AutoCloner

Multiple sequence alignment - TraesCS5D01G319200

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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	TraesCS5D01G319200	chr5D	100.000	2681	0	0	1	2681	412148813	412146133	0.000000e+00	4951
1	TraesCS5D01G319200	chr5D	82.692	156	27	0	1085	1240	87173729	87173574	3.600000e-29	139
2	TraesCS5D01G319200	chr5A	92.972	2106	80	22	4	2073	523880668	523878595	0.000000e+00	3007
3	TraesCS5D01G319200	chr5A	89.247	372	30	3	2087	2452	523878522	523878155	8.750000e-125	457
4	TraesCS5D01G319200	chr5A	94.565	92	4	1	4	95	523885292	523885202	1.000000e-29	141
5	TraesCS5D01G319200	chr5A	82.692	156	27	0	1085	1240	80155787	80155632	3.600000e-29	139
6	TraesCS5D01G319200	chr5B	93.799	1274	61	13	516	1787	495474053	495472796	0.000000e+00	1899
7	TraesCS5D01G319200	chr5B	87.965	914	48	18	1813	2680	495472797	495471900	0.000000e+00	1022
8	TraesCS5D01G319200	chr5B	95.020	502	24	1	11	512	495474598	495474098	0.000000e+00	787
9	TraesCS5D01G319200	chr3D	86.824	1017	102	18	672	1682	322682227	322683217	0.000000e+00	1107
10	TraesCS5D01G319200	chr6A	87.072	642	45	9	672	1301	420552984	420552369	0.000000e+00	691
11	TraesCS5D01G319200	chr2B	87.279	621	48	15	672	1291	769581248	769581838	0.000000e+00	680
12	TraesCS5D01G319200	chr2B	88.199	161	18	1	1550	1709	769588760	769588920	9.800000e-45	191
13	TraesCS5D01G319200	chr1B	87.146	529	59	3	1181	1709	489694751	489695270	2.300000e-165	592
14	TraesCS5D01G319200	chr1B	82.946	258	18	14	672	918	489693240	489693482	2.700000e-50	209
15	TraesCS5D01G319200	chr1A	86.151	556	50	9	1067	1622	585231637	585231109	2.310000e-160	575
16	TraesCS5D01G319200	chr1A	87.535	361	30	7	672	1031	585231989	585231643	1.160000e-108	403
17	TraesCS5D01G319200	chr1A	91.579	95	8	0	1615	1709	585220643	585220549	6.020000e-27	132
18	TraesCS5D01G319200	chr7B	87.220	313	19	9	672	981	50603039	50602745	1.190000e-88	337
19	TraesCS5D01G319200	chr7B	81.790	324	28	15	974	1296	50601050	50600757	2.670000e-60	243
20	TraesCS5D01G319200	chr7D	87.197	289	37	0	1421	1709	292242948	292242660	1.990000e-86	329
21	TraesCS5D01G319200	chr7D	88.263	213	20	3	817	1029	292243286	292243079	1.590000e-62	250
22	TraesCS5D01G319200	chr7D	93.662	142	8	1	1067	1208	292243079	292242939	7.520000e-51	211
23	TraesCS5D01G319200	chr7D	87.333	150	9	4	691	838	292249467	292249326	2.140000e-36	163

