AutoCloner

Multiple sequence alignment - TraesCS1D01G013800

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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	TraesCS1D01G013800	chr1D	100.000	4532	0	0	1	4532	6897456	6901987	0.000000e+00	8370.0
1	TraesCS1D01G013800	chr1D	85.186	2842	353	34	730	3539	6714866	6712061	0.000000e+00	2854.0
2	TraesCS1D01G013800	chr1D	82.796	2790	380	61	937	3682	6721658	6718925	0.000000e+00	2401.0
3	TraesCS1D01G013800	chr1D	98.503	334	5	0	4199	4532	204293018	204292685	1.400000e-164	590.0
4	TraesCS1D01G013800	chr1D	80.787	432	39	25	3778	4172	407674383	407673959	9.530000e-77	298.0
5	TraesCS1D01G013800	chr1D	90.476	63	6	0	10	72	407674719	407674657	2.910000e-12	84.2
6	TraesCS1D01G013800	chr1A	92.449	3708	192	40	1	3673	8326162	8329816	0.000000e+00	5216.0
7	TraesCS1D01G013800	chr1A	85.196	2756	337	37	820	3539	8144673	8141953	0.000000e+00	2763.0
8	TraesCS1D01G013800	chr1A	83.258	2658	362	47	937	3553	8159920	8157305	0.000000e+00	2366.0
9	TraesCS1D01G013800	chr1A	80.450	3069	436	83	896	3876	8341943	8344935	0.000000e+00	2193.0
10	TraesCS1D01G013800	chr1A	75.789	380	45	24	456	798	8089153	8088784	1.020000e-31	148.0
11	TraesCS1D01G013800	chr1A	80.620	129	23	2	418	545	8336995	8337122	1.040000e-16	99.0
12	TraesCS1D01G013800	chr5B	93.419	3100	167	20	587	3682	549547587	549550653	0.000000e+00	4560.0
13	TraesCS1D01G013800	chr5B	82.320	2715	366	68	985	3649	13776148	13773498	0.000000e+00	2250.0
14	TraesCS1D01G013800	chr5B	83.498	303	22	15	3888	4162	549553248	549553550	1.620000e-64	257.0
15	TraesCS1D01G013800	chr1B	90.796	3140	221	28	590	3681	548200321	548197202	0.000000e+00	4135.0
16	TraesCS1D01G013800	chr1B	91.765	2295	145	19	883	3168	9175260	9177519	0.000000e+00	3151.0
17	TraesCS1D01G013800	chr1B	83.402	2657	358	40	938	3553	9161738	9164352	0.000000e+00	2386.0
18	TraesCS1D01G013800	chr1B	82.864	2661	367	45	937	3553	8867294	8864679	0.000000e+00	2305.0
19	TraesCS1D01G013800	chr1B	91.904	877	54	11	887	1762	9281161	9282021	0.000000e+00	1210.0
20	TraesCS1D01G013800	chr1B	90.802	511	36	6	287	792	9280657	9281161	0.000000e+00	673.0
21	TraesCS1D01G013800	chr1B	80.787	432	39	25	3778	4172	548195752	548195328	9.530000e-77	298.0
22	TraesCS1D01G013800	chr1B	84.360	211	31	2	379	588	8867674	8867465	5.940000e-49	206.0
23	TraesCS1D01G013800	chr1B	88.073	109	8	1	139	242	9280537	9280645	1.710000e-24	124.0
24	TraesCS1D01G013800	chr1B	90.244	82	8	0	824	905	548200239	548200158	1.720000e-19	108.0
25	TraesCS1D01G013800	chr1B	88.889	63	7	0	10	72	548200869	548200807	1.350000e-10	78.7
26	TraesCS1D01G013800	chr5A	82.981	2603	344	57	985	3539	12194231	12191680	0.000000e+00	2261.0
27	TraesCS1D01G013800	chr5A	78.041	296	32	21	3856	4121	12196082	12195790	6.070000e-34	156.0
