AutoCloner

Multiple sequence alignment - TraesCS7A01G484500

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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	TraesCS7A01G484500	chr7A	100.000	2325	0	0	1	2325	675494211	675496535	0.000000e+00	4294
1	TraesCS7A01G484500	chr7A	100.000	1746	0	0	2631	4376	675496841	675498586	0.000000e+00	3225
2	TraesCS7A01G484500	chr7A	86.311	2345	285	28	1	2325	102055223	102057551	0.000000e+00	2519
3	TraesCS7A01G484500	chr7A	84.126	1178	159	19	2631	3791	102057567	102058733	0.000000e+00	1114
4	TraesCS7A01G484500	chr7D	96.360	2335	67	7	1	2325	86073231	86070905	0.000000e+00	3825
5	TraesCS7A01G484500	chr7D	95.195	1748	72	7	2631	4376	86070889	86069152	0.000000e+00	2752
6	TraesCS7A01G484500	chr2D	95.718	1378	45	6	1	1366	431392434	431391059	0.000000e+00	2206
7	TraesCS7A01G484500	chr2B	86.783	1778	186	23	2631	4374	259688153	259689915	0.000000e+00	1936
8	TraesCS7A01G484500	chr2B	89.210	1177	113	9	1159	2325	259686965	259688137	0.000000e+00	1458
9	TraesCS7A01G484500	chr2B	89.943	1054	102	3	1	1054	259685535	259686584	0.000000e+00	1356
10	TraesCS7A01G484500	chr2B	77.540	748	124	31	2712	3426	11908541	11909277	1.130000e-110	411
11	TraesCS7A01G484500	chr2B	74.757	618	123	25	1715	2325	11907851	11908442	3.380000e-61	246
12	TraesCS7A01G484500	chr5B	89.153	1429	134	16	912	2325	126444430	126445852	0.000000e+00	1760
13	TraesCS7A01G484500	chr5B	89.626	829	74	7	2975	3793	126446494	126447320	0.000000e+00	1044
14	TraesCS7A01G484500	chr5B	87.917	240	29	0	4	243	126444190	126444429	2.580000e-72	283
15	TraesCS7A01G484500	chr5B	83.489	321	28	9	2631	2950	126445867	126446163	4.310000e-70	276
16	TraesCS7A01G484500	chrUn	86.217	1052	124	16	1	1043	48372857	48371818	0.000000e+00	1120
17	TraesCS7A01G484500	chrUn	86.217	1052	124	16	1	1043	318400736	318401775	0.000000e+00	1120
18	TraesCS7A01G484500	chr1A	86.572	849	95	14	201	1042	570105510	570104674	0.000000e+00	918
19	TraesCS7A01G484500	chr5A	81.635	795	145	1	58	852	570228446	570227653	0.000000e+00	658
20	TraesCS7A01G484500	chr5A	77.538	463	81	17	3154	3606	570216289	570215840	1.560000e-64	257
21	TraesCS7A01G484500	chr3B	77.819	1073	209	20	58	1120	232563370	232564423	1.720000e-178	636
22	TraesCS7A01G484500	chr3B	84.982	273	40	1	3154	3426	232567548	232567819	4.310000e-70	276
23	TraesCS7A01G484500	chr3B	78.571	210	39	5	3200	3406	648183351	648183145	2.750000e-27	134