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	TraesCS5D01G319200	chr5D	412146133	412148813	2680	True	4951.000000	4951	100.000000	1	2681	1	chr5D.!!$R2	2680
1	TraesCS5D01G319200	chr5A	523878155	523880668	2513	True	1732.000000	3007	91.109500	4	2452	2	chr5A.!!$R3	2448
2	TraesCS5D01G319200	chr5B	495471900	495474598	2698	True	1236.000000	1899	92.261333	11	2680	3	chr5B.!!$R1	2669
3	TraesCS5D01G319200	chr3D	322682227	322683217	990	False	1107.000000	1107	86.824000	672	1682	1	chr3D.!!$F1	1010
4	TraesCS5D01G319200	chr6A	420552369	420552984	615	True	691.000000	691	87.072000	672	1301	1	chr6A.!!$R1	629
5	TraesCS5D01G319200	chr2B	769581248	769581838	590	False	680.000000	680	87.279000	672	1291	1	chr2B.!!$F1	619
6	TraesCS5D01G319200	chr1B	489693240	489695270	2030	False	400.500000	592	85.046000	672	1709	2	chr1B.!!$F1	1037
7	TraesCS5D01G319200	chr1A	585231109	585231989	880	True	489.000000	575	86.843000	672	1622	2	chr1A.!!$R2	950
8	TraesCS5D01G319200	chr7B	50600757	50603039	2282	True	290.000000	337	84.505000	672	1296	2	chr7B.!!$R1	624
9	TraesCS5D01G319200	chr7D	292242660	292243286	626	True	263.333333	329	89.707333	817	1709	3	chr7D.!!$R2	892

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
873	943	0.034059	GTGGAGTGGAGGTCTGTGTG	59.966	60.0	0.0	0.0	0.0	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2588	5581	0.310854	GGTGCTTTTGTTCGTGAGGG	59.689	55.0	0.0	0.0	0.0	4.3	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
183	184	0.178953	AACCACAGCTTTCTGGGCAT	60.179	50.000	6.76	0.00	42.40	4.40
194	195	8.775891	CAGCTTTCTGGGCATGGAATGTTTAG	62.776	46.154	0.00	0.00	40.65	1.85
319	320	1.009829	GCCAATGATCTCACCACGAC	58.990	55.000	0.00	0.00	0.00	4.34
512	520	0.247736	GTCCTCGTGTGGAGCATCTT	59.752	55.000	0.00	0.00	41.71	2.40
549	597	4.079970	ACAGAGGTCTTGATCACTTCGTA	58.920	43.478	0.00	0.00	0.00	3.43
550	598	4.156922	ACAGAGGTCTTGATCACTTCGTAG	59.843	45.833	0.00	0.00	0.00	3.51
551	599	3.129638	AGAGGTCTTGATCACTTCGTAGC	59.870	47.826	0.00	0.00	0.00	3.58
552	600	2.826128	AGGTCTTGATCACTTCGTAGCA	59.174	45.455	0.00	0.00	0.00	3.49
553	601	3.119316	AGGTCTTGATCACTTCGTAGCAG	60.119	47.826	0.00	0.00	0.00	4.24
635	684	4.261994	GGGCACTAAACAAGAAGATTGCAA	60.262	41.667	0.00	0.00	0.00	4.08
765	815	2.553727	GGTAGTAGCTCCCGCTCCG	61.554	68.421	0.00	0.00	45.15	4.63
794	861	3.186409	GCGTCATGTGCAAAAGAACTAGA	59.814	43.478	0.00	0.00	0.00	2.43
797	864	5.349817	CGTCATGTGCAAAAGAACTAGAGAT	59.650	40.000	0.00	0.00	0.00	2.75
