AutoCloner

Multiple sequence alignment - TraesCS5A01G221300

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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	TraesCS5A01G221300	chr5A	100.000	3022	0	0	1	3022	437394262	437391241	0.000000e+00	5581.0
1	TraesCS5A01G221300	chr5A	87.748	1763	135	45	406	2152	437413333	437411636	0.000000e+00	1984.0
2	TraesCS5A01G221300	chr5A	87.451	1267	102	32	802	2039	437400271	437399033	0.000000e+00	1406.0
3	TraesCS5A01G221300	chr5A	82.203	236	24	11	454	678	437400668	437400440	1.430000e-43	187.0
4	TraesCS5A01G221300	chr5D	94.511	2168	80	20	1	2135	336313842	336316003	0.000000e+00	3308.0
5	TraesCS5A01G221300	chr5D	95.937	1329	34	11	1	1312	336258966	336257641	0.000000e+00	2137.0
6	TraesCS5A01G221300	chr5D	88.020	1636	106	44	428	2002	336240469	336238863	0.000000e+00	1853.0
7	TraesCS5A01G221300	chr5D	85.663	1674	121	61	428	2039	336337937	336339553	0.000000e+00	1652.0
8	TraesCS5A01G221300	chr5D	88.731	1198	94	29	967	2150	336381453	336380283	0.000000e+00	1426.0
9	TraesCS5A01G221300	chr5D	84.496	1032	50	34	2074	3019	336238861	336237854	0.000000e+00	918.0
10	TraesCS5A01G221300	chr5D	87.473	463	39	11	1692	2138	336257245	336256786	1.610000e-142	516.0
11	TraesCS5A01G221300	chr5D	84.848	462	25	14	434	866	336382031	336381586	1.000000e-114	424.0
12	TraesCS5A01G221300	chr5D	80.357	168	23	8	157	320	354279784	354279623	5.290000e-23	119.0
13	TraesCS5A01G221300	chr5B	85.956	1773	155	44	434	2141	394628753	394627010	0.000000e+00	1808.0
14	TraesCS5A01G221300	chr5B	92.474	1249	67	13	947	2182	394572563	394571329	0.000000e+00	1760.0
15	TraesCS5A01G221300	chr5B	86.605	1411	107	42	729	2088	394581432	394580053	0.000000e+00	1483.0
16	TraesCS5A01G221300	chr5B	82.536	899	68	30	2184	3017	394570440	394569566	0.000000e+00	708.0
17	TraesCS5A01G221300	chr5B	83.155	374	43	12	348	706	394573106	394572738	1.040000e-84	324.0
18	TraesCS5A01G221300	chr5B	91.304	69	2	2	802	866	394572681	394572613	1.150000e-14	91.6
19	TraesCS5A01G221300	chr7B	85.401	137	16	4	179	315	187760985	187760853	4.060000e-29	139.0
20	TraesCS5A01G221300	chr7A	83.117	154	20	6	152	303	225638212	225638361	5.260000e-28	135.0
21	TraesCS5A01G221300	chr4D	81.595	163	23	5	156	317	82571240	82571396	8.790000e-26	128.0
22	TraesCS5A01G221300	chr1D	79.878	164	29	4	158	320	299593479	299593639	1.900000e-22	117.0
