AutoCloner

Multiple sequence alignment - TraesCS3A01G466300

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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	TraesCS3A01G466300	chr3A	100.000	2714	0	0	1	2714	700248557	700251270	0.000000e+00	5012.0
1	TraesCS3A01G466300	chr3A	76.364	880	153	29	1176	2011	699983064	699983932	3.230000e-114	422.0
2	TraesCS3A01G466300	chr3A	88.060	201	17	6	455	650	699533377	699533575	5.840000e-57	231.0
3	TraesCS3A01G466300	chr3A	86.567	201	24	3	451	650	701359338	701359536	4.550000e-53	219.0
4	TraesCS3A01G466300	chr3A	76.092	435	85	13	1404	1827	697584660	697584234	2.740000e-50	209.0
5	TraesCS3A01G466300	chr3A	85.500	200	22	5	455	649	699540248	699540445	4.580000e-48	202.0
6	TraesCS3A01G466300	chr3A	83.333	84	8	1	1900	1983	655921561	655921638	3.750000e-09	73.1
7	TraesCS3A01G466300	chr3A	83.333	84	8	1	1900	1983	658200173	658200096	3.750000e-09	73.1
8	TraesCS3A01G466300	chr3B	93.106	1233	73	5	791	2011	754308325	754309557	0.000000e+00	1796.0
9	TraesCS3A01G466300	chr3B	76.959	1072	183	28	794	1835	754330574	754331611	1.100000e-153	553.0
10	TraesCS3A01G466300	chr3B	90.647	417	26	6	243	650	754307873	754308285	2.380000e-150	542.0
11	TraesCS3A01G466300	chr3B	75.449	668	138	17	1181	1835	753995038	753995692	4.390000e-78	302.0
12	TraesCS3A01G466300	chr3B	87.864	206	19	6	447	650	752973259	752973058	1.260000e-58	237.0
13	TraesCS3A01G466300	chr3B	83.459	266	24	7	402	650	754330271	754330533	2.100000e-56	230.0
14	TraesCS3A01G466300	chr3B	73.958	576	131	14	1250	1816	763604842	763605407	5.890000e-52	215.0
15	TraesCS3A01G466300	chr3B	87.719	57	7	0	1253	1309	756252267	756252211	1.740000e-07	67.6
16	TraesCS3A01G466300	chr2A	92.441	635	35	4	2080	2714	735613888	735614509	0.000000e+00	894.0
17	TraesCS3A01G466300	chr2A	85.572	201	27	2	446	645	45080054	45080253	2.740000e-50	209.0
18	TraesCS3A01G466300	chr3D	74.972	895	196	24	951	1830	565642301	565643182	1.180000e-103	387.0
19	TraesCS3A01G466300	chr3D	85.714	259	19	5	409	650	565830681	565830938	9.640000e-65	257.0
20	TraesCS3A01G466300	chr3D	81.588	277	46	3	1556	1830	562418620	562418347	9.780000e-55	224.0
21	TraesCS3A01G466300	chr3D	86.802	197	24	2	455	650	565641914	565642109	4.550000e-53	219.0
22	TraesCS3A01G466300	chr3D	75.520	433	90	12	1404	1827	562465300	562464875	5.930000e-47	198.0
23	TraesCS3A01G466300	chr6B	92.275	233	18	0	2232	2464	346409684	346409452	5.600000e-87	331.0
24	TraesCS3A01G466300	chrUn	76.923	481	98	11	1328	1803	48293507	48293035	7.450000e-66	261.0
25	TraesCS3A01G466300	chr4D	90.210	143	13	1	652	794	353463884	353464025	4.610000e-43	185.0
26	TraesCS3A01G466300	chr6A	94.937	79	4	0	2636	2714	517897858	517897936	1.020000e-24	124.0