831	901	3.690460	CCAGGGAGAATTTAGCAAGTGT	58.310	45.455	0.00	0.00	0.00	3.55
866	936	1.059913	CTCTTTGGTGGAGTGGAGGT	58.940	55.000	0.00	0.00	0.00	3.85
873	943	0.034059	GTGGAGTGGAGGTCTGTGTG	59.966	60.000	0.00	0.00	0.00	3.82
880	971	0.532862	GGAGGTCTGTGTGGTGTGTG	60.533	60.000	0.00	0.00	0.00	3.82
966	1360	5.238868	GGCTAGGTGCTTAAGCTAATTAACC	59.761	44.000	26.90	22.89	38.38	2.85
1611	4497	0.602905	CGGAGAAGGCGTTCAAGGTT	60.603	55.000	20.38	0.00	34.82	3.50
1783	4669	5.703130	AGCAGTGAAATGAAGTCCTACTTTC	59.297	40.000	0.00	0.00	38.80	2.62
1789	4675	6.486657	TGAAATGAAGTCCTACTTTCCAACAG	59.513	38.462	0.00	0.00	38.80	3.16
1790	4676	5.825593	ATGAAGTCCTACTTTCCAACAGA	57.174	39.130	0.00	0.00	38.80	3.41
1982	4868	8.558973	AAACAAAATTTGACTGAATTTGGTCA	57.441	26.923	13.19	9.40	40.52	4.02
2001	4905	6.133356	TGGTCAAGGTGGAAAAACTAAGATT	58.867	36.000	0.00	0.00	0.00	2.40
2125	5090	5.021033	ACCAAAATCAACATTGTTCAGCA	57.979	34.783	0.00	0.00	0.00	4.41
2129	5094	6.128661	CCAAAATCAACATTGTTCAGCATCAG	60.129	38.462	0.00	0.00	0.00	2.90
2299	5288	2.091665	GGGGTCACCATCCATCATCTTT	60.092	50.000	0.00	0.00	39.85	2.52
2455	5447	5.248248	CCAAAATGAAATGGTACTTTCCCCT	59.752	40.000	5.43	0.00	34.83	4.79
2457	5449	7.125659	CCAAAATGAAATGGTACTTTCCCCTAT	59.874	37.037	5.43	0.00	34.83	2.57
2523	5516	7.256286	AGAAATAAGCTTGAGCAAACATCATC	58.744	34.615	9.86	0.00	45.16	2.92
2524	5517	6.519679	AATAAGCTTGAGCAAACATCATCA	57.480	33.333	9.86	0.00	45.16	3.07
2525	5518	4.859304	AAGCTTGAGCAAACATCATCAA	57.141	36.364	0.00	0.00	45.16	2.57
2543	5536	2.886523	TCAAAAGCACAACCATCCTCAG	59.113	45.455	0.00	0.00	0.00	3.35
2577	5570	4.323417	ACGATCATCAACAAAAGCACCTA	58.677	39.130	0.00	0.00	0.00	3.08
2580	5573	4.829064	TCATCAACAAAAGCACCTACAC	57.171	40.909	0.00	0.00	0.00	2.90
2587	5580	3.217242	AAGCACCTACACGCTTCAG	57.783	52.632	0.00	0.00	45.10	3.02
2588	5581	0.951040	AAGCACCTACACGCTTCAGC	60.951	55.000	0.00	0.00	45.10	4.26
2594	5587	0.737715	CTACACGCTTCAGCCCTCAC	60.738	60.000	0.00	0.00	37.91	3.51
2607	5600	0.310854	CCCTCACGAACAAAAGCACC	59.689	55.000	0.00	0.00	0.00	5.01
2618	5611	3.836949	ACAAAAGCACCAGCAAATATCG	58.163	40.909	0.00	0.00	45.49	2.92
2643	5636	2.692709	ACCATCATCACCAAAACCCA	57.307	45.000	0.00	0.00	0.00	4.51
2666	5659	6.204882	CCACCATCCGTAAGAAAATAGAATCC	59.795	42.308	0.00	0.00	43.02	3.01
2670	5663	7.715249	CCATCCGTAAGAAAATAGAATCCAGAA	59.285	37.037	0.00	0.00	43.02	3.02
