AutoCloner

Multiple sequence alignment - TraesCS3A01G492500

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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	TraesCS3A01G492500	chr3A	100.000	2459	0	0	1	2459	719355069	719352611	0.000000e+00	4542.0
1	TraesCS3A01G492500	chr3A	87.836	781	53	26	989	1734	719360804	719360031	0.000000e+00	878.0
2	TraesCS3A01G492500	chr3A	86.376	756	70	20	989	1734	719337323	719336591	0.000000e+00	795.0
3	TraesCS3A01G492500	chr3A	86.792	477	55	5	1985	2459	719360013	719359543	2.170000e-145	525.0
4	TraesCS3A01G492500	chr3A	82.353	408	31	11	537	922	719361281	719360893	1.420000e-82	316.0
5	TraesCS3A01G492500	chr3B	84.252	1797	157	51	30	1734	787989222	787990984	0.000000e+00	1635.0
6	TraesCS3A01G492500	chr3B	87.732	1239	85	32	537	1732	787472094	787473308	0.000000e+00	1384.0
7	TraesCS3A01G492500	chr3B	88.245	1157	93	16	790	1925	788058786	788057652	0.000000e+00	1343.0
8	TraesCS3A01G492500	chr3B	91.071	448	35	2	2012	2459	788057623	788057181	3.500000e-168	601.0
9	TraesCS3A01G492500	chr3B	85.504	476	59	7	1989	2459	787992064	787992534	2.840000e-134	488.0
10	TraesCS3A01G492500	chr3B	86.652	442	34	9	1310	1734	787991337	787991770	1.330000e-127	466.0
11	TraesCS3A01G492500	chr3B	90.365	301	25	2	204	500	788059140	788058840	2.290000e-105	392.0
12	TraesCS3A01G492500	chr3B	83.654	416	34	15	586	971	788074041	788073630	6.460000e-96	361.0
13	TraesCS3A01G492500	chr3B	83.747	363	49	7	30	383	788078207	788077846	3.920000e-88	335.0
14	TraesCS3A01G492500	chr3B	90.654	107	5	3	610	715	787986634	787986736	1.190000e-28	137.0
15	TraesCS3A01G492500	chr3D	85.902	1596	132	49	1	1553	589494166	589492621	0.000000e+00	1615.0
16	TraesCS3A01G492500	chr3D	87.821	1404	116	18	991	2378	589572851	589571487	0.000000e+00	1594.0
17	TraesCS3A01G492500	chr3D	90.248	1087	56	25	536	1580	589506471	589505393	0.000000e+00	1375.0
18	TraesCS3A01G492500	chr3D	88.153	996	71	22	765	1734	589433034	589432060	0.000000e+00	1142.0
19	TraesCS3A01G492500	chr3D	90.361	830	56	11	729	1540	589426843	589426020	0.000000e+00	1068.0
20	TraesCS3A01G492500	chr3D	88.603	544	52	9	1	536	589564093	589563552	0.000000e+00	652.0
21	TraesCS3A01G492500	chr3D	85.882	510	54	10	1	497	589437731	589437227	6.020000e-146	527.0
22	TraesCS3A01G492500	chr3D	83.617	470	37	18	537	988	589418226	589417779	2.940000e-109	405.0
23	TraesCS3A01G492500	chr3D	85.385	390	23	16	610	971	589573294	589572911	8.300000e-100	374.0
