AutoCloner

Multiple sequence alignment - TraesCS7D01G361500

Loading Multiple Alignment...

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	TraesCS7D01G361500	chr7D	100.000	2320	0	0	1	2320	463977592	463979911	0.000000e+00	4285.0
1	TraesCS7D01G361500	chr2D	97.708	2269	50	2	53	2320	63681756	63684023	0.000000e+00	3901.0
2	TraesCS7D01G361500	chr4D	97.964	2210	43	2	112	2320	496006351	496008559	0.000000e+00	3831.0
3	TraesCS7D01G361500	chr4D	98.182	55	1	0	1	55	277837453	277837399	1.900000e-16	97.1
4	TraesCS7D01G361500	chr5D	97.051	2272	60	6	53	2320	60521580	60519312	0.000000e+00	3818.0
5	TraesCS7D01G361500	chr6D	97.043	2266	64	3	53	2317	80672970	80670707	0.000000e+00	3810.0
6	TraesCS7D01G361500	chr7A	96.933	2250	68	1	72	2320	89990547	89988298	0.000000e+00	3771.0
7	TraesCS7D01G361500	chr3A	96.000	2275	83	7	53	2320	328922708	328924981	0.000000e+00	3690.0
8	TraesCS7D01G361500	chr3A	94.828	58	3	0	1	58	750255575	750255518	8.830000e-15	91.6
9	TraesCS7D01G361500	chr1B	95.936	2264	84	5	53	2309	615476984	615479246	0.000000e+00	3664.0
10	TraesCS7D01G361500	chr2B	95.890	2263	85	5	53	2309	90758888	90761148	0.000000e+00	3657.0
11	TraesCS7D01G361500	chr2B	95.690	2274	90	5	53	2320	631382516	631380245	0.000000e+00	3650.0
12	TraesCS7D01G361500	chr2B	93.548	62	2	2	1	61	769274792	769274852	8.830000e-15	91.6
13	TraesCS7D01G361500	chr7B	98.276	58	1	0	1	58	590148601	590148658	4.080000e-18	102.0
14	TraesCS7D01G361500	chr6B	98.182	55	1	0	1	55	720503126	720503180	1.900000e-16	97.1
15	TraesCS7D01G361500	chr6B	93.750	64	0	4	1	62	101221258	101221319	2.450000e-15	93.5
16	TraesCS7D01G361500	chrUn	96.552	58	0	2	1	57	40599811	40599755	6.820000e-16	95.3
17	TraesCS7D01G361500	chr3D	94.915	59	1	2	1	58	498280635	498280692	8.830000e-15	91.6
18	TraesCS7D01G361500	chr5B	90.909	66	5	1	2	67	641394130	641394194	1.140000e-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	TraesCS7D01G361500	chr7D	463977592	463979911	2319	False	4285	4285	100.000	1	2320	1	chr7D.!!$F1	2319
1	TraesCS7D01G361500	chr2D	63681756	63684023	2267	False	3901	3901	97.708	53	2320	1	chr2D.!!$F1	2267
2	TraesCS7D01G361500	chr4D	496006351	496008559	2208	False	3831	3831	97.964	112	2320	1	chr4D.!!$F1	2208
3	TraesCS7D01G361500	chr5D	60519312	60521580	2268	True	3818	3818	97.051	53	2320	1	chr5D.!!$R1	2267
4	TraesCS7D01G361500	chr6D	80670707	80672970	2263	True	3810	3810	97.043	53	2317	1	chr6D.!!$R1	2264
5	TraesCS7D01G361500	chr7A	89988298	89990547	2249	True	3771	3771	96.933	72	2320	1	chr7A.!!$R1	2248
6	TraesCS7D01G361500	chr3A	328922708	328924981	2273	False	3690	3690	96.000	53	2320	1	chr3A.!!$F1	2267
7	TraesCS7D01G361500	chr1B	615476984	615479246	2262	False	3664	3664	95.936	53	2309	1	chr1B.!!$F1	2256
8	TraesCS7D01G361500	chr2B	90758888	90761148	2260	False	3657	3657	95.890	53	2309	1	chr2B.!!$F1	2256