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	TraesCS7A01G484500	chr7A	675494211	675498586	4375	False	3759.500000	4294	100.000000	1	4376	2	chr7A.!!$F2	4375
1	TraesCS7A01G484500	chr7A	102055223	102058733	3510	False	1816.500000	2519	85.218500	1	3791	2	chr7A.!!$F1	3790
2	TraesCS7A01G484500	chr7D	86069152	86073231	4079	True	3288.500000	3825	95.777500	1	4376	2	chr7D.!!$R1	4375
3	TraesCS7A01G484500	chr2D	431391059	431392434	1375	True	2206.000000	2206	95.718000	1	1366	1	chr2D.!!$R1	1365
4	TraesCS7A01G484500	chr2B	259685535	259689915	4380	False	1583.333333	1936	88.645333	1	4374	3	chr2B.!!$F2	4373
5	TraesCS7A01G484500	chr2B	11907851	11909277	1426	False	328.500000	411	76.148500	1715	3426	2	chr2B.!!$F1	1711
6	TraesCS7A01G484500	chr5B	126444190	126447320	3130	False	840.750000	1760	87.546250	4	3793	4	chr5B.!!$F1	3789
7	TraesCS7A01G484500	chrUn	48371818	48372857	1039	True	1120.000000	1120	86.217000	1	1043	1	chrUn.!!$R1	1042
8	TraesCS7A01G484500	chrUn	318400736	318401775	1039	False	1120.000000	1120	86.217000	1	1043	1	chrUn.!!$F1	1042
9	TraesCS7A01G484500	chr1A	570104674	570105510	836	True	918.000000	918	86.572000	201	1042	1	chr1A.!!$R1	841
10	TraesCS7A01G484500	chr5A	570227653	570228446	793	True	658.000000	658	81.635000	58	852	1	chr5A.!!$R2	794
11	TraesCS7A01G484500	chr3B	232563370	232567819	4449	False	456.000000	636	81.400500	58	3426	2	chr3B.!!$F1	3368

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
784	787	1.202806	TGTTCCAAGCTGTGAGGAAGG	60.203	52.381	9.63	41.74	3.46	F
2014	2335	1.661197	CCGCAACACCAACATGTGC	60.661	57.895	0.00	39.93	4.57	F
2747	4448	1.134699	TGCATCCTAAGCCAAGACTCG	60.135	52.381	0.00	0.00	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2228	3929	3.000819	ACTGATCCGGCGACCCAA	61.001	61.111	9.30	0.00	4.12	R
3180	5237	0.326264	AGACAGTCCAACCATCAGGC	59.674	55.000	0.00	39.06	4.85	R
3659	5727	0.740149	CAAGTGTGTCCTGCAGCAAA	59.260	50.000	8.66	0.00	3.68	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
53	55	3.105283	TCAAGGGGCCTTAGTTCTAGAC	58.895	50.000	0.84	0.00	34.50	2.59
55	57	1.287146	AGGGGCCTTAGTTCTAGACGA	59.713	52.381	0.84	0.00	0.00	4.20
450	453	1.347378	GTTTTTGGCATCCCATGTGGT	59.653	47.619	0.00	0.00	41.78	4.16
591	594	2.145958	ATCGAGCCATCACAGAATCG	57.854	50.000	0.00	0.00	0.00	3.34
784	787	1.202806	TGTTCCAAGCTGTGAGGAAGG	60.203	52.381	9.63	0.00	41.74	3.46
869	873	5.592282	TGCAGGTATTTTTCACTCTGTTTCA	59.408	36.000	0.00	0.00	0.00	2.69
