AutoCloner

Multiple sequence alignment - TraesCS1D01G394900

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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	TraesCS1D01G394900	chr1D	100.000	2375	0	0	1	2375	463793643	463791269	0.000000e+00	4386.0
1	TraesCS1D01G394900	chr4D	94.974	2348	91	9	1	2328	236672657	236670317	0.000000e+00	3657.0
2	TraesCS1D01G394900	chr4D	92.000	975	36	8	901	1833	125802840	125801866	0.000000e+00	1330.0
3	TraesCS1D01G394900	chr4D	85.591	930	80	34	1438	2328	261222281	261221367	0.000000e+00	926.0
4	TraesCS1D01G394900	chr4D	87.683	479	24	6	1390	1833	125903980	125903502	2.090000e-145	525.0
5	TraesCS1D01G394900	chr2A	94.694	2337	96	13	1	2332	610789242	610791555	0.000000e+00	3603.0
6	TraesCS1D01G394900	chr2A	97.872	47	1	0	2329	2375	601990962	601990916	5.440000e-12	82.4
7	TraesCS1D01G394900	chr2A	91.667	60	4	1	2317	2375	656799467	656799408	5.440000e-12	82.4
8	TraesCS1D01G394900	chr3A	94.404	2341	85	8	1	2329	615136719	615134413	0.000000e+00	3555.0
9	TraesCS1D01G394900	chr3A	93.157	833	52	5	546	1375	706571677	706570847	0.000000e+00	1218.0
10	TraesCS1D01G394900	chr2D	94.113	2361	92	14	1	2335	645236663	645234324	0.000000e+00	3546.0
11	TraesCS1D01G394900	chr7A	93.473	2344	117	21	1	2328	56073899	56076222	0.000000e+00	3448.0
12	TraesCS1D01G394900	chr5A	92.809	2350	120	10	1	2328	235675095	235677417	0.000000e+00	3358.0
13	TraesCS1D01G394900	chr5A	92.862	1429	87	12	904	2329	178859734	178858318	0.000000e+00	2060.0
14	TraesCS1D01G394900	chr5A	92.982	57	3	1	2317	2372	634688851	634688795	5.440000e-12	82.4
15	TraesCS1D01G394900	chr5A	97.727	44	1	0	2329	2372	439951770	439951727	2.530000e-10	76.8
16	TraesCS1D01G394900	chr5B	92.460	2122	103	21	1	2117	56336221	56338290	0.000000e+00	2979.0
17	TraesCS1D01G394900	chr5B	88.710	62	6	1	2309	2369	268619912	268619973	9.100000e-10	75.0
18	TraesCS1D01G394900	chr7D	93.330	1844	70	15	504	2329	17927137	17925329	0.000000e+00	2675.0
19	TraesCS1D01G394900	chr7D	94.283	892	40	5	524	1412	501764687	501765570	0.000000e+00	1354.0
20	TraesCS1D01G394900	chr7D	97.872	47	1	0	2329	2375	366642312	366642266	5.440000e-12	82.4
21	TraesCS1D01G394900	chr4B	86.649	1865	137	55	523	2328	200943067	200944878	0.000000e+00	1962.0
22	TraesCS1D01G394900	chr4B	88.422	881	60	13	1471	2330	505002039	505001180	0.000000e+00	1024.0
23	TraesCS1D01G394900	chr3D	93.411	1199	43	7	1133	2328	57608386	57609551	0.000000e+00	1744.0
24	TraesCS1D01G394900	chr5D	96.855	922	29	0	1	922	384512118	384511197	0.000000e+00	1543.0
25	TraesCS1D01G394900	chr6D	95.987	922	37	0	1	922	297171498	297170577	0.000000e+00	1498.0
26	TraesCS1D01G394900	chr4A	95.974	919	35	2	1	918	433607523	433606606	0.000000e+00	1491.0
