AutoCloner

Multiple sequence alignment - TraesCS1B01G198100

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	TraesCS1B01G198100	chr1B	100.000	3233	0	0	1	3233	356283582	356280350	0.000000e+00	5971.0
1	TraesCS1B01G198100	chr1B	76.331	338	74	6	18	352	621445631	621445965	3.310000e-40	176.0
2	TraesCS1B01G198100	chr1A	94.489	1869	46	15	628	2458	330686547	330688396	0.000000e+00	2828.0
3	TraesCS1B01G198100	chr1D	94.220	1834	75	10	628	2435	256971457	256973285	0.000000e+00	2771.0
4	TraesCS1B01G198100	chr1D	78.671	647	100	25	2565	3185	213374391	213373757	2.340000e-106	396.0
5	TraesCS1B01G198100	chr1D	76.695	708	118	25	2503	3185	131630897	131630212	1.850000e-92	350.0
6	TraesCS1B01G198100	chr1D	81.633	98	13	5	3095	3189	163704707	163704802	3.460000e-10	76.8
7	TraesCS1B01G198100	chr1D	100.000	39	0	0	873	911	256971735	256971697	4.470000e-09	73.1
8	TraesCS1B01G198100	chr3D	89.324	562	57	1	1	562	74445675	74446233	0.000000e+00	702.0
9	TraesCS1B01G198100	chr3D	89.165	563	59	2	1	562	18798228	18798789	0.000000e+00	701.0
10	TraesCS1B01G198100	chr3D	77.419	713	125	16	2496	3185	451893994	451894693	3.020000e-105	392.0
11	TraesCS1B01G198100	chr3D	91.667	60	5	0	563	622	527563038	527563097	2.070000e-12	84.2
12	TraesCS1B01G198100	chr7B	85.409	562	82	0	1	562	535693834	535693273	4.650000e-163	584.0
13	TraesCS1B01G198100	chr7B	79.126	709	111	26	2503	3185	707963833	707963136	3.800000e-124	455.0
14	TraesCS1B01G198100	chr7B	77.353	680	118	19	2539	3185	145727497	145728173	1.420000e-98	370.0
15	TraesCS1B01G198100	chr7B	92.188	64	4	1	559	622	381917866	381917928	4.440000e-14	89.8
16	TraesCS1B01G198100	chr7B	92.188	64	4	1	559	622	381920361	381920423	4.440000e-14	89.8
17	TraesCS1B01G198100	chr7B	92.188	64	4	1	559	622	381942412	381942474	4.440000e-14	89.8
18	TraesCS1B01G198100	chr6B	85.409	562	81	1	1	562	620278094	620277534	1.670000e-162	582.0
19	TraesCS1B01G198100	chr6B	79.045	649	95	27	2565	3185	65134609	65133974	1.080000e-109	407.0
20	TraesCS1B01G198100	chr6B	75.063	397	60	25	2807	3186	568448693	568448319	7.230000e-32	148.0
21	TraesCS1B01G198100	chr3B	79.669	605	95	19	2504	3093	671576560	671577151	8.350000e-111	411.0
22	TraesCS1B01G198100	chr3B	83.516	91	14	1	3095	3185	819808528	819808617	2.070000e-12	84.2
23	TraesCS1B01G198100	chr4D	78.783	608	99	20	2503	3096	468394451	468395042	6.550000e-102	381.0
24	TraesCS1B01G198100	chr4D	77.985	536	91	17	2670	3185	96514537	96514009	8.710000e-81	311.0
25	TraesCS1B01G198100	chr4B	77.280	669	123	22	2540	3186	481491889	481491228	1.830000e-97	366.0
26	TraesCS1B01G198100	chr6D	76.869	709	120	25	2503	3182	390005340	390004647	8.530000e-96	361.0
27	TraesCS1B01G198100	chr6D	80.514	467	74	16	2542	2999	58531339	58530881	3.090000e-90	342.0
28	TraesCS1B01G198100	chrUn	80.810	469	74	10	2542	2999	45258883	45258420	1.430000e-93	353.0
29	TraesCS1B01G198100	chr2B	80.942	467	71	12	2545	2999	651134569	651134109	1.430000e-93	353.0
30	TraesCS1B01G198100	chr2B	77.960	549	98	13	2659	3190	198516159	198515617	4.020000e-84	322.0
31	TraesCS1B01G198100	chr5D	79.528	508	83	13	2503	2999	423231380	423231877	3.090000e-90	342.0
32	TraesCS1B01G198100	chr5D	81.176	170	20	7	3028	3185	294426119	294425950	3.390000e-25	126.0
33	TraesCS1B01G198100	chr7D	79.878	492	74	18	2713	3185	179526215	179526700	1.440000e-88	337.0
34	TraesCS1B01G198100	chr2D	79.331	508	81	14	2503	2999	68737186	68736692	5.170000e-88	335.0
35	TraesCS1B01G198100	chr2D	78.269	543	94	14	2659	3184	568947067	568947602	8.650000e-86	327.0
36	TraesCS1B01G198100	chr5B	78.937	508	86	13	2503	2999	617174534	617174037	3.110000e-85	326.0
37	TraesCS1B01G198100	chr4A	78.269	543	87	16	2659	3185	705177207	705177734	1.450000e-83	320.0
38	TraesCS1B01G198100	chr4A	84.058	69	9	2	563	629	563094915	563094983	7.490000e-07	65.8
39	TraesCS1B01G198100	chr3A	78.022	546	90	19	2659	3186	108507810	108508343	1.870000e-82	316.0
40	TraesCS1B01G198100	chr5A	92.727	55	4	0	3129	3183	311985614	311985668	2.670000e-11	80.5

