AutoCloner

Multiple sequence alignment - TraesCS3B01G076200

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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	TraesCS3B01G076200	chr3B	100.000	3140	0	0	1	3140	47120348	47123487	0.000000e+00	5799.0
1	TraesCS3B01G076200	chr3B	94.938	1699	71	5	768	2462	46366172	46364485	0.000000e+00	2647.0
2	TraesCS3B01G076200	chr3B	95.192	624	7	3	2518	3140	46364211	46363610	0.000000e+00	965.0
3	TraesCS3B01G076200	chr3B	77.660	846	163	18	1308	2134	47202136	47202974	2.810000e-135	492.0
4	TraesCS3B01G076200	chr3B	76.543	972	176	30	1323	2257	47193040	47193996	4.710000e-133	484.0
5	TraesCS3B01G076200	chr3B	79.091	330	51	9	2546	2858	47195406	47195734	8.820000e-51	211.0
6	TraesCS3B01G076200	chr3B	90.826	109	10	0	341	449	46366635	46366527	2.520000e-31	147.0
7	TraesCS3B01G076200	chr3B	78.808	151	31	1	2669	2819	46307800	46307949	1.990000e-17	100.0
8	TraesCS3B01G076200	chr3B	100.000	28	0	0	3080	3107	79132281	79132254	6.000000e-03	52.8
9	TraesCS3B01G076200	chr3A	93.756	2146	100	16	850	2983	37823990	37821867	0.000000e+00	3190.0
10	TraesCS3B01G076200	chr3A	95.000	160	8	0	2981	3140	37821744	37821585	5.200000e-63	252.0
11	TraesCS3B01G076200	chr3A	84.076	157	23	2	1040	1195	10940608	10940763	1.950000e-32	150.0
12	TraesCS3B01G076200	chr3A	80.247	162	27	5	1459	1619	10613087	10613244	1.980000e-22	117.0
13	TraesCS3B01G076200	chr3D	88.976	1524	129	13	850	2344	27948418	27949931	0.000000e+00	1847.0
14	TraesCS3B01G076200	chr3D	91.315	783	26	11	2377	3140	27949926	27950685	0.000000e+00	1031.0
15	TraesCS3B01G076200	chr3D	76.464	837	152	25	1451	2255	27681531	27680708	2.250000e-111	412.0
16	TraesCS3B01G076200	chr3D	81.457	151	22	4	2669	2818	4924771	4924626	5.500000e-23	119.0
17	TraesCS3B01G076200	chrUn	79.039	229	44	4	1052	1278	225561566	225561340	1.510000e-33	154.0
18	TraesCS3B01G076200	chrUn	78.571	238	47	4	1040	1275	237462792	237463027	1.510000e-33	154.0
19	TraesCS3B01G076200	chrUn	78.571	238	47	4	1040	1275	257674508	257674743	1.510000e-33	154.0
20	TraesCS3B01G076200	chrUn	78.571	238	47	4	1040	1275	279684649	279684884	1.510000e-33	154.0
21	TraesCS3B01G076200	chrUn	79.039	229	44	4	1052	1278	294339206	294338980	1.510000e-33	154.0
22	TraesCS3B01G076200	chr5A	77.574	272	35	8	520	768	483540366	483540098	1.170000e-29	141.0
23	TraesCS3B01G076200	chr4D	77.253	233	32	9	551	768	502490329	502490103	1.980000e-22	117.0
24	TraesCS3B01G076200	chr4D	87.879	66	5	2	2271	2334	218516255	218516191	1.210000e-09	75.0
25	TraesCS3B01G076200	chr5B	91.667	60	3	1	2271	2328	540361809	540361750	7.220000e-12	82.4
26	TraesCS3B01G076200	chr5B	90.164	61	4	1	2270	2328	559771434	559771494	9.340000e-11	78.7
27	TraesCS3B01G076200	chr6B	91.525	59	3	1	2270	2326	226867899	226867957	2.600000e-11	80.5
28	TraesCS3B01G076200	chr7D	86.111	72	8	2	2270	2339	443416090	443416019	3.360000e-10	76.8
29	TraesCS3B01G076200	chr1D	88.889	63	5	1	2271	2331	337065245	337065183	3.360000e-10	76.8
30	TraesCS3B01G076200	chr7B	100.000	29	0	0	511	539	435116298	435116270	2.000000e-03	54.7

