AutoCloner

Multiple sequence alignment - TraesCS7A01G398800

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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	TraesCS7A01G398800	chr7A	100.000	2969	0	0	1	2969	578573512	578576480	0.000000e+00	5483.0
1	TraesCS7A01G398800	chr7A	93.765	1636	96	3	1059	2690	578325710	578327343	0.000000e+00	2451.0
2	TraesCS7A01G398800	chr7A	95.390	282	13	0	2688	2969	578338167	578338448	1.620000e-122	449.0
3	TraesCS7A01G398800	chr7A	78.361	610	119	12	779	1382	578237908	578237306	1.670000e-102	383.0
4	TraesCS7A01G398800	chr7B	94.031	2982	164	10	1	2969	536560119	536563099	0.000000e+00	4508.0
5	TraesCS7A01G398800	chr7B	78.636	557	96	18	786	1340	536357394	536357929	6.090000e-92	348.0
6	TraesCS7A01G398800	chr7D	93.962	2981	164	12	1	2969	508318316	508321292	0.000000e+00	4494.0
7	TraesCS7A01G398800	chr7D	77.597	491	104	6	824	1313	508300937	508300452	2.890000e-75	292.0
8	TraesCS7A01G398800	chr7D	74.684	237	50	6	5	237	65520573	65520343	2.440000e-16	97.1
9	TraesCS7A01G398800	chr7D	86.842	76	10	0	797	872	508275851	508275776	5.270000e-13	86.1
10	TraesCS7A01G398800	chr7D	86.842	76	10	0	797	872	508301012	508300937	5.270000e-13	86.1
11	TraesCS7A01G398800	chr7D	85.484	62	9	0	172	233	256282090	256282151	6.870000e-07	65.8
12	TraesCS7A01G398800	chr1D	85.714	1988	212	37	298	2264	79172282	79174218	0.000000e+00	2032.0
13	TraesCS7A01G398800	chr1B	84.601	2091	235	44	181	2248	10127819	10125793	0.000000e+00	1997.0
14	TraesCS7A01G398800	chr1B	84.642	1452	200	15	1529	2969	130425115	130426554	0.000000e+00	1424.0
15	TraesCS7A01G398800	chr1B	85.111	947	128	8	591	1533	130422444	130423381	0.000000e+00	955.0
16	TraesCS7A01G398800	chr1B	86.626	658	82	6	2313	2969	10125792	10125140	0.000000e+00	723.0
17	TraesCS7A01G398800	chr1B	89.547	287	30	0	300	586	130366688	130366974	6.050000e-97	364.0
18	TraesCS7A01G398800	chr2A	88.174	1057	115	5	1444	2492	103506051	103504997	0.000000e+00	1251.0
19	TraesCS7A01G398800	chr2A	89.639	415	40	2	2555	2969	103504999	103504588	2.620000e-145	525.0
20	TraesCS7A01G398800	chr1A	87.124	831	86	17	298	1119	98024758	98025576	0.000000e+00	922.0
21	TraesCS7A01G398800	chr1A	85.672	677	89	7	2296	2969	98222885	98223556	0.000000e+00	706.0
22	TraesCS7A01G398800	chr1A	83.988	687	103	5	1169	1852	98025854	98026536	0.000000e+00	652.0
23	TraesCS7A01G398800	chr1A	84.802	454	60	6	1846	2294	98182756	98183205	5.840000e-122	448.0
24	TraesCS7A01G398800	chr5D	81.385	231	37	4	4	233	135706118	135705893	1.820000e-42	183.0
