AutoCloner

Multiple sequence alignment - TraesCS4B01G321200

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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	TraesCS4B01G321200	chr4B	100.000	3457	0	0	1	3457	612259030	612262486	0.000000e+00	6384.0
1	TraesCS4B01G321200	chr4D	92.474	2405	82	36	410	2787	482689432	482691764	0.000000e+00	3347.0
2	TraesCS4B01G321200	chr5A	90.891	2492	128	38	531	2966	659880932	659878484	0.000000e+00	3253.0
3	TraesCS4B01G321200	chr5A	84.110	365	37	12	3094	3457	659878440	659878096	1.990000e-87	333.0
4	TraesCS4B01G321200	chr5A	89.524	105	3	4	437	537	659881218	659881118	3.620000e-25	126.0
5	TraesCS4B01G321200	chrUn	83.547	468	66	5	1376	1834	91652912	91652447	8.870000e-116	427.0
6	TraesCS4B01G321200	chrUn	83.439	471	67	5	1373	1834	239778791	239779259	8.870000e-116	427.0
7	TraesCS4B01G321200	chr6B	86.022	186	24	2	11	195	468252383	468252199	7.570000e-47	198.0
8	TraesCS4B01G321200	chr6B	94.737	38	2	0	1950	1987	89566059	89566022	3.730000e-05	60.2
9	TraesCS4B01G321200	chr6D	85.326	184	25	2	11	193	302578786	302578604	4.550000e-44	189.0
10	TraesCS4B01G321200	chr7B	79.184	245	51	0	1813	2057	748457716	748457960	1.650000e-38	171.0
11	TraesCS4B01G321200	chr7B	93.333	105	7	0	2970	3074	484454840	484454944	4.620000e-34	156.0
12	TraesCS4B01G321200	chr7B	90.000	60	6	0	1300	1359	601265253	601265312	1.030000e-10	78.7
13	TraesCS4B01G321200	chr6A	82.540	189	30	3	5	192	413212023	413212209	2.760000e-36	163.0
14	TraesCS4B01G321200	chr6A	91.150	113	8	2	2972	3083	315625368	315625257	5.980000e-33	152.0
15	TraesCS4B01G321200	chr6A	86.301	73	9	1	1300	1371	534597099	534597171	1.030000e-10	78.7
16	TraesCS4B01G321200	chr5B	95.000	100	5	0	2975	3074	695894739	695894838	1.280000e-34	158.0
17	TraesCS4B01G321200	chr5B	89.831	118	9	2	2977	3093	306435383	306435268	7.730000e-32	148.0
18	TraesCS4B01G321200	chr1D	94.118	102	6	0	2978	3079	420554542	420554643	4.620000e-34	156.0
19	TraesCS4B01G321200	chr7D	91.071	112	8	2	2965	3075	561963318	561963428	2.150000e-32	150.0
20	TraesCS4B01G321200	chr3B	89.256	121	11	2	2965	3084	490924668	490924549	2.150000e-32	150.0
21	TraesCS4B01G321200	chr2B	90.435	115	9	2	2969	3082	774087848	774087961	2.150000e-32	150.0
22	TraesCS4B01G321200	chr2B	93.617	47	2	1	12	58	524006550	524006595	6.190000e-08	69.4
23	TraesCS4B01G321200	chr3A	84.722	144	20	2	9	151	489305228	489305086	3.600000e-30	143.0
24	TraesCS4B01G321200	chr3A	78.689	122	22	3	1	122	360820201	360820318	1.030000e-10	78.7
25	TraesCS4B01G321200	chr1B	86.260	131	15	3	2950	3078	150801847	150801976	4.650000e-29	139.0
26	TraesCS4B01G321200	chr1B	91.781	73	6	0	1300	1372	561545958	561546030	6.100000e-18	102.0

