AutoCloner

Multiple sequence alignment - TraesCS5D01G533900

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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	TraesCS5D01G533900	chr5D	100.000	4283	0	0	1	4283	548276744	548281026	0.000000e+00	7910
1	TraesCS5D01G533900	chr6B	87.684	2038	237	12	1527	3562	164043328	164045353	0.000000e+00	2361
2	TraesCS5D01G533900	chr6B	75.817	3395	743	69	200	3552	50337650	50341008	0.000000e+00	1650
3	TraesCS5D01G533900	chr6B	74.914	3476	778	77	117	3550	583293299	583296722	0.000000e+00	1502
4	TraesCS5D01G533900	chr4B	75.638	3604	775	85	1	3552	448807312	448810864	0.000000e+00	1696
5	TraesCS5D01G533900	chr4D	96.266	723	25	2	3558	4280	47308922	47309642	0.000000e+00	1184
6	TraesCS5D01G533900	chr4D	94.562	662	36	0	2901	3562	47308204	47308865	0.000000e+00	1024
7	TraesCS5D01G533900	chr1A	75.226	2430	536	53	206	2600	6302776	6305174	0.000000e+00	1092
8	TraesCS5D01G533900	chr7A	76.972	1559	335	19	2004	3552	644731919	644730375	0.000000e+00	869
9	TraesCS5D01G533900	chr7A	74.862	724	177	5	3558	4280	404499484	404500203	1.490000e-84	324
10	TraesCS5D01G533900	chr7A	78.281	221	36	10	1917	2131	50594198	50593984	9.660000e-27	132
11	TraesCS5D01G533900	chr5B	74.146	1756	409	40	1817	3552	257907742	257906012	0.000000e+00	686
12	TraesCS5D01G533900	chr5B	76.236	728	159	12	3561	4282	309671359	309672078	1.450000e-99	374
13	TraesCS5D01G533900	chr5B	76.264	712	153	15	3580	4283	642843261	642842558	8.750000e-97	364
14	TraesCS5D01G533900	chr1B	73.923	1764	417	38	1808	3552	279518029	279519768	0.000000e+00	669
15	TraesCS5D01G533900	chr7B	74.568	1506	353	26	2059	3552	739555809	739557296	2.170000e-177	632
16	TraesCS5D01G533900	chr4A	73.879	1673	398	34	1898	3552	565427288	565425637	2.170000e-177	632
17	TraesCS5D01G533900	chr4A	74.776	559	118	19	3679	4226	47734546	47734000	3.330000e-56	230
18	TraesCS5D01G533900	chr4A	73.703	559	124	19	3679	4226	563448312	563448858	3.380000e-46	196
19	TraesCS5D01G533900	chr7D	72.105	1373	327	47	1384	2726	113763128	113764474	3.150000e-96	363
20	TraesCS5D01G533900	chr3A	75.207	726	178	2	3558	4283	727541875	727541152	4.100000e-90	342
21	TraesCS5D01G533900	chr3A	72.291	729	167	19	3559	4278	724218305	724217603	1.220000e-45	195
22	TraesCS5D01G533900	chr2A	72.018	1308	311	47	2059	3340	492822397	492823675	1.910000e-88	337
23	TraesCS5D01G533900	chr2A	75.397	630	138	16	3646	4267	767395065	767395685	5.420000e-74	289
24	TraesCS5D01G533900	chr5A	74.240	559	121	19	3679	4226	569312894	569313440	3.350000e-51	213

