AutoCloner

Multiple sequence alignment - TraesCS6D01G140400

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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	TraesCS6D01G140400	chr6D	100.000	1913	0	0	1	1913	110153215	110151303	0.000000e+00	3533.0
1	TraesCS6D01G140400	chr6D	100.000	329	0	0	2152	2480	110151064	110150736	2.110000e-170	608.0
2	TraesCS6D01G140400	chr6D	85.520	221	29	3	1683	1901	109787238	109787019	6.900000e-56	228.0
3	TraesCS6D01G140400	chr6D	94.393	107	6	0	2298	2404	109787284	109787178	5.490000e-37	165.0
4	TraesCS6D01G140400	chr6D	90.110	91	9	0	2152	2242	110151409	110151319	4.330000e-23	119.0
5	TraesCS6D01G140400	chr6D	83.582	134	8	4	1	134	109589958	109590077	2.020000e-21	113.0
6	TraesCS6D01G140400	chr6D	92.453	53	4	0	2152	2204	110151355	110151303	2.640000e-10	76.8
7	TraesCS6D01G140400	chr6D	92.683	41	2	1	2152	2192	109787058	109787019	9.580000e-05	58.4
8	TraesCS6D01G140400	chr6B	94.628	1936	77	17	1	1913	198913428	198911497	0.000000e+00	2974.0
9	TraesCS6D01G140400	chr6B	82.310	1108	118	39	845	1913	633415216	633416284	0.000000e+00	889.0
10	TraesCS6D01G140400	chr6B	90.164	183	16	2	1721	1901	198911072	198910890	1.150000e-58	237.0
11	TraesCS6D01G140400	chr6B	92.000	150	11	1	2253	2401	198911049	198910900	2.500000e-50	209.0
12	TraesCS6D01G140400	chr6B	78.912	147	18	4	2152	2298	198911033	198910900	1.220000e-13	87.9
13	TraesCS6D01G140400	chr6B	90.323	62	6	0	2152	2213	198911549	198911488	5.680000e-12	82.4
14	TraesCS6D01G140400	chr6B	95.122	41	2	0	2152	2192	198910930	198910890	5.730000e-07	65.8
15	TraesCS6D01G140400	chr5D	90.443	1015	84	12	785	1794	542031702	542032708	0.000000e+00	1325.0
16	TraesCS6D01G140400	chr5D	87.976	657	58	11	134	772	542030942	542031595	0.000000e+00	756.0
17	TraesCS6D01G140400	chr5D	86.275	204	14	7	1695	1893	542066955	542067149	2.500000e-50	209.0
18	TraesCS6D01G140400	chr5D	85.507	207	21	7	2278	2480	542032582	542032783	8.990000e-50	207.0
19	TraesCS6D01G140400	chr5D	85.500	200	19	4	1695	1893	542067008	542067198	1.500000e-47	200.0
20	TraesCS6D01G140400	chr4D	87.653	1142	95	21	809	1913	425097927	425096795	0.000000e+00	1286.0
21	TraesCS6D01G140400	chr4D	84.669	724	97	11	17	731	425098752	425098034	0.000000e+00	710.0
22	TraesCS6D01G140400	chr4D	80.738	244	31	11	1683	1913	425096820	425096580	2.530000e-40	176.0
23	TraesCS6D01G140400	chr2D	85.581	1075	108	27	843	1911	481542026	481543059	0.000000e+00	1083.0
24	TraesCS6D01G140400	chr2D	96.703	91	3	0	2390	2480	511723653	511723563	4.270000e-33	152.0
25	TraesCS6D01G140400	chr2D	95.604	91	2	2	2390	2480	458183790	458183878	7.150000e-31	145.0
26	TraesCS6D01G140400	chr2D	95.402	87	4	0	2394	2480	511809467	511809381	3.330000e-29	139.0
27	TraesCS6D01G140400	chr1D	85.357	1079	108	28	843	1913	10923037	10924073	0.000000e+00	1072.0
28	TraesCS6D01G140400	chr1D	82.749	684	86	23	17	693	10922148	10922806	4.600000e-162	580.0
29	TraesCS6D01G140400	chr1D	95.604	91	3	1	2391	2480	384820208	384820298	7.150000e-31	145.0
30	TraesCS6D01G140400	chr3D	90.075	796	73	4	843	1637	577391227	577390437	0.000000e+00	1027.0
