AutoCloner

Multiple sequence alignment - TraesCS2B01G197700

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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	TraesCS2B01G197700	chr2B	100.000	2357	0	0	1	2357	175453756	175456112	0.000000e+00	4353.0
1	TraesCS2B01G197700	chr2B	95.406	849	37	2	1	849	452911023	452910177	0.000000e+00	1351.0
2	TraesCS2B01G197700	chr3B	96.226	848	32	0	1	848	824304206	824305053	0.000000e+00	1389.0
3	TraesCS2B01G197700	chr3B	94.982	857	38	3	1	855	708391918	708392771	0.000000e+00	1339.0
4	TraesCS2B01G197700	chr3B	85.171	263	34	4	1853	2113	550653105	550652846	4.990000e-67	265.0
5	TraesCS2B01G197700	chr1B	96.204	843	31	1	5	847	94009975	94009134	0.000000e+00	1378.0
6	TraesCS2B01G197700	chr1B	95.882	850	34	1	1	849	643025799	643024950	0.000000e+00	1375.0
7	TraesCS2B01G197700	chr6B	95.873	848	35	0	1	848	26218587	26217740	0.000000e+00	1373.0
8	TraesCS2B01G197700	chr4B	95.755	848	36	0	1	848	665294666	665293819	0.000000e+00	1367.0
9	TraesCS2B01G197700	chrUn	95.182	851	39	2	1	849	263186143	263185293	0.000000e+00	1343.0
10	TraesCS2B01G197700	chr7B	95.283	848	39	1	1	848	498598923	498599769	0.000000e+00	1343.0
11	TraesCS2B01G197700	chr2D	93.168	805	49	5	1438	2241	122562861	122563660	0.000000e+00	1177.0
12	TraesCS2B01G197700	chr2D	95.207	605	19	7	845	1445	122560782	122561380	0.000000e+00	948.0
13	TraesCS2B01G197700	chr2D	84.151	265	36	5	1854	2116	172409404	172409664	3.890000e-63	252.0
14	TraesCS2B01G197700	chr2A	91.003	678	58	3	1681	2357	126992209	126992884	0.000000e+00	911.0
15	TraesCS2B01G197700	chr2A	96.591	528	15	2	921	1445	126656589	126657116	0.000000e+00	872.0
16	TraesCS2B01G197700	chr2A	95.984	249	9	1	1438	1685	126658217	126658465	1.010000e-108	403.0
17	TraesCS2B01G197700	chr2A	84.211	266	37	4	1854	2116	177658674	177658411	1.080000e-63	254.0
18	TraesCS2B01G197700	chr2A	88.325	197	21	1	2161	2357	61503566	61503372	3.920000e-58	235.0
19	TraesCS2B01G197700	chr2A	86.935	199	24	1	2159	2357	13009175	13009371	3.050000e-54	222.0
20	TraesCS2B01G197700	chr2A	96.491	57	2	0	845	901	126651547	126651603	6.930000e-16	95.3
21	TraesCS2B01G197700	chr5D	88.115	244	25	4	1871	2113	5223939	5223699	1.070000e-73	287.0
22	TraesCS2B01G197700	chr5D	86.122	245	30	3	1872	2113	517846931	517846688	6.460000e-66	261.0
23	TraesCS2B01G197700	chr3D	84.791	263	37	2	1853	2113	422529058	422528797	6.460000e-66	261.0
24	TraesCS2B01G197700	chr3A	84.791	263	37	3	1853	2113	566874370	566874631	6.460000e-66	261.0
25	TraesCS2B01G197700	chr3A	85.514	214	26	3	2147	2357	726338784	726338995	3.940000e-53	219.0
26	TraesCS2B01G197700	chr6D	89.055	201	19	2	2157	2357	454889538	454889341	1.810000e-61	246.0
27	TraesCS2B01G197700	chr6D	88.557	201	20	2	2157	2357	454923093	454922896	8.420000e-60	241.0
28	TraesCS2B01G197700	chr7A	87.500	200	20	4	2159	2357	734933593	734933788	2.360000e-55	226.0
