AutoCloner

Multiple sequence alignment - TraesCS7D01G138100

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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	TraesCS7D01G138100	chr7D	100.000	2114	0	0	1	2114	88606444	88608557	0.000000e+00	3904
1	TraesCS7D01G138100	chr7D	93.573	389	17	4	1	382	556309129	556308742	6.540000e-160	573
2	TraesCS7D01G138100	chr7D	92.765	387	22	3	1	382	171327874	171328259	2.370000e-154	555
3	TraesCS7D01G138100	chr7D	92.765	387	22	3	1	382	171334669	171335054	2.370000e-154	555
4	TraesCS7D01G138100	chr7D	80.556	360	47	17	495	847	556307480	556307137	2.690000e-64	255
5	TraesCS7D01G138100	chr7D	94.483	145	6	2	713	856	556309316	556309459	2.730000e-54	222
6	TraesCS7D01G138100	chr7D	96.923	130	4	0	713	842	171327688	171327559	3.530000e-53	219
7	TraesCS7D01G138100	chr7D	96.154	130	5	0	713	842	171334483	171334354	1.640000e-51	213
8	TraesCS7D01G138100	chr2A	96.733	857	18	3	1268	2114	726900441	726901297	0.000000e+00	1419
9	TraesCS7D01G138100	chr7B	96.616	857	19	3	1268	2114	622431956	622432812	0.000000e+00	1413
10	TraesCS7D01G138100	chr7B	95.434	438	9	2	841	1267	386362936	386362499	0.000000e+00	688
11	TraesCS7D01G138100	chr7B	94.989	439	10	2	841	1267	262233991	262234429	0.000000e+00	678
12	TraesCS7D01G138100	chr3B	96.616	857	19	3	1268	2114	757830443	757831299	0.000000e+00	1413
13	TraesCS7D01G138100	chr3B	96.721	854	18	3	1271	2114	813250379	813249526	0.000000e+00	1413
14	TraesCS7D01G138100	chr3B	96.604	854	19	3	1271	2114	201545528	201544675	0.000000e+00	1408
15	TraesCS7D01G138100	chr3B	94.749	438	12	2	841	1267	201507113	201507550	0.000000e+00	671
16	TraesCS7D01G138100	chr3B	91.123	383	32	2	1	382	315388738	315389119	3.110000e-143	518
17	TraesCS7D01G138100	chr3A	96.616	857	19	3	1268	2114	65999466	66000322	0.000000e+00	1413
18	TraesCS7D01G138100	chr5D	96.499	857	20	3	1268	2114	503258763	503259619	0.000000e+00	1408
19	TraesCS7D01G138100	chr5D	94.989	439	10	2	841	1267	554200880	554201318	0.000000e+00	678
20	TraesCS7D01G138100	chr5D	94.989	439	9	3	841	1267	554200465	554200028	0.000000e+00	676
21	TraesCS7D01G138100	chr5D	94.508	437	14	2	841	1267	6207287	6206851	0.000000e+00	665
22	TraesCS7D01G138100	chr3D	96.604	854	19	3	1271	2114	589255651	589254798	0.000000e+00	1408
23	TraesCS7D01G138100	chr2D	96.604	854	19	3	1271	2114	591991683	591990830	0.000000e+00	1408
24	TraesCS7D01G138100	chr2D	91.239	468	31	1	381	838	46870054	46870521	1.380000e-176	628
25	TraesCS7D01G138100	chr6D	95.216	439	9	3	841	1267	431403679	431403241	0.000000e+00	684
26	TraesCS7D01G138100	chr6D	94.749	438	12	3	841	1267	431400561	431400998	0.000000e+00	671
27	TraesCS7D01G138100	chr6D	91.990	387	19	5	1	382	6238225	6237846	1.110000e-147	532
28	TraesCS7D01G138100	chr6D	90.840	393	24	5	1	382	50999751	50999360	1.120000e-142	516
29	TraesCS7D01G138100	chr6D	80.692	347	45	16	504	843	6236749	6236418	1.250000e-62	250
30	TraesCS7D01G138100	chr6D	96.875	128	4	0	713	840	6238412	6238539	4.570000e-52	215
31	TraesCS7D01G138100	chr1D	94.954	436	13	1	841	1267	254490235	254490670	0.000000e+00	675
32	TraesCS7D01G138100	chr1D	94.773	440	10	2	841	1267	394179450	394179889	0.000000e+00	673
33	TraesCS7D01G138100	chr1D	94.521	438	12	5	841	1267	483922422	483921986	0.000000e+00	665
34	TraesCS7D01G138100	chr1D	92.784	388	21	5	1	382	288098773	288099159	2.370000e-154	555
35	TraesCS7D01G138100	chrUn	94.318	440	12	2	841	1267	317472653	317472214	0.000000e+00	662
36	TraesCS7D01G138100	chrUn	94.886	352	6	2	841	1180	404958773	404959124	6.640000e-150	540
37	TraesCS7D01G138100	chr7A	92.228	386	23	5	3	382	78195870	78195486	6.640000e-150	540
38	TraesCS7D01G138100	chr7A	86.258	473	50	4	381	838	218243330	218243802	1.130000e-137	499
39	TraesCS7D01G138100	chr7A	79.320	353	51	16	495	840	78184157	78183820	5.870000e-56	228
40	TraesCS7D01G138100	chr1A	91.123	383	30	2	3	382	30359758	30360139	1.120000e-142	516
41	TraesCS7D01G138100	chr1A	85.294	476	53	7	381	840	524401114	524401588	1.900000e-130	475
42	TraesCS7D01G138100	chr4D	86.853	464	55	2	381	839	373808050	373808512	4.020000e-142	514
43	TraesCS7D01G138100	chr4B	86.134	476	51	4	381	841	42230947	42231422	1.130000e-137	499
44	TraesCS7D01G138100	chr5A	86.017	472	51	4	384	840	544506313	544505842	1.880000e-135	492
45	TraesCS7D01G138100	chr5A	80.260	461	82	7	389	840	140597469	140597009	2.600000e-89	339
46	TraesCS7D01G138100	chr6A	85.270	482	54	6	381	846	1955968	1956448	4.080000e-132	481
47	TraesCS7D01G138100	chr5B	85.412	473	52	6	384	840	643304766	643304295	1.900000e-130	475

