AutoCloner

Multiple sequence alignment - TraesCS7B01G216100

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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	TraesCS7B01G216100	chr7B	100.000	2487	0	0	1	2487	397829121	397831607	0.000000e+00	4593.0
1	TraesCS7B01G216100	chr2D	96.234	2496	74	8	1	2487	595722137	595719653	0.000000e+00	4071.0
2	TraesCS7B01G216100	chr3D	93.304	687	41	4	1179	1864	91313682	91314364	0.000000e+00	1009.0
3	TraesCS7B01G216100	chr3D	90.148	406	27	8	6	411	91312400	91312792	1.320000e-142	516.0
4	TraesCS7B01G216100	chr3D	86.207	58	4	4	752	805	574518168	574518111	2.670000e-05	60.2
5	TraesCS7B01G216100	chr3A	91.087	460	30	4	2033	2487	713316609	713316156	1.640000e-171	612.0
6	TraesCS7B01G216100	chr3A	97.143	35	1	0	752	786	432604414	432604380	2.670000e-05	60.2
7	TraesCS7B01G216100	chr1B	90.591	457	39	3	2033	2487	525798643	525799097	9.840000e-169	603.0
8	TraesCS7B01G216100	chr1B	85.846	325	32	11	90	411	172382893	172383206	1.430000e-87	333.0
9	TraesCS7B01G216100	chr1B	82.143	140	20	2	897	1035	520820099	520819964	5.620000e-22	115.0
10	TraesCS7B01G216100	chr1B	89.583	48	4	1	754	800	449389044	449388997	2.670000e-05	60.2
11	TraesCS7B01G216100	chr6B	87.629	485	48	9	874	1351	712236772	712236293	1.010000e-153	553.0
12	TraesCS7B01G216100	chr6B	87.838	370	32	9	1500	1861	713262391	713262027	2.960000e-114	422.0
13	TraesCS7B01G216100	chr6B	85.194	412	46	11	2	411	59411936	59411538	2.300000e-110	409.0
14	TraesCS7B01G216100	chr6A	88.789	446	44	5	909	1353	613328618	613328178	2.180000e-150	542.0
15	TraesCS7B01G216100	chr6D	87.447	470	48	10	890	1353	467032585	467032121	4.710000e-147	531.0
16	TraesCS7B01G216100	chr4B	86.313	453	55	6	1411	1861	444593059	444592612	1.030000e-133	486.0
17	TraesCS7B01G216100	chr4A	84.348	460	61	11	1408	1861	344038791	344039245	8.160000e-120	440.0
18	TraesCS7B01G216100	chr4A	97.297	37	1	0	752	788	548275646	548275610	2.060000e-06	63.9
19	TraesCS7B01G216100	chrUn	84.709	412	48	11	2	411	407365565	407365167	4.980000e-107	398.0
20	TraesCS7B01G216100	chrUn	86.900	229	22	6	183	411	266952259	266952039	1.480000e-62	250.0
21	TraesCS7B01G216100	chrUn	86.900	229	22	6	183	411	289877896	289877676	1.480000e-62	250.0
22	TraesCS7B01G216100	chrUn	86.900	229	22	6	183	411	328413746	328413526	1.480000e-62	250.0
23	TraesCS7B01G216100	chr5B	81.098	492	67	12	2007	2485	575966299	575965821	1.090000e-98	370.0
24	TraesCS7B01G216100	chr1A	86.349	315	31	10	100	411	12409892	12409587	1.430000e-87	333.0
25	TraesCS7B01G216100	chr7D	97.143	35	1	0	752	786	278231040	278231074	2.670000e-05	60.2
