AutoCloner

Multiple sequence alignment - TraesCS3B01G409500

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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	TraesCS3B01G409500	chr3B	100.000	3032	0	0	1	3032	645181351	645184382	0.000000e+00	5600
1	TraesCS3B01G409500	chr3B	90.371	2887	251	25	160	3030	71908422	71911297	0.000000e+00	3766
2	TraesCS3B01G409500	chr3B	86.699	2917	333	43	141	3030	74831158	74828270	0.000000e+00	3186
3	TraesCS3B01G409500	chr3B	88.221	1214	106	27	1852	3032	284885577	284884368	0.000000e+00	1415
4	TraesCS3B01G409500	chr3B	87.500	1216	109	29	1852	3030	361554921	361556130	0.000000e+00	1363
5	TraesCS3B01G409500	chr3B	85.383	1293	136	37	1780	3030	40496414	40497695	0.000000e+00	1291
6	TraesCS3B01G409500	chr3B	87.120	955	87	25	2111	3030	115674057	115673104	0.000000e+00	1050
7	TraesCS3B01G409500	chr3B	95.918	343	12	2	1	341	652590833	652590491	3.420000e-154	555
8	TraesCS3B01G409500	chr3B	86.550	342	39	7	1	339	128991938	128991601	1.330000e-98	370
9	TraesCS3B01G409500	chr4B	90.135	2970	255	29	86	3030	569591570	569594526	0.000000e+00	3827
10	TraesCS3B01G409500	chr5B	90.440	2908	251	24	139	3030	370324969	370322073	0.000000e+00	3805
11	TraesCS3B01G409500	chr5B	91.480	223	18	1	2809	3030	4634660	4634438	3.800000e-79	305
12	TraesCS3B01G409500	chr2B	87.247	3058	334	41	7	3032	115615189	115612156	0.000000e+00	3435
13	TraesCS3B01G409500	chr2B	87.181	3058	335	42	7	3032	115619634	115616602	0.000000e+00	3422
14	TraesCS3B01G409500	chr2B	87.157	3060	332	44	7	3032	115610777	115607745	0.000000e+00	3417
15	TraesCS3B01G409500	chr2B	83.626	342	37	10	1	339	405165799	405166124	1.370000e-78	303
16	TraesCS3B01G409500	chr7B	86.965	2992	327	48	79	3030	550727728	550724760	0.000000e+00	3306
17	TraesCS3B01G409500	chr4D	87.037	2862	316	37	193	3030	292635079	292637909	0.000000e+00	3179

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	TraesCS3B01G409500	chr3B	645181351	645184382	3031	False	5600.000000	5600	100.000	1	3032	1	chr3B.!!$F4	3031
1	TraesCS3B01G409500	chr3B	71908422	71911297	2875	False	3766.000000	3766	90.371	160	3030	1	chr3B.!!$F2	2870
2	TraesCS3B01G409500	chr3B	74828270	74831158	2888	True	3186.000000	3186	86.699	141	3030	1	chr3B.!!$R1	2889
3	TraesCS3B01G409500	chr3B	284884368	284885577	1209	True	1415.000000	1415	88.221	1852	3032	1	chr3B.!!$R4	1180
4	TraesCS3B01G409500	chr3B	361554921	361556130	1209	False	1363.000000	1363	87.500	1852	3030	1	chr3B.!!$F3	1178
5	TraesCS3B01G409500	chr3B	40496414	40497695	1281	False	1291.000000	1291	85.383	1780	3030	1	chr3B.!!$F1	1250