31	TraesCS6D01G140400	chr3D	83.611	1080	113	32	843	1913	550435408	550436432	0.000000e+00	955.0
32	TraesCS6D01G140400	chr3D	82.969	687	98	15	17	693	550434500	550435177	9.810000e-169	603.0
33	TraesCS6D01G140400	chr3D	83.138	682	90	14	17	693	577392119	577391458	1.270000e-167	599.0
34	TraesCS6D01G140400	chr3D	96.629	89	1	2	2393	2480	153609922	153610009	1.990000e-31	147.0
35	TraesCS6D01G140400	chr3B	85.766	822	82	17	845	1637	684652684	684651869	0.000000e+00	837.0
36	TraesCS6D01G140400	chrUn	88.824	680	60	8	845	1520	36390656	36391323	0.000000e+00	821.0
37	TraesCS6D01G140400	chrUn	80.583	206	31	7	8	208	43398431	43398230	1.540000e-32	150.0
38	TraesCS6D01G140400	chr1B	83.503	788	109	14	5	777	447549357	447550138	0.000000e+00	715.0
39	TraesCS6D01G140400	chr1B	79.639	388	51	18	5	385	34257364	34257730	1.140000e-63	254.0
40	TraesCS6D01G140400	chr7B	80.994	684	99	20	17	693	516867908	516868567	4.730000e-142	514.0
41	TraesCS6D01G140400	chr7B	80.335	239	31	10	1687	1913	516870124	516870358	1.530000e-37	167.0
42	TraesCS6D01G140400	chr7D	83.189	577	77	16	17	582	600059438	600060005	6.120000e-141	510.0
43	TraesCS6D01G140400	chr7D	95.604	91	2	2	2391	2480	244849635	244849546	7.150000e-31	145.0
44	TraesCS6D01G140400	chr5B	85.500	200	22	4	1695	1893	113068852	113069045	4.180000e-48	202.0
45	TraesCS6D01G140400	chr5A	85.000	200	23	4	1695	1893	94730050	94729857	1.950000e-46	196.0
46	TraesCS6D01G140400	chr6A	91.919	99	7	1	2382	2480	70445021	70445118	1.200000e-28	137.0
47	TraesCS6D01G140400	chr4A	90.476	105	6	4	2379	2480	613468984	613469087	4.300000e-28	135.0

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	TraesCS6D01G140400	chr6D	110150736	110153215	2479	True	1084.200000	3533	95.640750	1	2480	4	chr6D.!!$R2	2479
1	TraesCS6D01G140400	chr6B	633415216	633416284	1068	False	889.000000	889	82.310000	845	1913	1	chr6B.!!$F1	1068
2	TraesCS6D01G140400	chr6B	198910890	198913428	2538	True	609.350000	2974	90.191500	1	2401	6	chr6B.!!$R1	2400
3	TraesCS6D01G140400	chr5D	542030942	542032783	1841	False	762.666667	1325	87.975333	134	2480	3	chr5D.!!$F1	2346
4	TraesCS6D01G140400	chr4D	425096580	425098752	2172	True	724.000000	1286	84.353333	17	1913	3	chr4D.!!$R1	1896
5	TraesCS6D01G140400	chr2D	481542026	481543059	1033	False	1083.000000	1083	85.581000	843	1911	1	chr2D.!!$F2	1068
6	TraesCS6D01G140400	chr1D	10922148	10924073	1925	False	826.000000	1072	84.053000	17	1913	2	chr1D.!!$F2	1896
7	TraesCS6D01G140400	chr3D	577390437	577392119	1682	True	813.000000	1027	86.606500	17	1637	2	chr3D.!!$R1	1620
8	TraesCS6D01G140400	chr3D	550434500	550436432	1932	False	779.000000	955	83.290000	17	1913	2	chr3D.!!$F2	1896
9	TraesCS6D01G140400	chr3B	684651869	684652684	815	True	837.000000	837	85.766000	845	1637	1	chr3B.!!$R1	792
10	TraesCS6D01G140400	chrUn	36390656	36391323	667	False	821.000000	821	88.824000	845	1520	1	chrUn.!!$F1	675
11	TraesCS6D01G140400	chr1B	447549357	447550138	781	False	715.000000	715	83.503000	5	777	1	chr1B.!!$F2	772