27	TraesCS1D01G394900	chr4A	95.228	922	44	0	1	922	192323419	192322498	0.000000e+00	1459.0
28	TraesCS1D01G394900	chr4A	94.271	803	28	9	1531	2328	129032020	129032809	0.000000e+00	1212.0
29	TraesCS1D01G394900	chr4A	95.745	47	2	0	2329	2375	44877043	44876997	2.530000e-10	76.8
30	TraesCS1D01G394900	chr6A	97.872	47	1	0	2329	2375	324786521	324786475	5.440000e-12	82.4
31	TraesCS1D01G394900	chr1A	90.476	63	5	1	2314	2375	435182957	435182895	5.440000e-12	82.4

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	TraesCS1D01G394900	chr1D	463791269	463793643	2374	True	4386	4386	100.000	1	2375	1	chr1D.!!$R1	2374
1	TraesCS1D01G394900	chr4D	236670317	236672657	2340	True	3657	3657	94.974	1	2328	1	chr4D.!!$R3	2327
2	TraesCS1D01G394900	chr4D	125801866	125802840	974	True	1330	1330	92.000	901	1833	1	chr4D.!!$R1	932
3	TraesCS1D01G394900	chr4D	261221367	261222281	914	True	926	926	85.591	1438	2328	1	chr4D.!!$R4	890
4	TraesCS1D01G394900	chr2A	610789242	610791555	2313	False	3603	3603	94.694	1	2332	1	chr2A.!!$F1	2331
5	TraesCS1D01G394900	chr3A	615134413	615136719	2306	True	3555	3555	94.404	1	2329	1	chr3A.!!$R1	2328
6	TraesCS1D01G394900	chr3A	706570847	706571677	830	True	1218	1218	93.157	546	1375	1	chr3A.!!$R2	829
7	TraesCS1D01G394900	chr2D	645234324	645236663	2339	True	3546	3546	94.113	1	2335	1	chr2D.!!$R1	2334
8	TraesCS1D01G394900	chr7A	56073899	56076222	2323	False	3448	3448	93.473	1	2328	1	chr7A.!!$F1	2327
9	TraesCS1D01G394900	chr5A	235675095	235677417	2322	False	3358	3358	92.809	1	2328	1	chr5A.!!$F1	2327
10	TraesCS1D01G394900	chr5A	178858318	178859734	1416	True	2060	2060	92.862	904	2329	1	chr5A.!!$R1	1425
11	TraesCS1D01G394900	chr5B	56336221	56338290	2069	False	2979	2979	92.460	1	2117	1	chr5B.!!$F1	2116
12	TraesCS1D01G394900	chr7D	17925329	17927137	1808	True	2675	2675	93.330	504	2329	1	chr7D.!!$R1	1825
13	TraesCS1D01G394900	chr7D	501764687	501765570	883	False	1354	1354	94.283	524	1412	1	chr7D.!!$F1	888
14	TraesCS1D01G394900	chr4B	200943067	200944878	1811	False	1962	1962	86.649	523	2328	1	chr4B.!!$F1	1805
15	TraesCS1D01G394900	chr4B	505001180	505002039	859	True	1024	1024	88.422	1471	2330	1	chr4B.!!$R1	859
16	TraesCS1D01G394900	chr3D	57608386	57609551	1165	False	1744	1744	93.411	1133	2328	1	chr3D.!!$F1	1195
17	TraesCS1D01G394900	chr5D	384511197	384512118	921	True	1543	1543	96.855	1	922	1	chr5D.!!$R1	921
18	TraesCS1D01G394900	chr6D	297170577	297171498	921	True	1498	1498	95.987	1	922	1	chr6D.!!$R1	921
19	TraesCS1D01G394900	chr4A	433606606	433607523	917	True	1491	1491	95.974	1	918	1	chr4A.!!$R3	917
20	TraesCS1D01G394900	chr4A	192322498	192323419	921	True	1459	1459	95.228	1	922	1	chr4A.!!$R2	921
21	TraesCS1D01G394900	chr4A	129032020	129032809	789	False	1212	1212	94.271	1531	2328	1	chr4A.!!$F1	797

