AutoCloner

Multiple sequence alignment - TraesCS6A01G201200

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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	TraesCS6A01G201200	chr6A	100.000	2351	0	0	1	2351	328875809	328878159	0.000000e+00	4342
1	TraesCS6A01G201200	chr6A	95.793	2258	87	6	100	2351	204306953	204304698	0.000000e+00	3637
2	TraesCS6A01G201200	chr6A	95.625	2240	95	3	113	2351	518075644	518073407	0.000000e+00	3591
3	TraesCS6A01G201200	chr6A	95.501	2245	100	1	108	2351	136164332	136162088	0.000000e+00	3585
4	TraesCS6A01G201200	chr6A	95.189	2245	98	5	108	2351	213994237	213992002	0.000000e+00	3539
5	TraesCS6A01G201200	chr6A	95.970	1985	75	5	369	2351	473515388	473517369	0.000000e+00	3217
6	TraesCS6A01G201200	chr5A	96.390	2244	77	4	110	2351	268344297	268346538	0.000000e+00	3692
7	TraesCS6A01G201200	chr5A	96.154	2236	79	5	117	2351	109667608	109669837	0.000000e+00	3646
8	TraesCS6A01G201200	chr5A	88.268	179	9	5	1	168	300479419	300479596	1.100000e-48	204
9	TraesCS6A01G201200	chr2A	95.428	2253	99	4	102	2351	616456368	616454117	0.000000e+00	3587
10	TraesCS6A01G201200	chr2A	90.000	190	14	3	1	188	668750882	668750696	8.400000e-60	241
11	TraesCS6A01G201200	chr3A	94.327	2274	102	7	100	2351	134617316	134619584	0.000000e+00	3459
12	TraesCS6A01G201200	chr1A	95.963	1833	71	3	520	2351	465251795	465253625	0.000000e+00	2972
13	TraesCS6A01G201200	chr1A	88.820	161	15	3	4	164	533542365	533542208	6.630000e-46	195
14	TraesCS6A01G201200	chr6B	88.889	207	19	4	1	205	443111764	443111560	3.880000e-63	252
15	TraesCS6A01G201200	chr7A	91.351	185	11	4	1	185	619739060	619738881	5.020000e-62	248
16	TraesCS6A01G201200	chr7A	89.119	193	15	4	1	188	539160250	539160441	3.910000e-58	235
17	TraesCS6A01G201200	chr5D	87.963	216	18	5	1	210	31615630	31615843	5.020000e-62	248
18	TraesCS6A01G201200	chr5B	91.111	180	13	3	3	181	341863838	341864015	8.400000e-60	241
19	TraesCS6A01G201200	chr4B	87.440	207	20	6	4	210	232973374	232973174	1.400000e-57	233

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	TraesCS6A01G201200	chr6A	328875809	328878159	2350	False	4342	4342	100.000	1	2351	1	chr6A.!!$F1	2350
1	TraesCS6A01G201200	chr6A	204304698	204306953	2255	True	3637	3637	95.793	100	2351	1	chr6A.!!$R2	2251
2	TraesCS6A01G201200	chr6A	518073407	518075644	2237	True	3591	3591	95.625	113	2351	1	chr6A.!!$R4	2238
3	TraesCS6A01G201200	chr6A	136162088	136164332	2244	True	3585	3585	95.501	108	2351	1	chr6A.!!$R1	2243
4	TraesCS6A01G201200	chr6A	213992002	213994237	2235	True	3539	3539	95.189	108	2351	1	chr6A.!!$R3	2243
5	TraesCS6A01G201200	chr6A	473515388	473517369	1981	False	3217	3217	95.970	369	2351	1	chr6A.!!$F2	1982