23	TraesCS5A01G221300	chr7D	86.869	99	11	2	183	281	213797961	213798057	3.190000e-20	110.0

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	TraesCS5A01G221300	chr5A	437391241	437394262	3021	True	5581.0	5581	100.00000	1	3022	1	chr5A.!!$R1	3021
1	TraesCS5A01G221300	chr5A	437411636	437413333	1697	True	1984.0	1984	87.74800	406	2152	1	chr5A.!!$R2	1746
2	TraesCS5A01G221300	chr5A	437399033	437400668	1635	True	796.5	1406	84.82700	454	2039	2	chr5A.!!$R3	1585
3	TraesCS5A01G221300	chr5D	336313842	336316003	2161	False	3308.0	3308	94.51100	1	2135	1	chr5D.!!$F1	2134
4	TraesCS5A01G221300	chr5D	336337937	336339553	1616	False	1652.0	1652	85.66300	428	2039	1	chr5D.!!$F2	1611
5	TraesCS5A01G221300	chr5D	336237854	336240469	2615	True	1385.5	1853	86.25800	428	3019	2	chr5D.!!$R2	2591
6	TraesCS5A01G221300	chr5D	336256786	336258966	2180	True	1326.5	2137	91.70500	1	2138	2	chr5D.!!$R3	2137
7	TraesCS5A01G221300	chr5D	336380283	336382031	1748	True	925.0	1426	86.78950	434	2150	2	chr5D.!!$R4	1716
8	TraesCS5A01G221300	chr5B	394627010	394628753	1743	True	1808.0	1808	85.95600	434	2141	1	chr5B.!!$R2	1707
9	TraesCS5A01G221300	chr5B	394580053	394581432	1379	True	1483.0	1483	86.60500	729	2088	1	chr5B.!!$R1	1359
10	TraesCS5A01G221300	chr5B	394569566	394573106	3540	True	720.9	1760	87.36725	348	3017	4	chr5B.!!$R3	2669

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
725	834	0.589223	TCCGTAAAAAGCTTGCCGTG	59.411	50.000	0.0	0.0	0.0	4.94	F
1765	2047	1.226974	CACCGGCGACATACTCCTG	60.227	63.158	9.3	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1796	2078	0.320771	GAAGCACTCACGGTGATGGT	60.321	55.0	11.86	13.8	44.41	3.55	R
2843	4135	0.682852	TGATGTTCTTTCCGGACGGT	59.317	50.0	1.83	0.0	36.47	4.83	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
96	97	2.224744	TGGAGTAGCAATCAACAGCCAA	60.225	45.455	0.00	0.00	0.00	4.52
276	278	6.153170	TGCATAACTGAATGTTGTGATGGATT	59.847	34.615	8.95	0.00	46.41	3.01
335	337	8.861086	ACTTATCCCATAGAGTACATAAGTGTG	58.139	37.037	9.10	0.00	39.39	3.82
356	364	1.530720	TGCTGACACGTTGCTTGTATG	59.469	47.619	0.00	0.00	0.00	2.39
393	404	8.920174	TGAAAAAGAAGTGGATATAGGATACGA	58.080	33.333	0.00	0.00	46.39	3.43
395	408	9.712305	AAAAAGAAGTGGATATAGGATACGATG	57.288	33.333	0.00	0.00	46.39	3.84
456	469	6.647334	TGTGCTCCAAAATAAGACAAATGA	57.353	33.333	0.00	0.00	0.00	2.57
