AutoCloner

Multiple sequence alignment - TraesCS1B01G140200

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	TraesCS1B01G140200	chr1B	100.000	2897	0	0	1	2897	185228729	185225833	0.000000e+00	5350.0
1	TraesCS1B01G140200	chr1B	100.000	1530	0	0	3230	4759	185225500	185223971	0.000000e+00	2826.0
2	TraesCS1B01G140200	chr1B	96.996	466	14	0	1	466	566121825	566121360	0.000000e+00	784.0
3	TraesCS1B01G140200	chr1B	93.571	280	16	2	536	814	396245988	396245710	2.650000e-112	416.0
4	TraesCS1B01G140200	chr1B	89.286	252	26	1	539	790	639977937	639978187	9.940000e-82	315.0
5	TraesCS1B01G140200	chr1B	88.492	252	25	4	540	790	500987683	500987435	7.740000e-78	302.0
6	TraesCS1B01G140200	chr1A	92.496	2039	96	16	890	2890	133174052	133172033	0.000000e+00	2865.0
7	TraesCS1B01G140200	chr1A	94.348	690	35	2	4073	4759	133166761	133166073	0.000000e+00	1055.0
8	TraesCS1B01G140200	chr1A	95.238	441	5	2	3524	3950	133171295	133170857	0.000000e+00	684.0
9	TraesCS1B01G140200	chr1A	97.619	294	6	1	3234	3527	133171750	133171458	1.980000e-138	503.0
10	TraesCS1B01G140200	chr1A	87.692	325	20	13	541	847	540286038	540286360	1.260000e-95	361.0
11	TraesCS1B01G140200	chr1D	91.659	2122	86	25	841	2897	121407865	121405770	0.000000e+00	2854.0
12	TraesCS1B01G140200	chr1D	93.249	1259	43	11	3524	4759	121405264	121404025	0.000000e+00	1816.0
13	TraesCS1B01G140200	chr1D	97.959	294	5	1	3234	3527	121405716	121405424	4.250000e-140	508.0
14	TraesCS1B01G140200	chr1D	93.307	254	14	3	538	790	432685609	432685860	5.820000e-99	372.0
15	TraesCS1B01G140200	chr1D	91.200	250	19	3	542	790	205988638	205988391	2.120000e-88	337.0
16	TraesCS1B01G140200	chr1D	88.327	257	22	3	541	790	36440800	36441055	7.740000e-78	302.0
17	TraesCS1B01G140200	chr1D	87.649	251	28	3	541	790	389432241	389432489	6.030000e-74	289.0
18	TraesCS1B01G140200	chr1D	88.073	218	22	4	590	805	382776313	382776098	6.110000e-64	255.0
19	TraesCS1B01G140200	chr1D	85.000	220	20	7	575	792	52181974	52182182	1.340000e-50	211.0
20	TraesCS1B01G140200	chr1D	85.496	131	17	2	2716	2844	286385483	286385353	8.310000e-28	135.0
21	TraesCS1B01G140200	chr1D	91.765	85	5	1	463	547	121407930	121407848	3.010000e-22	117.0
22	TraesCS1B01G140200	chr1D	86.747	83	9	2	2716	2796	128505301	128505383	1.820000e-14	91.6
23	TraesCS1B01G140200	chr6B	97.021	470	13	1	1	470	283227973	283227505	0.000000e+00	789.0
24	TraesCS1B01G140200	chr6B	92.606	284	19	2	532	814	98690564	98690846	1.590000e-109	407.0
25	TraesCS1B01G140200	chr6B	92.254	284	20	2	532	814	98678412	98678694	7.420000e-108	401.0
26	TraesCS1B01G140200	chr4B	96.632	475	14	2	1	474	13967038	13966565	0.000000e+00	787.0
27	TraesCS1B01G140200	chr4B	96.000	475	16	3	1	473	510842416	510841943	0.000000e+00	769.0
28	TraesCS1B01G140200	chr4B	89.781	137	12	2	2716	2851	363314764	363314899	1.760000e-39	174.0
29	TraesCS1B01G140200	chr4A	96.596	470	14	2	1	470	714278434	714278901	0.000000e+00	778.0
30	TraesCS1B01G140200	chr4A	88.112	143	15	1	2716	2856	405575899	405575757	8.190000e-38	169.0
31	TraesCS1B01G140200	chr2D	96.781	466	15	0	1	466	610245579	610245114	0.000000e+00	778.0
32	TraesCS1B01G140200	chr2D	89.510	143	12	2	2716	2856	98988213	98988072	1.360000e-40	178.0
33	TraesCS1B01G140200	chr2D	88.811	143	13	2	2716	2856	388833805	388833664	6.330000e-39	172.0
