AutoCloner

Multiple sequence alignment - TraesCS4B01G133400

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	TraesCS4B01G133400	chr4B	100.000	2222	0	0	1	2222	173173315	173175536	0.000000e+00	4104.0
1	TraesCS4B01G133400	chr4B	84.141	227	24	7	11	229	400330985	400330763	2.240000e-50	209.0
2	TraesCS4B01G133400	chr4D	93.214	840	25	12	670	1488	112723966	112724794	0.000000e+00	1206.0
3	TraesCS4B01G133400	chr4D	91.745	424	30	2	1801	2222	112725101	112725521	3.180000e-163	584.0
4	TraesCS4B01G133400	chr4D	84.171	398	47	9	11	400	112226715	112226326	2.690000e-99	372.0
5	TraesCS4B01G133400	chr4D	88.506	261	14	3	1477	1737	112724835	112725079	3.590000e-78	302.0
6	TraesCS4B01G133400	chr4A	93.018	845	30	6	671	1488	464697294	464696452	0.000000e+00	1206.0
7	TraesCS4B01G133400	chr4A	90.255	431	25	9	1801	2222	464695847	464695425	4.170000e-152	547.0
8	TraesCS4B01G133400	chr4A	90.411	292	17	3	1477	1758	464696411	464696121	7.490000e-100	374.0
9	TraesCS4B01G133400	chr4A	87.288	118	5	2	1663	1770	464696059	464695942	2.320000e-25	126.0
10	TraesCS4B01G133400	chr3B	97.424	621	15	1	1	621	787921831	787921212	0.000000e+00	1057.0
11	TraesCS4B01G133400	chr3B	96.618	621	20	1	1	621	680917073	680916454	0.000000e+00	1029.0
12	TraesCS4B01G133400	chr3B	93.750	48	3	0	584	631	680908429	680908382	3.060000e-09	73.1
13	TraesCS4B01G133400	chr3B	90.566	53	4	1	584	635	809077016	809077068	3.960000e-08	69.4
14	TraesCS4B01G133400	chr2A	90.665	632	32	12	1	632	178136456	178137060	0.000000e+00	815.0
15	TraesCS4B01G133400	chr5B	95.575	226	10	0	997	1222	246181016	246181241	1.620000e-96	363.0
16	TraesCS4B01G133400	chr5B	92.157	51	3	1	584	634	42173724	42173675	1.100000e-08	71.3
17	TraesCS4B01G133400	chr5A	95.575	226	10	0	997	1222	299504522	299504297	1.620000e-96	363.0
18	TraesCS4B01G133400	chr5D	95.133	226	11	0	997	1222	224944013	224943788	7.550000e-95	357.0
19	TraesCS4B01G133400	chr6A	81.951	410	48	13	12	409	515074633	515075028	7.650000e-85	324.0
20	TraesCS4B01G133400	chr6B	93.878	49	3	0	584	632	430555122	430555074	8.510000e-10	75.0
21	TraesCS4B01G133400	chr6B	80.899	89	15	2	536	623	428608678	428608765	3.960000e-08	69.4
22	TraesCS4B01G133400	chr1B	100.000	40	0	0	584	623	5094240	5094279	8.510000e-10	75.0
23	TraesCS4B01G133400	chr1B	94.286	35	2	0	1766	1800	489201331	489201297	1.000000e-03	54.7
24	TraesCS4B01G133400	chr7B	91.071	56	1	4	578	632	21192078	21192026	3.060000e-09	73.1
25	TraesCS4B01G133400	chr1A	96.875	32	1	0	1768	1799	259204339	259204370	1.000000e-03	54.7

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	TraesCS4B01G133400	chr4B	173173315	173175536	2221	False	4104.000000	4104	100.000	1	2222	1	chr4B.!!$F1	2221
