AutoCloner

Multiple sequence alignment - TraesCS4B01G284100

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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	TraesCS4B01G284100	chr4B	100.000	2305	0	0	950	3254	567430663	567428359	0.000000e+00	4257.0
1	TraesCS4B01G284100	chr4B	85.262	1547	196	18	1416	2947	567590062	567588533	0.000000e+00	1565.0
2	TraesCS4B01G284100	chr4B	100.000	675	0	0	1	675	567431612	567430938	0.000000e+00	1247.0
3	TraesCS4B01G284100	chr4B	100.000	225	0	0	3697	3921	567427916	567427692	2.180000e-112	416.0
4	TraesCS4B01G284100	chr4B	91.818	110	8	1	90	198	567430195	567430086	6.790000e-33	152.0
5	TraesCS4B01G284100	chr4B	88.034	117	10	3	86	198	567590064	567589948	6.830000e-28	135.0
6	TraesCS4B01G284100	chr4B	78.646	192	27	8	2942	3125	567588497	567588312	8.900000e-22	115.0
7	TraesCS4B01G284100	chr4B	90.741	54	4	1	3860	3913	567587892	567587840	1.950000e-08	71.3
8	TraesCS4B01G284100	chr4A	94.288	2066	99	9	1075	3125	13162875	13164936	0.000000e+00	3144.0
9	TraesCS4B01G284100	chr4A	90.953	1669	130	9	1418	3069	13524969	13526633	0.000000e+00	2226.0
10	TraesCS4B01G284100	chr4A	89.369	1552	148	11	1400	2938	13517976	13519523	0.000000e+00	1936.0
11	TraesCS4B01G284100	chr4A	85.844	1547	188	15	1408	2947	13150691	13152213	0.000000e+00	1615.0
12	TraesCS4B01G284100	chr4A	89.270	466	45	5	18	482	13160644	13161105	2.630000e-161	579.0
13	TraesCS4B01G284100	chr4A	92.045	176	13	1	476	651	13162560	13162734	3.030000e-61	246.0
14	TraesCS4B01G284100	chr4A	93.252	163	10	1	37	198	13524916	13525078	5.060000e-59	239.0
15	TraesCS4B01G284100	chr4A	75.078	321	47	18	2942	3254	13157099	13157394	6.880000e-23	119.0
16	TraesCS4B01G284100	chr4D	88.625	1556	152	15	1408	2947	454991208	454989662	0.000000e+00	1869.0
17	TraesCS4B01G284100	chr4D	94.948	1148	33	10	1075	2204	454835426	454834286	0.000000e+00	1775.0
18	TraesCS4B01G284100	chr4D	84.343	1552	200	20	1408	2947	455090442	455088922	0.000000e+00	1480.0
19	TraesCS4B01G284100	chr4D	89.180	915	85	5	1418	2322	454809771	454808861	0.000000e+00	1129.0
20	TraesCS4B01G284100	chr4D	91.810	757	54	2	2196	2947	454833966	454833213	0.000000e+00	1048.0
21	TraesCS4B01G284100	chr4D	90.368	789	71	5	1665	2452	454839413	454838629	0.000000e+00	1031.0
22	TraesCS4B01G284100	chr4D	89.068	622	55	7	5	613	454836203	454835582	0.000000e+00	760.0
23	TraesCS4B01G284100	chr4D	88.655	238	20	5	1	233	455070113	455069878	2.310000e-72	283.0
24	TraesCS4B01G284100	chr4D	93.252	163	10	1	37	198	454809824	454809662	5.060000e-59	239.0
25	TraesCS4B01G284100	chr4D	88.034	117	10	3	86	198	455090436	455090320	6.830000e-28	135.0
26	TraesCS4B01G284100	chr4D	92.045	88	5	1	2942	3027	455088886	455088799	5.320000e-24	122.0
27	TraesCS4B01G284100	chr4D	78.646	192	27	10	2942	3125	454989626	454989441	8.900000e-22	115.0
28	TraesCS4B01G284100	chr4D	89.773	88	7	2	2942	3027	454833177	454833090	1.150000e-20	111.0
29	TraesCS4B01G284100	chr4D	95.238	42	2	0	3872	3913	455088263	455088222	2.530000e-07	67.6
30	TraesCS4B01G284100	chr4D	78.512	121	11	8	3796	3914	454806160	454806053	9.090000e-07	65.8
31	TraesCS4B01G284100	chr5A	94.771	918	42	1	1075	1992	53220297	53219386	0.000000e+00	1424.0
32	TraesCS4B01G284100	chr5A	91.209	182	16	0	470	651	53220596	53220415	8.410000e-62	248.0
33	TraesCS4B01G284100	chr3D	76.658	754	148	17	1419	2149	435489218	435488470	3.670000e-105	392.0
34	TraesCS4B01G284100	chr3B	80.645	186	30	4	467	651	3890839	3891019	5.280000e-29	139.0
35	TraesCS4B01G284100	chr3B	80.645	186	30	4	467	651	4777759	4777939	5.280000e-29	139.0

