AutoCloner

Multiple sequence alignment - TraesCS3D01G307300

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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	TraesCS3D01G307300	chr3D	100.000	2699	0	0	1	2699	421290138	421292836	0.000000e+00	4985.0
1	TraesCS3D01G307300	chr3D	87.694	837	84	6	990	1817	421314386	421315212	0.000000e+00	957.0
2	TraesCS3D01G307300	chr3D	93.509	570	36	1	83	652	421313509	421314077	0.000000e+00	846.0
3	TraesCS3D01G307300	chr3D	80.449	312	51	8	1212	1521	421704311	421704614	2.090000e-56	230.0
4	TraesCS3D01G307300	chr3D	79.167	312	51	10	1212	1521	422022876	422023175	1.270000e-48	204.0
5	TraesCS3D01G307300	chr3D	97.917	48	1	0	662	709	421314133	421314180	1.720000e-12	84.2
6	TraesCS3D01G307300	chr3A	95.330	1863	64	6	1	1849	529844466	529842613	0.000000e+00	2937.0
7	TraesCS3D01G307300	chr3A	86.619	837	87	10	990	1820	529777568	529776751	0.000000e+00	902.0
8	TraesCS3D01G307300	chr3A	89.734	526	43	6	177	691	529779797	529779272	0.000000e+00	662.0
9	TraesCS3D01G307300	chr3A	94.215	121	6	1	1852	1971	529841583	529841463	1.650000e-42	183.0
10	TraesCS3D01G307300	chr3A	96.000	100	4	0	83	182	529840366	529840267	2.150000e-36	163.0
11	TraesCS3D01G307300	chr3B	95.336	1844	68	8	1	1832	548038343	548040180	0.000000e+00	2913.0
12	TraesCS3D01G307300	chr3B	87.770	834	87	11	990	1817	548045031	548045855	0.000000e+00	961.0
13	TraesCS3D01G307300	chr3B	91.270	630	52	2	83	709	548044195	548044824	0.000000e+00	856.0
14	TraesCS3D01G307300	chr3B	93.555	481	29	2	2218	2697	99673225	99673704	0.000000e+00	715.0
15	TraesCS3D01G307300	chr3B	85.169	236	25	8	1966	2195	144212321	144212090	1.620000e-57	233.0
16	TraesCS3D01G307300	chr3B	79.167	312	55	7	1212	1521	549427491	549427794	9.790000e-50	207.0
17	TraesCS3D01G307300	chr3B	92.126	127	10	0	1839	1965	548042755	548042881	2.130000e-41	180.0
18	TraesCS3D01G307300	chr2B	86.401	728	71	9	1977	2699	5016832	5017536	0.000000e+00	771.0
19	TraesCS3D01G307300	chr2B	93.933	478	27	2	2221	2697	29220800	29220324	0.000000e+00	721.0
20	TraesCS3D01G307300	chr6B	93.294	507	30	4	2195	2699	158163901	158164405	0.000000e+00	745.0
21	TraesCS3D01G307300	chr6B	86.611	239	28	4	1966	2203	158163599	158163834	7.410000e-66	261.0
22	TraesCS3D01G307300	chrUn	92.578	512	31	6	2194	2699	26662864	26663374	0.000000e+00	728.0
23	TraesCS3D01G307300	chrUn	92.478	226	15	2	1972	2195	93758444	93758669	3.350000e-84	322.0
24	TraesCS3D01G307300	chr7B	94.142	478	26	2	2221	2697	697431859	697431383	0.000000e+00	726.0
25	TraesCS3D01G307300	chr7B	86.726	226	24	5	1978	2200	684596154	684596376	2.080000e-61	246.0
