AutoCloner

Multiple sequence alignment - TraesCS4D01G038900

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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	TraesCS4D01G038900	chr4D	100.000	7773	0	0	1	7773	16662524	16654752	0.000000e+00	14355.0
1	TraesCS4D01G038900	chr4D	85.638	188	16	4	130	316	236269520	236269343	3.700000e-43	187.0
2	TraesCS4D01G038900	chr4A	90.376	2525	124	45	332	2813	583899180	583901628	0.000000e+00	3206.0
3	TraesCS4D01G038900	chr4A	89.630	1350	76	31	4963	6289	583903352	583904660	0.000000e+00	1659.0
4	TraesCS4D01G038900	chr4A	88.748	1022	77	17	6474	7481	583904814	583905811	0.000000e+00	1216.0
5	TraesCS4D01G038900	chr4A	85.637	926	72	21	4029	4922	583902459	583903355	0.000000e+00	917.0
6	TraesCS4D01G038900	chr4A	95.853	434	15	3	3242	3675	583902048	583902478	0.000000e+00	699.0
7	TraesCS4D01G038900	chr4A	95.467	375	16	1	3656	4029	450790066	450790440	1.440000e-166	597.0
8	TraesCS4D01G038900	chr4A	95.610	205	8	1	3005	3208	583901777	583901981	2.090000e-85	327.0
9	TraesCS4D01G038900	chr4A	93.119	218	15	0	16	233	583898065	583898282	3.500000e-83	320.0
10	TraesCS4D01G038900	chr4B	91.663	2135	103	42	5211	7319	28623030	28620945	0.000000e+00	2887.0
11	TraesCS4D01G038900	chr4B	91.220	2073	83	38	496	2536	28627510	28625505	0.000000e+00	2728.0
12	TraesCS4D01G038900	chr4B	88.966	1015	68	14	4029	5029	28624016	28623032	0.000000e+00	1214.0
13	TraesCS4D01G038900	chr4B	94.017	468	13	8	3212	3673	28624457	28623999	0.000000e+00	695.0
14	TraesCS4D01G038900	chr4B	96.206	369	13	1	3672	4039	609476405	609476037	3.100000e-168	603.0
15	TraesCS4D01G038900	chr4B	86.640	494	37	22	2524	2993	28625490	28625002	3.210000e-143	520.0
16	TraesCS4D01G038900	chr4B	88.298	282	24	5	7373	7651	28620596	28620321	5.810000e-86	329.0
17	TraesCS4D01G038900	chr4B	93.069	202	11	1	3005	3206	28624700	28624502	7.630000e-75	292.0
18	TraesCS4D01G038900	chr4B	84.615	234	16	6	16	229	28627963	28627730	1.700000e-51	215.0
19	TraesCS4D01G038900	chr6D	84.194	930	111	25	6393	7319	414559470	414560366	0.000000e+00	870.0
20	TraesCS4D01G038900	chr6D	90.785	586	33	11	4029	4608	414705391	414704821	0.000000e+00	763.0
21	TraesCS4D01G038900	chr6D	92.443	397	25	4	3280	3675	414705764	414705372	5.270000e-156	562.0
22	TraesCS4D01G038900	chr6D	87.984	491	32	6	3210	3675	414746172	414745684	8.810000e-154	555.0
23	TraesCS4D01G038900	chr6D	86.200	500	41	8	5471	5955	414558248	414558734	4.160000e-142	516.0
24	TraesCS4D01G038900	chr6D	90.588	340	28	4	3337	3675	414557782	414558118	1.540000e-121	448.0
