AutoCloner

Multiple sequence alignment - TraesCS2A01G329900

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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	TraesCS2A01G329900	chr2A	100.000	3572	0	0	1	3572	562507017	562510588	0.000000e+00	6597.0
1	TraesCS2A01G329900	chr2D	97.276	2827	61	8	753	3572	426435194	426432377	0.000000e+00	4780.0
2	TraesCS2A01G329900	chr2D	89.521	773	58	19	1	761	426435994	426435233	0.000000e+00	957.0
3	TraesCS2A01G329900	chr2D	100.000	48	0	0	2633	2680	426433262	426433215	4.910000e-14	89.8
4	TraesCS2A01G329900	chr2B	97.436	2691	65	3	883	3572	503454165	503451478	0.000000e+00	4584.0
5	TraesCS2A01G329900	chr2B	91.916	569	41	5	2	570	503460680	503460117	0.000000e+00	791.0
6	TraesCS2A01G329900	chr2B	92.254	142	5	5	756	894	503459793	503459655	2.810000e-46	196.0
7	TraesCS2A01G329900	chr2B	97.917	48	1	0	2633	2680	503452367	503452320	2.290000e-12	84.2
8	TraesCS2A01G329900	chr3B	80.640	594	105	7	1960	2548	825290313	825290901	5.440000e-123	451.0
9	TraesCS2A01G329900	chr3B	82.969	458	74	4	1960	2413	823976843	823977300	9.230000e-111	411.0
10	TraesCS2A01G329900	chr3B	84.010	394	61	2	1367	1759	825289858	825290250	9.360000e-101	377.0
11	TraesCS2A01G329900	chr3B	79.177	413	73	7	2068	2478	823719538	823719939	1.260000e-69	274.0
12	TraesCS2A01G329900	chr3B	81.279	219	35	4	1542	1759	823976567	823976780	4.740000e-39	172.0
13	TraesCS2A01G329900	chr4B	80.750	587	98	6	2068	2653	1767391	1766819	9.100000e-121	444.0
14	TraesCS2A01G329900	chr4B	80.620	387	66	3	1384	1761	1767928	1767542	1.250000e-74	291.0
15	TraesCS2A01G329900	chr5B	81.655	447	77	4	2033	2478	88977556	88977114	2.030000e-97	366.0
16	TraesCS2A01G329900	chr5B	73.035	649	118	42	1121	1737	619190909	619191532	3.670000e-40	176.0
17	TraesCS2A01G329900	chr5B	78.231	147	19	10	1193	1337	619106962	619107097	8.220000e-12	82.4
18	TraesCS2A01G329900	chr4A	80.928	388	63	5	1384	1761	603468903	603469289	2.700000e-76	296.0
19	TraesCS2A01G329900	chr4A	80.670	388	64	4	1384	1761	603390111	603389725	1.250000e-74	291.0
20	TraesCS2A01G329900	chr4D	81.223	229	30	7	1544	1761	1311738	1311512	4.740000e-39	172.0

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	TraesCS2A01G329900	chr2A	562507017	562510588	3571	False	6597.000000	6597	100.0000	1	3572	1	chr2A.!!$F1	3571
1	TraesCS2A01G329900	chr2D	426432377	426435994	3617	True	1942.266667	4780	95.5990	1	3572	3	chr2D.!!$R1	3571
2	TraesCS2A01G329900	chr2B	503451478	503454165	2687	True	2334.100000	4584	97.6765	883	3572	2	chr2B.!!$R1	2689
3	TraesCS2A01G329900	chr2B	503459655	503460680	1025	True	493.500000	791	92.0850	2	894	2	chr2B.!!$R2	892
4	TraesCS2A01G329900	chr3B	825289858	825290901	1043	False	414.000000	451	82.3250	1367	2548	2	chr3B.!!$F3	1181