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	TraesCS4B01G321200	chr4B	612259030	612262486	3456	False	6384.000000	6384	100.000	1	3457	1	chr4B.!!$F1	3456
1	TraesCS4B01G321200	chr4D	482689432	482691764	2332	False	3347.000000	3347	92.474	410	2787	1	chr4D.!!$F1	2377
2	TraesCS4B01G321200	chr5A	659878096	659881218	3122	True	1237.333333	3253	88.175	437	3457	3	chr5A.!!$R1	3020

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
367	368	0.031449	GCTTGCTTTTACCGGTGCAA	59.969	50.0	23.78	23.78	42.16	4.08	F
982	1197	0.313043	CATTTCAGCGCCATCCATCC	59.687	55.0	2.29	0.00	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2295	2525	0.739112	CCGCTCTCTCTGCTTTCACC	60.739	60.0	0.0	0.0	0.0	4.02	R
2513	2758	0.036765	GCAAGGGATGTGTCGGTGTA	60.037	55.0	0.0	0.0	0.0	2.90	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
20	21	3.969117	GAACAACACATGAGCAACTCA	57.031	42.857	0.00	0.00	44.99	3.41
21	22	4.291540	GAACAACACATGAGCAACTCAA	57.708	40.909	0.00	0.00	44.04	3.02
22	23	3.976793	ACAACACATGAGCAACTCAAG	57.023	42.857	0.00	0.00	44.04	3.02
23	24	3.544684	ACAACACATGAGCAACTCAAGA	58.455	40.909	0.00	0.00	44.04	3.02
24	25	3.947196	ACAACACATGAGCAACTCAAGAA	59.053	39.130	0.00	0.00	44.04	2.52
25	26	4.398988	ACAACACATGAGCAACTCAAGAAA	59.601	37.500	0.00	0.00	44.04	2.52
26	27	4.825546	ACACATGAGCAACTCAAGAAAG	57.174	40.909	0.00	0.19	44.04	2.62
27	28	4.454678	ACACATGAGCAACTCAAGAAAGA	58.545	39.130	0.00	0.00	44.04	2.52
28	29	5.068636	ACACATGAGCAACTCAAGAAAGAT	58.931	37.500	0.00	0.00	44.04	2.40
29	30	5.533903	ACACATGAGCAACTCAAGAAAGATT	59.466	36.000	0.00	0.00	44.04	2.40
30	31	6.040166	ACACATGAGCAACTCAAGAAAGATTT	59.960	34.615	0.00	0.00	44.04	2.17
31	32	6.362551	CACATGAGCAACTCAAGAAAGATTTG	59.637	38.462	0.00	0.00	44.04	2.32
32	33	6.263842	ACATGAGCAACTCAAGAAAGATTTGA	59.736	34.615	0.00	0.00	44.04	2.69
33	34	6.889301	TGAGCAACTCAAGAAAGATTTGAT	57.111	33.333	0.00	0.00	37.57	2.57
34	35	7.281040	TGAGCAACTCAAGAAAGATTTGATT	57.719	32.000	0.00	0.00	37.57	2.57
35	36	7.143340	TGAGCAACTCAAGAAAGATTTGATTG	58.857	34.615	0.00	0.00	37.57	2.67
36	37	7.013559	TGAGCAACTCAAGAAAGATTTGATTGA	59.986	33.333	0.00	0.00	37.57	2.57
38	39	6.089150	GCAACTCAAGAAAGATTTGATTGAGC	59.911	38.462	19.80	10.51	46.88	4.26
39	40	6.889301	ACTCAAGAAAGATTTGATTGAGCA	57.111	33.333	19.80	0.00	46.88	4.26
40	41	6.675987	ACTCAAGAAAGATTTGATTGAGCAC	58.324	36.000	19.80	0.00	46.88	4.40
41	42	6.017400	TCAAGAAAGATTTGATTGAGCACC	57.983	37.500	0.00	0.00	30.03	5.01
42	43	5.771666	TCAAGAAAGATTTGATTGAGCACCT	59.228	36.000	0.00	0.00	30.03	4.00
43	44	5.640189	AGAAAGATTTGATTGAGCACCTG	57.360	39.130	0.00	0.00	0.00	4.00
44	45	3.863142	AAGATTTGATTGAGCACCTGC	57.137	42.857	0.00	0.00	42.49	4.85
55	56	2.670251	CACCTGCGGGCGGTTAAA	60.670	61.111	12.89	0.00	35.63	1.52