26	TraesCS7B01G216100	chr2B	97.222	36	0	1	751	786	637106639	637106605	2.670000e-05	60.2
27	TraesCS7B01G216100	chr2A	87.273	55	3	3	752	802	423069784	423069838	2.670000e-05	60.2
28	TraesCS7B01G216100	chr1D	90.909	44	4	0	752	795	210925684	210925641	2.670000e-05	60.2

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	TraesCS7B01G216100	chr7B	397829121	397831607	2486	False	4593.0	4593	100.000	1	2487	1	chr7B.!!$F1	2486
1	TraesCS7B01G216100	chr2D	595719653	595722137	2484	True	4071.0	4071	96.234	1	2487	1	chr2D.!!$R1	2486
2	TraesCS7B01G216100	chr3D	91312400	91314364	1964	False	762.5	1009	91.726	6	1864	2	chr3D.!!$F1	1858

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
515	516	0.179018	GTGTGGGTCTGGACTTGCTT	60.179	55.0	0.67	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2052	2652	0.329596	AGCCCAATCCAACTCAGGTC	59.67	55.0	0.0	0.0	0.0	3.85	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
25	26	1.913778	TGGCACATTTGATGCAGAGT	58.086	45.000	0.00	0.00	45.27	3.24
28	29	1.814394	GCACATTTGATGCAGAGTGGA	59.186	47.619	0.00	0.00	42.88	4.02
58	59	9.322769	TGTAAGTTTCTCCTCCTTATCTACTTT	57.677	33.333	0.00	0.00	0.00	2.66
87	88	6.448202	TCAGATTCCTCTCCCTTCTCTAATT	58.552	40.000	0.00	0.00	0.00	1.40
126	127	3.920231	TGCTATTTGATGGAGAGCAGT	57.080	42.857	0.00	0.00	38.20	4.40
222	223	4.214119	GCTACAGAATGATGTGTGTGTGTT	59.786	41.667	0.00	0.00	39.69	3.32
223	224	5.277974	GCTACAGAATGATGTGTGTGTGTTT	60.278	40.000	0.00	0.00	39.69	2.83
301	302	5.163663	GCAAAATATTTCCCGTGAGATGTGA	60.164	40.000	0.10	0.00	0.00	3.58
480	481	1.133598	CACGACAGGGCGATGTACTTA	59.866	52.381	0.00	0.00	32.25	2.24
515	516	0.179018	GTGTGGGTCTGGACTTGCTT	60.179	55.000	0.67	0.00	0.00	3.91
524	525	2.654877	GACTTGCTTCGGTCCGGA	59.345	61.111	12.29	0.00	0.00	5.14
580	581	1.281867	TGCCCGAGTTGAAGATGGATT	59.718	47.619	0.00	0.00	0.00	3.01
593	594	7.202016	TGAAGATGGATTGTTGTTTCTACAC	57.798	36.000	0.00	0.00	32.98	2.90
607	608	3.257469	TCTACACTAGACGACGTGGAT	57.743	47.619	4.58	0.00	35.51	3.41
628	629	4.804868	TGGTTGGGATTGATCACATTTG	57.195	40.909	0.00	0.00	40.43	2.32
630	631	4.021280	TGGTTGGGATTGATCACATTTGTG	60.021	41.667	4.29	4.29	40.43	3.33
655	657	2.922740	TAGGTGGATAATTGGCCGTC	57.077	50.000	0.00	0.00	0.00	4.79
662	664	1.195448	GATAATTGGCCGTCATCAGCG	59.805	52.381	0.00	0.00	0.00	5.18
672	674	3.549471	GCCGTCATCAGCGATTATATGAG	59.451	47.826	0.00	0.00	0.00	2.90
722	724	2.095372	GTGCCTAATGCGTGTAAGGAAC	59.905	50.000	6.44	2.73	45.60	3.62
945	954	3.198635	CCTTGGCATCTCCTACTCTTGAA	59.801	47.826	0.00	0.00	35.26	2.69
946	955	4.323792	CCTTGGCATCTCCTACTCTTGAAA	60.324	45.833	0.00	0.00	35.26	2.69
