AutoCloner

Multiple sequence alignment - TraesCS3D01G211000

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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	TraesCS3D01G211000	chr3D	100.000	3005	0	0	1	3005	281084444	281087448	0.000000e+00	5550.0
1	TraesCS3D01G211000	chr3D	96.296	2673	77	9	1	2671	450572980	450570328	0.000000e+00	4368.0
2	TraesCS3D01G211000	chr4D	97.569	2674	48	5	1	2670	500039410	500042070	0.000000e+00	4562.0
3	TraesCS3D01G211000	chr1A	96.890	2154	49	7	1	2146	493290296	493292439	0.000000e+00	3591.0
4	TraesCS3D01G211000	chr1A	96.395	527	17	2	2145	2670	493292526	493293051	0.000000e+00	867.0
5	TraesCS3D01G211000	chr1A	92.063	63	5	0	2941	3003	493934495	493934433	4.130000e-14	89.8
6	TraesCS3D01G211000	chr1B	89.375	1120	89	13	958	2077	601257570	601258659	0.000000e+00	1382.0
7	TraesCS3D01G211000	chr4A	90.330	817	72	5	955	1770	519159506	519160316	0.000000e+00	1064.0
8	TraesCS3D01G211000	chr4A	83.404	235	20	9	2771	3005	400761478	400761693	1.830000e-47	200.0
9	TraesCS3D01G211000	chr4A	86.957	115	15	0	2750	2864	597723008	597723122	2.430000e-26	130.0
10	TraesCS3D01G211000	chr4A	100.000	29	0	0	2819	2847	597723133	597723161	2.000000e-03	54.7
11	TraesCS3D01G211000	chr5D	86.935	819	90	8	961	1770	558499136	558498326	0.000000e+00	904.0
12	TraesCS3D01G211000	chr5D	85.421	439	34	13	223	657	524597969	524598381	2.140000e-116	429.0
13	TraesCS3D01G211000	chr5D	89.431	123	13	0	846	968	558499612	558499490	4.010000e-34	156.0
14	TraesCS3D01G211000	chr2A	86.242	785	92	13	1299	2076	692641808	692641033	0.000000e+00	837.0
15	TraesCS3D01G211000	chr2D	85.969	784	95	13	1299	2076	551871494	551870720	0.000000e+00	824.0
16	TraesCS3D01G211000	chr2D	89.127	607	59	5	963	1568	211559853	211559253	0.000000e+00	749.0
17	TraesCS3D01G211000	chr2B	86.629	531	57	7	958	1487	652282593	652283110	2.600000e-160	575.0
18	TraesCS3D01G211000	chr2B	89.391	443	43	2	1631	2072	652283132	652283571	3.380000e-154	555.0
19	TraesCS3D01G211000	chr2B	88.856	341	34	4	966	1305	657078011	657077674	1.670000e-112	416.0
20	TraesCS3D01G211000	chrUn	90.612	245	20	3	499	742	31916737	31916979	3.740000e-84	322.0
21	TraesCS3D01G211000	chrUn	87.454	271	21	6	238	495	31913440	31913710	1.750000e-77	300.0
22	TraesCS3D01G211000	chrUn	90.000	170	9	2	84	253	31913259	31913420	2.350000e-51	213.0
23	TraesCS3D01G211000	chr1D	93.750	208	12	1	2799	3005	163708205	163707998	8.090000e-81	311.0
24	TraesCS3D01G211000	chr1D	95.370	108	5	0	2670	2777	163709582	163709475	3.980000e-39	172.0
25	TraesCS3D01G211000	chr6B	90.777	206	16	2	449	652	257587344	257587140	3.820000e-69	272.0
26	TraesCS3D01G211000	chr6B	91.538	130	10	1	277	405	257596177	257596048	8.560000e-41	178.0
27	TraesCS3D01G211000	chr6B	97.015	67	2	0	225	291	257597152	257597086	2.450000e-21	113.0
28	TraesCS3D01G211000	chr6A	100.000	36	0	0	182	217	146741431	146741466	1.930000e-07	67.6
