AutoCloner

Multiple sequence alignment - TraesCS3B01G325200

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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	TraesCS3B01G325200	chr3B	100.000	2573	0	0	1	2573	526125708	526123136	0.000000e+00	4752.0
1	TraesCS3B01G325200	chr3B	95.378	238	11	0	129	366	526151503	526151266	1.870000e-101	379.0
2	TraesCS3B01G325200	chr3A	88.761	2171	159	40	438	2568	519275129	519273004	0.000000e+00	2579.0
3	TraesCS3B01G325200	chr3D	96.118	850	27	4	883	1731	400339804	400338960	0.000000e+00	1382.0
4	TraesCS3B01G325200	chr3D	86.720	753	64	10	1722	2440	400338914	400338164	0.000000e+00	804.0
5	TraesCS3B01G325200	chr3D	81.053	475	63	15	438	895	400340280	400339816	1.130000e-93	353.0
6	TraesCS3B01G325200	chr3D	90.455	220	17	4	129	348	112738489	112738704	1.170000e-73	287.0
7	TraesCS3B01G325200	chr3D	90.909	209	17	2	129	337	112734007	112734213	1.950000e-71	279.0
8	TraesCS3B01G325200	chr3D	75.000	292	54	17	449	726	587448707	587448993	1.620000e-22	117.0
9	TraesCS3B01G325200	chr2D	90.909	209	17	2	129	337	127039161	127038955	1.950000e-71	279.0
10	TraesCS3B01G325200	chr2D	87.552	241	24	6	129	367	127046975	127046739	9.070000e-70	274.0
11	TraesCS3B01G325200	chr7D	90.686	204	17	2	129	332	529576443	529576242	1.170000e-68	270.0
12	TraesCS3B01G325200	chr6D	87.983	233	22	6	192	424	401586400	401586174	1.170000e-68	270.0
13	TraesCS3B01G325200	chr6D	97.436	39	1	0	1695	1733	60610193	60610231	1.650000e-07	67.6
14	TraesCS3B01G325200	chr4D	85.597	243	18	10	128	367	338106794	338107022	3.310000e-59	239.0
15	TraesCS3B01G325200	chr6B	96.377	138	4	1	1	137	406131164	406131301	2.580000e-55	226.0
16	TraesCS3B01G325200	chr6B	95.683	139	6	0	1	139	378608504	378608366	9.260000e-55	224.0
17	TraesCS3B01G325200	chr6B	86.275	204	26	2	1031	1233	77111887	77112089	1.200000e-53	220.0
18	TraesCS3B01G325200	chr6B	84.112	107	14	2	304	410	338765216	338765113	1.630000e-17	100.0
19	TraesCS3B01G325200	chr4B	97.015	134	4	0	1	134	538313746	538313879	2.580000e-55	226.0
20	TraesCS3B01G325200	chr4B	88.820	161	17	1	264	424	311771731	311771890	2.020000e-46	196.0
21	TraesCS3B01G325200	chr4B	89.474	152	15	1	264	415	280785617	280785767	9.400000e-45	191.0
22	TraesCS3B01G325200	chr5B	95.683	139	6	0	1	139	267531450	267531312	9.260000e-55	224.0
23	TraesCS3B01G325200	chrUn	95.070	142	6	1	1	141	190129904	190129763	3.330000e-54	222.0
24	TraesCS3B01G325200	chrUn	95.070	142	6	1	1	141	221769138	221769279	3.330000e-54	222.0
25	TraesCS3B01G325200	chrUn	95.070	142	6	1	1	141	342422606	342422465	3.330000e-54	222.0
26	TraesCS3B01G325200	chrUn	89.474	152	15	1	264	415	470843512	470843662	9.400000e-45	191.0
27	TraesCS3B01G325200	chrUn	88.816	152	15	2	264	415	182176355	182176504	4.370000e-43	185.0
28	TraesCS3B01G325200	chrUn	90.164	61	6	0	364	424	474231739	474231679	2.120000e-11	80.5
29	TraesCS3B01G325200	chr7B	95.070	142	6	1	1	141	739812383	739812242	3.330000e-54	222.0
30	TraesCS3B01G325200	chr1B	94.928	138	5	2	1	138	486645295	486645430	5.580000e-52	215.0
31	TraesCS3B01G325200	chr1D	89.103	156	12	4	129	279	106544571	106544726	3.380000e-44	189.0
32	TraesCS3B01G325200	chr4A	87.059	85	11	0	340	424	629442259	629442175	2.110000e-16	97.1

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	TraesCS3B01G325200	chr3B	526123136	526125708	2572	True	4752.000000	4752	100.000000	1	2573	1	chr3B.!!$R1	2572
1	TraesCS3B01G325200	chr3A	519273004	519275129	2125	True	2579.000000	2579	88.761000	438	2568	1	chr3A.!!$R1	2130
2	TraesCS3B01G325200	chr3D	400338164	400340280	2116	True	846.333333	1382	87.963667	438	2440	3	chr3D.!!$R1	2002

