AutoCloner

Multiple sequence alignment - TraesCS3A01G511700

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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	TraesCS3A01G511700	chr3A	100.000	6760	0	0	876	7635	731083587	731090346	0.000000e+00	12484.0
1	TraesCS3A01G511700	chr3A	100.000	375	0	0	1	375	731082712	731083086	0.000000e+00	693.0
2	TraesCS3A01G511700	chr3A	97.222	36	1	0	4657	4692	731087261	731087296	2.300000e-05	62.1
3	TraesCS3A01G511700	chr3A	97.222	36	1	0	4550	4585	731087368	731087403	2.300000e-05	62.1
4	TraesCS3A01G511700	chr3B	92.600	6351	348	55	881	7172	808879848	808873561	0.000000e+00	9012.0
5	TraesCS3A01G511700	chr3B	84.104	2271	257	56	4735	6933	808710328	808712566	0.000000e+00	2098.0
6	TraesCS3A01G511700	chr3B	87.638	453	54	2	3712	4164	808709293	808709743	6.790000e-145	525.0
7	TraesCS3A01G511700	chr3B	90.286	350	17	6	1	335	808880416	808880069	7.030000e-120	442.0
8	TraesCS3A01G511700	chr3B	87.138	311	27	3	4163	4460	808709902	808710212	2.640000e-89	340.0
9	TraesCS3A01G511700	chr3B	90.476	84	6	2	4584	4667	284561689	284561608	8.100000e-20	110.0
10	TraesCS3A01G511700	chr3B	100.000	36	0	0	4550	4585	808876077	808876042	4.940000e-07	67.6
11	TraesCS3A01G511700	chr3B	97.222	36	1	0	4657	4692	808876183	808876148	2.300000e-05	62.1
12	TraesCS3A01G511700	chr3D	92.600	3527	193	21	881	4382	601925074	601921591	0.000000e+00	5005.0
13	TraesCS3A01G511700	chr3D	92.786	2523	107	27	4657	7145	601920400	601917919	0.000000e+00	3581.0
14	TraesCS3A01G511700	chr3D	92.368	380	15	4	1	375	601925596	601925226	5.250000e-146	529.0
15	TraesCS3A01G511700	chr3D	87.828	419	41	6	7221	7635	601917920	601917508	4.140000e-132	483.0
16	TraesCS3A01G511700	chr6B	91.196	1045	63	16	923	1943	429704084	429705123	0.000000e+00	1393.0
17	TraesCS3A01G511700	chr1D	95.946	74	3	0	4584	4657	211684857	211684930	3.740000e-23	121.0
18	TraesCS3A01G511700	chr1D	94.595	74	4	0	4584	4657	86918609	86918682	1.740000e-21	115.0
19	TraesCS3A01G511700	chr6D	94.595	74	4	0	4584	4657	319689492	319689419	1.740000e-21	115.0
20	TraesCS3A01G511700	chr5D	94.595	74	4	0	4584	4657	162425225	162425298	1.740000e-21	115.0
21	TraesCS3A01G511700	chr2D	94.595	74	4	0	4584	4657	298290221	298290294	1.740000e-21	115.0
22	TraesCS3A01G511700	chr2D	91.463	82	6	1	4584	4665	459298776	459298696	2.250000e-20	111.0
23	TraesCS3A01G511700	chr5A	88.764	89	9	1	4584	4671	585407250	585407162	2.910000e-19	108.0

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	TraesCS3A01G511700	chr3A	731082712	731090346	7634	False	3325.300000	12484	98.611000	1	7635	4	chr3A.!!$F1	7634
1	TraesCS3A01G511700	chr3B	808873561	808880416	6855	True	2395.925000	9012	95.027000	1	7172	4	chr3B.!!$R2	7171
2	TraesCS3A01G511700	chr3B	808709293	808712566	3273	False	987.666667	2098	86.293333	3712	6933	3	chr3B.!!$F1	3221
3	TraesCS3A01G511700	chr3D	601917508	601925596	8088	True	2399.500000	5005	91.395500	1	7635	4	chr3D.!!$R1	7634
4	TraesCS3A01G511700	chr6B	429704084	429705123	1039	False	1393.000000	1393	91.196000	923	1943	1	chr6B.!!$F1	1020

