AutoCloner

Multiple sequence alignment - TraesCS3A01G028600

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	TraesCS3A01G028600	chr3A	100.000	5119	0	0	1	5119	15298873	15293755	0.000000e+00	9454.0
1	TraesCS3A01G028600	chr3A	87.083	929	108	6	3194	4119	15291461	15292380	0.000000e+00	1040.0
2	TraesCS3A01G028600	chr3A	85.561	838	120	1	1290	2127	15289522	15290358	0.000000e+00	876.0
3	TraesCS3A01G028600	chr3A	83.410	868	110	17	1273	2140	15287856	15288689	0.000000e+00	774.0
4	TraesCS3A01G028600	chr3A	81.116	842	140	14	3194	4030	15065112	15064285	0.000000e+00	656.0
5	TraesCS3A01G028600	chr3A	87.591	411	43	7	2146	2555	15288806	15289209	2.160000e-128	470.0
6	TraesCS3A01G028600	chr3A	87.198	414	41	8	2135	2547	15290473	15290875	1.300000e-125	460.0
7	TraesCS3A01G028600	chr3A	77.315	745	128	24	3393	4121	14925533	14924814	7.980000e-108	401.0
8	TraesCS3A01G028600	chr3A	79.290	507	85	12	1609	2097	15066931	15066427	2.280000e-88	337.0
9	TraesCS3A01G028600	chr3A	82.843	204	20	10	2616	2815	15290911	15291103	8.810000e-38	169.0
10	TraesCS3A01G028600	chr3A	92.000	75	3	1	2974	3045	15291235	15291309	9.070000e-18	102.0
11	TraesCS3A01G028600	chr3A	89.286	56	2	3	604	656	533623243	533623297	3.310000e-07	67.6
12	TraesCS3A01G028600	chrUn	91.603	3549	190	46	1250	4724	244505808	244509322	0.000000e+00	4804.0
13	TraesCS3A01G028600	chrUn	84.607	929	130	7	3194	4119	244512638	244511720	0.000000e+00	911.0
14	TraesCS3A01G028600	chrUn	85.680	838	119	1	1290	2127	244514968	244514132	0.000000e+00	881.0
15	TraesCS3A01G028600	chrUn	85.444	845	100	18	1285	2127	244516637	244515814	0.000000e+00	857.0
16	TraesCS3A01G028600	chrUn	89.687	543	34	7	653	1173	244505244	244505786	0.000000e+00	673.0
17	TraesCS3A01G028600	chrUn	84.412	417	52	9	2146	2555	244515691	244515281	1.030000e-106	398.0
18	TraesCS3A01G028600	chrUn	89.531	277	25	4	4845	5119	244509882	244510156	1.050000e-91	348.0
19	TraesCS3A01G028600	chrUn	92.174	115	7	2	2619	2731	244513181	244513067	1.480000e-35	161.0
20	TraesCS3A01G028600	chrUn	87.838	74	3	3	2974	3044	244512861	244512791	1.180000e-11	82.4
21	TraesCS3A01G028600	chr3D	93.785	2478	118	10	653	3105	5869618	5872084	0.000000e+00	3690.0
22	TraesCS3A01G028600	chr3D	87.926	1673	94	36	3109	4724	5872117	5873738	0.000000e+00	1871.0
23	TraesCS3A01G028600	chr3D	85.699	930	111	12	3194	4119	5876697	5875786	0.000000e+00	961.0
24	TraesCS3A01G028600	chr3D	86.277	838	114	1	1290	2127	5878645	5877809	0.000000e+00	909.0
25	TraesCS3A01G028600	chr3D	85.900	844	98	16	1285	2127	5880311	5879488	0.000000e+00	880.0
26	TraesCS3A01G028600	chr3D	79.812	852	136	21	3194	4031	6033166	6033995	5.710000e-164	588.0
27	TraesCS3A01G028600	chr3D	88.862	413	33	5	4718	5119	5873761	5874171	3.560000e-136	496.0
28	TraesCS3A01G028600	chr3D	88.293	410	41	6	2147	2555	5879361	5878958	7.710000e-133	484.0
29	TraesCS3A01G028600	chr3D	86.553	409	46	7	2146	2553	5877678	5877278	4.700000e-120	442.0
30	TraesCS3A01G028600	chr3D	77.477	777	129	31	3362	4121	6067827	6068574	1.700000e-114	424.0
31	TraesCS3A01G028600	chr3D	83.085	201	19	10	2619	2815	5877245	5877056	8.810000e-38	169.0
32	TraesCS3A01G028600	chr3D	93.636	110	7	0	1	110	5868225	5868334	1.140000e-36	165.0
33	TraesCS3A01G028600	chr3D	90.909	55	1	4	605	656	313101808	313101861	2.560000e-08	71.3
34	TraesCS3A01G028600	chr3B	80.963	914	139	17	3225	4121	7595510	7594615	0.000000e+00	691.0
35	TraesCS3A01G028600	chr3B	77.992	777	128	25	3362	4121	7482963	7482213	1.010000e-121	448.0
36	TraesCS3A01G028600	chr3B	77.215	158	29	3	2903	3055	7595874	7595719	9.130000e-13	86.1
37	TraesCS3A01G028600	chr3B	80.851	94	16	1	5028	5119	420720177	420720270	7.110000e-09	73.1
38	TraesCS3A01G028600	chr3B	87.931	58	3	3	602	656	678629094	678629150	1.190000e-06	65.8
39	TraesCS3A01G028600	chr7A	87.000	100	12	1	4625	4724	729442706	729442608	1.510000e-20	111.0
40	TraesCS3A01G028600	chr7A	87.000	100	12	1	4625	4724	729489594	729489496	1.510000e-20	111.0
41	TraesCS3A01G028600	chr5A	86.000	100	13	1	4625	4724	678622516	678622418	7.010000e-19	106.0
42	TraesCS3A01G028600	chr1D	80.000	145	24	5	4377	4520	119263354	119263494	9.070000e-18	102.0
43	TraesCS3A01G028600	chr4B	80.800	125	18	6	4377	4499	122633167	122633287	5.460000e-15	93.5
44	TraesCS3A01G028600	chr6B	82.222	90	15	1	357	446	476338677	476338589	5.500000e-10	76.8
45	TraesCS3A01G028600	chr7B	95.556	45	0	2	613	656	66320630	66320587	2.560000e-08	71.3
46	TraesCS3A01G028600	chr2D	92.000	50	3	1	608	656	511922691	511922642	9.200000e-08	69.4
47	TraesCS3A01G028600	chr5B	87.931	58	3	3	602	656	182745422	182745366	1.190000e-06	65.8
48	TraesCS3A01G028600	chr5B	90.000	50	4	1	608	656	679686676	679686627	4.280000e-06	63.9
49	TraesCS3A01G028600	chr5B	89.796	49	4	1	609	656	69131972	69131924	1.540000e-05	62.1
50	TraesCS3A01G028600	chr1B	87.719	57	5	2	602	656	56271358	56271302	1.190000e-06	65.8
51	TraesCS3A01G028600	chr4D	92.500	40	3	0	316	355	463702383	463702344	1.990000e-04	58.4

