AutoCloner

Multiple sequence alignment - TraesCS4B01G326600

Loading Multiple Alignment...

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	TraesCS4B01G326600	chr4B	100.000	2681	0	0	1	2681	617425515	617422835	0.000000e+00	4951.0
1	TraesCS4B01G326600	chr4B	92.950	1234	57	12	485	1699	617404769	617403547	0.000000e+00	1770.0
2	TraesCS4B01G326600	chr4B	91.212	990	60	18	1700	2681	617403466	617402496	0.000000e+00	1321.0
3	TraesCS4B01G326600	chr4B	92.699	452	28	3	1	448	617405228	617404778	0.000000e+00	647.0
4	TraesCS4B01G326600	chr4B	75.904	249	50	9	1883	2125	26580437	26580193	4.690000e-23	119.0
5	TraesCS4B01G326600	chr4D	88.435	1712	95	39	1	1688	484722518	484720886	0.000000e+00	1969.0
6	TraesCS4B01G326600	chr4D	90.192	469	45	1	1700	2167	484716646	484716178	6.350000e-171	610.0
7	TraesCS4B01G326600	chr4D	92.035	339	25	2	2341	2679	484714062	484713726	2.420000e-130	475.0
8	TraesCS4B01G326600	chr4D	92.086	139	9	1	2159	2295	484716073	484715935	7.570000e-46	195.0
9	TraesCS4B01G326600	chr4D	80.729	192	30	7	1771	1957	121548412	121548601	2.780000e-30	143.0
10	TraesCS4B01G326600	chr5A	88.915	1254	70	25	459	1686	665763186	665761976	0.000000e+00	1482.0
11	TraesCS4B01G326600	chr5A	90.799	413	24	8	1	403	665763605	665763197	8.440000e-150	540.0
12	TraesCS4B01G326600	chr5A	76.371	237	44	10	633	865	429255338	429255566	1.690000e-22	117.0
13	TraesCS4B01G326600	chr2D	78.947	323	53	12	173	490	3972690	3972378	3.500000e-49	206.0
14	TraesCS4B01G326600	chr1D	83.422	187	21	4	717	900	268952514	268952693	5.940000e-37	165.0
15	TraesCS4B01G326600	chr2B	77.228	303	51	15	166	461	6959594	6959303	7.680000e-36	161.0
16	TraesCS4B01G326600	chr2B	80.631	222	27	11	634	850	747809052	747809262	9.940000e-35	158.0
17	TraesCS4B01G326600	chr2B	76.645	304	51	15	166	461	6873010	6872719	1.660000e-32	150.0
18	TraesCS4B01G326600	chr2B	78.846	208	32	12	166	368	6876963	6876763	2.170000e-26	130.0
19	TraesCS4B01G326600	chr2B	92.308	39	1	2	1205	1243	636820560	636820596	1.000000e-03	54.7
20	TraesCS4B01G326600	chr7B	77.686	242	46	8	628	864	562095184	562095422	1.000000e-29	141.0
21	TraesCS4B01G326600	chr2A	78.059	237	40	9	631	860	48854516	48854285	3.600000e-29	139.0
22	TraesCS4B01G326600	chr2A	79.508	122	14	6	330	446	44108050	44108165	2.860000e-10	76.8
23	TraesCS4B01G326600	chr6A	79.793	193	32	7	1771	1958	127000922	127001112	1.670000e-27	134.0
24	TraesCS4B01G326600	chr7A	78.894	199	31	7	633	828	303960951	303961141	1.010000e-24	124.0