5	TraesCS2A01G329900	chr3B	823976567	823977300	733	False	291.500000	411	82.1240	1542	2413	2	chr3B.!!$F2	871
6	TraesCS2A01G329900	chr4B	1766819	1767928	1109	True	367.500000	444	80.6850	1384	2653	2	chr4B.!!$R1	1269

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
835	1010	1.007964	CGAGCTGGGCTGTATCGAG	60.008	63.158	0.0	0.0	39.88	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2592	2791	0.460284	CGGTGGTGCTCACTATGTCC	60.46	60.0	9.83	0.0	45.38	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
174	175	4.732784	CAAAGTTTCCACCATGAATACCG	58.267	43.478	0.00	0.00	0.00	4.02
268	269	4.829492	AGAAATTCCCTTGGACAGACAAAG	59.171	41.667	0.00	0.00	0.00	2.77
285	287	3.228749	CAAAGCACTGACATAGCAAACG	58.771	45.455	2.61	0.00	0.00	3.60
291	293	3.679980	CACTGACATAGCAAACGCTAGTT	59.320	43.478	0.28	0.00	44.96	2.24
320	322	1.467342	GCCACAATTCGTTACCTCCAC	59.533	52.381	0.00	0.00	0.00	4.02
325	327	4.863131	CACAATTCGTTACCTCCACTAGAC	59.137	45.833	0.00	0.00	0.00	2.59
335	337	3.064931	CCTCCACTAGACAACGGTTTTC	58.935	50.000	0.00	0.00	0.00	2.29
345	347	2.166829	CAACGGTTTTCCCATCCATCA	58.833	47.619	0.00	0.00	36.42	3.07
355	357	7.069826	GGTTTTCCCATCCATCATTGAATTCTA	59.930	37.037	7.05	0.00	0.00	2.10
362	364	9.826574	CCATCCATCATTGAATTCTATGTTTTT	57.173	29.630	23.32	9.42	32.32	1.94
395	397	3.733443	AAAGTGCCTGAAACAATCACC	57.267	42.857	0.00	0.00	33.47	4.02
437	439	3.157087	CAGGCAACCCAAGATACTTGTT	58.843	45.455	9.99	0.00	37.17	2.83
441	443	5.007682	GGCAACCCAAGATACTTGTTAGAA	58.992	41.667	9.99	0.00	0.00	2.10
493	495	5.814188	TGACAAATCTCAGATCATGCAGTAC	59.186	40.000	0.00	0.00	0.00	2.73
506	508	3.040147	TGCAGTACCAGAAGTGTTAGC	57.960	47.619	0.00	0.00	0.00	3.09
557	559	1.533625	CAACTGGCCCGAATTCTGAA	58.466	50.000	0.00	0.00	0.00	3.02
570	668	7.579723	GCCCGAATTCTGAATGTAGGTATCTAT	60.580	40.741	3.22	0.00	0.00	1.98
607	705	9.461312	AAGGAAGTTACATTTAATACATCTGCA	57.539	29.630	0.00	0.00	0.00	4.41
697	805	2.005451	GCGAATGCACACTCTCTCATT	58.995	47.619	0.00	0.00	42.15	2.57
703	811	3.544684	TGCACACTCTCTCATTGTGTTT	58.455	40.909	3.14	0.00	42.19	2.83
751	859	4.269183	TCTCATTGTGGTGACAACAACTT	58.731	39.130	7.85	0.00	44.90	2.66
752	860	4.096231	TCTCATTGTGGTGACAACAACTTG	59.904	41.667	7.85	3.92	44.90	3.16
753	861	3.130164	TCATTGTGGTGACAACAACTTGG	59.870	43.478	7.85	0.00	44.90	3.61
770	942	3.879295	ACTTGGATCGCAACATATTGAGG	59.121	43.478	0.00	0.00	38.15	3.86
835	1010	1.007964	CGAGCTGGGCTGTATCGAG	60.008	63.158	0.00	0.00	39.88	4.04
852	1027	4.436998	GAGTGAGTGGCCCGGTCG	62.437	72.222	0.00	0.00	0.00	4.79
1509	1688	2.348998	CGCTGGGTCTCCAAGCTT	59.651	61.111	12.53	0.00	43.51	3.74
1893	2081	2.890371	CAGCAGCTCCCAATTGCC	59.110	61.111	0.00	0.00	38.58	4.52
2064	2259	1.632046	CGCCATACAACACGGTGTCC	61.632	60.000	15.09	0.00	32.75	4.02
