AutoCloner

Multiple sequence alignment - TraesCS6A01G000400

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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	TraesCS6A01G000400	chr6A	100.000	4590	0	0	1	4590	287242	291831	0.000000e+00	8477.0
1	TraesCS6A01G000400	chr6A	82.812	256	27	15	493	745	571190460	571190701	3.600000e-51	213.0
2	TraesCS6A01G000400	chr6A	100.000	28	0	0	4195	4222	447622361	447622334	8.000000e-03	52.8
3	TraesCS6A01G000400	chr6B	98.470	4379	38	9	27	4389	3383876	3388241	0.000000e+00	7688.0
4	TraesCS6A01G000400	chr6B	96.040	202	8	0	4386	4587	3388379	3388580	3.420000e-86	329.0
5	TraesCS6A01G000400	chr6B	82.869	251	29	11	493	743	642223392	642223628	3.600000e-51	213.0
6	TraesCS6A01G000400	chr6B	81.250	256	31	14	493	745	642265974	642266215	1.690000e-44	191.0
7	TraesCS6A01G000400	chr6B	90.714	140	12	1	4386	4525	719526941	719526803	7.840000e-43	185.0
8	TraesCS6A01G000400	chr6B	90.714	140	12	1	4386	4525	719596301	719596163	7.840000e-43	185.0
9	TraesCS6A01G000400	chr6B	90.714	140	12	1	4386	4525	719601903	719601765	7.840000e-43	185.0
10	TraesCS6A01G000400	chr6B	80.753	239	27	16	493	727	642120301	642120524	7.900000e-38	169.0
11	TraesCS6A01G000400	chr6B	76.761	142	28	4	1524	1663	663794587	663794725	1.770000e-09	75.0
12	TraesCS6A01G000400	chr6B	92.593	54	1	2	3399	3452	687291357	687291307	1.770000e-09	75.0
13	TraesCS6A01G000400	chr6D	92.264	2314	105	23	1437	3729	805946	808206	0.000000e+00	3214.0
14	TraesCS6A01G000400	chr6D	87.579	1433	59	36	28	1422	804539	805890	0.000000e+00	1550.0
15	TraesCS6A01G000400	chr6D	87.901	405	26	6	3786	4167	808387	808791	5.410000e-124	455.0
16	TraesCS6A01G000400	chr6D	81.641	256	30	15	493	745	426859782	426860023	3.620000e-46	196.0
17	TraesCS6A01G000400	chr5B	89.468	978	73	18	2228	3193	402845776	402844817	0.000000e+00	1208.0
18	TraesCS6A01G000400	chr5B	89.143	175	19	0	188	362	516031102	516030928	7.730000e-53	219.0
19	TraesCS6A01G000400	chr5B	79.000	100	18	3	3904	4001	590069301	590069399	1.070000e-06	65.8
20	TraesCS6A01G000400	chr7A	87.106	349	34	10	27	367	8382706	8383051	7.200000e-103	385.0
21	TraesCS6A01G000400	chr7D	86.257	342	32	10	27	367	7455355	7455682	1.570000e-94	357.0
22	TraesCS6A01G000400	chr7D	76.650	591	100	21	33	617	632362950	632363508	4.490000e-75	292.0
23	TraesCS6A01G000400	chr7D	76.481	591	102	21	33	617	632354559	632355118	2.090000e-73	287.0
24	TraesCS6A01G000400	chr4A	81.425	463	53	18	27	462	732780352	732780808	9.450000e-92	348.0
25	TraesCS6A01G000400	chr4A	86.408	103	12	1	2407	2509	657199350	657199250	1.350000e-20	111.0
26	TraesCS6A01G000400	chr4A	80.208	96	16	3	1524	1619	592757106	592757198	8.240000e-08	69.4
27	TraesCS6A01G000400	chr4A	80.208	96	16	3	1524	1619	593045185	593045277	8.240000e-08	69.4