29	TraesCS2B01G197700	chr1A	87.000	200	23	2	2159	2357	456286377	456286180	3.050000e-54	222.0
30	TraesCS2B01G197700	chr1A	87.374	198	20	4	2161	2357	520860758	520860951	3.050000e-54	222.0

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	TraesCS2B01G197700	chr2B	175453756	175456112	2356	False	4353.0	4353	100.0000	1	2357	1	chr2B.!!$F1	2356
1	TraesCS2B01G197700	chr2B	452910177	452911023	846	True	1351.0	1351	95.4060	1	849	1	chr2B.!!$R1	848
2	TraesCS2B01G197700	chr3B	824304206	824305053	847	False	1389.0	1389	96.2260	1	848	1	chr3B.!!$F2	847
3	TraesCS2B01G197700	chr3B	708391918	708392771	853	False	1339.0	1339	94.9820	1	855	1	chr3B.!!$F1	854
4	TraesCS2B01G197700	chr1B	94009134	94009975	841	True	1378.0	1378	96.2040	5	847	1	chr1B.!!$R1	842
5	TraesCS2B01G197700	chr1B	643024950	643025799	849	True	1375.0	1375	95.8820	1	849	1	chr1B.!!$R2	848
6	TraesCS2B01G197700	chr6B	26217740	26218587	847	True	1373.0	1373	95.8730	1	848	1	chr6B.!!$R1	847
7	TraesCS2B01G197700	chr4B	665293819	665294666	847	True	1367.0	1367	95.7550	1	848	1	chr4B.!!$R1	847
8	TraesCS2B01G197700	chrUn	263185293	263186143	850	True	1343.0	1343	95.1820	1	849	1	chrUn.!!$R1	848
9	TraesCS2B01G197700	chr7B	498598923	498599769	846	False	1343.0	1343	95.2830	1	848	1	chr7B.!!$F1	847
10	TraesCS2B01G197700	chr2D	122560782	122563660	2878	False	1062.5	1177	94.1875	845	2241	2	chr2D.!!$F2	1396
11	TraesCS2B01G197700	chr2A	126992209	126992884	675	False	911.0	911	91.0030	1681	2357	1	chr2A.!!$F3	676
12	TraesCS2B01G197700	chr2A	126656589	126658465	1876	False	637.5	872	96.2875	921	1685	2	chr2A.!!$F4	764

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
276	278	0.186873	ATGGTTGGGGATGGATCTGC	59.813	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1636	3254	0.034477	AATGGTAGGTTGGGAAGCGG	60.034	55.0	0.0	0.0	0.0	5.52	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
66	67	1.439679	GATCTTCCAACGCCGTTCTT	58.560	50.000	0.00	0.00	0.00	2.52
78	79	4.083862	GTTCTTCGGCGGCTCCCT	62.084	66.667	7.21	0.00	0.00	4.20
251	253	0.250234	CTTTCCTGACGAGGCCATCA	59.750	55.000	5.01	4.69	39.57	3.07
276	278	0.186873	ATGGTTGGGGATGGATCTGC	59.813	55.000	0.00	0.00	0.00	4.26
382	384	4.617520	TTTGCTCCAGCGTCGGCA	62.618	61.111	0.00	0.00	45.83	5.69
485	487	1.003839	GTGGTTCGTGGATGGCAGA	60.004	57.895	0.00	0.00	0.00	4.26
694	696	3.735591	TCCGTCATTCTTTTCTTCGGTT	58.264	40.909	0.00	0.00	38.04	4.44
711	714	3.719646	TTGCTGCTGTGGTGGTGCT	62.720	57.895	0.00	0.00	0.00	4.40
908	912	1.967319	TGATTAAAGCGGGCCTCATC	58.033	50.000	0.84	0.00	0.00	2.92
914	918	5.499004	TTAAAGCGGGCCTCATCTTATAT	57.501	39.130	0.84	0.00	0.00	0.86
915	919	6.614694	TTAAAGCGGGCCTCATCTTATATA	57.385	37.500	0.84	0.00	0.00	0.86
916	920	4.744795	AAGCGGGCCTCATCTTATATAG	57.255	45.455	0.84	0.00	0.00	1.31
917	921	3.034635	AGCGGGCCTCATCTTATATAGG	58.965	50.000	0.84	0.00	0.00	2.57
918	922	3.031736	GCGGGCCTCATCTTATATAGGA	58.968	50.000	0.84	0.00	0.00	2.94