976	985	2.679837	AGCAGCAATATTTCGTGGTGAG	59.320	45.455	8.20	0.00	44.17	3.51
980	989	4.629634	CAGCAATATTTCGTGGTGAGTACA	59.370	41.667	0.00	0.00	44.17	2.90
1224	1823	5.950883	TCGAGATCTGAAACTAAACGTCAT	58.049	37.500	0.00	0.00	0.00	3.06
1265	1864	3.448686	CCTCAGCTTTATAGGACACGTG	58.551	50.000	15.48	15.48	31.64	4.49
1430	2029	1.435577	GGTGTACTACCGGCACAAAG	58.564	55.000	0.00	0.00	40.26	2.77
1432	2031	1.796459	GTGTACTACCGGCACAAAGTG	59.204	52.381	0.00	0.00	36.51	3.16
1472	2071	0.246360	GAATTTGGTTTGGGCCCTCG	59.754	55.000	25.70	0.00	0.00	4.63
1515	2114	5.129980	TGATGTTGTCCTCTTCTGCTATGAT	59.870	40.000	0.00	0.00	0.00	2.45
1516	2115	5.426689	TGTTGTCCTCTTCTGCTATGATT	57.573	39.130	0.00	0.00	0.00	2.57
1531	2130	9.412460	TCTGCTATGATTTTGATGTTAAATCCT	57.588	29.630	0.00	0.00	39.92	3.24
1690	2289	4.893424	ACACCAACGGATGTATTTATGC	57.107	40.909	0.00	0.00	0.00	3.14
1706	2305	8.970020	TGTATTTATGCAGGAAATTGATGTTCT	58.030	29.630	13.01	0.00	0.00	3.01
1742	2341	8.074972	GCTTATTTTCACAATTTTGAAATGGCA	58.925	29.630	17.94	6.21	43.38	4.92
2052	2652	5.954296	TCTTTCTTTTCTCAATGCAGGAG	57.046	39.130	11.02	11.02	0.00	3.69
2053	2653	5.624159	TCTTTCTTTTCTCAATGCAGGAGA	58.376	37.500	14.89	14.89	39.53	3.71
2118	2718	5.908341	TGTATACCTCACATATTGCACGAA	58.092	37.500	0.00	0.00	0.00	3.85
2128	2728	4.630069	ACATATTGCACGAAACCTACTGAC	59.370	41.667	0.00	0.00	0.00	3.51
2162	2762	7.469043	GCTGTTGCCACATCAATTTCATATAGA	60.469	37.037	0.00	0.00	30.39	1.98
2215	2815	5.336150	TGGTGAAAAGCAATGACAGAAAA	57.664	34.783	0.00	0.00	0.00	2.29
2226	2826	4.574599	ATGACAGAAAACAGCACCTTTC	57.425	40.909	0.00	0.00	32.72	2.62
2286	2886	2.622436	CTTGATTCGGTGTCTCCTTCC	58.378	52.381	0.00	0.00	0.00	3.46
2304	2904	1.211703	TCCTGTTCTGCCAACAAGACA	59.788	47.619	0.47	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	3.323979	GGAGGAGAAACTTACAGTGTCCA	59.676	47.826	0.00	0.00	32.79	4.02
28	29	6.726764	AGATAAGGAGGAGAAACTTACAGTGT	59.273	38.462	0.00	0.00	30.33	3.55
50	51	8.646900	GGAGAGGAATCTGAATACAAAGTAGAT	58.353	37.037	0.00	0.00	0.00	1.98
55	56	6.245890	AGGGAGAGGAATCTGAATACAAAG	57.754	41.667	0.00	0.00	0.00	2.77
58	59	5.533112	AGAAGGGAGAGGAATCTGAATACA	58.467	41.667	0.00	0.00	0.00	2.29
222	223	6.293900	CCATCACATTAGCAAGTAACACACAA	60.294	38.462	0.00	0.00	0.00	3.33
223	224	5.181056	CCATCACATTAGCAAGTAACACACA	59.819	40.000	0.00	0.00	0.00	3.72
382	383	8.325421	TCAACCGTATTGTGCTTTTCTATTTA	57.675	30.769	0.00	0.00	0.00	1.40
439	440	0.750546	CTGGGCATGGTGGTCATCTG	60.751	60.000	0.00	0.00	32.92	2.90
480	481	0.694771	ACACACAGGCATCACCAGAT	59.305	50.000	0.00	0.00	43.14	2.90