28	TraesCS1D01G013800	chr2A	82.571	2645	361	50	936	3533	733628844	733631435	0.000000e+00	2239.0
29	TraesCS1D01G013800	chr2A	80.598	2675	403	70	935	3540	611302764	611305391	0.000000e+00	1958.0
30	TraesCS1D01G013800	chr2D	82.465	2629	357	54	953	3533	599926383	599928955	0.000000e+00	2206.0
31	TraesCS1D01G013800	chr2B	80.796	2687	397	65	935	3553	548623923	548626558	0.000000e+00	1993.0
32	TraesCS1D01G013800	chr5D	83.596	1207	144	32	2371	3539	18085120	18086310	0.000000e+00	1083.0
33	TraesCS1D01G013800	chrUn	98.802	334	4	0	4199	4532	366840408	366840075	3.020000e-166	595.0
34	TraesCS1D01G013800	chrUn	98.503	334	5	0	4199	4532	90088053	90087720	1.400000e-164	590.0
35	TraesCS1D01G013800	chr7D	98.802	334	4	0	4199	4532	586403688	586403355	3.020000e-166	595.0
36	TraesCS1D01G013800	chr6D	98.802	334	4	0	4199	4532	100234	99901	3.020000e-166	595.0
37	TraesCS1D01G013800	chr6D	98.220	337	6	0	4196	4532	2077097	2077433	1.400000e-164	590.0
38	TraesCS1D01G013800	chr6D	98.220	337	6	0	4196	4532	68363642	68363978	1.400000e-164	590.0
39	TraesCS1D01G013800	chr6D	98.503	334	5	0	4199	4532	433657584	433657251	1.400000e-164	590.0
40	TraesCS1D01G013800	chr6D	98.503	334	5	0	4199	4532	464776346	464776013	1.400000e-164	590.0
41	TraesCS1D01G013800	chr4B	80.089	447	53	21	379	798	36636304	36635867	2.650000e-77	300.0

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	TraesCS1D01G013800	chr1D	6897456	6901987	4531	False	8370.000	8370	100.000000	1	4532	1	chr1D.!!$F1	4531
1	TraesCS1D01G013800	chr1D	6712061	6714866	2805	True	2854.000	2854	85.186000	730	3539	1	chr1D.!!$R1	2809
2	TraesCS1D01G013800	chr1D	6718925	6721658	2733	True	2401.000	2401	82.796000	937	3682	1	chr1D.!!$R2	2745
3	TraesCS1D01G013800	chr1A	8326162	8329816	3654	False	5216.000	5216	92.449000	1	3673	1	chr1A.!!$F1	3672
4	TraesCS1D01G013800	chr1A	8141953	8144673	2720	True	2763.000	2763	85.196000	820	3539	1	chr1A.!!$R2	2719
5	TraesCS1D01G013800	chr1A	8157305	8159920	2615	True	2366.000	2366	83.258000	937	3553	1	chr1A.!!$R3	2616
6	TraesCS1D01G013800	chr1A	8341943	8344935	2992	False	2193.000	2193	80.450000	896	3876	1	chr1A.!!$F3	2980
7	TraesCS1D01G013800	chr5B	549547587	549553550	5963	False	2408.500	4560	88.458500	587	4162	2	chr5B.!!$F1	3575
8	TraesCS1D01G013800	chr5B	13773498	13776148	2650	True	2250.000	2250	82.320000	985	3649	1	chr5B.!!$R1	2664
9	TraesCS1D01G013800	chr1B	9175260	9177519	2259	False	3151.000	3151	91.765000	883	3168	1	chr1B.!!$F2	2285
10	TraesCS1D01G013800	chr1B	9161738	9164352	2614	False	2386.000	2386	83.402000	938	3553	1	chr1B.!!$F1	2615
11	TraesCS1D01G013800	chr1B	8864679	8867674	2995	True	1255.500	2305	83.612000	379	3553	2	chr1B.!!$R1	3174