28	TraesCS6A01G000400	chr3D	90.341	176	17	0	190	365	594958024	594957849	9.930000e-57	231.0
29	TraesCS6A01G000400	chr3B	89.773	176	18	0	190	365	798408526	798408351	4.620000e-55	226.0
30	TraesCS6A01G000400	chr3B	78.541	233	28	14	551	767	43731524	43731750	2.880000e-27	134.0
31	TraesCS6A01G000400	chr3B	92.857	70	4	1	4518	4587	322689158	322689090	2.920000e-17	100.0
32	TraesCS6A01G000400	chr5D	89.714	175	18	0	188	362	426162550	426162376	1.660000e-54	224.0
33	TraesCS6A01G000400	chr5A	89.714	175	18	0	188	362	540364446	540364272	1.660000e-54	224.0
34	TraesCS6A01G000400	chr5A	89.381	113	11	1	27	138	568161701	568161589	1.720000e-29	141.0
35	TraesCS6A01G000400	chr5A	91.549	71	6	0	4517	4587	583775613	583775683	1.050000e-16	99.0
36	TraesCS6A01G000400	chr1B	91.489	141	9	3	4386	4525	4752313	4752175	1.690000e-44	191.0
37	TraesCS6A01G000400	chrUn	90.714	140	12	1	4386	4525	282274679	282274541	7.840000e-43	185.0
38	TraesCS6A01G000400	chrUn	90.714	140	12	1	4386	4525	282279144	282279006	7.840000e-43	185.0
39	TraesCS6A01G000400	chrUn	90.714	140	12	1	4386	4525	383461402	383461264	7.840000e-43	185.0
40	TraesCS6A01G000400	chrUn	90.714	140	12	1	4386	4525	454430599	454430737	7.840000e-43	185.0
41	TraesCS6A01G000400	chrUn	80.791	177	23	6	2407	2578	459903794	459903624	1.340000e-25	128.0
42	TraesCS6A01G000400	chrUn	80.226	177	24	6	2407	2578	460612493	460612663	6.240000e-24	122.0
43	TraesCS6A01G000400	chrUn	80.208	96	16	3	1524	1619	332731891	332731983	8.240000e-08	69.4
44	TraesCS6A01G000400	chr1A	80.385	260	23	17	493	748	557050306	557050071	6.110000e-39	172.0
45	TraesCS6A01G000400	chr1A	96.825	63	2	0	4525	4587	68998336	68998398	6.280000e-19	106.0
46	TraesCS6A01G000400	chr1A	96.875	32	1	0	3956	3987	433738900	433738931	2.000000e-03	54.7
47	TraesCS6A01G000400	chr1A	96.875	32	1	0	3956	3987	481218307	481218338	2.000000e-03	54.7
48	TraesCS6A01G000400	chr4B	98.413	63	1	0	4525	4587	536736909	536736971	1.350000e-20	111.0
49	TraesCS6A01G000400	chr4B	92.857	70	4	1	4518	4587	10004889	10004821	2.920000e-17	100.0
50	TraesCS6A01G000400	chr4B	100.000	29	0	0	3959	3987	451241136	451241108	2.000000e-03	54.7
51	TraesCS6A01G000400	chr4B	100.000	29	0	0	3959	3987	451260586	451260558	2.000000e-03	54.7
52	TraesCS6A01G000400	chr2A	95.385	65	3	0	4523	4587	74511911	74511847	2.260000e-18	104.0
53	TraesCS6A01G000400	chr2A	79.006	181	12	10	496	674	748817083	748817239	2.920000e-17	100.0
54	TraesCS6A01G000400	chr2A	93.617	47	3	0	1276	1322	770683237	770683191	2.290000e-08	71.3
55	TraesCS6A01G000400	chr7B	95.312	64	3	0	4524	4587	105800734	105800671	8.120000e-18	102.0
56	TraesCS6A01G000400	chr7B	95.312	64	3	0	4524	4587	251490984	251490921	8.120000e-18	102.0
57	TraesCS6A01G000400	chr1D	86.000	100	9	3	634	729	433416039	433415941	8.120000e-18	102.0