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
907	959	1.441016	GCCGTTTCAGCTGCGAAAG	60.441	57.895	9.47	8.55	35.62	2.62	F
1706	1789	1.228245	TGAACAGTTGAGGCCTGCC	60.228	57.895	12.00	0.00	33.09	4.85	F
2298	2386	1.472728	CGGGAGTTATCTTTGTCCGGG	60.473	57.143	0.00	0.00	33.27	5.73	F
2872	2962	1.070601	GCCAATTGTTCTGCCCAAGTT	59.929	47.619	4.43	0.00	0.00	2.66	F
4317	4593	0.331616	TAAAGGGGGCTGGCTTCTTC	59.668	55.000	0.00	0.00	0.00	2.87	F
4616	5923	0.790993	TAGTGGTCAGACCCTTCCCT	59.209	55.000	17.59	7.46	37.50	4.20	F
4618	5925	0.836400	GTGGTCAGACCCTTCCCTGA	60.836	60.000	17.59	0.00	37.50	3.86	F
6142	7514	0.883370	GGAAGCGTTTCTCCCACGTT	60.883	55.000	11.94	0.00	39.92	3.99	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1839	1923	1.211457	CTGGTAGAAGCCTGCAATCCT	59.789	52.381	0.00	0.00	0.00	3.24	R
2849	2938	1.243342	TGGGCAGAACAATTGGCTCG	61.243	55.000	10.83	4.34	40.61	5.03	R
4134	4238	0.991146	TGCCAAGGAAGCTGTATGGA	59.009	50.000	11.16	0.00	32.82	3.41	R
4648	5955	0.538287	GACTCCATATTGGGCAGCCC	60.538	60.000	25.54	25.54	45.71	5.19	R
6239	7611	0.468226	ACGACCTTGGAGAAGTGCAA	59.532	50.000	0.00	0.00	32.33	4.08	R
6391	7781	0.948623	CCGCCGAGTTGATGTTCACA	60.949	55.000	0.00	0.00	0.00	3.58	R
6614	8004	4.844884	TCCTAGAACTCGTCATCAAGAGA	58.155	43.478	0.00	0.00	37.87	3.10	R
7218	8617	0.105709	TGGCATCCAGATACTCCGGA	60.106	55.000	2.93	2.93	0.00	5.14	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
21	22	4.957759	CTAAACCTACCACCAAAATCGG	57.042	45.455	0.00	0.00	0.00	4.18
116	122	9.920946	AGATAATTTATCTCCCAGCTACAAAAA	57.079	29.630	12.26	0.00	41.55	1.94
120	126	6.817765	TTATCTCCCAGCTACAAAAACAAG	57.182	37.500	0.00	0.00	0.00	3.16
323	372	3.083997	GGCACCGTCCTCCTCCAT	61.084	66.667	0.00	0.00	0.00	3.41
324	373	2.501610	GCACCGTCCTCCTCCATC	59.498	66.667	0.00	0.00	0.00	3.51
325	374	2.808315	CACCGTCCTCCTCCATCG	59.192	66.667	0.00	0.00	0.00	3.84
326	375	3.148279	ACCGTCCTCCTCCATCGC	61.148	66.667	0.00	0.00	0.00	4.58
327	376	3.917760	CCGTCCTCCTCCATCGCC	61.918	72.222	0.00	0.00	0.00	5.54
328	377	2.835431	CGTCCTCCTCCATCGCCT	60.835	66.667	0.00	0.00	0.00	5.52
329	378	2.851071	CGTCCTCCTCCATCGCCTC	61.851	68.421	0.00	0.00	0.00	4.70
330	379	2.519541	TCCTCCTCCATCGCCTCG	60.520	66.667	0.00	0.00	0.00	4.63
907	959	1.441016	GCCGTTTCAGCTGCGAAAG	60.441	57.895	9.47	8.55	35.62	2.62
965	1021	4.974438	TTCCGGCTCCAGGGGTGT	62.974	66.667	0.00	0.00	0.00	4.16
974	1030	2.488347	GCTCCAGGGGTGTTGAAGTTTA	60.488	50.000	0.00	0.00	0.00	2.01
1302	1367	4.576330	ATGCTTTCTTGTAGGCCTACTT	57.424	40.909	36.49	5.92	37.00	2.24
1374	1439	6.936968	AGAACCACCTATTCTGAGTAACTT	57.063	37.500	0.00	0.00	35.06	2.66
1456	1537	2.582052	CACCAAACACTTTGAGGCCTA	58.418	47.619	4.42	0.00	43.26	3.93
1500	1581	6.019108	ACTTCCAGGCAGAATAATTTTCCTT	58.981	36.000	0.00	0.00	0.00	3.36
1536	1617	9.378551	TGTTGAGGTGTATGTAGATAATGTTTC	57.621	33.333	0.00	0.00	0.00	2.78
1538	1619	8.002984	TGAGGTGTATGTAGATAATGTTTCGA	57.997	34.615	0.00	0.00	0.00	3.71
1540	1621	9.477484	GAGGTGTATGTAGATAATGTTTCGATT	57.523	33.333	0.00	0.00	0.00	3.34
1559	1640	6.570692	TCGATTGTTACCAGATTAGAAGGTC	58.429	40.000	0.00	0.00	36.87	3.85
1564	1645	5.105877	TGTTACCAGATTAGAAGGTCGTCAG	60.106	44.000	0.00	0.00	36.87	3.51
1614	1695	2.258109	GGAAACTCTGGGACTGTAGGT	58.742	52.381	0.00	0.00	0.00	3.08
1621	1702	4.773149	ACTCTGGGACTGTAGGTTTCTTAG	59.227	45.833	0.00	0.00	0.00	2.18