919	923	3.068873	GCGGGCCTCATCTTATATAGGAG	59.931	52.174	0.84	0.00	0.00	3.69
1081	1088	1.374947	CACCGGTCAGTGGAATGGT	59.625	57.895	2.59	0.00	34.16	3.55
1393	1400	4.503314	GCAGCTTTGCCCGGCATC	62.503	66.667	14.30	5.84	38.76	3.91
1424	1431	3.064207	CCTGCTAGTGCTTTTACGTTGA	58.936	45.455	0.00	0.00	40.48	3.18
1454	3070	3.758931	GGTTCGCATGTTGGGGCC	61.759	66.667	0.00	0.00	0.00	5.80
1477	3093	4.328983	CGGCGAATGTACATCTTGTTTACT	59.671	41.667	9.23	0.00	0.00	2.24
1735	3353	7.486647	ACTAATCGTAAATCATACAACGGACT	58.513	34.615	0.00	0.00	36.08	3.85
1748	3366	4.369182	ACAACGGACTCAAAGACACTAAG	58.631	43.478	0.00	0.00	0.00	2.18
1750	3368	2.299297	ACGGACTCAAAGACACTAAGGG	59.701	50.000	0.00	0.00	0.00	3.95
1755	3373	6.107343	GGACTCAAAGACACTAAGGGTATTC	58.893	44.000	0.00	0.00	0.00	1.75
1778	3396	1.271054	CCTCCTAATCCAATGGCTCCG	60.271	57.143	0.00	0.00	0.00	4.63
1790	3408	2.661866	GCTCCGTCGCAACACACT	60.662	61.111	0.00	0.00	0.00	3.55
1866	3485	8.127954	GCAAAGAAGATCAATACTCCTTTCATC	58.872	37.037	0.00	0.00	0.00	2.92
1885	3504	6.540438	TCATCCCGGAATATAAGGTGTATC	57.460	41.667	0.73	0.00	0.00	2.24
1887	3506	4.665451	TCCCGGAATATAAGGTGTATCGA	58.335	43.478	0.73	0.00	0.00	3.59
1896	3515	9.188588	GAATATAAGGTGTATCGATTTTCGTGA	57.811	33.333	1.71	0.00	41.35	4.35
2036	3656	7.253883	CGGTACCGTAGATGTTGATACTTTTTC	60.254	40.741	26.39	0.00	34.35	2.29
2117	3737	2.950990	AGGATGGAGGGAGTACAACT	57.049	50.000	0.00	0.00	0.00	3.16
2118	3738	2.753247	AGGATGGAGGGAGTACAACTC	58.247	52.381	0.00	0.00	44.32	3.01
2168	3788	1.808411	ATCAATCACGCGAACCAACT	58.192	45.000	15.93	0.00	0.00	3.16
2194	3814	1.285280	TGGGATGGTTAGGTGGACAG	58.715	55.000	0.00	0.00	0.00	3.51
2203	3823	3.105283	GTTAGGTGGACAGTGGTATCCT	58.895	50.000	0.00	0.00	35.86	3.24
2211	3831	1.135094	CAGTGGTATCCTCAGCCCAT	58.865	55.000	0.00	0.00	0.00	4.00
2233	3853	3.366052	AGGGTTTAATTCCTGATGCGT	57.634	42.857	0.00	0.00	31.11	5.24
2245	3865	3.947196	TCCTGATGCGTGCATTTATTCTT	59.053	39.130	8.98	0.00	36.70	2.52
2265	3885	8.986477	ATTCTTGATTTATTTCAGGTTTTCCG	57.014	30.769	0.00	0.00	46.35	4.30
2269	3889	2.476126	TATTTCAGGTTTTCCGGCGA	57.524	45.000	9.30	0.00	46.35	5.54
2273	3893	0.458889	TCAGGTTTTCCGGCGATACG	60.459	55.000	9.30	0.00	46.35	3.06
2285	3905	2.006772	CGATACGCTTTCAGTGGGC	58.993	57.895	0.00	0.00	0.00	5.36
2319	3939	3.379372	AGTCAACTATACGAAGCGCCTAA	59.621	43.478	2.29	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	3.299977	CCTCACCACCGACGACCA	61.300	66.667	0.00	0.00	0.00	4.02
251	253	1.010793	TCCATCCCCAACCATAGGACT	59.989	52.381	0.00	0.00	30.97	3.85
276	278	4.276678	TCCTTGCTTGAACAGACTGATTTG	59.723	41.667	10.08	0.00	0.00	2.32
382	384	1.501582	GACTACCTCCCAAGCTCCAT	58.498	55.000	0.00	0.00	0.00	3.41
450	452	1.450669	ACGAACCCAGCACACGTTT	60.451	52.632	0.00	0.00	33.48	3.60
694	696	4.193893	AGCACCACCACAGCAGCA	62.194	61.111	0.00	0.00	0.00	4.41
850	853	2.352388	GTATGCTACCTTTTGGCGTGA	58.648	47.619	0.00	0.00	45.59	4.35
