AutoCloner

Multiple sequence alignment - TraesCS5D01G169900

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	TraesCS5D01G169900	chr5D	100.000	2621	0	0	1	2621	266327007	266324387	0.000000e+00	4841.0
1	TraesCS5D01G169900	chr5D	94.531	640	33	1	1210	1847	266086036	266086675	0.000000e+00	987.0
2	TraesCS5D01G169900	chr5D	92.322	521	15	6	716	1214	266085494	266086011	0.000000e+00	717.0
3	TraesCS5D01G169900	chr5D	85.053	281	24	11	514	780	266085220	266085496	1.200000e-68	270.0
4	TraesCS5D01G169900	chr5D	81.940	299	45	6	25	317	14562355	14562650	7.250000e-61	244.0
5	TraesCS5D01G169900	chr5B	95.188	1413	60	6	1210	2620	300097935	300096529	0.000000e+00	2226.0
6	TraesCS5D01G169900	chr5B	87.531	1227	81	30	25	1214	300099151	300097960	0.000000e+00	1352.0
7	TraesCS5D01G169900	chr5B	93.935	643	33	3	1210	1847	299847707	299848348	0.000000e+00	966.0
8	TraesCS5D01G169900	chr5B	93.416	562	14	6	675	1214	299847122	299847682	0.000000e+00	811.0
9	TraesCS5D01G169900	chr5B	82.474	291	47	3	25	314	563712128	563711841	4.330000e-63	252.0
10	TraesCS5D01G169900	chr5B	95.833	48	2	0	582	629	299847002	299847049	7.780000e-11	78.7
11	TraesCS5D01G169900	chr5B	100.000	30	0	0	643	672	299847036	299847065	3.640000e-04	56.5
12	TraesCS5D01G169900	chr5A	92.179	1432	85	20	1210	2620	353988821	353990246	0.000000e+00	1999.0
13	TraesCS5D01G169900	chr5A	91.624	1170	43	14	736	1850	354315816	354314647	0.000000e+00	1567.0
14	TraesCS5D01G169900	chr5A	92.402	895	31	12	352	1214	353987819	353988708	0.000000e+00	1242.0
15	TraesCS5D01G169900	chr5A	86.222	225	18	8	527	739	354316252	354316029	5.640000e-57	231.0
16	TraesCS5D01G169900	chr2A	86.223	646	57	20	999	1623	30021457	30020823	0.000000e+00	671.0
17	TraesCS5D01G169900	chr2A	93.282	387	24	2	1238	1623	30072292	30071907	1.050000e-158	569.0
18	TraesCS5D01G169900	chr2A	92.746	386	26	2	1238	1622	30079875	30079491	8.190000e-155	556.0
19	TraesCS5D01G169900	chr2A	88.889	153	17	0	998	1150	30127269	30127117	3.440000e-44	189.0
20	TraesCS5D01G169900	chr2A	87.582	153	19	0	998	1150	30086811	30086659	7.450000e-41	178.0
21	TraesCS5D01G169900	chr2D	92.746	386	26	2	1238	1622	27888285	27887901	8.190000e-155	556.0
22	TraesCS5D01G169900	chr7B	83.882	304	44	5	31	330	633915663	633915361	4.270000e-73	285.0
23	TraesCS5D01G169900	chr4D	83.067	313	50	3	25	334	439750201	439750513	5.520000e-72	281.0
24	TraesCS5D01G169900	chr7A	83.946	299	41	7	25	317	9409656	9409953	1.990000e-71	279.0
25	TraesCS5D01G169900	chr7A	83.056	301	42	8	25	317	68780964	68781263	5.560000e-67	265.0
26	TraesCS5D01G169900	chr3B	83.442	308	42	6	25	330	61647539	61647839	7.140000e-71	278.0
27	TraesCS5D01G169900	chr3A	82.258	310	49	6	25	329	50001169	50001477	2.000000e-66	263.0
28	TraesCS5D01G169900	chr3A	89.524	105	8	3	1892	1996	709066666	709066767	2.120000e-26	130.0
