AutoCloner

Multiple sequence alignment - TraesCS5B01G133700

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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	TraesCS5B01G133700	chr5B	100.000	4789	0	0	1	4789	250236920	250232132	0.000000e+00	8844
1	TraesCS5B01G133700	chr5A	95.792	4515	131	22	1	4464	304541733	304537227	0.000000e+00	7230
2	TraesCS5B01G133700	chr5D	95.697	4462	138	28	22	4461	222736897	222741326	0.000000e+00	7127
3	TraesCS5B01G133700	chr3A	86.916	535	62	6	4253	4782	44221863	44222394	1.150000e-165	593
4	TraesCS5B01G133700	chr3A	85.769	527	65	4	4261	4778	31829261	31828736	2.520000e-152	549
5	TraesCS5B01G133700	chr3A	78.267	750	135	25	2466	3198	716758250	716758988	1.570000e-124	457
6	TraesCS5B01G133700	chr3A	90.566	159	15	0	1086	1244	716756679	716756837	1.350000e-50	211
7	TraesCS5B01G133700	chr4B	86.200	529	67	5	4259	4782	481492140	481491613	6.960000e-158	568
8	TraesCS5B01G133700	chr1B	87.064	487	57	6	4299	4781	600979702	600980186	3.260000e-151	545
9	TraesCS5B01G133700	chr2B	85.102	537	65	10	4260	4789	421078127	421077599	7.050000e-148	534
10	TraesCS5B01G133700	chr2D	87.041	463	56	4	4329	4789	625456134	625455674	1.980000e-143	520
11	TraesCS5B01G133700	chr2D	84.023	532	73	10	4259	4782	626769309	626769836	7.160000e-138	501
12	TraesCS5B01G133700	chr3B	85.253	495	67	6	4299	4789	753268237	753267745	5.530000e-139	505
13	TraesCS5B01G133700	chr3B	85.253	495	67	6	4299	4789	815161041	815161533	5.530000e-139	505
14	TraesCS5B01G133700	chr3B	78.133	750	136	25	2466	3198	777580272	777581010	7.310000e-123	451
15	TraesCS5B01G133700	chr3B	89.937	159	16	0	1086	1244	777578686	777578844	6.280000e-49	206
16	TraesCS5B01G133700	chr3D	78.926	745	130	25	2466	3198	581114580	581113851	9.320000e-132	481
17	TraesCS5B01G133700	chr3D	92.000	150	12	0	1095	1244	581116131	581115982	1.350000e-50	211
18	TraesCS5B01G133700	chr7D	81.716	536	52	16	4259	4789	179525822	179526316	5.770000e-109	405

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	TraesCS5B01G133700	chr5B	250232132	250236920	4788	True	8844.0	8844	100.0000	1	4789	1	chr5B.!!$R1	4788
1	TraesCS5B01G133700	chr5A	304537227	304541733	4506	True	7230.0	7230	95.7920	1	4464	1	chr5A.!!$R1	4463
2	TraesCS5B01G133700	chr5D	222736897	222741326	4429	False	7127.0	7127	95.6970	22	4461	1	chr5D.!!$F1	4439
3	TraesCS5B01G133700	chr3A	44221863	44222394	531	False	593.0	593	86.9160	4253	4782	1	chr3A.!!$F1	529
4	TraesCS5B01G133700	chr3A	31828736	31829261	525	True	549.0	549	85.7690	4261	4778	1	chr3A.!!$R1	517