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	TraesCS3B01G076200	chr3B	47120348	47123487	3139	False	5799.0	5799	100.0000	1	3140	1	chr3B.!!$F2	3139
1	TraesCS3B01G076200	chr3B	46363610	46366635	3025	True	1253.0	2647	93.6520	341	3140	3	chr3B.!!$R2	2799
2	TraesCS3B01G076200	chr3B	47202136	47202974	838	False	492.0	492	77.6600	1308	2134	1	chr3B.!!$F3	826
3	TraesCS3B01G076200	chr3B	47193040	47195734	2694	False	347.5	484	77.8170	1323	2858	2	chr3B.!!$F4	1535
4	TraesCS3B01G076200	chr3A	37821585	37823990	2405	True	1721.0	3190	94.3780	850	3140	2	chr3A.!!$R1	2290
5	TraesCS3B01G076200	chr3D	27948418	27950685	2267	False	1439.0	1847	90.1455	850	3140	2	chr3D.!!$F1	2290
6	TraesCS3B01G076200	chr3D	27680708	27681531	823	True	412.0	412	76.4640	1451	2255	1	chr3D.!!$R2	804

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
553	847	0.034059	CTTAGGAGCGGGCATGTAGG	59.966	60.0	0.0	0.0	0.0	3.18	F
555	849	0.178932	TAGGAGCGGGCATGTAGGAT	60.179	55.0	0.0	0.0	0.0	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1561	1891	0.528684	GAGTAGACACATGCGAGGGC	60.529	60.000	0.0	0.0	40.52	5.19	R
2316	2706	4.284746	AGCAGTTTACTCAGCTACTCCTTT	59.715	41.667	0.0	0.0	35.19	3.11	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
19	20	2.935481	GCTTTGCTCATTCCTTCTGG	57.065	50.000	0.00	0.00	0.00	3.86
20	21	1.135170	GCTTTGCTCATTCCTTCTGGC	60.135	52.381	0.00	0.00	0.00	4.85
21	22	2.165167	CTTTGCTCATTCCTTCTGGCA	58.835	47.619	0.00	0.00	0.00	4.92
22	23	1.538047	TTGCTCATTCCTTCTGGCAC	58.462	50.000	0.00	0.00	0.00	5.01
23	24	0.694771	TGCTCATTCCTTCTGGCACT	59.305	50.000	0.00	0.00	0.00	4.40
24	25	1.093159	GCTCATTCCTTCTGGCACTG	58.907	55.000	0.00	0.00	0.00	3.66
25	26	1.612726	GCTCATTCCTTCTGGCACTGT	60.613	52.381	0.00	0.00	0.00	3.55
26	27	2.355108	GCTCATTCCTTCTGGCACTGTA	60.355	50.000	0.00	0.00	0.00	2.74
27	28	3.683847	GCTCATTCCTTCTGGCACTGTAT	60.684	47.826	0.00	0.00	0.00	2.29
28	29	4.521146	CTCATTCCTTCTGGCACTGTATT	58.479	43.478	0.00	0.00	0.00	1.89
29	30	4.922206	TCATTCCTTCTGGCACTGTATTT	58.078	39.130	0.00	0.00	0.00	1.40
30	31	4.943705	TCATTCCTTCTGGCACTGTATTTC	59.056	41.667	0.00	0.00	0.00	2.17
31	32	4.365514	TTCCTTCTGGCACTGTATTTCA	57.634	40.909	0.00	0.00	0.00	2.69
32	33	4.574674	TCCTTCTGGCACTGTATTTCAT	57.425	40.909	0.00	0.00	0.00	2.57
33	34	4.922206	TCCTTCTGGCACTGTATTTCATT	58.078	39.130	0.00	0.00	0.00	2.57
34	35	4.701651	TCCTTCTGGCACTGTATTTCATTG	59.298	41.667	0.00	0.00	0.00	2.82
35	36	4.460382	CCTTCTGGCACTGTATTTCATTGT	59.540	41.667	0.00	0.00	0.00	2.71
36	37	5.647658	CCTTCTGGCACTGTATTTCATTGTA	59.352	40.000	0.00	0.00	0.00	2.41
37	38	6.150976	CCTTCTGGCACTGTATTTCATTGTAA	59.849	38.462	0.00	0.00	0.00	2.41
38	39	7.148018	CCTTCTGGCACTGTATTTCATTGTAAT	60.148	37.037	0.00	0.00	0.00	1.89
39	40	7.701539	TCTGGCACTGTATTTCATTGTAATT	57.298	32.000	0.00	0.00	0.00	1.40
40	41	7.537715	TCTGGCACTGTATTTCATTGTAATTG	58.462	34.615	0.00	0.00	0.00	2.32
41	42	7.176515	TCTGGCACTGTATTTCATTGTAATTGT	59.823	33.333	0.00	0.00	0.00	2.71
42	43	7.665690	TGGCACTGTATTTCATTGTAATTGTT	58.334	30.769	0.00	0.00	0.00	2.83
43	44	8.147058	TGGCACTGTATTTCATTGTAATTGTTT	58.853	29.630	0.00	0.00	0.00	2.83