25	TraesCS4D01G038900	chr6D	83.497	509	52	16	5474	5953	414745553	414745048	5.530000e-121	446.0
26	TraesCS4D01G038900	chr6D	93.793	145	8	1	3210	3353	414557626	414557770	4.720000e-52	217.0
27	TraesCS4D01G038900	chr6D	91.339	127	11	0	3072	3198	414746345	414746219	2.880000e-39	174.0
28	TraesCS4D01G038900	chr6D	91.270	126	11	0	3073	3198	414557454	414557579	1.040000e-38	172.0
29	TraesCS4D01G038900	chr6D	79.911	224	32	7	7334	7554	414560417	414560630	1.350000e-32	152.0
30	TraesCS4D01G038900	chr6D	85.950	121	12	4	6163	6281	414706537	414706420	2.940000e-24	124.0
31	TraesCS4D01G038900	chr6D	100.000	31	0	0	4029	4059	414745703	414745673	3.030000e-04	58.4
32	TraesCS4D01G038900	chr6D	100.000	30	0	0	5702	5731	414745394	414745365	1.000000e-03	56.5
33	TraesCS4D01G038900	chr7A	98.300	353	5	1	3678	4029	465760863	465761215	1.110000e-172	617.0
34	TraesCS4D01G038900	chr5B	97.772	359	7	1	3672	4029	222365789	222365431	1.110000e-172	617.0
35	TraesCS4D01G038900	chr3B	97.772	359	7	1	3672	4029	39816300	39815942	1.110000e-172	617.0
36	TraesCS4D01G038900	chr3B	96.216	370	11	3	3672	4038	22779783	22780152	3.100000e-168	603.0
37	TraesCS4D01G038900	chr2B	96.486	370	11	2	3672	4039	636550231	636549862	1.850000e-170	610.0
38	TraesCS4D01G038900	chr1B	97.230	361	7	2	3670	4029	478710510	478710868	6.670000e-170	608.0
39	TraesCS4D01G038900	chr6B	95.745	376	10	4	3673	4047	15713000	15713370	1.120000e-167	601.0

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	TraesCS4D01G038900	chr4D	16654752	16662524	7772	True	14355.000000	14355	100.000000	1	7773	1	chr4D.!!$R1	7772
1	TraesCS4D01G038900	chr4A	583898065	583905811	7746	False	1192.000000	3206	91.281857	16	7481	7	chr4A.!!$F2	7465
2	TraesCS4D01G038900	chr4B	28620321	28627963	7642	True	1110.000000	2887	89.811000	16	7651	8	chr4B.!!$R2	7635
3	TraesCS4D01G038900	chr6D	414704821	414706537	1716	True	483.000000	763	89.726000	3280	6281	3	chr6D.!!$R1	3001
4	TraesCS4D01G038900	chr6D	414557454	414560630	3176	False	395.833333	870	87.659333	3073	7554	6	chr6D.!!$F1	4481
5	TraesCS4D01G038900	chr6D	414745048	414746345	1297	True	257.980000	555	92.564000	3072	5953	5	chr6D.!!$R2	2881

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
731	1630	0.321653	CTTCCCCAAAGAGACCACGG	60.322	60.000	0.00	37.12	4.94	F
2451	3395	0.664166	GTCCAAACAGCCGCATTGTG	60.664	55.000	0.00	0.00	3.33	F
2842	3840	0.036765	GTCTGGATGTGTTACCGCCA	60.037	55.000	0.00	0.00	5.69	F
3764	5135	0.031111	CCCAGGAGGTCACCATCCTA	60.031	60.000	12.96	44.30	2.94	F