908	912	7.284944	CCTGTAACCCGGATACTCCTATATAAG	59.715	44.444	0.73	0.00	33.30	1.73
914	918	2.754186	GCCTGTAACCCGGATACTCCTA	60.754	54.545	0.73	0.00	33.30	2.94
915	919	2.033208	GCCTGTAACCCGGATACTCCT	61.033	57.143	0.73	0.00	33.30	3.69
916	920	0.391966	GCCTGTAACCCGGATACTCC	59.608	60.000	0.73	0.00	0.00	3.85
917	921	1.340568	GAGCCTGTAACCCGGATACTC	59.659	57.143	0.73	0.00	0.00	2.59
918	922	1.411041	GAGCCTGTAACCCGGATACT	58.589	55.000	0.73	0.00	0.00	2.12
919	923	0.391966	GGAGCCTGTAACCCGGATAC	59.608	60.000	0.73	6.73	0.00	2.24
1065	1069	0.036164	TCAACCATTCCACTGACCGG	59.964	55.000	0.00	0.00	0.00	5.28
1081	1088	4.124910	GCCGATGGCGAAGATCAA	57.875	55.556	0.00	0.00	39.62	2.57
1335	1342	7.804954	TTCTTACCTGAGAAGTACGCGAACG	62.805	48.000	15.93	0.00	36.94	3.95
1393	1400	0.109086	CACTAGCAGGTGAGGTCGTG	60.109	60.000	3.43	0.00	39.34	4.35
1424	1431	2.032681	GAACCTTGCAGCTCCGGT	59.967	61.111	0.00	0.00	0.00	5.28
1454	3070	3.740044	AAACAAGATGTACATTCGCCG	57.260	42.857	10.30	0.41	0.00	6.46
1555	3173	8.928448	TGCCTTCTATAAAGATGTTAGTCTCAT	58.072	33.333	0.00	0.00	0.00	2.90
1636	3254	0.034477	AATGGTAGGTTGGGAAGCGG	60.034	55.000	0.00	0.00	0.00	5.52
1735	3353	5.337009	GGTCGAATACCCTTAGTGTCTTTGA	60.337	44.000	0.00	0.00	43.16	2.69
1750	3368	5.238583	CCATTGGATTAGGAGGTCGAATAC	58.761	45.833	0.00	0.00	0.00	1.89
1755	3373	1.417890	AGCCATTGGATTAGGAGGTCG	59.582	52.381	6.95	0.00	0.00	4.79
1866	3485	5.593679	ATCGATACACCTTATATTCCGGG	57.406	43.478	0.00	0.00	0.00	5.73
1885	3504	7.586300	ACATAAGTTTGACTTTCACGAAAATCG	59.414	33.333	0.00	0.00	41.56	3.34
2000	3619	5.009911	ACATCTACGGTACCGCATTTGTATA	59.990	40.000	33.62	14.75	44.19	1.47
2010	3629	4.825546	AGTATCAACATCTACGGTACCG	57.174	45.455	32.22	32.22	46.03	4.02
2036	3656	5.355596	TGCTTGTTTGACCAAGTATTTTGG	58.644	37.500	4.45	4.45	43.03	3.28
2117	3737	6.662755	ACTATATTGGCAATTCCTCTGTTGA	58.337	36.000	19.21	0.00	35.26	3.18
2118	3738	6.543465	TGACTATATTGGCAATTCCTCTGTTG	59.457	38.462	19.21	0.00	35.26	3.33
2168	3788	1.783979	ACCTAACCATCCCAACCACAA	59.216	47.619	0.00	0.00	0.00	3.33
2194	3814	1.071385	CTGATGGGCTGAGGATACCAC	59.929	57.143	0.00	0.00	35.52	4.16
2222	3842	3.947196	AGAATAAATGCACGCATCAGGAA	59.053	39.130	4.73	0.00	35.31	3.36
2228	3848	8.876275	AATAAATCAAGAATAAATGCACGCAT	57.124	26.923	0.00	0.00	38.46	4.73
2245	3865	4.380023	CGCCGGAAAACCTGAAATAAATCA	60.380	41.667	5.05	0.00	0.00	2.57
2269	3889	4.201951	CGCCCACTGAAAGCGTAT	57.798	55.556	0.00	0.00	44.65	3.06
2273	3893	2.035442	GTCTCCGCCCACTGAAAGC	61.035	63.158	0.00	0.00	37.60	3.51
2285	3905	2.135664	AGTTGACTGAAACGTCTCCG	57.864	50.000	0.00	0.00	40.83	4.63
2295	3915	2.479049	GGCGCTTCGTATAGTTGACTGA	60.479	50.000	7.64	0.00	0.00	3.41
2308	3928	0.389948	AAGTCACCTTAGGCGCTTCG	60.390	55.000	7.64	0.00	0.00	3.79
2319	3939	4.041198	TCTTGGGATTTTACGAAGTCACCT	59.959	41.667	0.00	0.00	43.93	4.00
2337	3957	1.446907	GAGCCGGCATATCATCTTGG	58.553	55.000	31.54	0.00	0.00	3.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.