AutoCloner

Multiple sequence alignment - TraesCS3A01G245800

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	TraesCS3A01G245800	chr3A	100.000	2657	0	0	1	2657	461154918	461152262	0.000000e+00	4907
1	TraesCS3A01G245800	chr3B	96.728	1681	47	6	981	2657	440677145	440678821	0.000000e+00	2793
2	TraesCS3A01G245800	chr3B	90.190	999	68	12	6	992	67998317	67997337	0.000000e+00	1275
3	TraesCS3A01G245800	chr3D	95.163	1075	47	5	981	2053	341885726	341886797	0.000000e+00	1692
4	TraesCS3A01G245800	chr3D	92.585	998	36	14	1	985	459086178	459087150	0.000000e+00	1399
5	TraesCS3A01G245800	chr3D	96.045	531	17	3	2130	2657	341886801	341887330	0.000000e+00	861
6	TraesCS3A01G245800	chr5A	96.247	986	19	9	1	985	705563998	705564966	0.000000e+00	1600
7	TraesCS3A01G245800	chr5A	82.838	303	29	7	1897	2177	619267533	619267232	1.580000e-62	250
8	TraesCS3A01G245800	chr1A	95.025	985	31	9	1	984	477415733	477416700	0.000000e+00	1531
9	TraesCS3A01G245800	chr7A	94.518	985	36	9	1	984	30323164	30324131	0.000000e+00	1504
10	TraesCS3A01G245800	chr7A	94.518	985	36	9	1	984	721211348	721212315	0.000000e+00	1504
11	TraesCS3A01G245800	chr7A	93.340	991	40	10	1	982	17741551	17740578	0.000000e+00	1441
12	TraesCS3A01G245800	chr7A	91.784	998	46	24	1	984	475974481	475975456	0.000000e+00	1356
13	TraesCS3A01G245800	chr1D	93.857	993	35	10	1	984	48477344	48478319	0.000000e+00	1472
14	TraesCS3A01G245800	chr1D	94.038	889	26	13	1	880	3882253	3883123	0.000000e+00	1323
15	TraesCS3A01G245800	chr1D	91.339	993	39	19	1	984	246001190	246002144	0.000000e+00	1314
16	TraesCS3A01G245800	chr1D	83.172	309	30	1	1891	2177	254396941	254397249	2.030000e-66	263
17	TraesCS3A01G245800	chr6A	93.656	993	38	7	1	984	587852234	587853210	0.000000e+00	1461
18	TraesCS3A01G245800	chr4A	90.462	996	63	21	1	984	684497654	684496679	0.000000e+00	1284
19	TraesCS3A01G245800	chr4A	88.387	155	16	2	2024	2177	73809942	73809789	4.520000e-43	185
20	TraesCS3A01G245800	chrUn	83.495	309	29	1	1891	2177	389446205	389445897	4.360000e-68	268
21	TraesCS3A01G245800	chrUn	83.172	309	30	1	1891	2177	346595325	346595633	2.030000e-66	263
22	TraesCS3A01G245800	chrUn	91.250	80	7	0	1891	1970	71296036	71296115	2.800000e-20	110
23	TraesCS3A01G245800	chr5D	83.495	309	29	1	1891	2177	503219387	503219079	4.360000e-68	268
24	TraesCS3A01G245800	chr4D	83.172	309	30	1	1891	2177	30386829	30387137	2.030000e-66	263
25	TraesCS3A01G245800	chr4D	81.848	303	33	5	1897	2177	19929737	19929435	4.420000e-58	235
26	TraesCS3A01G245800	chr6D	83.388	307	25	5	1895	2177	168256091	168255787	7.300000e-66	261
27	TraesCS3A01G245800	chr2B	88.722	133	15	0	1891	2023	465000060	465000192	2.120000e-36	163

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	TraesCS3A01G245800	chr3A	461152262	461154918	2656	True	4907.0	4907	100.000	1	2657	1	chr3A.!!$R1	2656