3845	5216	0.034089	GCCAAGCCTATCACAACCCT	60.034	55.000	0.00	0.00	4.34	F
3975	5346	0.034089	GCCAAGCCTATCACAACCCT	60.034	55.000	0.00	0.00	4.34	F
5043	6452	0.039911	AAGGCGAGTACCAGAGGAGT	59.960	55.000	0.00	0.00	3.85	F
5131	6545	0.404040	CTTCCCCCTTGGCTACAACA	59.596	55.000	0.00	32.14	3.33	F
5214	6634	1.064758	ACAGCAACCACACCTTCAAGA	60.065	47.619	0.00	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2466	3410	0.254747	GTGGTGCTGCCCCTGTTATA	59.745	55.000	2.15	36.04	0.98	R
3745	5116	0.031111	TAGGATGGTGACCTCCTGGG	60.031	60.000	24.07	41.96	4.45	R
3826	5197	0.034089	AGGGTTGTGATAGGCTTGGC	60.034	55.000	0.00	0.00	4.52	R
5043	6452	0.177141	GTGAGCAGGCCGTATTACCA	59.823	55.000	0.00	0.00	3.25	R
5046	6455	0.464036	CAGGTGAGCAGGCCGTATTA	59.536	55.000	0.00	0.00	0.98	R
5560	6987	1.246737	GGCTCACCTCCTTTGCCAAG	61.247	60.000	0.00	42.79	3.61	R
6201	7981	0.037590	TGGACAGTTCCCAAATCCCG	59.962	55.000	0.00	42.01	5.14	R
6595	8469	0.407918	TGGGAATGGGAGGTTGTTCC	59.592	55.000	0.00	39.47	3.62	R
6978	8857	2.438392	CTCCTAAAGTATGGTCCCCCAC	59.562	54.545	0.00	45.65	4.61	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
70	71	4.824166	CGTAGACACGGCCGGACG	62.824	72.222	32.33	32.33	44.59	4.79
96	98	4.817517	CCGGAGAAAGTTAGTAAAGCTCA	58.182	43.478	0.00	0.00	0.00	4.26
108	110	0.901124	AAAGCTCAGCCGATCTGTCT	59.099	50.000	0.00	2.12	43.32	3.41
158	179	2.595750	TCAAACCAATCCACCCGAAT	57.404	45.000	0.00	0.00	0.00	3.34
183	204	3.120408	CGCAACATTCTTCTTCCAGACAG	60.120	47.826	0.00	0.00	0.00	3.51
185	206	4.516698	GCAACATTCTTCTTCCAGACAGAA	59.483	41.667	0.00	0.00	31.26	3.02
236	257	3.165058	TCAACATTTCCGATCGAGGAG	57.835	47.619	18.66	4.87	41.98	3.69
238	259	2.586258	ACATTTCCGATCGAGGAGTG	57.414	50.000	18.66	10.86	41.98	3.51
243	264	2.473760	CCGATCGAGGAGTGCTCGT	61.474	63.158	29.65	18.78	43.87	4.18
244	265	1.010574	CGATCGAGGAGTGCTCGTC	60.011	63.158	29.65	23.69	43.87	4.20
245	266	1.706287	CGATCGAGGAGTGCTCGTCA	61.706	60.000	29.65	15.07	42.71	4.35
246	267	0.452184	GATCGAGGAGTGCTCGTCAA	59.548	55.000	29.65	14.36	42.71	3.18
247	268	0.453793	ATCGAGGAGTGCTCGTCAAG	59.546	55.000	29.65	5.61	42.71	3.02
248	269	0.889638	TCGAGGAGTGCTCGTCAAGT	60.890	55.000	29.65	0.00	42.71	3.16
251	272	2.085320	GAGGAGTGCTCGTCAAGTAGA	58.915	52.381	14.67	0.00	42.29	2.59
254	275	2.229302	GGAGTGCTCGTCAAGTAGAAGT	59.771	50.000	0.00	0.00	0.00	3.01
256	277	4.437659	GGAGTGCTCGTCAAGTAGAAGTAG	60.438	50.000	0.00	0.00	0.00	2.57
257	278	4.073549	AGTGCTCGTCAAGTAGAAGTAGT	58.926	43.478	0.00	0.00	0.00	2.73
