AutoCloner

Multiple sequence alignment - TraesCS4A01G181700

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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	TraesCS4A01G181700	chr4A	100.000	2675	0	0	1	2675	456450968	456448294	0.000000e+00	4940.0
1	TraesCS4A01G181700	chr4A	98.022	910	9	6	1771	2675	586689597	586688692	0.000000e+00	1572.0
2	TraesCS4A01G181700	chr4A	87.251	1153	105	22	571	1698	586683169	586682034	0.000000e+00	1277.0
3	TraesCS4A01G181700	chr4A	86.159	1156	114	27	571	1698	456437576	456436439	0.000000e+00	1206.0
4	TraesCS4A01G181700	chr4A	90.839	906	59	8	795	1698	456456106	456455223	0.000000e+00	1192.0
5	TraesCS4A01G181700	chr4A	99.089	549	5	0	1	549	706948208	706947660	0.000000e+00	987.0
6	TraesCS4A01G181700	chr4A	98.907	549	5	1	1	549	706972443	706971896	0.000000e+00	979.0
7	TraesCS4A01G181700	chr4A	88.679	53	4	2	1675	1726	586699200	586699251	2.220000e-06	63.9
8	TraesCS4A01G181700	chr4D	91.983	1160	67	14	550	1692	14914170	14915320	0.000000e+00	1604.0
9	TraesCS4A01G181700	chr4D	90.480	1145	82	17	571	1698	14908949	14910083	0.000000e+00	1485.0
10	TraesCS4A01G181700	chr4D	93.161	965	48	11	745	1692	14862538	14863501	0.000000e+00	1400.0
11	TraesCS4A01G181700	chr4D	88.382	1162	90	11	571	1701	14460183	14459036	0.000000e+00	1356.0
12	TraesCS4A01G181700	chr4D	91.247	914	67	6	795	1698	14434611	14433701	0.000000e+00	1232.0
13	TraesCS4A01G181700	chr4D	96.420	419	11	3	2049	2463	307814743	307814325	0.000000e+00	688.0
14	TraesCS4A01G181700	chr4D	96.181	419	11	3	2049	2463	383855346	383854929	0.000000e+00	680.0
15	TraesCS4A01G181700	chr4D	98.558	208	3	0	2465	2672	14864526	14864733	4.210000e-98	368.0
16	TraesCS4A01G181700	chr4D	89.161	286	2	4	1771	2048	14864266	14864530	1.990000e-86	329.0
17	TraesCS4A01G181700	chr4D	82.486	354	35	12	571	899	14895804	14896155	4.360000e-73	285.0
18	TraesCS4A01G181700	chr4D	90.863	197	12	2	550	746	14850857	14851047	2.640000e-65	259.0
19	TraesCS4A01G181700	chr4D	87.204	211	24	3	2465	2674	14854368	14854576	1.240000e-58	237.0
20	TraesCS4A01G181700	chr4D	93.125	160	8	1	550	709	14862386	14862542	5.760000e-57	231.0
21	TraesCS4A01G181700	chr4D	92.308	104	6	2	2465	2567	14897133	14897235	2.150000e-31	147.0
22	TraesCS4A01G181700	chr4D	100.000	32	0	0	1695	1726	14433722	14433753	2.880000e-05	60.2
23	TraesCS4A01G181700	chr4D	100.000	32	0	0	1695	1726	14915305	14915274	2.880000e-05	60.2
24	TraesCS4A01G181700	chr4B	89.073	1089	86	19	622	1692	24759056	24760129	0.000000e+00	1321.0
25	TraesCS4A01G181700	chr4B	87.577	1143	99	25	571	1698	24741227	24742341	0.000000e+00	1284.0
26	TraesCS4A01G181700	chr4B	87.060	1136	103	21	571	1683	24745351	24746465	0.000000e+00	1243.0
