AutoCloner

Multiple sequence alignment - TraesCS3B01G500900

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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	TraesCS3B01G500900	chr3B	100.000	3912	0	0	1	3912	745204397	745200486	0.000000e+00	7225.0
1	TraesCS3B01G500900	chr3B	93.091	1954	79	31	1637	3566	746357136	746355215	0.000000e+00	2809.0
2	TraesCS3B01G500900	chr3B	86.929	1400	137	22	984	2344	747493022	747494414	0.000000e+00	1530.0
3	TraesCS3B01G500900	chr3B	86.315	1403	146	21	984	2347	744419878	744418483	0.000000e+00	1485.0
4	TraesCS3B01G500900	chr3B	92.774	941	54	7	4	940	746361099	746360169	0.000000e+00	1349.0
5	TraesCS3B01G500900	chr3B	84.270	1424	170	29	945	2346	744590523	744591914	0.000000e+00	1339.0
6	TraesCS3B01G500900	chr3B	84.170	1434	171	28	945	2356	746856435	746855036	0.000000e+00	1339.0
7	TraesCS3B01G500900	chr3B	84.053	1367	177	30	928	2281	747093650	747094988	0.000000e+00	1279.0
8	TraesCS3B01G500900	chr3B	81.127	816	103	30	2346	3134	745243465	745242674	1.200000e-169	606.0
9	TraesCS3B01G500900	chr3B	81.852	540	72	19	2450	2981	747095236	747095757	7.770000e-117	431.0
10	TraesCS3B01G500900	chr3B	83.755	474	56	14	2450	2914	744545205	744544744	2.790000e-116	429.0
11	TraesCS3B01G500900	chr3B	81.797	434	71	7	2482	2911	747385904	747386333	1.340000e-94	357.0
12	TraesCS3B01G500900	chr3B	90.650	246	23	0	2048	2293	745449329	745449084	1.050000e-85	327.0
13	TraesCS3B01G500900	chr3B	95.294	85	4	0	3563	3647	746354921	746354837	6.820000e-28	135.0
14	TraesCS3B01G500900	chr3D	86.452	1395	151	21	984	2347	560235130	560233743	0.000000e+00	1495.0
15	TraesCS3B01G500900	chr3D	85.406	1391	167	19	983	2363	560826869	560828233	0.000000e+00	1411.0
16	TraesCS3B01G500900	chr3D	89.043	940	97	5	968	1905	560269625	560268690	0.000000e+00	1160.0
17	TraesCS3B01G500900	chr3D	82.218	1001	128	32	2051	3039	560784703	560783741	0.000000e+00	817.0
18	TraesCS3B01G500900	chr3D	80.966	725	89	27	2346	3045	560703156	560702456	2.680000e-146	529.0
19	TraesCS3B01G500900	chr3D	83.087	473	61	14	2450	2914	560285205	560284744	2.810000e-111	412.0
20	TraesCS3B01G500900	chr3D	83.848	421	53	8	2501	2916	560645411	560645001	1.700000e-103	387.0
21	TraesCS3B01G500900	chr3D	84.164	341	40	9	2049	2381	560197917	560197583	6.310000e-83	318.0
22	TraesCS3B01G500900	chr3D	87.821	156	17	2	3746	3900	281350824	281350670	8.630000e-42	182.0
23	TraesCS3B01G500900	chr3D	86.179	123	10	7	3738	3853	126958058	126958180	4.100000e-25	126.0
24	TraesCS3B01G500900	chr3D	75.916	191	30	9	622	809	82548017	82548194	2.500000e-12	84.2