24	TraesCS3A01G492500	chr3D	88.412	233	14	6	553	772	589437201	589436969	4.030000e-68	268.0
25	TraesCS3A01G492500	chr3D	87.113	194	16	3	1549	1733	589474905	589474712	6.890000e-51	211.0
26	TraesCS3A01G492500	chr4A	93.548	124	8	0	1850	1973	592264760	592264883	4.180000e-43	185.0
27	TraesCS3A01G492500	chr4A	93.548	124	8	0	1850	1973	592602178	592602301	4.180000e-43	185.0
28	TraesCS3A01G492500	chr4A	93.548	124	8	0	1850	1973	592891298	592891421	4.180000e-43	185.0
29	TraesCS3A01G492500	chr4A	93.548	124	8	0	1850	1973	593162768	593162891	4.180000e-43	185.0
30	TraesCS3A01G492500	chr4A	91.935	124	10	0	1850	1973	591452672	591452549	9.040000e-40	174.0
31	TraesCS3A01G492500	chr1D	93.388	121	8	0	1850	1970	206049296	206049176	1.940000e-41	180.0
32	TraesCS3A01G492500	chr2D	94.737	114	6	0	1850	1963	24923149	24923036	6.990000e-41	178.0
33	TraesCS3A01G492500	chr2D	86.087	115	15	1	1738	1851	353586806	353586692	3.320000e-24	122.0
34	TraesCS3A01G492500	chr1A	86.047	86	9	3	337	420	20963183	20963099	3.370000e-14	89.8
35	TraesCS3A01G492500	chr2B	73.206	209	50	6	198	402	756566223	756566017	1.220000e-08	71.3
36	TraesCS3A01G492500	chr2A	100.000	29	0	0	86	114	699643211	699643183	1.000000e-03	54.7
37	TraesCS3A01G492500	chr7B	100.000	28	0	0	87	114	714452957	714452930	4.000000e-03	52.8

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	TraesCS3A01G492500	chr3A	719352611	719355069	2458	True	4542.000000	4542	100.000000	1	2459	1	chr3A.!!$R2	2458
1	TraesCS3A01G492500	chr3A	719336591	719337323	732	True	795.000000	795	86.376000	989	1734	1	chr3A.!!$R1	745
2	TraesCS3A01G492500	chr3A	719359543	719361281	1738	True	573.000000	878	85.660333	537	2459	3	chr3A.!!$R3	1922
3	TraesCS3A01G492500	chr3B	787472094	787473308	1214	False	1384.000000	1384	87.732000	537	1732	1	chr3B.!!$F1	1195
4	TraesCS3A01G492500	chr3B	788057181	788059140	1959	True	778.666667	1343	89.893667	204	2459	3	chr3B.!!$R1	2255
5	TraesCS3A01G492500	chr3B	787986634	787992534	5900	False	681.500000	1635	86.765500	30	2459	4	chr3B.!!$F2	2429
6	TraesCS3A01G492500	chr3B	788073630	788078207	4577	True	348.000000	361	83.700500	30	971	2	chr3B.!!$R2	941
7	TraesCS3A01G492500	chr3D	589492621	589494166	1545	True	1615.000000	1615	85.902000	1	1553	1	chr3D.!!$R4	1552
8	TraesCS3A01G492500	chr3D	589505393	589506471	1078	True	1375.000000	1375	90.248000	536	1580	1	chr3D.!!$R5	1044