Showing 1 to 25 of 198 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	2.777832	AGTGAGAGCCATTGACTTCC	57.222	50.000	0.00	0.00	0.00	3.46
21	22	4.083057	GGAAAAGTGAGAGCCATTGACTTC	60.083	45.833	0.00	0.00	0.00	3.01
116	122	6.071391	AGTGACATTCCACTTTTGTTTCTTGT	60.071	34.615	0.00	0.00	44.32	3.16
120	126	5.650543	ACAGTGACATTCCACTTTTGTTTC	58.349	37.500	0.00	0.00	44.32	2.78
907	959	0.457337	ACGACGCGGTTAGACAATCC	60.457	55.000	12.47	0.00	0.00	3.01
965	1021	0.806241	GGCGCCGGAATAAACTTCAA	59.194	50.000	12.58	0.00	0.00	2.69
1284	1340	5.407407	TCTGAAGTAGGCCTACAAGAAAG	57.593	43.478	37.94	26.77	38.48	2.62
1292	1348	3.786553	TCCTTGTTCTGAAGTAGGCCTA	58.213	45.455	8.91	8.91	0.00	3.93
1294	1350	3.008049	TCTTCCTTGTTCTGAAGTAGGCC	59.992	47.826	11.17	0.00	39.19	5.19
1302	1367	5.551305	TTCTGTCATCTTCCTTGTTCTGA	57.449	39.130	0.00	0.00	0.00	3.27
1374	1439	8.635765	AGGATGATTTTACTCTTAAAAGTGCA	57.364	30.769	0.00	0.00	39.89	4.57
1456	1537	7.455953	TGGAAGTGGCAGAATACATATCTCTAT	59.544	37.037	0.00	0.00	0.00	1.98
1500	1581	6.530120	ACATACACCTCAACATTACTCACAA	58.470	36.000	0.00	0.00	0.00	3.33
1512	1593	8.471609	TCGAAACATTATCTACATACACCTCAA	58.528	33.333	0.00	0.00	0.00	3.02
1559	1640	8.141909	TCCAAATATCTAACCTGATAACTGACG	58.858	37.037	0.00	0.00	33.31	4.35
1607	1688	3.437049	GCAACCTGCTAAGAAACCTACAG	59.563	47.826	0.00	0.00	40.96	2.74
1678	1761	3.743396	CCTCAACTGTTCAGTGCTTCTAC	59.257	47.826	6.22	0.00	0.00	2.59
1688	1771	1.228245	GGCAGGCCTCAACTGTTCA	60.228	57.895	0.00	0.00	38.22	3.18
1706	1789	4.902443	TCTTCCAGCTGAATACGTCTAG	57.098	45.455	17.39	0.00	31.06	2.43
1731	1815	9.643693	CATTAGCATTACTCAAACTGGAAAAAT	57.356	29.630	0.00	0.00	0.00	1.82
1838	1922	1.635487	TGGTAGAAGCCTGCAATCCTT	59.365	47.619	0.00	0.00	0.00	3.36
1839	1923	1.211457	CTGGTAGAAGCCTGCAATCCT	59.789	52.381	0.00	0.00	0.00	3.24
1846	1930	2.191128	AGCAAACTGGTAGAAGCCTG	57.809	50.000	0.00	0.00	0.00	4.85
1944	2028	4.044065	AGGTGGAAATGGACAAACCTATCA	59.956	41.667	0.00	0.00	36.28	2.15
1978	2062	4.139786	AGAACAGCATCACAACTGAATGT	58.860	39.130	0.00	0.00	37.35	2.71

Showing 1 to 25 of 181 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.