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	3.969117	TGAGTTGCTCATGTGTTGTTC	57.031	42.857	0.00	0.00	35.39	3.18
2	3	3.544684	TCTTGAGTTGCTCATGTGTTGT	58.455	40.909	10.44	0.00	40.39	3.32
3	4	4.556942	TTCTTGAGTTGCTCATGTGTTG	57.443	40.909	10.44	0.00	40.39	3.33
4	5	4.883585	TCTTTCTTGAGTTGCTCATGTGTT	59.116	37.500	10.44	0.00	40.39	3.32
6	7	5.624344	ATCTTTCTTGAGTTGCTCATGTG	57.376	39.130	10.44	0.00	40.39	3.21
8	9	6.675026	TCAAATCTTTCTTGAGTTGCTCATG	58.325	36.000	0.00	3.07	40.39	3.07
9	10	6.889301	TCAAATCTTTCTTGAGTTGCTCAT	57.111	33.333	0.00	0.00	40.39	2.90
10	11	6.889301	ATCAAATCTTTCTTGAGTTGCTCA	57.111	33.333	0.00	0.00	40.49	4.26
11	12	7.365741	TCAATCAAATCTTTCTTGAGTTGCTC	58.634	34.615	0.00	0.00	40.49	4.26
12	13	7.281040	TCAATCAAATCTTTCTTGAGTTGCT	57.719	32.000	0.00	0.00	40.49	3.91
13	14	6.089150	GCTCAATCAAATCTTTCTTGAGTTGC	59.911	38.462	17.38	7.92	42.92	4.17
14	15	7.114529	GTGCTCAATCAAATCTTTCTTGAGTTG	59.885	37.037	17.38	5.44	42.92	3.16
15	16	7.144000	GTGCTCAATCAAATCTTTCTTGAGTT	58.856	34.615	17.38	0.00	42.92	3.01
16	17	6.294397	GGTGCTCAATCAAATCTTTCTTGAGT	60.294	38.462	17.38	0.35	42.92	3.41
17	18	6.072064	AGGTGCTCAATCAAATCTTTCTTGAG	60.072	38.462	14.46	14.46	43.51	3.02
18	19	5.771666	AGGTGCTCAATCAAATCTTTCTTGA	59.228	36.000	0.00	0.00	37.22	3.02
19	20	5.862323	CAGGTGCTCAATCAAATCTTTCTTG	59.138	40.000	0.00	0.00	0.00	3.02
20	21	5.566230	GCAGGTGCTCAATCAAATCTTTCTT	60.566	40.000	0.00	0.00	38.21	2.52
21	22	4.082354	GCAGGTGCTCAATCAAATCTTTCT	60.082	41.667	0.00	0.00	38.21	2.52
22	23	4.171754	GCAGGTGCTCAATCAAATCTTTC	58.828	43.478	0.00	0.00	38.21	2.62
23	24	3.366679	CGCAGGTGCTCAATCAAATCTTT	60.367	43.478	0.00	0.00	39.32	2.52
24	25	2.163010	CGCAGGTGCTCAATCAAATCTT	59.837	45.455	0.00	0.00	39.32	2.40
25	26	1.741706	CGCAGGTGCTCAATCAAATCT	59.258	47.619	0.00	0.00	39.32	2.40
26	27	2.184385	CGCAGGTGCTCAATCAAATC	57.816	50.000	0.00	0.00	39.32	2.17
41	42	2.106683	CCTCTTTAACCGCCCGCAG	61.107	63.158	0.00	0.00	0.00	5.18

Showing 1 to 25 of 447 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.