AutoCloner

Multiple sequence alignment - TraesCS3B01G380800

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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	TraesCS3B01G380800	chr3B	100.000	9145	0	0	1	9145	598187708	598196852	0.000000e+00	16888.0
1	TraesCS3B01G380800	chr3B	90.162	2094	203	2	5112	7205	478082606	478084696	0.000000e+00	2723.0
2	TraesCS3B01G380800	chr3B	92.481	266	17	2	395	657	427264692	427264427	2.410000e-100	377.0
3	TraesCS3B01G380800	chr3B	82.955	88	5	3	8499	8584	744654333	744654254	4.580000e-08	71.3
4	TraesCS3B01G380800	chr3B	82.895	76	13	0	1254	1329	598188889	598188964	1.650000e-07	69.4
5	TraesCS3B01G380800	chr3B	82.895	76	13	0	1182	1257	598188961	598189036	1.650000e-07	69.4
6	TraesCS3B01G380800	chr3B	94.595	37	2	0	8499	8535	420304160	420304196	3.570000e-04	58.4
7	TraesCS3B01G380800	chr1B	97.232	2095	56	1	5112	7206	188912218	188910126	0.000000e+00	3546.0
8	TraesCS3B01G380800	chr1B	90.553	2096	194	4	5112	7206	390344514	390342422	0.000000e+00	2771.0
9	TraesCS3B01G380800	chr1B	89.260	2095	220	5	5112	7205	301272069	301269979	0.000000e+00	2617.0
10	TraesCS3B01G380800	chr1B	81.013	237	37	5	1629	1861	529396255	529396023	2.030000e-41	182.0
11	TraesCS3B01G380800	chr1B	88.889	144	15	1	4351	4494	529393987	529393845	9.440000e-40	176.0
12	TraesCS3B01G380800	chr1B	94.444	36	1	1	3313	3347	415223257	415223292	5.000000e-03	54.7
13	TraesCS3B01G380800	chr3D	90.541	2590	152	47	668	3201	455051042	455053594	0.000000e+00	3339.0
14	TraesCS3B01G380800	chr3D	95.518	1718	46	6	3397	5112	455053650	455055338	0.000000e+00	2717.0
15	TraesCS3B01G380800	chr3D	93.726	1291	61	11	7220	8503	455055338	455056615	0.000000e+00	1917.0
16	TraesCS3B01G380800	chr3D	93.718	589	19	4	8575	9145	455056617	455057205	0.000000e+00	867.0
17	TraesCS3B01G380800	chr3D	95.019	261	11	2	398	657	306028960	306029219	8.550000e-110	409.0
18	TraesCS3B01G380800	chr3D	88.854	314	31	3	83	396	455050714	455051023	5.180000e-102	383.0
19	TraesCS3B01G380800	chr3D	96.875	32	0	1	3317	3347	371367038	371367007	1.700000e-02	52.8
20	TraesCS3B01G380800	chr7A	90.662	2099	185	10	5112	7206	482730227	482728136	0.000000e+00	2780.0
21	TraesCS3B01G380800	chr7A	90.123	2106	204	1	5101	7206	299592298	299590197	0.000000e+00	2734.0
22	TraesCS3B01G380800	chr7A	100.000	28	0	0	3374	3401	628705055	628705082	1.700000e-02	52.8
23	TraesCS3B01G380800	chr6D	90.847	2065	183	2	5107	7171	237758982	237756924	0.000000e+00	2761.0
24	TraesCS3B01G380800	chr6A	89.737	2095	215	0	5112	7206	14748117	14746023	0.000000e+00	2678.0
25	TraesCS3B01G380800	chr6A	94.118	34	2	0	3314	3347	610234749	610234782	1.700000e-02	52.8
26	TraesCS3B01G380800	chr7B	89.695	2096	214	2	5112	7206	615167828	615169922	0.000000e+00	2673.0