870	874	6.145535	GCAGGTATTTTTCACTCTGTTTCAG	58.854	40.000	0.00	0.00	0.00	3.02
888	892	8.827832	TGTTTCAGGGATCTTCATGAATAATT	57.172	30.769	8.96	0.00	32.13	1.40
965	974	8.032451	GCTAATGGGCTTTTTATCACAACTTTA	58.968	33.333	0.00	0.00	0.00	1.85
1009	1018	2.350007	GGCGTTCTAAACATGTTGCGAA	60.350	45.455	12.82	14.25	0.00	4.70
1702	2008	5.233689	CGAAGGAACAAATACTTACGATCCC	59.766	44.000	0.00	0.00	0.00	3.85
1736	2042	8.853077	TGTATCAACAGATCAAACTCAATTCT	57.147	30.769	0.00	0.00	0.00	2.40
1847	2154	8.786937	AAATTTGAATGCATATACACGATGAC	57.213	30.769	0.00	0.00	0.00	3.06
2014	2335	1.661197	CCGCAACACCAACATGTGC	60.661	57.895	0.00	0.00	39.93	4.57
2067	2388	3.087031	CAGGATGCAACTGTCAAGGAAT	58.913	45.455	12.26	0.00	0.00	3.01
2144	3844	3.699538	ACTATGCTGAGATACGTCCAACA	59.300	43.478	0.00	0.00	0.00	3.33
2275	3976	3.283751	CACCAAACCCAACTGTACTCAA	58.716	45.455	0.00	0.00	0.00	3.02
2747	4448	1.134699	TGCATCCTAAGCCAAGACTCG	60.135	52.381	0.00	0.00	0.00	4.18
3106	5162	5.350633	CCGAATGGTAGGTCGTGTTATTAA	58.649	41.667	0.00	0.00	35.48	1.40
3180	5237	1.951602	TGGTACATCCCGACGATACTG	59.048	52.381	0.00	0.00	34.77	2.74
3219	5276	4.672413	GTCTATGCTTTTGATATGTTGCGC	59.328	41.667	0.00	0.00	0.00	6.09
3449	5507	1.079127	CATCGACCACTCGCCCTTT	60.079	57.895	0.00	0.00	39.96	3.11
3468	5526	8.832521	CGCCCTTTGTAATTAGTTCACATATTA	58.167	33.333	0.00	0.00	0.00	0.98
3469	5527	9.946165	GCCCTTTGTAATTAGTTCACATATTAC	57.054	33.333	0.00	0.00	35.21	1.89
3520	5578	2.739885	TTTGAATCCACCCAAATGCG	57.260	45.000	0.00	0.00	0.00	4.73
3525	5583	0.552848	ATCCACCCAAATGCGGAGAT	59.447	50.000	0.00	0.00	0.00	2.75
3595	5653	5.408356	ACAAGCTACAGATACCACTAAACG	58.592	41.667	0.00	0.00	0.00	3.60
3606	5664	7.010183	CAGATACCACTAAACGAAGTATGTTGG	59.990	40.741	0.00	0.00	45.00	3.77
3608	5667	4.992951	ACCACTAAACGAAGTATGTTGGTC	59.007	41.667	0.00	0.00	45.00	4.02
3688	5756	1.675483	GGACACACTTGCATCACACAA	59.325	47.619	0.00	0.00	0.00	3.33
3740	5808	2.582052	CAAGGCAACCAAACTCCAGTA	58.418	47.619	0.00	0.00	37.17	2.74
3773	5841	3.334691	CCTTGAAGCGGTCAAAGTATCA	58.665	45.455	7.21	0.00	45.67	2.15
3818	5903	6.148315	CCGTTCTAACTACCGGAAATTTCTTT	59.852	38.462	17.42	5.27	43.01	2.52
3907	5992	6.134730	GTCTGACGATCGGTTACTACTTATG	58.865	44.000	20.98	0.00	0.00	1.90
3950	6035	7.568349	TCTAGCACATCTGATAGAAACCAAAT	58.432	34.615	0.00	0.00	41.45	2.32
4010	6095	3.380479	TCGGAGGTACAAGTTCAACTG	57.620	47.619	0.00	0.00	0.00	3.16