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	TraesCS1B01G198100	chr1B	356280350	356283582	3232	True	5971	5971	100.000	1	3233	1	chr1B.!!$R1	3232
1	TraesCS1B01G198100	chr1A	330686547	330688396	1849	False	2828	2828	94.489	628	2458	1	chr1A.!!$F1	1830
2	TraesCS1B01G198100	chr1D	256971457	256973285	1828	False	2771	2771	94.220	628	2435	1	chr1D.!!$F2	1807
3	TraesCS1B01G198100	chr1D	213373757	213374391	634	True	396	396	78.671	2565	3185	1	chr1D.!!$R2	620
4	TraesCS1B01G198100	chr1D	131630212	131630897	685	True	350	350	76.695	2503	3185	1	chr1D.!!$R1	682
5	TraesCS1B01G198100	chr3D	74445675	74446233	558	False	702	702	89.324	1	562	1	chr3D.!!$F2	561
6	TraesCS1B01G198100	chr3D	18798228	18798789	561	False	701	701	89.165	1	562	1	chr3D.!!$F1	561
7	TraesCS1B01G198100	chr3D	451893994	451894693	699	False	392	392	77.419	2496	3185	1	chr3D.!!$F3	689
8	TraesCS1B01G198100	chr7B	535693273	535693834	561	True	584	584	85.409	1	562	1	chr7B.!!$R1	561
9	TraesCS1B01G198100	chr7B	707963136	707963833	697	True	455	455	79.126	2503	3185	1	chr7B.!!$R2	682
10	TraesCS1B01G198100	chr7B	145727497	145728173	676	False	370	370	77.353	2539	3185	1	chr7B.!!$F1	646
11	TraesCS1B01G198100	chr6B	620277534	620278094	560	True	582	582	85.409	1	562	1	chr6B.!!$R3	561
12	TraesCS1B01G198100	chr6B	65133974	65134609	635	True	407	407	79.045	2565	3185	1	chr6B.!!$R1	620
13	TraesCS1B01G198100	chr3B	671576560	671577151	591	False	411	411	79.669	2504	3093	1	chr3B.!!$F1	589
14	TraesCS1B01G198100	chr4D	468394451	468395042	591	False	381	381	78.783	2503	3096	1	chr4D.!!$F1	593
15	TraesCS1B01G198100	chr4D	96514009	96514537	528	True	311	311	77.985	2670	3185	1	chr4D.!!$R1	515
16	TraesCS1B01G198100	chr4B	481491228	481491889	661	True	366	366	77.280	2540	3186	1	chr4B.!!$R1	646
17	TraesCS1B01G198100	chr6D	390004647	390005340	693	True	361	361	76.869	2503	3182	1	chr6D.!!$R2	679
18	TraesCS1B01G198100	chr2B	198515617	198516159	542	True	322	322	77.960	2659	3190	1	chr2B.!!$R1	531
19	TraesCS1B01G198100	chr2D	568947067	568947602	535	False	327	327	78.269	2659	3184	1	chr2D.!!$F1	525
20	TraesCS1B01G198100	chr4A	705177207	705177734	527	False	320	320	78.269	2659	3185	1	chr4A.!!$F2	526
21	TraesCS1B01G198100	chr3A	108507810	108508343	533	False	316	316	78.022	2659	3186	1	chr3A.!!$F1	527