Showing 1 to 25 of 415 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.135170	GCCAGAAGGAATGAGCAAAGC	60.135	52.381	0.00	0.00	36.89	3.51
1	2	2.094854	GTGCCAGAAGGAATGAGCAAAG	60.095	50.000	0.00	0.00	36.89	2.77
2	3	1.888512	GTGCCAGAAGGAATGAGCAAA	59.111	47.619	0.00	0.00	36.89	3.68
3	4	1.074405	AGTGCCAGAAGGAATGAGCAA	59.926	47.619	0.00	0.00	36.89	3.91
4	5	0.694771	AGTGCCAGAAGGAATGAGCA	59.305	50.000	0.00	0.00	36.89	4.26
5	6	1.093159	CAGTGCCAGAAGGAATGAGC	58.907	55.000	0.00	0.00	36.89	4.26
6	7	2.486472	ACAGTGCCAGAAGGAATGAG	57.514	50.000	0.00	0.00	36.89	2.90
7	8	4.574674	AATACAGTGCCAGAAGGAATGA	57.425	40.909	0.00	0.00	36.89	2.57
8	9	4.701651	TGAAATACAGTGCCAGAAGGAATG	59.298	41.667	0.00	0.00	36.89	2.67
9	10	4.922206	TGAAATACAGTGCCAGAAGGAAT	58.078	39.130	0.00	0.00	36.89	3.01
10	11	4.365514	TGAAATACAGTGCCAGAAGGAA	57.634	40.909	0.00	0.00	36.89	3.36
11	12	4.574674	ATGAAATACAGTGCCAGAAGGA	57.425	40.909	0.00	0.00	36.89	3.36
12	13	4.460382	ACAATGAAATACAGTGCCAGAAGG	59.540	41.667	0.00	0.00	46.68	3.46
13	14	5.633830	ACAATGAAATACAGTGCCAGAAG	57.366	39.130	0.00	0.00	46.68	2.85
14	15	7.701539	ATTACAATGAAATACAGTGCCAGAA	57.298	32.000	0.00	0.00	46.68	3.02
15	16	7.176515	ACAATTACAATGAAATACAGTGCCAGA	59.823	33.333	0.00	0.00	46.68	3.86
16	17	7.315142	ACAATTACAATGAAATACAGTGCCAG	58.685	34.615	0.00	0.00	46.68	4.85
17	18	7.225784	ACAATTACAATGAAATACAGTGCCA	57.774	32.000	0.00	0.00	46.68	4.92
18	19	8.532977	AAACAATTACAATGAAATACAGTGCC	57.467	30.769	0.00	0.00	46.68	5.01
19	20	9.796062	CAAAACAATTACAATGAAATACAGTGC	57.204	29.630	0.00	0.00	46.68	4.40
21	22	9.762933	AGCAAAACAATTACAATGAAATACAGT	57.237	25.926	0.00	0.00	0.00	3.55
23	24	9.755804	TGAGCAAAACAATTACAATGAAATACA	57.244	25.926	0.00	0.00	0.00	2.29
25	26	9.979578	AGTGAGCAAAACAATTACAATGAAATA	57.020	25.926	0.00	0.00	0.00	1.40
26	27	8.891671	AGTGAGCAAAACAATTACAATGAAAT	57.108	26.923	0.00	0.00	0.00	2.17
27	28	8.602328	CAAGTGAGCAAAACAATTACAATGAAA	58.398	29.630	0.00	0.00	0.00	2.69

Showing 1 to 25 of 392 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.