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	TraesCS5D01G533900	chr5D	548276744	548281026	4282	False	7910	7910	100.000	1	4283	1	chr5D.!!$F1	4282
1	TraesCS5D01G533900	chr6B	164043328	164045353	2025	False	2361	2361	87.684	1527	3562	1	chr6B.!!$F2	2035
2	TraesCS5D01G533900	chr6B	50337650	50341008	3358	False	1650	1650	75.817	200	3552	1	chr6B.!!$F1	3352
3	TraesCS5D01G533900	chr6B	583293299	583296722	3423	False	1502	1502	74.914	117	3550	1	chr6B.!!$F3	3433
4	TraesCS5D01G533900	chr4B	448807312	448810864	3552	False	1696	1696	75.638	1	3552	1	chr4B.!!$F1	3551
5	TraesCS5D01G533900	chr4D	47308204	47309642	1438	False	1104	1184	95.414	2901	4280	2	chr4D.!!$F1	1379
6	TraesCS5D01G533900	chr1A	6302776	6305174	2398	False	1092	1092	75.226	206	2600	1	chr1A.!!$F1	2394
7	TraesCS5D01G533900	chr7A	644730375	644731919	1544	True	869	869	76.972	2004	3552	1	chr7A.!!$R2	1548
8	TraesCS5D01G533900	chr7A	404499484	404500203	719	False	324	324	74.862	3558	4280	1	chr7A.!!$F1	722
9	TraesCS5D01G533900	chr5B	257906012	257907742	1730	True	686	686	74.146	1817	3552	1	chr5B.!!$R1	1735
10	TraesCS5D01G533900	chr5B	309671359	309672078	719	False	374	374	76.236	3561	4282	1	chr5B.!!$F1	721
11	TraesCS5D01G533900	chr5B	642842558	642843261	703	True	364	364	76.264	3580	4283	1	chr5B.!!$R2	703
12	TraesCS5D01G533900	chr1B	279518029	279519768	1739	False	669	669	73.923	1808	3552	1	chr1B.!!$F1	1744
13	TraesCS5D01G533900	chr7B	739555809	739557296	1487	False	632	632	74.568	2059	3552	1	chr7B.!!$F1	1493
14	TraesCS5D01G533900	chr4A	565425637	565427288	1651	True	632	632	73.879	1898	3552	1	chr4A.!!$R2	1654
15	TraesCS5D01G533900	chr4A	47734000	47734546	546	True	230	230	74.776	3679	4226	1	chr4A.!!$R1	547
16	TraesCS5D01G533900	chr7D	113763128	113764474	1346	False	363	363	72.105	1384	2726	1	chr7D.!!$F1	1342
17	TraesCS5D01G533900	chr3A	727541152	727541875	723	True	342	342	75.207	3558	4283	1	chr3A.!!$R2	725
18	TraesCS5D01G533900	chr2A	492822397	492823675	1278	False	337	337	72.018	2059	3340	1	chr2A.!!$F1	1281
19	TraesCS5D01G533900	chr2A	767395065	767395685	620	False	289	289	75.397	3646	4267	1	chr2A.!!$F2	621
20	TraesCS5D01G533900	chr5A	569312894	569313440	546	False	213	213	74.240	3679	4226	1	chr5A.!!$F1	547

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	Hairpin	End Stability	Orientation
402	403	0.037303	CATGGGAGTGTGTTCCTGCT	59.963	55.0	0.00	37.40	4.24	F
825	827	0.039035	GTGGCCTGGTTGGGATTACA	59.961	55.0	3.32	36.00	2.41	F
1151	1162	0.179161	CGTCTACTGCCAACCGAGAG	60.179	60.0	0.00	0.00	3.20	F
1251	1262	0.252467	AGGAAGAGGACACCCAGGAG	60.252	60.0	0.00	33.88	3.69	F
1285	1296	0.475906	AGTGCCTCTGAAGCCAGTTT	59.524	50.0	0.00	41.16	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2265	2288	0.034477	CCCCACACAGAATACCACCC	60.034	60.000	0.00	0.00	4.61	R
2754	2780	0.830648	CCTCATCACCCGAGGCTAAA	59.169	55.000	0.00	43.50	1.85	R
2791	2817	3.146847	GGTCAAACCGAAATTCTCTGGT	58.853	45.455	0.00	33.92	4.00	R
2989	3015	9.593134	CTCTTCTAGCATGTATAATTCCATACC	57.407	37.037	0.00	31.52	2.73	R
3282	3308	2.206576	CTGGGCCAACTAGCTCTTTT	57.793	50.000	8.04	33.00	2.27	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
21	22	2.434359	GGCGACTCCGGGTTTGAG	60.434	66.667	0.00	0.00	36.06	3.02
23	24	1.218316	GCGACTCCGGGTTTGAGAT	59.782	57.895	0.00	0.00	36.06	2.75
30	31	2.639839	CTCCGGGTTTGAGATATGGGAT	59.360	50.000	0.00	0.00	31.26	3.85
33	34	3.557898	CCGGGTTTGAGATATGGGATGAG	60.558	52.174	0.00	0.00	0.00	2.90
45	46	3.928779	GATGAGGCGGCCGATGGA	61.929	66.667	33.48	9.91	0.00	3.41
47	48	2.738213	GATGAGGCGGCCGATGGAAT	62.738	60.000	33.48	15.06	0.00	3.01
51	52	3.957535	GCGGCCGATGGAATGCAG	61.958	66.667	33.48	0.00	0.00	4.41
52	53	3.282157	CGGCCGATGGAATGCAGG	61.282	66.667	24.07	0.00	0.00	4.85
53	54	3.599704	GGCCGATGGAATGCAGGC	61.600	66.667	2.37	2.37	46.51	4.85
54	55	2.517875	GCCGATGGAATGCAGGCT	60.518	61.111	3.76	0.00	44.06	4.58
56	57	2.719979	CGATGGAATGCAGGCTGC	59.280	61.111	31.91	31.91	45.29	5.25
57	58	1.822613	CGATGGAATGCAGGCTGCT	60.823	57.895	36.50	20.70	45.31	4.24
61	62	1.273986	TGGAATGCAGGCTGCTCCTA	61.274	55.000	34.23	23.37	45.52	2.94
71	72	1.261238	GCTGCTCCTACTCACCAGGT	61.261	60.000	0.00	0.00	34.56	4.00
73	74	1.219393	GCTCCTACTCACCAGGTGC	59.781	63.158	15.64	0.00	43.25	5.01
119	120	2.507452	CCATCCGCATGAGCCTGA	59.493	61.111	0.00	0.00	37.52	3.86
127	128	0.593618	GCATGAGCCTGATGATGCAG	59.406	55.000	1.97	0.00	40.78	4.41
137	138	1.450531	GATGATGCAGGGGGAAAGCG	61.451	60.000	0.00	0.00	0.00	4.68
138	139	1.925285	ATGATGCAGGGGGAAAGCGA	61.925	55.000	0.00	0.00	0.00	4.93
141	142	4.722700	GCAGGGGGAAAGCGAGCA	62.723	66.667	0.00	0.00	0.00	4.26
159	160	2.202676	GCTCCGCCTCGACAAGAG	60.203	66.667	0.00	0.00	46.44	2.85
160	161	2.995872	GCTCCGCCTCGACAAGAGT	61.996	63.158	0.00	0.00	45.44	3.24
162	163	1.867919	CTCCGCCTCGACAAGAGTGT	61.868	60.000	0.00	0.00	45.44	3.55
173	174	0.673985	CAAGAGTGTCGTGGTGGAGA	59.326	55.000	0.00	0.00	0.00	3.71
174	175	0.674534	AAGAGTGTCGTGGTGGAGAC	59.325	55.000	0.00	0.00	37.85	3.36