2674	5667	9.765795	CCGTAAGAAAATAGAATCCAGAACTAT	57.234	33.333	0.00	0.00	43.02	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.986572	GACAAGTGAGTGAGTGAGTGATG	59.013	47.826	0.00	0.00	0.00	3.07
194	195	2.036387	AGGGCCTTGTTTGTTTACCAC	58.964	47.619	0.00	0.00	0.00	4.16
228	229	4.562757	GGCAAATGGATGGCGACTAGTATA	60.563	45.833	0.00	0.00	36.07	1.47
319	320	6.861065	AATGAACACCGTAGCCAATAATAG	57.139	37.500	0.00	0.00	0.00	1.73
453	461	4.838152	CAGGTCGGCCCATCCACG	62.838	72.222	0.08	0.00	34.66	4.94
488	496	0.389166	GCTCCACACGAGGACTGAAG	60.389	60.000	0.00	0.00	39.22	3.02
512	520	2.886523	CCTCTGTCATTTTTGAGGCACA	59.113	45.455	0.00	0.00	39.46	4.57
520	528	6.302269	AGTGATCAAGACCTCTGTCATTTTT	58.698	36.000	0.00	0.00	44.33	1.94
549	597	3.612247	CTTACCGTGCTGGCCTGCT	62.612	63.158	31.50	16.40	43.94	4.24
550	598	3.127533	CTTACCGTGCTGGCCTGC	61.128	66.667	26.46	26.46	43.94	4.85
551	599	2.034879	CACTTACCGTGCTGGCCTG	61.035	63.158	3.32	4.26	43.94	4.85
552	600	2.214216	TCACTTACCGTGCTGGCCT	61.214	57.895	3.32	0.00	43.46	5.19
553	601	2.033194	GTCACTTACCGTGCTGGCC	61.033	63.158	0.00	0.00	43.46	5.36
635	684	6.247903	CGAACATACAAGTTCATTATTGCGT	58.752	36.000	7.49	0.00	46.32	5.24
765	815	1.855213	TTGCACATGACGCCTTGCTC	61.855	55.000	0.00	0.00	35.91	4.26
794	861	1.566231	CCTGGCCCCTTTGTCTTATCT	59.434	52.381	0.00	0.00	0.00	1.98
797	864	0.476808	TCCCTGGCCCCTTTGTCTTA	60.477	55.000	0.00	0.00	0.00	2.10
831	901	4.267536	CAAAGAGGATGGAAAGCATCTGA	58.732	43.478	0.00	0.00	0.00	3.27
866	936	4.882842	ACATATACACACACCACACAGA	57.117	40.909	0.00	0.00	0.00	3.41
873	943	6.075762	TCCATACGTACATATACACACACC	57.924	41.667	0.00	0.00	0.00	4.16
880	971	4.154737	TCGCCACTCCATACGTACATATAC	59.845	45.833	0.00	0.00	0.00	1.47
966	1360	0.027063	CGCGCGTTTTATAACCTGGG	59.973	55.000	24.19	0.00	0.00	4.45
1221	4074	1.368850	GAAGTTGGTGCGCGTGTTC	60.369	57.895	8.43	0.00	0.00	3.18
1611	4497	0.728129	GCACGATCACAGACGACGAA	60.728	55.000	0.00	0.00	0.00	3.85
1658	4544	1.153127	AAACCGTCGAGGCCAAACA	60.153	52.632	5.01	0.00	46.52	2.83
1803	4689	1.065418	GGCATCTTCCTTCCTTCGGAA	60.065	52.381	0.00	0.00	39.66	4.30
1804	4690	0.541863	GGCATCTTCCTTCCTTCGGA	59.458	55.000	0.00	0.00	0.00	4.55
1805	4691	0.543749	AGGCATCTTCCTTCCTTCGG	59.456	55.000	0.00	0.00	30.82	4.30
1806	4692	2.432510	ACTAGGCATCTTCCTTCCTTCG	59.567	50.000	0.00	0.00	37.66	3.79
1807	4693	4.495690	AACTAGGCATCTTCCTTCCTTC	57.504	45.455	0.00	0.00	37.66	3.46
1808	4694	4.043435	ACAAACTAGGCATCTTCCTTCCTT	59.957	41.667	0.00	0.00	37.66	3.36
1809	4695	3.589288	ACAAACTAGGCATCTTCCTTCCT	59.411	43.478	0.00	0.00	37.66	3.36
