AutoCloner

Multiple sequence alignment - TraesCS1B01G204500

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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	TraesCS1B01G204500	chr1B	100.000	2864	0	0	1	2864	368551586	368548723	0.000000e+00	5289.0
1	TraesCS1B01G204500	chr1A	92.955	2555	120	26	348	2864	313743709	313746241	0.000000e+00	3666.0
2	TraesCS1B01G204500	chr1A	87.926	323	13	4	1	323	313743423	313743719	9.760000e-95	357.0
3	TraesCS1B01G204500	chr1D	93.272	2081	86	31	348	2396	233902262	233900204	0.000000e+00	3018.0
4	TraesCS1B01G204500	chr1D	89.970	329	14	6	1	323	233902567	233902252	9.550000e-110	407.0
5	TraesCS1B01G204500	chr2A	87.683	682	71	10	2144	2819	665683607	665684281	0.000000e+00	782.0
6	TraesCS1B01G204500	chr2A	88.950	181	15	2	1046	1226	573418644	573418819	4.800000e-53	219.0
7	TraesCS1B01G204500	chr2A	85.417	192	23	2	1035	1226	98887946	98887760	8.100000e-46	195.0
8	TraesCS1B01G204500	chr2A	86.614	127	16	1	1035	1161	98888771	98888646	3.850000e-29	139.0
9	TraesCS1B01G204500	chr2A	97.143	35	1	0	2826	2860	665684327	665684361	3.080000e-05	60.2
10	TraesCS1B01G204500	chr5A	84.457	682	86	14	2146	2816	402121621	402122293	0.000000e+00	654.0
11	TraesCS1B01G204500	chr2D	84.320	676	89	10	2151	2816	561060596	561059928	0.000000e+00	645.0
12	TraesCS1B01G204500	chr2D	88.021	192	18	2	1035	1226	234337205	234337019	3.710000e-54	222.0
13	TraesCS1B01G204500	chr3B	83.918	684	91	14	2144	2816	279666726	279666051	1.120000e-178	636.0
14	TraesCS1B01G204500	chr3B	88.950	181	15	2	1046	1226	5770054	5769879	4.800000e-53	219.0
15	TraesCS1B01G204500	chr7D	83.602	683	91	13	2147	2816	104082294	104082968	3.130000e-174	621.0
16	TraesCS1B01G204500	chr7D	81.912	680	104	12	2147	2816	106365367	106366037	8.960000e-155	556.0
17	TraesCS1B01G204500	chr2B	83.235	680	88	16	2147	2816	206686520	206685857	4.080000e-168	601.0
18	TraesCS1B01G204500	chr7B	82.396	676	103	11	2151	2816	621768194	621767525	2.470000e-160	575.0
19	TraesCS1B01G204500	chr5D	87.500	192	19	2	1035	1226	58253556	58253370	1.730000e-52	217.0
20	TraesCS1B01G204500	chr5D	90.780	141	13	0	1086	1226	17818171	17818031	3.770000e-44	189.0

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	TraesCS1B01G204500	chr1B	368548723	368551586	2863	True	5289.0	5289	100.0000	1	2864	1	chr1B.!!$R1	2863
1	TraesCS1B01G204500	chr1A	313743423	313746241	2818	False	2011.5	3666	90.4405	1	2864	2	chr1A.!!$F1	2863
2	TraesCS1B01G204500	chr1D	233900204	233902567	2363	True	1712.5	3018	91.6210	1	2396	2	chr1D.!!$R1	2395
3	TraesCS1B01G204500	chr2A	665683607	665684361	754	False	421.1	782	92.4130	2144	2860	2	chr2A.!!$F2	716
4	TraesCS1B01G204500	chr5A	402121621	402122293	672	False	654.0	654	84.4570	2146	2816	1	chr5A.!!$F1	670