29	TraesCS3D01G211000	chr7D	100.000	34	0	0	905	938	502878986	502879019	2.500000e-06	63.9
30	TraesCS3D01G211000	chr7B	100.000	34	0	0	905	938	531660351	531660384	2.500000e-06	63.9
31	TraesCS3D01G211000	chr7A	97.059	34	1	0	905	938	570117978	570118011	1.160000e-04	58.4
32	TraesCS3D01G211000	chr4B	100.000	29	0	0	2819	2847	10519830	10519802	2.000000e-03	54.7

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	TraesCS3D01G211000	chr3D	281084444	281087448	3004	False	5550.000000	5550	100.000000	1	3005	1	chr3D.!!$F1	3004
1	TraesCS3D01G211000	chr3D	450570328	450572980	2652	True	4368.000000	4368	96.296000	1	2671	1	chr3D.!!$R1	2670
2	TraesCS3D01G211000	chr4D	500039410	500042070	2660	False	4562.000000	4562	97.569000	1	2670	1	chr4D.!!$F1	2669
3	TraesCS3D01G211000	chr1A	493290296	493293051	2755	False	2229.000000	3591	96.642500	1	2670	2	chr1A.!!$F1	2669
4	TraesCS3D01G211000	chr1B	601257570	601258659	1089	False	1382.000000	1382	89.375000	958	2077	1	chr1B.!!$F1	1119
5	TraesCS3D01G211000	chr4A	519159506	519160316	810	False	1064.000000	1064	90.330000	955	1770	1	chr4A.!!$F2	815
6	TraesCS3D01G211000	chr5D	558498326	558499612	1286	True	530.000000	904	88.183000	846	1770	2	chr5D.!!$R1	924
7	TraesCS3D01G211000	chr2A	692641033	692641808	775	True	837.000000	837	86.242000	1299	2076	1	chr2A.!!$R1	777
8	TraesCS3D01G211000	chr2D	551870720	551871494	774	True	824.000000	824	85.969000	1299	2076	1	chr2D.!!$R2	777
9	TraesCS3D01G211000	chr2D	211559253	211559853	600	True	749.000000	749	89.127000	963	1568	1	chr2D.!!$R1	605
10	TraesCS3D01G211000	chr2B	652282593	652283571	978	False	565.000000	575	88.010000	958	2072	2	chr2B.!!$F1	1114
11	TraesCS3D01G211000	chrUn	31913259	31916979	3720	False	278.333333	322	89.355333	84	742	3	chrUn.!!$F1	658
12	TraesCS3D01G211000	chr1D	163707998	163709582	1584	True	241.500000	311	94.560000	2670	3005	2	chr1D.!!$R1	335

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
850	3924	1.001974	ACTACAACCGCAGCTGATTCA	59.998	47.619	20.43	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2620	6191	0.179032	TCCTGAGCGGAAACTTTGCA	60.179	50.0	0.0	0.0	39.4	4.08	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
102	104	5.365619	GTTTCTTCCGATAAATCCCTGCTA	58.634	41.667	0.00	0.00	0.00	3.49
269	306	5.398176	TGGATTTGCGAATCGTGTAATAC	57.602	39.130	18.46	3.49	42.12	1.89
447	496	4.870636	TGATCAGGCATGGGTATTCTTTT	58.129	39.130	0.00	0.00	0.00	2.27
724	3798	3.181450	ACTTGCTGAAGCTCCTACAAACT	60.181	43.478	3.61	0.00	42.66	2.66
728	3802	3.368236	GCTGAAGCTCCTACAAACTTACG	59.632	47.826	0.00	0.00	38.21	3.18
850	3924	1.001974	ACTACAACCGCAGCTGATTCA	59.998	47.619	20.43	0.00	0.00	2.57
1011	4452	9.918630	AATATAAAGTATTGCATGATTCCTTGC	57.081	29.630	0.00	2.61	42.01	4.01
1100	4541	9.196139	GTCTCCTAGCTATGACAAGGATTATAT	57.804	37.037	13.41	0.00	37.50	0.86