25	TraesCS7A01G398800	chr3B	75.074	337	56	19	408	718	154452601	154452267	6.680000e-27	132.0
26	TraesCS7A01G398800	chr3D	74.777	337	60	15	406	718	103822000	103821665	8.640000e-26	128.0
27	TraesCS7A01G398800	chr6B	74.333	300	69	7	913	1206	16996243	16996540	1.450000e-23	121.0
28	TraesCS7A01G398800	chrUn	76.543	162	34	4	4	163	20102950	20103109	5.270000e-13	86.1
29	TraesCS7A01G398800	chr3A	74.654	217	38	11	4	210	658836195	658836404	2.450000e-11	80.5
30	TraesCS7A01G398800	chr3A	100.000	34	0	0	198	231	97910445	97910478	2.470000e-06	63.9
31	TraesCS7A01G398800	chr6D	85.135	74	11	0	2736	2809	441868901	441868828	3.170000e-10	76.8
32	TraesCS7A01G398800	chr6D	92.308	52	4	0	2751	2802	441789700	441789649	1.140000e-09	75.0

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	TraesCS7A01G398800	chr7A	578573512	578576480	2968	False	5483.0	5483	100.0000	1	2969	1	chr7A.!!$F3	2968
1	TraesCS7A01G398800	chr7A	578325710	578327343	1633	False	2451.0	2451	93.7650	1059	2690	1	chr7A.!!$F1	1631
2	TraesCS7A01G398800	chr7A	578237306	578237908	602	True	383.0	383	78.3610	779	1382	1	chr7A.!!$R1	603
3	TraesCS7A01G398800	chr7B	536560119	536563099	2980	False	4508.0	4508	94.0310	1	2969	1	chr7B.!!$F2	2968
4	TraesCS7A01G398800	chr7B	536357394	536357929	535	False	348.0	348	78.6360	786	1340	1	chr7B.!!$F1	554
5	TraesCS7A01G398800	chr7D	508318316	508321292	2976	False	4494.0	4494	93.9620	1	2969	1	chr7D.!!$F2	2968
6	TraesCS7A01G398800	chr1D	79172282	79174218	1936	False	2032.0	2032	85.7140	298	2264	1	chr1D.!!$F1	1966
7	TraesCS7A01G398800	chr1B	10125140	10127819	2679	True	1360.0	1997	85.6135	181	2969	2	chr1B.!!$R1	2788
8	TraesCS7A01G398800	chr1B	130422444	130426554	4110	False	1189.5	1424	84.8765	591	2969	2	chr1B.!!$F2	2378
9	TraesCS7A01G398800	chr2A	103504588	103506051	1463	True	888.0	1251	88.9065	1444	2969	2	chr2A.!!$R1	1525
10	TraesCS7A01G398800	chr1A	98024758	98026536	1778	False	787.0	922	85.5560	298	1852	2	chr1A.!!$F3	1554
11	TraesCS7A01G398800	chr1A	98222885	98223556	671	False	706.0	706	85.6720	2296	2969	1	chr1A.!!$F2	673

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
994	1054	0.530288	TTGCCGCTTTATCCCTTTGC	59.47	50.0	0.0	0.0	0.0	3.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2859	4940	0.035152	ATGCCTCACGGATTGCTTCA	60.035	50.0	0.0	0.0	0.0	3.02	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
33	34	3.433598	CCGAATCTATTTCAGGCCTTCCA	60.434	47.826	0.00	0.00	33.66	3.53
63	64	2.810400	CGTTGTGTGGGAGGAGACATTT	60.810	50.000	0.00	0.00	0.00	2.32
92	93	0.747255	ACGAAGGCATCTGTAGCGAT	59.253	50.000	0.00	0.00	0.00	4.58