Showing 1 to 25 of 225 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.545952	CCATATCTCAAACCCGGAGTCG	60.546	54.545	0.73	0.00	34.04	4.18
9	10	2.047061	TCCCATATCTCAAACCCGGAG	58.953	52.381	0.73	0.00	0.00	4.63
15	16	3.070018	CGCCTCATCCCATATCTCAAAC	58.930	50.000	0.00	0.00	0.00	2.93
21	22	1.078143	GGCCGCCTCATCCCATATC	60.078	63.158	0.71	0.00	0.00	1.63
23	24	3.625897	CGGCCGCCTCATCCCATA	61.626	66.667	14.67	0.00	0.00	2.74
30	31	3.479203	ATTCCATCGGCCGCCTCA	61.479	61.111	23.51	2.57	0.00	3.86
51	52	1.519719	CTGGTGAGTAGGAGCAGCC	59.480	63.158	0.00	0.00	32.56	4.85
52	53	1.261238	ACCTGGTGAGTAGGAGCAGC	61.261	60.000	0.00	0.00	37.57	5.25
53	54	0.534412	CACCTGGTGAGTAGGAGCAG	59.466	60.000	22.33	0.00	38.71	4.24
54	55	1.544825	GCACCTGGTGAGTAGGAGCA	61.545	60.000	30.23	0.00	46.84	4.26
56	57	0.534412	CTGCACCTGGTGAGTAGGAG	59.466	60.000	30.23	9.56	38.71	3.69
57	58	0.178932	ACTGCACCTGGTGAGTAGGA	60.179	55.000	30.23	2.92	38.71	2.94
60	61	1.480212	CCCACTGCACCTGGTGAGTA	61.480	60.000	30.23	13.87	35.23	2.59
61	62	2.822637	CCCACTGCACCTGGTGAGT	61.823	63.158	30.23	23.90	35.23	3.41
101	102	2.407440	ATCAGGCTCATGCGGATGGG	62.407	60.000	17.41	15.39	40.82	4.00
103	104	0.250166	TCATCAGGCTCATGCGGATG	60.250	55.000	11.15	11.15	45.11	3.51
104	105	0.691332	ATCATCAGGCTCATGCGGAT	59.309	50.000	0.00	0.00	40.82	4.18
106	107	1.853114	GCATCATCAGGCTCATGCGG	61.853	60.000	0.00	0.00	40.82	5.69
108	109	0.593618	CTGCATCATCAGGCTCATGC	59.406	55.000	0.00	2.08	41.75	4.06
109	110	1.239347	CCTGCATCATCAGGCTCATG	58.761	55.000	0.00	0.00	46.11	3.07
110	111	3.727738	CCTGCATCATCAGGCTCAT	57.272	52.632	0.00	0.00	46.11	2.90
119	120	1.454479	CGCTTTCCCCCTGCATCAT	60.454	57.895	0.00	0.00	0.00	2.45
153	154	0.389391	CTCCACCACGACACTCTTGT	59.611	55.000	0.00	0.00	39.32	3.16
159	160	2.049433	CCGTCTCCACCACGACAC	60.049	66.667	0.00	0.00	39.75	3.67
160	161	3.986006	GCCGTCTCCACCACGACA	61.986	66.667	0.00	0.00	39.75	4.35

Showing 1 to 25 of 235 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.