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
421	422	0.033405	AGCGTAAGGGTGAGGAGCTA	60.033	55.0	0.0	0.0	38.28	3.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1497	1604	1.071471	ACAAGTGCTCCCAGGTTCG	59.929	57.895	0.0	0.0	0.0	3.95	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
224	225	3.194005	ACCTGTGTGTCGAACAAGATT	57.806	42.857	0.00	0.00	41.57	2.40
360	361	8.114331	TGAATAACATTTCTGATTCTTGCTGT	57.886	30.769	0.00	0.00	31.03	4.40
421	422	0.033405	AGCGTAAGGGTGAGGAGCTA	60.033	55.000	0.00	0.00	38.28	3.32
624	661	1.328680	CACACGCTATGTTCCATGCTC	59.671	52.381	0.00	0.00	40.64	4.26
868	906	9.646427	GTCAAGTTACTAGTCATCATCTTCTTT	57.354	33.333	0.00	0.00	0.00	2.52
883	921	8.279970	TCATCTTCTTTTGTTTGAGTTTGAGA	57.720	30.769	0.00	0.00	0.00	3.27
926	974	1.408702	TGCTGGTTTGGTTTCTCTTGC	59.591	47.619	0.00	0.00	0.00	4.01
1025	1091	1.862602	AAAATGAAGGACGCACCGGC	61.863	55.000	0.00	0.00	44.74	6.13
1028	1094	4.681978	GAAGGACGCACCGGCACT	62.682	66.667	0.00	0.00	44.74	4.40
1083	1149	4.142609	TGTTGAAGAAGTGCTCAAGACT	57.857	40.909	0.00	0.00	0.00	3.24
1198	1264	2.481568	CGTGATCTTGAGCAAAAGCTGA	59.518	45.455	0.00	0.00	0.00	4.26
1385	1451	4.235079	AGGTAGTTTGATGGCTATGCAA	57.765	40.909	0.00	0.00	0.00	4.08
1418	1484	3.759581	ACCTGTGATCTGATGCAGTTTT	58.240	40.909	14.02	1.26	32.61	2.43
1435	1501	5.578776	CAGTTTTTCGTAGTTTGAAGGCTT	58.421	37.500	0.00	0.00	0.00	4.35
1436	1502	6.721321	CAGTTTTTCGTAGTTTGAAGGCTTA	58.279	36.000	0.00	0.00	0.00	3.09
1444	1510	6.865205	TCGTAGTTTGAAGGCTTAGAAGTTAC	59.135	38.462	0.00	3.81	0.00	2.50
1559	1736	1.268539	GGAGCACTTGTTGTTGAACCG	60.269	52.381	0.00	0.00	0.00	4.44
1627	1936	5.300286	GGCTCATTTTGGAAGCTATGTGTAT	59.700	40.000	0.00	0.00	0.00	2.29
1908	2225	7.722949	AAATCATCAGAAAAAGGCTCCATTA	57.277	32.000	0.00	0.00	0.00	1.90
1929	2246	7.334171	CCATTACCAGAAAATAAAAGGCCAAAG	59.666	37.037	5.01	0.00	0.00	2.77
2021	2350	1.822186	GCCCATGTAAACGGCCGAT	60.822	57.895	35.90	19.90	36.63	4.18
2341	2674	9.814899	ATTTCTTGTAGTGTAGATGAATCTGAG	57.185	33.333	2.99	0.00	37.76	3.35
2342	2675	8.581253	TTCTTGTAGTGTAGATGAATCTGAGA	57.419	34.615	2.99	0.00	37.76	3.27
2343	2676	8.759481	TCTTGTAGTGTAGATGAATCTGAGAT	57.241	34.615	2.99	0.00	37.76	2.75
2344	2677	9.194972	TCTTGTAGTGTAGATGAATCTGAGATT	57.805	33.333	7.53	7.53	37.76	2.40
2345	2678	9.247126	CTTGTAGTGTAGATGAATCTGAGATTG	57.753	37.037	13.18	0.00	37.76	2.67
2346	2679	8.298729	TGTAGTGTAGATGAATCTGAGATTGT	57.701	34.615	13.18	0.73	37.76	2.71
2347	2680	8.193438	TGTAGTGTAGATGAATCTGAGATTGTG	58.807	37.037	13.18	0.00	37.76	3.33
2348	2681	7.180322	AGTGTAGATGAATCTGAGATTGTGT	57.820	36.000	13.18	2.55	37.76	3.72
2349	2682	7.040494	AGTGTAGATGAATCTGAGATTGTGTG	58.960	38.462	13.18	0.00	37.76	3.82