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
232	233	0.032813	CCTAGGTGACCGGAACCCTA	60.033	60.0	22.31	18.08	38.57	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2198	2334	0.327924	ATGAATGCTCCGGTGGACAA	59.672	50.0	0.0	0.0	0.0	3.18	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	Hairpin	End Stability
29	30	2.355502	TCGAGAGAGCCCGAACCT	59.644	61.111	0.00	34.84	3.50
30	31	2.046864	TCGAGAGAGCCCGAACCTG	61.047	63.158	0.00	34.84	4.00
31	32	2.896443	GAGAGAGCCCGAACCTGG	59.104	66.667	0.00	0.00	4.45
40	41	1.984066	CCCGAACCTGGGTAAAAACA	58.016	50.000	0.00	44.76	2.83
41	42	2.521126	CCCGAACCTGGGTAAAAACAT	58.479	47.619	0.00	44.76	2.71
42	43	2.490509	CCCGAACCTGGGTAAAAACATC	59.509	50.000	0.00	44.76	3.06
43	44	2.160813	CCGAACCTGGGTAAAAACATCG	59.839	50.000	0.00	0.00	3.84
44	45	2.809696	CGAACCTGGGTAAAAACATCGT	59.190	45.455	0.00	0.00	3.73
45	46	3.364565	CGAACCTGGGTAAAAACATCGTG	60.365	47.826	0.00	0.00	4.35
46	47	3.217681	ACCTGGGTAAAAACATCGTGT	57.782	42.857	0.00	0.00	4.49
47	48	3.143728	ACCTGGGTAAAAACATCGTGTC	58.856	45.455	0.00	0.00	3.67
48	49	2.486592	CCTGGGTAAAAACATCGTGTCC	59.513	50.000	0.00	0.00	4.02
49	50	2.486592	CTGGGTAAAAACATCGTGTCCC	59.513	50.000	0.00	31.92	4.46
50	51	2.106857	TGGGTAAAAACATCGTGTCCCT	59.893	45.455	10.79	32.37	4.20
51	52	3.151554	GGGTAAAAACATCGTGTCCCTT	58.848	45.455	0.00	29.50	3.95
52	53	3.057806	GGGTAAAAACATCGTGTCCCTTG	60.058	47.826	0.00	29.50	3.61
53	54	3.566742	GGTAAAAACATCGTGTCCCTTGT	59.433	43.478	0.00	0.00	3.16
54	55	3.982576	AAAAACATCGTGTCCCTTGTC	57.017	42.857	0.00	0.00	3.18
55	56	2.930826	AAACATCGTGTCCCTTGTCT	57.069	45.000	0.00	0.00	3.41
56	57	2.457366	AACATCGTGTCCCTTGTCTC	57.543	50.000	0.00	0.00	3.36
57	58	0.608640	ACATCGTGTCCCTTGTCTCC	59.391	55.000	0.00	0.00	3.71
58	59	0.898320	CATCGTGTCCCTTGTCTCCT	59.102	55.000	0.00	0.00	3.69
59	60	0.898320	ATCGTGTCCCTTGTCTCCTG	59.102	55.000	0.00	0.00	3.86
60	61	0.469331	TCGTGTCCCTTGTCTCCTGT	60.469	55.000	0.00	0.00	4.00
61	62	0.393077	CGTGTCCCTTGTCTCCTGTT	59.607	55.000	0.00	0.00	3.16

Showing 1 to 25 of 364 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	3.449632	GCTCTCTCGATGGAGGTAAAAC	58.550	50.000	4.78	40.85	2.43
1	2	2.431057	GGCTCTCTCGATGGAGGTAAAA	59.569	50.000	4.78	40.85	1.52
2	3	2.032620	GGCTCTCTCGATGGAGGTAAA	58.967	52.381	4.78	40.85	2.01
3	4	1.693627	GGCTCTCTCGATGGAGGTAA	58.306	55.000	4.78	40.85	2.85
5	6	1.456705	GGGCTCTCTCGATGGAGGT	60.457	63.158	4.78	40.85	3.85
6	7	2.560119	CGGGCTCTCTCGATGGAGG	61.560	68.421	4.78	40.85	4.30
7	8	1.103987	TTCGGGCTCTCTCGATGGAG	61.104	60.000	0.00	41.89	3.86
8	9	1.076995	TTCGGGCTCTCTCGATGGA	60.077	57.895	0.00	35.25	3.41
9	10	1.066587	GTTCGGGCTCTCTCGATGG	59.933	63.158	0.00	35.25	3.51
10	11	1.066587	GGTTCGGGCTCTCTCGATG	59.933	63.158	0.00	35.25	3.84
11	12	1.076632	AGGTTCGGGCTCTCTCGAT	60.077	57.895	0.00	35.25	3.59
12	13	2.046864	CAGGTTCGGGCTCTCTCGA	61.047	63.158	0.00	0.00	4.04
13	14	2.492090	CAGGTTCGGGCTCTCTCG	59.508	66.667	0.00	0.00	4.04
14	15	2.726351	CCCAGGTTCGGGCTCTCTC	61.726	68.421	0.00	40.07	3.20
15	16	2.685380	CCCAGGTTCGGGCTCTCT	60.685	66.667	0.00	40.07	3.10
22	23	2.160813	CGATGTTTTTACCCAGGTTCGG	59.839	50.000	0.00	0.00	4.30
23	24	2.809696	ACGATGTTTTTACCCAGGTTCG	59.190	45.455	0.00	0.00	3.95
24	25	3.566742	ACACGATGTTTTTACCCAGGTTC	59.433	43.478	0.00	0.00	3.62
25	26	3.558033	ACACGATGTTTTTACCCAGGTT	58.442	40.909	0.00	0.00	3.50
26	27	3.143728	GACACGATGTTTTTACCCAGGT	58.856	45.455	0.00	0.00	4.00
27	28	2.486592	GGACACGATGTTTTTACCCAGG	59.513	50.000	0.00	0.00	4.45
28	29	2.486592	GGGACACGATGTTTTTACCCAG	59.513	50.000	0.00	31.68	4.45
29	30	2.106857	AGGGACACGATGTTTTTACCCA	59.893	45.455	0.00	33.25	4.51
30	31	2.786777	AGGGACACGATGTTTTTACCC	58.213	47.619	0.00	31.54	3.69
31	32	3.566742	ACAAGGGACACGATGTTTTTACC	59.433	43.478	0.00	0.00	2.85

Showing 1 to 25 of 379 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.