29	TraesCS5D01G169900	chr7D	82.667	300	44	6	25	317	9373730	9374028	2.590000e-65	259.0
30	TraesCS5D01G169900	chr7D	92.632	95	6	1	1890	1984	30293648	30293555	4.550000e-28	135.0
31	TraesCS5D01G169900	chr7D	89.623	106	8	2	1886	1991	22260870	22260972	5.890000e-27	132.0
32	TraesCS5D01G169900	chr2B	88.235	153	18	0	998	1150	44361838	44361686	1.600000e-42	183.0
33	TraesCS5D01G169900	chr2B	88.889	108	8	4	1893	1998	794520180	794520285	2.120000e-26	130.0
34	TraesCS5D01G169900	chr3D	92.857	98	4	2	1892	1989	141424363	141424269	3.520000e-29	139.0
35	TraesCS5D01G169900	chr6A	93.478	92	4	2	1897	1988	362228893	362228804	4.550000e-28	135.0
36	TraesCS5D01G169900	chr6B	91.837	98	5	2	1892	1989	708941568	708941474	1.640000e-27	134.0
37	TraesCS5D01G169900	chr1D	89.423	104	9	1	1890	1993	379468011	379467910	2.120000e-26	130.0

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	TraesCS5D01G169900	chr5D	266324387	266327007	2620	True	4841.00	4841	100.000000	1	2621	1	chr5D.!!$R1	2620
1	TraesCS5D01G169900	chr5D	266085220	266086675	1455	False	658.00	987	90.635333	514	1847	3	chr5D.!!$F2	1333
2	TraesCS5D01G169900	chr5B	300096529	300099151	2622	True	1789.00	2226	91.359500	25	2620	2	chr5B.!!$R2	2595
3	TraesCS5D01G169900	chr5B	299847002	299848348	1346	False	478.05	966	95.796000	582	1847	4	chr5B.!!$F1	1265
4	TraesCS5D01G169900	chr5A	353987819	353990246	2427	False	1620.50	1999	92.290500	352	2620	2	chr5A.!!$F1	2268
5	TraesCS5D01G169900	chr5A	354314647	354316252	1605	True	899.00	1567	88.923000	527	1850	2	chr5A.!!$R1	1323
6	TraesCS5D01G169900	chr2A	30020823	30021457	634	True	671.00	671	86.223000	999	1623	1	chr2A.!!$R1	624

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
283	285	0.034059	CTTATAGGTGCGGAGGCTGG	59.966	60.0	0.0	0.0	40.82	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1755	2274	1.442769	TGCTTTCTCGAGCCATGTTC	58.557	50.0	7.81	0.0	42.01	3.18	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.777075	GAGGGGGAGAGGAGAGGA	58.223	66.667	0.00	0.00	0.00	3.71
18	19	1.541672	GAGGGGGAGAGGAGAGGAG	59.458	68.421	0.00	0.00	0.00	3.69
19	20	2.123033	GGGGGAGAGGAGAGGAGC	60.123	72.222	0.00	0.00	0.00	4.70
20	21	2.123033	GGGGAGAGGAGAGGAGCC	60.123	72.222	0.00	0.00	0.00	4.70
21	22	2.693017	GGGAGAGGAGAGGAGCCA	59.307	66.667	0.00	0.00	0.00	4.75
22	23	1.235696	GGGAGAGGAGAGGAGCCAT	59.764	63.158	0.00	0.00	0.00	4.40
23	24	0.831711	GGGAGAGGAGAGGAGCCATC	60.832	65.000	0.00	0.00	0.00	3.51
30	31	0.823356	GAGAGGAGCCATCGAGAGCT	60.823	60.000	11.46	11.46	43.55	4.09
52	53	2.505405	GGACTTCTCCAGGGTGAAAAC	58.495	52.381	4.57	2.35	36.42	2.43
53	54	2.106684	GGACTTCTCCAGGGTGAAAACT	59.893	50.000	4.57	0.00	36.42	2.66
60	61	6.200878	TCTCCAGGGTGAAAACTTAAGATT	57.799	37.500	10.09	0.00	0.00	2.40