2350	2683	7.038048	GTGTAGATGAATCTGAGATTGTGTGA	58.962	38.462	13.18	0.00	37.76	3.58
2351	2684	7.710044	GTGTAGATGAATCTGAGATTGTGTGAT	59.290	37.037	13.18	0.00	37.76	3.06
2352	2685	7.709613	TGTAGATGAATCTGAGATTGTGTGATG	59.290	37.037	13.18	0.00	37.76	3.07
2353	2686	5.527951	AGATGAATCTGAGATTGTGTGATGC	59.472	40.000	13.18	0.00	35.42	3.91
2354	2687	4.581868	TGAATCTGAGATTGTGTGATGCA	58.418	39.130	13.18	0.00	0.00	3.96
2355	2688	5.190677	TGAATCTGAGATTGTGTGATGCAT	58.809	37.500	13.18	0.00	0.00	3.96
2356	2689	6.350906	TGAATCTGAGATTGTGTGATGCATA	58.649	36.000	13.18	0.00	0.00	3.14
2357	2690	6.996282	TGAATCTGAGATTGTGTGATGCATAT	59.004	34.615	13.18	0.00	0.00	1.78
2358	2691	7.172703	TGAATCTGAGATTGTGTGATGCATATC	59.827	37.037	13.18	0.00	0.00	1.63
2359	2692	4.986659	TCTGAGATTGTGTGATGCATATCG	59.013	41.667	0.00	0.00	36.04	2.92
2360	2693	4.696455	TGAGATTGTGTGATGCATATCGT	58.304	39.130	0.00	0.00	36.04	3.73
2361	2694	5.841810	TGAGATTGTGTGATGCATATCGTA	58.158	37.500	0.00	0.00	36.04	3.43
2362	2695	6.458210	TGAGATTGTGTGATGCATATCGTAT	58.542	36.000	0.00	0.00	36.04	3.06
2363	2696	7.601856	TGAGATTGTGTGATGCATATCGTATA	58.398	34.615	0.00	0.00	36.04	1.47
2364	2697	8.087750	TGAGATTGTGTGATGCATATCGTATAA	58.912	33.333	0.00	0.00	36.04	0.98
2365	2698	9.091784	GAGATTGTGTGATGCATATCGTATAAT	57.908	33.333	0.00	0.00	36.04	1.28
2366	2699	9.091784	AGATTGTGTGATGCATATCGTATAATC	57.908	33.333	0.00	5.02	36.04	1.75
2367	2700	8.776376	ATTGTGTGATGCATATCGTATAATCA	57.224	30.769	0.00	0.00	36.04	2.57
2368	2701	8.776376	TTGTGTGATGCATATCGTATAATCAT	57.224	30.769	0.00	0.00	36.04	2.45
2369	2702	9.868277	TTGTGTGATGCATATCGTATAATCATA	57.132	29.630	0.00	0.00	36.04	2.15
2370	2703	9.301153	TGTGTGATGCATATCGTATAATCATAC	57.699	33.333	0.00	0.00	36.96	2.39
2371	2704	8.755941	GTGTGATGCATATCGTATAATCATACC	58.244	37.037	0.00	0.00	34.62	2.73
2372	2705	8.695456	TGTGATGCATATCGTATAATCATACCT	58.305	33.333	0.00	0.00	34.62	3.08

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
224	225	9.047371	TGATTGTACACAACTTTTTCTCGATTA	57.953	29.630	0.00	0.00	38.86	1.75
297	298	6.072064	CGGTAAGGTCTCTAGAGAAAAGTTCA	60.072	42.308	23.96	3.61	39.48	3.18
421	422	4.811557	GCCTTAAACAAGTCTATCGCAGAT	59.188	41.667	0.00	0.00	45.12	2.90
430	431	1.497286	TGGGTGGCCTTAAACAAGTCT	59.503	47.619	3.32	0.00	0.00	3.24
624	661	8.854979	TTTGTTGAACTATCAAACAACATCAG	57.145	30.769	0.00	0.00	46.66	2.90
837	875	5.714047	TGATGACTAGTAACTTGACAGCAG	58.286	41.667	0.00	0.00	28.24	4.24
909	957	2.430332	CCAAGCAAGAGAAACCAAACCA	59.570	45.455	0.00	0.00	0.00	3.67
910	958	2.430694	ACCAAGCAAGAGAAACCAAACC	59.569	45.455	0.00	0.00	0.00	3.27
926	974	4.394300	TCACATTTTGCAAACCAAACCAAG	59.606	37.500	12.39	0.00	42.81	3.61
1020	1086	0.608640	CTTCACCTTCTAGTGCCGGT	59.391	55.000	1.90	0.00	37.68	5.28