1	TraesCS4B01G133400	chr4D	112723966	112725521	1555	False	697.333333	1206	91.155	670	2222	3	chr4D.!!$F1	1552
2	TraesCS4B01G133400	chr4A	464695425	464697294	1869	True	563.250000	1206	90.243	671	2222	4	chr4A.!!$R1	1551
3	TraesCS4B01G133400	chr3B	787921212	787921831	619	True	1057.000000	1057	97.424	1	621	1	chr3B.!!$R3	620
4	TraesCS4B01G133400	chr3B	680916454	680917073	619	True	1029.000000	1029	96.618	1	621	1	chr3B.!!$R2	620
5	TraesCS4B01G133400	chr2A	178136456	178137060	604	False	815.000000	815	90.665	1	632	1	chr2A.!!$F1	631

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
114	115	0.042131	TATTGGAGGACGGGGTCACT	59.958	55.0	0.0	0.0	33.68	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	2288	1.067354	GCAAAATCAAGGGAGGTGCTG	60.067	52.381	0.0	0.0	0.0	4.41	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
114	115	0.042131	TATTGGAGGACGGGGTCACT	59.958	55.000	0.00	0.00	33.68	3.41
354	355	0.766288	GAGGGGAGGGGGATGAAGAG	60.766	65.000	0.00	0.00	0.00	2.85
561	562	6.869388	GCGGGTTTATTTCCATAAAACTCAAA	59.131	34.615	3.42	0.00	40.95	2.69
591	592	9.240159	GTTTCTGTAAATTTGTTAACGGTGAAT	57.760	29.630	0.00	0.00	0.00	2.57
607	608	0.837272	GAATCCGGAGACCCAATCCA	59.163	55.000	11.34	0.00	36.57	3.41
624	625	8.179487	ACCCAATCCATGCTTTATTATTAGGAT	58.821	33.333	0.00	0.00	36.25	3.24
625	626	9.699410	CCCAATCCATGCTTTATTATTAGGATA	57.301	33.333	0.00	0.00	33.75	2.59
654	655	6.926630	AGGATTAGGAAGAGATATGTCACC	57.073	41.667	2.30	5.47	0.00	4.02
655	656	6.385443	AGGATTAGGAAGAGATATGTCACCA	58.615	40.000	14.90	0.92	0.00	4.17
656	657	7.021873	AGGATTAGGAAGAGATATGTCACCAT	58.978	38.462	14.90	4.64	34.97	3.55
657	658	7.515514	AGGATTAGGAAGAGATATGTCACCATT	59.484	37.037	14.90	0.00	32.29	3.16
658	659	7.605691	GGATTAGGAAGAGATATGTCACCATTG	59.394	40.741	14.90	0.00	32.29	2.82
659	660	5.965033	AGGAAGAGATATGTCACCATTGT	57.035	39.130	14.90	0.00	32.29	2.71
660	661	8.547481	TTAGGAAGAGATATGTCACCATTGTA	57.453	34.615	14.90	1.22	32.29	2.41
661	662	6.821388	AGGAAGAGATATGTCACCATTGTAC	58.179	40.000	14.90	0.00	32.29	2.90
662	663	6.384015	AGGAAGAGATATGTCACCATTGTACA	59.616	38.462	14.90	0.00	32.29	2.90
663	664	7.071698	AGGAAGAGATATGTCACCATTGTACAT	59.928	37.037	14.90	0.00	37.58	2.29
664	665	7.716998	GGAAGAGATATGTCACCATTGTACATT	59.283	37.037	2.30	0.00	35.54	2.71
665	666	8.442632	AAGAGATATGTCACCATTGTACATTG	57.557	34.615	10.21	10.21	35.54	2.82
666	667	6.484643	AGAGATATGTCACCATTGTACATTGC	59.515	38.462	11.46	0.47	35.54	3.56
667	668	5.532406	AGATATGTCACCATTGTACATTGCC	59.468	40.000	11.46	1.65	35.54	4.52
668	669	2.166829	TGTCACCATTGTACATTGCCC	58.833	47.619	11.46	1.37	0.00	5.36