104	105	6.694411	GCATCTGTAGCGATTTCATCAATTTT	59.306	34.615	0.00	0.00	0.00	1.82
119	120	6.318396	TCATCAATTTTAAGATGATGTGCCGA	59.682	34.615	18.67	5.14	46.61	5.54
162	163	6.659668	GCTCATAGGGATAGAGTATGTGTGTA	59.340	42.308	0.00	0.00	0.00	2.90
164	165	6.946583	TCATAGGGATAGAGTATGTGTGTACC	59.053	42.308	0.00	0.00	0.00	3.34
173	174	0.947180	ATGTGTGTACCCGTGCGTTC	60.947	55.000	0.00	0.00	0.00	3.95
177	178	1.000618	TGTGTACCCGTGCGTTCATAA	59.999	47.619	0.00	0.00	0.00	1.90
211	212	7.970614	CGTATGTGTGTATGTATGAGCATCTAT	59.029	37.037	0.00	0.00	34.92	1.98
264	267	9.814129	CATAATTTTGACACGCAAATATTTACG	57.186	29.630	17.27	17.27	45.30	3.18
272	275	8.130469	TGACACGCAAATATTTACGACTATAGA	58.870	33.333	23.99	2.40	31.69	1.98
281	284	9.765795	AATATTTACGACTATAGAAAAGCTGCT	57.234	29.630	6.78	0.00	0.00	4.24
311	314	8.207545	CCTAGCTTAACCAGACATCTAAAGAAT	58.792	37.037	0.00	0.00	0.00	2.40
851	879	5.716979	AGCACCTCCTTATCCTATCAACTA	58.283	41.667	0.00	0.00	0.00	2.24
898	957	4.002982	ACGCTGCATCTTAATTGTCTTGA	58.997	39.130	0.00	0.00	0.00	3.02
994	1054	0.530288	TTGCCGCTTTATCCCTTTGC	59.470	50.000	0.00	0.00	0.00	3.68
1044	1104	5.510861	CCTCCGGTACATCCTCGATAAAAAT	60.511	44.000	0.00	0.00	0.00	1.82
1157	1217	1.228769	TATATGGCGAGGGCGAGGT	60.229	57.895	0.00	0.00	41.24	3.85
1269	1557	5.408356	GTGAATCATGCAAGCTTTCTCAAT	58.592	37.500	0.00	0.00	0.00	2.57
1280	1568	6.565247	GCAAGCTTTCTCAATCAACATTTTGG	60.565	38.462	0.00	0.00	33.06	3.28
1313	1601	1.719063	AAGGGCCACAAGCTCCAAGA	61.719	55.000	6.18	0.00	46.61	3.02
1466	1755	1.205417	CATGGGGGAAAGCATCACAAC	59.795	52.381	0.00	0.00	30.77	3.32
1495	1784	0.474184	CCAACCACCTGTCTTCCAGT	59.526	55.000	0.00	0.00	39.74	4.00
1590	3616	2.472695	ACGTCACCAACTACATGCAT	57.527	45.000	0.00	0.00	0.00	3.96
1591	3617	2.076100	ACGTCACCAACTACATGCATG	58.924	47.619	25.09	25.09	0.00	4.06
1742	3810	4.082125	CCTTCCACAATGTTTAAGGCTCT	58.918	43.478	9.71	0.00	31.04	4.09
1762	3830	1.798735	CCGCAGCAACAAGAGGATG	59.201	57.895	0.00	0.00	0.00	3.51
1876	3944	3.069586	TGTCTTCCCTAGCGGTGATATTG	59.930	47.826	0.00	0.00	0.00	1.90
1977	4045	2.806945	TCCCAATGTAAGCAAGGAGG	57.193	50.000	0.00	0.00	0.00	4.30
2052	4128	6.558009	TCTTTGAGCACAAGCATATTTCATC	58.442	36.000	0.00	0.00	45.49	2.92
2066	4142	8.512956	AGCATATTTCATCTAGTCATTGCAATC	58.487	33.333	9.53	0.00	0.00	2.67
2085	4161	6.366061	TGCAATCGTTATTATGGATCTCTTCG	59.634	38.462	0.00	0.00	0.00	3.79
2151	4227	4.253685	TCTATGTTGCACCTACTCTTTGC	58.746	43.478	0.00	0.00	36.76	3.68
2172	4248	3.181531	GCGTAAACATGCATGCTTTTTCC	60.182	43.478	26.53	9.76	0.00	3.13
