AutoCloner

Multiple sequence alignment - TraesCS4B01G344300

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	TraesCS4B01G344300	chr4B	100.000	4515	0	0	1	4515	637740597	637736083	0.000000e+00	8338.0
1	TraesCS4B01G344300	chr4B	93.023	43	2	1	3	45	627060645	627060686	1.360000e-05	62.1
2	TraesCS4B01G344300	chr4D	90.875	1874	84	36	1700	3522	497167985	497166148	0.000000e+00	2433.0
3	TraesCS4B01G344300	chr4D	90.021	1453	56	40	212	1585	497169622	497168180	0.000000e+00	1797.0
4	TraesCS4B01G344300	chr4D	91.711	374	23	6	3630	4000	497166107	497165739	3.120000e-141	512.0
5	TraesCS4B01G344300	chr4D	87.104	473	34	13	4048	4503	497165620	497165158	1.120000e-140	510.0
6	TraesCS4B01G344300	chr5A	89.775	1868	108	52	1700	3522	676967765	676965936	0.000000e+00	2314.0
7	TraesCS4B01G344300	chr5A	88.085	1410	71	31	225	1606	676969288	676967948	0.000000e+00	1583.0
8	TraesCS4B01G344300	chr5A	86.929	635	46	20	3568	4181	676964763	676964145	0.000000e+00	678.0
9	TraesCS4B01G344300	chr5A	90.415	313	14	7	3630	3927	676965880	676965569	9.100000e-107	398.0
10	TraesCS4B01G344300	chr5A	84.365	307	40	6	4201	4504	676965086	676964785	1.230000e-75	294.0
11	TraesCS4B01G344300	chr5A	90.845	142	12	1	4185	4326	676964165	676964025	5.960000e-44	189.0
12	TraesCS4B01G344300	chr1A	81.202	649	112	9	2732	3373	253728763	253728118	8.660000e-142	514.0
13	TraesCS4B01G344300	chr1A	80.795	604	92	14	2788	3383	254351401	254351988	6.890000e-123	451.0
14	TraesCS4B01G344300	chr1A	91.860	172	14	0	40	211	431032674	431032845	1.620000e-59	241.0
15	TraesCS4B01G344300	chr1A	79.795	292	53	6	1281	1568	254350469	254350758	1.650000e-49	207.0
16	TraesCS4B01G344300	chr1A	81.111	180	34	0	1288	1467	253731646	253731467	1.310000e-30	145.0
17	TraesCS4B01G344300	chr1A	88.073	109	12	1	1465	1573	253729563	253729456	1.320000e-25	128.0
18	TraesCS4B01G344300	chr1A	92.982	57	4	0	3939	3995	396427640	396427696	2.890000e-12	84.2
19	TraesCS4B01G344300	chr1A	100.000	33	0	0	3968	4000	482962090	482962058	1.360000e-05	62.1
20	TraesCS4B01G344300	chr1A	97.222	36	1	0	3965	4000	548733202	548733167	1.360000e-05	62.1
21	TraesCS4B01G344300	chr1B	79.085	612	104	14	2788	3391	288757739	288758334	2.530000e-107	399.0
22	TraesCS4B01G344300	chr1B	93.023	172	12	0	40	211	54995382	54995553	7.500000e-63	252.0
23	TraesCS4B01G344300	chr1B	79.730	296	46	9	1281	1568	288756808	288757097	7.660000e-48	202.0
24	TraesCS4B01G344300	chr1D	81.704	399	50	14	3114	3505	200464599	200464217	1.220000e-80	311.0
25	TraesCS4B01G344300	chr1D	81.703	317	46	5	3075	3391	200869277	200869581	2.080000e-63	254.0
26	TraesCS4B01G344300	chr1D	80.137	292	52	6	1281	1568	200868701	200868990	3.540000e-51	213.0
27	TraesCS4B01G344300	chr1D	96.970	33	1	0	3968	4000	383176761	383176729	6.310000e-04	56.5
28	TraesCS4B01G344300	chr3B	93.023	172	12	0	40	211	715068857	715069028	7.500000e-63	252.0
29	TraesCS4B01G344300	chr3B	91.279	172	15	0	40	211	23767745	23767574	7.550000e-58	235.0
30	TraesCS4B01G344300	chr5B	92.442	172	13	0	40	211	400101720	400101891	3.490000e-61	246.0
31	TraesCS4B01G344300	chr5B	91.279	172	15	0	40	211	43276721	43276550	7.550000e-58	235.0
32	TraesCS4B01G344300	chr5B	97.059	34	0	1	3962	3995	696165725	696165693	6.310000e-04	56.5
33	TraesCS4B01G344300	chr7B	91.860	172	14	0	40	211	602024634	602024463	1.620000e-59	241.0
34	TraesCS4B01G344300	chr7B	100.000	39	0	0	3	41	456344316	456344278	6.270000e-09	73.1
35	TraesCS4B01G344300	chr7D	91.228	171	15	0	41	211	506107089	506106919	2.720000e-57	233.0
36	TraesCS4B01G344300	chr7D	91.228	57	5	0	3939	3995	519273383	519273439	1.350000e-10	78.7
37	TraesCS4B01G344300	chr2B	90.643	171	16	0	41	211	722369124	722369294	1.260000e-55	228.0
38	TraesCS4B01G344300	chr6A	81.778	225	24	5	2793	3007	139896381	139896598	6.000000e-39	172.0
39	TraesCS4B01G344300	chr5D	91.228	57	5	0	3939	3995	430065202	430065258	1.350000e-10	78.7
40	TraesCS4B01G344300	chr5D	100.000	40	0	0	3	42	458628601	458628640	1.740000e-09	75.0