9	TraesCS3A01G492500	chr3D	589426020	589426843	823	True	1068.000000	1068	90.361000	729	1540	1	chr3D.!!$R2	811
10	TraesCS3A01G492500	chr3D	589571487	589573294	1807	True	984.000000	1594	86.603000	610	2378	2	chr3D.!!$R8	1768
11	TraesCS3A01G492500	chr3D	589563552	589564093	541	True	652.000000	652	88.603000	1	536	1	chr3D.!!$R6	535
12	TraesCS3A01G492500	chr3D	589432060	589437731	5671	True	645.666667	1142	87.482333	1	1734	3	chr3D.!!$R7	1733

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
243	2821	0.61326	ACGCATTTACAGCAGGAGGA	59.387	50.0	0.0	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	13008	0.107897	TCCTATCGTGCGCCAAACAT	60.108	50.0	4.18	0.0	0.0	2.71	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
126	2694	5.657302	ACTACCACATTTAAGGTCTCGATCT	59.343	40.000	0.00	0.00	39.31	2.75
130	2698	6.070995	ACCACATTTAAGGTCTCGATCTTACA	60.071	38.462	0.00	0.00	34.04	2.41
170	2738	4.079980	TGTGAGCAAAAACTACCAGCTA	57.920	40.909	0.00	0.00	35.36	3.32
171	2739	4.065088	TGTGAGCAAAAACTACCAGCTAG	58.935	43.478	0.00	0.00	35.36	3.42
243	2821	0.613260	ACGCATTTACAGCAGGAGGA	59.387	50.000	0.00	0.00	0.00	3.71
260	2838	1.077429	GAGCCTGCTTGTTAGGGGG	60.077	63.158	0.00	0.00	35.80	5.40
275	2853	4.646877	GGGGGCGTGACGGGAAAA	62.647	66.667	7.25	0.00	0.00	2.29
287	2865	3.505680	TGACGGGAAAATCAACTCCATTG	59.494	43.478	0.00	0.00	39.94	2.82
356	2943	1.168714	GCATGAACTTTCTTCCGCCT	58.831	50.000	0.00	0.00	0.00	5.52
368	2955	1.136110	CTTCCGCCTCTCTTTCTCTCC	59.864	57.143	0.00	0.00	0.00	3.71
383	3271	6.484643	TCTTTCTCTCCTTGACAATTCAACTG	59.515	38.462	0.00	0.00	36.79	3.16
451	5761	2.508663	GGCAGCCCGTACTCGAAC	60.509	66.667	0.00	0.00	39.71	3.95
452	5762	2.879462	GCAGCCCGTACTCGAACG	60.879	66.667	2.65	2.65	42.49	3.95
453	5763	2.564975	CAGCCCGTACTCGAACGT	59.435	61.111	8.68	0.00	41.27	3.99
454	5764	1.513586	CAGCCCGTACTCGAACGTC	60.514	63.158	8.68	0.98	41.27	4.34
707	6984	1.011968	TCACGCCAAGTCACGTATGC	61.012	55.000	0.00	0.00	41.32	3.14
712	6995	1.298340	CAAGTCACGTATGCCCCCA	59.702	57.895	0.00	0.00	0.00	4.96
831	11083	2.430610	GCGACCAGGGCATCTCTCT	61.431	63.158	0.00	0.00	0.00	3.10
1434	11763	2.510238	GGCGTGCTCAGCTTCGAT	60.510	61.111	16.53	0.00	34.52	3.59
1478	11807	1.762460	GCTAGCTAGCCTGACCCCA	60.762	63.158	31.67	0.00	43.39	4.96
1488	11817	3.612247	CTGACCCCAGACCCAAGCG	62.612	68.421	0.00	0.00	43.02	4.68
1509	11850	0.322322	ATACCCGTTCCGTCTTGCAA	59.678	50.000	0.00	0.00	0.00	4.08