6	TraesCS3B01G409500	chr3B	115673104	115674057	953	True	1050.000000	1050	87.120	2111	3030	1	chr3B.!!$R2	919
7	TraesCS3B01G409500	chr4B	569591570	569594526	2956	False	3827.000000	3827	90.135	86	3030	1	chr4B.!!$F1	2944
8	TraesCS3B01G409500	chr5B	370322073	370324969	2896	True	3805.000000	3805	90.440	139	3030	1	chr5B.!!$R2	2891
9	TraesCS3B01G409500	chr2B	115607745	115619634	11889	True	3424.666667	3435	87.195	7	3032	3	chr2B.!!$R1	3025
10	TraesCS3B01G409500	chr7B	550724760	550727728	2968	True	3306.000000	3306	86.965	79	3030	1	chr7B.!!$R1	2951
11	TraesCS3B01G409500	chr4D	292635079	292637909	2830	False	3179.000000	3179	87.037	193	3030	1	chr4D.!!$F1	2837

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	Hairpin	End Stability	Orientation
310	330	0.035820	GACATCCGTAGTTTGGGGCA	60.036	55.000	0.00	5.36	F
1101	1127	2.227388	GCCCACACAAGATGACTTTGAG	59.773	50.000	33.70	3.02	F
1157	1183	2.082231	CACTTGGAGTGCTGAAGATGG	58.918	52.381	39.62	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1157	1183	0.468226	TATCACCGGCCTCATTGGAC	59.532	55.000	41.70	4.02	R
2017	2046	0.676184	TCTCCTCATCGCCATGCTAC	59.324	55.000	0.00	3.58	R
2744	2811	1.076350	CCCCAAAGGAACATACCACCA	59.924	52.381	38.24	4.17	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
75	76	3.756963	GTCTTTTCAATTCCCTAGCCGTT	59.243	43.478	0.00	0.00	0.00	4.44
76	77	3.756434	TCTTTTCAATTCCCTAGCCGTTG	59.244	43.478	0.00	0.00	0.00	4.10
83	84	3.469008	TTCCCTAGCCGTTGATGTATG	57.531	47.619	0.00	0.00	0.00	2.39
109	111	8.427774	GCTTGTGTTAGCATTTTATTTCTCAAC	58.572	33.333	0.00	0.00	40.89	3.18
111	113	9.462174	TTGTGTTAGCATTTTATTTCTCAACTG	57.538	29.630	0.00	0.00	0.00	3.16
130	133	9.097257	CTCAACTGAAACAAATACACCAAAAAT	57.903	29.630	0.00	0.00	0.00	1.82
204	221	5.219633	GGCGACAATCATGTTTTGTTTAGT	58.780	37.500	14.85	0.00	40.74	2.24
234	254	1.869774	TGCATTCATCTCCCGAATCG	58.130	50.000	0.00	0.00	30.65	3.34
240	260	4.459390	TTCATCTCCCGAATCGTGTTAA	57.541	40.909	0.82	0.00	0.00	2.01
250	270	5.577945	CCCGAATCGTGTTAACTAGCTTTAA	59.422	40.000	7.22	0.00	0.00	1.52
253	273	6.089820	CGAATCGTGTTAACTAGCTTTAACCA	59.910	38.462	15.26	4.65	40.03	3.67
310	330	0.035820	GACATCCGTAGTTTGGGGCA	60.036	55.000	0.00	0.00	0.00	5.36
402	425	4.161754	TGAGGCTTTAGACTAGGTTTAGCC	59.838	45.833	13.92	13.92	45.38	3.93
574	599	4.364415	AGCAACATTACAAACAACACGT	57.636	36.364	0.00	0.00	0.00	4.49
796	822	4.271661	TGATTGTTATGGCATGAGCTTCA	58.728	39.130	10.98	5.29	41.70	3.02
988	1014	6.155910	CCATTCAGCTCCTACTCATATACCAT	59.844	42.308	0.00	0.00	0.00	3.55
1027	1053	5.016831	GTCCAATGGAGTTAAATGGTCCTT	58.983	41.667	0.27	0.00	29.39	3.36
1101	1127	2.227388	GCCCACACAAGATGACTTTGAG	59.773	50.000	0.00	0.00	33.70	3.02