705	706	6.476706	GTGAAGGAAGGAAACAAATTGTTCTG	59.523	38.462	12.11	0.00	40.14	3.02
710	711	4.359706	AGGAAACAAATTGTTCTGAACGC	58.640	39.130	12.11	0.00	40.14	4.84
762	763	3.425758	CGGACGGTTTTATCAAAGAAGGC	60.426	47.826	0.00	0.00	0.00	4.35
894	895	3.706373	GCTCCCTCCTGCGACCAA	61.706	66.667	0.00	0.00	0.00	3.67
901	905	3.353836	CCTGCGACCAAACCACCG	61.354	66.667	0.00	0.00	0.00	4.94
917	921	1.152963	CCGCCCCCGATTCTCAATT	60.153	57.895	0.00	0.00	36.29	2.32
931	935	4.589216	TCTCAATTGAAAAGCACAAGGG	57.411	40.909	9.88	0.00	0.00	3.95
966	970	2.271173	GGGCTAGGGTTTGGTCGG	59.729	66.667	0.00	0.00	0.00	4.79
1170	1174	1.149101	ACAAGGACCACATCACCCTT	58.851	50.000	0.00	0.00	39.42	3.95
1247	1251	2.622210	TCACCCCGGCCATGTATATTA	58.378	47.619	2.24	0.00	0.00	0.98
1256	1260	5.468746	CCGGCCATGTATATTATTATTCCCG	59.531	44.000	2.24	0.00	0.00	5.14
1266	1270	2.702592	ATTATTCCCGTCGCCTTTGA	57.297	45.000	0.00	0.00	0.00	2.69
1340	1365	5.333645	CGGGATGAGAATCTCAAATTAAGCG	60.334	44.000	17.59	0.00	44.04	4.68
1472	1500	7.661040	CAATGAACTAGAAATTGTGGGTTTCT	58.339	34.615	0.00	6.40	45.23	2.52
1478	1506	7.264947	ACTAGAAATTGTGGGTTTCTGTTTTG	58.735	34.615	10.45	1.04	43.62	2.44
1494	1573	5.761234	TCTGTTTTGCCGTGAGTTATAGTTT	59.239	36.000	0.00	0.00	0.00	2.66
1508	1587	5.648092	AGTTATAGTTTTCAGATGGTGGTGC	59.352	40.000	0.00	0.00	0.00	5.01
1518	1597	2.171448	AGATGGTGGTGCTAGATTGGTC	59.829	50.000	0.00	0.00	0.00	4.02
1603	1682	7.393515	GGGATTGCTTAGGAGAACTTTTCTTAA	59.606	37.037	0.00	0.00	40.87	1.85
1612	1691	7.661968	AGGAGAACTTTTCTTAATGGCTTTTC	58.338	34.615	0.00	0.00	40.87	2.29
1643	1722	2.895404	TGTTCGTTGGTAGGTTCTAGCT	59.105	45.455	0.00	0.00	0.00	3.32
1648	1727	3.097614	GTTGGTAGGTTCTAGCTCCTCA	58.902	50.000	8.46	1.13	35.51	3.86
1653	1732	4.162509	GGTAGGTTCTAGCTCCTCAACAAT	59.837	45.833	8.46	0.00	35.51	2.71
1758	2014	6.683974	ACAGCTGTAACATTGGTATGATTC	57.316	37.500	20.16	0.00	35.65	2.52
1771	2063	7.973048	TTGGTATGATTCAACTAGTACTCCT	57.027	36.000	0.00	0.00	0.00	3.69
1792	2084	8.414778	ACTCCTTCTGTTCCTAAATATAAGACG	58.585	37.037	0.00	0.00	0.00	4.18
1793	2085	8.302515	TCCTTCTGTTCCTAAATATAAGACGT	57.697	34.615	0.00	0.00	0.00	4.34
1795	2087	9.032420	CCTTCTGTTCCTAAATATAAGACGTTC	57.968	37.037	0.00	0.00	0.00	3.95
1799	2091	6.759827	TGTTCCTAAATATAAGACGTTCTGGC	59.240	38.462	0.00	0.00	0.00	4.85
1860	2180	4.158764	AGACGGTTTGTTTGGTCATGAAAA	59.841	37.500	0.00	0.00	31.93	2.29
1905	2225	3.429960	CGAGTGATGCATCTGAAGGAGAA	60.430	47.826	26.32	0.72	33.12	2.87
1911	2231	8.435187	AGTGATGCATCTGAAGGAGAATAATTA	58.565	33.333	26.32	0.00	33.12	1.40
1964	2288	7.374491	GCTCGAACTTGATAATTCATTTACAGC	59.626	37.037	0.00	0.00	0.00	4.40