259	280	4.617645	GTGCTCGTCAAGTAGAAGTAGTTG	59.382	45.833	0.00	0.00	39.92	3.16
261	282	4.852650	GCTCGTCAAGTAGAAGTAGTTGTC	59.147	45.833	0.00	0.00	39.65	3.18
262	283	5.562307	GCTCGTCAAGTAGAAGTAGTTGTCA	60.562	44.000	0.00	0.00	39.65	3.58
263	284	6.381481	TCGTCAAGTAGAAGTAGTTGTCAA	57.619	37.500	0.00	0.00	39.65	3.18
265	286	6.261603	TCGTCAAGTAGAAGTAGTTGTCAAGA	59.738	38.462	0.00	0.00	39.65	3.02
266	287	6.360148	CGTCAAGTAGAAGTAGTTGTCAAGAC	59.640	42.308	0.00	0.00	39.65	3.01
267	288	7.427214	GTCAAGTAGAAGTAGTTGTCAAGACT	58.573	38.462	1.53	0.00	39.65	3.24

Showing 1 to 25 of 553 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	1.374252	CGACCCGTGGAAGTGGAAG	60.374	63.158	0.00	0.00	3.46
1	2	2.738480	CGACCCGTGGAAGTGGAA	59.262	61.111	0.00	0.00	3.53
2	3	3.998672	GCGACCCGTGGAAGTGGA	61.999	66.667	0.00	0.00	4.02
70	71	0.174162	TACTAACTTTCTCCGGCGGC	59.826	55.000	23.83	0.00	6.53
96	98	2.492090	GCGTGAGACAGATCGGCT	59.508	61.111	0.00	0.00	5.52
158	179	0.881118	GGAAGAAGAATGTTGCGCCA	59.119	50.000	4.18	0.00	5.69
173	194	6.314896	GGTGTGAGATTATTTCTGTCTGGAAG	59.685	42.308	0.00	33.74	3.46
183	204	5.642063	TGGAGAAACGGTGTGAGATTATTTC	59.358	40.000	0.00	0.00	2.17
185	206	5.160607	TGGAGAAACGGTGTGAGATTATT	57.839	39.130	0.00	0.00	1.40
236	257	4.422546	ACTACTTCTACTTGACGAGCAC	57.577	45.455	0.00	0.00	4.40
238	259	4.796369	ACAACTACTTCTACTTGACGAGC	58.204	43.478	0.00	0.00	5.03
243	264	7.284716	TCAGTCTTGACAACTACTTCTACTTGA	59.715	37.037	3.49	0.00	3.02
244	265	7.426410	TCAGTCTTGACAACTACTTCTACTTG	58.574	38.462	3.49	0.00	3.16
245	266	7.502895	TCTCAGTCTTGACAACTACTTCTACTT	59.497	37.037	3.49	0.00	2.24
246	267	6.999272	TCTCAGTCTTGACAACTACTTCTACT	59.001	38.462	3.49	0.00	2.57
247	268	7.040961	AGTCTCAGTCTTGACAACTACTTCTAC	60.041	40.741	3.49	35.81	2.59
248	269	6.999272	AGTCTCAGTCTTGACAACTACTTCTA	59.001	38.462	3.49	35.81	2.10
251	272	5.361285	ACAGTCTCAGTCTTGACAACTACTT	59.639	40.000	3.49	35.81	2.24
254	275	6.954487	TTACAGTCTCAGTCTTGACAACTA	57.046	37.500	3.49	35.81	2.24
256	277	6.510317	GCTTTTACAGTCTCAGTCTTGACAAC	60.510	42.308	3.49	35.81	3.32
257	278	5.523916	GCTTTTACAGTCTCAGTCTTGACAA	59.476	40.000	3.49	35.81	3.18
259	280	5.050490	TGCTTTTACAGTCTCAGTCTTGAC	58.950	41.667	0.00	0.00	3.18
261	282	4.084118	GCTGCTTTTACAGTCTCAGTCTTG	60.084	45.833	0.00	39.96	3.02
262	283	4.061596	GCTGCTTTTACAGTCTCAGTCTT	58.938	43.478	0.00	39.96	3.01
263	284	3.070159	TGCTGCTTTTACAGTCTCAGTCT	59.930	43.478	0.00	39.96	3.24

Showing 1 to 25 of 559 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.