27	TraesCS3B01G380800	chr7B	93.233	266	16	2	393	657	149805437	149805701	3.100000e-104	390.0
28	TraesCS3B01G380800	chr7B	100.000	28	0	0	3374	3401	686527469	686527496	1.700000e-02	52.8
29	TraesCS3B01G380800	chr3A	94.122	1310	57	10	7204	8503	597333753	597335052	0.000000e+00	1975.0
30	TraesCS3B01G380800	chr3A	88.828	1271	83	31	673	1916	597329149	597330387	0.000000e+00	1506.0
31	TraesCS3B01G380800	chr3A	96.579	643	21	1	2699	3340	597331326	597331968	0.000000e+00	1064.0
32	TraesCS3B01G380800	chr3A	92.946	723	25	3	3397	4095	597331981	597332701	0.000000e+00	1029.0
33	TraesCS3B01G380800	chr3A	89.176	813	61	13	1916	2714	597330437	597331236	0.000000e+00	989.0
34	TraesCS3B01G380800	chr3A	97.070	512	14	1	4604	5114	597333255	597333766	0.000000e+00	861.0
35	TraesCS3B01G380800	chr3A	95.178	477	11	5	4129	4604	597332699	597333164	0.000000e+00	743.0
36	TraesCS3B01G380800	chr3A	88.682	592	34	11	8575	9145	597335054	597335633	0.000000e+00	691.0
37	TraesCS3B01G380800	chr3A	83.721	86	4	3	8499	8582	709895641	709895718	1.270000e-08	73.1
38	TraesCS3B01G380800	chr3A	83.721	86	4	3	8499	8582	709923637	709923714	1.270000e-08	73.1
39	TraesCS3B01G380800	chr3A	100.000	30	0	0	3319	3348	645146584	645146555	1.000000e-03	56.5
40	TraesCS3B01G380800	chr2D	93.870	261	15	1	398	657	644999394	644999134	8.610000e-105	392.0
41	TraesCS3B01G380800	chr1A	94.118	255	12	3	395	648	174960563	174960815	1.440000e-102	385.0
42	TraesCS3B01G380800	chr1A	86.525	282	34	4	2822	3101	492126553	492126274	3.210000e-79	307.0
43	TraesCS3B01G380800	chr1A	84.916	179	25	2	2361	2539	492127355	492127179	7.300000e-41	180.0
44	TraesCS3B01G380800	chr1A	80.841	214	35	3	1629	1839	492127881	492127671	7.350000e-36	163.0
45	TraesCS3B01G380800	chr1A	87.050	139	18	0	4351	4489	492125639	492125501	3.420000e-34	158.0
46	TraesCS3B01G380800	chr1A	100.000	31	0	0	3310	3340	457957373	457957403	3.570000e-04	58.4
47	TraesCS3B01G380800	chr1A	96.875	32	1	0	3316	3347	428668203	428668172	5.000000e-03	54.7
48	TraesCS3B01G380800	chr1D	92.481	266	18	2	394	658	365804557	365804821	6.700000e-101	379.0
49	TraesCS3B01G380800	chr1D	86.879	282	33	4	2822	3101	393734666	393734945	6.890000e-81	313.0
50	TraesCS3B01G380800	chr1D	81.308	214	34	3	1629	1839	393733332	393733542	1.580000e-37	169.0
51	TraesCS3B01G380800	chr1D	85.366	82	5	3	8500	8579	22502947	22503023	2.740000e-10	78.7
52	TraesCS3B01G380800	chr1D	84.146	82	5	2	8499	8580	183020110	183020037	1.270000e-08	73.1
53	TraesCS3B01G380800	chr5A	92.481	266	17	3	396	658	34841903	34842168	2.410000e-100	377.0
54	TraesCS3B01G380800	chr5A	86.905	84	6	5	8499	8580	535656944	535657024	1.260000e-13	89.8
55	TraesCS3B01G380800	chr5A	96.875	32	0	1	3316	3347	236871307	236871277	1.700000e-02	52.8