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	TraesCS3A01G028600	chr3A	15293755	15298873	5118	True	9454.000000	9454	100.000000	1	5119	1	chr3A.!!$R2	5118
1	TraesCS3A01G028600	chr3A	15287856	15292380	4524	False	555.857143	1040	86.526571	1273	4119	7	chr3A.!!$F2	2846
2	TraesCS3A01G028600	chr3A	15064285	15066931	2646	True	496.500000	656	80.203000	1609	4030	2	chr3A.!!$R3	2421
3	TraesCS3A01G028600	chr3A	14924814	14925533	719	True	401.000000	401	77.315000	3393	4121	1	chr3A.!!$R1	728
4	TraesCS3A01G028600	chrUn	244505244	244510156	4912	False	1941.666667	4804	90.273667	653	5119	3	chrUn.!!$F1	4466
5	TraesCS3A01G028600	chrUn	244511720	244516637	4917	True	548.400000	911	86.692500	1285	4119	6	chrUn.!!$R1	2834
6	TraesCS3A01G028600	chr3D	5868225	5874171	5946	False	1555.500000	3690	91.052250	1	5119	4	chr3D.!!$F4	5118
7	TraesCS3A01G028600	chr3D	5875786	5880311	4525	True	640.833333	961	85.967833	1285	4119	6	chr3D.!!$R1	2834
8	TraesCS3A01G028600	chr3D	6033166	6033995	829	False	588.000000	588	79.812000	3194	4031	1	chr3D.!!$F1	837
9	TraesCS3A01G028600	chr3D	6067827	6068574	747	False	424.000000	424	77.477000	3362	4121	1	chr3D.!!$F2	759
10	TraesCS3A01G028600	chr3B	7482213	7482963	750	True	448.000000	448	77.992000	3362	4121	1	chr3B.!!$R1	759
11	TraesCS3A01G028600	chr3B	7594615	7595874	1259	True	388.550000	691	79.089000	2903	4121	2	chr3B.!!$R2	1218