68	69	6.806739	GGGTGAAAACTTAAGATTTTGGATCG	59.193	38.462	10.09	0.00	29.44	3.69
107	108	4.202141	TGTGCATTGTTTTCTTCTTGGAGG	60.202	41.667	0.00	0.00	0.00	4.30
136	137	8.785329	TGCTTTTGAAGACCTTTTATGTTTTT	57.215	26.923	0.00	0.00	0.00	1.94
162	163	2.158534	TGCTGTATCTGGTGGTGGTTTT	60.159	45.455	0.00	0.00	0.00	2.43
172	173	1.315981	TGGTGGTTTTTGTGCGCTGA	61.316	50.000	9.73	0.00	0.00	4.26
179	180	2.168326	TTTTGTGCGCTGATGAGAGA	57.832	45.000	9.73	0.00	0.00	3.10
189	190	3.551082	CGCTGATGAGAGAAGTTGATCAC	59.449	47.826	0.00	0.00	0.00	3.06
197	198	3.070018	GAGAAGTTGATCACTGTGGTGG	58.930	50.000	8.11	0.00	43.17	4.61
198	199	2.705658	AGAAGTTGATCACTGTGGTGGA	59.294	45.455	8.11	0.00	43.17	4.02
248	250	5.389859	TTCTTTTGGTATGTGCATTCTGG	57.610	39.130	0.00	0.00	0.00	3.86
257	259	5.822519	GGTATGTGCATTCTGGATGTCTTTA	59.177	40.000	0.00	0.00	38.07	1.85
275	277	7.396190	GTCTTTAAGACATCTTATAGGTGCG	57.604	40.000	19.00	0.00	44.45	5.34
279	281	2.894126	AGACATCTTATAGGTGCGGAGG	59.106	50.000	0.00	0.00	0.00	4.30
283	285	0.034059	CTTATAGGTGCGGAGGCTGG	59.966	60.000	0.00	0.00	40.82	4.85
300	302	4.975794	AGGCTGGGTGTAATAGGTATCTTT	59.024	41.667	0.00	0.00	0.00	2.52
302	304	6.042897	AGGCTGGGTGTAATAGGTATCTTTAC	59.957	42.308	0.00	0.00	0.00	2.01
348	350	5.437289	AAAACAAAGACAATGATCTCGCA	57.563	34.783	0.00	0.00	0.00	5.10
349	351	5.437289	AAACAAAGACAATGATCTCGCAA	57.563	34.783	0.00	0.00	0.00	4.85
350	352	5.437289	AACAAAGACAATGATCTCGCAAA	57.563	34.783	0.00	0.00	0.00	3.68
351	353	5.437289	ACAAAGACAATGATCTCGCAAAA	57.563	34.783	0.00	0.00	0.00	2.44
352	354	5.830912	ACAAAGACAATGATCTCGCAAAAA	58.169	33.333	0.00	0.00	0.00	1.94
564	584	2.458006	GAAGGAAGCCGTGTTTGCCG	62.458	60.000	0.00	0.00	0.00	5.69
847	1202	2.471815	ATCCCGACCTTATCAGGACA	57.528	50.000	0.00	0.00	44.19	4.02
903	1276	2.082231	CATCTTGGTGTTGCTCAGGAG	58.918	52.381	0.00	0.00	0.00	3.69
912	1285	3.661648	GCTCAGGAGGGGCCCAAA	61.662	66.667	27.72	3.63	37.37	3.28
939	1313	0.476338	TAAGCCTTGCTGACCCAACA	59.524	50.000	0.00	0.00	39.62	3.33
1458	1972	0.178068	GGAAGCTGCCTATGTTCGGA	59.822	55.000	2.27	0.00	0.00	4.55
1755	2274	4.867608	TGTGTATGTCCATGTTCATGTACG	59.132	41.667	11.13	0.00	0.00	3.67
1891	2414	3.606687	GAAAATATCTCCACCACCGTGT	58.393	45.455	0.00	0.00	38.41	4.49
1900	2423	3.929094	TCCACCACCGTGTTTATTACTC	58.071	45.455	0.00	0.00	38.41	2.59
1911	2434	5.289434	CGTGTTTATTACTCCCTCCGTAAAC	59.711	44.000	0.00	0.00	34.38	2.01
1928	2451	9.669353	CTCCGTAAACTAATATAAGAGCGTTTA	57.331	33.333	0.00	0.00	0.00	2.01
2011	2544	2.291209	TAGTAGTGGACGGTTGGACA	57.709	50.000	0.00	0.00	0.00	4.02
2151	2686	8.349983	CACGGTATAATTAAAGGGAAAATGAGG	58.650	37.037	0.00	0.00	0.00	3.86
2191	2726	9.684448	TTTCGTGCAAAGATGAAATTATTACAA	57.316	25.926	0.00	0.00	0.00	2.41
2262	2797	8.477419	AAAACAAGATCTATCAAAGGAAACCA	57.523	30.769	0.00	0.00	0.00	3.67