27	TraesCS4A01G181700	chr4B	100.000	32	0	0	1695	1726	24746459	24746428	2.880000e-05	60.2
28	TraesCS4A01G181700	chr4B	100.000	32	0	0	1695	1726	24760114	24760083	2.880000e-05	60.2
29	TraesCS4A01G181700	chr3B	86.847	1148	97	26	571	1692	452717370	452716251	0.000000e+00	1234.0
30	TraesCS4A01G181700	chr3B	100.000	32	0	0	1695	1726	452716266	452716297	2.880000e-05	60.2
31	TraesCS4A01G181700	chr1A	98.198	555	4	3	1	550	592803500	592804053	0.000000e+00	965.0
32	TraesCS4A01G181700	chr1A	98.364	550	6	2	1	550	174049995	174050541	0.000000e+00	963.0
33	TraesCS4A01G181700	chr1B	94.000	550	8	5	1	550	1952534	1953058	0.000000e+00	809.0
34	TraesCS4A01G181700	chr7D	95.281	445	13	6	2031	2467	388994267	388993823	0.000000e+00	699.0
35	TraesCS4A01G181700	chr5D	96.471	425	11	2	2043	2463	435585204	435585628	0.000000e+00	699.0
36	TraesCS4A01G181700	chr5D	95.476	420	14	3	2049	2463	59938417	59937998	0.000000e+00	665.0
37	TraesCS4A01G181700	chr2D	95.724	421	12	4	2049	2464	20920477	20920058	0.000000e+00	673.0
38	TraesCS4A01G181700	chr3A	95.238	420	15	4	2049	2463	672427120	672427539	0.000000e+00	660.0
39	TraesCS4A01G181700	chr6B	94.393	428	17	4	2041	2463	151201273	151201698	0.000000e+00	651.0
40	TraesCS4A01G181700	chr6B	98.684	76	1	0	474	549	714777610	714777535	4.650000e-28	135.0
41	TraesCS4A01G181700	chr7A	96.648	179	5	1	372	549	539403861	539403683	2.010000e-76	296.0
42	TraesCS4A01G181700	chr7A	92.308	91	5	2	183	272	539404054	539403965	7.770000e-26	128.0
43	TraesCS4A01G181700	chr7A	98.148	54	1	0	498	551	721488675	721488622	7.880000e-16	95.3
44	TraesCS4A01G181700	chr7A	100.000	33	0	0	317	349	539403894	539403862	8.000000e-06	62.1
45	TraesCS4A01G181700	chr2A	94.915	118	6	0	432	549	20864299	20864416	4.550000e-43	185.0
46	TraesCS4A01G181700	chr2A	93.671	79	3	2	359	437	20862936	20863012	1.680000e-22	117.0
47	TraesCS4A01G181700	chr6D	90.698	43	4	0	53	95	7240477	7240519	1.030000e-04	58.4

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	TraesCS4A01G181700	chr4A	456448294	456450968	2674	True	4940.0	4940	100.00000	1	2675	1	chr4A.!!$R2	2674
1	TraesCS4A01G181700	chr4A	586688692	586689597	905	True	1572.0	1572	98.02200	1771	2675	1	chr4A.!!$R5	904
2	TraesCS4A01G181700	chr4A	586682034	586683169	1135	True	1277.0	1277	87.25100	571	1698	1	chr4A.!!$R4	1127
3	TraesCS4A01G181700	chr4A	456436439	456437576	1137	True	1206.0	1206	86.15900	571	1698	1	chr4A.!!$R1	1127
4	TraesCS4A01G181700	chr4A	456455223	456456106	883	True	1192.0	1192	90.83900	795	1698	1	chr4A.!!$R3	903
5	TraesCS4A01G181700	chr4A	706947660	706948208	548	True	987.0	987	99.08900	1	549	1	chr4A.!!$R6	548
