AutoCloner

Multiple sequence alignment - TraesCS6D01G248600

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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	TraesCS6D01G248600	chr6D	100.000	3166	0	0	1	3166	351985872	351989037	0.000000e+00	5847.0
1	TraesCS6D01G248600	chr6D	85.512	918	126	6	1000	1913	351986643	351987557	0.000000e+00	952.0
2	TraesCS6D01G248600	chr6D	85.512	918	126	6	772	1686	351986871	351987784	0.000000e+00	952.0
3	TraesCS6D01G248600	chr6D	96.525	259	9	0	2528	2786	460832791	460832533	2.260000e-116	429.0
4	TraesCS6D01G248600	chr6D	95.753	259	11	0	2530	2788	448351775	448351517	4.880000e-113	418.0
5	TraesCS6D01G248600	chr6D	95.076	264	12	1	2530	2792	20243930	20243667	6.320000e-112	414.0
6	TraesCS6D01G248600	chr6D	100.000	39	0	0	2497	2535	20243950	20243912	4.380000e-09	73.1
7	TraesCS6D01G248600	chr6D	100.000	39	0	0	2497	2535	448351795	448351757	4.380000e-09	73.1
8	TraesCS6D01G248600	chr6B	93.392	1695	83	12	1	1686	526798915	526797241	0.000000e+00	2483.0
9	TraesCS6D01G248600	chr6B	88.948	1511	137	13	1000	2500	526798153	526796663	0.000000e+00	1838.0
10	TraesCS6D01G248600	chr6B	87.773	229	16	5	2819	3036	526796621	526796394	1.130000e-64	257.0
11	TraesCS6D01G248600	chr6A	94.306	1247	55	6	955	2190	490999195	490997954	0.000000e+00	1895.0
12	TraesCS6D01G248600	chr6A	94.030	938	41	6	24	958	491000424	490999499	0.000000e+00	1408.0
13	TraesCS6D01G248600	chr6A	85.542	913	127	4	775	1686	490999147	490998239	0.000000e+00	950.0
14	TraesCS6D01G248600	chr6A	84.636	729	106	5	1187	1913	490999191	490998467	0.000000e+00	721.0
15	TraesCS6D01G248600	chr6A	91.958	286	13	8	2819	3098	490991782	490991501	2.960000e-105	392.0
16	TraesCS6D01G248600	chr6A	88.506	261	25	3	2536	2793	23330109	23329851	8.530000e-81	311.0
17	TraesCS6D01G248600	chr6A	94.937	79	4	0	2418	2496	490991901	490991823	1.190000e-24	124.0
18	TraesCS6D01G248600	chr6A	98.413	63	1	0	3098	3160	490991320	490991258	9.280000e-21	111.0
19	TraesCS6D01G248600	chr7D	82.443	917	156	5	1000	1914	562149187	562148274	0.000000e+00	797.0
20	TraesCS6D01G248600	chr7D	96.911	259	8	0	2530	2788	537292565	537292307	4.850000e-118	435.0
21	TraesCS6D01G248600	chr7D	94.382	267	13	2	2521	2786	550600365	550600630	2.940000e-110	409.0
22	TraesCS6D01G248600	chr7D	100.000	41	0	0	2495	2535	537292587	537292547	3.390000e-10	76.8
23	TraesCS6D01G248600	chr7A	82.386	880	152	3	1010	1888	647307230	647306353	0.000000e+00	763.0
24	TraesCS6D01G248600	chr2D	83.988	687	104	5	771	1455	520583525	520582843	0.000000e+00	654.0
25	TraesCS6D01G248600	chr5B	95.785	261	11	0	2526	2786	532730355	532730615	3.780000e-114	422.0
26	TraesCS6D01G248600	chr5B	95.385	260	12	0	2530	2789	439840220	439839961	6.320000e-112	414.0
27	TraesCS6D01G248600	chr2B	96.109	257	10	0	2530	2786	139650343	139650087	1.360000e-113	420.0
28	TraesCS6D01G248600	chr2B	84.615	390	56	3	771	1158	613037667	613037280	4.950000e-103	385.0
29	TraesCS6D01G248600	chr2B	96.875	32	0	1	1673	1703	461199293	461199262	6.000000e-03	52.8
30	TraesCS6D01G248600	chr4B	96.094	256	10	0	2530	2785	514215911	514215656	4.880000e-113	418.0
31	TraesCS6D01G248600	chr4A	95.257	253	12	0	2536	2788	541775663	541775915	4.920000e-108	401.0
32	TraesCS6D01G248600	chr4A	100.000	40	0	0	2499	2538	614550625	614550586	1.220000e-09	75.0
33	TraesCS6D01G248600	chr1D	92.424	264	16	3	2530	2789	16639179	16639442	1.070000e-99	374.0
34	TraesCS6D01G248600	chr3D	89.041	292	19	5	2495	2786	590370962	590370684	1.810000e-92	350.0
35	TraesCS6D01G248600	chr3A	85.714	294	18	3	2495	2788	194833978	194833709	4.000000e-74	289.0
36	TraesCS6D01G248600	chr7B	87.050	139	18	0	775	913	611730746	611730608	1.180000e-34	158.0