26	TraesCS3D01G307300	chr7B	85.909	220	29	2	1977	2195	746356799	746356581	1.620000e-57	233.0
27	TraesCS3D01G307300	chr5B	93.347	481	30	2	2218	2697	560003417	560003896	0.000000e+00	710.0
28	TraesCS3D01G307300	chr1B	92.231	502	37	2	2199	2699	58085832	58086332	0.000000e+00	710.0
29	TraesCS3D01G307300	chr1B	92.032	502	38	2	2199	2699	58112482	58112982	0.000000e+00	704.0
30	TraesCS3D01G307300	chr1B	86.547	223	22	7	1979	2195	73038907	73038687	3.470000e-59	239.0
31	TraesCS3D01G307300	chr1B	85.650	223	25	6	1978	2195	377663343	377663123	7.520000e-56	228.0
32	TraesCS3D01G307300	chr7A	91.929	508	38	3	2194	2699	506287570	506287064	0.000000e+00	708.0
33	TraesCS3D01G307300	chr4A	89.270	233	25	0	269	501	538833223	538833455	2.630000e-75	292.0
34	TraesCS3D01G307300	chr4A	93.333	45	3	0	131	175	538833184	538833228	1.730000e-07	67.6
35	TraesCS3D01G307300	chr2A	80.000	340	62	6	1195	1532	15815548	15815213	2.080000e-61	246.0
36	TraesCS3D01G307300	chr5D	85.135	222	25	7	1979	2195	438431757	438431539	1.260000e-53	220.0
37	TraesCS3D01G307300	chr4D	94.937	79	4	0	368	446	450198733	450198655	1.010000e-24	124.0

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	TraesCS3D01G307300	chr3D	421290138	421292836	2698	False	4985.000000	4985	100.000000	1	2699	1	chr3D.!!$F1	2698
1	TraesCS3D01G307300	chr3D	421313509	421315212	1703	False	629.066667	957	93.040000	83	1817	3	chr3D.!!$F4	1734
2	TraesCS3D01G307300	chr3A	529840267	529844466	4199	True	1094.333333	2937	95.181667	1	1971	3	chr3A.!!$R2	1970
3	TraesCS3D01G307300	chr3A	529776751	529779797	3046	True	782.000000	902	88.176500	177	1820	2	chr3A.!!$R1	1643
4	TraesCS3D01G307300	chr3B	548038343	548045855	7512	False	1227.500000	2913	91.625500	1	1965	4	chr3B.!!$F3	1964
5	TraesCS3D01G307300	chr2B	5016832	5017536	704	False	771.000000	771	86.401000	1977	2699	1	chr2B.!!$F1	722
6	TraesCS3D01G307300	chr6B	158163599	158164405	806	False	503.000000	745	89.952500	1966	2699	2	chr6B.!!$F1	733
7	TraesCS3D01G307300	chrUn	26662864	26663374	510	False	728.000000	728	92.578000	2194	2699	1	chrUn.!!$F1	505
8	TraesCS3D01G307300	chr1B	58085832	58086332	500	False	710.000000	710	92.231000	2199	2699	1	chr1B.!!$F1	500
9	TraesCS3D01G307300	chr1B	58112482	58112982	500	False	704.000000	704	92.032000	2199	2699	1	chr1B.!!$F2	500
10	TraesCS3D01G307300	chr7A	506287064	506287570	506	True	708.000000	708	91.929000	2194	2699	1	chr7A.!!$R1	505

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
658	670	0.755079	TCTTCCATGGATGCTCCGAG	59.245	55.0	17.06	8.2	40.17	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1869	10161	0.603569	AACGCCAGTTCGACTCAGAT	59.396	50.0	0.0	0.0	35.23	2.9	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