58	TraesCS6A01G000400	chr1D	81.395	86	11	4	3919	4002	83128754	83128836	1.070000e-06	65.8

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	TraesCS6A01G000400	chr6A	287242	291831	4589	False	8477.000000	8477	100.000	1	4590	1	chr6A.!!$F1	4589
1	TraesCS6A01G000400	chr6B	3383876	3388580	4704	False	4008.500000	7688	97.255	27	4587	2	chr6B.!!$F5	4560
2	TraesCS6A01G000400	chr6D	804539	808791	4252	False	1739.666667	3214	89.248	28	4167	3	chr6D.!!$F2	4139
3	TraesCS6A01G000400	chr5B	402844817	402845776	959	True	1208.000000	1208	89.468	2228	3193	1	chr5B.!!$R1	965
4	TraesCS6A01G000400	chr7D	632362950	632363508	558	False	292.000000	292	76.650	33	617	1	chr7D.!!$F3	584
5	TraesCS6A01G000400	chr7D	632354559	632355118	559	False	287.000000	287	76.481	33	617	1	chr7D.!!$F2	584

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
219	227	0.779997	ACCTGAACATCAAGGGGCTT	59.220	50.0	0.0	0.0	0.0	4.35	F
1148	1197	0.907486	TGGATCAAGCTCCTCACTGG	59.093	55.0	0.0	0.0	36.2	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1493	1583	8.738645	ACTTGAAACAAGACATAAAGAAGAGT	57.261	30.769	16.65	0.0	0.00	3.24	R
4394	4653	3.927548	ACGTAAACGCACCCCGGT	61.928	61.111	0.00	0.0	44.43	5.28	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
24	25	7.308782	CCCTGTTATGCTCTAGTTACTTTTG	57.691	40.000	0.00	0.00	0.00	2.44
25	26	6.183360	CCCTGTTATGCTCTAGTTACTTTTGC	60.183	42.308	0.00	0.00	0.00	3.68
113	119	5.585390	GCAAAGCATCTACATACTGCAATT	58.415	37.500	0.00	0.00	38.37	2.32
155	161	7.108194	TGTAAATGAATGCTTCTCTCTGACAT	58.892	34.615	0.00	0.00	0.00	3.06
219	227	0.779997	ACCTGAACATCAAGGGGCTT	59.220	50.000	0.00	0.00	0.00	4.35
220	228	1.147817	ACCTGAACATCAAGGGGCTTT	59.852	47.619	0.00	0.00	0.00	3.51
403	420	3.414700	CGCCGCGCTGAAAGAACT	61.415	61.111	5.56	0.00	34.07	3.01
408	425	1.057361	GCGCTGAAAGAACTACGCG	59.943	57.895	3.53	3.53	43.03	6.01
476	493	6.987992	TGTCGTAATGGGTTGTAATTATCCTC	59.012	38.462	0.00	0.00	0.00	3.71
608	626	1.614903	TCAAGTGGATGCTTTGCTTGG	59.385	47.619	0.00	0.00	37.65	3.61
699	730	6.071391	GGATGCTGGTTCTTTAAGATTGGAAA	60.071	38.462	0.00	0.00	0.00	3.13
700	731	6.084326	TGCTGGTTCTTTAAGATTGGAAAC	57.916	37.500	0.00	0.00	0.00	2.78
786	823	3.244526	TGTTGTGCCTGAGAGAGCAAATA	60.245	43.478	0.00	0.00	41.48	1.40
787	824	3.701205	TGTGCCTGAGAGAGCAAATAA	57.299	42.857	0.00	0.00	41.48	1.40
788	825	4.019792	TGTGCCTGAGAGAGCAAATAAA	57.980	40.909	0.00	0.00	41.48	1.40
789	826	4.592942	TGTGCCTGAGAGAGCAAATAAAT	58.407	39.130	0.00	0.00	41.48	1.40
790	827	5.012239	TGTGCCTGAGAGAGCAAATAAATT	58.988	37.500	0.00	0.00	41.48	1.82
791	828	5.106038	TGTGCCTGAGAGAGCAAATAAATTG	60.106	40.000	0.00	0.00	41.48	2.32
792	829	5.124457	GTGCCTGAGAGAGCAAATAAATTGA	59.876	40.000	0.00	0.00	41.85	2.57
