AutoCloner

Multiple sequence alignment - TraesCS4A01G234500

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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	TraesCS4A01G234500	chr4A	100.000	3304	0	0	1	3304	543373607	543376910	0.000000e+00	6102.0
1	TraesCS4A01G234500	chr4A	94.643	56	3	0	3135	3190	192625206	192625151	1.630000e-13	87.9
2	TraesCS4A01G234500	chr4A	96.970	33	1	0	3103	3135	594531621	594531653	4.610000e-04	56.5
3	TraesCS4A01G234500	chr4A	96.970	33	1	0	3103	3135	594531996	594532028	4.610000e-04	56.5
4	TraesCS4A01G234500	chr4D	95.160	3223	111	17	120	3304	53753485	53750270	0.000000e+00	5046.0
5	TraesCS4A01G234500	chr4D	93.333	195	10	3	2	195	53755027	53754835	5.400000e-73	285.0
6	TraesCS4A01G234500	chr4D	94.915	59	3	0	3132	3190	296729457	296729515	3.510000e-15	93.5
7	TraesCS4A01G234500	chr4D	96.970	33	1	0	3103	3135	8782444	8782412	4.610000e-04	56.5
8	TraesCS4A01G234500	chr4D	96.970	33	1	0	3103	3135	8783471	8783439	4.610000e-04	56.5
9	TraesCS4A01G234500	chr4B	93.491	3349	147	35	1	3304	78606145	78602823	0.000000e+00	4911.0
10	TraesCS4A01G234500	chr5D	72.115	624	122	40	1688	2276	78804891	78805497	1.240000e-29	141.0
11	TraesCS4A01G234500	chr5D	94.643	56	3	0	3135	3190	233044526	233044471	1.630000e-13	87.9
12	TraesCS4A01G234500	chr5A	71.820	621	126	42	1688	2277	74948837	74949439	7.440000e-27	132.0
13	TraesCS4A01G234500	chr5B	71.704	622	124	44	1688	2277	88359046	88359647	3.460000e-25	126.0
14	TraesCS4A01G234500	chr1B	98.148	54	1	0	3135	3188	529387041	529386988	9.760000e-16	95.3
15	TraesCS4A01G234500	chr6D	96.364	55	2	0	3135	3189	410398345	410398399	1.260000e-14	91.6
16	TraesCS4A01G234500	chr6B	96.364	55	2	0	3135	3189	617176648	617176702	1.260000e-14	91.6
17	TraesCS4A01G234500	chr6A	96.364	55	2	0	3135	3189	555729257	555729311	1.260000e-14	91.6
18	TraesCS4A01G234500	chr3A	100.000	33	0	0	3103	3135	671139546	671139514	9.900000e-06	62.1
19	TraesCS4A01G234500	chr3D	100.000	30	0	0	3106	3135	535782660	535782631	4.610000e-04	56.5
20	TraesCS4A01G234500	chr2D	100.000	29	0	0	3107	3135	482662492	482662520	2.000000e-03	54.7
21	TraesCS4A01G234500	chr2B	100.000	29	0	0	3107	3135	566624827	566624855	2.000000e-03	54.7

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	TraesCS4A01G234500	chr4A	543373607	543376910	3303	False	6102.0	6102	100.0000	1	3304	1	chr4A.!!$F1	3303