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	TraesCS4B01G284100	chr4B	567427692	567431612	3920	True	1518.000000	4257	97.954500	1	3921	4	chr4B.!!$R1	3920
1	TraesCS4B01G284100	chr4B	567587840	567590064	2224	True	471.575000	1565	85.670750	86	3913	4	chr4B.!!$R2	3827
2	TraesCS4B01G284100	chr4A	13517976	13519523	1547	False	1936.000000	1936	89.369000	1400	2938	1	chr4A.!!$F2	1538
3	TraesCS4B01G284100	chr4A	13150691	13152213	1522	False	1615.000000	1615	85.844000	1408	2947	1	chr4A.!!$F1	1539
4	TraesCS4B01G284100	chr4A	13524916	13526633	1717	False	1232.500000	2226	92.102500	37	3069	2	chr4A.!!$F4	3032
5	TraesCS4B01G284100	chr4A	13157099	13164936	7837	False	1022.000000	3144	87.670250	18	3254	4	chr4A.!!$F3	3236
6	TraesCS4B01G284100	chr4D	454989441	454991208	1767	True	992.000000	1869	83.635500	1408	3125	2	chr4D.!!$R4	1717
7	TraesCS4B01G284100	chr4D	454833090	454839413	6323	True	945.000000	1775	91.193400	5	3027	5	chr4D.!!$R3	3022
8	TraesCS4B01G284100	chr4D	454806053	454809824	3771	True	477.933333	1129	86.981333	37	3914	3	chr4D.!!$R2	3877
9	TraesCS4B01G284100	chr4D	455088222	455090442	2220	True	451.150000	1480	89.915000	86	3913	4	chr4D.!!$R5	3827
10	TraesCS4B01G284100	chr5A	53219386	53220596	1210	True	836.000000	1424	92.990000	470	1992	2	chr5A.!!$R1	1522
11	TraesCS4B01G284100	chr3D	435488470	435489218	748	True	392.000000	392	76.658000	1419	2149	1	chr3D.!!$R1	730

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	Hairpin	End Stability	Orientation
351	3881	0.177604	CTGGACCTGCCTGTCAGATC	59.822	60.0	45.72	2.75	F
1064	4603	0.181587	TGTTTGCTTTCCTCACCCGA	59.818	50.0	0.00	5.14	F
1379	4918	0.385390	CTTGCAGCCGAACAAAACCT	59.615	50.0	0.00	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1391	4930	0.107643	GCAGGCTGGAAGGAGGATAC	59.892	60.0	17.64	2.24	R
2902	11228	0.456653	GCATTCGGCGCACTTTTGAT	60.457	50.0	10.83	2.57	R
3108	11646	0.976641	TCCATGAGACGCCAAAGAGT	59.023	50.0	0.00	3.24	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
121	3650	1.479757	GGATACTTCCTCGCCTCCTCT	60.480	57.143	0.00	0.00	39.14	3.69
143	3672	3.681835	AGCCACCCGTCGTCACTC	61.682	66.667	0.00	0.00	0.00	3.51
145	3674	3.667282	CCACCCGTCGTCACTCGT	61.667	66.667	0.00	0.00	40.80	4.18
151	3680	2.335369	GTCGTCACTCGTGCCAGT	59.665	61.111	0.00	0.00	40.80	4.00
155	3684	3.545574	TCACTCGTGCCAGTGCCA	61.546	61.111	3.26	0.00	43.18	4.92
156	3685	3.046087	CACTCGTGCCAGTGCCAG	61.046	66.667	0.00	0.00	37.58	4.85
228	3758	3.947841	GCGGTTTCAGTGTGCGCA	61.948	61.111	5.66	5.66	0.00	6.09
245	3775	1.230635	GCACGCACAGTCATGAAGGT	61.231	55.000	0.00	0.00	0.00	3.50
248	3778	1.878775	GCACAGTCATGAAGGTGGC	59.121	57.895	22.42	14.26	0.00	5.01
253	3783	1.450312	GTCATGAAGGTGGCGGAGG	60.450	63.158	0.00	0.00	0.00	4.30
282	3812	3.942829	TCTACTAGTTCCCGAGTTTCGA	58.057	45.455	0.00	0.00	43.74	3.71
283	3813	4.521146	TCTACTAGTTCCCGAGTTTCGAT	58.479	43.478	0.00	0.00	43.74	3.59
316	3846	3.391049	GAAGGCGAACAGTCAAGTAACT	58.609	45.455	0.00	0.00	0.00	2.24
343	3873	4.704103	TCCTCGCTGGACCTGCCT	62.704	66.667	16.88	0.00	40.56	4.75
350	3880	1.908340	GCTGGACCTGCCTGTCAGAT	61.908	60.000	12.17	0.00	45.72	2.90
351	3881	0.177604	CTGGACCTGCCTGTCAGATC	59.822	60.000	0.00	0.00	45.72	2.75
353	3883	1.323271	GGACCTGCCTGTCAGATCGA	61.323	60.000	0.00	0.00	45.72	3.59
390	3920	3.050619	GGTGAAGAACTCGGCATATACG	58.949	50.000	0.00	0.00	0.00	3.06
438	3968	3.327172	TGTGGGAATACTTGTTAACCCGA	59.673	43.478	2.48	0.00	40.08	5.14
441	3971	4.225492	TGGGAATACTTGTTAACCCGATGA	59.775	41.667	2.48	0.00	40.08	2.92
443	3973	4.573607	GGAATACTTGTTAACCCGATGACC	59.426	45.833	2.48	0.00	0.00	4.02
446	3976	0.322322	TTGTTAACCCGATGACCGCT	59.678	50.000	2.48	0.00	36.84	5.52
463	3993	2.223971	CCGCTCGAAGTTGGTGGTATAT	60.224	50.000	0.00	0.00	0.00	0.86
465	3995	4.500205	CCGCTCGAAGTTGGTGGTATATAA	60.500	45.833	0.00	0.00	0.00	0.98
466	3996	5.045215	CGCTCGAAGTTGGTGGTATATAAA	58.955	41.667	0.00	0.00	0.00	1.40