5	TraesCS5B01G133700	chr3A	716756679	716758988	2309	False	334.0	457	84.4165	1086	3198	2	chr3A.!!$F2	2112
6	TraesCS5B01G133700	chr4B	481491613	481492140	527	True	568.0	568	86.2000	4259	4782	1	chr4B.!!$R1	523
7	TraesCS5B01G133700	chr2B	421077599	421078127	528	True	534.0	534	85.1020	4260	4789	1	chr2B.!!$R1	529
8	TraesCS5B01G133700	chr2D	626769309	626769836	527	False	501.0	501	84.0230	4259	4782	1	chr2D.!!$F1	523
9	TraesCS5B01G133700	chr3B	777578686	777581010	2324	False	328.5	451	84.0350	1086	3198	2	chr3B.!!$F2	2112
10	TraesCS5B01G133700	chr3D	581113851	581116131	2280	True	346.0	481	85.4630	1095	3198	2	chr3D.!!$R1	2103

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
567	589	0.110373	GAAAACCTAACGTGCGCCAG	60.110	55.000	4.18	0.15	0.00	4.85	F
945	998	0.478507	CCTCCTCTCCTCTCCTCTCC	59.521	65.000	0.00	0.00	0.00	3.71	F
2664	3294	1.008424	GATCGAGGAGATTCGCGCA	60.008	57.895	8.75	0.00	40.26	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1953	2264	1.978580	AGAAAATGGACTGACGAGGGT	59.021	47.619	0.0	0.0	0.0	4.34	R
2718	3348	1.878211	TGATGGGCAGATAGTGGTGA	58.122	50.000	0.0	0.0	0.0	4.02	R
3933	4587	0.748450	TATCGTCCAAAGCCCTACCG	59.252	55.000	0.0	0.0	0.0	4.02	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
24	26	2.508526	GGCCTTCCCTGCTGTATTATG	58.491	52.381	0.00	0.00	0.00	1.90
26	28	2.508526	CCTTCCCTGCTGTATTATGCC	58.491	52.381	0.00	0.00	0.00	4.40
61	66	2.492088	GCCCATAGTTGTTTGGTCCTTC	59.508	50.000	0.00	0.00	0.00	3.46
84	91	9.177608	CTTCCCTTTGTTGTCAATATTCAGATA	57.822	33.333	0.00	0.00	33.32	1.98
179	186	3.181412	ACACCCATCCCACAATAAACCTT	60.181	43.478	0.00	0.00	0.00	3.50
396	418	7.222000	TGTAAATACATGTGAAAAAGGGTCC	57.778	36.000	9.11	0.00	0.00	4.46
406	428	5.663556	TGTGAAAAAGGGTCCCATAGTTTTT	59.336	36.000	11.55	13.69	33.98	1.94
507	529	6.152379	CGAGATCTATCGAATCAACCAATCA	58.848	40.000	0.00	0.00	45.56	2.57
518	540	2.955660	TCAACCAATCACAAACTCCACC	59.044	45.455	0.00	0.00	0.00	4.61
567	589	0.110373	GAAAACCTAACGTGCGCCAG	60.110	55.000	4.18	0.15	0.00	4.85
598	633	6.791867	ACCACTACACACATACAGATACAT	57.208	37.500	0.00	0.00	0.00	2.29
653	688	2.267351	CCTGTGGCGTCATTGGCAA	61.267	57.895	0.68	0.68	46.76	4.52
662	697	0.539438	GTCATTGGCAAGTGGGGTCA	60.539	55.000	5.96	0.00	0.00	4.02
769	804	1.423845	GCCAACAGTATTGGTCGCG	59.576	57.895	0.00	0.00	41.53	5.87
942	995	1.850345	TCTTCCTCCTCTCCTCTCCTC	59.150	57.143	0.00	0.00	0.00	3.71
943	996	1.852965	CTTCCTCCTCTCCTCTCCTCT	59.147	57.143	0.00	0.00	0.00	3.69