25	TraesCS4B01G326600	chr7A	77.169	219	41	8	633	846	694036452	694036238	4.690000e-23	119.0
26	TraesCS4B01G326600	chr5D	82.609	115	14	6	330	441	5005581	5005692	2.200000e-16	97.1
27	TraesCS4B01G326600	chr5D	76.440	191	38	5	1772	1957	121595510	121595698	2.200000e-16	97.1
28	TraesCS4B01G326600	chr4A	83.505	97	13	3	171	266	739069193	739069099	1.320000e-13	87.9
29	TraesCS4B01G326600	chr1B	94.444	36	2	0	1212	1247	442953804	442953769	3.730000e-04	56.5
30	TraesCS4B01G326600	chr6D	100.000	28	0	0	1216	1243	16972057	16972084	5.000000e-03	52.8

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	TraesCS4B01G326600	chr4B	617422835	617425515	2680	True	4951.000000	4951	100.000000	1	2681	1	chr4B.!!$R2	2680
1	TraesCS4B01G326600	chr4B	617402496	617405228	2732	True	1246.000000	1770	92.287000	1	2681	3	chr4B.!!$R3	2680
2	TraesCS4B01G326600	chr4D	484720886	484722518	1632	True	1969.000000	1969	88.435000	1	1688	1	chr4D.!!$R1	1687
3	TraesCS4B01G326600	chr4D	484713726	484716646	2920	True	426.666667	610	91.437667	1700	2679	3	chr4D.!!$R2	979
4	TraesCS4B01G326600	chr5A	665761976	665763605	1629	True	1011.000000	1482	89.857000	1	1686	2	chr5A.!!$R1	1685

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
701	736	0.035152	ATCTCCGCCATCAAACAGCA	60.035	50.0	0.00	0.0	0.00	4.41	F
976	1023	0.534427	GGATACGCTTACCAAGGGGC	60.534	60.0	7.73	0.0	44.93	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1654	1718	0.033109	CTGTTTGATCCCCTTCCCCC	60.033	60.0	0.00	0.0	0.0	5.40	R
1864	2008	0.179067	AAAGTTCTTCCGGCGTGTCA	60.179	50.0	6.01	0.0	0.0	3.58	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
204	212	2.223548	GCAACATGCTTGAGTGTGTGAA	60.224	45.455	6.60	0.00	40.96	3.18
205	213	3.551454	GCAACATGCTTGAGTGTGTGAAT	60.551	43.478	6.60	0.00	40.96	2.57
206	214	4.613944	CAACATGCTTGAGTGTGTGAATT	58.386	39.130	6.60	0.00	0.00	2.17
211	219	3.002246	TGCTTGAGTGTGTGAATTTCGTC	59.998	43.478	0.00	0.00	0.00	4.20
248	256	1.107538	TAGACATTCGAGGAGCCCGG	61.108	60.000	0.00	0.00	0.00	5.73
260	268	1.454201	GAGCCCGGGAGAAAAGAAAG	58.546	55.000	29.31	0.00	0.00	2.62
283	291	3.945285	ACAAAATGACCTTCGAACAGTGT	59.055	39.130	0.00	0.00	0.00	3.55
452	469	3.562781	CGAATTTACTATTCGCGCACA	57.437	42.857	8.75	0.00	43.20	4.57
550	573	3.423058	AGATAGCTTGGGTAAGAGGGT	57.577	47.619	0.00	0.00	35.92	4.34
701	736	0.035152	ATCTCCGCCATCAAACAGCA	60.035	50.000	0.00	0.00	0.00	4.41
774	810	9.573166	TTAGCATGCAATTAATAACATACTCCT	57.427	29.630	21.98	0.00	0.00	3.69
776	812	9.003658	AGCATGCAATTAATAACATACTCCTAC	57.996	33.333	21.98	0.00	0.00	3.18