9	TraesCS7D01G361500	chr2B	631380245	631382516	2271	True	3650	3650	95.690	53	2320	1	chr2B.!!$R1	2267

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
321	333	3.064931	GTTCCTCCAGTACTTCGTTTGG	58.935	50.0	0.0	0.0	0.0	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1901	1919	0.530744	TACCACTCGGTCATGCAGAC	59.469	55.0	7.52	7.52	44.71	3.51	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
46	47	8.480643	AAGTTGAGTCATCTATTTTAGAACGG	57.519	34.615	4.14	0.00	38.50	4.44
47	48	7.837863	AGTTGAGTCATCTATTTTAGAACGGA	58.162	34.615	1.70	0.00	38.50	4.69
48	49	7.976734	AGTTGAGTCATCTATTTTAGAACGGAG	59.023	37.037	1.70	0.00	38.50	4.63
49	50	6.806751	TGAGTCATCTATTTTAGAACGGAGG	58.193	40.000	0.00	0.00	38.50	4.30
50	51	6.163135	AGTCATCTATTTTAGAACGGAGGG	57.837	41.667	0.00	0.00	38.50	4.30
51	52	5.897824	AGTCATCTATTTTAGAACGGAGGGA	59.102	40.000	0.00	0.00	38.50	4.20
55	56	7.562454	TCATCTATTTTAGAACGGAGGGAGTAA	59.438	37.037	0.00	0.00	38.50	2.24
61	62	8.593945	TTTTAGAACGGAGGGAGTAATAGTTA	57.406	34.615	0.00	0.00	0.00	2.24
291	303	7.684670	AGAAGTATATAAATTGTGCGTGTGTG	58.315	34.615	0.00	0.00	0.00	3.82
321	333	3.064931	GTTCCTCCAGTACTTCGTTTGG	58.935	50.000	0.00	0.00	0.00	3.28
591	603	3.300013	CCGGGAAGGTGAGGTCTC	58.700	66.667	0.00	0.00	34.51	3.36
924	936	5.523369	GTCAGGTAATGCTAATTTGATGCC	58.477	41.667	0.00	0.00	0.00	4.40
1050	1064	1.763545	GGTTTTGTTTGGGCCCTACAA	59.236	47.619	28.45	28.45	0.00	2.41
1424	1440	1.959085	CGTTGCCCCATGATATGCC	59.041	57.895	0.00	0.00	0.00	4.40
1521	1539	0.304705	GTTGAGACAAGTGTGGTGCG	59.695	55.000	0.00	0.00	0.00	5.34
1590	1608	6.015010	ACCACGGAAAAATGAAATTGATACCA	60.015	34.615	0.00	0.00	36.10	3.25
1689	1707	2.161855	GTGGACATGTGGAATGCTCAA	58.838	47.619	1.15	0.00	0.00	3.02
1901	1919	1.291877	GCGCACCTAGATTATGGCCG	61.292	60.000	0.30	0.00	0.00	6.13
1933	1951	3.435671	CCGAGTGGTATGTCTTTTTGTCC	59.564	47.826	0.00	0.00	0.00	4.02
1963	1981	6.016213	TGAACATGTGTCATTTCTTCATGG	57.984	37.500	0.00	0.00	39.76	3.66
2063	2082	2.547218	GCACCTGGTAGAGAAACGAACA	60.547	50.000	0.00	0.00	0.00	3.18
2068	2087	5.221661	ACCTGGTAGAGAAACGAACATTCTT	60.222	40.000	0.00	0.00	37.26	2.52
2280	2299	8.049117	TCAGTATAGAATGGATGTGCTTTCTTT	58.951	33.333	7.71	4.04	31.29	2.52
2281	2300	9.330063	CAGTATAGAATGGATGTGCTTTCTTTA	57.670	33.333	7.71	3.27	31.29	1.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	8.936864	CCGTTCTAAAATAGATGACTCAACTTT	58.063	33.333	0.00	0.00	34.22	2.66
21	22	8.311836	TCCGTTCTAAAATAGATGACTCAACTT	58.688	33.333	0.00	0.00	34.22	2.66
22	23	7.837863	TCCGTTCTAAAATAGATGACTCAACT	58.162	34.615	0.00	0.00	34.22	3.16
23	24	7.222999	CCTCCGTTCTAAAATAGATGACTCAAC	59.777	40.741	0.00	0.00	34.22	3.18
24	25	7.265673	CCTCCGTTCTAAAATAGATGACTCAA	58.734	38.462	0.00	0.00	34.22	3.02
25	26	6.183360	CCCTCCGTTCTAAAATAGATGACTCA	60.183	42.308	0.00	0.00	34.22	3.41
26	27	6.040616	TCCCTCCGTTCTAAAATAGATGACTC	59.959	42.308	0.00	0.00	34.22	3.36