5	TraesCS1B01G204500	chr2D	561059928	561060596	668	True	645.0	645	84.3200	2151	2816	1	chr2D.!!$R2	665
6	TraesCS1B01G204500	chr3B	279666051	279666726	675	True	636.0	636	83.9180	2144	2816	1	chr3B.!!$R2	672
7	TraesCS1B01G204500	chr7D	104082294	104082968	674	False	621.0	621	83.6020	2147	2816	1	chr7D.!!$F1	669
8	TraesCS1B01G204500	chr7D	106365367	106366037	670	False	556.0	556	81.9120	2147	2816	1	chr7D.!!$F2	669
9	TraesCS1B01G204500	chr2B	206685857	206686520	663	True	601.0	601	83.2350	2147	2816	1	chr2B.!!$R1	669
10	TraesCS1B01G204500	chr7B	621767525	621768194	669	True	575.0	575	82.3960	2151	2816	1	chr7B.!!$R1	665

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
792	799	0.322008	CAGCCTTGAACCCCAGAGAC	60.322	60.0	0.0	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2551	2629	0.109723	TGGTGTGGGTTGCCTCTTAC	59.89	55.0	0.0	0.0	0.0	2.34	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
93	94	1.068610	GCGCCTGCAGAAATACAAACA	60.069	47.619	17.39	0.00	42.15	2.83
220	221	0.604780	CCCCACAGACTTCACTGCTG	60.605	60.000	0.00	0.00	41.06	4.41
221	222	0.394192	CCCACAGACTTCACTGCTGA	59.606	55.000	0.00	0.00	41.06	4.26
222	223	1.202687	CCCACAGACTTCACTGCTGAA	60.203	52.381	0.00	0.00	41.06	3.02
223	224	1.869767	CCACAGACTTCACTGCTGAAC	59.130	52.381	0.00	0.00	41.06	3.18
224	225	2.554142	CACAGACTTCACTGCTGAACA	58.446	47.619	0.00	0.00	41.06	3.18
307	314	4.717233	AATGAGCCGCATTGACAAATTA	57.283	36.364	0.00	0.00	45.27	1.40
308	315	3.485947	TGAGCCGCATTGACAAATTAC	57.514	42.857	0.00	0.00	0.00	1.89
309	316	2.816672	TGAGCCGCATTGACAAATTACA	59.183	40.909	0.00	0.00	0.00	2.41
310	317	3.254411	TGAGCCGCATTGACAAATTACAA	59.746	39.130	0.00	0.00	0.00	2.41
311	318	4.233789	GAGCCGCATTGACAAATTACAAA	58.766	39.130	0.00	0.00	0.00	2.83
312	319	4.819769	AGCCGCATTGACAAATTACAAAT	58.180	34.783	0.00	0.00	0.00	2.32
313	320	5.237048	AGCCGCATTGACAAATTACAAATT	58.763	33.333	0.00	0.00	0.00	1.82
314	321	6.393990	AGCCGCATTGACAAATTACAAATTA	58.606	32.000	0.00	0.00	0.00	1.40
315	322	6.310224	AGCCGCATTGACAAATTACAAATTAC	59.690	34.615	0.00	0.00	0.00	1.89
316	323	6.090088	GCCGCATTGACAAATTACAAATTACA	59.910	34.615	0.00	0.00	0.00	2.41
317	324	7.359598	GCCGCATTGACAAATTACAAATTACAA	60.360	33.333	0.00	0.00	0.00	2.41
318	325	8.491152	CCGCATTGACAAATTACAAATTACAAA	58.509	29.630	0.00	0.00	0.00	2.83
339	346	8.647143	ACAAATTACAAATTTCAAGTCTGTGG	57.353	30.769	0.00	0.00	0.00	4.17
340	347	8.257306	ACAAATTACAAATTTCAAGTCTGTGGT	58.743	29.630	0.00	0.00	0.00	4.16
341	348	9.097257	CAAATTACAAATTTCAAGTCTGTGGTT	57.903	29.630	0.00	0.00	0.00	3.67
343	350	9.744468	AATTACAAATTTCAAGTCTGTGGTTAC	57.256	29.630	0.00	0.00	0.00	2.50
344	351	6.767524	ACAAATTTCAAGTCTGTGGTTACA	57.232	33.333	0.00	0.00	35.08	2.41
345	352	7.164230	ACAAATTTCAAGTCTGTGGTTACAA	57.836	32.000	0.00	0.00	36.14	2.41