34	TraesCS1B01G140200	chr3B	96.767	464	15	0	1	464	52192998	52192535	0.000000e+00	774.0
35	TraesCS1B01G140200	chr7A	96.567	466	16	0	1	466	46140108	46139643	0.000000e+00	773.0
36	TraesCS1B01G140200	chr7A	89.286	252	25	2	540	790	314444595	314444345	9.940000e-82	315.0
37	TraesCS1B01G140200	chr7A	89.268	205	20	2	587	790	148573724	148573521	6.110000e-64	255.0
38	TraesCS1B01G140200	chr7A	90.411	146	11	2	2716	2859	252184599	252184455	6.290000e-44	189.0
39	TraesCS1B01G140200	chr2B	96.375	469	15	2	1	469	795927594	795927128	0.000000e+00	771.0
40	TraesCS1B01G140200	chr2B	93.478	276	16	2	540	814	438882712	438882986	4.430000e-110	409.0
41	TraesCS1B01G140200	chr2B	93.165	278	16	3	538	813	642615386	642615110	5.730000e-109	405.0
42	TraesCS1B01G140200	chr5B	93.502	277	16	2	541	816	293834060	293833785	1.230000e-110	411.0
43	TraesCS1B01G140200	chr5B	93.773	273	15	2	542	813	507315325	507315596	4.430000e-110	409.0
44	TraesCS1B01G140200	chr5B	89.655	145	13	1	2712	2854	304628590	304628734	2.930000e-42	183.0
45	TraesCS1B01G140200	chr5D	90.879	307	21	4	540	845	494644926	494644626	5.730000e-109	405.0
46	TraesCS1B01G140200	chr5D	93.116	276	17	2	539	813	447769398	447769124	2.060000e-108	403.0
47	TraesCS1B01G140200	chr5D	89.510	143	12	2	2716	2856	360541999	360541858	1.360000e-40	178.0
48	TraesCS1B01G140200	chr5D	89.313	131	12	1	2716	2844	200643631	200643761	3.810000e-36	163.0
49	TraesCS1B01G140200	chr5D	86.897	145	17	1	2712	2854	268905658	268905802	1.370000e-35	161.0
50	TraesCS1B01G140200	chr4D	94.071	253	13	2	539	790	64046162	64046413	2.690000e-102	383.0
51	TraesCS1B01G140200	chr4D	92.032	251	18	2	541	790	57766721	57766970	7.580000e-93	351.0
52	TraesCS1B01G140200	chr4D	90.370	270	22	4	538	805	454833964	454834231	7.580000e-93	351.0
53	TraesCS1B01G140200	chr4D	91.633	251	19	2	541	790	319700919	319701168	3.530000e-91	346.0
54	TraesCS1B01G140200	chr4D	90.299	134	11	2	2716	2848	294454438	294454570	1.760000e-39	174.0
55	TraesCS1B01G140200	chr4D	88.571	140	13	2	2716	2853	163760010	163760148	2.950000e-37	167.0
56	TraesCS1B01G140200	chr4D	88.148	135	14	2	2716	2848	473136013	473136147	4.930000e-35	159.0
57	TraesCS1B01G140200	chr4D	86.014	143	18	2	2716	2856	287550824	287550966	8.250000e-33	152.0
58	TraesCS1B01G140200	chr4D	85.714	147	14	3	2716	2856	346468043	346468188	1.070000e-31	148.0
59	TraesCS1B01G140200	chr7D	93.385	257	15	2	535	790	635569224	635569479	3.480000e-101	379.0
60	TraesCS1B01G140200	chr7D	90.411	146	11	2	2716	2859	236827522	236827378	6.290000e-44	189.0
61	TraesCS1B01G140200	chr7D	88.811	143	13	3	2716	2856	175941671	175941812	6.330000e-39	172.0
62	TraesCS1B01G140200	chr5A	89.243	251	25	2	541	790	550496790	550497039	3.580000e-81	313.0
63	TraesCS1B01G140200	chr7B	89.726	146	12	2	2716	2859	213463582	213463438	2.930000e-42	183.0
64	TraesCS1B01G140200	chr6D	87.857	140	15	1	2719	2856	210769664	210769525	3.810000e-36	163.0
65	TraesCS1B01G140200	chr6D	86.620	142	16	2	2717	2856	105578891	105579031	2.290000e-33	154.0
66	TraesCS1B01G140200	chr6D	85.315	143	19	1	2716	2856	126868442	126868584	3.840000e-31	147.0
67	TraesCS1B01G140200	chr6D	88.393	112	13	0	2741	2852	372144900	372144789	8.310000e-28	135.0