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
784	796	0.390735	CACCTACGAAACTTCCCCGG	60.391	60.0	0.0	0.0	0.0	5.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2490	2554	0.107848	AACTTTATGACGGCGGAGGG	60.108	55.0	13.24	0.0	0.0	4.3	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
31	32	3.753272	TCTTCTTACAGCATTGGACAAGC	59.247	43.478	0.00	0.00	0.00	4.01
34	35	1.725641	TACAGCATTGGACAAGCTCG	58.274	50.000	0.00	0.00	36.26	5.03
37	38	2.787249	CATTGGACAAGCTCGGCG	59.213	61.111	0.00	0.00	0.00	6.46
64	65	2.338500	ACGAAGTTCTCCGAAATGCTC	58.662	47.619	0.56	0.00	37.78	4.26
67	68	0.608640	AGTTCTCCGAAATGCTCCGT	59.391	50.000	0.00	0.00	0.00	4.69
73	74	0.807667	CCGAAATGCTCCGTCCAGAG	60.808	60.000	0.00	0.00	36.92	3.35
136	137	1.079543	CTGAAGCCGAGTGGTGAGG	60.080	63.158	0.00	0.00	37.67	3.86
145	146	3.948719	GTGGTGAGGCCCCGACAA	61.949	66.667	0.00	0.00	36.04	3.18
151	152	1.303282	GAGGCCCCGACAAAGGATT	59.697	57.895	0.00	0.00	0.00	3.01
175	176	0.596577	CGTCACCGTTCTGGAGAGAA	59.403	55.000	0.00	0.00	38.08	2.87
238	239	2.042537	AGGAGAGCGATGAGGGCA	60.043	61.111	0.00	0.00	0.00	5.36
250	251	2.610859	AGGGCACGGTTGATCCCT	60.611	61.111	0.00	0.00	43.98	4.20
253	254	2.668632	GCACGGTTGATCCCTCCA	59.331	61.111	0.00	0.00	0.00	3.86
256	257	1.026718	CACGGTTGATCCCTCCAAGC	61.027	60.000	0.00	0.00	38.30	4.01
412	413	3.755628	CGGACTTCGGAGCGGGAA	61.756	66.667	0.00	0.00	34.75	3.97
525	527	1.187087	AGCTAGTTGGCGTAGAAGCT	58.813	50.000	0.00	0.00	35.55	3.74
528	530	2.186076	CTAGTTGGCGTAGAAGCTTCG	58.814	52.381	20.43	11.07	37.29	3.79
556	558	0.602905	CCTCCTTGTCGTTGTGGGAC	60.603	60.000	0.00	0.00	34.99	4.46
570	572	2.450609	TGGGACACGAGAGTTTTAGC	57.549	50.000	0.00	0.00	46.40	3.09
571	573	1.689813	TGGGACACGAGAGTTTTAGCA	59.310	47.619	0.00	0.00	46.40	3.49
572	574	2.067013	GGGACACGAGAGTTTTAGCAC	58.933	52.381	0.00	0.00	46.40	4.40
573	575	2.067013	GGACACGAGAGTTTTAGCACC	58.933	52.381	0.00	0.00	46.40	5.01
574	576	2.547218	GGACACGAGAGTTTTAGCACCA	60.547	50.000	0.00	0.00	46.40	4.17
575	577	3.128349	GACACGAGAGTTTTAGCACCAA	58.872	45.455	0.00	0.00	46.40	3.67
576	578	3.537580	ACACGAGAGTTTTAGCACCAAA	58.462	40.909	0.00	0.00	46.40	3.28

