AutoCloner

Multiple sequence alignment - TraesCS5D01G541000

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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	TraesCS5D01G541000	chr5D	100.000	3276	0	0	1	3276	552034542	552031267	0.000000e+00	6050
1	TraesCS5D01G541000	chr5D	89.744	2496	208	22	564	3042	551989513	551987049	0.000000e+00	3147
2	TraesCS5D01G541000	chr5D	72.417	1200	260	51	820	1976	543508795	543507624	1.900000e-82	316
3	TraesCS5D01G541000	chr5D	97.345	113	3	0	1	113	560286241	560286129	3.340000e-45	193
4	TraesCS5D01G541000	chr4A	95.045	2866	128	9	422	3276	616213184	616210322	0.000000e+00	4494
5	TraesCS5D01G541000	chr4A	94.062	2863	144	15	422	3276	616297061	616299905	0.000000e+00	4322
6	TraesCS5D01G541000	chr4A	95.202	1855	78	5	1311	3156	616230056	616228204	0.000000e+00	2922
7	TraesCS5D01G541000	chr4A	87.304	1725	172	21	564	2266	616315011	616316710	0.000000e+00	1929
8	TraesCS5D01G541000	chr4A	97.297	111	3	0	1	111	455027808	455027918	4.320000e-44	189
9	TraesCS5D01G541000	chr4A	83.974	156	22	2	3042	3194	561518894	561518739	2.630000e-31	147
10	TraesCS5D01G541000	chr4A	83.333	156	23	2	3044	3196	65058000	65058155	1.230000e-29	141
11	TraesCS5D01G541000	chr5B	95.649	2459	96	10	538	2988	699949676	699952131	0.000000e+00	3938
12	TraesCS5D01G541000	chr5B	89.815	1620	115	25	532	2140	700229903	700228323	0.000000e+00	2032
13	TraesCS5D01G541000	chr5B	88.419	639	63	6	2414	3042	700228019	700227382	0.000000e+00	760
14	TraesCS5D01G541000	chr5B	93.284	268	18	0	115	382	408958243	408958510	2.370000e-106	396
15	TraesCS5D01G541000	chr5B	72.712	1213	276	41	790	1967	703529332	703530524	4.020000e-94	355
16	TraesCS5D01G541000	chr5B	86.129	310	41	2	2068	2377	700228325	700228018	1.880000e-87	333
17	TraesCS5D01G541000	chr5B	90.244	123	7	4	422	542	699949528	699949647	4.380000e-34	156
18	TraesCS5D01G541000	chr5B	94.030	67	2	2	3199	3265	700227387	700227323	2.080000e-17	100
19	TraesCS5D01G541000	chr1D	81.882	861	130	12	609	1456	457779293	457780140	0.000000e+00	702
20	TraesCS5D01G541000	chr7B	93.309	269	18	0	116	384	396334092	396333824	6.590000e-107	398
21	TraesCS5D01G541000	chr7B	92.937	269	19	0	116	384	607728378	607728646	3.060000e-105	392
22	TraesCS5D01G541000	chr3B	93.284	268	18	0	117	384	586266082	586265815	2.370000e-106	396
23	TraesCS5D01G541000	chr3B	93.258	267	18	0	117	383	557194177	557193911	8.520000e-106	394
24	TraesCS5D01G541000	chr2B	93.585	265	17	0	117	381	503482246	503481982	2.370000e-106	396
25	TraesCS5D01G541000	chrUn	93.258	267	18	0	117	383	66272817	66273083	8.520000e-106	394
26	TraesCS5D01G541000	chr6B	93.284	268	17	1	117	383	446119746	446120013	8.520000e-106	394
27	TraesCS5D01G541000	chr3D	91.815	281	21	2	112	390	281948416	281948696	1.100000e-104	390
28	TraesCS5D01G541000	chr4B	77.435	421	91	3	1558	1976	581072794	581072376	7.020000e-62	248
29	TraesCS5D01G541000	chr2D	98.198	111	2	0	1	111	314360671	314360781	9.270000e-46	195
30	TraesCS5D01G541000	chr2D	97.345	113	3	0	1	113	480541507	480541619	3.340000e-45	193
31	TraesCS5D01G541000	chr2D	96.491	114	4	0	1	114	35246702	35246589	4.320000e-44	189
32	TraesCS5D01G541000	chr2D	92.248	129	7	3	1	128	131274057	131273931	2.600000e-41	180
33	TraesCS5D01G541000	chr6D	97.345	113	3	0	1	113	107938629	107938741	3.340000e-45	193
34	TraesCS5D01G541000	chr6D	83.226	155	23	2	3043	3194	465143928	465143774	4.410000e-29	139
35	TraesCS5D01G541000	chr4D	96.491	114	4	0	1	114	487284394	487284281	4.320000e-44	189
36	TraesCS5D01G541000	chr7A	95.690	116	5	0	1	116	43173044	43172929	1.550000e-43	187
37	TraesCS5D01G541000	chr7A	81.935	155	25	2	3043	3194	54687336	54687182	9.540000e-26	128
38	TraesCS5D01G541000	chr7A	81.457	151	25	2	3047	3194	437071111	437070961	1.600000e-23	121
39	TraesCS5D01G541000	chr2A	85.806	155	19	2	3043	3194	281234187	281234033	9.410000e-36	161
40	TraesCS5D01G541000	chr2A	83.117	154	23	2	3044	3194	453894253	453894100	1.590000e-28	137
41	TraesCS5D01G541000	chr1B	84.000	150	21	2	3043	3189	142518866	142518717	1.230000e-29	141