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	TraesCS1B01G140200	chr1B	185223971	185228729	4758	True	4088.000000	5350	100.000000	1	4759	2	chr1B.!!$R4	4758
1	TraesCS1B01G140200	chr1A	133170857	133174052	3195	True	1350.666667	2865	95.117667	890	3950	3	chr1A.!!$R2	3060
2	TraesCS1B01G140200	chr1A	133166073	133166761	688	True	1055.000000	1055	94.348000	4073	4759	1	chr1A.!!$R1	686
3	TraesCS1B01G140200	chr1D	121404025	121407930	3905	True	1323.750000	2854	93.658000	463	4759	4	chr1D.!!$R4	4296

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
331	332	0.039764	ATGACACAGGACTCCGGAGA	59.960	55.0	37.69	12.51	0.00	3.71	F
1585	1609	0.032815	TGGCGTGTCACATTCTTCGA	59.967	50.0	3.42	0.00	0.00	3.71	F
2101	2134	0.322187	AAATGGGACGTGGTGGCTAC	60.322	55.0	0.00	0.00	0.00	3.58	F
2144	2177	0.663269	TGTACAGCGTGAACTCTGCG	60.663	55.0	0.43	0.00	32.25	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1998	2031	0.035458	CCAGTGGTGGTGAGTTCCTC	59.965	60.000	0.00	0.0	39.3	3.71	R
2712	2766	0.404040	TGGCTAGTTCTTTGGTGGGG	59.596	55.000	0.00	0.0	0.0	4.96	R
3633	3867	2.679716	GGGGCACTGCAGAGGAAT	59.320	61.111	23.35	0.0	0.0	3.01	R
4114	4366	1.134788	CCCCACTACGATTCTGTCACC	60.135	57.143	0.00	0.0	0.0	4.02	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
17	18	3.292656	CTCCTTCCTCTGCGCTGA	58.707	61.111	16.55	16.55	0.00	4.26
18	19	1.821936	CTCCTTCCTCTGCGCTGAT	59.178	57.895	17.78	0.00	0.00	2.90
19	20	0.530211	CTCCTTCCTCTGCGCTGATG	60.530	60.000	17.78	14.79	0.00	3.07
20	21	2.178890	CCTTCCTCTGCGCTGATGC	61.179	63.158	17.78	0.00	0.00	3.91
21	22	1.153409	CTTCCTCTGCGCTGATGCT	60.153	57.895	17.78	0.00	36.97	3.79
22	23	1.429927	CTTCCTCTGCGCTGATGCTG	61.430	60.000	17.78	5.89	36.97	4.41
23	24	2.864378	TTCCTCTGCGCTGATGCTGG	62.864	60.000	17.78	14.71	36.97	4.85
24	25	2.125229	CTCTGCGCTGATGCTGGT	60.125	61.111	17.78	0.00	36.97	4.00
25	26	2.435410	TCTGCGCTGATGCTGGTG	60.435	61.111	13.46	0.00	36.97	4.17
26	27	3.506096	CTGCGCTGATGCTGGTGG	61.506	66.667	9.73	0.00	36.97	4.61
28	29	4.783621	GCGCTGATGCTGGTGGGA	62.784	66.667	0.00	0.00	36.97	4.37
29	30	2.513204	CGCTGATGCTGGTGGGAG	60.513	66.667	0.00	0.00	36.97	4.30
30	31	2.993008	GCTGATGCTGGTGGGAGA	59.007	61.111	0.00	0.00	36.03	3.71
31	32	1.530771	GCTGATGCTGGTGGGAGAT	59.469	57.895	0.00	0.00	36.03	2.75
32	33	0.534652	GCTGATGCTGGTGGGAGATC	60.535	60.000	0.00	0.00	36.03	2.75
33	34	0.108207	CTGATGCTGGTGGGAGATCC	59.892	60.000	0.00	0.00	0.00	3.36
34	35	0.326904	TGATGCTGGTGGGAGATCCT	60.327	55.000	0.00	0.00	36.20	3.24
35	36	0.108207	GATGCTGGTGGGAGATCCTG	59.892	60.000	0.00	0.00	36.20	3.86
36	37	1.992519	ATGCTGGTGGGAGATCCTGC	61.993	60.000	0.00	0.00	44.87	4.85
37	38	2.373707	GCTGGTGGGAGATCCTGCT	61.374	63.158	0.00	0.00	42.58	4.24
38	39	1.919600	GCTGGTGGGAGATCCTGCTT	61.920	60.000	0.00	0.00	42.58	3.91
39	40	0.622665	CTGGTGGGAGATCCTGCTTT	59.377	55.000	0.00	0.00	36.20	3.51
40	41	0.329261	TGGTGGGAGATCCTGCTTTG	59.671	55.000	0.00	0.00	36.20	2.77
41	42	1.034292	GGTGGGAGATCCTGCTTTGC	61.034	60.000	0.00	0.00	36.20	3.68
42	43	1.034292	GTGGGAGATCCTGCTTTGCC	61.034	60.000	0.00	0.00	36.20	4.52