1	TraesCS3A01G245800	chr3B	440677145	440678821	1676	False	2793.0	2793	96.728	981	2657	1	chr3B.!!$F1	1676
2	TraesCS3A01G245800	chr3B	67997337	67998317	980	True	1275.0	1275	90.190	6	992	1	chr3B.!!$R1	986
3	TraesCS3A01G245800	chr3D	459086178	459087150	972	False	1399.0	1399	92.585	1	985	1	chr3D.!!$F1	984
4	TraesCS3A01G245800	chr3D	341885726	341887330	1604	False	1276.5	1692	95.604	981	2657	2	chr3D.!!$F2	1676
5	TraesCS3A01G245800	chr5A	705563998	705564966	968	False	1600.0	1600	96.247	1	985	1	chr5A.!!$F1	984
6	TraesCS3A01G245800	chr1A	477415733	477416700	967	False	1531.0	1531	95.025	1	984	1	chr1A.!!$F1	983
7	TraesCS3A01G245800	chr7A	30323164	30324131	967	False	1504.0	1504	94.518	1	984	1	chr7A.!!$F1	983
8	TraesCS3A01G245800	chr7A	721211348	721212315	967	False	1504.0	1504	94.518	1	984	1	chr7A.!!$F3	983
9	TraesCS3A01G245800	chr7A	17740578	17741551	973	True	1441.0	1441	93.340	1	982	1	chr7A.!!$R1	981
10	TraesCS3A01G245800	chr7A	475974481	475975456	975	False	1356.0	1356	91.784	1	984	1	chr7A.!!$F2	983
11	TraesCS3A01G245800	chr1D	48477344	48478319	975	False	1472.0	1472	93.857	1	984	1	chr1D.!!$F2	983
12	TraesCS3A01G245800	chr1D	3882253	3883123	870	False	1323.0	1323	94.038	1	880	1	chr1D.!!$F1	879
13	TraesCS3A01G245800	chr1D	246001190	246002144	954	False	1314.0	1314	91.339	1	984	1	chr1D.!!$F3	983
14	TraesCS3A01G245800	chr6A	587852234	587853210	976	False	1461.0	1461	93.656	1	984	1	chr6A.!!$F1	983
15	TraesCS3A01G245800	chr4A	684496679	684497654	975	True	1284.0	1284	90.462	1	984	1	chr4A.!!$R2	983

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
573	581	0.251297	TCCAGTGTTTCATGCCAGGG	60.251	55.0	0.0	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2124	2150	0.605319	TTTTCCGTGCCTGCCTAGTG	60.605	55.0	0.0	0.0	0.0	2.74	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
146	147	6.862209	TCTTTTGCTGTCAACAAAGTATGTT	58.138	32.000	1.92	0.00	45.86	2.71
277	280	5.027206	CACTTGTCAGTGCATTCTACTTG	57.973	43.478	0.00	0.00	44.16	3.16
278	281	4.512944	CACTTGTCAGTGCATTCTACTTGT	59.487	41.667	0.00	0.00	44.16	3.16
279	282	4.752101	ACTTGTCAGTGCATTCTACTTGTC	59.248	41.667	0.00	0.00	0.00	3.18
280	283	4.335400	TGTCAGTGCATTCTACTTGTCA	57.665	40.909	0.00	0.00	0.00	3.58
281	284	4.309933	TGTCAGTGCATTCTACTTGTCAG	58.690	43.478	0.00	0.00	0.00	3.51
282	285	4.202253	TGTCAGTGCATTCTACTTGTCAGT	60.202	41.667	0.00	0.00	36.99	3.41
283	286	4.151335	GTCAGTGCATTCTACTTGTCAGTG	59.849	45.833	0.00	0.00	34.06	3.66
284	287	3.070018	AGTGCATTCTACTTGTCAGTGC	58.930	45.455	0.00	0.00	34.06	4.40
285	288	2.807967	GTGCATTCTACTTGTCAGTGCA	59.192	45.455	0.00	0.00	38.62	4.57
286	289	3.438087	GTGCATTCTACTTGTCAGTGCAT	59.562	43.478	0.00	0.00	42.23	3.96
287	290	4.074259	TGCATTCTACTTGTCAGTGCATT	58.926	39.130	0.00	0.00	36.33	3.56
288	291	4.154737	TGCATTCTACTTGTCAGTGCATTC	59.845	41.667	0.00	0.00	36.33	2.67