25	TraesCS3B01G500900	chr3A	85.766	1391	150	26	984	2334	629086990	629088372	0.000000e+00	1428.0
26	TraesCS3B01G500900	chr3A	85.489	1392	154	26	984	2335	696332975	696331592	0.000000e+00	1408.0
27	TraesCS3B01G500900	chr3A	82.840	338	48	9	2049	2381	696289176	696288844	1.060000e-75	294.0
28	TraesCS3B01G500900	chr3A	79.907	428	62	18	1960	2371	696599537	696599118	3.820000e-75	292.0
29	TraesCS3B01G500900	chrUn	81.181	813	102	30	2346	3131	301718583	301719371	1.200000e-169	606.0
30	TraesCS3B01G500900	chr2D	100.000	85	0	0	3649	3733	542253425	542253509	1.460000e-34	158.0
31	TraesCS3B01G500900	chr2B	100.000	85	0	0	3649	3733	647315799	647315883	1.460000e-34	158.0
32	TraesCS3B01G500900	chr6A	79.116	249	29	7	573	809	34305229	34304992	2.430000e-32	150.0
33	TraesCS3B01G500900	chr6A	81.879	149	22	4	666	809	34258177	34258029	1.910000e-23	121.0
34	TraesCS3B01G500900	chr2A	96.429	84	3	0	3650	3733	685222597	685222680	5.270000e-29	139.0
35	TraesCS3B01G500900	chr6D	81.301	123	22	1	668	790	466385098	466384977	8.950000e-17	99.0
36	TraesCS3B01G500900	chr1B	77.128	188	29	10	632	809	368462444	368462627	3.220000e-16	97.1
37	TraesCS3B01G500900	chr4B	75.519	241	31	20	622	840	40523289	40523523	4.160000e-15	93.5
38	TraesCS3B01G500900	chr4D	79.775	89	12	3	721	809	485493849	485493767	4.220000e-05	60.2
39	TraesCS3B01G500900	chr7B	92.308	39	3	0	632	670	514511206	514511168	5.460000e-04	56.5

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	TraesCS3B01G500900	chr3B	745200486	745204397	3911	True	7225	7225	100.000000	1	3912	1	chr3B.!!$R3	3911
1	TraesCS3B01G500900	chr3B	747493022	747494414	1392	False	1530	1530	86.929000	984	2344	1	chr3B.!!$F3	1360
2	TraesCS3B01G500900	chr3B	744418483	744419878	1395	True	1485	1485	86.315000	984	2347	1	chr3B.!!$R1	1363
3	TraesCS3B01G500900	chr3B	746354837	746361099	6262	True	1431	2809	93.719667	4	3647	3	chr3B.!!$R7	3643
4	TraesCS3B01G500900	chr3B	744590523	744591914	1391	False	1339	1339	84.270000	945	2346	1	chr3B.!!$F1	1401
5	TraesCS3B01G500900	chr3B	746855036	746856435	1399	True	1339	1339	84.170000	945	2356	1	chr3B.!!$R6	1411
6	TraesCS3B01G500900	chr3B	747093650	747095757	2107	False	855	1279	82.952500	928	2981	2	chr3B.!!$F4	2053
7	TraesCS3B01G500900	chr3B	745242674	745243465	791	True	606	606	81.127000	2346	3134	1	chr3B.!!$R4	788
8	TraesCS3B01G500900	chr3D	560233743	560235130	1387	True	1495	1495	86.452000	984	2347	1	chr3D.!!$R3	1363
9	TraesCS3B01G500900	chr3D	560826869	560828233	1364	False	1411	1411	85.406000	983	2363	1	chr3D.!!$F3	1380