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
404	748	0.108992	GTACCATCGAAGGTGTGCGA	60.109	55.0	22.16	0.00	43.14	5.10	F
1147	1976	0.036388	TGGACCGGATTCAGTTCAGC	60.036	55.0	9.46	0.00	0.00	4.26	F
1379	2208	0.106819	GCCTGCTGTCCATGGAAGAT	60.107	55.0	18.20	0.00	0.00	2.40	F
2742	6028	0.471591	AATTGGCAAGGCTTGTCCCA	60.472	50.0	27.49	22.86	33.37	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1379	2208	0.039618	GGGCCCTGTCCATCTCAAAA	59.960	55.000	17.04	0.0	0.0	2.44	R
2454	5716	0.537143	TCAGCACATGTTCCGCCTTT	60.537	50.000	0.00	0.0	0.0	3.11	R
3117	6505	1.067354	CAATCTGCAAAGGAACCAGGC	60.067	52.381	0.00	0.0	0.0	4.85	R
4380	7868	0.317770	CACTCGCGCCAAAACACAAT	60.318	50.000	0.00	0.0	0.0	2.71	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
41	42	9.209175	GATATAAGTTAAGGACCTAAGTGCATG	57.791	37.037	0.00	0.00	36.65	4.06
60	61	5.983118	TGCATGAGTACAACTCCATATTACG	59.017	40.000	0.00	0.00	44.44	3.18
61	62	6.183360	TGCATGAGTACAACTCCATATTACGA	60.183	38.462	0.00	0.00	44.44	3.43
63	64	8.027189	GCATGAGTACAACTCCATATTACGATA	58.973	37.037	0.00	0.00	44.44	2.92
68	69	8.298140	AGTACAACTCCATATTACGATAGAAGC	58.702	37.037	0.00	0.00	41.38	3.86
227	529	5.754406	TCTGGAAATGCACACAAATTTTGAG	59.246	36.000	15.81	10.28	0.00	3.02
344	688	6.003234	GTTTAGGAACCTTCTGAAAGCTTC	57.997	41.667	0.00	0.00	0.00	3.86
345	689	3.147553	AGGAACCTTCTGAAAGCTTCC	57.852	47.619	0.00	10.37	43.40	3.46
346	690	2.163509	GGAACCTTCTGAAAGCTTCCC	58.836	52.381	0.00	0.00	39.72	3.97
348	692	3.222603	GAACCTTCTGAAAGCTTCCCAA	58.777	45.455	0.00	0.00	0.00	4.12
350	694	3.642141	ACCTTCTGAAAGCTTCCCAAAA	58.358	40.909	0.00	0.00	0.00	2.44
351	695	3.384789	ACCTTCTGAAAGCTTCCCAAAAC	59.615	43.478	0.00	0.00	0.00	2.43
352	696	3.243873	CCTTCTGAAAGCTTCCCAAAACC	60.244	47.826	0.00	0.00	0.00	3.27
354	698	1.000274	CTGAAAGCTTCCCAAAACCGG	60.000	52.381	0.00	0.00	0.00	5.28
355	699	1.037493	GAAAGCTTCCCAAAACCGGT	58.963	50.000	0.00	0.00	0.00	5.28
357	701	2.368311	AAGCTTCCCAAAACCGGTAA	57.632	45.000	8.00	0.00	0.00	2.85
359	703	2.668625	AGCTTCCCAAAACCGGTAAAA	58.331	42.857	8.00	0.00	0.00	1.52
360	704	3.032459	AGCTTCCCAAAACCGGTAAAAA	58.968	40.909	8.00	0.00	0.00	1.94
380	724	0.668535	AAAAGACAAAGTGAGCCGGC	59.331	50.000	21.89	21.89	0.00	6.13
381	725	1.172812	AAAGACAAAGTGAGCCGGCC	61.173	55.000	26.15	15.80	0.00	6.13
382	726	3.056328	GACAAAGTGAGCCGGCCC	61.056	66.667	26.15	13.59	0.00	5.80
383	727	3.842925	GACAAAGTGAGCCGGCCCA	62.843	63.158	26.15	17.08	0.00	5.36
384	728	2.361610	CAAAGTGAGCCGGCCCAT	60.362	61.111	26.15	3.93	0.00	4.00
385	729	2.361610	AAAGTGAGCCGGCCCATG	60.362	61.111	26.15	0.00	0.00	3.66
386	730	3.210012	AAAGTGAGCCGGCCCATGT	62.210	57.895	26.15	6.35	0.00	3.21