289	292	4.394300	GCATTCTACTTGTCAGTGCATTCT	59.606	41.667	0.00	0.00	34.06	2.40
295	298	5.411831	ACTTGTCAGTGCATTCTCTGATA	57.588	39.130	7.88	3.12	42.57	2.15
304	307	5.129980	AGTGCATTCTCTGATACTGATTGGA	59.870	40.000	0.00	0.00	0.00	3.53
316	319	2.906389	ACTGATTGGACAGGCTGTCTTA	59.094	45.455	38.04	28.23	46.19	2.10
400	404	1.151668	CGCAAGCAAGCTACAGTCTT	58.848	50.000	0.00	0.00	0.00	3.01
573	581	0.251297	TCCAGTGTTTCATGCCAGGG	60.251	55.000	0.00	0.00	0.00	4.45
693	701	2.610232	GGATTCACAAAAGCATTGCCGT	60.610	45.455	4.70	0.00	0.00	5.68
894	919	5.745227	TCTCCAAGAATGTAATCTCAACCC	58.255	41.667	0.00	0.00	0.00	4.11
1235	1260	3.244353	GGTGACTTGGATCGGATGATGAT	60.244	47.826	0.00	0.00	34.09	2.45
1319	1344	2.235402	GGGATGAGAACGGAAAGGTACA	59.765	50.000	0.00	0.00	0.00	2.90
1404	1429	3.494626	ACGCTGCGGTTGAATATAAGATG	59.505	43.478	26.95	0.00	0.00	2.90
1429	1454	6.917533	ACATTTCTAGACTTTTTCCATGCAG	58.082	36.000	0.00	0.00	0.00	4.41
1626	1651	2.217510	TCCCAGTCTCTCCACAGTAC	57.782	55.000	0.00	0.00	0.00	2.73
1911	1937	1.613270	GTTGAATGGTTAAAGCGCCG	58.387	50.000	2.29	0.00	0.00	6.46
2061	2087	9.476202	CATAACATAGGAACAATATGAACTCGA	57.524	33.333	0.24	0.00	35.15	4.04
2184	2210	6.599638	GTGAAAGAAGCAATATACCAGGAGTT	59.400	38.462	0.00	0.00	0.00	3.01
2200	2226	4.919754	CAGGAGTTGATAGCTTGTTTTTGC	59.080	41.667	0.00	0.00	0.00	3.68
2327	2355	4.650734	TGCATTCTTGAAGTCATACCACA	58.349	39.130	0.00	0.00	0.00	4.17
2444	2473	2.732366	CAGAGCGCGTGTATGTATCTT	58.268	47.619	8.43	0.00	0.00	2.40
2498	2527	1.405526	CCCCACATCGTACCTGAACAG	60.406	57.143	0.00	0.00	0.00	3.16
2596	2625	3.958147	ACTGGAGTTTAAGGGTTTTGGTG	59.042	43.478	0.00	0.00	0.00	4.17
2600	2629	2.698274	AGTTTAAGGGTTTTGGTGGCAG	59.302	45.455	0.00	0.00	0.00	4.85
2610	2640	1.722034	TTGGTGGCAGAACTCTCTCT	58.278	50.000	0.00	0.00	0.00	3.10
2611	2641	1.261480	TGGTGGCAGAACTCTCTCTC	58.739	55.000	0.00	0.00	0.00	3.20
2624	2654	1.143305	CTCTCTCACTTGTGCAACCG	58.857	55.000	0.00	0.00	34.36	4.44
2636	2666	1.226379	GCAACCGCATGATGGAACG	60.226	57.895	11.03	0.00	38.36	3.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
146	147	4.286032	AGTTGTAGGTGCATGAAGGAACTA	59.714	41.667	0.00	0.00	38.49	2.24
273	276	3.758755	TCAGAGAATGCACTGACAAGT	57.241	42.857	0.00	0.00	36.92	3.16
274	277	5.291371	CAGTATCAGAGAATGCACTGACAAG	59.709	44.000	2.54	0.00	43.02	3.16
275	278	5.047092	TCAGTATCAGAGAATGCACTGACAA	60.047	40.000	2.54	0.00	43.02	3.18
276	279	4.463891	TCAGTATCAGAGAATGCACTGACA	59.536	41.667	2.54	0.00	43.02	3.58
277	280	5.003692	TCAGTATCAGAGAATGCACTGAC	57.996	43.478	2.54	0.00	43.02	3.51
278	281	5.866159	ATCAGTATCAGAGAATGCACTGA	57.134	39.130	3.02	3.02	46.12	3.41
279	282	5.236695	CCAATCAGTATCAGAGAATGCACTG	59.763	44.000	0.00	0.00	40.39	3.66
280	283	5.129980	TCCAATCAGTATCAGAGAATGCACT	59.870	40.000	0.00	0.00	0.00	4.40
281	284	5.236047	GTCCAATCAGTATCAGAGAATGCAC	59.764	44.000	0.00	0.00	0.00	4.57