450	454	2.809601	CGTTCTTGACGCGGAGGG	60.810	66.667	12.47	0.00	45.86	4.30
653	665	3.627395	TTACGTTCTTCCATGGATGCT	57.373	42.857	17.06	4.06	0.00	3.79
654	666	2.029838	ACGTTCTTCCATGGATGCTC	57.970	50.000	17.06	12.41	0.00	4.26
655	667	1.303309	CGTTCTTCCATGGATGCTCC	58.697	55.000	17.06	7.92	36.96	4.70
656	668	1.303309	GTTCTTCCATGGATGCTCCG	58.697	55.000	17.06	0.52	40.17	4.63
657	669	1.134401	GTTCTTCCATGGATGCTCCGA	60.134	52.381	17.06	0.00	40.17	4.55
658	670	0.755079	TCTTCCATGGATGCTCCGAG	59.245	55.000	17.06	8.20	40.17	4.63
770	2314	6.288941	TCCTCCAGAAAATACACGTATGAA	57.711	37.500	0.00	0.00	0.00	2.57
808	2352	2.463752	ACAGGCCGTTCCTAACAGATA	58.536	47.619	0.00	0.00	45.52	1.98
850	2394	2.104170	GAGGGAGTTCGGTTGAGATCT	58.896	52.381	0.00	0.00	0.00	2.75
953	2517	3.879892	GGCATCTCCAACAAATACTCCTC	59.120	47.826	0.00	0.00	34.01	3.71
1135	2709	3.055385	CGGACCCACCTTTCTAATCTTGA	60.055	47.826	0.00	0.00	36.31	3.02
1221	2795	3.745803	GCGTCCTTCTCCGTCGGT	61.746	66.667	11.88	0.00	0.00	4.69
1296	2870	2.664851	TTCAACCTCACGCTGCGG	60.665	61.111	26.95	15.00	0.00	5.69
1714	3288	5.855045	ACTCGTAGACTGTCTTTGGATTTT	58.145	37.500	16.53	0.00	0.00	1.82
1820	9085	9.613428	AAGCTGAATGTACTGCTGTAATTTATA	57.387	29.630	4.88	0.00	42.48	0.98
1844	9109	6.796705	AAAATTCGTAGTAACCACCTTCAG	57.203	37.500	0.00	0.00	0.00	3.02
1849	9114	4.218417	TCGTAGTAACCACCTTCAGTAACC	59.782	45.833	0.00	0.00	0.00	2.85
1866	10158	0.666274	ACCTCGTGTACATGCGTGTG	60.666	55.000	21.92	4.77	39.39	3.82
1869	10161	2.321263	CTCGTGTACATGCGTGTGTTA	58.679	47.619	21.92	4.80	39.39	2.41
1885	10177	2.924290	GTGTTATCTGAGTCGAACTGGC	59.076	50.000	0.00	0.00	0.00	4.85
1915	10207	7.458038	TTGAATAAAAAGCACGAAAACCTTC	57.542	32.000	0.00	0.00	0.00	3.46
2069	10362	2.285180	CCCTCCTCCTCCCTCCTG	59.715	72.222	0.00	0.00	0.00	3.86
2140	10433	2.282180	GGCGGGGCTTGTTCTTCA	60.282	61.111	0.00	0.00	0.00	3.02
2153	10446	2.884087	TTCTTCATCCTCCGCGCGAC	62.884	60.000	34.63	0.00	0.00	5.19
2263	10697	4.704833	GGTTCAGGCTGCTGGCGA	62.705	66.667	10.34	9.15	44.18	5.54
2392	10826	2.345244	CTTGGCGGCTCTCTGTGT	59.655	61.111	11.43	0.00	0.00	3.72
2396	10830	3.695606	GCGGCTCTCTGTGTGGGA	61.696	66.667	0.00	0.00	0.00	4.37
2596	11189	2.202743	GTGCCGACGATGCTGCTA	60.203	61.111	0.00	0.00	0.00	3.49
2597	11190	2.202743	TGCCGACGATGCTGCTAC	60.203	61.111	0.00	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
485	489	1.118356	CCAGCTTCGAGGGCCTAGAT	61.118	60.000	17.47	1.39	0.00	1.98
488	500	1.758514	CTCCAGCTTCGAGGGCCTA	60.759	63.158	5.73	0.00	0.00	3.93