Showing 1 to 25 of 196 entries

Previous1 2 3 4 5…8Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	4.532521	ACTCATGCACTTAGGTCCTTAACT	59.467	41.667	0.00	0.00	0.00	2.24
41	42	9.828852	CTTCTATCGTAATATGGAGTTGTACTC	57.171	37.037	0.00	0.00	44.32	2.59
140	440	5.625921	ATTGTGTTTTGCAAAAGCTGTTT	57.374	30.435	24.46	6.17	0.00	2.83
141	441	5.625921	AATTGTGTTTTGCAAAAGCTGTT	57.374	30.435	24.46	12.82	0.00	3.16
202	504	6.111382	TCAAAATTTGTGTGCATTTCCAGAA	58.889	32.000	5.56	0.00	0.00	3.02
204	506	5.524646	ACTCAAAATTTGTGTGCATTTCCAG	59.475	36.000	11.94	0.00	36.17	3.86
360	704	1.067060	GCCGGCTCACTTTGTCTTTTT	59.933	47.619	22.15	0.00	0.00	1.94
361	705	0.668535	GCCGGCTCACTTTGTCTTTT	59.331	50.000	22.15	0.00	0.00	2.27
362	706	1.172812	GGCCGGCTCACTTTGTCTTT	61.173	55.000	28.56	0.00	0.00	2.52
363	707	1.600916	GGCCGGCTCACTTTGTCTT	60.601	57.895	28.56	0.00	0.00	3.01
364	708	2.032681	GGCCGGCTCACTTTGTCT	59.967	61.111	28.56	0.00	0.00	3.41
365	709	3.056328	GGGCCGGCTCACTTTGTC	61.056	66.667	28.56	5.59	0.00	3.18
366	710	3.210012	ATGGGCCGGCTCACTTTGT	62.210	57.895	35.86	13.67	0.00	2.83
367	711	2.361610	ATGGGCCGGCTCACTTTG	60.362	61.111	35.86	0.00	0.00	2.77
368	712	1.847798	TACATGGGCCGGCTCACTTT	61.848	55.000	35.86	21.37	0.00	2.66
369	713	2.297895	TACATGGGCCGGCTCACTT	61.298	57.895	35.86	24.24	0.00	3.16
370	714	2.687200	TACATGGGCCGGCTCACT	60.687	61.111	35.86	22.73	0.00	3.41
371	715	2.513897	GTACATGGGCCGGCTCAC	60.514	66.667	35.86	16.28	0.00	3.51
372	716	3.792736	GGTACATGGGCCGGCTCA	61.793	66.667	35.14	35.14	0.00	4.26
373	717	3.792736	TGGTACATGGGCCGGCTC	61.793	66.667	28.56	25.91	0.00	4.70
384	728	4.739683	TATCGCACACCTTCGATGGTACA	61.740	47.826	21.46	5.74	44.10	2.90
385	729	0.108992	TCGCACACCTTCGATGGTAC	60.109	55.000	21.46	13.29	38.45	3.34
386	730	0.821517	ATCGCACACCTTCGATGGTA	59.178	50.000	21.46	7.45	42.95	3.25
387	731	0.821517	TATCGCACACCTTCGATGGT	59.178	50.000	16.84	16.84	44.10	3.55
388	732	1.794701	CATATCGCACACCTTCGATGG	59.205	52.381	15.45	15.45	44.10	3.51

Showing 1 to 25 of 185 entries

Previous1 2 3 4 5…8Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.