777	813	8.237267	GCATGCAATTAATAACATACTCCTACC	58.763	37.037	14.21	0.00	0.00	3.18
976	1023	0.534427	GGATACGCTTACCAAGGGGC	60.534	60.000	7.73	0.00	44.93	5.80
1018	1065	7.115520	CAGGAACTCTATATAAGCACAACATCG	59.884	40.741	0.00	0.00	34.60	3.84
1020	1067	7.096023	GGAACTCTATATAAGCACAACATCGTG	60.096	40.741	0.00	0.00	40.00	4.35
1037	1084	1.345741	CGTGCATCCTCCTGGACATAT	59.654	52.381	0.00	0.00	46.51	1.78
1041	1088	4.284490	GTGCATCCTCCTGGACATATTCTA	59.716	45.833	0.00	0.00	46.51	2.10
1045	1092	3.471306	TCCTCCTGGACATATTCTACCCT	59.529	47.826	0.00	0.00	37.46	4.34
1091	1138	4.412199	CCCAAAACTATCTACCCATCCTCA	59.588	45.833	0.00	0.00	0.00	3.86
1108	1155	6.434028	CCATCCTCAAGGTTTATCAAGAAACA	59.566	38.462	3.02	0.00	40.43	2.83
1208	1256	1.401670	CCGGTTCGTGTTCTCTCTCTG	60.402	57.143	0.00	0.00	0.00	3.35
1274	1322	4.809426	CGGAGGGAGTATATTGTTGTGAAC	59.191	45.833	0.00	0.00	0.00	3.18
1370	1420	2.429058	CTGCCGCTATGCCAGGAT	59.571	61.111	0.00	0.00	0.00	3.24
1373	1423	2.256591	GCCGCTATGCCAGGATGTG	61.257	63.158	0.00	0.00	0.00	3.21
1428	1478	1.598601	TGGTGAACGCCGAAGTAAAAC	59.401	47.619	0.00	0.00	0.00	2.43
1433	1483	1.134226	ACGCCGAAGTAAAACAGTCG	58.866	50.000	0.00	0.00	0.00	4.18
1436	1486	1.725164	GCCGAAGTAAAACAGTCGAGG	59.275	52.381	0.00	0.00	35.54	4.63
1448	1498	3.822192	TCGAGGTGCGTGGGATCG	61.822	66.667	0.00	0.00	41.80	3.69
1626	1685	6.488683	CAGTAGTGTTATCCTTTTGTGGGAAA	59.511	38.462	0.00	0.00	36.37	3.13
1636	1695	3.593442	TTTGTGGGAAACAGTGGATCT	57.407	42.857	0.00	0.00	40.74	2.75
1663	1727	3.466395	TCTATTTTTGTGGGGGAAGGG	57.534	47.619	0.00	0.00	0.00	3.95
1664	1728	2.043801	TCTATTTTTGTGGGGGAAGGGG	59.956	50.000	0.00	0.00	0.00	4.79
1720	1864	4.637091	TCTGTTGCACATATGAACCATCTG	59.363	41.667	10.38	6.66	0.00	2.90
1734	1878	2.028112	ACCATCTGCGACAATAGTGTGT	60.028	45.455	0.00	0.00	38.41	3.72
1792	1936	1.326548	GTTCACACACGAACAGGTCAC	59.673	52.381	0.00	0.00	43.89	3.67
1848	1992	2.899339	GCCGGAGCAGCCTCATTC	60.899	66.667	5.05	0.00	39.96	2.67
1864	2008	0.032130	ATTCGGAGCGCGATACACAT	59.968	50.000	12.10	0.00	0.00	3.21
1906	2051	6.855763	TTAAGAACCCGAAACCTCATACTA	57.144	37.500	0.00	0.00	0.00	1.82
1959	2104	1.681229	ATGGGCTTCCCTAGGTCAAA	58.319	50.000	8.29	0.00	45.70	2.69
1970	2115	0.174845	TAGGTCAAACTGATCGCCCG	59.825	55.000	0.00	0.00	31.44	6.13
2005	2150	0.584396	CGCTACCGTGCAACAAGAAA	59.416	50.000	0.00	0.00	35.74	2.52
2011	2156	3.855858	ACCGTGCAACAAGAAAAACAAT	58.144	36.364	0.00	0.00	35.74	2.71
2050	2197	3.332968	ACTGGGGTAAAGAAGAAAGGGA	58.667	45.455	0.00	0.00	0.00	4.20