1129	4570	3.193263	CTGTATGGCAGCTACACTCTTG	58.807	50.000	0.00	0.00	38.52	3.02
1317	4762	9.406828	GTCCTTGGTAGTTATTGATTTGTTTTC	57.593	33.333	0.00	0.00	0.00	2.29
1615	5077	7.538678	GCAAAACTGTGAACATTAAGTAGATGG	59.461	37.037	0.00	0.00	0.00	3.51
1888	5354	3.313012	TTGGTGTGGTCTCTTCGTATG	57.687	47.619	0.00	0.00	0.00	2.39
1901	5368	4.806330	TCTTCGTATGGTCTCAAGTTGAC	58.194	43.478	0.08	0.00	0.00	3.18
1957	5424	1.618487	TGTGATGGCTTTCATGTGCA	58.382	45.000	9.44	0.00	35.97	4.57
2138	5605	2.483014	TAGGTACGCAGGCAACATTT	57.517	45.000	0.00	0.00	41.41	2.32
2168	5723	3.858247	TCACTTGCATCTCAGATCACTG	58.142	45.455	0.00	0.00	44.66	3.66
2171	5726	2.573941	TGCATCTCAGATCACTGTCG	57.426	50.000	0.00	0.00	43.81	4.35
2172	5727	1.821136	TGCATCTCAGATCACTGTCGT	59.179	47.619	0.00	0.00	43.81	4.34
2173	5728	3.016736	TGCATCTCAGATCACTGTCGTA	58.983	45.455	0.00	0.00	43.81	3.43
2174	5729	3.443681	TGCATCTCAGATCACTGTCGTAA	59.556	43.478	0.00	0.00	43.81	3.18
2175	5730	4.082245	TGCATCTCAGATCACTGTCGTAAA	60.082	41.667	0.00	0.00	43.81	2.01
2176	5731	4.864806	GCATCTCAGATCACTGTCGTAAAA	59.135	41.667	0.00	0.00	43.81	1.52
2177	5732	5.348724	GCATCTCAGATCACTGTCGTAAAAA	59.651	40.000	0.00	0.00	43.81	1.94
2178	5733	6.036517	GCATCTCAGATCACTGTCGTAAAAAT	59.963	38.462	0.00	0.00	43.81	1.82
2240	5810	2.965831	TGTGCCTCTCCAGGATATACAC	59.034	50.000	0.00	0.00	43.65	2.90
2241	5811	2.965831	GTGCCTCTCCAGGATATACACA	59.034	50.000	0.00	0.00	43.65	3.72
2414	5984	7.491681	AGGGAGTATGATCCTCCTATATTTGT	58.508	38.462	14.06	0.00	46.43	2.83
2453	6023	8.510243	TGATCTATTTTATGAATGTGTGCTGT	57.490	30.769	0.00	0.00	0.00	4.40
2532	6103	3.330701	TCTGGTCAGCACTAAGGGATTTT	59.669	43.478	0.00	0.00	0.00	1.82
2578	6149	1.441738	CATTCACATGTGCGTCCAGA	58.558	50.000	21.38	0.00	0.00	3.86
2620	6191	3.807368	GGTGACCTACCTGGCACT	58.193	61.111	0.00	0.00	46.51	4.40
2624	6195	1.374947	GACCTACCTGGCACTGCAA	59.625	57.895	2.82	0.00	40.22	4.08
2676	6247	3.427573	GCCCCAACCACTAGTGTTTAAT	58.572	45.455	21.18	0.17	0.00	1.40
2724	6295	2.154462	CATCGATTGCCCACTAATCCC	58.846	52.381	0.00	0.00	32.26	3.85
2752	6323	3.067601	ACCCCTTTTCGTTGTCATCAAAC	59.932	43.478	0.00	0.00	35.20	2.93
2754	6325	4.290155	CCCTTTTCGTTGTCATCAAACTG	58.710	43.478	0.00	0.00	35.20	3.16
2765	6336	2.041485	TCATCAAACTGCCATTCCCTCA	59.959	45.455	0.00	0.00	0.00	3.86
2817	7636	4.655527	CGCACCACGTCTTCTTCT	57.344	55.556	0.00	0.00	36.87	2.85
2829	7648	0.676151	CTTCTTCTCCCTGCTGCCAC	60.676	60.000	0.00	0.00	0.00	5.01
2914	7733	2.155194	CGCTTCTCGTCTGCTTCCG	61.155	63.158	0.00	0.00	0.00	4.30
2915	7734	1.213013	GCTTCTCGTCTGCTTCCGA	59.787	57.895	0.00	0.00	0.00	4.55
2916	7735	1.073768	GCTTCTCGTCTGCTTCCGAC	61.074	60.000	0.00	0.00	0.00	4.79
2926	7746	0.669318	TGCTTCCGACGGACATGAAC	60.669	55.000	18.12	3.15	0.00	3.18
2937	7757	2.227089	GACATGAACGCGGGTCTCCT	62.227	60.000	12.47	0.00	0.00	3.69
2996	7816	1.589113	GAGGACTGAAGCTGAGCGT	59.411	57.895	0.00	0.00	0.00	5.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