4053	6138	2.936919	ACTCAACAACAGCTGATGGA	57.063	45.000	25.57	14.16	0.00	3.41
4131	6217	2.457366	AAGTTCACTGCTCCTAACCG	57.543	50.000	0.00	0.00	0.00	4.44
4144	6230	1.464997	CCTAACCGAAGAAGCACTTGC	59.535	52.381	1.06	0.00	39.13	4.01
4185	6271	1.110442	TGAACAGTGCAAACCCCTTG	58.890	50.000	0.00	0.00	38.15	3.61
4196	6282	0.625849	AACCCCTTGACATAGCCAGG	59.374	55.000	0.00	0.00	0.00	4.45
4208	6294	3.461085	ACATAGCCAGGTCCTTGATTCAT	59.539	43.478	0.00	0.00	0.00	2.57
4278	6364	2.832661	TGTGCCACCACACTTGCC	60.833	61.111	0.00	0.00	46.51	4.52
4282	6368	2.985282	CCACCACACTTGCCGCAT	60.985	61.111	0.00	0.00	0.00	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	6.012421	GGCCCCTTGATTAGAAATCCTATAGT	60.012	42.308	0.00	0.00	0.00	2.12
17	18	6.216456	AGGCCCCTTGATTAGAAATCCTATAG	59.784	42.308	0.00	0.00	0.00	1.31
31	32	3.712218	GTCTAGAACTAAGGCCCCTTGAT	59.288	47.826	9.79	0.00	37.47	2.57
53	55	8.217115	CACTAAATAAATCGGACATCTTCATCG	58.783	37.037	0.00	0.00	0.00	3.84
55	57	7.445402	CCCACTAAATAAATCGGACATCTTCAT	59.555	37.037	0.00	0.00	0.00	2.57
450	453	6.382859	TGCCTTCACCTTCTATGACTGTATTA	59.617	38.462	0.00	0.00	0.00	0.98
591	594	4.020543	AGTCCTTCTCTATCTGTGTGGAC	58.979	47.826	0.00	0.00	41.95	4.02
784	787	3.141398	TCTTGGACACATCTGCTTTGAC	58.859	45.455	0.00	0.00	0.00	3.18
888	892	9.465985	GAATAACATCAAAAAGTACGGGAAAAA	57.534	29.630	0.00	0.00	0.00	1.94
965	974	7.307870	CGCCTAGATCAAGACTATTTAGTACGT	60.308	40.741	0.00	0.00	36.50	3.57
973	982	7.584122	TTAGAACGCCTAGATCAAGACTATT	57.416	36.000	0.00	0.00	0.00	1.73
1009	1018	0.458669	CCTATCCGCGGTGTTACACT	59.541	55.000	27.15	3.46	34.40	3.55
1157	1175	9.825109	ATGTCATGAATGAAAATGATTGCATTA	57.175	25.926	0.00	0.00	43.52	1.90
1678	1984	5.233689	GGGATCGTAAGTATTTGTTCCTTCG	59.766	44.000	0.00	0.00	39.48	3.79
1808	2114	8.695284	TGCATTCAAATTTCATAACGTAAACAC	58.305	29.630	0.00	0.00	0.00	3.32
1847	2154	3.652057	AATGGGTAGTGTCAGATTGGG	57.348	47.619	0.00	0.00	0.00	4.12
2014	2335	3.624326	TTTGATTGAGTGGTTCTTGCG	57.376	42.857	0.00	0.00	0.00	4.85
2144	3844	4.243793	TCCAAACAATATGAATCCGGGT	57.756	40.909	0.00	0.00	0.00	5.28
2228	3929	3.000819	ACTGATCCGGCGACCCAA	61.001	61.111	9.30	0.00	0.00	4.12
2275	3976	3.525199	ACTCATCCAGTCTTTTATGGCCT	59.475	43.478	3.32	0.00	36.47	5.19
2747	4448	6.657541	TGGATTTCAACACCCTCTAATGTTAC	59.342	38.462	0.00	0.00	36.92	2.50
2946	4675	4.067192	GGTTTTCATCAAAGCAGCCAAAT	58.933	39.130	0.00	0.00	41.73	2.32