2286	2821	8.899771	CCAGTTATTCCATTTATTCGGTAAAGT	58.100	33.333	0.00	0.00	35.83	2.66
2337	2872	7.728148	TGGTTTGTATACTCTTGTTGTGTCTA	58.272	34.615	4.17	0.00	0.00	2.59
2363	2898	3.130633	GGCATTGGTTGTGGTTTTCTTC	58.869	45.455	0.00	0.00	0.00	2.87
2367	2902	5.427378	CATTGGTTGTGGTTTTCTTCCTTT	58.573	37.500	0.00	0.00	0.00	3.11
2431	2966	6.972901	GTGCTTTAATATTAACAAGCCACCTC	59.027	38.462	21.18	9.17	29.61	3.85
2450	2985	6.072286	CCACCTCGAAAACTAGTGAAGTAGTA	60.072	42.308	0.00	0.00	37.50	1.82
2496	3031	3.730215	TGCTTTTGAGGCCAGGTATTA	57.270	42.857	5.01	0.00	0.00	0.98
2506	3041	6.827727	TGAGGCCAGGTATTAGAGTTTATTC	58.172	40.000	5.01	0.00	0.00	1.75
2585	3125	2.158564	CCCAATATCTCACATGCCCACT	60.159	50.000	0.00	0.00	0.00	4.00
2601	3141	1.002087	CCACTTATCGTGCCCCTATCC	59.998	57.143	0.00	0.00	42.42	2.59
2614	3154	5.250774	GTGCCCCTATCCCATCTCTTTAATA	59.749	44.000	0.00	0.00	0.00	0.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.541672	CTCCTCTCCTCTCCCCCTC	59.458	68.421	0.00	0.00	0.00	4.30
2	3	2.123033	GCTCCTCTCCTCTCCCCC	60.123	72.222	0.00	0.00	0.00	5.40
3	4	2.123033	GGCTCCTCTCCTCTCCCC	60.123	72.222	0.00	0.00	0.00	4.81
4	5	0.831711	GATGGCTCCTCTCCTCTCCC	60.832	65.000	0.00	0.00	0.00	4.30
5	6	1.178534	CGATGGCTCCTCTCCTCTCC	61.179	65.000	0.00	0.00	0.00	3.71
6	7	0.179004	TCGATGGCTCCTCTCCTCTC	60.179	60.000	0.00	0.00	0.00	3.20
8	9	0.179004	TCTCGATGGCTCCTCTCCTC	60.179	60.000	0.00	0.00	0.00	3.71
9	10	0.178992	CTCTCGATGGCTCCTCTCCT	60.179	60.000	0.00	0.00	0.00	3.69
10	11	1.805428	GCTCTCGATGGCTCCTCTCC	61.805	65.000	3.02	0.00	0.00	3.71
11	12	0.823356	AGCTCTCGATGGCTCCTCTC	60.823	60.000	6.47	0.00	32.98	3.20
12	13	0.823356	GAGCTCTCGATGGCTCCTCT	60.823	60.000	21.63	0.00	46.32	3.69
13	14	1.659794	GAGCTCTCGATGGCTCCTC	59.340	63.158	21.63	5.50	46.32	3.71
14	15	3.854856	GAGCTCTCGATGGCTCCT	58.145	61.111	21.63	0.51	46.32	3.69
34	35	3.953542	AAGTTTTCACCCTGGAGAAGT	57.046	42.857	0.00	0.00	0.00	3.01
52	53	4.672409	GTTGCCCGATCCAAAATCTTAAG	58.328	43.478	0.00	0.00	0.00	1.85
53	54	3.127895	CGTTGCCCGATCCAAAATCTTAA	59.872	43.478	0.00	0.00	39.56	1.85
68	69	4.025401	CAAGCACCGTCGTTGCCC	62.025	66.667	11.46	0.00	0.00	5.36
96	97	0.108585	AAGCAACGCCTCCAAGAAGA	59.891	50.000	0.00	0.00	0.00	2.87
100	101	0.667993	TCAAAAGCAACGCCTCCAAG	59.332	50.000	0.00	0.00	0.00	3.61
107	108	2.492019	AAGGTCTTCAAAAGCAACGC	57.508	45.000	0.00	0.00	0.00	4.84
136	137	1.419762	ACCACCAGATACAGCACACAA	59.580	47.619	0.00	0.00	0.00	3.33
137	138	1.055849	ACCACCAGATACAGCACACA	58.944	50.000	0.00	0.00	0.00	3.72
151	152	1.880796	GCGCACAAAAACCACCACC	60.881	57.895	0.30	0.00	0.00	4.61
162	163	1.001293	ACTTCTCTCATCAGCGCACAA	59.999	47.619	11.47	0.00	0.00	3.33
172	173	4.285517	ACCACAGTGATCAACTTCTCTCAT	59.714	41.667	0.62	0.00	36.83	2.90