56	TraesCS3B01G380800	chr2B	92.748	262	17	2	398	658	603430010	603430270	2.410000e-100	377.0
57	TraesCS3B01G380800	chr4D	92.135	267	18	3	396	660	55965604	55965339	3.120000e-99	374.0
58	TraesCS3B01G380800	chr4A	80.371	377	54	9	8752	9114	612520147	612519777	1.510000e-67	268.0
59	TraesCS3B01G380800	chr4A	81.707	82	7	3	8499	8579	314860946	314860872	2.760000e-05	62.1
60	TraesCS3B01G380800	chr4A	81.707	82	7	3	8499	8579	315036780	315036706	2.760000e-05	62.1
61	TraesCS3B01G380800	chr6B	84.211	95	4	5	8499	8592	49403904	49403988	2.120000e-11	82.4
62	TraesCS3B01G380800	chr6B	72.650	234	55	7	30	257	488894068	488893838	1.650000e-07	69.4
63	TraesCS3B01G380800	chrUn	83.721	86	4	3	8499	8582	478445748	478445671	1.270000e-08	73.1
64	TraesCS3B01G380800	chr4B	83.951	81	7	2	8499	8579	39245367	39245293	1.270000e-08	73.1
65	TraesCS3B01G380800	chr5D	81.707	82	14	1	8500	8580	551876827	551876746	5.930000e-07	67.6
66	TraesCS3B01G380800	chr5D	100.000	29	0	0	3376	3404	244629635	244629663	5.000000e-03	54.7
67	TraesCS3B01G380800	chr7D	83.099	71	6	4	8499	8567	611229613	611229679	9.920000e-05	60.2
68	TraesCS3B01G380800	chr7D	100.000	29	0	0	3320	3348	453144811	453144783	5.000000e-03	54.7
69	TraesCS3B01G380800	chr5B	100.000	28	0	0	3374	3401	554776690	554776663	1.700000e-02	52.8
70	TraesCS3B01G380800	chr2A	100.000	28	0	0	3374	3401	350738160	350738133	1.700000e-02	52.8

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	TraesCS3B01G380800	chr3B	598187708	598196852	9144	False	16888.00	16888	100.000000	1	9145	1	chr3B.!!$F3	9144
1	TraesCS3B01G380800	chr3B	478082606	478084696	2090	False	2723.00	2723	90.162000	5112	7205	1	chr3B.!!$F2	2093
2	TraesCS3B01G380800	chr1B	188910126	188912218	2092	True	3546.00	3546	97.232000	5112	7206	1	chr1B.!!$R1	2094
3	TraesCS3B01G380800	chr1B	390342422	390344514	2092	True	2771.00	2771	90.553000	5112	7206	1	chr1B.!!$R3	2094
4	TraesCS3B01G380800	chr1B	301269979	301272069	2090	True	2617.00	2617	89.260000	5112	7205	1	chr1B.!!$R2	2093
5	TraesCS3B01G380800	chr3D	455050714	455057205	6491	False	1844.60	3339	92.471400	83	9145	5	chr3D.!!$F2	9062
6	TraesCS3B01G380800	chr7A	482728136	482730227	2091	True	2780.00	2780	90.662000	5112	7206	1	chr7A.!!$R2	2094
7	TraesCS3B01G380800	chr7A	299590197	299592298	2101	True	2734.00	2734	90.123000	5101	7206	1	chr7A.!!$R1	2105
8	TraesCS3B01G380800	chr6D	237756924	237758982	2058	True	2761.00	2761	90.847000	5107	7171	1	chr6D.!!$R1	2064
9	TraesCS3B01G380800	chr6A	14746023	14748117	2094	True	2678.00	2678	89.737000	5112	7206	1	chr6A.!!$R1	2094
10	TraesCS3B01G380800	chr7B	615167828	615169922	2094	False	2673.00	2673	89.695000	5112	7206	1	chr7B.!!$F2	2094
11	TraesCS3B01G380800	chr3A	597329149	597335633	6484	False	1107.25	1975	92.822625	673	9145	8	chr3A.!!$F3	8472