12	TraesCS1D01G013800	chr1B	548195328	548200869	5541	True	1154.925	4135	87.679000	10	4172	4	chr1B.!!$R2	4162
13	TraesCS1D01G013800	chr1B	9280537	9282021	1484	False	669.000	1210	90.259667	139	1762	3	chr1B.!!$F3	1623
14	TraesCS1D01G013800	chr5A	12191680	12196082	4402	True	1208.500	2261	80.511000	985	4121	2	chr5A.!!$R1	3136
15	TraesCS1D01G013800	chr2A	733628844	733631435	2591	False	2239.000	2239	82.571000	936	3533	1	chr2A.!!$F2	2597
16	TraesCS1D01G013800	chr2A	611302764	611305391	2627	False	1958.000	1958	80.598000	935	3540	1	chr2A.!!$F1	2605
17	TraesCS1D01G013800	chr2D	599926383	599928955	2572	False	2206.000	2206	82.465000	953	3533	1	chr2D.!!$F1	2580
18	TraesCS1D01G013800	chr2B	548623923	548626558	2635	False	1993.000	1993	80.796000	935	3553	1	chr2B.!!$F1	2618
19	TraesCS1D01G013800	chr5D	18085120	18086310	1190	False	1083.000	1083	83.596000	2371	3539	1	chr5D.!!$F1	1168

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
561	627	0.821711	TTGGACGCTTGGTGGAAAGG	60.822	55.000	0.00	0.00	3.11	F
803	921	1.153529	CCAGAGCAGAGCAGAGCAG	60.154	63.158	0.00	0.00	4.24	F
2465	3439	1.226746	AGAGTTGTAACTGCCGCAAC	58.773	50.000	1.35	39.88	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2069	3025	0.035056	CTCCCAATCCTGTGGTGACC	60.035	60.0	0.00	36.90	4.02	R
2544	3538	0.883833	CACCACCAGTGCCTTGATTC	59.116	55.0	0.00	40.28	2.52	R
4389	8038	0.034896	GCTCAGGTTCGTTTCTGGGA	59.965	55.0	5.89	33.51	4.37	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
71	104	5.926542	TCAACTAGTTGGATTTCGAAGAGTG	59.073	40.000	30.35	4.90	40.78	3.51
104	142	6.486253	TCTGCAGTTGACATGTAGAAATTC	57.514	37.500	14.67	0.00	36.61	2.17
161	199	6.292168	CCCTTATAACATCTTAGTTGCGTTCG	60.292	42.308	0.00	0.00	33.07	3.95
207	264	4.830600	TGGGTTGGTCAGTAAAAGGATTTC	59.169	41.667	0.00	0.00	37.28	2.17
249	306	9.479549	AAGACAACCCTTGAATATGTCAATAAT	57.520	29.630	6.94	0.00	45.27	1.28
252	309	9.131791	ACAACCCTTGAATATGTCAATAATACC	57.868	33.333	0.00	0.00	45.27	2.73
253	310	9.130661	CAACCCTTGAATATGTCAATAATACCA	57.869	33.333	0.00	0.00	45.27	3.25
307	364	5.646360	GCTGACCCTTTTTACAGTTAGCATA	59.354	40.000	0.00	0.00	40.46	3.14
309	366	7.624360	TGACCCTTTTTACAGTTAGCATATG	57.376	36.000	0.00	0.00	0.00	1.78
334	391	4.380531	TGCTTGTACTCTGTTTCTTCCTG	58.619	43.478	0.00	0.00	0.00	3.86
455	513	3.376546	GTGGAAGCCTCATGATTGACTTC	59.623	47.826	14.22	14.22	35.64	3.01
548	614	2.001812	CCTCATGACTGACTTGGACG	57.998	55.000	0.00	0.00	0.00	4.79
561	627	0.821711	TTGGACGCTTGGTGGAAAGG	60.822	55.000	0.00	0.00	0.00	3.11
593	675	4.254709	TCCTTGGTGTGCGCTGCT	62.255	61.111	9.73	0.00	0.00	4.24
728	819	2.514013	GGCGTAGTGACATTCCGCG	61.514	63.158	0.00	0.00	44.90	6.46
785	903	8.744568	ATACATCCTCTTCTTCCTTTGAATTC	57.255	34.615	0.00	0.00	0.00	2.17
803	921	1.153529	CCAGAGCAGAGCAGAGCAG	60.154	63.158	0.00	0.00	0.00	4.24
