTCACAGGAATTAC	57.867	33.333	0.00	0.00	31.93	1.89
33	34	8.408043	ACATTCATCTTTTCACAGGAATTACA	57.592	30.769	0.00	0.00	31.93	2.41
34	35	8.859090	ACATTCATCTTTTCACAGGAATTACAA	58.141	29.630	0.00	0.00	31.93	2.41
35	36	9.695526	CATTCATCTTTTCACAGGAATTACAAA	57.304	29.630	0.00	0.00	31.93	2.83
38	39	9.528018	TCATCTTTTCACAGGAATTACAAAAAC	57.472	29.630	0.00	0.00	31.93	2.43
39	40	7.979115	TCTTTTCACAGGAATTACAAAAACG	57.021	32.000	0.00	0.00	31.93	3.60
40	41	7.540299	TCTTTTCACAGGAATTACAAAAACGT	58.460	30.769	0.00	0.00	31.93	3.99
41	42	7.486551	TCTTTTCACAGGAATTACAAAAACGTG	59.513	33.333	0.00	0.00	31.93	4.49
42	43	5.821516	TCACAGGAATTACAAAAACGTGT	57.178	34.783	0.00	0.00	35.43	4.49
43	44	5.812652	TCACAGGAATTACAAAAACGTGTC	58.187	37.500	0.00	0.00	32.75	3.67
44	45	5.354513	TCACAGGAATTACAAAAACGTGTCA	59.645	36.000	0.00	0.00	32.75	3.58
45	46	6.038825	TCACAGGAATTACAAAAACGTGTCAT	59.961	34.615	0.00	0.00	32.75	3.06
46	47	6.695278	CACAGGAATTACAAAAACGTGTCATT	59.305	34.615	0.00	0.00	29.96	2.57
47	48	7.858382	CACAGGAATTACAAAAACGTGTCATTA	59.142	33.333	0.00	0.00	27.98	1.90
48	49	8.073768	ACAGGAATTACAAAAACGTGTCATTAG	58.926	33.333	0.00	0.00	27.98	1.73
49	50	8.286800	CAGGAATTACAAAAACGTGTCATTAGA	58.713	33.333	0.00	0.00	27.98	2.10

Showing 1 to 25 of 499 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.598005	TGTGAAAAGATGAATGTTGAACCCT	59.402	36.000	0.00	0.00	0.00	4.34
1	2	5.841810	TGTGAAAAGATGAATGTTGAACCC	58.158	37.500	0.00	0.00	0.00	4.11
2	3	5.922544	CCTGTGAAAAGATGAATGTTGAACC	59.077	40.000	0.00	0.00	0.00	3.62
3	4	6.738114	TCCTGTGAAAAGATGAATGTTGAAC	58.262	36.000	0.00	0.00	0.00	3.18
4	5	6.957920	TCCTGTGAAAAGATGAATGTTGAA	57.042	33.333	0.00	0.00	0.00	2.69
5	6	6.957920	TTCCTGTGAAAAGATGAATGTTGA	57.042	33.333	0.00	0.00	0.00	3.18
6	7	9.132521	GTAATTCCTGTGAAAAGATGAATGTTG	57.867	33.333	0.00	0.00	33.32	3.33
7	8	8.859090	TGTAATTCCTGTGAAAAGATGAATGTT	58.141	29.630	0.00	0.00	33.32	2.71
8	9	8.408043	TGTAATTCCTGTGAAAAGATGAATGT	57.592	30.769	0.00	0.00	33.32	2.71
9	10	9.695526	TTTGTAATTCCTGTGAAAAGATGAATG	57.304	29.630	0.00	0.00	33.32	2.67
12	13	9.528018	GTTTTTGTAATTCCTGTGAAAAGATGA	57.472	29.630	0.00	0.00	33.32	2.92
13	14	8.479280	CGTTTTTGTAATTCCTGTGAAAAGATG	58.521	33.333	0.00	0.00	33.32	2.90
14	15	8.194769	ACGTTTTTGTAATTCCTGTGAAAAGAT	58.805	29.630	0.00	0.00	33.32	2.40
15	16	7.486551	CACGTTTTTGTAATTCCTGTGAAAAGA	59.513	33.333	0.00	0.00	33.32	2.52
16	17	7.274686	ACACGTTTTTGTAATTCCTGTGAAAAG	59.725	33.333	0.00	0.00	33.32	2.27
17	18	7.091443	ACACGTTTTTGTAATTCCTGTGAAAA	58.909	30.769	0.00	0.00	33.32	2.29
18	19	6.622549	ACACGTTTTTGTAATTCCTGTGAAA	58.377	32.000	0.00	0.00	33.32	2.69
19	20	6.127980	TGACACGTTTTTGTAATTCCTGTGAA	60.128	34.615	0.00	0.00	34.33	3.18
20	21	5.354513	TGACACGTTTTTGTAATTCCTGTGA	59.645	36.000	0.00	0.00	0.00	3.58
21	22	5.574082	TGACACGTTTTTGTAATTCCTGTG	58.426	37.500	0.00	0.00	0.00	3.66
22	23	5.821516	TGACACGTTTTTGTAATTCCTGT	57.178	34.783	0.00	0.00	0.00	4.00
23	24	8.286800	TCTAATGACACGTTTTTGTAATTCCTG	58.713	33.333	0.00	0.00	33.31	3.86
24	25	8.385898	TCTAATGACACGTTTTTGTAATTCCT	57.614	30.769	0.00	0.00	33.31	3.36
25	26	9.620660	ATTCTAATGACACGTTTTTGTAATTCC	57.379	29.630	0.00	0.00	33.31	3.01
27	28	8.911662	GCATTCTAATGACACGTTTTTGTAATT	58.088	29.630	6.87	0.00	38.70	1.40

Showing 1 to 25 of 500 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.