2194	2389	3.736252	CCGTGTAGCCGAGAATGAAATAG	59.264	47.826	0.00	0.00	0.00	1.73
2387	2582	2.951787	GCATGGTCTTTGACATGGGGAT	60.952	50.000	0.00	0.00	33.68	3.85
2402	2597	1.625508	GGGGATTGGGAGGTCTACACT	60.626	57.143	0.00	0.00	0.00	3.55
2460	2655	2.233271	CCTCCACAAAGCACAATCTGT	58.767	47.619	0.00	0.00	0.00	3.41
2620	2819	4.722700	GCACCACCGGCCACATCT	62.723	66.667	0.00	0.00	0.00	2.90
2739	2938	1.805869	CACTGAAGAACTGGCAGAGG	58.194	55.000	23.66	0.00	33.94	3.69
2840	3039	6.015265	GGTTTGTACTCTAGTCCCTATCATCC	60.015	46.154	0.00	0.00	0.00	3.51
3258	3458	0.035439	GGTGGTGTCCGTGGATGAAT	60.035	55.000	0.00	0.00	0.00	2.57
3295	3495	1.563435	CTGCAGCGACCTCACAACTG	61.563	60.000	0.00	0.00	0.00	3.16
3459	3659	1.826385	GCACCCAGCTAACAATGTCT	58.174	50.000	0.00	0.00	41.15	3.41
3516	3716	2.664081	GGTGACCAGCTCCAGGAGG	61.664	68.421	18.83	5.07	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
123	124	4.576330	AAAAGTGAAGGAGGTATGGGAG	57.424	45.455	0.00	0.00	0.00	4.30
238	239	6.272324	TCTGTCCAAGGGAATTTCTAAAGAGA	59.728	38.462	0.00	0.00	31.38	3.10
268	269	3.296516	GCGTTTGCTATGTCAGTGC	57.703	52.632	0.00	0.00	38.39	4.40
291	293	1.173043	CGAATTGTGGCCCAAGCTAA	58.827	50.000	0.00	0.00	39.73	3.09
320	322	3.007635	GGATGGGAAAACCGTTGTCTAG	58.992	50.000	1.43	0.00	44.64	2.43
325	327	2.166829	TGATGGATGGGAAAACCGTTG	58.833	47.619	0.00	0.00	44.64	4.10
335	337	7.534723	AACATAGAATTCAATGATGGATGGG	57.465	36.000	8.44	0.00	0.00	4.00
363	365	9.023962	TGTTTCAGGCACTTTATTTGAGATAAT	57.976	29.630	0.00	0.00	34.60	1.28
365	367	7.994425	TGTTTCAGGCACTTTATTTGAGATA	57.006	32.000	0.00	0.00	34.60	1.98
366	368	6.899393	TGTTTCAGGCACTTTATTTGAGAT	57.101	33.333	0.00	0.00	34.60	2.75
367	369	6.707440	TTGTTTCAGGCACTTTATTTGAGA	57.293	33.333	0.00	0.00	34.60	3.27
368	370	7.115378	GTGATTGTTTCAGGCACTTTATTTGAG	59.885	37.037	0.00	0.00	34.60	3.02
369	371	6.922957	GTGATTGTTTCAGGCACTTTATTTGA	59.077	34.615	0.00	0.00	34.60	2.69
370	372	6.146021	GGTGATTGTTTCAGGCACTTTATTTG	59.854	38.462	0.00	0.00	34.60	2.32
371	373	6.223120	GGTGATTGTTTCAGGCACTTTATTT	58.777	36.000	0.00	0.00	34.60	1.40
395	397	2.042686	CATGGTGGGTGTAGACATGG	57.957	55.000	0.00	0.00	36.25	3.66
437	439	6.484643	GCATATTGATGGTGAAGCTCTTTCTA	59.515	38.462	0.00	0.00	33.76	2.10
441	443	4.529897	TGCATATTGATGGTGAAGCTCTT	58.470	39.130	0.00	0.00	33.26	2.85
515	517	5.538433	TGGTTAGCTTGGCAAAATCTAGTTT	59.462	36.000	0.00	0.00	0.00	2.66
590	688	7.989170	TCTCATGAGTGCAGATGTATTAAATGT	59.011	33.333	21.92	0.00	0.00	2.71
594	692	8.206189	TGATTCTCATGAGTGCAGATGTATTAA	58.794	33.333	21.92	4.98	0.00	1.40
607	705	9.902684	ACTGATAATTTCTTGATTCTCATGAGT	57.097	29.630	21.92	3.90	33.06	3.41
667	766	2.975851	GTGTGCATTCGCTCAAGAAAAG	59.024	45.455	0.00	0.00	42.84	2.27