6	TraesCS6A01G201200	chr5A	268344297	268346538	2241	False	3692	3692	96.390	110	2351	1	chr5A.!!$F2	2241
7	TraesCS6A01G201200	chr5A	109667608	109669837	2229	False	3646	3646	96.154	117	2351	1	chr5A.!!$F1	2234
8	TraesCS6A01G201200	chr2A	616454117	616456368	2251	True	3587	3587	95.428	102	2351	1	chr2A.!!$R1	2249
9	TraesCS6A01G201200	chr3A	134617316	134619584	2268	False	3459	3459	94.327	100	2351	1	chr3A.!!$F1	2251
10	TraesCS6A01G201200	chr1A	465251795	465253625	1830	False	2972	2972	95.963	520	2351	1	chr1A.!!$F1	1831

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
731	764	0.179145	CGAACTTCCGTCTACGCCAT	60.179	55.0	0.0	0.0	38.18	4.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1634	1681	0.813184	ATCCAGCCGCAATTCTTGTG	59.187	50.0	0.0	0.0	40.74	3.33	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	7.938563	ACGTATACTAGTACTGCTACTGTAC	57.061	40.000	4.31	6.65	38.48	2.90
25	26	7.721402	ACGTATACTAGTACTGCTACTGTACT	58.279	38.462	17.62	17.62	45.91	2.73
26	27	8.851145	ACGTATACTAGTACTGCTACTGTACTA	58.149	37.037	17.88	17.88	43.65	1.82
27	28	9.123709	CGTATACTAGTACTGCTACTGTACTAC	57.876	40.741	16.05	10.44	43.65	2.73
31	32	8.940768	ACTAGTACTGCTACTGTACTACTTAC	57.059	38.462	16.05	0.00	43.65	2.34
32	33	8.757877	ACTAGTACTGCTACTGTACTACTTACT	58.242	37.037	16.05	1.58	43.65	2.24
35	36	8.976353	AGTACTGCTACTGTACTACTTACTAGA	58.024	37.037	13.54	0.00	43.65	2.43
36	37	9.762933	GTACTGCTACTGTACTACTTACTAGAT	57.237	37.037	0.00	0.00	36.38	1.98
37	38	8.665643	ACTGCTACTGTACTACTTACTAGATG	57.334	38.462	0.00	0.00	0.00	2.90
38	39	8.266473	ACTGCTACTGTACTACTTACTAGATGT	58.734	37.037	0.00	0.00	0.00	3.06
39	40	9.761504	CTGCTACTGTACTACTTACTAGATGTA	57.238	37.037	0.00	0.00	0.00	2.29
82	83	7.586714	ACATAGGTTTAACTAACAAGTACGC	57.413	36.000	0.00	0.00	38.55	4.42
83	84	7.153985	ACATAGGTTTAACTAACAAGTACGCA	58.846	34.615	0.00	0.00	38.55	5.24
84	85	5.912360	AGGTTTAACTAACAAGTACGCAC	57.088	39.130	0.00	0.00	38.55	5.34
85	86	5.604565	AGGTTTAACTAACAAGTACGCACT	58.395	37.500	0.00	0.00	38.55	4.40
86	87	6.051074	AGGTTTAACTAACAAGTACGCACTT	58.949	36.000	0.00	0.00	46.15	3.16
95	96	3.396260	AAGTACGCACTTGAAGCCTAA	57.604	42.857	0.00	0.00	43.50	2.69
96	97	3.611766	AGTACGCACTTGAAGCCTAAT	57.388	42.857	0.00	0.00	0.00	1.73
97	98	3.939066	AGTACGCACTTGAAGCCTAATT	58.061	40.909	0.00	0.00	0.00	1.40
98	99	3.684788	AGTACGCACTTGAAGCCTAATTG	59.315	43.478	0.00	0.00	0.00	2.32
168	169	9.812347	ATTAGAATAACTATTTGGATCATGGCA	57.188	29.630	0.00	0.00	0.00	4.92
264	267	2.824880	CCCACCCACTTCCCACGAA	61.825	63.158	0.00	0.00	0.00	3.85
553	561	1.220206	CGGATCCAGCTGCAACTCT	59.780	57.895	13.41	0.00	0.00	3.24