1	TraesCS4A01G234500	chr4D	53750270	53755027	4757	True	2665.5	5046	94.2465	2	3304	2	chr4D.!!$R2	3302
2	TraesCS4A01G234500	chr4B	78602823	78606145	3322	True	4911.0	4911	93.4910	1	3304	1	chr4B.!!$R1	3303

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
615	2052	0.179084	CCCTATTGGTGCATCGACGT	60.179	55.0	0.0	0.0	0.0	4.34	F
1287	2724	0.331278	TGGGCGACTCAAATGGGATT	59.669	50.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1648	3085	0.246360	CAGTAGTGGTGCCATCGTCA	59.754	55.0	0.00	0.00	0.0	4.35	R
2751	4225	1.726853	ATTAGCTGTCTGACAACCGC	58.273	50.0	12.16	11.69	0.0	5.68	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	0.250234	ACCACCGGACAGATGTCATG	59.750	55.000	9.46	9.10	46.47	3.07
118	119	5.723492	AGTTACAAACGTGTACAGGTTTC	57.277	39.130	32.82	24.28	44.50	2.78
162	163	7.914427	AGATCTATATCACACTGTTTGGGTA	57.086	36.000	0.00	0.00	34.28	3.69
219	1647	7.032580	CGAAAGGTAAATGATTGGTGCAATTA	58.967	34.615	0.00	0.00	33.90	1.40
256	1687	6.203145	TGGCTTTGTTTCAATTTGATGATGTG	59.797	34.615	0.00	0.00	0.00	3.21
310	1741	2.032550	CGGGCAGATGCTGTTGAAATAG	59.967	50.000	4.59	0.00	41.70	1.73
311	1742	2.360165	GGGCAGATGCTGTTGAAATAGG	59.640	50.000	4.59	0.00	41.70	2.57
347	1780	9.890629	AAGCTGTACATTTTGAGTATAAGATGA	57.109	29.630	0.00	0.00	0.00	2.92
407	1840	7.967908	TGTCCAATCCCTTTTAAGCATTTAAA	58.032	30.769	0.00	0.00	37.06	1.52
474	1909	5.012664	TGCAACTCTAGTTTATTGGGAGTGA	59.987	40.000	0.00	0.00	37.34	3.41
505	1940	5.279607	CCATTCCAACAACATTCTCCACAAT	60.280	40.000	0.00	0.00	0.00	2.71
615	2052	0.179084	CCCTATTGGTGCATCGACGT	60.179	55.000	0.00	0.00	0.00	4.34
642	2079	3.629398	GGAGAATTCTCGGCAATCATTGT	59.371	43.478	25.40	0.00	43.76	2.71
674	2111	0.601311	GACACTTGCCACTCGAGCTT	60.601	55.000	13.61	0.00	0.00	3.74
1021	2458	3.757947	TGGAGTCTGGAGGAGTGATTA	57.242	47.619	0.00	0.00	0.00	1.75
1041	2478	3.706373	GAAGCGGGCTGGGACTCA	61.706	66.667	0.00	0.00	0.00	3.41
1134	2571	0.689623	AGGAAGAACACCAGGAGCTG	59.310	55.000	0.00	0.00	0.00	4.24
1240	2677	4.157289	GTGTTGGTAGTCTCGTCCTTGATA	59.843	45.833	0.00	0.00	0.00	2.15
1287	2724	0.331278	TGGGCGACTCAAATGGGATT	59.669	50.000	0.00	0.00	0.00	3.01
1296	2733	1.358787	TCAAATGGGATTGGCTCCTGT	59.641	47.619	0.00	0.00	44.28	4.00
1459	2896	3.195661	GACACGTCCAACAAGAGAAAGT	58.804	45.455	0.00	0.00	0.00	2.66
1470	2907	3.008330	CAAGAGAAAGTGCCAGGATCAG	58.992	50.000	0.00	0.00	0.00	2.90
1648	3085	0.251922	AGGCCATGCAATGTGAAGGT	60.252	50.000	5.01	0.00	44.81	3.50