1157	1183	2.082231	CACTTGGAGTGCTGAAGATGG	58.918	52.381	0.00	0.00	39.62	3.51
1164	1190	2.681848	GAGTGCTGAAGATGGTCCAATG	59.318	50.000	0.00	0.00	0.00	2.82
1307	1333	3.881688	AGTGTTGCTGAGATATCCATTGC	59.118	43.478	0.00	0.18	0.00	3.56
1311	1337	3.917988	TGCTGAGATATCCATTGCTACG	58.082	45.455	0.00	0.00	0.00	3.51
1407	1433	5.278463	CCAAGAAGAAATTCTCGAAGCCAAA	60.278	40.000	0.00	0.00	0.00	3.28
1706	1732	6.597672	CCTGTTAGTGGCATTACTCACATTAA	59.402	38.462	0.00	0.00	35.10	1.40
1822	1848	5.334414	CCTCATGTTAGTGTTGACTTTGCTC	60.334	44.000	0.00	0.00	33.21	4.26
1834	1860	6.265196	TGTTGACTTTGCTCATTTCTACCATT	59.735	34.615	0.00	0.00	0.00	3.16
1900	1926	7.237263	ACTCTATTGATGATTTAGAGGGCATCT	59.763	37.037	6.96	6.96	42.04	2.90
1917	1943	4.589374	GGCATCTACCCTATCACTTGTAGT	59.411	45.833	0.00	0.00	33.91	2.73
1918	1944	5.070580	GGCATCTACCCTATCACTTGTAGTT	59.929	44.000	0.00	0.00	33.91	2.24
1919	1945	5.986135	GCATCTACCCTATCACTTGTAGTTG	59.014	44.000	0.00	0.00	35.56	3.16
2129	2167	2.158623	TGGTGAGGTGATTGAGCAAGTT	60.159	45.455	0.00	0.00	0.00	2.66
2146	2186	4.156556	GCAAGTTCTACATGATCAAAGCCA	59.843	41.667	0.00	0.00	0.00	4.75
2161	2201	2.957402	AGCCAGGTGAGATGTTTCAA	57.043	45.000	0.00	0.00	0.00	2.69
2267	2321	4.879545	TGAATTTTACCTTCGACATAGGGC	59.120	41.667	6.59	0.00	37.09	5.19
2692	2755	6.808321	AATCTGGTAGCTTGGACAGTAATA	57.192	37.500	0.00	0.00	32.92	0.98
2696	2759	8.313944	TCTGGTAGCTTGGACAGTAATAAATA	57.686	34.615	0.00	0.00	32.92	1.40
2744	2811	4.202326	GGTGTATACCATGTTCTCGGGATT	60.202	45.833	3.35	0.00	46.71	3.01
2768	2835	2.990284	TGGTATGTTCCTTTGGGGAGAA	59.010	45.455	0.00	0.00	46.01	2.87
3005	7561	8.650714	GTTGATCCTCTTTTATCATTGCAAAAC	58.349	33.333	1.71	0.00	32.40	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	9.349713	ACTGTTTAACATTCAACATAGGAAAGA	57.650	29.630	0.00	0.00	32.50	2.52
12	13	9.965824	AACTGTTTAACATTCAACATAGGAAAG	57.034	29.630	0.00	0.00	32.50	2.62
51	52	3.947834	CGGCTAGGGAATTGAAAAGACAT	59.052	43.478	0.00	0.00	0.00	3.06
60	61	2.643551	ACATCAACGGCTAGGGAATTG	58.356	47.619	0.00	0.00	0.00	2.32
65	66	1.070758	AGCATACATCAACGGCTAGGG	59.929	52.381	0.00	0.00	32.09	3.53
83	84	8.427774	GTTGAGAAATAAAATGCTAACACAAGC	58.572	33.333	0.00	0.00	43.08	4.01
99	101	9.126151	TGGTGTATTTGTTTCAGTTGAGAAATA	57.874	29.630	0.00	0.00	39.46	1.40
109	111	9.810231	GCATTATTTTTGGTGTATTTGTTTCAG	57.190	29.630	0.00	0.00	0.00	3.02
132	135	8.844244	GGTAGATTCAGATTTTACTCAATGCAT	58.156	33.333	0.00	0.00	0.00	3.96
133	136	8.049117	AGGTAGATTCAGATTTTACTCAATGCA	58.951	33.333	0.00	0.00	0.00	3.96
134	137	8.443953	AGGTAGATTCAGATTTTACTCAATGC	57.556	34.615	0.00	0.00	0.00	3.56