565	573	1.893808	CAACTCTGCCACACGCCTT	60.894	57.895	0.00	0.00	36.24	4.35
577	585	4.473520	CGCCTTGGATCCGGCTGT	62.474	66.667	23.47	0.00	44.11	4.40
731	764	0.179145	CGAACTTCCGTCTACGCCAT	60.179	55.000	0.00	0.00	38.18	4.40
891	924	1.153647	CAGCCAATCGGACGCTACA	60.154	57.895	0.00	0.00	0.00	2.74
1031	1064	1.899437	GATCTGCGACCACCTTGGGA	61.899	60.000	0.00	0.00	43.37	4.37
1033	1066	1.002134	CTGCGACCACCTTGGGATT	60.002	57.895	0.00	0.00	43.37	3.01
1152	1185	2.024273	TCATCCCCTTCTTCTAGGTCGT	60.024	50.000	0.00	0.00	33.17	4.34
1159	1192	3.695060	CCTTCTTCTAGGTCGTGAAGCTA	59.305	47.826	0.00	0.00	39.41	3.32
1239	1272	2.278857	CTCGGCAAGATCGACCCG	60.279	66.667	12.74	12.74	41.97	5.28
1262	1295	3.257561	CATCAAGCTCGCCGACGG	61.258	66.667	10.29	10.29	40.63	4.79
1357	1402	2.667470	TCAAGGGGAAGTAGATCGAGG	58.333	52.381	0.00	0.00	0.00	4.63
1513	1560	3.960571	AGCTGCCTGTATGTGAGAAAAT	58.039	40.909	0.00	0.00	0.00	1.82
1520	1567	5.528690	GCCTGTATGTGAGAAAATCATGCTA	59.471	40.000	0.00	0.00	40.92	3.49
1634	1681	8.627487	TGTATTTTGACATTTCACAACAACTC	57.373	30.769	0.00	0.00	0.00	3.01
1703	1750	4.025858	AGTGCATCACCGGCAGCT	62.026	61.111	0.00	0.00	42.85	4.24
1801	1848	2.665537	CAGCAGAGTTCTTAGCGTCTTG	59.334	50.000	0.00	0.00	0.00	3.02
1858	1906	3.121929	AGGAATAGTCTCCTTCTGGCA	57.878	47.619	0.00	0.00	43.76	4.92
2112	2162	3.656559	CTGACCAAGCAATTCAAAAGGG	58.343	45.455	0.00	0.00	0.00	3.95
2130	2180	1.362355	GGCAGGTGGTTTCGTTTGG	59.638	57.895	0.00	0.00	0.00	3.28
2200	2250	0.039180	TCCTAACTCGAGGGAGCACA	59.961	55.000	18.41	0.00	44.48	4.57
2271	2322	4.342378	TGAGGAATGAGAGGTACAGTATGC	59.658	45.833	0.00	0.00	42.53	3.14

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.938563	GTACAGTAGCAGTACTAGTATACGT	57.061	40.000	5.75	9.11	37.40	3.57
10	11	9.762933	ATCTAGTAAGTAGTACAGTAGCAGTAC	57.237	37.037	2.52	0.00	41.59	2.73
11	12	9.761504	CATCTAGTAAGTAGTACAGTAGCAGTA	57.238	37.037	2.52	0.00	34.88	2.74
12	13	8.266473	ACATCTAGTAAGTAGTACAGTAGCAGT	58.734	37.037	2.52	0.13	34.88	4.40
13	14	8.665643	ACATCTAGTAAGTAGTACAGTAGCAG	57.334	38.462	2.52	0.00	34.88	4.24
56	57	9.305925	GCGTACTTGTTAGTTAAACCTATGTAT	57.694	33.333	0.00	0.00	37.27	2.29
57	58	8.303156	TGCGTACTTGTTAGTTAAACCTATGTA	58.697	33.333	0.00	0.00	37.27	2.29
58	59	7.116805	GTGCGTACTTGTTAGTTAAACCTATGT	59.883	37.037	0.00	0.00	37.27	2.29
59	60	7.330208	AGTGCGTACTTGTTAGTTAAACCTATG	59.670	37.037	0.00	0.00	37.27	2.23
60	61	7.381323	AGTGCGTACTTGTTAGTTAAACCTAT	58.619	34.615	0.00	0.00	37.27	2.57
61	62	6.748132	AGTGCGTACTTGTTAGTTAAACCTA	58.252	36.000	0.00	0.00	37.27	3.08
62	63	5.604565	AGTGCGTACTTGTTAGTTAAACCT	58.395	37.500	0.00	0.00	37.27	3.50