793	830	5.711506	TGCCTGAGAGAGCAAATAAATTGAA	59.288	36.000	0.00	0.00	41.85	2.69
794	831	6.209192	TGCCTGAGAGAGCAAATAAATTGAAA	59.791	34.615	0.00	0.00	41.85	2.69
795	832	7.093640	TGCCTGAGAGAGCAAATAAATTGAAAT	60.094	33.333	0.00	0.00	41.85	2.17
971	1020	6.769512	TCAACCTGATAAGAAAAGCACTACT	58.230	36.000	0.00	0.00	0.00	2.57
984	1033	4.543590	AGCACTACTTGTAGCTTGTCAT	57.456	40.909	7.62	0.00	32.11	3.06
1148	1197	0.907486	TGGATCAAGCTCCTCACTGG	59.093	55.000	0.00	0.00	36.20	4.00
3367	3474	9.462174	CTCTGATCTTAGTTAGCTAAAGACATG	57.538	37.037	7.99	0.00	36.82	3.21
4304	4562	8.477419	TTGTGAACCCTTTTCTAATTTGAGAT	57.523	30.769	0.00	0.00	0.00	2.75
4390	4649	9.558648	TTTCATAATCTGATGTTTCATTTGACG	57.441	29.630	0.00	0.00	32.72	4.35
4391	4650	7.696755	TCATAATCTGATGTTTCATTTGACGG	58.303	34.615	0.00	0.00	0.00	4.79
4392	4651	5.964958	AATCTGATGTTTCATTTGACGGT	57.035	34.783	0.00	0.00	0.00	4.83
4393	4652	5.551760	ATCTGATGTTTCATTTGACGGTC	57.448	39.130	0.00	0.00	0.00	4.79
4394	4653	4.384940	TCTGATGTTTCATTTGACGGTCA	58.615	39.130	6.76	6.76	0.00	4.02
4447	4847	4.980434	CACTTGAAGTTTTGGCTGATTCTG	59.020	41.667	0.00	0.00	0.00	3.02
4464	4864	2.754254	GGCCCCGTTTCATGGACC	60.754	66.667	0.00	0.00	0.00	4.46
4519	4919	0.181824	ATGATTAACGAACCCCGGGG	59.818	55.000	39.18	39.18	43.93	5.73
4587	4987	1.818674	CCGGCTAGAGTTTGGCAATTT	59.181	47.619	0.00	0.00	0.00	1.82
4588	4988	2.415893	CCGGCTAGAGTTTGGCAATTTG	60.416	50.000	0.00	0.00	0.00	2.32
4589	4989	2.610433	GGCTAGAGTTTGGCAATTTGC	58.390	47.619	13.04	13.04	44.08	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.183360	GCAAAAGTAACTAGAGCATAACAGGG	60.183	42.308	0.00	0.00	0.00	4.45
1	2	6.595716	AGCAAAAGTAACTAGAGCATAACAGG	59.404	38.462	0.00	0.00	0.00	4.00
2	3	7.118390	ACAGCAAAAGTAACTAGAGCATAACAG	59.882	37.037	0.00	0.00	0.00	3.16
4	5	7.365840	ACAGCAAAAGTAACTAGAGCATAAC	57.634	36.000	0.00	0.00	0.00	1.89
6	7	7.386851	AGAACAGCAAAAGTAACTAGAGCATA	58.613	34.615	0.00	0.00	0.00	3.14
7	8	6.234177	AGAACAGCAAAAGTAACTAGAGCAT	58.766	36.000	0.00	0.00	0.00	3.79
8	9	5.611374	AGAACAGCAAAAGTAACTAGAGCA	58.389	37.500	0.00	0.00	0.00	4.26
9	10	6.366630	CAAGAACAGCAAAAGTAACTAGAGC	58.633	40.000	0.00	0.00	0.00	4.09
10	11	6.483640	ACCAAGAACAGCAAAAGTAACTAGAG	59.516	38.462	0.00	0.00	0.00	2.43
11	12	6.354130	ACCAAGAACAGCAAAAGTAACTAGA	58.646	36.000	0.00	0.00	0.00	2.43
12	13	6.619801	ACCAAGAACAGCAAAAGTAACTAG	57.380	37.500	0.00	0.00	0.00	2.57
13	14	7.399245	AAACCAAGAACAGCAAAAGTAACTA	57.601	32.000	0.00	0.00	0.00	2.24
14	15	5.914898	AACCAAGAACAGCAAAAGTAACT	57.085	34.783	0.00	0.00	0.00	2.24
15	16	6.588373	TCAAAACCAAGAACAGCAAAAGTAAC	59.412	34.615	0.00	0.00	0.00	2.50
16	17	6.692486	TCAAAACCAAGAACAGCAAAAGTAA	58.308	32.000	0.00	0.00	0.00	2.24
17	18	6.274157	TCAAAACCAAGAACAGCAAAAGTA	57.726	33.333	0.00	0.00	0.00	2.24