515	516	1.133699	AGTATGGTGTATCCGGACCGA	60.134	52.381	17.49	1.45	39.52	4.69
580	581	4.035558	ACGTCGTCTAGTGTAGAAACAACA	59.964	41.667	0.00	0.00	37.36	3.33
593	594	1.469251	CCAACCATCCACGTCGTCTAG	60.469	57.143	0.00	0.00	0.00	2.43
607	608	4.158786	ACAAATGTGATCAATCCCAACCA	58.841	39.130	0.00	0.00	0.00	3.67
628	629	4.278419	GCCAATTATCCACCTATTCACCAC	59.722	45.833	0.00	0.00	0.00	4.16
630	631	3.826729	GGCCAATTATCCACCTATTCACC	59.173	47.826	0.00	0.00	0.00	4.02
655	657	6.427853	TGGTTTTCCTCATATAATCGCTGATG	59.572	38.462	0.00	0.00	41.38	3.07
662	664	8.159344	CCACTTCTGGTTTTCCTCATATAATC	57.841	38.462	0.00	0.00	41.38	1.75
688	690	5.293324	CGCATTAGGCACTCTATTTGTGTTA	59.707	40.000	0.00	0.00	45.17	2.41
692	694	3.623060	CACGCATTAGGCACTCTATTTGT	59.377	43.478	0.00	0.00	45.17	2.83
779	781	3.200605	TGTGATAAGGACAGACATGGCAT	59.799	43.478	0.00	0.00	35.42	4.40
976	985	9.973246	CATATGAAAGTGTAGTTCATGTTGTAC	57.027	33.333	9.36	0.00	43.76	2.90
980	989	8.635765	AACCATATGAAAGTGTAGTTCATGTT	57.364	30.769	3.65	3.63	43.76	2.71
1141	1645	3.456280	GCAGAAAACAATCACCTGCAAA	58.544	40.909	0.00	0.00	46.68	3.68
1224	1823	7.934120	GCTGAGGCTTTCCTAAATTTATCTCTA	59.066	37.037	0.00	0.00	44.46	2.43
1265	1864	5.068723	TGGAATCCCGTAACTCTTCAGATAC	59.931	44.000	0.00	0.00	34.29	2.24
1472	2071	0.818296	AGCCGTCATGACCTACAGAC	59.182	55.000	20.03	0.00	0.00	3.51
1515	2114	9.762933	CTTGGAAGAAAGGATTTAACATCAAAA	57.237	29.630	0.00	0.00	39.27	2.44
1531	2130	7.723616	TGATTTGTCTGATTACCTTGGAAGAAA	59.276	33.333	0.00	0.00	0.00	2.52
1535	2134	5.710099	GGTGATTTGTCTGATTACCTTGGAA	59.290	40.000	0.00	0.00	32.17	3.53
1676	2275	6.969366	TCAATTTCCTGCATAAATACATCCG	58.031	36.000	7.40	0.00	0.00	4.18
1690	2289	7.161773	ACAATACCAGAACATCAATTTCCTG	57.838	36.000	0.00	0.00	0.00	3.86
2052	2652	0.329596	AGCCCAATCCAACTCAGGTC	59.670	55.000	0.00	0.00	0.00	3.85
2053	2653	0.329596	GAGCCCAATCCAACTCAGGT	59.670	55.000	0.00	0.00	0.00	4.00
2118	2718	1.671742	CAGGTGGCGTCAGTAGGTT	59.328	57.895	0.00	0.00	0.00	3.50
2162	2762	6.711277	TGTTATTCAGGATAAGCTTGTCAGT	58.289	36.000	22.69	8.29	31.01	3.41
2226	2826	4.210955	GTCTTCTGTGAGCTTGAGAAACAG	59.789	45.833	0.00	0.00	39.66	3.16
2286	2886	3.144506	AGATGTCTTGTTGGCAGAACAG	58.855	45.455	1.34	0.00	31.78	3.16
2328	2928	5.764487	TGCTGTACACAATGATTTCACAA	57.236	34.783	0.00	0.00	0.00	3.33
2336	2936	7.138081	CAGTTTACAAATGCTGTACACAATGA	58.862	34.615	15.05	4.13	41.69	2.57
2348	2948	2.415697	ACGCACCAGTTTACAAATGC	57.584	45.000	0.00	0.00	0.00	3.56
2459	3060	7.074494	AGGTGGCTGGTATATTAAATAGGGAAA	59.926	37.037	0.00	0.00	0.00	3.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.