1674	3111	1.210722	TGGCACCACTACTGACACAAA	59.789	47.619	0.00	0.00	0.00	2.83
1722	3159	6.091441	ACGTCTGAAATTGACTCTAATGCTTC	59.909	38.462	0.00	0.00	32.70	3.86
1754	3191	0.973632	TGTTGCCTCTAAGCCGAAGA	59.026	50.000	0.00	0.00	0.00	2.87
1819	3256	1.953559	ATGCAAGGGTATGCTACACG	58.046	50.000	0.00	0.00	46.54	4.49
1984	3436	3.273434	TCAGCAACATGTCCTTCATAGC	58.727	45.455	0.00	0.00	34.67	2.97
1989	3441	4.860907	GCAACATGTCCTTCATAGCTTTTG	59.139	41.667	0.00	0.00	34.67	2.44
2035	3487	3.552890	GGGCAACAACTCAAAGATCAACC	60.553	47.826	0.00	0.00	39.74	3.77
2100	3552	3.073062	AGGCAGTGGAGTATGTGAAGTTT	59.927	43.478	0.00	0.00	0.00	2.66
2115	3567	5.642919	TGTGAAGTTTTTGCAGCTTCAAATT	59.357	32.000	12.34	4.27	46.55	1.82
2162	3614	7.428826	GTTCAGTTCAGAACTTCATCCATTTT	58.571	34.615	13.53	0.00	43.46	1.82
2169	3621	5.287752	CAGAACTTCATCCATTTTGAATGCG	59.712	40.000	0.00	0.00	32.94	4.73
2170	3622	3.514645	ACTTCATCCATTTTGAATGCGC	58.485	40.909	0.00	0.00	32.94	6.09
2185	3643	4.390603	TGAATGCGCGTGTTAAAGAGTTAT	59.609	37.500	8.43	0.00	0.00	1.89
2408	3868	1.082756	CGCGCAAGTGGTTTCTGAC	60.083	57.895	8.75	0.00	46.11	3.51
2458	3918	2.625790	CTCTCAGGCGTAAATAGAGGCT	59.374	50.000	0.00	0.00	41.64	4.58
2476	3936	4.521146	AGGCTGAATACAATGTTCTCCAG	58.479	43.478	0.00	0.00	0.00	3.86
2481	3941	5.809001	TGAATACAATGTTCTCCAGAAGCT	58.191	37.500	0.00	0.00	34.27	3.74
2526	3991	0.532862	GAGTGTCATGTATGGCCCGG	60.533	60.000	0.00	0.00	0.00	5.73
2546	4011	3.422085	CGGAAAATACGCGAAAAAGACGA	60.422	43.478	15.93	0.00	0.00	4.20
2663	4135	2.545106	GGCCGTGTCGTTTTTCTTCTTA	59.455	45.455	0.00	0.00	0.00	2.10
2751	4225	1.202879	TGTGGTTAGCTGGAACTTGGG	60.203	52.381	0.00	0.00	0.00	4.12
2775	4249	4.870426	CGGTTGTCAGACAGCTAATAATGT	59.130	41.667	16.17	0.00	29.63	2.71
2932	4406	6.414732	TCCTCATATTCTTTTCATCGTTGGT	58.585	36.000	0.00	0.00	0.00	3.67
2946	4420	6.411376	TCATCGTTGGTTGTTAGTGGAATAT	58.589	36.000	0.00	0.00	0.00	1.28
2975	4449	4.144297	ACTGTTGTATTGCTGGTGTCATT	58.856	39.130	0.00	0.00	0.00	2.57
3065	4541	3.319972	GGTCCCTTTTACCCTGTTTTCAC	59.680	47.826	0.00	0.00	0.00	3.18
3120	4596	9.095065	GTACTTGATCCGTTCACAAATATAAGT	57.905	33.333	0.00	0.00	32.84	2.24
3122	4598	8.450964	ACTTGATCCGTTCACAAATATAAGTTG	58.549	33.333	0.00	0.00	32.84	3.16
3147	4636	7.433719	TGTTTTGGATATTTGAGTGAACAAACG	59.566	33.333	0.00	0.00	41.49	3.60