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	TraesCS3A01G466300	chr3A	700248557	700251270	2713	False	5012.0	5012	100.0000	1	2714	1	chr3A.!!$F5	2713
1	TraesCS3A01G466300	chr3A	699983064	699983932	868	False	422.0	422	76.3640	1176	2011	1	chr3A.!!$F4	835
2	TraesCS3A01G466300	chr3B	754307873	754309557	1684	False	1169.0	1796	91.8765	243	2011	2	chr3B.!!$F3	1768
3	TraesCS3A01G466300	chr3B	754330271	754331611	1340	False	391.5	553	80.2090	402	1835	2	chr3B.!!$F4	1433
4	TraesCS3A01G466300	chr3B	753995038	753995692	654	False	302.0	302	75.4490	1181	1835	1	chr3B.!!$F1	654
5	TraesCS3A01G466300	chr3B	763604842	763605407	565	False	215.0	215	73.9580	1250	1816	1	chr3B.!!$F2	566
6	TraesCS3A01G466300	chr2A	735613888	735614509	621	False	894.0	894	92.4410	2080	2714	1	chr2A.!!$F2	634
7	TraesCS3A01G466300	chr3D	565641914	565643182	1268	False	303.0	387	80.8870	455	1830	2	chr3D.!!$F2	1375

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
678	698	0.034337	TCAGTTACCAAGCCGTGACC	59.966	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2227	2337	0.02877	CAAGAAAAACGCCACGCTGA	59.971	50.0	0.0	0.0	0.0	4.26	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
24	25	6.708285	CCTGGTATCTGGTTATATGGTAACC	58.292	44.000	12.53	12.53	45.37	2.85
25	26	6.500751	CCTGGTATCTGGTTATATGGTAACCT	59.499	42.308	17.60	5.78	45.38	3.50
26	27	7.311092	TGGTATCTGGTTATATGGTAACCTG	57.689	40.000	17.60	16.86	45.38	4.00
27	28	6.171213	GGTATCTGGTTATATGGTAACCTGC	58.829	44.000	17.60	8.60	45.38	4.85
28	29	5.904984	ATCTGGTTATATGGTAACCTGCA	57.095	39.130	17.60	10.60	45.38	4.41
29	30	5.904984	TCTGGTTATATGGTAACCTGCAT	57.095	39.130	17.60	0.00	45.38	3.96
30	31	6.260700	TCTGGTTATATGGTAACCTGCATT	57.739	37.500	17.60	0.00	45.38	3.56
31	32	6.061441	TCTGGTTATATGGTAACCTGCATTG	58.939	40.000	17.60	0.00	45.38	2.82
32	33	4.582656	TGGTTATATGGTAACCTGCATTGC	59.417	41.667	17.60	0.46	45.38	3.56
33	34	4.582656	GGTTATATGGTAACCTGCATTGCA	59.417	41.667	11.50	11.50	42.68	4.08
34	35	5.507315	GGTTATATGGTAACCTGCATTGCAC	60.507	44.000	7.38	0.00	42.68	4.57
35	36	1.185315	ATGGTAACCTGCATTGCACC	58.815	50.000	7.38	7.74	33.79	5.01
36	37	0.112218	TGGTAACCTGCATTGCACCT	59.888	50.000	7.38	0.00	33.79	4.00
37	38	1.352687	TGGTAACCTGCATTGCACCTA	59.647	47.619	7.38	0.00	33.79	3.08
38	39	2.017049	GGTAACCTGCATTGCACCTAG	58.983	52.381	7.38	0.00	33.79	3.02
39	40	2.355716	GGTAACCTGCATTGCACCTAGA	60.356	50.000	7.38	0.00	33.79	2.43
40	41	2.119801	AACCTGCATTGCACCTAGAG	57.880	50.000	7.38	0.00	33.79	2.43
41	42	0.393537	ACCTGCATTGCACCTAGAGC	60.394	55.000	7.38	0.00	33.79	4.09
42	43	1.434622	CCTGCATTGCACCTAGAGCG	61.435	60.000	7.38	0.00	33.79	5.03
43	44	1.434622	CTGCATTGCACCTAGAGCGG	61.435	60.000	7.38	0.00	33.79	5.52
44	45	2.828128	GCATTGCACCTAGAGCGGC	61.828	63.158	3.15	0.00	33.85	6.53
45	46	1.450134	CATTGCACCTAGAGCGGCA	60.450	57.895	1.45	0.00	33.85	5.69
46	47	0.816825	CATTGCACCTAGAGCGGCAT	60.817	55.000	1.45	0.00	35.98	4.40
47	48	0.816825	ATTGCACCTAGAGCGGCATG	60.817	55.000	1.45	0.00	35.98	4.06
48	49	2.590007	GCACCTAGAGCGGCATGG	60.590	66.667	1.45	0.79	0.00	3.66