10	TraesCS3B01G500900	chr3D	560268690	560269625	935	True	1160	1160	89.043000	968	1905	1	chr3D.!!$R4	937
11	TraesCS3B01G500900	chr3D	560783741	560784703	962	True	817	817	82.218000	2051	3039	1	chr3D.!!$R8	988
12	TraesCS3B01G500900	chr3D	560702456	560703156	700	True	529	529	80.966000	2346	3045	1	chr3D.!!$R7	699
13	TraesCS3B01G500900	chr3A	629086990	629088372	1382	False	1428	1428	85.766000	984	2334	1	chr3A.!!$F1	1350
14	TraesCS3B01G500900	chr3A	696331592	696332975	1383	True	1408	1408	85.489000	984	2335	1	chr3A.!!$R2	1351
15	TraesCS3B01G500900	chrUn	301718583	301719371	788	False	606	606	81.181000	2346	3131	1	chrUn.!!$F1	785

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
215	216	0.108585	GAACCTCTCACCCACTTGCA	59.891	55.0	0.00	0.0	0.0	4.08	F
711	721	0.254747	TATTGAAGGGGCCTGGTTCG	59.745	55.0	0.84	0.0	0.0	3.95	F
2034	4396	0.185901	AGCAACAGTTGGTGGTGGAT	59.814	50.0	17.24	0.0	45.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2034	4396	0.659427	CTACCACGAGATCGGCGTTA	59.341	55.0	6.85	5.11	44.95	3.18	R
2561	5087	0.038251	TTCTTCACGCTCTGCACGAT	60.038	50.0	1.86	0.00	0.00	3.73	R
3727	6612	0.107945	GCGAGCCATCAGAGGAACTT	60.108	55.0	0.00	0.00	41.55	2.66	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
64	65	0.172578	TTGACCCGTGCGATCACTAG	59.827	55.000	0.00	0.00	40.99	2.57
66	67	2.005960	GACCCGTGCGATCACTAGCT	62.006	60.000	0.00	0.00	40.99	3.32
74	75	4.477780	GTGCGATCACTAGCTAGGTATTC	58.522	47.826	24.35	13.68	40.03	1.75
78	79	2.940158	TCACTAGCTAGGTATTCGGCA	58.060	47.619	24.35	0.00	0.00	5.69
109	110	4.392138	CGAATTACCTCACTTCCTGTTTCC	59.608	45.833	0.00	0.00	0.00	3.13
111	112	1.518367	ACCTCACTTCCTGTTTCCCA	58.482	50.000	0.00	0.00	0.00	4.37
119	120	1.444933	TCCTGTTTCCCAGTCACCAT	58.555	50.000	0.00	0.00	39.74	3.55
183	184	4.184649	AGGGTTTTGGAGAAGAACACAT	57.815	40.909	0.00	0.00	0.00	3.21
215	216	0.108585	GAACCTCTCACCCACTTGCA	59.891	55.000	0.00	0.00	0.00	4.08
263	264	1.676678	TACTTGCCCTAGCCAGAGCG	61.677	60.000	0.00	0.00	46.67	5.03
278	279	3.181461	CCAGAGCGAAAATAGTGAGGGAT	60.181	47.826	0.00	0.00	0.00	3.85
317	318	4.325344	CCCATGAGAGGAAATAAAGTGGGT	60.325	45.833	0.00	0.00	39.09	4.51
347	348	2.666596	CTAGCCCGCCCAGATTGGAC	62.667	65.000	0.00	0.00	40.96	4.02
365	366	1.136305	GACAATGTAGCTCCGCCACTA	59.864	52.381	0.00	0.00	0.00	2.74
445	449	2.159254	TCATGTCAACGATGCGAGATCA	60.159	45.455	0.00	0.00	0.00	2.92
520	525	8.574251	ACACAAGCATGACCACTTATTTATTA	57.426	30.769	0.00	0.00	0.00	0.98
521	526	9.019656	ACACAAGCATGACCACTTATTTATTAA	57.980	29.630	0.00	0.00	0.00	1.40
522	527	9.289303	CACAAGCATGACCACTTATTTATTAAC	57.711	33.333	0.00	0.00	0.00	2.01