137	140	8.730680	GCAAAGGTAGATTCAGATTTTACTCAA	58.269	33.333	0.00	0.00	0.00	3.02
168	171	2.420628	TGTCGCCAAAGAAAATGCAG	57.579	45.000	0.00	0.00	0.00	4.41
204	221	6.349280	CGGGAGATGAATGCAAGAAAGTAAAA	60.349	38.462	0.00	0.00	0.00	1.52
209	226	3.273434	TCGGGAGATGAATGCAAGAAAG	58.727	45.455	0.00	0.00	0.00	2.62
250	270	2.094752	GGCGATAACAACAATGCTTGGT	60.095	45.455	0.00	0.00	34.12	3.67
253	273	4.261801	ACTAGGCGATAACAACAATGCTT	58.738	39.130	0.00	0.00	0.00	3.91
310	330	8.967664	TCAGTTGTAATATAGCGGGTTTTTAT	57.032	30.769	0.00	0.00	0.00	1.40
552	577	4.739195	ACGTGTTGTTTGTAATGTTGCTT	58.261	34.783	0.00	0.00	0.00	3.91
560	585	9.705471	CTTGAATACTTTACGTGTTGTTTGTAA	57.295	29.630	0.00	0.00	0.00	2.41
639	664	4.505324	AGGCCTATCCTCAAAAACTACC	57.495	45.455	1.29	0.00	43.20	3.18
796	822	0.031111	TATGAGCTAGGCTGTGGGGT	60.031	55.000	0.00	0.00	39.88	4.95
988	1014	1.195115	GGACACATCTCCTGGTGCTA	58.805	55.000	0.00	0.00	38.57	3.49
1101	1127	5.303971	AGCAATGTGAGCTTGTCTATATCC	58.696	41.667	0.00	0.00	39.87	2.59
1157	1183	0.468226	TATCACCGGCCTCATTGGAC	59.532	55.000	0.00	0.00	41.70	4.02
1164	1190	2.515854	TCATCTAGTATCACCGGCCTC	58.484	52.381	0.00	0.00	0.00	4.70
1307	1333	2.132762	GTGTTGGAACCTCACACGTAG	58.867	52.381	9.75	0.00	33.04	3.51
1407	1433	1.838715	AGCTCTGGATCATCTTGTGCT	59.161	47.619	0.00	2.63	0.00	4.40
1706	1732	6.950842	TGAGGAAAGTAACTGTGATCATCAT	58.049	36.000	0.00	0.00	0.00	2.45
1764	1790	9.448438	TTTTCATTAAGCTCAAGACTAGCATAA	57.552	29.630	0.22	0.00	42.62	1.90
1765	1791	9.448438	TTTTTCATTAAGCTCAAGACTAGCATA	57.552	29.630	0.22	0.00	42.62	3.14
1822	1848	7.765307	AGCACATGTTTAGAATGGTAGAAATG	58.235	34.615	0.00	0.00	0.00	2.32
1900	1926	6.675413	ACAACAACTACAAGTGATAGGGTA	57.325	37.500	0.00	0.00	0.00	3.69
1917	1943	6.767524	AAATAGGACTCACACAAACAACAA	57.232	33.333	0.00	0.00	0.00	2.83
1918	1944	6.767524	AAAATAGGACTCACACAAACAACA	57.232	33.333	0.00	0.00	0.00	3.33
1962	1991	4.333649	CGAACTTGGTCAGCATGTATTGAT	59.666	41.667	0.00	0.00	37.40	2.57
1966	1995	3.195610	TCTCGAACTTGGTCAGCATGTAT	59.804	43.478	0.00	0.00	37.40	2.29
2017	2046	0.676184	TCTCCTCATCGCCATGCTAC	59.324	55.000	0.00	0.00	0.00	3.58
2129	2167	3.519107	TCACCTGGCTTTGATCATGTAGA	59.481	43.478	0.00	0.00	0.00	2.59
2146	2186	2.711009	TGGGTCTTGAAACATCTCACCT	59.289	45.455	0.00	0.00	0.00	4.00
2267	2321	7.010830	ACTCAGTTCACATATTCACATCAATCG	59.989	37.037	0.00	0.00	0.00	3.34
2744	2811	1.076350	CCCCAAAGGAACATACCACCA	59.924	52.381	0.00	0.00	38.24	4.17
3005	7561	8.985805	ACACTAGTAAACTCGACCATTTTAAAG	58.014	33.333	0.00	0.00	0.00	1.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.