822	940	3.126514	GCAGATTCACATTCACACTCCTG	59.873	47.826	0.00	0.00	0.00	3.86
844	962	2.776370	ATTGGGCCACTGCTGTCCTG	62.776	60.000	5.23	0.00	37.74	3.86
893	1011	2.159476	TCCTAGTGACATTACGCGTGAC	60.159	50.000	24.59	6.35	0.00	3.67
931	1054	6.486657	GCATATTATTGCTTCCTGTTCCAGTA	59.513	38.462	0.00	0.00	39.57	2.74
1020	1889	4.323333	CCCATGCCTCTCCTCTACATATTG	60.323	50.000	0.00	0.00	0.00	1.90
1194	2093	3.338249	CACCATCAGTAAGTCCCACAAG	58.662	50.000	0.00	0.00	0.00	3.16
1257	2183	6.405065	GGTTCAATAAGATCCCGGTTTTTACC	60.405	42.308	0.00	0.00	31.08	2.85
1406	2332	4.380867	CCTTGTTTGGTCCACTCATATTGC	60.381	45.833	0.00	0.00	0.00	3.56

Showing 1 to 25 of 376 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	1.121240	CATGACCGTACGAATCGAGC	58.879	55.000	18.76	0.08	0.00	5.03
10	11	0.099968	GCAGTAGCATGACCGTACGA	59.900	55.000	18.76	0.00	41.58	3.43
71	104	7.584987	ACATGTCAACTGCAGAAAGTAATTAC	58.415	34.615	23.35	7.57	0.00	1.89
125	163	5.940470	AGATGTTATAAGGGGATCATTTCGC	59.060	40.000	0.00	0.00	36.58	4.70
161	199	6.974622	CCACAATATTTGCTTCAATGGTCTAC	59.025	38.462	0.00	0.00	0.00	2.59
249	306	4.987963	AGCCTGAATGATCATCATGGTA	57.012	40.909	9.06	0.00	37.15	3.25
250	307	3.878237	AGCCTGAATGATCATCATGGT	57.122	42.857	9.06	8.56	37.15	3.55
251	308	5.393135	GCAATAGCCTGAATGATCATCATGG	60.393	44.000	9.06	11.79	33.96	3.66
252	309	5.641709	GCAATAGCCTGAATGATCATCATG	58.358	41.667	9.06	7.24	33.96	3.07
253	310	5.899120	GCAATAGCCTGAATGATCATCAT	57.101	39.130	9.06	0.00	34.75	2.45
282	339	3.120304	GCTAACTGTAAAAAGGGTCAGCG	60.120	47.826	0.00	0.00	0.00	5.18
307	364	5.220710	AGAAACAGAGTACAAGCAGACAT	57.779	39.130	0.00	0.00	0.00	3.06
309	366	4.449405	GGAAGAAACAGAGTACAAGCAGAC	59.551	45.833	0.00	0.00	0.00	3.51
334	391	6.833342	AAGTTTTGTGCATCTTTCATTGAC	57.167	33.333	0.00	0.00	0.00	3.18
548	614	2.087646	GAGTGATCCTTTCCACCAAGC	58.912	52.381	0.00	0.00	34.00	4.01
561	627	3.008485	ACCAAGGAGGACTTTGAGTGATC	59.992	47.826	0.00	0.00	41.22	2.92
593	675	3.684305	CCATGAAAACGATGTGCTAGTCA	59.316	43.478	0.00	0.00	0.00	3.41
710	801	2.514013	CGCGGAATGTCACTACGCC	61.514	63.158	5.13	0.00	46.72	5.68
784	902	1.605971	CTGCTCTGCTCTGCTCTGGA	61.606	60.000	0.00	0.00	0.00	3.86
785	903	1.153529	CTGCTCTGCTCTGCTCTGG	60.154	63.158	0.00	0.00	0.00	3.86
803	921	3.942829	TCCAGGAGTGTGAATGTGAATC	58.057	45.455	0.00	0.00	0.00	2.52
822	940	1.598701	GACAGCAGTGGCCCAATTCC	61.599	60.000	0.00	0.00	42.56	3.01
844	962	3.430453	TGGGACCAACCAAATTCAGATC	58.570	45.455	0.00	0.00	41.20	2.75
893	1011	5.560375	GCAATAATATGCTCAGCTGACTGTG	60.560	44.000	13.74	4.09	43.06	3.66
1020	1889	1.483004	GAGAGGAGAAGCCCAAGTACC	59.517	57.143	0.00	0.00	37.37	3.34

Showing 1 to 25 of 336 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.