6	TraesCS4A01G181700	chr4A	706971896	706972443	547	True	979.0	979	98.90700	1	549	1	chr4A.!!$R7	548
7	TraesCS4A01G181700	chr4D	14914170	14915320	1150	False	1604.0	1604	91.98300	550	1692	1	chr4D.!!$F3	1142
8	TraesCS4A01G181700	chr4D	14908949	14910083	1134	False	1485.0	1485	90.48000	571	1698	1	chr4D.!!$F2	1127
9	TraesCS4A01G181700	chr4D	14459036	14460183	1147	True	1356.0	1356	88.38200	571	1701	1	chr4D.!!$R2	1130
10	TraesCS4A01G181700	chr4D	14433701	14434611	910	True	1232.0	1232	91.24700	795	1698	1	chr4D.!!$R1	903
11	TraesCS4A01G181700	chr4D	14862386	14864733	2347	False	582.0	1400	93.50125	550	2672	4	chr4D.!!$F5	2122
12	TraesCS4A01G181700	chr4D	14850857	14854576	3719	False	248.0	259	89.03350	550	2674	2	chr4D.!!$F4	2124
13	TraesCS4A01G181700	chr4D	14895804	14897235	1431	False	216.0	285	87.39700	571	2567	2	chr4D.!!$F6	1996
14	TraesCS4A01G181700	chr4B	24759056	24760129	1073	False	1321.0	1321	89.07300	622	1692	1	chr4B.!!$F1	1070
15	TraesCS4A01G181700	chr4B	24741227	24746465	5238	False	1263.5	1284	87.31850	571	1698	2	chr4B.!!$F2	1127
16	TraesCS4A01G181700	chr3B	452716251	452717370	1119	True	1234.0	1234	86.84700	571	1692	1	chr3B.!!$R1	1121
17	TraesCS4A01G181700	chr1A	592803500	592804053	553	False	965.0	965	98.19800	1	550	1	chr1A.!!$F2	549
18	TraesCS4A01G181700	chr1A	174049995	174050541	546	False	963.0	963	98.36400	1	550	1	chr1A.!!$F1	549
19	TraesCS4A01G181700	chr1B	1952534	1953058	524	False	809.0	809	94.00000	1	550	1	chr1B.!!$F1	549

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
928	1074	0.595095	GCTTAGCAGCAGCAACAACT	59.405	50.0	3.17	0.0	46.49	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1765	6521	7.76997	TGGAACTACAAGTATATTTAAACCGGG	59.23	37.037	6.32	0.0	0.0	5.73	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
107	108	5.124457	CGATCTTTCACAATTTGTCCCATCT	59.876	40.000	0.00	0.00	0.00	2.90
677	704	2.621526	GTCTGTTCGTTGGTCCCATTTT	59.378	45.455	0.00	0.00	0.00	1.82
712	739	1.140312	TGGCCTTGACTCTGACCTTT	58.860	50.000	3.32	0.00	0.00	3.11
713	740	1.494721	TGGCCTTGACTCTGACCTTTT	59.505	47.619	3.32	0.00	0.00	2.27
715	742	2.487265	GGCCTTGACTCTGACCTTTTGA	60.487	50.000	0.00	0.00	0.00	2.69
792	881	0.767375	TGAACTCTCTGCCTTGCCTT	59.233	50.000	0.00	0.00	0.00	4.35
864	994	0.683828	ATTGCGTGCATCAATCCCCA	60.684	50.000	10.27	0.00	28.76	4.96
900	1046	2.119801	ATGCCTCACCATTCACTCAC	57.880	50.000	0.00	0.00	0.00	3.51
928	1074	0.595095	GCTTAGCAGCAGCAACAACT	59.405	50.000	3.17	0.00	46.49	3.16
1082	1240	2.363925	GGCTACCGACCCTGACCT	60.364	66.667	0.00	0.00	0.00	3.85
1146	1304	1.896660	GGTGAATGGGCACACGTGT	60.897	57.895	17.22	17.22	40.52	4.49
1278	1438	1.670083	GCCCGGTACCAACACACTC	60.670	63.158	13.54	0.00	0.00	3.51