1642	12814	1.672881	CGGTGCTCTTGGAATTGGATC	59.327	52.381	0.00	0.00	0.00	3.36
1699	12875	7.410800	TGAATGAAAAACATGAATGTGAAGC	57.589	32.000	0.00	0.00	41.61	3.86
1766	12942	4.163839	TGGCAATATTTGGAAAGGGGAATG	59.836	41.667	0.00	0.00	0.00	2.67
1782	12958	5.043281	AGGGGAATGAGAGTTTAGAGTAGGA	60.043	44.000	0.00	0.00	0.00	2.94
1800	12976	7.982354	AGAGTAGGAAGTTGTATTGTGATTAGC	59.018	37.037	0.00	0.00	0.00	3.09
1802	12978	5.193679	AGGAAGTTGTATTGTGATTAGCCC	58.806	41.667	0.00	0.00	0.00	5.19
1810	12987	3.565764	TTGTGATTAGCCCTGAGATGG	57.434	47.619	0.00	0.00	0.00	3.51
1828	13006	3.722908	TGGGTCGTTTATTCCCAATCA	57.277	42.857	0.00	0.00	46.78	2.57
1830	13008	5.375283	TGGGTCGTTTATTCCCAATCATA	57.625	39.130	0.00	0.00	46.78	2.15
1879	13057	7.609532	CCCATGACTATTCCCTTATGAATTCTC	59.390	40.741	7.05	0.00	36.41	2.87
1887	13065	6.596869	TCCCTTATGAATTCTCAATCCCTT	57.403	37.500	7.05	0.00	34.49	3.95
1928	13106	8.530269	TTTAAAGTCTCGTACCTCTTCAATTC	57.470	34.615	0.00	0.00	0.00	2.17
1929	13107	5.723672	AAGTCTCGTACCTCTTCAATTCA	57.276	39.130	0.00	0.00	0.00	2.57
1930	13108	5.317733	AGTCTCGTACCTCTTCAATTCAG	57.682	43.478	0.00	0.00	0.00	3.02
1936	13114	4.811557	CGTACCTCTTCAATTCAGATTCCC	59.188	45.833	0.00	0.00	0.00	3.97
1980	13185	3.196939	ACACGTTGTTAGGCCTTGTTA	57.803	42.857	12.58	0.00	0.00	2.41
1986	13191	4.259356	GTTGTTAGGCCTTGTTAGGTAGG	58.741	47.826	12.58	0.00	44.00	3.18
2009	13224	1.697754	AACCCCCTAGGCCATCCAG	60.698	63.158	5.01	0.00	40.58	3.86
2018	13233	2.044946	GCCATCCAGTCCACCCAC	60.045	66.667	0.00	0.00	0.00	4.61
2051	13266	0.995024	CCCACTCCCTCAACCAATCT	59.005	55.000	0.00	0.00	0.00	2.40
2129	13344	1.205460	TAAACCCCTCCTGGCAGGTC	61.205	60.000	31.60	0.00	36.53	3.85
2130	13345	3.810687	AACCCCTCCTGGCAGGTCA	62.811	63.158	31.60	14.02	36.53	4.02
2131	13346	2.693864	CCCCTCCTGGCAGGTCAT	60.694	66.667	31.60	0.00	36.53	3.06
2136	13351	2.202987	CCTGGCAGGTCATCGCTC	60.203	66.667	25.74	0.00	0.00	5.03
2140	13355	4.148825	GCAGGTCATCGCTCCCGT	62.149	66.667	0.00	0.00	35.54	5.28
2219	13435	1.338890	TTTCCACGGGTGAGGTGACA	61.339	55.000	0.00	0.00	37.60	3.58
2304	13523	2.818130	TAACTAAACCCGCACGAACT	57.182	45.000	0.00	0.00	0.00	3.01
2397	13617	0.539986	ATGGGCGTAATCGGACAAGT	59.460	50.000	0.00	0.00	37.56	3.16
2403	13623	4.040376	GGCGTAATCGGACAAGTACTTAG	58.960	47.826	8.04	5.71	37.56	2.18
2404	13624	4.201950	GGCGTAATCGGACAAGTACTTAGA	60.202	45.833	8.04	6.29	37.56	2.10
2405	13625	4.968788	GCGTAATCGGACAAGTACTTAGAG	59.031	45.833	8.04	0.00	37.56	2.43