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	TraesCS5D01G541000	chr5D	552031267	552034542	3275	True	6050.00	6050	100.00000	1	3276	1	chr5D.!!$R3	3275
1	TraesCS5D01G541000	chr5D	551987049	551989513	2464	True	3147.00	3147	89.74400	564	3042	1	chr5D.!!$R2	2478
2	TraesCS5D01G541000	chr5D	543507624	543508795	1171	True	316.00	316	72.41700	820	1976	1	chr5D.!!$R1	1156
3	TraesCS5D01G541000	chr4A	616210322	616213184	2862	True	4494.00	4494	95.04500	422	3276	1	chr4A.!!$R2	2854
4	TraesCS5D01G541000	chr4A	616297061	616299905	2844	False	4322.00	4322	94.06200	422	3276	1	chr4A.!!$F3	2854
5	TraesCS5D01G541000	chr4A	616228204	616230056	1852	True	2922.00	2922	95.20200	1311	3156	1	chr4A.!!$R3	1845
6	TraesCS5D01G541000	chr4A	616315011	616316710	1699	False	1929.00	1929	87.30400	564	2266	1	chr4A.!!$F4	1702
7	TraesCS5D01G541000	chr5B	699949528	699952131	2603	False	2047.00	3938	92.94650	422	2988	2	chr5B.!!$F3	2566
8	TraesCS5D01G541000	chr5B	700227323	700229903	2580	True	806.25	2032	89.59825	532	3265	4	chr5B.!!$R1	2733
9	TraesCS5D01G541000	chr5B	703529332	703530524	1192	False	355.00	355	72.71200	790	1967	1	chr5B.!!$F2	1177
10	TraesCS5D01G541000	chr1D	457779293	457780140	847	False	702.00	702	81.88200	609	1456	1	chr1D.!!$F1	847

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
392	393	0.034896	AACAACCCCTAGTGTCAGCG	59.965	55.0	0.0	0.0	0.00	5.18	F
397	398	0.108615	CCCCTAGTGTCAGCGTTCTG	60.109	60.0	0.0	0.0	41.67	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2140	2334	3.375699	AGGTGTAACATTCGAGGATCCT	58.624	45.455	16.13	16.13	39.98	3.24	R
2313	2507	6.456181	GCTGATTATCTTTCTTGTTGACGAGG	60.456	42.308	0.00	0.00	0.00	4.63	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	4.876701	GCTGCCGACCCATATGAA	57.123	55.556	3.65	0.00	0.00	2.57
18	19	3.094386	GCTGCCGACCCATATGAAA	57.906	52.632	3.65	0.00	0.00	2.69
19	20	1.388547	GCTGCCGACCCATATGAAAA	58.611	50.000	3.65	0.00	0.00	2.29
20	21	1.748493	GCTGCCGACCCATATGAAAAA	59.252	47.619	3.65	0.00	0.00	1.94
21	22	2.479560	GCTGCCGACCCATATGAAAAAC	60.480	50.000	3.65	0.00	0.00	2.43
22	23	2.752354	CTGCCGACCCATATGAAAAACA	59.248	45.455	3.65	0.00	0.00	2.83
23	24	2.752354	TGCCGACCCATATGAAAAACAG	59.248	45.455	3.65	0.00	0.00	3.16
24	25	2.099098	GCCGACCCATATGAAAAACAGG	59.901	50.000	3.65	0.00	0.00	4.00
25	26	2.687935	CCGACCCATATGAAAAACAGGG	59.312	50.000	3.65	0.00	37.47	4.45
26	27	2.099098	CGACCCATATGAAAAACAGGGC	59.901	50.000	3.65	0.00	35.63	5.19
27	28	2.099098	GACCCATATGAAAAACAGGGCG	59.901	50.000	3.65	0.00	35.63	6.13
28	29	1.408702	CCCATATGAAAAACAGGGCGG	59.591	52.381	3.65	0.00	0.00	6.13
29	30	2.374184	CCATATGAAAAACAGGGCGGA	58.626	47.619	3.65	0.00	0.00	5.54
30	31	2.099098	CCATATGAAAAACAGGGCGGAC	59.901	50.000	3.65	0.00	0.00	4.79
31	32	1.444836	TATGAAAAACAGGGCGGACG	58.555	50.000	0.00	0.00	0.00	4.79
32	33	1.862602	ATGAAAAACAGGGCGGACGC	61.863	55.000	8.39	8.39	41.06	5.19
88	89	2.413837	ACGAAATCTCCGTCTGTTTGG	58.586	47.619	0.00	0.00	34.97	3.28
89	90	1.732259	CGAAATCTCCGTCTGTTTGGG	59.268	52.381	0.00	0.00	0.00	4.12
90	91	2.779506	GAAATCTCCGTCTGTTTGGGT	58.220	47.619	0.00	0.00	0.00	4.51
91	92	2.474410	AATCTCCGTCTGTTTGGGTC	57.526	50.000	0.00	0.00	0.00	4.46
92	93	0.246635	ATCTCCGTCTGTTTGGGTCG	59.753	55.000	0.00	0.00	0.00	4.79
93	94	1.374252	CTCCGTCTGTTTGGGTCGG	60.374	63.158	0.00	0.00	42.12	4.79
94	95	3.047877	CCGTCTGTTTGGGTCGGC	61.048	66.667	0.00	0.00	35.01	5.54
95	96	3.047877	CGTCTGTTTGGGTCGGCC	61.048	66.667	0.00	0.00	0.00	6.13
105	106	4.324991	GGTCGGCCCGTTGGAGTT	62.325	66.667	1.63	0.00	0.00	3.01