346	353	7.033185	ACAAATTTCAAGTCTGTGGTTACAAC	58.967	34.615	0.00	0.00	36.14	3.32
501	508	0.466372	TCGCCGATGACCTGAGAGAT	60.466	55.000	0.00	0.00	0.00	2.75
513	520	2.416747	CTGAGAGATGGCACGAAACAA	58.583	47.619	0.00	0.00	0.00	2.83
514	521	3.005554	CTGAGAGATGGCACGAAACAAT	58.994	45.455	0.00	0.00	0.00	2.71
624	631	1.364678	TGGTGGAATAGAGGGAGGTCA	59.635	52.381	0.00	0.00	0.00	4.02
648	655	1.187087	GGAAGGCGAGAAGGAGAGAA	58.813	55.000	0.00	0.00	0.00	2.87
789	796	1.059584	TCACAGCCTTGAACCCCAGA	61.060	55.000	0.00	0.00	0.00	3.86
790	797	0.607489	CACAGCCTTGAACCCCAGAG	60.607	60.000	0.00	0.00	0.00	3.35
791	798	0.768221	ACAGCCTTGAACCCCAGAGA	60.768	55.000	0.00	0.00	0.00	3.10
792	799	0.322008	CAGCCTTGAACCCCAGAGAC	60.322	60.000	0.00	0.00	0.00	3.36
794	801	1.296715	CCTTGAACCCCAGAGACGG	59.703	63.158	0.00	0.00	0.00	4.79
848	891	1.335964	GGCAGAAAAGGAAAAGCCGTC	60.336	52.381	0.00	0.00	43.43	4.79
1521	1565	0.034089	ACAAGCTGGGTTATGGCCTC	60.034	55.000	3.32	0.00	0.00	4.70
1779	1826	3.933332	GGTAGTGTCATTGTAGAAGGCAC	59.067	47.826	0.00	0.00	0.00	5.01
1836	1884	8.352137	TCCATCATGATTGTTTCTGTGTATTT	57.648	30.769	5.16	0.00	0.00	1.40
1852	1900	6.894682	TGTGTATTTCTTGGATGCAGGTATA	58.105	36.000	0.00	0.00	0.00	1.47
1873	1921	1.766143	GCGTCGATGATGCAAGGGTC	61.766	60.000	9.31	0.00	43.32	4.46
2043	2110	9.208022	TCATGTTTTACTCTCACTCTGTTTATG	57.792	33.333	0.00	0.00	0.00	1.90
2046	2113	7.042051	TGTTTTACTCTCACTCTGTTTATGTGC	60.042	37.037	0.00	0.00	0.00	4.57
2137	2204	3.256879	TGTGGACTTGTGCAAACAGAAAA	59.743	39.130	0.00	0.00	0.00	2.29
2143	2210	4.937015	ACTTGTGCAAACAGAAAAGCAATT	59.063	33.333	0.00	0.00	38.91	2.32
2148	2215	6.085573	GTGCAAACAGAAAAGCAATTGTTTT	58.914	32.000	13.80	13.80	40.62	2.43
2149	2216	6.249050	GTGCAAACAGAAAAGCAATTGTTTTC	59.751	34.615	23.90	23.90	40.62	2.29
2221	2288	0.895530	GTGAAGAGACCCATCCACGA	59.104	55.000	0.00	0.00	0.00	4.35
2236	2303	2.538037	TCCACGATTCGAATACAATGCG	59.462	45.455	11.38	11.56	0.00	4.73
2280	2355	1.633432	CCCTGGGATTAGAACCACACA	59.367	52.381	7.01	0.00	32.33	3.72
2352	2427	1.301401	CGAAGAAGACGGGGCACAA	60.301	57.895	0.00	0.00	0.00	3.33
2374	2449	1.019278	CAAACAGGCCGCGTCACTAT	61.019	55.000	4.92	0.00	0.00	2.12
2416	2491	3.110358	TCACAACAACGACTACAGAACG	58.890	45.455	0.00	0.00	0.00	3.95
2500	2578	2.035632	CTAGCCGGACCTGAAGAAGAT	58.964	52.381	5.05	0.00	0.00	2.40
2551	2629	4.181010	CCCTGGAGGCCCATGTCG	62.181	72.222	0.00	0.00	42.59	4.35
2574	2653	0.827368	GAGGCAACCCACACCAAAAA	59.173	50.000	0.00	0.00	37.17	1.94
2603	2682	1.065854	CCAAACTCCAGCTTCGAGGAT	60.066	52.381	11.38	0.00	32.53	3.24
2625	2704	3.741476	CGAACAGCCAAGGCAGCC	61.741	66.667	14.40	1.84	44.88	4.85
2683	2765	1.497309	TTCTGGGGAGCCGGAACAAT	61.497	55.000	5.05	0.00	31.05	2.71
2759	2842	4.309950	AAGGACACGACACCCGCC	62.310	66.667	0.00	0.00	43.32	6.13