1810	4696	3.956744	ACAAACTAGGCATCTTCCTTCC	58.043	45.455	0.00	0.00	37.66	3.46
1811	4697	5.735766	AGTACAAACTAGGCATCTTCCTTC	58.264	41.667	0.00	0.00	37.66	3.46
1812	4698	5.763876	AGTACAAACTAGGCATCTTCCTT	57.236	39.130	0.00	0.00	37.66	3.36
1813	4699	5.958987	AGTAGTACAAACTAGGCATCTTCCT	59.041	40.000	2.52	0.00	38.89	3.36
1978	4864	6.650427	AATCTTAGTTTTTCCACCTTGACC	57.350	37.500	0.00	0.00	0.00	4.02
2125	5090	3.845178	TCGTGAAAGATGTTACGCTGAT	58.155	40.909	0.00	0.00	36.56	2.90
2129	5094	4.953269	TGAAATCGTGAAAGATGTTACGC	58.047	39.130	0.00	0.00	36.56	4.42
2138	5103	8.393395	TCTTTGAACTTTTGAAATCGTGAAAG	57.607	30.769	0.00	0.00	35.72	2.62
2203	5168	1.608717	GGACTGAGGACCGCTGACAT	61.609	60.000	9.08	0.00	0.00	3.06
2204	5169	2.276116	GGACTGAGGACCGCTGACA	61.276	63.158	9.08	0.00	0.00	3.58
2299	5288	2.440253	ACCTACTGTGGTGCTTTTGGTA	59.560	45.455	1.87	0.00	39.17	3.25
2369	5361	5.539048	TGTTAACTTGAGTTGTAGCTCTCC	58.461	41.667	7.22	0.00	38.90	3.71
2488	5481	6.765512	GCTCAAGCTTATTTCTCTAGGAACAT	59.234	38.462	0.00	0.00	38.21	2.71
2490	5483	6.109359	TGCTCAAGCTTATTTCTCTAGGAAC	58.891	40.000	0.00	0.00	42.66	3.62
2494	5487	7.369803	TGTTTGCTCAAGCTTATTTCTCTAG	57.630	36.000	0.00	0.00	42.66	2.43
2496	5489	6.432162	TGATGTTTGCTCAAGCTTATTTCTCT	59.568	34.615	0.00	0.00	42.66	3.10
2497	5490	6.615088	TGATGTTTGCTCAAGCTTATTTCTC	58.385	36.000	0.00	0.00	42.66	2.87
2509	5502	4.202131	TGTGCTTTTGATGATGTTTGCTCA	60.202	37.500	0.00	0.00	0.00	4.26
2523	5516	2.608752	GCTGAGGATGGTTGTGCTTTTG	60.609	50.000	0.00	0.00	0.00	2.44
2524	5517	1.615392	GCTGAGGATGGTTGTGCTTTT	59.385	47.619	0.00	0.00	0.00	2.27
2525	5518	1.251251	GCTGAGGATGGTTGTGCTTT	58.749	50.000	0.00	0.00	0.00	3.51
2543	5536	5.106712	TGTTGATGATCGTTAGACCTTTTGC	60.107	40.000	0.00	0.00	0.00	3.68
2577	5570	2.031163	GTGAGGGCTGAAGCGTGT	59.969	61.111	0.00	0.00	43.26	4.49
2580	5573	2.048222	TTCGTGAGGGCTGAAGCG	60.048	61.111	0.00	0.00	43.26	4.68
2587	5580	0.317854	GTGCTTTTGTTCGTGAGGGC	60.318	55.000	0.00	0.00	0.00	5.19
2588	5581	0.310854	GGTGCTTTTGTTCGTGAGGG	59.689	55.000	0.00	0.00	0.00	4.30
2594	5587	1.919918	TTTGCTGGTGCTTTTGTTCG	58.080	45.000	0.00	0.00	40.48	3.95
2607	5600	4.096231	TGATGGTTTGGACGATATTTGCTG	59.904	41.667	0.00	0.00	0.00	4.41
2618	5611	4.306600	GTTTTGGTGATGATGGTTTGGAC	58.693	43.478	0.00	0.00	0.00	4.02
2643	5636	6.895782	TGGATTCTATTTTCTTACGGATGGT	58.104	36.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.