18	19	5.146010	TCAAAACCAAGAACAGCAAAAGT	57.854	34.783	0.00	0.00	0.00	2.66
19	20	6.313411	TGATTCAAAACCAAGAACAGCAAAAG	59.687	34.615	0.00	0.00	0.00	2.27
20	21	6.169094	TGATTCAAAACCAAGAACAGCAAAA	58.831	32.000	0.00	0.00	0.00	2.44
21	22	5.728471	TGATTCAAAACCAAGAACAGCAAA	58.272	33.333	0.00	0.00	0.00	3.68
22	23	5.336150	TGATTCAAAACCAAGAACAGCAA	57.664	34.783	0.00	0.00	0.00	3.91
23	24	4.998671	TGATTCAAAACCAAGAACAGCA	57.001	36.364	0.00	0.00	0.00	4.41
24	25	8.031277	AGATATTGATTCAAAACCAAGAACAGC	58.969	33.333	2.68	0.00	0.00	4.40
113	119	8.846943	TCATTTACAAGAACAGAGCTAATCAA	57.153	30.769	0.00	0.00	0.00	2.57
155	161	2.875296	AGGGCAACAAGAATAACAGCA	58.125	42.857	0.00	0.00	39.74	4.41
219	227	3.071023	CAGTCTGACAGGTTAGGTCCAAA	59.929	47.826	10.88	0.00	34.36	3.28
220	228	2.632996	CAGTCTGACAGGTTAGGTCCAA	59.367	50.000	10.88	0.00	34.36	3.53
403	420	3.557185	AGACATGACGAATACTACGCGTA	59.443	43.478	19.40	19.40	38.51	4.42
408	425	8.851960	TGAAATACAGACATGACGAATACTAC	57.148	34.615	0.00	0.00	0.00	2.73
476	493	1.064208	CGACACCACCTCATAGACTCG	59.936	57.143	0.00	0.00	0.00	4.18
608	626	7.856145	ACAATCAGAACAGGAAGATGATAAC	57.144	36.000	0.00	0.00	30.65	1.89
786	823	4.102996	AGAGGCCCACAACAATTTCAATTT	59.897	37.500	0.00	0.00	0.00	1.82
787	824	3.647590	AGAGGCCCACAACAATTTCAATT	59.352	39.130	0.00	0.00	0.00	2.32
788	825	3.007182	CAGAGGCCCACAACAATTTCAAT	59.993	43.478	0.00	0.00	0.00	2.57
789	826	2.364970	CAGAGGCCCACAACAATTTCAA	59.635	45.455	0.00	0.00	0.00	2.69
790	827	1.962807	CAGAGGCCCACAACAATTTCA	59.037	47.619	0.00	0.00	0.00	2.69
791	828	2.238521	TCAGAGGCCCACAACAATTTC	58.761	47.619	0.00	0.00	0.00	2.17
792	829	2.380064	TCAGAGGCCCACAACAATTT	57.620	45.000	0.00	0.00	0.00	1.82
793	830	2.610438	ATCAGAGGCCCACAACAATT	57.390	45.000	0.00	0.00	0.00	2.32
794	831	2.610438	AATCAGAGGCCCACAACAAT	57.390	45.000	0.00	0.00	0.00	2.71
795	832	2.158475	AGAAATCAGAGGCCCACAACAA	60.158	45.455	0.00	0.00	0.00	2.83
904	953	6.153340	CCAGGATTTTCTGCTATTTTGGAAGA	59.847	38.462	0.00	0.00	33.64	2.87
971	1020	3.769739	AGTGGTGATGACAAGCTACAA	57.230	42.857	0.00	0.00	0.00	2.41
984	1033	2.568956	AGAAGCTAGATGCAAGTGGTGA	59.431	45.455	0.00	0.00	45.94	4.02
1493	1583	8.738645	ACTTGAAACAAGACATAAAGAAGAGT	57.261	30.769	16.65	0.00	0.00	3.24
4394	4653	3.927548	ACGTAAACGCACCCCGGT	61.928	61.111	0.00	0.00	44.43	5.28
4447	4847	2.754254	GGTCCATGAAACGGGGCC	60.754	66.667	0.00	0.00	42.68	5.80
4464	4864	3.947834	GGACCCCAAATCAGTGAGTAATG	59.052	47.826	0.00	0.00	0.00	1.90
4519	4919	1.494824	GTTATATCCCCGACACGCAC	58.505	55.000	0.00	0.00	0.00	5.34
4541	4941	1.483415	ACATCCGGCGGTTTATACTGT	59.517	47.619	27.32	14.92	32.95	3.55
4543	4943	3.575256	TCATACATCCGGCGGTTTATACT	59.425	43.478	27.32	3.08	0.00	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.