2950	4679	1.338105	GGGGTTTTCATCAAAGCAGCC	60.338	52.381	0.00	0.00	43.59	4.85
3106	5162	7.497249	TGGCATTGCAAACTTAAACAATACTTT	59.503	29.630	11.39	0.00	31.75	2.66
3180	5237	0.326264	AGACAGTCCAACCATCAGGC	59.674	55.000	0.00	0.00	39.06	4.85
3219	5276	9.736023	GCTGGGTCTAATACAATTATTCTTTTG	57.264	33.333	0.00	0.00	0.00	2.44
3449	5507	9.758651	ATGCGAGTAATATGTGAACTAATTACA	57.241	29.630	14.97	0.00	37.30	2.41
3468	5526	4.261447	GGGACAAGTTAAAACAATGCGAGT	60.261	41.667	0.00	0.00	0.00	4.18
3469	5527	4.023193	AGGGACAAGTTAAAACAATGCGAG	60.023	41.667	0.00	0.00	0.00	5.03
3520	5578	1.625818	ACACAACCCAGTCTGATCTCC	59.374	52.381	0.00	0.00	0.00	3.71
3525	5583	1.148273	GGCACACAACCCAGTCTGA	59.852	57.895	0.00	0.00	0.00	3.27
3584	5642	6.015180	AGACCAACATACTTCGTTTAGTGGTA	60.015	38.462	0.00	0.00	0.00	3.25
3595	5653	7.644986	GTATGATGCTAGACCAACATACTTC	57.355	40.000	16.58	0.57	42.93	3.01
3606	5664	3.834813	TCCATGGGAGTATGATGCTAGAC	59.165	47.826	13.02	0.00	0.00	2.59
3608	5667	4.897509	TTCCATGGGAGTATGATGCTAG	57.102	45.455	13.02	0.00	31.21	3.42
3659	5727	0.740149	CAAGTGTGTCCTGCAGCAAA	59.260	50.000	8.66	0.00	0.00	3.68
3688	5756	6.710597	TTAGTTCGTAGATCATTAGGCTGT	57.289	37.500	0.00	0.00	35.04	4.40
3740	5808	1.507141	CTTCAAGGGCGTCGTTTGCT	61.507	55.000	0.00	0.00	0.00	3.91
3773	5841	5.978814	ACGGTATTCTAAAGAGCAGTGAAT	58.021	37.500	0.00	0.00	0.00	2.57
3873	5958	4.174009	CCGATCGTCAGACATAGTTTTGT	58.826	43.478	15.09	0.00	0.00	2.83
3907	5992	3.609103	AGAAATTTGCACTCGACACAC	57.391	42.857	0.00	0.00	0.00	3.82
3950	6035	8.479313	CTAGTGTGAACTAGTTGCATATGAAA	57.521	34.615	14.14	0.00	36.01	2.69
4010	6095	1.953686	TGCCTTTGTTTGTGTCCTAGC	59.046	47.619	0.00	0.00	0.00	3.42
4053	6138	4.775780	TGTGATAGTTGTAACCCTAGCAGT	59.224	41.667	0.00	0.00	30.87	4.40
4115	6201	2.244695	TCTTCGGTTAGGAGCAGTGAA	58.755	47.619	0.00	0.00	0.00	3.18
4131	6217	3.698029	TTCTGTTGCAAGTGCTTCTTC	57.302	42.857	0.00	0.00	42.66	2.87
4144	6230	4.883026	GCTGGCAGCATTCTGTTG	57.117	55.556	33.33	0.00	41.89	3.33
4185	6271	3.118261	TGAATCAAGGACCTGGCTATGTC	60.118	47.826	0.00	0.00	0.00	3.06
4196	6282	8.443953	AGACAATTTAGCTATGAATCAAGGAC	57.556	34.615	0.00	0.00	0.00	3.85
4208	6294	7.010771	TCCTGCTCCTATAGACAATTTAGCTA	58.989	38.462	0.00	0.00	0.00	3.32
4278	6364	2.848887	CAACTCAGAGTTACGAGATGCG	59.151	50.000	15.73	0.00	40.51	4.73
4282	6368	4.590918	AGGATCAACTCAGAGTTACGAGA	58.409	43.478	15.73	9.25	36.03	4.04

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.