12	TraesCS3B01G380800	chr1A	492125501	492127881	2380	True	202.00	307	84.833000	1629	4489	4	chr1A.!!$R2	2860
13	TraesCS3B01G380800	chr1D	393733332	393734945	1613	False	241.00	313	84.093500	1629	3101	2	chr1D.!!$F3	1472

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
344	345	0.033504	ATGACGGCGTGAAGTGAAGT	59.966	50.000	21.19	0.00	0.00	3.01	F
1174	1225	0.105709	CTCCTCCTCCTCCTTCTCCC	60.106	65.000	0.00	0.00	0.00	4.30	F
1352	1403	0.320771	GCATCTCCACACGGAACAGT	60.321	55.000	0.00	0.00	42.21	3.55	F
1933	2050	1.165907	TGTTTGCTAGTGCTTGCGCT	61.166	50.000	9.73	13.32	40.48	5.92	F
2251	2380	1.688735	CCACTAGATGAGATTCGGGCA	59.311	52.381	0.00	0.00	0.00	5.36	F
3606	4620	2.142292	ATCCACCTCTTTTGCCCGCT	62.142	55.000	0.00	0.00	0.00	5.52	F
4658	5840	1.757731	GCTGCATTGGTGGGCCATA	60.758	57.895	10.70	0.00	45.56	2.74	F
5491	6673	1.087771	GGCGGTTGTGAAGGTATCCG	61.088	60.000	0.00	0.00	40.72	4.18	F
7158	8345	0.179089	GCTGACCATGTCTCGCAGAT	60.179	55.000	0.00	0.00	33.89	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1481	1532	0.790207	CTTTGTGTCGACCGATGTGG	59.210	55.000	14.12	0.00	46.41	4.17	R
1995	2112	2.170607	ACACAGCACAACACTACCTCTT	59.829	45.455	0.00	0.00	0.00	2.85	R
2289	2418	2.214387	GCAACTTGCAAGCTTGAACT	57.786	45.000	30.39	4.16	44.26	3.01	R
2838	3851	3.509442	TCTTGCATGAGTTCCCCATTTT	58.491	40.909	0.00	0.00	0.00	1.82	R
4047	5137	2.005451	CTGACACAGCTACCTCATTGC	58.995	52.381	0.00	0.00	0.00	3.56	R
5285	6467	2.162608	CGTAGATAGGATCAAGGCCGAG	59.837	54.545	0.00	0.00	0.00	4.63	R
5723	6909	0.179029	CAACCTTTCACGGGTCCACT	60.179	55.000	0.00	0.00	35.83	4.00	R
7217	8404	0.392193	CGGGATCAAGCAGAAGCACT	60.392	55.000	0.00	0.00	45.49	4.40	R
8972	10202	0.453950	CGTCGTCGGTGGTAGAACAG	60.454	60.000	0.00	0.00	0.00	3.16	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	Hairpin	End Stability
23	24	6.782298	CAGACTATGCCTCATAACAATCTG	57.218	41.667	0.00	0.00	2.90
24	25	6.519382	CAGACTATGCCTCATAACAATCTGA	58.481	40.000	0.00	31.34	3.27
25	26	6.988580	CAGACTATGCCTCATAACAATCTGAA	59.011	38.462	0.00	31.34	3.02
26	27	7.496920	CAGACTATGCCTCATAACAATCTGAAA	59.503	37.037	0.00	31.34	2.69
27	28	7.714377	AGACTATGCCTCATAACAATCTGAAAG	59.286	37.037	0.00	0.00	2.62
43	44	4.449068	TCTGAAAGAAGATGTCAAAGTCGC	59.551	41.667	0.00	42.31	5.19
44	45	3.498397	TGAAAGAAGATGTCAAAGTCGCC	59.502	43.478	0.00	0.00	5.54
45	46	1.714794	AGAAGATGTCAAAGTCGCCG	58.285	50.000	0.00	0.00	6.46
46	47	0.721718	GAAGATGTCAAAGTCGCCGG	59.278	55.000	0.00	0.00	6.13
47	48	0.320374	AAGATGTCAAAGTCGCCGGA	59.680	50.000	5.05	0.00	5.14
48	49	0.389948	AGATGTCAAAGTCGCCGGAC	60.390	55.000	5.05	43.76	4.79
49	50	1.359459	GATGTCAAAGTCGCCGGACC	61.359	60.000	5.05	44.54	4.46
50	51	2.029964	GTCAAAGTCGCCGGACCA	59.970	61.111	5.05	44.54	4.02