Showing 1 to 25 of 172 entries

Previous1 2 3 4 5 6 7Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	4.170062	TTCGTCTACGCCGCCGAG	62.170	66.667	0.00	0.00	39.60	4.63
34	35	2.126189	AACTTCGTCTACGCCGCC	60.126	61.111	0.00	0.00	39.60	6.13
37	38	0.522915	CGGAGAACTTCGTCTACGCC	60.523	60.000	0.00	0.00	44.58	5.68
58	59	0.324738	TCCTCTCTGGACGGAGCATT	60.325	55.000	3.25	0.00	40.56	3.56
64	65	1.608717	CTGGGTTCCTCTCTGGACGG	61.609	65.000	0.00	0.00	46.14	4.79
67	68	2.191400	CAATCTGGGTTCCTCTCTGGA	58.809	52.381	0.00	0.00	44.51	3.86
73	74	1.210722	GAGGACCAATCTGGGTTCCTC	59.789	57.143	13.65	13.65	43.37	3.71
136	137	1.067846	GTGAAAATCCTTTGTCGGGGC	60.068	52.381	0.00	0.00	0.00	5.80
175	176	2.095978	CTGGTGACTTCCGTCCCGTT	62.096	60.000	0.00	0.00	39.47	4.44
238	239	1.299976	GCTTGGAGGGATCAACCGT	59.700	57.895	0.00	0.00	40.11	4.83
267	268	0.317603	CTTCGACGTCGTCCACAACT	60.318	55.000	34.40	0.00	40.80	3.16
400	401	2.357760	CCGTTTTCCCGCTCCGAA	60.358	61.111	0.00	0.00	0.00	4.30
412	413	4.264638	GCGCTGGTTGCACCGTTT	62.265	61.111	0.00	0.00	42.58	3.60
457	459	3.121019	GACCTGTCGGCGCTCTAT	58.879	61.111	7.64	0.00	0.00	1.98
468	470	3.622826	CGTGGGGGTTCGACCTGT	61.623	66.667	4.41	0.00	38.64	4.00
505	507	2.376109	AGCTTCTACGCCAACTAGCTA	58.624	47.619	0.00	0.00	37.21	3.32
509	511	2.273370	CGAAGCTTCTACGCCAACTA	57.727	50.000	23.50	0.00	0.00	2.24
536	538	1.302511	CCCACAACGACAAGGAGGG	60.303	63.158	0.00	0.00	0.00	4.30
556	558	3.560068	AGTTTGGTGCTAAAACTCTCGTG	59.440	43.478	6.27	0.00	42.75	4.35
562	564	5.983118	GCATGTTTAGTTTGGTGCTAAAACT	59.017	36.000	13.79	13.79	46.72	2.66
563	565	5.751028	TGCATGTTTAGTTTGGTGCTAAAAC	59.249	36.000	0.00	2.47	39.29	2.43
564	566	5.907207	TGCATGTTTAGTTTGGTGCTAAAA	58.093	33.333	0.00	0.00	39.29	1.52
565	567	5.521906	TGCATGTTTAGTTTGGTGCTAAA	57.478	34.783	0.00	0.00	36.44	1.85
566	568	5.285651	GTTGCATGTTTAGTTTGGTGCTAA	58.714	37.500	0.00	0.00	33.95	3.09
567	569	4.555708	CGTTGCATGTTTAGTTTGGTGCTA	60.556	41.667	0.00	0.00	33.95	3.49

Showing 1 to 25 of 138 entries

Previous1 2 3 4 5 6Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.