1704	6004	5.902681	GGAGACTGCCCATAAATTAAAACC	58.097	41.667	0.00	0.00	0.00	3.27
1705	6005	5.163447	GGAGACTGCCCATAAATTAAAACCC	60.163	44.000	0.00	0.00	0.00	4.11
1706	6006	5.337788	AGACTGCCCATAAATTAAAACCCA	58.662	37.500	0.00	0.00	0.00	4.51
1707	6007	5.422012	AGACTGCCCATAAATTAAAACCCAG	59.578	40.000	0.00	0.00	0.00	4.45
1708	6008	4.081142	ACTGCCCATAAATTAAAACCCAGC	60.081	41.667	0.00	0.00	0.00	4.85
1709	6009	3.118956	TGCCCATAAATTAAAACCCAGCG	60.119	43.478	0.00	0.00	0.00	5.18
1710	6010	3.739830	GCCCATAAATTAAAACCCAGCGG	60.740	47.826	0.00	0.00	0.00	5.52
1711	6011	3.453424	CCATAAATTAAAACCCAGCGGC	58.547	45.455	0.00	0.00	0.00	6.53
1712	6012	2.923605	TAAATTAAAACCCAGCGGCG	57.076	45.000	0.51	0.51	0.00	6.46
1713	6013	1.249407	AAATTAAAACCCAGCGGCGA	58.751	45.000	12.98	0.00	0.00	5.54
1715	6015	0.524414	ATTAAAACCCAGCGGCGAAC	59.476	50.000	12.98	0.00	0.00	3.95
1718	6018	2.070654	AAAACCCAGCGGCGAACTTG	62.071	55.000	12.98	2.33	0.00	3.16
1720	6020	4.697756	CCCAGCGGCGAACTTGGA	62.698	66.667	12.98	0.00	32.34	3.53
1721	6021	3.423154	CCAGCGGCGAACTTGGAC	61.423	66.667	12.98	0.00	32.34	4.02
1722	6022	2.357517	CAGCGGCGAACTTGGACT	60.358	61.111	12.98	0.00	0.00	3.85
1723	6023	1.961277	CAGCGGCGAACTTGGACTT	60.961	57.895	12.98	0.00	0.00	3.01
1724	6024	1.961277	AGCGGCGAACTTGGACTTG	60.961	57.895	12.98	0.00	0.00	3.16
1725	6025	1.959226	GCGGCGAACTTGGACTTGA	60.959	57.895	12.98	0.00	0.00	3.02
1726	6026	1.503818	GCGGCGAACTTGGACTTGAA	61.504	55.000	12.98	0.00	0.00	2.69
1727	6027	0.512952	CGGCGAACTTGGACTTGAAG	59.487	55.000	0.00	0.00	0.00	3.02
1728	6028	1.594331	GGCGAACTTGGACTTGAAGT	58.406	50.000	0.00	0.00	35.08	3.01
1729	6029	1.947456	GGCGAACTTGGACTTGAAGTT	59.053	47.619	0.00	0.00	44.51	2.66
1730	6030	3.135994	GGCGAACTTGGACTTGAAGTTA	58.864	45.455	0.00	0.00	42.42	2.24
1731	6031	3.751698	GGCGAACTTGGACTTGAAGTTAT	59.248	43.478	0.00	0.00	42.42	1.89
1736	6492	8.662141	GCGAACTTGGACTTGAAGTTATAAATA	58.338	33.333	0.00	0.00	42.42	1.40
1983	8296	5.479027	GGTGCCTTAACTCCCTATTTCAAAA	59.521	40.000	0.00	0.00	0.00	2.44
1984	8297	6.014925	GGTGCCTTAACTCCCTATTTCAAAAA	60.015	38.462	0.00	0.00	0.00	1.94
2270	8692	8.807948	AATAGTATCATGTGTTAAACAGCCTT	57.192	30.769	0.00	0.00	43.64	4.35
2313	8735	3.612423	GCCCTCATTTCAACGTATTTTGC	59.388	43.478	0.00	0.00	0.00	3.68
2356	8778	7.728847	TGTGTGTTATGCCTTCATGTATATC	57.271	36.000	0.00	0.00	34.22	1.63
2457	8879	0.693049	AGCTCGGTCACCAAAAGGAT	59.307	50.000	0.00	0.00	0.00	3.24
2460	8882	2.095212	GCTCGGTCACCAAAAGGATTTC	60.095	50.000	0.00	0.00	37.28	2.17
2462	8884	1.199097	CGGTCACCAAAAGGATTTCCG	59.801	52.381	0.00	0.00	37.28	4.30
2463	8885	2.235891	GGTCACCAAAAGGATTTCCGT	58.764	47.619	0.00	0.00	37.28	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	2.682352	CAGCGACTGAGAGAGAGATTGA	59.318	50.000	1.18	0.00	32.44	2.57