3159	4648	6.037281	TGAGTGAACAAACGCACTAAAATGTA	59.963	34.615	0.00	0.00	44.77	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	70	7.436933	TCATCAGTATAACATGACATCTGTCC	58.563	38.462	0.00	0.00	44.15	4.02
104	105	2.037144	ACTGAGGAAACCTGTACACGT	58.963	47.619	0.00	0.00	31.76	4.49
105	106	2.814280	ACTGAGGAAACCTGTACACG	57.186	50.000	0.00	0.00	31.76	4.49
106	107	4.202223	TGAGAACTGAGGAAACCTGTACAC	60.202	45.833	0.00	0.00	31.76	2.90
118	119	5.713792	TCTAGACAAACTGAGAACTGAGG	57.286	43.478	0.00	0.00	0.00	3.86
148	149	1.069513	TCCGAGTACCCAAACAGTGTG	59.930	52.381	0.00	0.00	0.00	3.82
149	150	1.343465	CTCCGAGTACCCAAACAGTGT	59.657	52.381	0.00	0.00	0.00	3.55
162	163	5.066764	GTGTATAGAAGAAAGAGCTCCGAGT	59.933	44.000	10.93	0.00	0.00	4.18
219	1647	5.301551	TGAAACAAAGCCACTGATACACAAT	59.698	36.000	0.00	0.00	0.00	2.71
256	1687	7.919091	TCGTGTCTGTTTCATACTTATGATACC	59.081	37.037	13.86	3.87	41.16	2.73
310	1741	1.004277	TGTACAGCTTTCCATCACCCC	59.996	52.381	0.00	0.00	0.00	4.95
311	1742	2.489938	TGTACAGCTTTCCATCACCC	57.510	50.000	0.00	0.00	0.00	4.61
347	1780	1.651987	CGTGTATCCCGATTGCTTGT	58.348	50.000	0.00	0.00	0.00	3.16
407	1840	3.528905	TGATGGAGGGAATCTGGACATTT	59.471	43.478	0.00	0.00	0.00	2.32
474	1909	8.260114	GGAGAATGTTGTTGGAATGGAATAATT	58.740	33.333	0.00	0.00	0.00	1.40
505	1940	9.812347	AATTAATACAGGATCAGGCATTATGAA	57.188	29.630	0.00	0.00	0.00	2.57
596	2033	0.179084	ACGTCGATGCACCAATAGGG	60.179	55.000	4.06	0.00	44.81	3.53
615	2052	1.449601	GCCGAGAATTCTCCCGCAA	60.450	57.895	26.08	0.00	39.79	4.85
631	2068	0.102300	GGCCGGTTACAATGATTGCC	59.898	55.000	4.84	0.00	0.00	4.52
642	2079	1.420532	AAGTGTCCCAAGGCCGGTTA	61.421	55.000	1.90	0.00	0.00	2.85
674	2111	4.717877	TCTTCAGAAGTCAAGCCAATCAA	58.282	39.130	10.09	0.00	0.00	2.57
1021	2458	4.021925	GTCCCAGCCCGCTTCAGT	62.022	66.667	0.00	0.00	0.00	3.41
1041	2478	3.865929	CTGCGACGTCAGGCCAAGT	62.866	63.158	17.16	0.00	0.00	3.16
1062	2499	0.965439	CCATCATCTCCGACTCCTCC	59.035	60.000	0.00	0.00	0.00	4.30
1134	2571	1.973812	GGCCTGAACAGACCAAGGC	60.974	63.158	3.92	3.92	41.32	4.35
1240	2677	1.374947	CCCCATAATCCGACGGCAT	59.625	57.895	9.66	2.45	0.00	4.40
1296	2733	1.005037	CAGGTCAAGTGCTGCGGTA	60.005	57.895	0.00	0.00	0.00	4.02
1459	2896	1.009997	ATTTTCCCCTGATCCTGGCA	58.990	50.000	0.00	0.00	0.00	4.92
1470	2907	3.161866	TGTTTGGTCAGCTATTTTCCCC	58.838	45.455	0.00	0.00	0.00	4.81
1648	3085	0.246360	CAGTAGTGGTGCCATCGTCA	59.754	55.000	0.00	0.00	0.00	4.35