1965	2289	8.262715	TCGAACTTGATAATTCATTTACAGCA	57.737	30.769	0.00	0.00	0.00	4.41
1966	2290	8.390354	TCGAACTTGATAATTCATTTACAGCAG	58.610	33.333	0.00	0.00	0.00	4.24
1967	2291	7.164826	CGAACTTGATAATTCATTTACAGCAGC	59.835	37.037	0.00	0.00	0.00	5.25
1978	2302	0.835971	TACAGCAGCACCTCCCTTGA	60.836	55.000	0.00	0.00	0.00	3.02
2021	2345	3.111098	CTGCTCTGTGTTTGCAAAGAAC	58.889	45.455	13.26	14.36	38.42	3.01
2073	2397	5.695816	TGTTGAAATTATGCTCTGTTTTGCC	59.304	36.000	0.00	0.00	0.00	4.52
2076	2400	6.523840	TGAAATTATGCTCTGTTTTGCCTTT	58.476	32.000	0.00	0.00	0.00	3.11
2077	2401	6.991531	TGAAATTATGCTCTGTTTTGCCTTTT	59.008	30.769	0.00	0.00	0.00	2.27
2113	2437	4.043750	CGAAGACAAAGCTGATTTTGCAA	58.956	39.130	0.00	0.00	40.80	4.08
2151	2480	5.300286	GCCTATTTCACTGCCACTAATCATT	59.700	40.000	0.00	0.00	0.00	2.57
2172	2501	0.963962	CTCCATTGCAGTGCAGGTTT	59.036	50.000	18.81	2.02	40.61	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
242	243	2.341101	CGGCCACGTCTCACCTAGT	61.341	63.158	2.24	0.00	34.81	2.57
267	268	2.685017	TCCTCCCGATGCACTGCT	60.685	61.111	1.98	0.00	0.00	4.24
511	512	2.094078	CCTGGTCACCGTTATCCGTAAA	60.094	50.000	0.00	0.00	33.66	2.01
561	562	6.239092	CCGTTAACAAATTTACAGAAACCCCT	60.239	38.462	6.39	0.00	0.00	4.79
591	592	1.983119	GCATGGATTGGGTCTCCGGA	61.983	60.000	2.93	2.93	35.41	5.14
632	633	6.672266	TGGTGACATATCTCTTCCTAATCC	57.328	41.667	0.00	0.00	33.40	3.01
647	648	9.033463	CATTAGGGCAATGTACAATGGTGACAT	62.033	40.741	12.73	5.43	45.23	3.06
648	649	7.800671	CATTAGGGCAATGTACAATGGTGACA	61.801	42.308	12.73	0.00	41.43	3.58
649	650	2.446435	AGGGCAATGTACAATGGTGAC	58.554	47.619	12.73	4.97	0.00	3.67
650	651	2.897271	AGGGCAATGTACAATGGTGA	57.103	45.000	12.73	0.00	0.00	4.02
651	652	4.935702	CATTAGGGCAATGTACAATGGTG	58.064	43.478	12.73	4.27	39.42	4.17
778	779	0.038251	TCCTGATCAGCACACGTCAC	60.038	55.000	17.76	0.00	0.00	3.67
787	788	2.279120	CTCGGCGTCCTGATCAGC	60.279	66.667	17.76	6.66	0.00	4.26
894	895	4.419921	GAATCGGGGGCGGTGGTT	62.420	66.667	0.00	0.00	0.00	3.67
901	905	1.762708	TTCAATTGAGAATCGGGGGC	58.237	50.000	8.41	0.00	38.61	5.80
907	911	5.636543	CCCTTGTGCTTTTCAATTGAGAATC	59.363	40.000	11.46	8.46	0.00	2.52
917	921	2.727544	GCGCCCTTGTGCTTTTCA	59.272	55.556	0.00	0.00	44.66	2.69
995	999	1.808133	GCACCACCTCGATCATCTTCC	60.808	57.143	0.00	0.00	0.00	3.46
1170	1174	1.712018	CGTGGATCTCGTAGTCGCCA	61.712	60.000	0.00	0.00	36.96	5.69
1247	1251	2.285977	GTCAAAGGCGACGGGAATAAT	58.714	47.619	0.00	0.00	0.00	1.28
1256	1260	2.159517	GGAATCATGTGTCAAAGGCGAC	60.160	50.000	0.00	0.00	36.40	5.19
1340	1365	3.807622	TGTTTGGCATAGCGCTAATAGAC	59.192	43.478	22.98	16.74	41.21	2.59
1472	1500	6.038382	TGAAAACTATAACTCACGGCAAAACA	59.962	34.615	0.00	0.00	0.00	2.83