2098	2245	8.296000	TGATTTGTCGATATGTGTTGTTCAATT	58.704	29.630	0.00	0.00	0.00	2.32
2108	2255	6.456795	TGTGTTGTTCAATTGGTCATTACA	57.543	33.333	5.42	9.91	0.00	2.41
2195	2456	8.180706	AGCCAAAAAGCAAATTAATCCATTTT	57.819	26.923	0.00	0.00	34.23	1.82
2196	2457	9.294614	AGCCAAAAAGCAAATTAATCCATTTTA	57.705	25.926	0.00	0.00	34.23	1.52
2259	2522	4.387026	TCATCTTGAGGGTGTTTTGGAT	57.613	40.909	0.00	0.00	0.00	3.41
2430	4520	5.818336	TCATTGTCAAACCTTACAGTTTCGA	59.182	36.000	0.00	0.00	37.87	3.71
2456	4546	3.482722	ACTTTTGCATGCGATCTTGAG	57.517	42.857	14.09	7.13	0.00	3.02
2459	4549	4.455533	ACTTTTGCATGCGATCTTGAGTTA	59.544	37.500	14.09	0.00	0.00	2.24
2500	4590	0.933097	CATTCATCTCGACAAGGCGG	59.067	55.000	0.00	0.00	0.00	6.13
2546	4636	7.851822	TTTCGTTTGAAGTCATCTTAATTGC	57.148	32.000	0.00	0.00	35.06	3.56
2547	4637	6.552859	TCGTTTGAAGTCATCTTAATTGCA	57.447	33.333	0.00	0.00	33.64	4.08
2555	4645	8.579006	TGAAGTCATCTTAATTGCATTTGTTCT	58.421	29.630	4.11	0.00	33.64	3.01
2606	4696	8.239314	TGCATCTCTGAAATTGTCATAACTTTC	58.761	33.333	0.00	0.00	35.07	2.62
2614	4704	4.678509	TTGTCATAACTTTCGCATCCAC	57.321	40.909	0.00	0.00	0.00	4.02
2627	4717	3.067601	TCGCATCCACGCTCTATTTAGAA	59.932	43.478	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	98	2.132996	AGCCGGGCTCAGAGATGAG	61.133	63.158	17.69	0.83	30.62	2.90
204	212	6.894339	ACTTCACCAAATTTAGGACGAAAT	57.106	33.333	11.98	3.97	0.00	2.17
205	213	6.702716	AACTTCACCAAATTTAGGACGAAA	57.297	33.333	11.98	0.00	0.00	3.46
206	214	6.702716	AAACTTCACCAAATTTAGGACGAA	57.297	33.333	11.98	11.73	0.00	3.85
211	219	9.626045	GAATGTCTAAACTTCACCAAATTTAGG	57.374	33.333	0.00	0.00	35.99	2.69
248	256	7.043961	AGGTCATTTTGTCTTTCTTTTCTCC	57.956	36.000	0.00	0.00	0.00	3.71
260	268	4.035208	ACACTGTTCGAAGGTCATTTTGTC	59.965	41.667	0.00	0.00	0.00	3.18
283	291	8.397906	CAGATATGCGAGAAAGTTTAAATTCCA	58.602	33.333	0.00	0.00	0.00	3.53
363	380	1.466167	AGATGTTTGAGTGCGTGATGC	59.534	47.619	0.00	0.00	46.70	3.91
550	573	8.821686	ATGAAATTGAATGTATGTTAGGGTGA	57.178	30.769	0.00	0.00	0.00	4.02
687	722	2.572191	ATTGATGCTGTTTGATGGCG	57.428	45.000	0.00	0.00	0.00	5.69
701	736	9.358406	TGAAGCAATATAGGTCATTGAATTGAT	57.642	29.630	10.70	3.45	35.77	2.57
886	925	1.812093	GGTACGCGCAATGCAGGTA	60.812	57.895	5.73	3.58	46.97	3.08
976	1023	1.621301	CCTGCGTGAGAGTTGAAGCG	61.621	60.000	0.00	0.00	0.00	4.68
1037	1084	3.627747	GCTAGGACCAGAGAAGGGTAGAA	60.628	52.174	0.00	0.00	39.19	2.10
1041	1088	0.413832	TGCTAGGACCAGAGAAGGGT	59.586	55.000	0.00	0.00	42.61	4.34
1045	1092	2.244695	TCGTTTGCTAGGACCAGAGAA	58.755	47.619	0.00	0.00	0.00	2.87