2406	13626	4.968788	CGTAATCGGACAAGTACTTAGAGC	59.031	45.833	8.04	0.00	0.00	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	2615	4.147321	AGCATCAGTTTCACCTGTTTCAT	58.853	39.130	0.00	0.00	34.02	2.57
130	2698	9.555727	TGCTCACAATTTTAAAGTAGTAGTTCT	57.444	29.630	0.00	0.00	0.00	3.01
152	2720	3.685272	GGTCTAGCTGGTAGTTTTTGCTC	59.315	47.826	13.09	0.00	35.47	4.26
202	2780	2.413310	AAATCGTCTAAACCGGCCAT	57.587	45.000	0.00	0.00	0.00	4.40
243	2821	3.090765	CCCCCTAACAAGCAGGCT	58.909	61.111	0.00	0.00	0.00	4.58
260	2838	1.238625	TTGATTTTCCCGTCACGCCC	61.239	55.000	0.00	0.00	0.00	6.13
287	2865	1.392510	GTCAACTTAACGGTCCATCGC	59.607	52.381	0.00	0.00	0.00	4.58
352	2936	1.821753	TCAAGGAGAGAAAGAGAGGCG	59.178	52.381	0.00	0.00	0.00	5.52
353	2937	2.564947	TGTCAAGGAGAGAAAGAGAGGC	59.435	50.000	0.00	0.00	0.00	4.70
356	2943	6.425210	TGAATTGTCAAGGAGAGAAAGAGA	57.575	37.500	0.00	0.00	32.74	3.10
368	2955	2.624838	AGGTGCCAGTTGAATTGTCAAG	59.375	45.455	0.00	0.00	44.44	3.02
433	5743	4.124351	TTCGAGTACGGGCTGCCG	62.124	66.667	13.40	10.64	40.21	5.69
434	5744	2.508663	GTTCGAGTACGGGCTGCC	60.509	66.667	11.05	11.05	40.21	4.85
435	5745	2.879462	CGTTCGAGTACGGGCTGC	60.879	66.667	1.67	0.00	40.21	5.25
436	5746	1.513586	GACGTTCGAGTACGGGCTG	60.514	63.158	13.69	0.00	45.44	4.85
437	5747	2.694760	GGACGTTCGAGTACGGGCT	61.695	63.158	13.69	0.00	45.44	5.19
438	5748	2.202531	GGACGTTCGAGTACGGGC	60.203	66.667	13.69	5.61	45.44	6.13
439	5749	2.099062	CGGACGTTCGAGTACGGG	59.901	66.667	11.86	0.00	44.19	5.28
442	5752	1.063951	CAGCACGGACGTTCGAGTAC	61.064	60.000	25.79	8.81	0.00	2.73
443	5753	1.208358	CAGCACGGACGTTCGAGTA	59.792	57.895	25.79	0.00	0.00	2.59
444	5754	2.050351	CAGCACGGACGTTCGAGT	60.050	61.111	25.79	3.31	0.00	4.18
445	5755	1.797933	CTCAGCACGGACGTTCGAG	60.798	63.158	25.79	17.36	0.00	4.04
446	5756	2.254350	CTCAGCACGGACGTTCGA	59.746	61.111	25.79	0.00	0.00	3.71
447	5757	2.050351	ACTCAGCACGGACGTTCG	60.050	61.111	16.31	16.31	0.00	3.95
448	5758	1.004277	CTCACTCAGCACGGACGTTC	61.004	60.000	0.00	0.00	0.00	3.95
449	5759	1.007271	CTCACTCAGCACGGACGTT	60.007	57.895	0.00	0.00	0.00	3.99
450	5760	2.645567	CTCACTCAGCACGGACGT	59.354	61.111	0.00	0.00	0.00	4.34
480	5895	0.175760	TAGTTGGATGGAGCGCTGAC	59.824	55.000	18.48	8.47	0.00	3.51
707	6984	2.480610	CGAAATGGATGCGTGGGGG	61.481	63.158	0.00	0.00	0.00	5.40
712	6995	2.386661	AGTCTTCGAAATGGATGCGT	57.613	45.000	0.00	0.00	0.00	5.24