Showing 1 to 25 of 138 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	8.853126	ACTGCACGTACCTAATATATAACAGAA	58.147	33.333	0.00	0.00	0.00	3.02
8	9	8.400184	ACTGCACGTACCTAATATATAACAGA	57.600	34.615	0.00	0.00	0.00	3.41
14	15	8.302438	GGAAACTACTGCACGTACCTAATATAT	58.698	37.037	0.00	0.00	0.00	0.86
16	17	6.097270	TGGAAACTACTGCACGTACCTAATAT	59.903	38.462	0.00	0.00	0.00	1.28
29	3558	6.095377	CAGATTGGATTTTGGAAACTACTGC	58.905	40.000	0.00	0.00	0.00	4.40
70	3599	0.170561	CCAGTACTTGCTAGTCGCGT	59.829	55.000	5.77	0.00	43.27	6.01
121	3650	3.524648	GACGACGGGTGGCTGGAAA	62.525	63.158	0.00	0.00	0.00	3.13
143	3672	3.121030	GTAGCTGGCACTGGCACG	61.121	66.667	0.07	0.00	43.71	5.34
228	3758	0.603707	CCACCTTCATGACTGTGCGT	60.604	55.000	15.28	0.00	0.00	5.24
237	3767	2.825836	GCCTCCGCCACCTTCATG	60.826	66.667	0.00	0.00	0.00	3.07
245	3775	1.609635	TAGAACATTCGCCTCCGCCA	61.610	55.000	0.00	0.00	0.00	5.69
248	3778	2.358267	ACTAGTAGAACATTCGCCTCCG	59.642	50.000	3.59	0.00	0.00	4.63
253	3783	3.114065	CGGGAACTAGTAGAACATTCGC	58.886	50.000	3.59	4.90	0.00	4.70
260	3790	4.326826	TCGAAACTCGGGAACTAGTAGAA	58.673	43.478	3.59	0.00	40.88	2.10
282	3812	0.603569	CGCCTTCCTATGCCGAGTAT	59.396	55.000	0.00	0.00	0.00	2.12
283	3813	0.466739	TCGCCTTCCTATGCCGAGTA	60.467	55.000	0.00	0.00	0.00	2.59
294	3824	2.450609	TACTTGACTGTTCGCCTTCC	57.549	50.000	0.00	0.00	0.00	3.46
316	3846	1.299850	CAGCGAGGACGTGTCAACA	60.300	57.895	0.00	0.00	41.98	3.33
339	3869	0.668535	CGGTATCGATCTGACAGGCA	59.331	55.000	0.00	0.00	39.00	4.75
340	3870	0.952280	TCGGTATCGATCTGACAGGC	59.048	55.000	0.00	0.00	40.88	4.85
343	3873	2.640184	ACACTCGGTATCGATCTGACA	58.360	47.619	0.00	0.00	45.04	3.58
350	3880	0.098200	CGCAGAACACTCGGTATCGA	59.902	55.000	0.00	0.00	43.86	3.59
351	3881	0.866061	CCGCAGAACACTCGGTATCG	60.866	60.000	0.00	0.00	38.47	2.92
407	3937	7.784633	AACAAGTATTCCCACAATTTGTTTG	57.215	32.000	0.00	2.46	41.36	2.93
411	3941	6.871492	GGGTTAACAAGTATTCCCACAATTTG	59.129	38.462	8.10	0.00	35.43	2.32

Showing 1 to 25 of 136 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.