944	997	1.518367	TCCTCCTCTCCTCTCCTCTC	58.482	60.000	0.00	0.00	0.00	3.20
945	998	0.478507	CCTCCTCTCCTCTCCTCTCC	59.521	65.000	0.00	0.00	0.00	3.71
946	999	1.522900	CTCCTCTCCTCTCCTCTCCT	58.477	60.000	0.00	0.00	0.00	3.69
1047	1100	4.580580	AGCTGGGATCTTTTTAATTAGCCG	59.419	41.667	0.00	0.00	0.00	5.52
1902	2213	4.363138	CCTTTCTGATCGATCGATTCACA	58.637	43.478	29.89	21.61	34.60	3.58
2204	2546	3.464907	CTCACATCACATCCATCTCCAC	58.535	50.000	0.00	0.00	0.00	4.02
2205	2547	2.171237	TCACATCACATCCATCTCCACC	59.829	50.000	0.00	0.00	0.00	4.61
2324	2666	3.119388	GCAGCATGTCATGGTATTGTTGT	60.119	43.478	16.82	0.00	39.29	3.32
2430	2777	9.809096	CTGGTTAATAGTATATCATACTGGCTG	57.191	37.037	8.72	0.00	0.00	4.85
2664	3294	1.008424	GATCGAGGAGATTCGCGCA	60.008	57.895	8.75	0.00	40.26	6.09
2718	3348	4.421479	CGCTCGCCGTTCCTCACT	62.421	66.667	0.00	0.00	0.00	3.41
3379	4033	1.377333	GAGGCGAGGAACAAAGGGG	60.377	63.158	0.00	0.00	0.00	4.79
3455	4109	1.068585	GGTCGTCAACAACTCCGGT	59.931	57.895	0.00	0.00	0.00	5.28
3513	4167	2.695147	TCACACATGCATATCTCCGTCT	59.305	45.455	0.00	0.00	0.00	4.18
3517	4171	2.037772	ACATGCATATCTCCGTCTTCCC	59.962	50.000	0.00	0.00	0.00	3.97
3577	4231	1.452110	TCTGTTGCATCATCGTTGGG	58.548	50.000	0.00	0.00	0.00	4.12
3934	4588	3.092081	GCAGCTTTTGGTTACTGCG	57.908	52.632	0.00	0.00	45.23	5.18
4047	4701	6.490040	GCCCTTGCATTTCTCCTATTATTACA	59.510	38.462	0.00	0.00	37.47	2.41
4116	4770	6.911250	AAATAACGAGAACTTCCCCAAAAT	57.089	33.333	0.00	0.00	0.00	1.82
4126	4780	6.660949	AGAACTTCCCCAAAATGATCTAACTG	59.339	38.462	0.00	0.00	0.00	3.16
4154	4808	0.310543	TGTCAAATGGCAACGCAGAC	59.689	50.000	0.00	0.00	42.51	3.51
4173	4827	7.167481	CGCAGACGTTTAAATTTTGTGAAAAA	58.833	30.769	0.00	0.00	31.94	1.94
4256	4913	3.508762	ACGTTCTTTCCACATAGCGTAG	58.491	45.455	0.00	0.00	0.00	3.51
4448	5112	2.698855	AGGATGTTCATCGTCTTGGG	57.301	50.000	6.70	0.00	33.00	4.12
4461	5125	4.912395	TTGGGTTTGGCAGCGGCT	62.912	61.111	9.17	0.00	40.87	5.52
4518	5183	1.603172	CGATGAGGCGATTGGTCCTAC	60.603	57.143	0.00	0.00	31.71	3.18
4607	5278	2.526873	ACCTGTGTCCTCGGGCTT	60.527	61.111	0.00	0.00	37.37	4.35
4631	5302	4.961511	TGCGACGGCGTTTGCTCT	62.962	61.111	29.28	1.73	44.10	4.09
4669	5340	1.558294	TGAGTGGTAGTCTAGGAGCGA	59.442	52.381	0.00	0.00	0.00	4.93
4681	5352	2.988010	AGGAGCGAATGCAGATTGTA	57.012	45.000	0.00	0.00	46.23	2.41
4695	5366	2.683362	AGATTGTAGTCTGCATCGACGA	59.317	45.455	0.00	0.00	38.90	4.20
4696	5367	3.316588	AGATTGTAGTCTGCATCGACGAT	59.683	43.478	4.05	4.05	38.90	3.73