555	567	2.106938	TGCGATCCTCATGACCGC	59.893	61.111	15.69	15.69	45.28	5.68
653	665	0.749818	CCTAGTCAGCTCAGCTCGGA	60.750	60.000	0.00	0.00	36.40	4.55
654	666	1.732917	CCTAGTCAGCTCAGCTCGG	59.267	63.158	0.00	0.00	36.40	4.63
655	667	1.065600	GCCTAGTCAGCTCAGCTCG	59.934	63.158	0.00	0.00	36.40	5.03
656	668	1.441311	GGCCTAGTCAGCTCAGCTC	59.559	63.158	0.00	0.00	36.40	4.09
657	669	2.422231	CGGCCTAGTCAGCTCAGCT	61.422	63.158	0.00	0.00	40.77	4.24
658	670	2.105930	CGGCCTAGTCAGCTCAGC	59.894	66.667	0.00	0.00	0.00	4.26
770	2314	3.118738	CCTGTACCTTAATTGTCCTCGCT	60.119	47.826	0.00	0.00	0.00	4.93
825	2369	0.249741	CAACCGAACTCCCTCACGTT	60.250	55.000	0.00	0.00	0.00	3.99
834	2378	6.657541	AGGATATCTAGATCTCAACCGAACTC	59.342	42.308	17.22	0.54	0.00	3.01
850	2394	5.071384	TCCGTATCCAGCGATAGGATATCTA	59.929	44.000	12.74	0.00	46.63	1.98
953	2517	3.932089	GCTGTCTTCAAGCTTCTTCTAGG	59.068	47.826	0.00	0.00	0.00	3.02
1135	2709	2.301870	TCACTCCAACCGAAAGTAGCAT	59.698	45.455	0.00	0.00	0.00	3.79
1296	2870	1.132640	GGCGCACGTCTTGTTCATC	59.867	57.895	10.83	0.00	0.00	2.92
1548	3122	1.827399	CGAAGTAGCCCCACCACAGT	61.827	60.000	0.00	0.00	0.00	3.55
1552	3126	3.712907	GCCGAAGTAGCCCCACCA	61.713	66.667	0.00	0.00	0.00	4.17
1714	3288	4.257731	TGACAATTCATCCGAAAATCCGA	58.742	39.130	0.00	0.00	34.01	4.55
1820	9085	6.769341	ACTGAAGGTGGTTACTACGAATTTTT	59.231	34.615	0.00	0.00	0.00	1.94
1838	9103	3.928727	TGTACACGAGGTTACTGAAGG	57.071	47.619	0.00	0.00	0.00	3.46
1844	9109	1.652124	CACGCATGTACACGAGGTTAC	59.348	52.381	12.29	0.00	0.00	2.50
1849	9114	1.136690	AACACACGCATGTACACGAG	58.863	50.000	12.29	1.73	36.72	4.18
1866	10158	2.186076	CGCCAGTTCGACTCAGATAAC	58.814	52.381	0.00	0.00	0.00	1.89
1869	10161	0.603569	AACGCCAGTTCGACTCAGAT	59.396	50.000	0.00	0.00	35.23	2.90
1910	10202	3.096852	TCATCGTGATAGGTGTGAAGGT	58.903	45.455	0.00	0.00	0.00	3.50
1915	10207	4.271049	GGACAAATCATCGTGATAGGTGTG	59.729	45.833	12.29	5.87	35.76	3.82
1950	10242	2.154462	AGCTCCAGTTTGCACATACAC	58.846	47.619	0.00	0.00	0.00	2.90
2029	10322	4.227134	CGGCGGTGGGAGGATCTG	62.227	72.222	0.00	0.00	33.73	2.90
2131	10424	1.019278	GCGCGGAGGATGAAGAACAA	61.019	55.000	8.83	0.00	0.00	2.83
2161	10455	3.074369	TCGATGAAGGAGCCCGCA	61.074	61.111	0.00	0.00	0.00	5.69
2396	10830	3.580319	AAACCGCTCCCCTGCCTT	61.580	61.111	0.00	0.00	0.00	4.35
2411	10845	4.278513	CCACCGCCCCTGTCCAAA	62.279	66.667	0.00	0.00	0.00	3.28
2588	11181	0.764752	GGGACTAGGGGTAGCAGCAT	60.765	60.000	0.00	0.00	0.00	3.79
2596	11189	4.477119	GGAGCCGGGACTAGGGGT	62.477	72.222	2.18	0.00	36.58	4.95
2597	11190	4.159108	AGGAGCCGGGACTAGGGG	62.159	72.222	2.18	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.