617	632	2.938451	CTGAATGGAGTATTGCGCTTGA	59.062	45.455	9.73	0.00	0.00	3.02
677	704	1.222661	CCACTGCTGGCTGCTATGA	59.777	57.895	17.45	0.00	43.37	2.15
712	739	3.824001	TGAAAATGGAGATGGGGTCAA	57.176	42.857	0.00	0.00	0.00	3.18
713	740	3.269118	TGATGAAAATGGAGATGGGGTCA	59.731	43.478	0.00	0.00	0.00	4.02
715	742	3.011595	TGTGATGAAAATGGAGATGGGGT	59.988	43.478	0.00	0.00	0.00	4.95
774	856	1.163554	CAAGGCAAGGCAGAGAGTTC	58.836	55.000	0.00	0.00	0.00	3.01
792	881	0.603439	ATGTCGTCACTGCATGCACA	60.603	50.000	18.46	11.98	0.00	4.57
864	994	7.398024	GTGAGGCATATGGAGTCCTTTATATT	58.602	38.462	11.33	0.00	0.00	1.28
900	1046	2.042831	GCTGCTAAGCTGTGGTGGG	61.043	63.158	0.00	0.00	46.60	4.61
928	1074	3.451402	TGGAGAGTGTCTAAGGCACTA	57.549	47.619	6.43	0.00	45.99	2.74
997	1154	1.337118	GTTTTGGAGCACCCCATTGA	58.663	50.000	0.00	0.00	35.87	2.57
1082	1240	0.603569	GACGCAGAAGTCCTGGAGAA	59.396	55.000	0.00	0.00	43.13	2.87
1122	1280	2.100631	GTGCCCATTCACCGAGACG	61.101	63.158	0.00	0.00	0.00	4.18
1146	1304	2.742116	GGCCTCCGACATGGGCTTA	61.742	63.158	9.42	0.00	44.70	3.09
1165	1323	0.806241	GAGAAGAGGAAGTCGTCGCT	59.194	55.000	0.00	0.00	38.60	4.93
1278	1438	3.561429	CGGTTCATGGACACACCG	58.439	61.111	6.44	6.70	45.75	4.94
1302	1462	1.832167	GGTGCCTCCAGGTGCAAAA	60.832	57.895	7.83	0.00	39.57	2.44
1505	1667	3.083997	AGACGACCATGGAGGCCC	61.084	66.667	21.47	3.27	43.14	5.80
1698	5998	0.535553	AAGTTCGCCGCTGGGTTTTA	60.536	50.000	0.00	0.00	34.97	1.52
1703	6003	4.697756	TCCAAGTTCGCCGCTGGG	62.698	66.667	0.00	0.00	0.00	4.45
1704	6004	3.423154	GTCCAAGTTCGCCGCTGG	61.423	66.667	0.00	0.00	0.00	4.85
1705	6005	1.961277	AAGTCCAAGTTCGCCGCTG	60.961	57.895	0.00	0.00	0.00	5.18
1706	6006	1.961277	CAAGTCCAAGTTCGCCGCT	60.961	57.895	0.00	0.00	0.00	5.52
1707	6007	1.503818	TTCAAGTCCAAGTTCGCCGC	61.504	55.000	0.00	0.00	0.00	6.53
1708	6008	0.512952	CTTCAAGTCCAAGTTCGCCG	59.487	55.000	0.00	0.00	0.00	6.46
1709	6009	1.594331	ACTTCAAGTCCAAGTTCGCC	58.406	50.000	0.00	0.00	29.29	5.54
1710	6010	6.476243	TTATAACTTCAAGTCCAAGTTCGC	57.524	37.500	1.17	0.00	42.03	4.70
1762	6518	9.519191	AACTACAAGTATATTTAAACCGGGTTT	57.481	29.630	26.79	26.79	39.24	3.27
1763	6519	9.166173	GAACTACAAGTATATTTAAACCGGGTT	57.834	33.333	10.96	10.96	0.00	4.11
1764	6520	7.770433	GGAACTACAAGTATATTTAAACCGGGT	59.230	37.037	6.32	0.00	0.00	5.28
1765	6521	7.769970	TGGAACTACAAGTATATTTAAACCGGG	59.230	37.037	6.32	0.00	0.00	5.73
1767	6523	9.374838	ACTGGAACTACAAGTATATTTAAACCG	57.625	33.333	0.00	0.00	0.00	4.44
1990	8303	8.697846	TCTTGTTATGTAATACTCCGAGTTTG	57.302	34.615	6.31	0.00	0.00	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.