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	TraesCS7D01G138100	chr7D	88606444	88608557	2113	False	3904	3904	100.0000	1	2114	1	chr7D.!!$F1	2113
1	TraesCS7D01G138100	chr7D	556307137	556309129	1992	True	414	573	87.0645	1	847	2	chr7D.!!$R3	846
2	TraesCS7D01G138100	chr2A	726900441	726901297	856	False	1419	1419	96.7330	1268	2114	1	chr2A.!!$F1	846
3	TraesCS7D01G138100	chr7B	622431956	622432812	856	False	1413	1413	96.6160	1268	2114	1	chr7B.!!$F2	846
4	TraesCS7D01G138100	chr3B	757830443	757831299	856	False	1413	1413	96.6160	1268	2114	1	chr3B.!!$F3	846
5	TraesCS7D01G138100	chr3B	813249526	813250379	853	True	1413	1413	96.7210	1271	2114	1	chr3B.!!$R2	843
6	TraesCS7D01G138100	chr3B	201544675	201545528	853	True	1408	1408	96.6040	1271	2114	1	chr3B.!!$R1	843
7	TraesCS7D01G138100	chr3A	65999466	66000322	856	False	1413	1413	96.6160	1268	2114	1	chr3A.!!$F1	846
8	TraesCS7D01G138100	chr5D	503258763	503259619	856	False	1408	1408	96.4990	1268	2114	1	chr5D.!!$F1	846
9	TraesCS7D01G138100	chr3D	589254798	589255651	853	True	1408	1408	96.6040	1271	2114	1	chr3D.!!$R1	843
10	TraesCS7D01G138100	chr2D	591990830	591991683	853	True	1408	1408	96.6040	1271	2114	1	chr2D.!!$R1	843
11	TraesCS7D01G138100	chr6D	6236418	6238225	1807	True	391	532	86.3410	1	843	2	chr6D.!!$R3	842

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
453	1932	0.105039	AGATAGGCGGCGAGAAAAGG	59.895	55.0	12.98	0.0	0.0	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1254	2763	0.815095	CACCCCTAACCCGATTTTGC	59.185	55.0	0.0	0.0	0.0	3.68	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
25	26	0.108233	GGCTCTGCTCCAGTGAGAAG	60.108	60.000	0.00	0.00	44.71	2.85
30	31	1.220477	GCTCCAGTGAGAAGAGGGC	59.780	63.158	0.00	0.00	41.42	5.19
33	34	2.286523	CCAGTGAGAAGAGGGCGGT	61.287	63.158	0.00	0.00	0.00	5.68
128	129	4.315803	CTCCTCCGCGATATGGTAATTTT	58.684	43.478	8.23	0.00	0.00	1.82
165	166	4.018779	CCCAATCCTACTGTTTAGTTCCCA	60.019	45.833	0.00	0.00	38.36	4.37
168	169	7.343357	CCAATCCTACTGTTTAGTTCCCATTA	58.657	38.462	0.00	0.00	38.36	1.90
173	174	8.483758	TCCTACTGTTTAGTTCCCATTATTCTC	58.516	37.037	0.00	0.00	38.36	2.87
174	175	8.265055	CCTACTGTTTAGTTCCCATTATTCTCA	58.735	37.037	0.00	0.00	38.36	3.27
228	231	0.827368	CTAGGACCACAAGAGGAGCC	59.173	60.000	0.00	0.00	0.00	4.70
304	311	5.464722	AGTCATATGTCGATGTCAAAGATGC	59.535	40.000	1.90	0.00	0.00	3.91
396	1875	0.982852	TAGTGTGGCAGCTAGGGCAT	60.983	55.000	3.54	0.00	45.62	4.40
413	1892	1.377202	ATGGTACCAACGGCAGCAG	60.377	57.895	20.76	0.00	0.00	4.24
414	1893	1.836999	ATGGTACCAACGGCAGCAGA	61.837	55.000	20.76	0.00	0.00	4.26
415	1894	1.078426	GGTACCAACGGCAGCAGAT	60.078	57.895	7.15	0.00	0.00	2.90
440	1919	2.126307	CGCCGGCGATGAGATAGG	60.126	66.667	44.86	10.04	42.83	2.57
441	1920	2.433318	GCCGGCGATGAGATAGGC	60.433	66.667	12.58	0.00	37.61	3.93
443	1922	2.126307	CGGCGATGAGATAGGCGG	60.126	66.667	0.00	0.00	46.89	6.13
444	1923	2.433318	GGCGATGAGATAGGCGGC	60.433	66.667	0.00	0.00	41.85	6.53
446	1925	2.954611	CGATGAGATAGGCGGCGA	59.045	61.111	12.98	0.00	0.00	5.54
447	1926	1.154131	CGATGAGATAGGCGGCGAG	60.154	63.158	12.98	0.00	0.00	5.03
448	1927	1.578206	CGATGAGATAGGCGGCGAGA	61.578	60.000	12.98	0.00	0.00	4.04
449	1928	0.598562	GATGAGATAGGCGGCGAGAA	59.401	55.000	12.98	0.00	0.00	2.87
450	1929	1.000163	GATGAGATAGGCGGCGAGAAA	60.000	52.381	12.98	0.00	0.00	2.52
451	1930	0.821517	TGAGATAGGCGGCGAGAAAA	59.178	50.000	12.98	0.00	0.00	2.29
453	1932	0.105039	AGATAGGCGGCGAGAAAAGG	59.895	55.000	12.98	0.00	0.00	3.11