1664	3101	2.493278	AGCTTTGCTTGTTTGTGTCAGT	59.507	40.909	0.00	0.00	33.89	3.41
1722	3159	0.676151	GGCAACAGGAGGCTCTTGAG	60.676	60.000	30.45	22.01	0.00	3.02
1754	3191	4.737177	GCCAGCCTGAGCCTTGCT	62.737	66.667	0.00	0.00	43.88	3.91
1783	3220	1.830883	GCATAGAGGCTCTGGGGATCT	60.831	57.143	26.95	0.16	0.00	2.75
1819	3256	3.683822	CAGCAGAAAACTGAGAGGATGAC	59.316	47.826	0.00	0.00	37.32	3.06
1996	3448	6.535540	TGTTGCCCTTCATTTTACAGTACTA	58.464	36.000	0.00	0.00	0.00	1.82
1998	3450	5.699097	TGTTGCCCTTCATTTTACAGTAC	57.301	39.130	0.00	0.00	0.00	2.73
2035	3487	2.119801	ACCTGCAAGATAGCACAAGG	57.880	50.000	0.00	0.00	40.11	3.61
2100	3552	5.301551	TCTCACCTTAATTTGAAGCTGCAAA	59.698	36.000	22.17	22.17	41.49	3.68
2115	3567	2.708861	TGTGGAAAAGCCTCTCACCTTA	59.291	45.455	0.00	0.00	37.63	2.69
2125	3577	2.687935	TGAACTGAACTGTGGAAAAGCC	59.312	45.455	0.00	0.00	37.10	4.35
2126	3578	3.627577	TCTGAACTGAACTGTGGAAAAGC	59.372	43.478	0.00	0.00	0.00	3.51
2162	3614	2.139917	ACTCTTTAACACGCGCATTCA	58.860	42.857	5.73	0.00	0.00	2.57
2169	3621	8.959734	AACCATTAAATAACTCTTTAACACGC	57.040	30.769	0.00	0.00	34.39	5.34
2225	3683	3.003585	GCGCATACATCCACATTTCATCA	59.996	43.478	0.30	0.00	0.00	3.07
2408	3868	2.154462	CTGCCCGGAATAGCTTATTGG	58.846	52.381	0.73	0.00	0.00	3.16
2458	3918	5.809001	AGCTTCTGGAGAACATTGTATTCA	58.191	37.500	0.00	0.00	0.00	2.57
2512	3973	2.746279	ATTTTCCGGGCCATACATGA	57.254	45.000	4.39	0.00	0.00	3.07
2526	3991	6.952083	AGTATTCGTCTTTTTCGCGTATTTTC	59.048	34.615	5.77	0.00	0.00	2.29
2546	4011	3.452627	AGCCTCTTCCGACATTCAGTATT	59.547	43.478	0.00	0.00	0.00	1.89
2722	4195	7.152645	AGTTCCAGCTAACCACATTATATACG	58.847	38.462	0.00	0.00	0.00	3.06
2751	4225	1.726853	ATTAGCTGTCTGACAACCGC	58.273	50.000	12.16	11.69	0.00	5.68
2775	4249	2.837498	CCACATCATGCCACGATCTTA	58.163	47.619	0.00	0.00	0.00	2.10
2898	4372	2.846206	AGAATATGAGGAAGGCACCACA	59.154	45.455	3.87	3.87	35.29	4.17
2946	4420	6.712998	ACACCAGCAATACAACAGTATACAAA	59.287	34.615	5.50	0.00	0.00	2.83
2975	4449	2.142356	AATGCCGGACCAATGATTCA	57.858	45.000	5.05	0.00	0.00	2.57
3065	4541	2.292569	GCATCATGGACTGTATTGCCTG	59.707	50.000	0.00	0.00	0.00	4.85
3120	4596	9.092876	GTTTGTTCACTCAAATATCCAAAACAA	57.907	29.630	0.00	0.00	39.09	2.83
3122	4598	7.566868	GCGTTTGTTCACTCAAATATCCAAAAC	60.567	37.037	0.00	0.00	39.09	2.43
3196	4687	5.408299	TCACCATAGAGAATGTTTGTTCACG	59.592	40.000	0.00	0.00	33.34	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.