1108	1155	2.224523	CCTGGCGTCCATGGTATGTATT	60.225	50.000	12.58	0.00	30.82	1.89
1247	1295	4.715297	ACAACAATATACTCCCTCCGTTCT	59.285	41.667	0.00	0.00	0.00	3.01
1251	1299	4.665833	TCACAACAATATACTCCCTCCG	57.334	45.455	0.00	0.00	0.00	4.63
1274	1322	7.855409	TCTCAACACACGAAAATGTTCATAAAG	59.145	33.333	0.00	0.00	36.92	1.85
1428	1478	2.890847	GATCCCACGCACCTCGACTG	62.891	65.000	0.00	0.00	41.67	3.51
1433	1483	4.530857	CCCGATCCCACGCACCTC	62.531	72.222	0.00	0.00	0.00	3.85
1539	1596	6.371825	GTCTTCAATTCAACTCGGTAGGATTT	59.628	38.462	0.00	0.00	0.00	2.17
1593	1651	7.916077	AAAGGATAACACTACTGGCTAGTAT	57.084	36.000	10.68	0.00	38.65	2.12
1647	1711	0.871024	ATCCCCTTCCCCCACAAAAA	59.129	50.000	0.00	0.00	0.00	1.94
1654	1718	0.033109	CTGTTTGATCCCCTTCCCCC	60.033	60.000	0.00	0.00	0.00	5.40
1659	1723	4.387026	TGATTCACTGTTTGATCCCCTT	57.613	40.909	0.00	0.00	32.84	3.95
1734	1878	3.228453	GACTGGACGGGAGATTATGGTA	58.772	50.000	0.00	0.00	0.00	3.25
1787	1931	4.073200	CCGGGGTACACGGTGACC	62.073	72.222	16.29	16.45	46.03	4.02
1814	1958	1.076533	GGCACGTGTCCTGTGTATCG	61.077	60.000	18.38	0.00	39.53	2.92
1848	1992	1.299089	TCATGTGTATCGCGCTCCG	60.299	57.895	5.56	0.00	38.61	4.63
1864	2008	0.179067	AAAGTTCTTCCGGCGTGTCA	60.179	50.000	6.01	0.00	0.00	3.58
1970	2115	1.591863	GCGAACCTCGAGGCCATAC	60.592	63.158	31.56	16.00	43.74	2.39
1993	2138	6.645700	TCTTCATTGTTTTTCTTGTTGCAC	57.354	33.333	0.00	0.00	0.00	4.57
2195	2456	5.291371	TCAACATGAAAGTTGTTCGTCGTTA	59.709	36.000	0.00	0.00	46.78	3.18
2196	2457	4.093703	TCAACATGAAAGTTGTTCGTCGTT	59.906	37.500	0.00	0.00	46.78	3.85
2259	2522	8.560355	TCTGCTGCATATAAGTTAGAAAACAA	57.440	30.769	1.31	0.00	38.12	2.83
2290	2553	2.093869	GCCGGACATGTTCCTTAGTACA	60.094	50.000	5.05	0.00	43.25	2.90
2295	2558	0.988832	AAGGCCGGACATGTTCCTTA	59.011	50.000	11.69	0.00	43.25	2.69
2297	2560	1.299976	GAAGGCCGGACATGTTCCT	59.700	57.895	11.69	0.00	43.25	3.36
2300	2563	1.675641	GCTGAAGGCCGGACATGTT	60.676	57.895	11.69	0.00	34.27	2.71
2301	2564	2.045926	GCTGAAGGCCGGACATGT	60.046	61.111	11.69	0.00	34.27	3.21
2343	2639	2.484417	CGGATGAAGGGAAGATGGACAG	60.484	54.545	0.00	0.00	0.00	3.51
2430	4520	3.753272	AGATCGCATGCAAAAGTTACAGT	59.247	39.130	19.57	0.00	0.00	3.55
2547	4637	9.228949	GGCATCAGATCATAGAATAGAACAAAT	57.771	33.333	0.00	0.00	0.00	2.32
2555	4645	5.012354	TGTGCAGGCATCAGATCATAGAATA	59.988	40.000	0.00	0.00	0.00	1.75
2606	4696	3.013276	TCTAAATAGAGCGTGGATGCG	57.987	47.619	0.00	0.00	40.67	4.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.