1478	1506	5.006746	CCATCTGAAAACTATAACTCACGGC	59.993	44.000	0.00	0.00	0.00	5.68
1494	1573	3.370846	CCAATCTAGCACCACCATCTGAA	60.371	47.826	0.00	0.00	0.00	3.02
1508	1587	7.383572	CCTCATCAACTAAATCGACCAATCTAG	59.616	40.741	0.00	0.00	0.00	2.43
1518	1597	6.204882	GGGGATAAACCTCATCAACTAAATCG	59.795	42.308	0.00	0.00	39.39	3.34
1603	1682	5.532557	GAACAAGTAGCAAAGAAAAGCCAT	58.467	37.500	0.00	0.00	0.00	4.40
1612	1691	3.963383	ACCAACGAACAAGTAGCAAAG	57.037	42.857	0.00	0.00	0.00	2.77
1643	1722	3.323691	TCGAGTTCTCCAATTGTTGAGGA	59.676	43.478	4.43	0.00	0.00	3.71
1648	1727	6.824305	AATCAATCGAGTTCTCCAATTGTT	57.176	33.333	4.43	9.40	0.00	2.83
1716	1962	9.836864	ACAGCTGTAGATTACATAATCAATCAA	57.163	29.630	20.16	0.00	43.43	2.57
1758	2014	5.986501	AGGAACAGAAGGAGTACTAGTTG	57.013	43.478	0.00	0.00	0.00	3.16
1771	2063	9.582431	CAGAACGTCTTATATTTAGGAACAGAA	57.418	33.333	0.00	0.00	0.00	3.02
1787	2079	4.163458	TCCCAAATATAGCCAGAACGTCTT	59.837	41.667	0.00	0.00	0.00	3.01
1789	2081	4.067972	TCCCAAATATAGCCAGAACGTC	57.932	45.455	0.00	0.00	0.00	4.34
1790	2082	4.196971	GTTCCCAAATATAGCCAGAACGT	58.803	43.478	0.00	0.00	0.00	3.99
1791	2083	4.196193	TGTTCCCAAATATAGCCAGAACG	58.804	43.478	0.00	0.00	35.93	3.95
1792	2084	5.437060	TCTGTTCCCAAATATAGCCAGAAC	58.563	41.667	0.00	0.00	34.23	3.01
1793	2085	5.397899	CCTCTGTTCCCAAATATAGCCAGAA	60.398	44.000	0.00	0.00	0.00	3.02
1795	2087	4.141390	ACCTCTGTTCCCAAATATAGCCAG	60.141	45.833	0.00	0.00	0.00	4.85
1799	2091	8.707796	TCTACTACCTCTGTTCCCAAATATAG	57.292	38.462	0.00	0.00	0.00	1.31
1807	2127	6.436847	AGTTACTTTCTACTACCTCTGTTCCC	59.563	42.308	0.00	0.00	0.00	3.97
1860	2180	8.514330	TCGGTAAATAGGCAAATAAATTCAGT	57.486	30.769	0.00	0.00	0.00	3.41
1964	2288	1.067354	GCAAAATCAAGGGAGGTGCTG	60.067	52.381	0.00	0.00	0.00	4.41
1965	2289	1.203100	AGCAAAATCAAGGGAGGTGCT	60.203	47.619	0.00	0.00	35.01	4.40
1966	2290	1.067354	CAGCAAAATCAAGGGAGGTGC	60.067	52.381	0.00	0.00	0.00	5.01
1967	2291	2.517959	TCAGCAAAATCAAGGGAGGTG	58.482	47.619	0.00	0.00	0.00	4.00
1978	2302	3.028850	AGCAGTGCCATATCAGCAAAAT	58.971	40.909	12.58	0.00	43.02	1.82
2021	2345	9.294030	GTACTTGCATGGAAGATTTTAATTCTG	57.706	33.333	30.84	3.39	0.00	3.02
2073	2397	6.583912	TCTTCGTCAGACTAAACACAAAAG	57.416	37.500	0.00	0.00	0.00	2.27
2113	2437	9.590451	CAGTGAAATAGGCATGTAAATTCAATT	57.410	29.630	0.00	0.00	0.00	2.32
2151	2480	1.974875	CCTGCACTGCAATGGAGCA	60.975	57.895	11.54	3.80	43.35	4.26
2172	2501	1.675714	CGCAGGCAAAGATAGGTGACA	60.676	52.381	0.00	0.00	0.00	3.58
2183	2512	2.042686	AAGCTATCATCGCAGGCAAA	57.957	45.000	0.00	0.00	0.00	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.