4702	5373	3.142174	AGTCTGCATCGACGATATCTGA	58.858	45.455	10.57	11.41	38.90	3.27
4706	5377	3.642705	TGCATCGACGATATCTGAAAGG	58.357	45.455	10.57	0.00	0.00	3.11
4716	5387	4.202253	CGATATCTGAAAGGTGGTGGATCA	60.202	45.833	0.34	0.00	0.00	2.92
4782	5453	1.471287	CCGACGTCTTAGTCATGTGGA	59.529	52.381	14.70	0.00	40.98	4.02
4784	5455	2.418976	CGACGTCTTAGTCATGTGGAGA	59.581	50.000	14.70	0.00	40.98	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	12	2.653726	TGTTGGCATAATACAGCAGGG	58.346	47.619	0.00	0.00	0.00	4.45
20	22	4.314121	GGCAATTGTCTTTGTTGGCATAA	58.686	39.130	7.40	0.00	44.77	1.90
24	26	1.202627	TGGGCAATTGTCTTTGTTGGC	60.203	47.619	10.38	2.72	44.70	4.52
26	28	5.138125	ACTATGGGCAATTGTCTTTGTTG	57.862	39.130	10.38	0.00	0.00	3.33
179	186	6.479972	AGTACATCATCGGTCCAAGAATTA	57.520	37.500	0.00	0.00	0.00	1.40
226	233	0.661020	ACTTGTTTTTCCGTGAGCCG	59.339	50.000	0.00	0.00	0.00	5.52
281	288	9.706691	TGTGAAAAGGTTTATACAGAGTAGAAG	57.293	33.333	0.00	0.00	0.00	2.85
310	317	7.357429	TCTGACTACTCATCACATGAATCAT	57.643	36.000	0.00	0.00	39.11	2.45
396	418	6.279513	TGGGCAAAGATGTAAAAACTATGG	57.720	37.500	0.00	0.00	0.00	2.74
406	428	0.251916	CGGTCCTGGGCAAAGATGTA	59.748	55.000	0.00	0.00	0.00	2.29
428	450	1.999634	ATACATGGGTCAGGGCCAGC	62.000	60.000	6.18	0.00	0.00	4.85
438	460	1.152963	GGGCTTCGCATACATGGGT	60.153	57.895	0.00	0.00	41.04	4.51
507	529	2.764010	GGGTGAAAAAGGTGGAGTTTGT	59.236	45.455	0.00	0.00	0.00	2.83
518	540	5.126384	TGGTAAAAGTGTGAGGGTGAAAAAG	59.874	40.000	0.00	0.00	0.00	2.27
567	589	4.785511	ATGTGTGTAGTGGTAGTGACTC	57.214	45.455	0.00	0.00	0.00	3.36
598	633	4.175787	TGTGTGTATGTGTATGCGTACA	57.824	40.909	14.85	14.85	38.20	2.90
703	738	2.237066	TCGAGCGCACTGTGTTGTG	61.237	57.895	11.47	0.00	40.62	3.33
769	804	2.019897	GAGAGGGAGCTGAGCTGAGC	62.020	65.000	18.32	18.32	39.88	4.26
796	831	2.370189	CTCTCTCTCTCTCTCTCTCCCC	59.630	59.091	0.00	0.00	0.00	4.81
942	995	1.075600	GTGGGGAGAGGGAGAGGAG	60.076	68.421	0.00	0.00	0.00	3.69
943	996	2.997584	CGTGGGGAGAGGGAGAGGA	61.998	68.421	0.00	0.00	0.00	3.71
944	997	2.443016	CGTGGGGAGAGGGAGAGG	60.443	72.222	0.00	0.00	0.00	3.69
945	998	2.443016	CCGTGGGGAGAGGGAGAG	60.443	72.222	0.00	0.00	34.06	3.20
946	999	3.273654	ACCGTGGGGAGAGGGAGA	61.274	66.667	0.00	0.00	36.97	3.71
1047	1100	5.823570	TCATGTAGCACTAGTACTCTCCTTC	59.176	44.000	0.00	0.00	0.00	3.46
1054	1107	7.213216	CATGATCTCATGTAGCACTAGTACT	57.787	40.000	11.26	0.00	46.40	2.73