63	64	5.912360	AGTGCGTACTTGTTAGTTAAACC	57.088	39.130	0.00	0.00	37.27	3.27
76	77	3.611766	ATTAGGCTTCAAGTGCGTACT	57.388	42.857	0.00	0.00	39.32	2.73
77	78	3.682858	TCAATTAGGCTTCAAGTGCGTAC	59.317	43.478	0.00	0.00	31.75	3.67
78	79	3.932822	TCAATTAGGCTTCAAGTGCGTA	58.067	40.909	0.00	0.00	0.00	4.42
79	80	2.778299	TCAATTAGGCTTCAAGTGCGT	58.222	42.857	0.00	0.00	0.00	5.24
80	81	5.679734	ATATCAATTAGGCTTCAAGTGCG	57.320	39.130	0.00	0.00	0.00	5.34
264	267	0.563672	GGAGAGGGTAGTGGAGGGAT	59.436	60.000	0.00	0.00	0.00	3.85
399	405	1.444672	CTGGATCAGCTCATCGGCA	59.555	57.895	0.00	0.00	34.17	5.69
410	416	3.610619	CTGGCGTGGTGCTGGATCA	62.611	63.158	0.00	0.00	45.43	2.92
553	561	2.359850	GATCCAAGGCGTGTGGCA	60.360	61.111	0.00	0.00	46.16	4.92
583	591	3.399181	GATCCTGCGGTGGGGACA	61.399	66.667	0.00	0.00	34.16	4.02
585	594	4.731853	TGGATCCTGCGGTGGGGA	62.732	66.667	14.23	0.00	35.96	4.81
721	754	0.739561	AAGGTCGAGATGGCGTAGAC	59.260	55.000	0.00	2.09	0.00	2.59
731	764	1.812113	AAGGGGAGGGAAGGTCGAGA	61.812	60.000	0.00	0.00	0.00	4.04
878	911	0.241749	TGTCGTTGTAGCGTCCGATT	59.758	50.000	0.00	0.00	0.00	3.34
891	924	1.667830	CAGTCGGCCACATGTCGTT	60.668	57.895	2.24	0.00	0.00	3.85
1031	1064	1.201429	AGCCCCGTCTTGACTCCAAT	61.201	55.000	0.00	0.00	0.00	3.16
1033	1066	2.203788	AGCCCCGTCTTGACTCCA	60.204	61.111	0.00	0.00	0.00	3.86
1152	1185	2.742053	GTCGCATTCCTTGTTAGCTTCA	59.258	45.455	0.00	0.00	0.00	3.02
1159	1192	0.534203	ACGGTGTCGCATTCCTTGTT	60.534	50.000	0.00	0.00	40.63	2.83
1239	1272	2.033662	GTCGGCGAGCTTGATGAAATAC	60.034	50.000	11.20	0.00	0.00	1.89
1262	1295	1.607509	CCTCGATCCAGATGACCATGC	60.608	57.143	0.00	0.00	0.00	4.06
1336	1381	3.031736	CCTCGATCTACTTCCCCTTGAA	58.968	50.000	0.00	0.00	0.00	2.69
1357	1402	3.404224	AAAAAGGTTCTCTCCCTCGAC	57.596	47.619	0.00	0.00	0.00	4.20
1388	1435	1.153745	CTCACCGCCTGCTCAGTAC	60.154	63.158	0.00	0.00	0.00	2.73
1634	1681	0.813184	ATCCAGCCGCAATTCTTGTG	59.187	50.000	0.00	0.00	40.74	3.33
1777	1824	1.819288	ACGCTAAGAACTCTGCTGCTA	59.181	47.619	0.00	0.00	0.00	3.49
1801	1848	5.993748	TTTCACATGGGGAAATTAGGAAC	57.006	39.130	9.85	0.00	29.78	3.62
1858	1906	2.911143	GGGATCACCGATGGCTGT	59.089	61.111	0.00	0.00	36.97	4.40
2000	2048	1.739562	GTCTGCAGGAGAAGCACGG	60.740	63.158	15.13	0.00	37.02	4.94
2067	2115	3.132289	AGGATAACACAACGGACATCGAT	59.868	43.478	0.00	0.00	42.43	3.59
2112	2162	1.362355	CCAAACGAAACCACCTGCC	59.638	57.895	0.00	0.00	0.00	4.85
2200	2250	7.902920	ATAAGAGCACATATTTGGATGGTTT	57.097	32.000	0.00	0.00	0.00	3.27
2301	2358	6.172630	AGTTTCAATTGTTTCCTGCTTGTTT	58.827	32.000	5.13	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.