Showing 1 to 25 of 275 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.752354	TGTTTTTCATATGGGTCGGCAG	59.248	45.455	2.13	0.00	0.00	4.85
2	3	2.752354	CTGTTTTTCATATGGGTCGGCA	59.248	45.455	2.13	0.00	0.00	5.69
6	7	2.099098	CGCCCTGTTTTTCATATGGGTC	59.901	50.000	2.13	0.00	37.09	4.46
9	10	2.099098	GTCCGCCCTGTTTTTCATATGG	59.901	50.000	2.13	0.00	0.00	2.74
10	11	2.223249	CGTCCGCCCTGTTTTTCATATG	60.223	50.000	0.00	0.00	0.00	1.78
11	12	2.014128	CGTCCGCCCTGTTTTTCATAT	58.986	47.619	0.00	0.00	0.00	1.78
12	13	1.444836	CGTCCGCCCTGTTTTTCATA	58.555	50.000	0.00	0.00	0.00	2.15
13	14	1.862602	GCGTCCGCCCTGTTTTTCAT	61.863	55.000	0.00	0.00	34.56	2.57
14	15	2.548295	GCGTCCGCCCTGTTTTTCA	61.548	57.895	0.00	0.00	34.56	2.69
15	16	2.254350	GCGTCCGCCCTGTTTTTC	59.746	61.111	0.00	0.00	34.56	2.29
42	43	4.629523	TGTCCGTTTGGGTCGGCC	62.630	66.667	0.00	0.00	46.49	6.13
43	44	1.726533	TTTTGTCCGTTTGGGTCGGC	61.727	55.000	0.00	0.00	46.49	5.54
68	69	2.413837	CCAAACAGACGGAGATTTCGT	58.586	47.619	0.00	0.00	44.03	3.85
69	70	1.732259	CCCAAACAGACGGAGATTTCG	59.268	52.381	0.00	0.00	0.00	3.46
70	71	2.742589	GACCCAAACAGACGGAGATTTC	59.257	50.000	0.00	0.00	0.00	2.17
71	72	2.779506	GACCCAAACAGACGGAGATTT	58.220	47.619	0.00	0.00	0.00	2.17
72	73	1.337823	CGACCCAAACAGACGGAGATT	60.338	52.381	0.00	0.00	0.00	2.40
73	74	0.246635	CGACCCAAACAGACGGAGAT	59.753	55.000	0.00	0.00	0.00	2.75
74	75	1.663739	CGACCCAAACAGACGGAGA	59.336	57.895	0.00	0.00	0.00	3.71
75	76	1.374252	CCGACCCAAACAGACGGAG	60.374	63.158	0.00	0.00	45.31	4.63
76	77	2.738480	CCGACCCAAACAGACGGA	59.262	61.111	0.00	0.00	45.31	4.69
77	78	3.047877	GCCGACCCAAACAGACGG	61.048	66.667	0.00	0.00	45.26	4.79
78	79	3.047877	GGCCGACCCAAACAGACG	61.048	66.667	0.00	0.00	0.00	4.18
88	89	4.324991	AACTCCAACGGGCCGACC	62.325	66.667	35.78	0.00	0.00	4.79
89	90	3.047877	CAACTCCAACGGGCCGAC	61.048	66.667	35.78	0.00	0.00	4.79

Showing 1 to 25 of 268 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.