557	562	8.049721	AGGATGACCACTTATTTAAGAAGGAAG	58.950	37.037	15.44	0.00	38.94	3.46
564	569	7.386848	CCACTTATTTAAGAAGGAAGTCGTTCA	59.613	37.037	14.30	0.00	41.65	3.18
600	605	3.065567	GCATCCCGGCCCGAAAAA	61.066	61.111	3.71	0.00	0.00	1.94
610	615	2.281900	CCGAAAAAGCCCGACCCA	60.282	61.111	0.00	0.00	0.00	4.51
620	625	1.295423	CCCGACCCAACGATTCACT	59.705	57.895	0.00	0.00	35.09	3.41
688	698	0.679640	CTGGGCCCGTCATTTTAGCA	60.680	55.000	19.37	0.00	0.00	3.49
694	704	4.202212	GGGCCCGTCATTTTAGCAATTTAT	60.202	41.667	5.69	0.00	0.00	1.40

Showing 1 to 25 of 200 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.554959	TGGAGGATATGTTTAATACTCCCTC	57.445	40.000	11.04	0.00	41.71	4.30
1	2	7.474936	GCTTGGAGGATATGTTTAATACTCCCT	60.475	40.741	11.04	0.00	41.71	4.20
2	3	6.655425	GCTTGGAGGATATGTTTAATACTCCC	59.345	42.308	11.04	0.00	41.71	4.30
64	65	1.419374	CGTGATGCCGAATACCTAGC	58.581	55.000	0.00	0.00	0.00	3.42
66	67	3.580904	GCGTGATGCCGAATACCTA	57.419	52.632	0.00	0.00	37.76	3.08
78	79	2.427453	AGTGAGGTAATTCGAGCGTGAT	59.573	45.455	0.00	0.00	0.00	3.06
109	110	0.321210	TTGTACGGCATGGTGACTGG	60.321	55.000	0.00	0.00	0.00	4.00
111	112	0.685097	AGTTGTACGGCATGGTGACT	59.315	50.000	0.00	0.00	0.00	3.41
119	120	3.786516	TCGATTATGAGTTGTACGGCA	57.213	42.857	0.00	0.00	0.00	5.69
183	184	1.774217	AGGTTCCTTGTGGGGCTCA	60.774	57.895	0.00	0.00	35.33	4.26
278	279	3.465210	TCATGGGCCCAATATGGTCTTAA	59.535	43.478	32.58	2.20	35.17	1.85
317	318	3.281158	GGGCGGGCTAGTACAAATAAAA	58.719	45.455	0.26	0.00	0.00	1.52
329	330	2.366301	TCCAATCTGGGCGGGCTA	60.366	61.111	0.26	0.00	38.32	3.93
330	331	4.115199	GTCCAATCTGGGCGGGCT	62.115	66.667	0.26	0.00	38.32	5.19
375	379	2.166664	GCTACCCTCTTTCACGAGTGAT	59.833	50.000	6.77	0.00	39.64	3.06
445	449	4.635699	AAAAATTACCCTCTCAGTCGGT	57.364	40.909	0.00	0.00	0.00	4.69
520	525	5.048846	AGTGGTCATCCTTGTGTAAAGTT	57.951	39.130	0.00	0.00	34.23	2.66
521	526	4.706842	AGTGGTCATCCTTGTGTAAAGT	57.293	40.909	0.00	0.00	34.23	2.66
522	527	7.687941	AATAAGTGGTCATCCTTGTGTAAAG	57.312	36.000	0.00	0.00	34.23	1.85
557	562	2.067013	GCCAGGACTACTTTGAACGAC	58.933	52.381	0.00	0.00	0.00	4.34
564	569	0.625849	CCCATGGCCAGGACTACTTT	59.374	55.000	21.32	0.00	0.00	2.66
590	595	3.744719	GTCGGGCTTTTTCGGGCC	61.745	66.667	0.00	0.00	46.89	5.80
591	596	3.744719	GGTCGGGCTTTTTCGGGC	61.745	66.667	0.00	0.00	0.00	6.13
592	597	3.060000	GGGTCGGGCTTTTTCGGG	61.060	66.667	0.00	0.00	0.00	5.14
593	598	1.899534	TTGGGTCGGGCTTTTTCGG	60.900	57.895	0.00	0.00	0.00	4.30

Showing 1 to 25 of 186 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.