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	TraesCS6D01G248600	chr6D	351985872	351989037	3165	False	2583.666667	5847	90.341333	1	3166	3	chr6D.!!$F1	3165
1	TraesCS6D01G248600	chr6B	526796394	526798915	2521	True	1526.000000	2483	90.037667	1	3036	3	chr6B.!!$R1	3035
2	TraesCS6D01G248600	chr6A	490997954	491000424	2470	True	1243.500000	1895	89.628500	24	2190	4	chr6A.!!$R3	2166
3	TraesCS6D01G248600	chr6A	490991258	490991901	643	True	209.000000	392	95.102667	2418	3160	3	chr6A.!!$R2	742
4	TraesCS6D01G248600	chr7D	562148274	562149187	913	True	797.000000	797	82.443000	1000	1914	1	chr7D.!!$R1	914
5	TraesCS6D01G248600	chr7A	647306353	647307230	877	True	763.000000	763	82.386000	1010	1888	1	chr7A.!!$R1	878
6	TraesCS6D01G248600	chr2D	520582843	520583525	682	True	654.000000	654	83.988000	771	1455	1	chr2D.!!$R1	684

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
987	1007	0.175989	CCCTCTACCTTGTTCTCCGC	59.824	60.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2228	3252	0.510359	CAGCGATAAGAATGCTCCGC	59.49	55.0	6.91	6.91	42.52	5.54	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
48	50	2.139917	TCAGTTTCCATTGTCGGTTCG	58.860	47.619	0.00	0.00	0.00	3.95
146	152	7.321271	GTCAGATTAATTGTTGTTTGACGACTG	59.679	37.037	0.00	0.00	33.63	3.51
193	199	2.025418	GTACGTTGCACCGTCAGGG	61.025	63.158	14.17	0.00	43.47	4.45
258	267	8.128582	TCTTTTTGGATCATATATTGTGCGTTC	58.871	33.333	0.00	0.00	0.00	3.95
282	291	5.008019	CGATGTGATTGGGATTTTGGAGTAG	59.992	44.000	0.00	0.00	0.00	2.57
417	426	5.001232	TGAAGTTTTTAGTTGAGGGATCGG	58.999	41.667	0.00	0.00	0.00	4.18
610	620	9.495572	AAGATTTCCTAGTGTAGAAAGAAGTTG	57.504	33.333	0.00	0.00	0.00	3.16
688	698	3.818210	TGTACACATGCTTTCCGTTTCAT	59.182	39.130	0.00	0.00	0.00	2.57
689	699	4.998033	TGTACACATGCTTTCCGTTTCATA	59.002	37.500	0.00	0.00	0.00	2.15
690	700	5.645929	TGTACACATGCTTTCCGTTTCATAT	59.354	36.000	0.00	0.00	0.00	1.78
691	701	4.985413	ACACATGCTTTCCGTTTCATATG	58.015	39.130	0.00	0.00	0.00	1.78
692	702	4.142403	ACACATGCTTTCCGTTTCATATGG	60.142	41.667	2.13	0.00	0.00	2.74
693	703	4.096231	CACATGCTTTCCGTTTCATATGGA	59.904	41.667	2.13	0.00	40.28	3.41
694	704	4.889409	ACATGCTTTCCGTTTCATATGGAT	59.111	37.500	2.13	0.00	41.61	3.41
695	705	5.009010	ACATGCTTTCCGTTTCATATGGATC	59.991	40.000	2.13	0.00	41.61	3.36
696	706	4.780815	TGCTTTCCGTTTCATATGGATCT	58.219	39.130	2.13	0.00	41.61	2.75
697	707	4.816385	TGCTTTCCGTTTCATATGGATCTC	59.184	41.667	2.13	0.00	41.61	2.75
933	953	2.739784	CAGCTAGAGGATGGCCGG	59.260	66.667	0.00	0.00	39.96	6.13
973	993	3.562108	TCCAAAAGGAGTCTACCCTCT	57.438	47.619	0.00	0.00	32.57	3.69
974	994	4.687262	TCCAAAAGGAGTCTACCCTCTA	57.313	45.455	0.00	0.00	32.57	2.43
975	995	4.351127	TCCAAAAGGAGTCTACCCTCTAC	58.649	47.826	0.00	0.00	32.57	2.59
976	996	3.451540	CCAAAAGGAGTCTACCCTCTACC	59.548	52.174	0.00	0.00	32.57	3.18
977	997	4.354662	CAAAAGGAGTCTACCCTCTACCT	58.645	47.826	0.00	0.00	32.57	3.08
978	998	4.696040	AAAGGAGTCTACCCTCTACCTT	57.304	45.455	0.00	0.00	37.79	3.50
979	999	3.673543	AGGAGTCTACCCTCTACCTTG	57.326	52.381	0.00	0.00	0.00	3.61