495	512	7.124347	AGCAGTTTCAATTTTACGTCGATTA	57.876	32.000	0.00	0.00	0.00	1.75
725	834	0.589223	TCCGTAAAAAGCTTGCCGTG	59.411	50.000	0.00	0.00	0.00	4.94
882	1039	4.279169	CCATGCAAAAAGAAGTCTCTCCAA	59.721	41.667	0.00	0.00	0.00	3.53
969	1157	3.372554	CTTCTTCCGACCGGCCTCC	62.373	68.421	0.00	0.00	34.68	4.30
999	1226	2.806856	CGCTTGTCGCCAGCTGATC	61.807	63.158	17.39	5.53	34.21	2.92
1000	1227	1.742880	GCTTGTCGCCAGCTGATCA	60.743	57.895	17.39	5.67	0.00	2.92
1419	1685	2.352805	GTGCCTCCTTGTCCAGGG	59.647	66.667	0.00	0.00	44.12	4.45
1765	2047	1.226974	CACCGGCGACATACTCCTG	60.227	63.158	9.30	0.00	0.00	3.86
1796	2078	2.436109	GCCTCTCCACCAGCCAAA	59.564	61.111	0.00	0.00	0.00	3.28
1840	2139	1.516161	AGCTATGTGGTGCATATGCG	58.484	50.000	22.21	6.88	45.83	4.73
1994	2310	8.629158	CAAGACTGAAGAATCATACTACTAGCT	58.371	37.037	0.00	0.00	34.37	3.32
2003	2319	2.819422	TACTACTAGCTTCGTGCACG	57.181	50.000	32.76	32.76	45.94	5.34
2010	2326	2.579207	AGCTTCGTGCACGTATATGT	57.421	45.000	35.74	15.94	45.94	2.29
2011	2327	2.460918	AGCTTCGTGCACGTATATGTC	58.539	47.619	35.74	19.09	45.94	3.06
2013	2329	1.779157	CTTCGTGCACGTATATGTCCG	59.221	52.381	35.74	11.48	40.80	4.79
2067	2387	3.758554	GGTGTTAATGCCAGATGACAACT	59.241	43.478	0.00	0.00	0.00	3.16
2070	2390	5.048782	GTGTTAATGCCAGATGACAACTTGA	60.049	40.000	0.00	0.00	0.00	3.02
2085	2405	7.874940	TGACAACTTGAAGTATTGGATTGAAG	58.125	34.615	0.00	0.00	0.00	3.02
2143	2470	7.812191	TGCAAATTGTTGTTGTTACATCTATCC	59.188	33.333	0.00	0.00	37.06	2.59
2153	2480	9.093970	TGTTGTTACATCTATCCTTTTGATACG	57.906	33.333	0.00	0.00	34.76	3.06
2274	3493	7.977789	TGCTGTTTATTTTAGAGTGTGATGA	57.022	32.000	0.00	0.00	0.00	2.92
2291	3510	4.931601	GTGATGATGTGCTGAAGTAAGACA	59.068	41.667	0.00	0.00	0.00	3.41
2324	3548	2.430694	TCCAACCCTGTATGATCGAGTG	59.569	50.000	0.00	0.00	0.00	3.51
2329	3553	2.223829	CCCTGTATGATCGAGTGTGGAC	60.224	54.545	0.00	0.00	0.00	4.02
2337	3561	2.509166	TCGAGTGTGGACTATGACCT	57.491	50.000	0.00	0.00	30.16	3.85
2347	3571	5.530915	TGTGGACTATGACCTCTTTGTTTTG	59.469	40.000	0.00	0.00	0.00	2.44
2474	3743	7.350744	TGGCAATTGTAAGAATATCATTGCT	57.649	32.000	7.40	0.00	41.75	3.91
2506	3775	3.566742	GGAACTTGTCAAAATACCACCGT	59.433	43.478	0.00	0.00	0.00	4.83
2568	3837	9.525409	GAAACGTACAAGAATACCACTATACAT	57.475	33.333	0.00	0.00	0.00	2.29
2661	3930	7.606839	ACCAAGGTCTAAAGCAAACTATAAGTC	59.393	37.037	0.00	0.00	0.00	3.01