2809	2892	1.078143	GCAGAGATTTCGCCCTGGT	60.078	57.895	0.00	0.00	0.00	4.00
2856	2978	2.494073	CCATAGGAAGGAGAGATACGCC	59.506	54.545	0.00	0.00	38.77	5.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	9.788960	GAATTCGTGATAATAGGCTTTTCTTTT	57.211	29.630	0.00	0.00	0.00	2.27
175	176	7.409465	TGTTCACTTGTTTGGTTGTTAAAAC	57.591	32.000	0.00	0.00	36.92	2.43
220	221	3.059800	GTGCAGAAGTAACTCGGTTGTTC	60.060	47.826	0.00	3.68	0.00	3.18
221	222	2.870411	GTGCAGAAGTAACTCGGTTGTT	59.130	45.455	0.00	0.00	0.00	2.83
222	223	2.159014	TGTGCAGAAGTAACTCGGTTGT	60.159	45.455	0.00	0.00	0.00	3.32
223	224	2.479837	TGTGCAGAAGTAACTCGGTTG	58.520	47.619	0.00	0.00	0.00	3.77
224	225	2.902705	TGTGCAGAAGTAACTCGGTT	57.097	45.000	0.00	0.00	0.00	4.44
313	320	9.743057	CCACAGACTTGAAATTTGTAATTTGTA	57.257	29.630	0.00	0.00	0.00	2.41
314	321	8.257306	ACCACAGACTTGAAATTTGTAATTTGT	58.743	29.630	0.00	0.00	0.00	2.83
315	322	8.647143	ACCACAGACTTGAAATTTGTAATTTG	57.353	30.769	0.00	0.00	0.00	2.32
317	324	9.744468	GTAACCACAGACTTGAAATTTGTAATT	57.256	29.630	0.00	0.00	0.00	1.40
318	325	8.908903	TGTAACCACAGACTTGAAATTTGTAAT	58.091	29.630	0.00	0.00	0.00	1.89
319	326	8.282455	TGTAACCACAGACTTGAAATTTGTAA	57.718	30.769	0.00	0.00	0.00	2.41
320	327	7.867305	TGTAACCACAGACTTGAAATTTGTA	57.133	32.000	0.00	0.00	0.00	2.41
321	328	6.767524	TGTAACCACAGACTTGAAATTTGT	57.232	33.333	0.00	0.00	0.00	2.83
322	329	7.257722	AGTTGTAACCACAGACTTGAAATTTG	58.742	34.615	0.00	0.00	35.67	2.32
323	330	7.404671	AGTTGTAACCACAGACTTGAAATTT	57.595	32.000	0.00	0.00	35.67	1.82
324	331	7.404671	AAGTTGTAACCACAGACTTGAAATT	57.595	32.000	0.00	0.00	36.02	1.82
325	332	7.554835	TGTAAGTTGTAACCACAGACTTGAAAT	59.445	33.333	11.88	0.00	37.00	2.17
326	333	6.879993	TGTAAGTTGTAACCACAGACTTGAAA	59.120	34.615	11.88	0.00	37.00	2.69
327	334	6.408035	TGTAAGTTGTAACCACAGACTTGAA	58.592	36.000	11.88	3.01	37.00	2.69
328	335	5.979993	TGTAAGTTGTAACCACAGACTTGA	58.020	37.500	11.88	2.13	37.00	3.02
329	336	6.671614	TTGTAAGTTGTAACCACAGACTTG	57.328	37.500	11.88	0.00	37.00	3.16
330	337	7.875327	ATTTGTAAGTTGTAACCACAGACTT	57.125	32.000	0.00	0.00	38.45	3.01
331	338	7.875327	AATTTGTAAGTTGTAACCACAGACT	57.125	32.000	0.00	0.00	35.67	3.24
332	339	8.071967	GGTAATTTGTAAGTTGTAACCACAGAC	58.928	37.037	0.00	0.00	35.67	3.51
333	340	7.994334	AGGTAATTTGTAAGTTGTAACCACAGA	59.006	33.333	0.00	0.00	35.67	3.41
334	341	8.073768	CAGGTAATTTGTAAGTTGTAACCACAG	58.926	37.037	0.00	0.00	35.67	3.66
335	342	7.556996	ACAGGTAATTTGTAAGTTGTAACCACA	59.443	33.333	0.00	0.00	0.00	4.17
336	343	7.858879	CACAGGTAATTTGTAAGTTGTAACCAC	59.141	37.037	0.00	0.00	0.00	4.16
337	344	7.774157	TCACAGGTAATTTGTAAGTTGTAACCA	59.226	33.333	0.00	0.00	0.00	3.67
338	345	8.156994	TCACAGGTAATTTGTAAGTTGTAACC	57.843	34.615	0.00	0.00	0.00	2.85