Showing 1 to 25 of 316 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	6.708285	GGTTACCATATAACCAGATACCAGG	58.292	44.000	10.34	0.00	44.72	4.45
10	11	4.582656	TGCAATGCAGGTTACCATATAACC	59.417	41.667	2.72	7.63	45.47	2.85
11	12	5.507315	GGTGCAATGCAGGTTACCATATAAC	60.507	44.000	8.73	0.00	40.08	1.89
12	13	4.582656	GGTGCAATGCAGGTTACCATATAA	59.417	41.667	8.73	0.00	40.08	0.98
13	14	4.141274	AGGTGCAATGCAGGTTACCATATA	60.141	41.667	8.73	0.00	40.08	0.86
14	15	2.958355	GGTGCAATGCAGGTTACCATAT	59.042	45.455	8.73	0.00	40.08	1.78
15	16	2.025416	AGGTGCAATGCAGGTTACCATA	60.025	45.455	8.73	0.00	40.08	2.74
16	17	1.185315	GGTGCAATGCAGGTTACCAT	58.815	50.000	8.73	0.00	40.08	3.55
17	18	0.112218	AGGTGCAATGCAGGTTACCA	59.888	50.000	8.73	0.00	40.08	3.25
18	19	2.017049	CTAGGTGCAATGCAGGTTACC	58.983	52.381	8.73	5.86	40.08	2.85
19	20	2.939103	CTCTAGGTGCAATGCAGGTTAC	59.061	50.000	8.73	0.00	40.08	2.50
20	21	2.680805	GCTCTAGGTGCAATGCAGGTTA	60.681	50.000	8.73	0.51	40.08	2.85
21	22	1.952367	GCTCTAGGTGCAATGCAGGTT	60.952	52.381	8.73	0.00	40.08	3.50
22	23	0.393537	GCTCTAGGTGCAATGCAGGT	60.394	55.000	8.73	0.60	40.08	4.00
23	24	1.434622	CGCTCTAGGTGCAATGCAGG	61.435	60.000	8.73	0.00	40.08	4.85
24	25	1.434622	CCGCTCTAGGTGCAATGCAG	61.435	60.000	8.73	0.00	40.08	4.41
25	26	1.450134	CCGCTCTAGGTGCAATGCA	60.450	57.895	2.72	2.72	35.60	3.96
26	27	2.828128	GCCGCTCTAGGTGCAATGC	61.828	63.158	0.00	0.00	0.00	3.56
27	28	0.816825	ATGCCGCTCTAGGTGCAATG	60.817	55.000	0.00	0.00	37.27	2.82
28	29	0.816825	CATGCCGCTCTAGGTGCAAT	60.817	55.000	0.00	0.00	37.27	3.56
29	30	1.450134	CATGCCGCTCTAGGTGCAA	60.450	57.895	0.00	0.00	37.27	4.08
30	31	2.187685	CATGCCGCTCTAGGTGCA	59.812	61.111	8.82	4.65	38.23	4.57
31	32	2.388890	ATCCATGCCGCTCTAGGTGC	62.389	60.000	0.00	0.00	0.00	5.01
32	33	0.602106	CATCCATGCCGCTCTAGGTG	60.602	60.000	0.00	0.00	0.00	4.00
33	34	1.750930	CATCCATGCCGCTCTAGGT	59.249	57.895	0.00	0.00	0.00	3.08

Showing 1 to 25 of 299 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.