2689	3960	1.000884	CAAACGCCGGTCGCTTTATA	58.999	50.000	16.48	0.00	43.23	0.98
2690	3961	1.595794	CAAACGCCGGTCGCTTTATAT	59.404	47.619	16.48	0.00	43.23	0.86
2742	4032	2.277084	CCACCTTACAATAGCCGTGTC	58.723	52.381	0.00	0.00	0.00	3.67
2789	4079	6.663093	AGCCGATCTAACTCATGAGAGATTAT	59.337	38.462	29.27	14.38	44.98	1.28
2790	4080	7.178274	AGCCGATCTAACTCATGAGAGATTATT	59.822	37.037	29.27	13.73	44.98	1.40
2821	4113	2.508526	AGGCAACGAATGAAAGAAGCT	58.491	42.857	0.00	0.00	46.39	3.74
2836	4128	7.556844	TGAAAGAAGCTGAAGTATAACCTAGG	58.443	38.462	7.41	7.41	0.00	3.02
2837	4129	6.487299	AAGAAGCTGAAGTATAACCTAGGG	57.513	41.667	14.81	0.00	0.00	3.53
2838	4130	5.778542	AGAAGCTGAAGTATAACCTAGGGA	58.221	41.667	14.81	0.06	0.00	4.20
2839	4131	6.203072	AGAAGCTGAAGTATAACCTAGGGAA	58.797	40.000	14.81	0.00	0.00	3.97
2840	4132	6.672657	AGAAGCTGAAGTATAACCTAGGGAAA	59.327	38.462	14.81	0.00	0.00	3.13
2841	4133	6.487299	AGCTGAAGTATAACCTAGGGAAAG	57.513	41.667	14.81	0.00	0.00	2.62
2842	4134	6.203072	AGCTGAAGTATAACCTAGGGAAAGA	58.797	40.000	14.81	0.00	0.00	2.52
2843	4135	6.672657	AGCTGAAGTATAACCTAGGGAAAGAA	59.327	38.462	14.81	0.00	0.00	2.52
2844	4136	6.762187	GCTGAAGTATAACCTAGGGAAAGAAC	59.238	42.308	14.81	3.56	0.00	3.01
2845	4137	7.191593	TGAAGTATAACCTAGGGAAAGAACC	57.808	40.000	14.81	0.00	0.00	3.62
2846	4138	5.866159	AGTATAACCTAGGGAAAGAACCG	57.134	43.478	14.81	0.00	0.00	4.44
2847	4139	5.275630	AGTATAACCTAGGGAAAGAACCGT	58.724	41.667	14.81	0.00	0.00	4.83
2848	4140	4.750021	ATAACCTAGGGAAAGAACCGTC	57.250	45.455	14.81	0.00	0.00	4.79
2849	4141	1.273759	ACCTAGGGAAAGAACCGTCC	58.726	55.000	14.81	0.00	0.00	4.79
2860	4152	1.346722	AGAACCGTCCGGAAAGAACAT	59.653	47.619	5.23	0.00	38.96	2.71
2888	4180	5.539582	TTCGCATAAATAGCAGTCGTTTT	57.460	34.783	0.00	0.00	0.00	2.43
2958	4250	2.358322	TTCTTCCACCACCAAGTTCC	57.642	50.000	0.00	0.00	0.00	3.62
2965	4257	0.840722	ACCACCAAGTTCCGGATCCT	60.841	55.000	4.15	0.69	0.00	3.24
3019	4311	1.886542	AGCATATGCCTACGTCATCGA	59.113	47.619	23.96	0.00	43.38	3.59
3020	4312	2.493675	AGCATATGCCTACGTCATCGAT	59.506	45.455	23.96	0.00	43.38	3.59
3021	4313	2.600420	GCATATGCCTACGTCATCGATG	59.400	50.000	19.61	19.61	36.57	3.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	3.748568	ACTCCAAGATTCGTGCTCTTTTC	59.251	43.478	0.00	0.00	30.60	2.29
124	125	1.591703	CTACCTGCAAGTCGCCTGA	59.408	57.895	0.00	0.00	41.33	3.86