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	TraesCS4B01G344300	chr4B	637736083	637740597	4514	True	8338.000000	8338	100.000000	1	4515	1	chr4B.!!$R1	4514
1	TraesCS4B01G344300	chr4D	497165158	497169622	4464	True	1313.000000	2433	89.927750	212	4503	4	chr4D.!!$R1	4291
2	TraesCS4B01G344300	chr5A	676964025	676969288	5263	True	909.333333	2314	88.402333	225	4504	6	chr5A.!!$R1	4279
3	TraesCS4B01G344300	chr1A	254350469	254351988	1519	False	329.000000	451	80.295000	1281	3383	2	chr1A.!!$F3	2102
4	TraesCS4B01G344300	chr1A	253728118	253731646	3528	True	262.333333	514	83.462000	1288	3373	3	chr1A.!!$R3	2085
5	TraesCS4B01G344300	chr1B	288756808	288758334	1526	False	300.500000	399	79.407500	1281	3391	2	chr1B.!!$F2	2110
6	TraesCS4B01G344300	chr1D	200868701	200869581	880	False	233.500000	254	80.920000	1281	3391	2	chr1D.!!$F1	2110

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
119	120	0.028902	AAAGCGGACACAAAGCGAAC	59.971	50.0	0.0	0.0	35.78	3.95	F
1649	3645	0.182299	TGTGTGCATGGTGGTCTCAA	59.818	50.0	0.0	0.0	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1887	4009	0.958091	CAAATCACCAACGGAAGCCA	59.042	50.0	0.0	0.0	0.0	4.75	R
3620	6072	0.040157	CTTCGTTCGGTCGGTACACA	60.040	55.0	0.0	0.0	0.0	3.72	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
40	41	1.776662	GGGGGTGGATAGAAAAAGGC	58.223	55.000	0.00	0.00	0.00	4.35
41	42	1.389555	GGGGTGGATAGAAAAAGGCG	58.610	55.000	0.00	0.00	0.00	5.52
42	43	1.340697	GGGGTGGATAGAAAAAGGCGT	60.341	52.381	0.00	0.00	0.00	5.68
43	44	2.014857	GGGTGGATAGAAAAAGGCGTC	58.985	52.381	0.00	0.00	0.00	5.19
44	45	2.014857	GGTGGATAGAAAAAGGCGTCC	58.985	52.381	0.00	0.00	0.00	4.79
45	46	1.664151	GTGGATAGAAAAAGGCGTCCG	59.336	52.381	0.00	0.00	0.00	4.79
46	47	0.656259	GGATAGAAAAAGGCGTCCGC	59.344	55.000	2.45	2.45	41.06	5.54
47	48	1.365699	GATAGAAAAAGGCGTCCGCA	58.634	50.000	14.19	0.00	44.11	5.69
48	49	1.940613	GATAGAAAAAGGCGTCCGCAT	59.059	47.619	14.19	2.98	44.11	4.73
49	50	1.083489	TAGAAAAAGGCGTCCGCATG	58.917	50.000	14.19	0.00	44.11	4.06
50	51	1.154035	GAAAAAGGCGTCCGCATGG	60.154	57.895	14.19	0.00	44.11	3.66
51	52	1.862602	GAAAAAGGCGTCCGCATGGT	61.863	55.000	14.19	0.00	44.11	3.55
52	53	2.141122	AAAAAGGCGTCCGCATGGTG	62.141	55.000	14.19	0.00	44.11	4.17
53	54	3.842925	AAAGGCGTCCGCATGGTGT	62.843	57.895	14.19	0.00	44.11	4.16
54	55	4.760047	AGGCGTCCGCATGGTGTC	62.760	66.667	14.19	0.00	44.11	3.67
57	58	4.735132	CGTCCGCATGGTGTCCGT	62.735	66.667	0.00	0.00	36.30	4.69
58	59	2.358247	GTCCGCATGGTGTCCGTT	60.358	61.111	0.00	0.00	36.30	4.44
59	60	1.964373	GTCCGCATGGTGTCCGTTT	60.964	57.895	0.00	0.00	36.30	3.60
60	61	1.669760	TCCGCATGGTGTCCGTTTC	60.670	57.895	0.00	0.00	36.30	2.78
61	62	1.963855	CCGCATGGTGTCCGTTTCA	60.964	57.895	0.00	0.00	0.00	2.69
62	63	1.206578	CGCATGGTGTCCGTTTCAC	59.793	57.895	0.00	0.00	35.36	3.18
66	67	2.511900	GGTGTCCGTTTCACCCCA	59.488	61.111	8.95	0.00	46.63	4.96
67	68	1.152922	GGTGTCCGTTTCACCCCAA	60.153	57.895	8.95	0.00	46.63	4.12
68	69	0.752376	GGTGTCCGTTTCACCCCAAA	60.752	55.000	8.95	0.00	46.63	3.28
69	70	1.104630	GTGTCCGTTTCACCCCAAAA	58.895	50.000	0.00	0.00	0.00	2.44