12	TraesCS6D01G140400	chr7B	516867908	516870358	2450	False	340.500000	514	80.664500	17	1913	2	chr7B.!!$F1	1896
13	TraesCS6D01G140400	chr7D	600059438	600060005	567	False	510.000000	510	83.189000	17	582	1	chr7D.!!$F1	565

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
32	33	0.606604	AGTTGTGACCCGCGACTAAT	59.393	50.000	8.23	0.0	36.90	1.73	F
484	522	1.417592	CACGTTGTGAGCATCGAGC	59.582	57.895	5.28	0.0	46.19	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1009	1274	0.612453	AACCTCTCGGTCACCTCCTC	60.612	60.0	0.0	0.0	44.73	3.71	R
2157	2518	0.463116	CCCAAAATAGGGGTCGTCGG	60.463	60.0	0.0	0.0	45.60	4.79	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
32	33	0.606604	AGTTGTGACCCGCGACTAAT	59.393	50.000	8.23	0.0	36.90	1.73
57	58	1.722034	AGCTGACATATCGACCCCAT	58.278	50.000	0.00	0.0	0.00	4.00
58	59	2.050144	AGCTGACATATCGACCCCATT	58.950	47.619	0.00	0.0	0.00	3.16
177	182	1.587054	CAACCGCTCTCTTCTCCGT	59.413	57.895	0.00	0.0	0.00	4.69
195	200	3.171828	TTTGTTCCCCTCTCGCGCA	62.172	57.895	8.75	0.0	0.00	6.09
273	310	3.909732	TGGTTTCTTGGTCTGATGGTTT	58.090	40.909	0.00	0.0	0.00	3.27
415	453	6.719370	ACTCATTTTCCTTATGTTTAGCCACA	59.281	34.615	0.00	0.0	0.00	4.17
484	522	1.417592	CACGTTGTGAGCATCGAGC	59.582	57.895	5.28	0.0	46.19	5.03
626	664	7.704472	TGCTTAGTTGTTTTAGTGATTTTGTGG	59.296	33.333	0.00	0.0	0.00	4.17
728	767	7.933577	TGCTCATAATTCTTGACATAAGTAGGG	59.066	37.037	0.00	0.0	0.00	3.53
1009	1274	5.359576	GCTAGGATCTGGACTATGTATGAGG	59.640	48.000	0.00	0.0	0.00	3.86
1075	1340	3.584848	AGAAGTCTGCAAGGTACTGGAAT	59.415	43.478	0.00	0.0	40.86	3.01
1117	1382	8.990163	AAATGACCTGAGGTTCTTTAAAGTTA	57.010	30.769	5.21	2.3	35.25	2.24
1403	1677	2.644798	AGAAAAGGCACCTGGAGTACAT	59.355	45.455	0.00	0.0	0.00	2.29
1557	1859	8.629158	ACATTTGTACTGAAATTTGTGCTTCTA	58.371	29.630	0.00	0.0	0.00	2.10
1697	2010	8.839310	ATGCTATTCATAGTGTTTAGATGGTC	57.161	34.615	0.00	0.0	32.59	4.02
1712	2025	1.364901	GGTCGGGTTGTTGTCGAGA	59.635	57.895	0.00	0.0	33.41	4.04
1715	2028	0.313043	TCGGGTTGTTGTCGAGAGTC	59.687	55.000	0.00	0.0	0.00	3.36
1720	2033	1.986378	GTTGTTGTCGAGAGTCCGATG	59.014	52.381	6.93	0.0	40.91	3.84
1728	2041	3.253677	GTCGAGAGTCCGATGACCATTAT	59.746	47.826	6.93	0.0	42.81	1.28
2174	2615	1.093496	GGCCGACGACCCCTATTTTG	61.093	60.000	0.00	0.0	0.00	2.44
2196	2637	3.464456	GGGGTAGGGTTTATATGGTTGGT	59.536	47.826	0.00	0.0	0.00	3.67
2199	2640	5.959594	GGGTAGGGTTTATATGGTTGGTTTT	59.040	40.000	0.00	0.0	0.00	2.43
2242	3168	6.971726	CCCTATTTTGGGGTAAGGTTTATC	57.028	41.667	0.00	0.0	43.45	1.75
2243	3169	5.836898	CCCTATTTTGGGGTAAGGTTTATCC	59.163	44.000	0.00	0.0	43.45	2.59
2246	3172	4.385478	TTTGGGGTAAGGTTTATCCGTT	57.615	40.909	0.00	0.0	41.99	4.44
2266	3234	5.279056	CCGTTTATATGGTTGGGTTGTTGTT	60.279	40.000	0.00	0.0	0.00	2.83
2276	3244	0.750249	GGTTGTTGTTGAGGGGTTGG	59.250	55.000	0.00	0.0	0.00	3.77
2304	3331	5.011840	CCACTATTTTAGGGTAGGCTAGGTC	59.988	48.000	0.00	0.0	0.00	3.85
2401	3481	3.715315	AGGACCACTATTTTAGGGTAGGC	59.285	47.826	0.00	0.0	32.03	3.93
2402	3482	3.715315	GGACCACTATTTTAGGGTAGGCT	59.285	47.826	0.00	0.0	32.03	4.58