335	337	0.934496	TACAAGCAACGTGTCAGCAC	59.066	50.000	0.00	0.00	41.97	4.40
404	417	6.845302	TGCAAACACTTCATATCATCAAGTC	58.155	36.000	0.00	0.00	0.00	3.01
456	469	4.429854	AACTGCTCCTTGAAGAGTTCTT	57.570	40.909	0.00	0.00	39.23	2.52
495	512	5.117355	TCATACGAAGAACGAAGAACACT	57.883	39.130	0.00	0.00	45.77	3.55
627	667	3.632145	AGACTTTGTCAAAATGCCGTTCT	59.368	39.130	0.00	0.00	34.60	3.01
725	834	2.738846	AGCACGAAATGATATGATCGGC	59.261	45.455	0.00	0.00	39.49	5.54
882	1039	1.832883	TTGGGAATACATGCACGCTT	58.167	45.000	0.00	0.00	0.00	4.68
969	1157	1.831343	GACAAGCGCTGGCATTTATG	58.169	50.000	12.58	5.08	43.41	1.90
999	1226	2.462255	GATTGGCTGCGGTGTGTGTG	62.462	60.000	0.00	0.00	0.00	3.82
1000	1227	2.203337	ATTGGCTGCGGTGTGTGT	60.203	55.556	0.00	0.00	0.00	3.72
1796	2078	0.320771	GAAGCACTCACGGTGATGGT	60.321	55.000	11.86	13.80	44.41	3.55
1840	2139	6.385033	GCAAATCAGATCCTATAACAATGGC	58.615	40.000	0.00	0.00	0.00	4.40
1841	2140	6.491062	TGGCAAATCAGATCCTATAACAATGG	59.509	38.462	0.00	0.00	0.00	3.16
1842	2141	7.230108	ACTGGCAAATCAGATCCTATAACAATG	59.770	37.037	0.00	0.00	38.11	2.82
1843	2142	7.293073	ACTGGCAAATCAGATCCTATAACAAT	58.707	34.615	0.00	0.00	38.11	2.71
1844	2143	6.662755	ACTGGCAAATCAGATCCTATAACAA	58.337	36.000	0.00	0.00	38.11	2.83
1846	2145	7.420800	CAAACTGGCAAATCAGATCCTATAAC	58.579	38.462	0.00	0.00	38.11	1.89
1847	2146	6.039717	GCAAACTGGCAAATCAGATCCTATAA	59.960	38.462	0.00	0.00	38.11	0.98
1994	2310	1.132834	ACGGACATATACGTGCACGAA	59.867	47.619	42.94	27.33	46.30	3.85
2067	2387	7.765695	AGCTTTCTTCAATCCAATACTTCAA	57.234	32.000	0.00	0.00	0.00	2.69
2070	2390	6.573094	GCCAAGCTTTCTTCAATCCAATACTT	60.573	38.462	0.00	0.00	0.00	2.24
2085	2405	3.375299	ACATAATCTGACGCCAAGCTTTC	59.625	43.478	0.00	0.00	0.00	2.62
2143	2470	8.377681	ACGACAACATGTTATACGTATCAAAAG	58.622	33.333	24.44	3.70	0.00	2.27
2153	2480	6.128499	TGCCTGTTAACGACAACATGTTATAC	60.128	38.462	11.53	4.91	37.75	1.47
2159	2486	2.095768	CCTGCCTGTTAACGACAACATG	60.096	50.000	0.26	0.00	37.75	3.21
2274	3493	6.882610	TTTCATTGTCTTACTTCAGCACAT	57.117	33.333	0.00	0.00	0.00	3.21
2291	3510	7.838696	TCATACAGGGTTGGACATAATTTCATT	59.161	33.333	0.00	0.00	0.00	2.57
2324	3548	5.531287	ACAAAACAAAGAGGTCATAGTCCAC	59.469	40.000	0.00	0.00	0.00	4.02
2354	3599	4.629200	CAGAAAGTAAGCAGCCTTAGACAG	59.371	45.833	0.00	0.00	34.35	3.51
2356	3601	3.372514	GCAGAAAGTAAGCAGCCTTAGAC	59.627	47.826	0.00	0.00	34.35	2.59