Showing 1 to 25 of 527 entries

Previous1 2 3 4 5…22Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.530211	CATCAGCGCAGAGGAAGGAG	60.530	60.000	11.47	0.00	0.00	3.69
1	2	1.519246	CATCAGCGCAGAGGAAGGA	59.481	57.895	11.47	0.00	0.00	3.36
2	3	2.178890	GCATCAGCGCAGAGGAAGG	61.179	63.158	18.96	1.64	0.00	3.46
3	4	3.407657	GCATCAGCGCAGAGGAAG	58.592	61.111	18.96	4.47	0.00	3.46
13	14	0.534652	GATCTCCCACCAGCATCAGC	60.535	60.000	0.00	0.00	42.56	4.26
14	15	0.108207	GGATCTCCCACCAGCATCAG	59.892	60.000	0.00	0.00	34.14	2.90
15	16	0.326904	AGGATCTCCCACCAGCATCA	60.327	55.000	0.00	0.00	37.41	3.07
16	17	0.108207	CAGGATCTCCCACCAGCATC	59.892	60.000	0.00	0.00	37.41	3.91
17	18	1.992519	GCAGGATCTCCCACCAGCAT	61.993	60.000	0.00	0.00	38.31	3.79
18	19	2.673200	GCAGGATCTCCCACCAGCA	61.673	63.158	0.00	0.00	38.31	4.41
19	20	1.919600	AAGCAGGATCTCCCACCAGC	61.920	60.000	0.00	0.00	38.63	4.85
20	21	0.622665	AAAGCAGGATCTCCCACCAG	59.377	55.000	0.00	0.00	37.41	4.00
21	22	0.329261	CAAAGCAGGATCTCCCACCA	59.671	55.000	0.00	0.00	37.41	4.17
22	23	1.034292	GCAAAGCAGGATCTCCCACC	61.034	60.000	0.00	0.00	37.41	4.61
23	24	1.034292	GGCAAAGCAGGATCTCCCAC	61.034	60.000	0.00	0.00	37.41	4.61
24	25	1.304282	GGCAAAGCAGGATCTCCCA	59.696	57.895	0.00	0.00	37.41	4.37
25	26	1.454663	GGGCAAAGCAGGATCTCCC	60.455	63.158	0.00	0.00	36.42	4.30
26	27	1.821332	CGGGCAAAGCAGGATCTCC	60.821	63.158	0.00	0.00	0.00	3.71
27	28	1.821332	CCGGGCAAAGCAGGATCTC	60.821	63.158	0.00	0.00	31.38	2.75
28	29	2.273449	CCGGGCAAAGCAGGATCT	59.727	61.111	0.00	0.00	31.38	2.75
29	30	2.830370	CCCGGGCAAAGCAGGATC	60.830	66.667	8.08	0.00	31.38	3.36
63	64	2.660064	ATCTGACCGGTCCAGCACC	61.660	63.158	31.19	6.16	42.69	5.01
64	65	1.448540	CATCTGACCGGTCCAGCAC	60.449	63.158	31.19	6.98	0.00	4.40
65	66	1.609210	TCATCTGACCGGTCCAGCA	60.609	57.895	31.19	12.87	0.00	4.41
66	67	1.153549	GTCATCTGACCGGTCCAGC	60.154	63.158	31.19	8.22	39.07	4.85

Showing 1 to 25 of 578 entries

Previous1 2 3 4 5…24Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.