Showing 1 to 25 of 450 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	50	4.759516	TCAAAACTCTATTTTCACCGGC	57.240	40.909	0.00	0.00	0.00	6.13
146	152	7.623268	AGTTCAGAAAAACAATAATGCGAAC	57.377	32.000	0.00	0.00	0.00	3.95
258	267	3.696051	ACTCCAAAATCCCAATCACATCG	59.304	43.478	0.00	0.00	0.00	3.84
282	291	4.148696	CAGGTTTTGCATCAACGAATGTTC	59.851	41.667	0.00	0.00	35.72	3.18
417	426	5.869753	ATACTGCAACATCAACAGACTTC	57.130	39.130	0.00	0.00	35.38	3.01
483	493	5.853936	ACAGATAACGCATCTATAGCCAAA	58.146	37.500	0.00	0.00	42.40	3.28
610	620	9.152595	GTATATACAGCCCAGAAATACTAAAGC	57.847	37.037	8.05	0.00	0.00	3.51
681	691	7.800380	GCAAAACATAGAGATCCATATGAAACG	59.200	37.037	17.40	7.64	34.24	3.60
688	698	4.751600	CAGCGCAAAACATAGAGATCCATA	59.248	41.667	11.47	0.00	0.00	2.74
689	699	3.562973	CAGCGCAAAACATAGAGATCCAT	59.437	43.478	11.47	0.00	0.00	3.41
690	700	2.938451	CAGCGCAAAACATAGAGATCCA	59.062	45.455	11.47	0.00	0.00	3.41
691	701	2.289002	CCAGCGCAAAACATAGAGATCC	59.711	50.000	11.47	0.00	0.00	3.36
692	702	2.939103	ACCAGCGCAAAACATAGAGATC	59.061	45.455	11.47	0.00	0.00	2.75
693	703	2.939103	GACCAGCGCAAAACATAGAGAT	59.061	45.455	11.47	0.00	0.00	2.75
694	704	2.028112	AGACCAGCGCAAAACATAGAGA	60.028	45.455	11.47	0.00	0.00	3.10
695	705	2.350522	AGACCAGCGCAAAACATAGAG	58.649	47.619	11.47	0.00	0.00	2.43
696	706	2.472695	AGACCAGCGCAAAACATAGA	57.527	45.000	11.47	0.00	0.00	1.98
697	707	3.248602	GGATAGACCAGCGCAAAACATAG	59.751	47.826	11.47	0.00	38.79	2.23
769	789	3.366422	GTCTTGACAAAGATCTGCGTCTC	59.634	47.826	19.94	8.88	44.18	3.36
773	793	1.734465	GGGTCTTGACAAAGATCTGCG	59.266	52.381	0.00	0.00	44.18	5.18
933	953	3.243068	GGATGTTGTAATCGGCCAATGTC	60.243	47.826	2.24	0.00	0.00	3.06
973	993	3.060828	TCAGGCGGAGAACAAGGTA	57.939	52.632	0.00	0.00	0.00	3.08
974	994	3.885814	TCAGGCGGAGAACAAGGT	58.114	55.556	0.00	0.00	0.00	3.50
982	1002	3.465403	CCCACCTCTCAGGCGGAG	61.465	72.222	8.46	8.46	40.03	4.63
983	1003	3.317436	ATCCCACCTCTCAGGCGGA	62.317	63.158	0.00	0.19	40.03	5.54

Showing 1 to 25 of 436 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.