Showing 1 to 25 of 342 entries

Previous1 2 3 4 5…14Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.918201	CCTTCCTCCGGCCGCATC	62.918	72.222	22.85	0.00	0.00	3.91
21	22	1.776662	GCCTTTTTCTATCCACCCCC	58.223	55.000	0.00	0.00	0.00	5.40
22	23	1.340697	ACGCCTTTTTCTATCCACCCC	60.341	52.381	0.00	0.00	0.00	4.95
23	24	2.014857	GACGCCTTTTTCTATCCACCC	58.985	52.381	0.00	0.00	0.00	4.61
24	25	2.014857	GGACGCCTTTTTCTATCCACC	58.985	52.381	0.00	0.00	0.00	4.61
25	26	1.664151	CGGACGCCTTTTTCTATCCAC	59.336	52.381	0.00	0.00	0.00	4.02
26	27	2.010043	GCGGACGCCTTTTTCTATCCA	61.010	52.381	5.20	0.00	34.56	3.41
27	28	0.656259	GCGGACGCCTTTTTCTATCC	59.344	55.000	5.20	0.00	34.56	2.59
28	29	1.365699	TGCGGACGCCTTTTTCTATC	58.634	50.000	14.61	0.00	41.09	2.08
29	30	1.670811	CATGCGGACGCCTTTTTCTAT	59.329	47.619	14.61	0.00	41.09	1.98
30	31	1.083489	CATGCGGACGCCTTTTTCTA	58.917	50.000	14.61	0.00	41.09	2.10
31	32	1.586154	CCATGCGGACGCCTTTTTCT	61.586	55.000	14.61	0.00	41.09	2.52
32	33	1.154035	CCATGCGGACGCCTTTTTC	60.154	57.895	14.61	0.00	41.09	2.29
33	34	1.901464	ACCATGCGGACGCCTTTTT	60.901	52.632	14.61	0.00	41.09	1.94
34	35	2.282180	ACCATGCGGACGCCTTTT	60.282	55.556	14.61	0.00	41.09	2.27
35	36	3.055719	CACCATGCGGACGCCTTT	61.056	61.111	14.61	0.00	41.09	3.11
36	37	4.329545	ACACCATGCGGACGCCTT	62.330	61.111	14.61	0.00	41.09	4.35
37	38	4.760047	GACACCATGCGGACGCCT	62.760	66.667	14.61	0.77	41.09	5.52
50	51	1.104630	TTTTGGGGTGAAACGGACAC	58.895	50.000	0.00	0.00	38.12	3.67
51	52	1.477295	GTTTTTGGGGTGAAACGGACA	59.523	47.619	0.00	0.00	38.12	4.02
52	53	2.212869	GTTTTTGGGGTGAAACGGAC	57.787	50.000	0.00	0.00	38.12	4.79
56	57	0.872451	CGCCGTTTTTGGGGTGAAAC	60.872	55.000	0.00	0.00	37.20	2.78
57	58	1.437986	CGCCGTTTTTGGGGTGAAA	59.562	52.632	0.00	0.00	37.20	2.69
58	59	3.121019	CGCCGTTTTTGGGGTGAA	58.879	55.556	0.00	0.00	37.20	3.18
59	60	3.597728	GCGCCGTTTTTGGGGTGA	61.598	61.111	0.00	0.00	43.50	4.02

Showing 1 to 25 of 353 entries

Previous1 2 3 4 5…15Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.