Showing 1 to 25 of 305 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	4.705519	CAAAAGCTGCCGCCACCG	62.706	66.667	0.00	0.00	36.60	4.94
33	34	3.294493	GGACAAAAGCTGCCGCCA	61.294	61.111	0.00	0.00	36.60	5.69
104	105	0.611062	TACCATATCGCGGAGGAGGG	60.611	60.000	6.13	2.76	0.00	4.30
128	129	4.042174	AGGATTGGGATTAGGGTTACGAA	58.958	43.478	0.00	0.00	0.00	3.85
168	169	7.014038	GGTCATTGATTCTGCCTAAATGAGAAT	59.986	37.037	0.00	0.00	37.79	2.40
173	174	4.576053	TCGGTCATTGATTCTGCCTAAATG	59.424	41.667	0.00	0.00	0.00	2.32
174	175	4.780815	TCGGTCATTGATTCTGCCTAAAT	58.219	39.130	0.00	0.00	0.00	1.40
261	268	2.017049	CTTCGATTTCCCAAATCCGCT	58.983	47.619	3.87	0.00	43.39	5.52
295	302	4.143543	TCCATCAAACACAGCATCTTTGA	58.856	39.130	0.00	0.00	38.07	2.69
304	311	5.934043	TCTACTTCACATCCATCAAACACAG	59.066	40.000	0.00	0.00	0.00	3.66
396	1875	1.836999	ATCTGCTGCCGTTGGTACCA	61.837	55.000	11.60	11.60	0.00	3.25
425	1904	2.126307	CGCCTATCTCATCGCCGG	60.126	66.667	0.00	0.00	0.00	6.13
427	1906	2.433318	GCCGCCTATCTCATCGCC	60.433	66.667	0.00	0.00	0.00	5.54
430	1909	0.598562	TTCTCGCCGCCTATCTCATC	59.401	55.000	0.00	0.00	0.00	2.92
431	1910	1.040646	TTTCTCGCCGCCTATCTCAT	58.959	50.000	0.00	0.00	0.00	2.90
435	1914	0.880718	CCCTTTTCTCGCCGCCTATC	60.881	60.000	0.00	0.00	0.00	2.08
436	1915	1.146263	CCCTTTTCTCGCCGCCTAT	59.854	57.895	0.00	0.00	0.00	2.57
437	1916	2.582436	CCCTTTTCTCGCCGCCTA	59.418	61.111	0.00	0.00	0.00	3.93
440	1919	1.095807	ATTAGCCCTTTTCTCGCCGC	61.096	55.000	0.00	0.00	0.00	6.53
441	1920	0.657840	CATTAGCCCTTTTCTCGCCG	59.342	55.000	0.00	0.00	0.00	6.46
442	1921	0.382158	GCATTAGCCCTTTTCTCGCC	59.618	55.000	0.00	0.00	33.58	5.54
443	1922	3.926289	GCATTAGCCCTTTTCTCGC	57.074	52.632	0.00	0.00	33.58	5.03
455	1934	0.830648	TCTTCCACCTCCGGCATTAG	59.169	55.000	0.00	0.00	0.00	1.73
456	1935	0.830648	CTCTTCCACCTCCGGCATTA	59.169	55.000	0.00	0.00	0.00	1.90
457	1936	1.604378	CTCTTCCACCTCCGGCATT	59.396	57.895	0.00	0.00	0.00	3.56

Showing 1 to 25 of 351 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.