269	306	1.273327	GAAAGCCCACATCCCAGTTTG	59.727	52.381	0.00	0.00	0.00	2.93
495	544	9.504708	TCATTTCATGGCACTGAAAATATTTTT	57.495	25.926	20.77	0.00	45.45	1.94
533	3605	7.862372	AGTTGTGTTGTTTGATACATGTGAATC	59.138	33.333	9.11	5.07	36.44	2.52
724	3798	2.396590	GGAGAACAATGGCTCCGTAA	57.603	50.000	8.31	0.00	41.10	3.18
850	3924	3.629855	TGGATCGAACAAACAACACACAT	59.370	39.130	0.00	0.00	0.00	3.21
1011	4452	4.400251	TGAGCATTTGGAAAGAGGCTAATG	59.600	41.667	0.00	0.00	0.00	1.90
1129	4570	2.561569	CCTCCCATCCGTGACATTTAC	58.438	52.381	0.00	0.00	0.00	2.01
1615	5077	4.331168	AGAGCTATGTTTCGTCTTTCATGC	59.669	41.667	0.00	0.00	0.00	4.06
1869	5335	1.548719	CCATACGAAGAGACCACACCA	59.451	52.381	0.00	0.00	0.00	4.17
1888	5354	5.867716	TCTTTAATAGCGTCAACTTGAGACC	59.132	40.000	0.00	0.00	32.41	3.85
1957	5424	5.995282	TGAAAACCATCAATAGACTTGACGT	59.005	36.000	0.00	0.00	0.00	4.34
2011	5478	6.488683	TCCATTCCAATTGGATATTACCGTTC	59.511	38.462	27.53	0.00	44.98	3.95
2163	5718	4.613944	ACGACAGATTTTTACGACAGTGA	58.386	39.130	0.00	0.00	0.00	3.41
2174	5729	9.730420	GTGCCATAATTATTTACGACAGATTTT	57.270	29.630	0.00	0.00	0.00	1.82
2175	5730	9.120538	AGTGCCATAATTATTTACGACAGATTT	57.879	29.630	0.00	0.00	0.00	2.17
2176	5731	8.559536	CAGTGCCATAATTATTTACGACAGATT	58.440	33.333	0.00	0.00	0.00	2.40
2177	5732	7.931407	TCAGTGCCATAATTATTTACGACAGAT	59.069	33.333	0.00	0.00	0.00	2.90
2178	5733	7.223971	GTCAGTGCCATAATTATTTACGACAGA	59.776	37.037	0.00	0.00	0.00	3.41
2240	5810	0.716108	GGACGTCATCGCTTCAGTTG	59.284	55.000	18.91	0.00	41.18	3.16
2241	5811	0.603569	AGGACGTCATCGCTTCAGTT	59.396	50.000	18.91	0.00	41.18	3.16
2414	5984	7.452880	AAAATAGATCAAAGCTACAAGCACA	57.547	32.000	1.22	0.00	45.56	4.57
2453	6023	7.775053	AGGTTGGAAAAATAAGATACAGCAA	57.225	32.000	0.00	0.00	0.00	3.91
2532	6103	8.570488	CAAGCATTGCTCATGGAATTATAACTA	58.430	33.333	12.39	0.00	40.39	2.24
2620	6191	0.179032	TCCTGAGCGGAAACTTTGCA	60.179	50.000	0.00	0.00	39.40	4.08
2624	6195	1.003233	GCCTCCTGAGCGGAAACTT	60.003	57.895	0.00	0.00	42.53	2.66
2676	6247	1.971167	GGATCCGTGGCTTGTTGCA	60.971	57.895	0.00	0.00	45.15	4.08
2724	6295	3.007635	GACAACGAAAAGGGGTATGGAG	58.992	50.000	0.00	0.00	0.00	3.86
2752	6323	2.425143	TTTAGCTGAGGGAATGGCAG	57.575	50.000	0.00	0.00	0.00	4.85
2754	6325	3.356290	TCTTTTTAGCTGAGGGAATGGC	58.644	45.455	0.00	0.00	0.00	4.40
2765	6336	4.520874	GGGAAGAGCAGTTTCTTTTTAGCT	59.479	41.667	0.00	0.00	37.53	3.32
2808	7627	0.392327	GGCAGCAGGGAGAAGAAGAC	60.392	60.000	0.00	0.00	0.00	3.01
2914	7733	3.186047	CCCGCGTTCATGTCCGTC	61.186	66.667	4.92	1.72	0.00	4.79
2915	7734	3.927163	GACCCGCGTTCATGTCCGT	62.927	63.158	4.92	0.00	0.00	4.69
2916	7735	3.186047	GACCCGCGTTCATGTCCG	61.186	66.667	4.92	0.00	0.00	4.79
2926	7746	4.570663	CGGCTAAGGAGACCCGCG	62.571	72.222	0.00	0.00	37.58	6.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.