715	823	4.020839	CACAATGAGAGGGATTGCCTTTTT	60.021	41.667	0.00	0.00	34.67	1.94
716	824	3.512724	CACAATGAGAGGGATTGCCTTTT	59.487	43.478	0.00	0.00	34.67	2.27
718	826	2.622452	CCACAATGAGAGGGATTGCCTT	60.622	50.000	0.00	0.00	34.67	4.35
719	827	1.064166	CCACAATGAGAGGGATTGCCT	60.064	52.381	0.00	0.00	34.67	4.75
720	828	1.341383	ACCACAATGAGAGGGATTGCC	60.341	52.381	0.00	0.00	34.67	4.52
727	835	2.849942	TGTTGTCACCACAATGAGAGG	58.150	47.619	0.00	0.00	44.47	3.69
751	859	2.158769	AGCCTCAATATGTTGCGATCCA	60.159	45.455	0.00	0.00	35.26	3.41
752	860	2.481952	GAGCCTCAATATGTTGCGATCC	59.518	50.000	0.00	0.00	35.26	3.36
753	861	2.156504	CGAGCCTCAATATGTTGCGATC	59.843	50.000	0.00	0.00	35.26	3.69
809	981	2.670934	GCCCAGCTCGCCATATGG	60.671	66.667	18.07	18.07	38.53	2.74
811	983	1.121407	TACAGCCCAGCTCGCCATAT	61.121	55.000	0.00	0.00	36.40	1.78
812	984	1.121407	ATACAGCCCAGCTCGCCATA	61.121	55.000	0.00	0.00	36.40	2.74
835	1010	4.436998	CGACCGGGCCACTCACTC	62.437	72.222	6.32	0.00	0.00	3.51
881	1056	1.153489	CACCTGCCGGATCTCACAG	60.153	63.158	5.05	0.63	0.00	3.66
1842	2030	4.590850	ACGATGTTCATAGCAGAGCATA	57.409	40.909	0.00	0.00	39.18	3.14
1884	2072	2.389962	CCTTCATTGTGGCAATTGGG	57.610	50.000	7.72	0.00	0.00	4.12
2064	2259	6.381801	CAGGTTCTTGGCACTAGTAAAAATG	58.618	40.000	0.00	0.00	0.00	2.32
2170	2365	1.153647	CATTCTCGGCTACACGGCA	60.154	57.895	0.00	0.00	38.27	5.69
2194	2389	4.377897	CGGGGATAATACCTCAGAACAAC	58.622	47.826	0.00	0.00	0.00	3.32
2387	2582	1.073284	GGCAAAGTGTAGACCTCCCAA	59.927	52.381	0.00	0.00	0.00	4.12
2402	2597	2.199652	CCAGCAACGGGAAGGCAAA	61.200	57.895	0.00	0.00	0.00	3.68
2460	2655	3.678056	ATGTCGCTGAGAAAGTACCAA	57.322	42.857	0.00	0.00	0.00	3.67
2550	2748	3.273434	TCAATCCTCCAAATCTTGCTCG	58.727	45.455	0.00	0.00	0.00	5.03
2592	2791	0.460284	CGGTGGTGCTCACTATGTCC	60.460	60.000	9.83	0.00	45.38	4.02
2620	2819	6.095300	CAGGCATGATAAACATAACTTCCACA	59.905	38.462	0.00	0.00	37.46	4.17
2699	2898	2.323999	CTCTCCATATGAGGGGCTCT	57.676	55.000	3.65	0.00	41.76	4.09
2840	3039	6.429692	TCCATTACAGGACATAAACACACAAG	59.570	38.462	0.00	0.00	31.23	3.16
2918	3118	7.951347	ACTTGCAAATATCTGAAAATCCTCT	57.049	32.000	0.00	0.00	0.00	3.69
3068	3268	1.400242	GCCTGTGTGATTCGCTTGTTC	60.400	52.381	0.00	0.00	0.00	3.18
3210	3410	5.645067	TCTGAAGTTGCTATGTGATCTTTGG	59.355	40.000	0.00	0.00	0.00	3.28
3258	3458	0.682852	AGGCGCTGTAGTTTGTACCA	59.317	50.000	7.64	0.00	0.00	3.25
3295	3495	0.882042	CAGAGGCCGGACATGTATGC	60.882	60.000	11.69	1.32	0.00	3.14
3387	3587	1.000283	CAGATACTCGACCCCAGCATC	60.000	57.143	0.00	0.00	0.00	3.91
3459	3659	2.343758	GCGTCCAAGGACTGCTCA	59.656	61.111	20.77	0.00	42.54	4.26
3516	3716	2.633488	GTCTACAGCTTTGGGGTCATC	58.367	52.381	0.00	0.00	0.00	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.