282	285	5.104817	TGTCCAATCAGTATCAGAGAATGCA	60.105	40.000	0.00	0.00	0.00	3.96
283	286	5.363101	TGTCCAATCAGTATCAGAGAATGC	58.637	41.667	0.00	0.00	0.00	3.56
284	287	5.990386	CCTGTCCAATCAGTATCAGAGAATG	59.010	44.000	0.00	0.00	34.02	2.67
285	288	5.454471	GCCTGTCCAATCAGTATCAGAGAAT	60.454	44.000	0.00	0.00	34.02	2.40
286	289	4.141846	GCCTGTCCAATCAGTATCAGAGAA	60.142	45.833	0.00	0.00	34.02	2.87
287	290	3.386078	GCCTGTCCAATCAGTATCAGAGA	59.614	47.826	0.00	0.00	34.02	3.10
288	291	3.387374	AGCCTGTCCAATCAGTATCAGAG	59.613	47.826	0.00	0.00	34.02	3.35
289	292	3.133542	CAGCCTGTCCAATCAGTATCAGA	59.866	47.826	0.00	0.00	34.02	3.27
295	298	3.944476	GACAGCCTGTCCAATCAGT	57.056	52.632	14.04	0.00	41.37	3.41
304	307	4.737946	GCGTCTATCATTAAGACAGCCTGT	60.738	45.833	0.00	0.00	42.91	4.00
316	319	3.319405	CCACCAGTAGAGCGTCTATCATT	59.681	47.826	0.00	0.00	30.76	2.57
400	404	4.779993	TCTGCCTCTGTACTAGATCTGA	57.220	45.455	5.18	0.00	34.21	3.27
573	581	5.886960	AAGTCTATCTCAATGTGTTTGGC	57.113	39.130	0.00	0.00	35.92	4.52
842	866	9.945633	AAGAAAGGAGGTAGAGATAAGAGTTAT	57.054	33.333	0.00	0.00	0.00	1.89
894	919	1.536766	CCCATAACAGCGCATACATGG	59.463	52.381	11.47	16.30	34.07	3.66
924	949	5.700722	ACGGCTTCGTGTTATATAGATGA	57.299	39.130	0.00	0.00	46.32	2.92
949	974	0.759346	AACGTCTTGCCTTCTCAGGT	59.241	50.000	0.00	0.00	43.18	4.00
1235	1260	4.284550	GCACCACAAGCCCTCCCA	62.285	66.667	0.00	0.00	0.00	4.37
1319	1344	0.876399	GAACGTGGCAAACCCGTATT	59.124	50.000	1.15	0.00	40.52	1.89
1404	1429	6.913170	TGCATGGAAAAAGTCTAGAAATGTC	58.087	36.000	0.00	0.00	0.00	3.06
1600	1625	0.693049	GGAGAGACTGGGAAGCCAAA	59.307	55.000	0.00	0.00	0.00	3.28
1626	1651	5.535753	AACAAATCTTTTGAAGACCCAGG	57.464	39.130	6.96	0.00	41.01	4.45
1790	1816	1.885887	GGTGCCAGCACTGTTCATTTA	59.114	47.619	21.19	0.00	45.52	1.40
1814	1840	8.926710	CAAAGACGTATCCAATATATTGTCCTC	58.073	37.037	21.20	10.02	36.06	3.71
1889	1915	2.595386	GCGCTTTAACCATTCAACCAG	58.405	47.619	0.00	0.00	0.00	4.00
1911	1937	8.749354	ACCCTCAAATTTACCAATTATGAGTTC	58.251	33.333	0.00	0.00	36.71	3.01
2061	2087	9.743057	CTCTGAGTTCGAGTATCAATAAGAATT	57.257	33.333	0.00	0.00	33.17	2.17
2124	2150	0.605319	TTTTCCGTGCCTGCCTAGTG	60.605	55.000	0.00	0.00	0.00	2.74
2160	2186	6.313519	ACTCCTGGTATATTGCTTCTTTCA	57.686	37.500	0.00	0.00	0.00	2.69
2184	2210	5.528043	TTCAAGGCAAAAACAAGCTATCA	57.472	34.783	0.00	0.00	0.00	2.15
2327	2355	1.525619	GCACGACGACTTAAAAGCTGT	59.474	47.619	0.00	0.00	0.00	4.40
2498	2527	3.364441	TGACAAGCATGCGGGCAC	61.364	61.111	15.77	8.98	35.83	5.01
2596	2625	2.298729	ACAAGTGAGAGAGAGTTCTGCC	59.701	50.000	0.00	0.00	32.53	4.85
2600	2629	3.377346	TGCACAAGTGAGAGAGAGTTC	57.623	47.619	4.04	0.00	0.00	3.01
2624	2654	1.394917	GACACACTCGTTCCATCATGC	59.605	52.381	0.00	0.00	0.00	4.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.