1953	2264	1.978580	AGAAAATGGACTGACGAGGGT	59.021	47.619	0.00	0.00	0.00	4.34
2204	2546	3.260100	AAGCAGTGGGTGGAGGGG	61.260	66.667	0.00	0.00	0.00	4.79
2205	2547	2.034687	CAAGCAGTGGGTGGAGGG	59.965	66.667	0.00	0.00	0.00	4.30
2607	3237	2.604686	AGGTGCTTGGCGAGGAGA	60.605	61.111	3.44	0.00	0.00	3.71
2718	3348	1.878211	TGATGGGCAGATAGTGGTGA	58.122	50.000	0.00	0.00	0.00	4.02
2934	3588	4.351938	CGGGAGTTGACGTCGGCA	62.352	66.667	11.62	0.00	0.00	5.69
3060	3714	4.760047	AGCGGCGTGACACCATCC	62.760	66.667	9.37	0.00	0.00	3.51
3138	3792	0.955428	GCTTGTTGGGCTCGATGTGA	60.955	55.000	0.00	0.00	0.00	3.58
3171	3825	1.661509	CGCTGACTGCACGAGTTCA	60.662	57.895	5.11	0.00	43.06	3.18
3455	4109	4.373116	GAACACTGAGGCGGCCGA	62.373	66.667	33.48	6.73	0.00	5.54
3513	4167	2.243774	ATCGAGAGCCAGAGGGGGAA	62.244	60.000	0.00	0.00	37.04	3.97
3517	4171	0.893270	ATCGATCGAGAGCCAGAGGG	60.893	60.000	23.84	0.00	37.18	4.30
3933	4587	0.748450	TATCGTCCAAAGCCCTACCG	59.252	55.000	0.00	0.00	0.00	4.02
3934	4588	1.070289	CCTATCGTCCAAAGCCCTACC	59.930	57.143	0.00	0.00	0.00	3.18
4047	4701	2.649531	TGGACGGGAAAATTGTCACT	57.350	45.000	0.00	0.00	34.32	3.41
4099	4753	4.265073	AGATCATTTTGGGGAAGTTCTCG	58.735	43.478	2.25	0.00	0.00	4.04
4116	4770	9.699410	ATTTGACAATTATTCCCAGTTAGATCA	57.301	29.630	0.00	0.00	0.00	2.92
4126	4780	4.566360	CGTTGCCATTTGACAATTATTCCC	59.434	41.667	0.00	0.00	0.00	3.97
4197	4854	8.350852	ACGTTAAATTATTTGTATTGGTCCCA	57.649	30.769	0.00	0.00	0.00	4.37
4432	5096	2.819608	CCAAACCCAAGACGATGAACAT	59.180	45.455	0.00	0.00	0.00	2.71
4448	5112	2.800736	CCATAGCCGCTGCCAAAC	59.199	61.111	2.16	0.00	38.69	2.93
4461	5125	1.669604	TTTTATTCAGCGCCGCCATA	58.330	45.000	4.98	0.00	0.00	2.74
4518	5183	1.846007	TTCAAATCCATCCCCAACCG	58.154	50.000	0.00	0.00	0.00	4.44
4631	5302	2.922950	AAGTTCCGTGCCGACGCTA	61.923	57.895	0.00	0.00	44.68	4.26
4646	5317	3.358118	GCTCCTAGACTACCACTCAAGT	58.642	50.000	0.00	0.00	0.00	3.16
4653	5324	1.681793	GCATTCGCTCCTAGACTACCA	59.318	52.381	0.00	0.00	34.30	3.25
4681	5352	3.142174	TCAGATATCGTCGATGCAGACT	58.858	45.455	17.98	6.78	38.90	3.24
4695	5366	5.133322	ACATGATCCACCACCTTTCAGATAT	59.867	40.000	0.00	0.00	0.00	1.63
4696	5367	4.474651	ACATGATCCACCACCTTTCAGATA	59.525	41.667	0.00	0.00	0.00	1.98
4702	5373	2.892852	CAACACATGATCCACCACCTTT	59.107	45.455	0.00	0.00	0.00	3.11
4706	5377	1.176527	CCCAACACATGATCCACCAC	58.823	55.000	0.00	0.00	0.00	4.16
4716	5387	1.874739	CGTACCACGAACCCAACACAT	60.875	52.381	0.00	0.00	46.05	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.