1025	1091	3.685139	TTGGCTCTTCACCTTCTAGTG	57.315	47.619	0.00	0.00	39.20	2.74
1028	1094	3.904339	AGACTTTGGCTCTTCACCTTCTA	59.096	43.478	0.00	0.00	0.00	2.10
1083	1149	3.569701	GGAATGTGCTTTCCTTGACTTCA	59.430	43.478	8.94	0.00	41.69	3.02
1198	1264	0.036858	GCTTGAAGCTCCGACCTCTT	60.037	55.000	10.44	0.00	38.45	2.85
1385	1451	6.064060	TCAGATCACAGGTTCAAAGACAAAT	58.936	36.000	0.00	0.00	0.00	2.32
1418	1484	5.850614	ACTTCTAAGCCTTCAAACTACGAA	58.149	37.500	0.00	0.00	0.00	3.85
1435	1501	4.798907	CGACCTACTACGACGTAACTTCTA	59.201	45.833	9.32	0.00	0.00	2.10
1436	1502	3.614616	CGACCTACTACGACGTAACTTCT	59.385	47.826	9.32	0.00	0.00	2.85
1444	1510	1.728971	AGTTCACGACCTACTACGACG	59.271	52.381	0.00	0.00	0.00	5.12
1497	1604	1.071471	ACAAGTGCTCCCAGGTTCG	59.929	57.895	0.00	0.00	0.00	3.95
1559	1736	5.841957	AAATGAGCCATCATAAGTTCACC	57.158	39.130	0.00	0.00	45.67	4.02
1694	2003	7.566709	CATTTTTGCAGTCCAACTCAATTTAC	58.433	34.615	0.00	0.00	31.97	2.01
1908	2225	5.887214	ACTTTGGCCTTTTATTTTCTGGT	57.113	34.783	3.32	0.00	0.00	4.00
1941	2258	1.547372	GTTTTGCTCATCTGCATGGGT	59.453	47.619	0.00	0.00	42.96	4.51
2012	2341	2.420043	CGGTCCATATCGGCCGTT	59.580	61.111	27.15	20.39	44.58	4.44
2021	2350	2.391926	TAGAATCAGCCCGGTCCATA	57.608	50.000	0.00	0.00	0.00	2.74
2064	2393	2.679837	CAAGCTGACGTGGCAGAATTAT	59.320	45.455	6.96	0.00	38.14	1.28
2330	2663	5.296035	TGCATCACACAATCTCAGATTCATC	59.704	40.000	0.00	0.00	0.00	2.92
2331	2664	5.190677	TGCATCACACAATCTCAGATTCAT	58.809	37.500	0.00	0.00	0.00	2.57
2332	2665	4.581868	TGCATCACACAATCTCAGATTCA	58.418	39.130	0.00	0.00	0.00	2.57
2333	2666	5.752892	ATGCATCACACAATCTCAGATTC	57.247	39.130	0.00	0.00	0.00	2.52
2334	2667	6.147328	CGATATGCATCACACAATCTCAGATT	59.853	38.462	0.19	0.00	0.00	2.40
2335	2668	5.638234	CGATATGCATCACACAATCTCAGAT	59.362	40.000	0.19	0.00	0.00	2.90
2336	2669	4.986659	CGATATGCATCACACAATCTCAGA	59.013	41.667	0.19	0.00	0.00	3.27
2337	2670	4.748600	ACGATATGCATCACACAATCTCAG	59.251	41.667	0.19	0.00	0.00	3.35
2338	2671	4.696455	ACGATATGCATCACACAATCTCA	58.304	39.130	0.19	0.00	0.00	3.27
2339	2672	6.957984	ATACGATATGCATCACACAATCTC	57.042	37.500	0.19	0.00	0.00	2.75
2340	2673	9.091784	GATTATACGATATGCATCACACAATCT	57.908	33.333	0.19	0.00	0.00	2.40
2341	2674	8.872845	TGATTATACGATATGCATCACACAATC	58.127	33.333	0.19	6.02	0.00	2.67
2342	2675	8.776376	TGATTATACGATATGCATCACACAAT	57.224	30.769	0.19	0.00	0.00	2.71
2343	2676	8.776376	ATGATTATACGATATGCATCACACAA	57.224	30.769	0.19	0.00	0.00	3.33
2344	2677	9.301153	GTATGATTATACGATATGCATCACACA	57.699	33.333	0.19	0.00	30.68	3.72
2345	2678	8.755941	GGTATGATTATACGATATGCATCACAC	58.244	37.037	0.19	0.00	40.07	3.82
2346	2679	8.695456	AGGTATGATTATACGATATGCATCACA	58.305	33.333	0.19	0.00	40.07	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.