27	28	5.897824	TCCCTCCGTTCTAAAATAGATGACT	59.102	40.000	0.00	0.00	34.22	3.41
28	29	6.158023	TCCCTCCGTTCTAAAATAGATGAC	57.842	41.667	0.00	0.00	34.22	3.06
29	30	5.897824	ACTCCCTCCGTTCTAAAATAGATGA	59.102	40.000	0.00	0.00	34.22	2.92
30	31	6.163135	ACTCCCTCCGTTCTAAAATAGATG	57.837	41.667	0.00	0.00	34.22	2.90
31	32	7.909485	TTACTCCCTCCGTTCTAAAATAGAT	57.091	36.000	0.00	0.00	34.22	1.98
32	33	7.909485	ATTACTCCCTCCGTTCTAAAATAGA	57.091	36.000	0.00	0.00	0.00	1.98
33	34	8.858094	ACTATTACTCCCTCCGTTCTAAAATAG	58.142	37.037	0.00	0.00	32.24	1.73
34	35	8.773033	ACTATTACTCCCTCCGTTCTAAAATA	57.227	34.615	0.00	0.00	0.00	1.40
35	36	7.672122	ACTATTACTCCCTCCGTTCTAAAAT	57.328	36.000	0.00	0.00	0.00	1.82
36	37	7.486407	AACTATTACTCCCTCCGTTCTAAAA	57.514	36.000	0.00	0.00	0.00	1.52
37	38	8.773033	ATAACTATTACTCCCTCCGTTCTAAA	57.227	34.615	0.00	0.00	0.00	1.85
38	39	8.000709	TGATAACTATTACTCCCTCCGTTCTAA	58.999	37.037	0.00	0.00	0.00	2.10
39	40	7.446625	GTGATAACTATTACTCCCTCCGTTCTA	59.553	40.741	0.00	0.00	0.00	2.10
40	41	6.264970	GTGATAACTATTACTCCCTCCGTTCT	59.735	42.308	0.00	0.00	0.00	3.01
41	42	6.040166	TGTGATAACTATTACTCCCTCCGTTC	59.960	42.308	0.00	0.00	0.00	3.95
42	43	5.895534	TGTGATAACTATTACTCCCTCCGTT	59.104	40.000	0.00	0.00	0.00	4.44
43	44	5.301298	GTGTGATAACTATTACTCCCTCCGT	59.699	44.000	0.00	0.00	0.00	4.69
44	45	5.562307	CGTGTGATAACTATTACTCCCTCCG	60.562	48.000	0.00	0.00	0.00	4.63
45	46	5.533903	TCGTGTGATAACTATTACTCCCTCC	59.466	44.000	0.00	0.00	0.00	4.30
46	47	6.630444	TCGTGTGATAACTATTACTCCCTC	57.370	41.667	0.00	0.00	0.00	4.30
47	48	7.598759	AATCGTGTGATAACTATTACTCCCT	57.401	36.000	0.00	0.00	33.40	4.20
48	49	8.548721	CAAAATCGTGTGATAACTATTACTCCC	58.451	37.037	0.00	0.00	33.40	4.30
49	50	9.095065	ACAAAATCGTGTGATAACTATTACTCC	57.905	33.333	0.00	0.00	33.40	3.85
61	62	7.498900	ACCACATCATATACAAAATCGTGTGAT	59.501	33.333	0.00	0.00	37.26	3.06
291	303	5.224821	AGTACTGGAGGAACCTACAAAAC	57.775	43.478	7.22	8.00	36.31	2.43
321	333	4.265056	ACGTGGGTTGTGGCCTCC	62.265	66.667	3.32	0.99	0.00	4.30
476	488	0.784778	GGTGAAAAGAGTGCGTCTCG	59.215	55.000	3.64	0.00	46.86	4.04
591	603	2.672996	CCTTTGTCGCCACCCCTG	60.673	66.667	0.00	0.00	0.00	4.45
1050	1064	2.799126	TACGCTCCCACATCCAAATT	57.201	45.000	0.00	0.00	0.00	1.82
1424	1440	1.007387	GCCACTCCACCGCAAAAAG	60.007	57.895	0.00	0.00	0.00	2.27
1521	1539	6.100668	GGTACAAGAAACTCTCACCTATGTC	58.899	44.000	0.00	0.00	0.00	3.06
1590	1608	5.812642	CGTCCTACAAAGCATGAGAAGTATT	59.187	40.000	0.00	0.00	0.00	1.89
1689	1707	1.351017	TCTTCAACTCGGGCATTCCTT	59.649	47.619	0.00	0.00	0.00	3.36
1901	1919	0.530744	TACCACTCGGTCATGCAGAC	59.469	55.000	7.52	7.52	44.71	3.51
1963	1981	4.976224	AAAACTTAAGTGACACACCACC	57.024	40.909	9.34	0.00	37.76	4.61
2063	2082	7.183460	ACCTGTAGAGTACTCCTAACAAGAAT	58.817	38.462	19.38	0.00	0.00	2.40
2068	2087	7.262990	TCTAACCTGTAGAGTACTCCTAACA	57.737	40.000	19.38	18.27	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.