2294	4371	5.462398	CGCACAACCTATAGAAATCTACCAC	59.538	44.000	0.00	0.00	0.00	4.16
2334	4411	3.951306	ACACATGACATTGTTTGACACG	58.049	40.909	0.00	0.00	32.88	4.49
2525	4604	3.409570	GAGTCCTCCCAAAACCTAACAC	58.590	50.000	0.00	0.00	0.00	3.32
2529	4608	1.265905	CTCCCAAAACCTAACACGTGC	59.734	52.381	17.22	0.00	0.00	5.34
2589	4670	3.001330	AGTCGTCTTCGCTTCACAAAAAG	59.999	43.478	0.00	0.00	36.96	2.27
2632	4713	3.955551	CAGGTTTCCTCTAGACCTAGGAC	59.044	52.174	17.98	9.98	41.72	3.85
2641	4722	5.768164	CCTCTAGACCTAGGACAGAATCTTC	59.232	48.000	17.98	0.00	34.58	2.87
2852	4933	9.309516	TCCTATTTACTAAATGACACTTTAGCG	57.690	33.333	13.08	0.00	40.72	4.26
2859	4940	5.880054	AAATGACACTTTAGCGCATTACT	57.120	34.783	11.47	0.00	0.00	2.24
2907	4989	0.460311	ACTGGAAAGGCGTATCCGAG	59.540	55.000	0.00	4.05	38.63	4.63
2951	5033	5.886609	TGGAAAATGAGGTTCTCAATGGTA	58.113	37.500	1.53	0.00	44.04	3.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	3.808728	TGGAAGGCCTGAAATAGATTCG	58.191	45.455	5.69	0.00	41.18	3.34
19	20	2.094675	CATCGTTGGAAGGCCTGAAAT	58.905	47.619	5.69	0.00	34.31	2.17
46	47	1.676014	CGGAAATGTCTCCTCCCACAC	60.676	57.143	0.00	0.00	32.82	3.82
104	105	4.406648	AATGAGTCGGCACATCATCTTA	57.593	40.909	0.00	0.00	32.59	2.10
119	120	3.244215	TGAGCACTTCCGAGAAAATGAGT	60.244	43.478	0.00	0.00	0.00	3.41
132	133	6.435904	ACATACTCTATCCCTATGAGCACTTC	59.564	42.308	0.00	0.00	0.00	3.01
134	135	5.714333	CACATACTCTATCCCTATGAGCACT	59.286	44.000	0.00	0.00	0.00	4.40
162	163	1.078708	CCCTTATGAACGCACGGGT	60.079	57.895	0.00	0.00	0.00	5.28
164	165	0.390603	TCACCCTTATGAACGCACGG	60.391	55.000	0.00	0.00	0.00	4.94
173	174	2.866156	CACACATACGCTCACCCTTATG	59.134	50.000	0.00	0.00	0.00	1.90
177	178	1.552578	TACACACATACGCTCACCCT	58.447	50.000	0.00	0.00	0.00	4.34
264	267	6.399639	AGGTAGAGCAGCTTTTCTATAGTC	57.600	41.667	0.00	0.00	0.00	2.59
281	284	5.767670	AGATGTCTGGTTAAGCTAGGTAGA	58.232	41.667	6.19	0.00	0.00	2.59
311	314	6.196918	TCTAGAAGATATGGACCGACCTTA	57.803	41.667	0.00	0.00	39.86	2.69
340	343	8.143193	CAGCATACATTCCAAGGCAATAATTAA	58.857	33.333	0.00	0.00	0.00	1.40
623	646	9.727627	GTTCTAAAGATGGATGCTTATTCAAAG	57.272	33.333	0.00	0.00	0.00	2.77
851	879	7.226523	GTGCCAATCCAGAAACTTTTAAATGTT	59.773	33.333	12.38	12.38	0.00	2.71
868	927	1.660560	AAGATGCAGCGTGCCAATCC	61.661	55.000	0.00	0.00	44.23	3.01
884	943	5.934625	GCCAAGAGACTCAAGACAATTAAGA	59.065	40.000	5.02	0.00	0.00	2.10
888	947	4.070716	CAGCCAAGAGACTCAAGACAATT	58.929	43.478	5.02	0.00	0.00	2.32
889	948	3.326006	TCAGCCAAGAGACTCAAGACAAT	59.674	43.478	5.02	0.00	0.00	2.71