51	52	1.595929	GTCAAAGTCGCCGGACCAA	60.596	57.895	5.05	44.54	3.67
52	53	0.953960	GTCAAAGTCGCCGGACCAAT	60.954	55.000	5.05	44.54	3.16
53	54	0.609151	TCAAAGTCGCCGGACCAATA	59.391	50.000	5.05	44.54	1.90
54	55	1.208535	TCAAAGTCGCCGGACCAATAT	59.791	47.619	5.05	44.54	1.28
55	56	2.014128	CAAAGTCGCCGGACCAATATT	58.986	47.619	5.05	44.54	1.28
56	57	1.949465	AAGTCGCCGGACCAATATTC	58.051	50.000	5.05	44.54	1.75
57	58	0.828022	AGTCGCCGGACCAATATTCA	59.172	50.000	5.05	44.54	2.57
58	59	1.208535	AGTCGCCGGACCAATATTCAA	59.791	47.619	5.05	44.54	2.69
59	60	1.329599	GTCGCCGGACCAATATTCAAC	59.670	52.381	5.05	37.19	3.18
60	61	0.661020	CGCCGGACCAATATTCAACC	59.339	55.000	5.05	0.00	3.77
61	62	1.757682	GCCGGACCAATATTCAACCA	58.242	50.000	5.05	0.00	3.67
62	63	2.096248	GCCGGACCAATATTCAACCAA	58.904	47.619	5.05	0.00	3.67

Showing 1 to 25 of 335 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
2	3	7.712639	TCTTTCAGATTGTTATGAGGCATAGTC	59.287	37.037	0.00	0.00	2.59
3	4	7.568349	TCTTTCAGATTGTTATGAGGCATAGT	58.432	34.615	0.00	0.00	2.12
4	5	8.442632	TTCTTTCAGATTGTTATGAGGCATAG	57.557	34.615	0.00	0.00	2.23
6	7	7.114754	TCTTCTTTCAGATTGTTATGAGGCAT	58.885	34.615	0.00	0.00	4.40
7	8	6.475504	TCTTCTTTCAGATTGTTATGAGGCA	58.524	36.000	0.00	0.00	4.75
8	9	6.992063	TCTTCTTTCAGATTGTTATGAGGC	57.008	37.500	0.00	0.00	4.70
9	10	8.503458	ACATCTTCTTTCAGATTGTTATGAGG	57.497	34.615	0.00	30.50	3.86
10	11	9.159364	TGACATCTTCTTTCAGATTGTTATGAG	57.841	33.333	0.00	30.50	2.90
11	12	9.506018	TTGACATCTTCTTTCAGATTGTTATGA	57.494	29.630	0.00	30.50	2.15
14	15	9.342308	ACTTTGACATCTTCTTTCAGATTGTTA	57.658	29.630	0.00	30.50	2.41
15	16	8.230472	ACTTTGACATCTTCTTTCAGATTGTT	57.770	30.769	0.00	30.50	2.83
16	17	7.307632	CGACTTTGACATCTTCTTTCAGATTGT	60.308	37.037	0.00	30.50	2.71
17	18	7.014115	CGACTTTGACATCTTCTTTCAGATTG	58.986	38.462	0.00	30.50	2.67
18	19	6.348050	GCGACTTTGACATCTTCTTTCAGATT	60.348	38.462	0.00	30.50	2.40
19	20	5.121454	GCGACTTTGACATCTTCTTTCAGAT	59.879	40.000	0.00	33.44	2.90
20	21	4.449068	GCGACTTTGACATCTTCTTTCAGA	59.551	41.667	0.00	0.00	3.27
21	22	4.377841	GGCGACTTTGACATCTTCTTTCAG	60.378	45.833	0.00	0.00	3.02
22	23	3.498397	GGCGACTTTGACATCTTCTTTCA	59.502	43.478	0.00	0.00	2.69
23	24	3.423645	CGGCGACTTTGACATCTTCTTTC	60.424	47.826	0.00	0.00	2.62
24	25	2.480419	CGGCGACTTTGACATCTTCTTT	59.520	45.455	0.00	0.00	2.52
25	26	2.069273	CGGCGACTTTGACATCTTCTT	58.931	47.619	0.00	0.00	2.52
26	27	1.673033	CCGGCGACTTTGACATCTTCT	60.673	52.381	9.30	0.00	2.85
27	28	0.721718	CCGGCGACTTTGACATCTTC	59.278	55.000	9.30	0.00	2.87
28	29	0.320374	TCCGGCGACTTTGACATCTT	59.680	50.000	9.30	0.00	2.40
29	30	0.389948	GTCCGGCGACTTTGACATCT	60.390	55.000	9.30	35.99	2.90

Showing 1 to 25 of 363 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.