1434	11763	5.354842	AGCTCATCATGATCTTGAACTCA	57.645	39.130	14.60	0.14	0.00	3.41
1478	11807	0.685458	ACGGGTATACGCTTGGGTCT	60.685	55.000	16.87	0.00	37.37	3.85
1509	11850	1.490490	TGAATGAGCGAAGGGGCTATT	59.510	47.619	0.00	0.00	44.93	1.73
1572	11943	9.498176	TTCACATAGATCAATTACCTCATCATG	57.502	33.333	0.00	0.00	0.00	3.07
1642	12814	2.000447	GAATTCCTCGAGAAACCCACG	59.000	52.381	15.71	0.00	38.21	4.94
1766	12942	9.575783	CAATACAACTTCCTACTCTAAACTCTC	57.424	37.037	0.00	0.00	0.00	3.20
1782	12958	5.815581	TCAGGGCTAATCACAATACAACTT	58.184	37.500	0.00	0.00	0.00	2.66
1802	12978	3.467803	GGGAATAAACGACCCATCTCAG	58.532	50.000	0.00	0.00	42.81	3.35
1810	12987	6.877611	ACATATGATTGGGAATAAACGACC	57.122	37.500	10.38	0.00	0.00	4.79
1828	13006	2.143122	CCTATCGTGCGCCAAACATAT	58.857	47.619	4.18	0.00	0.00	1.78
1830	13008	0.107897	TCCTATCGTGCGCCAAACAT	60.108	50.000	4.18	0.00	0.00	2.71
1879	13057	6.588719	TCTATTGTTTGGTTGAAGGGATTG	57.411	37.500	0.00	0.00	0.00	2.67
1928	13106	4.505742	GGGTAATTAGAGCTGGGGAATCTG	60.506	50.000	0.00	0.00	0.00	2.90
1929	13107	3.653352	GGGTAATTAGAGCTGGGGAATCT	59.347	47.826	0.00	0.00	0.00	2.40
1930	13108	3.244946	GGGGTAATTAGAGCTGGGGAATC	60.245	52.174	0.00	0.00	0.00	2.52
1936	13114	2.422945	GGTTGGGGGTAATTAGAGCTGG	60.423	54.545	0.00	0.00	0.00	4.85
1986	13191	3.417779	GGCCTAGGGGGTTGGTCC	61.418	72.222	11.72	0.00	37.43	4.46
2051	13266	6.553852	GGATCTAGAGGTTTAATCCCTACACA	59.446	42.308	0.00	0.00	31.56	3.72
2078	13293	1.198094	TGGGTGAGCGAGGGATTGAA	61.198	55.000	0.00	0.00	0.00	2.69
2136	13351	1.019278	CCCAATGTGAACTCGACGGG	61.019	60.000	0.00	0.00	0.00	5.28
2140	13355	1.808411	GAAGCCCAATGTGAACTCGA	58.192	50.000	0.00	0.00	0.00	4.04
2192	13407	1.036707	CACCCGTGGAAACAAACCAT	58.963	50.000	0.00	0.00	46.06	3.55
2219	13435	4.800784	CGAAAACACGGGGAAACATAATT	58.199	39.130	0.00	0.00	0.00	1.40
2290	13509	1.234615	CCATCAGTTCGTGCGGGTTT	61.235	55.000	0.00	0.00	0.00	3.27
2304	13523	2.363975	GGTGTACCTCGGCCCATCA	61.364	63.158	0.00	0.00	0.00	3.07
2345	13564	1.389609	CCTGCTCAATCCACATGGGC	61.390	60.000	0.00	0.00	44.70	5.36
2397	13617	0.683179	TGCAGCCCTCGCTCTAAGTA	60.683	55.000	0.00	0.00	43.95	2.24
2403	13623	2.584261	TTCAGATGCAGCCCTCGCTC	62.584	60.000	0.00	0.00	43.95	5.03
2405	13625	0.250038	TATTCAGATGCAGCCCTCGC	60.250	55.000	0.00	0.00	0.00	5.03
2406	13626	1.069823	ACTATTCAGATGCAGCCCTCG	59.930	52.381	0.00	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.