2358	3603	3.338249	TGCAGAAAGTAAGCAGCCTTAG	58.662	45.455	0.00	0.00	34.35	2.18
2474	3743	3.070476	TGACAAGTTCCATGCATGCTA	57.930	42.857	21.69	8.51	0.00	3.49
2506	3775	7.763172	AGCATTTTAACAAATTTCGTGTTGA	57.237	28.000	4.58	0.00	39.50	3.18
2675	3946	5.463061	TGTAAAGTAATATAAAGCGACCGGC	59.537	40.000	0.00	0.00	44.05	6.13
2690	3961	9.784680	GAACGATCTATCTGTCTTGTAAAGTAA	57.215	33.333	0.00	0.00	46.34	2.24
2709	3980	2.029838	AAGGTGGCTGATGAACGATC	57.970	50.000	0.00	0.00	0.00	3.69
2715	3986	3.433598	GGCTATTGTAAGGTGGCTGATGA	60.434	47.826	0.00	0.00	0.00	2.92
2760	4050	4.517075	TCTCATGAGTTAGATCGGCTAGTG	59.483	45.833	21.92	0.00	0.00	2.74
2761	4051	4.720046	TCTCATGAGTTAGATCGGCTAGT	58.280	43.478	21.92	0.00	0.00	2.57
2789	4079	3.478857	TCGTTGCCTAAGGAAGACAAA	57.521	42.857	0.00	0.00	0.00	2.83
2790	4080	3.478857	TTCGTTGCCTAAGGAAGACAA	57.521	42.857	0.00	0.00	36.19	3.18
2821	4113	6.127253	CGGTTCTTTCCCTAGGTTATACTTCA	60.127	42.308	8.29	0.00	0.00	3.02
2836	4128	1.154197	CTTTCCGGACGGTTCTTTCC	58.846	55.000	1.83	0.00	36.47	3.13
2837	4129	2.159327	TCTTTCCGGACGGTTCTTTC	57.841	50.000	1.83	0.00	36.47	2.62
2838	4130	2.216046	GTTCTTTCCGGACGGTTCTTT	58.784	47.619	1.83	0.00	36.47	2.52
2839	4131	1.139455	TGTTCTTTCCGGACGGTTCTT	59.861	47.619	1.83	0.00	36.47	2.52
2840	4132	0.754472	TGTTCTTTCCGGACGGTTCT	59.246	50.000	1.83	0.00	36.47	3.01
2841	4133	1.730612	GATGTTCTTTCCGGACGGTTC	59.269	52.381	1.83	0.00	36.47	3.62
2842	4134	1.071071	TGATGTTCTTTCCGGACGGTT	59.929	47.619	1.83	0.00	36.47	4.44
2843	4135	0.682852	TGATGTTCTTTCCGGACGGT	59.317	50.000	1.83	0.00	36.47	4.83
2844	4136	2.024176	ATGATGTTCTTTCCGGACGG	57.976	50.000	1.83	3.96	0.00	4.79
2845	4137	5.556382	CGAATTATGATGTTCTTTCCGGACG	60.556	44.000	1.83	0.00	0.00	4.79
2846	4138	5.738370	CGAATTATGATGTTCTTTCCGGAC	58.262	41.667	1.83	0.00	0.00	4.79
2847	4139	4.272504	GCGAATTATGATGTTCTTTCCGGA	59.727	41.667	0.00	0.00	0.00	5.14
2848	4140	4.035091	TGCGAATTATGATGTTCTTTCCGG	59.965	41.667	0.00	0.00	0.00	5.14
2849	4141	5.155509	TGCGAATTATGATGTTCTTTCCG	57.844	39.130	0.00	0.00	0.00	4.30
2860	4152	6.645003	ACGACTGCTATTTATGCGAATTATGA	59.355	34.615	0.00	0.00	0.00	2.15
2958	4250	1.364626	GCACAGCAACTCAGGATCCG	61.365	60.000	5.98	1.36	0.00	4.18
2965	4257	3.076621	CCAATTCTAGCACAGCAACTCA	58.923	45.455	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.