890	949	2.700371	TCAGCCAAGAGACTCAAGACAA	59.300	45.455	5.02	0.00	0.00	3.18
891	950	2.319844	TCAGCCAAGAGACTCAAGACA	58.680	47.619	5.02	0.00	0.00	3.41
898	957	1.273495	TGGAGGATCAGCCAAGAGACT	60.273	52.381	3.51	0.00	40.02	3.24
994	1054	1.131883	CTTCTTGCGAGCCATTTCCAG	59.868	52.381	0.00	0.00	0.00	3.86
1044	1104	6.874134	GCTTCTTTGAAGTACTACATCTGGAA	59.126	38.462	0.00	0.00	0.00	3.53
1157	1217	0.107081	CGGGAACACTTGTGGTACCA	59.893	55.000	18.99	11.60	0.00	3.25
1230	1518	4.511454	TGATTCACCGTCTTCTTGAAGTTG	59.489	41.667	9.80	4.53	32.91	3.16
1269	1557	2.036217	CTGGAGCTTGCCAAAATGTTGA	59.964	45.455	0.00	0.00	37.52	3.18
1280	1568	3.066814	CCTTGGCCTGGAGCTTGC	61.067	66.667	3.32	0.00	43.05	4.01
1313	1601	4.040829	TGGTCTCATTGTCTTCACAGATGT	59.959	41.667	0.00	0.00	32.71	3.06
1466	1755	0.965363	AGGTGGTTGGCCGCTAATTG	60.965	55.000	0.00	0.00	44.44	2.32
1495	1784	1.001120	TGACGTATGGCTCCTGGGA	59.999	57.895	0.00	0.00	0.00	4.37
1590	3616	3.664495	GTCGACGGAGACTCCACA	58.336	61.111	21.49	0.00	35.91	4.17
1762	3830	3.562973	CCATACCTCATCATGTCAAGTGC	59.437	47.826	0.00	0.00	0.00	4.40
2037	4113	7.283807	TGCAATGACTAGATGAAATATGCTTGT	59.716	33.333	0.00	0.00	0.00	3.16
2052	4128	8.310406	TCCATAATAACGATTGCAATGACTAG	57.690	34.615	18.59	5.38	0.00	2.57
2066	4142	6.390721	ACCATCGAAGAGATCCATAATAACG	58.609	40.000	0.00	0.00	43.63	3.18
2085	4161	4.917415	CGGAGATCAAACAAACAAACCATC	59.083	41.667	0.00	0.00	0.00	3.51
2151	4227	3.059306	CGGAAAAAGCATGCATGTTTACG	59.941	43.478	26.28	24.63	30.81	3.18
2189	4266	5.212194	CGTCAAGGGTCAACAAAAACTATG	58.788	41.667	0.00	0.00	0.00	2.23
2419	4496	7.816995	GCTTAGTCATGTCATAATAGAAGAGGG	59.183	40.741	0.00	0.00	0.00	4.30
2490	4569	1.003233	AGGACTCGTGGTTGGGAATTC	59.997	52.381	0.00	0.00	0.00	2.17
2492	4571	0.613777	GAGGACTCGTGGTTGGGAAT	59.386	55.000	0.00	0.00	0.00	3.01
2525	4604	1.390123	CACTGTCAAGGATTACGCACG	59.610	52.381	0.00	0.00	0.00	5.34
2529	4608	6.020599	CGAAACTATCACTGTCAAGGATTACG	60.021	42.308	0.00	0.00	0.00	3.18
2589	4670	2.885266	GAGGACTCCCACTTTTTGGTTC	59.115	50.000	0.00	0.00	45.25	3.62
2632	4713	2.906691	AGATGGGCTCGAAGATTCTG	57.093	50.000	0.00	0.00	33.89	3.02
2738	4819	2.420547	CCTTCGAGATTGGCATGGAGAA	60.421	50.000	0.00	0.00	0.00	2.87
2842	4923	3.125316	GCTTCAGTAATGCGCTAAAGTGT	59.875	43.478	9.73	0.00	0.00	3.55
2852	4933	2.677836	TCACGGATTGCTTCAGTAATGC	59.322	45.455	0.00	0.00	35.72	3.56
2859	4940	0.035152	ATGCCTCACGGATTGCTTCA	60.035	50.000	0.00	0.00	0.00	3.02
2907	4989	4.436332	CATTGCCCCTTTAGCATTTCTTC	58.564	43.478	0.00	0.00	40.59	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.