223	224	6.705381	CCAGAATGCACATACCAAAAGAAAAA	59.295	34.615	0.00	0.00	31.97	1.94
229	230	4.771577	ACATCCAGAATGCACATACCAAAA	59.228	37.500	0.00	0.00	39.12	2.44
236	237	6.094603	GTCTTAAAGACATCCAGAATGCACAT	59.905	38.462	0.00	0.00	44.45	3.21
257	259	3.322254	CCTCCGCACCTATAAGATGTCTT	59.678	47.826	0.45	0.45	39.85	3.01
267	269	3.164269	CCCAGCCTCCGCACCTAT	61.164	66.667	0.00	0.00	37.52	2.57
275	277	1.508256	ACCTATTACACCCAGCCTCC	58.492	55.000	0.00	0.00	0.00	4.30
279	281	5.924825	CGTAAAGATACCTATTACACCCAGC	59.075	44.000	0.00	0.00	31.45	4.85
325	327	5.830912	TGCGAGATCATTGTCTTTGTTTTT	58.169	33.333	0.00	0.00	0.00	1.94
326	328	5.437289	TGCGAGATCATTGTCTTTGTTTT	57.563	34.783	0.00	0.00	0.00	2.43
327	329	5.437289	TTGCGAGATCATTGTCTTTGTTT	57.563	34.783	0.00	0.00	0.00	2.83
328	330	5.437289	TTTGCGAGATCATTGTCTTTGTT	57.563	34.783	0.00	0.00	0.00	2.83
329	331	5.437289	TTTTGCGAGATCATTGTCTTTGT	57.563	34.783	0.00	0.00	0.00	2.83
354	356	8.883731	CCACGTAGAATTATCTTTCATTGTCTT	58.116	33.333	0.00	0.00	37.10	3.01
355	357	7.495934	CCCACGTAGAATTATCTTTCATTGTCT	59.504	37.037	0.00	0.00	37.10	3.41
356	358	7.494625	TCCCACGTAGAATTATCTTTCATTGTC	59.505	37.037	0.00	0.00	37.10	3.18
428	447	2.032302	TCGAATTTGGTCACCGTTTGTG	59.968	45.455	0.00	0.00	46.88	3.33
434	453	1.785321	CGGTCGAATTTGGTCACCG	59.215	57.895	9.37	9.37	43.71	4.94
783	1138	5.243981	CCTTATCCTCTGCACCATAGAATG	58.756	45.833	0.00	0.00	0.00	2.67
890	1263	2.360475	GCCCCTCCTGAGCAACAC	60.360	66.667	0.00	0.00	0.00	3.32
903	1276	3.162666	GCTTATATAACCTTTGGGCCCC	58.837	50.000	22.27	0.85	35.63	5.80
912	1285	4.202472	GGGTCAGCAAGGCTTATATAACCT	60.202	45.833	0.00	9.53	36.40	3.50
939	1313	1.123861	TCTGGCTTGAGGACTGCTGT	61.124	55.000	0.00	0.00	0.00	4.40
1234	1748	3.064324	GATGGGCCACACCTGCAC	61.064	66.667	9.28	0.00	39.10	4.57
1755	2274	1.442769	TGCTTTCTCGAGCCATGTTC	58.557	50.000	7.81	0.00	42.01	3.18
1900	2423	6.091437	CGCTCTTATATTAGTTTACGGAGGG	58.909	44.000	0.00	0.00	0.00	4.30
2116	2651	3.753294	AATTATACCGTGGCCTGAGAG	57.247	47.619	3.32	0.00	0.00	3.20
2151	2686	6.984740	TTGCACGAAATTCAATACAACTTC	57.015	33.333	0.00	0.00	0.00	3.01
2262	2797	9.457436	ACACTTTACCGAATAAATGGAATAACT	57.543	29.630	0.00	0.00	32.23	2.24
2337	2872	2.675658	ACCACAACCAATGCCTTACT	57.324	45.000	0.00	0.00	0.00	2.24
2363	2898	3.554960	GGTTTGGCTTCTGGCTTAAAAGG	60.555	47.826	0.00	0.00	41.46	3.11
2367	2902	2.373335	TGGTTTGGCTTCTGGCTTAA	57.627	45.000	0.00	0.00	41.46	1.85
2450	2985	9.642343	AACAAAAGGACCTCTTAGACTAATTTT	57.358	29.630	0.00	0.00	34.78	1.82
2496	3031	7.272144	ACTATCAACTTGGGGAATAAACTCT	57.728	36.000	0.00	0.00	0.00	3.24
2506	3041	6.320418	GTGGGTAAATAACTATCAACTTGGGG	59.680	42.308	0.00	0.00	0.00	4.96
2585	3125	1.906574	GATGGGATAGGGGCACGATAA	59.093	52.381	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.