342	349	9.787435	TCTATTCACAGGTAATTTGTAAGTTGT	57.213	29.630	0.00	0.00	0.00	3.32
345	352	9.227777	GGTTCTATTCACAGGTAATTTGTAAGT	57.772	33.333	0.00	0.00	0.00	2.24
346	353	8.674607	GGGTTCTATTCACAGGTAATTTGTAAG	58.325	37.037	0.00	0.00	0.00	2.34
475	482	2.181777	GTCATCGGCGAGCTGACA	59.818	61.111	28.96	3.73	43.42	3.58
501	508	1.872952	CTCAGTGATTGTTTCGTGCCA	59.127	47.619	0.00	0.00	0.00	4.92
562	569	4.805719	CGCTTCACTATTATTCTGTGCTCA	59.194	41.667	0.00	0.00	0.00	4.26
624	631	0.395862	TCCTTCTCGCCTTCCTCGAT	60.396	55.000	0.00	0.00	35.25	3.59
648	655	1.913762	CGACCTCCCTTCCACCACT	60.914	63.158	0.00	0.00	0.00	4.00
738	745	4.607025	TTCCGGCCCCCGCTTTTT	62.607	61.111	0.00	0.00	46.86	1.94
1298	1342	1.833049	GAGACGACGGGGGATGGAT	60.833	63.158	0.00	0.00	0.00	3.41
1426	1470	1.774856	AGGGTTTGGCTTAGTGTCTGT	59.225	47.619	0.00	0.00	0.00	3.41
1540	1584	1.537814	TTCGACATGTACCAGGGCGT	61.538	55.000	0.00	0.00	45.74	5.68
1710	1754	3.366396	CCTCTCCTTCCTTGCTGTAGTA	58.634	50.000	0.00	0.00	0.00	1.82
1836	1884	2.368548	ACGCATATACCTGCATCCAAGA	59.631	45.455	0.00	0.00	42.40	3.02
1852	1900	1.162181	CCCTTGCATCATCGACGCAT	61.162	55.000	0.00	0.00	28.98	4.73
1873	1921	5.821470	AGATCCTGCAGATAAAATCACACAG	59.179	40.000	17.39	0.00	34.42	3.66
1983	2038	6.317140	TGATTCTATTTAAGCTTGGACTGCAG	59.683	38.462	13.48	13.48	0.00	4.41
2031	2086	6.147656	TCAGTACAATGCACATAAACAGAGTG	59.852	38.462	0.00	0.00	36.39	3.51
2043	2110	3.003689	ACTTGTTGCTCAGTACAATGCAC	59.996	43.478	6.25	4.01	34.10	4.57
2046	2113	4.275689	TCCAACTTGTTGCTCAGTACAATG	59.724	41.667	7.89	0.00	34.10	2.82
2137	2204	6.377327	TCGAGAGAAAAGAAAACAATTGCT	57.623	33.333	5.05	0.00	37.03	3.91
2154	2221	1.629013	TGCTTGTGCGTATTCGAGAG	58.371	50.000	0.00	0.00	43.34	3.20
2221	2288	4.142491	TGCCTTTTCGCATTGTATTCGAAT	60.142	37.500	16.15	16.15	41.09	3.34
2236	2303	1.069049	AGCATGGTGTGTTGCCTTTTC	59.931	47.619	0.00	0.00	39.72	2.29
2280	2355	6.655848	AGTTCTCTCTTTCTCGTGTGTAGTAT	59.344	38.462	0.00	0.00	0.00	2.12
2352	2427	3.660111	GACGCGGCCTGTTTGCTT	61.660	61.111	12.47	0.00	0.00	3.91
2374	2449	1.315981	TTGGTTGTGGCTTGCAACGA	61.316	50.000	0.00	7.18	45.01	3.85
2416	2491	2.104963	GGGAGGTACATTGATCCAGTCC	59.895	54.545	0.00	0.00	33.24	3.85
2514	2592	0.670239	CGCTATGTATGCCATCGCCA	60.670	55.000	0.00	0.00	38.65	5.69
2551	2629	0.109723	TGGTGTGGGTTGCCTCTTAC	59.890	55.000	0.00	0.00	0.00	2.34
2574	2653	0.537371	CTGGAGTTTGGGGCGTCTTT	60.537	55.000	0.00	0.00	0.00	2.52
2603	2682	1.896660	GCCTTGGCTGTTCGTGGAA	60.897	57.895	4.11	0.00	0.00	3.53
2789	2872	0.465097	CCAGGGCGAAATCTCTGCAT	60.465	55.000	0.00	0.00	0.00	3.96
2809	2892	1.022982	ACTCTACGCACGGTCATCGA	61.023	55.000	0.00	0.00	42.43	3.59
2823	2945	0.554305	TCCTATGGCGGTGGACTCTA	59.446	55.000	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.