2403	3483	4.903649	GGACCACTATTTTAGGGTAGGCTA	59.096	45.833	0.00	0.0	32.03	3.93
2413	3493	6.841781	TTTAGGGTAGGCTATGAAGGAAAT	57.158	37.500	0.00	0.0	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	3.531538	GGTCGATATGTCAGCTTTCCAA	58.468	45.455	0.00	0.00	0.00	3.53
57	58	2.181521	GCCACGTGGTTCCGACAAA	61.182	57.895	33.92	0.00	37.57	2.83
58	59	2.589442	GCCACGTGGTTCCGACAA	60.589	61.111	33.92	0.00	37.57	3.18
177	182	2.358247	GCGCGAGAGGGGAACAAA	60.358	61.111	12.10	0.00	45.27	2.83
273	310	0.602106	AGACGACGAGGACGAGTCAA	60.602	55.000	0.00	0.00	44.89	3.18
415	453	0.674581	CGTGCACTCCATGGTCACAT	60.675	55.000	16.19	0.00	37.99	3.21
560	598	7.822822	ACTTTAACACCTAATTGCACTACTAGG	59.177	37.037	7.66	7.66	37.52	3.02
565	603	7.932491	TGTACACTTTAACACCTAATTGCACTA	59.068	33.333	0.00	0.00	0.00	2.74
701	740	9.330063	CCTACTTATGTCAAGAATTATGAGCAA	57.670	33.333	0.00	0.00	0.00	3.91
1009	1274	0.612453	AACCTCTCGGTCACCTCCTC	60.612	60.000	0.00	0.00	44.73	3.71
1075	1340	8.213679	CAGGTCATTTTCCATCTTCCTCTTATA	58.786	37.037	0.00	0.00	0.00	0.98
1117	1382	3.640967	TCAGCCACCATTTTAGCAAAGTT	59.359	39.130	0.00	0.00	0.00	2.66
1403	1677	8.646004	CCTTCTCTTTGAATAGATCACCTATGA	58.354	37.037	0.00	0.00	38.08	2.15
1516	1817	8.216453	CAGTACAAATGTCTTGCAATTTTTAGC	58.784	33.333	0.00	0.00	0.00	3.09
1685	1998	3.142951	CAACAACCCGACCATCTAAACA	58.857	45.455	0.00	0.00	0.00	2.83
1697	2010	0.666577	GGACTCTCGACAACAACCCG	60.667	60.000	0.00	0.00	0.00	5.28
1728	2041	1.374572	CCAACCTACCCTACCCCAAA	58.625	55.000	0.00	0.00	0.00	3.28
2154	2515	2.261430	AAAATAGGGGTCGTCGGCCC	62.261	60.000	27.40	27.40	45.35	5.80
2155	2516	1.093496	CAAAATAGGGGTCGTCGGCC	61.093	60.000	7.54	7.54	0.00	6.13
2156	2517	1.093496	CCAAAATAGGGGTCGTCGGC	61.093	60.000	0.00	0.00	0.00	5.54
2157	2518	0.463116	CCCAAAATAGGGGTCGTCGG	60.463	60.000	0.00	0.00	45.60	4.79
2158	2519	3.074594	CCCAAAATAGGGGTCGTCG	57.925	57.895	0.00	0.00	45.60	5.12
2166	2607	6.951778	CCATATAAACCCTACCCCAAAATAGG	59.048	42.308	0.00	0.00	38.18	2.57
2174	2615	3.464456	ACCAACCATATAAACCCTACCCC	59.536	47.826	0.00	0.00	0.00	4.95
2234	3160	6.066032	CCCAACCATATAAACGGATAAACCT	58.934	40.000	0.00	0.00	36.31	3.50
2239	3165	6.003859	ACAACCCAACCATATAAACGGATA	57.996	37.500	0.00	0.00	0.00	2.59
2240	3166	4.862371	ACAACCCAACCATATAAACGGAT	58.138	39.130	0.00	0.00	0.00	4.18
2241	3167	4.304048	ACAACCCAACCATATAAACGGA	57.696	40.909	0.00	0.00	0.00	4.69
2242	3168	4.218852	ACAACAACCCAACCATATAAACGG	59.781	41.667	0.00	0.00	0.00	4.44
2243	3169	5.379732	ACAACAACCCAACCATATAAACG	57.620	39.130	0.00	0.00	0.00	3.60
2246	3172	5.478679	CCTCAACAACAACCCAACCATATAA	59.521	40.000	0.00	0.00	0.00	0.98
2276	3244	4.163649	AGCCTACCCTAAAATAGTGGTCAC	59.836	45.833	0.00	0.00	33.38	3.67
2304	3331	1.941999	GACCCCTCGACAACTACCCG	61.942	65.000	0.00	0.00	0.00	5.28
2332	3359	6.858306	ACCATATAGACCCTACCCCAAAATAA	59.142	38.462	0.00	0.00	0.00	1.40
2385	3412	7.080353	TCCTTCATAGCCTACCCTAAAATAGT	58.920	38.462	0.00	0.00	0.00	2.12
2393	3473	5.280727	GCATATTTCCTTCATAGCCTACCCT	60.281	44.000	0.00	0.00	0.00	4.34
2401	3481	6.648192	CCTCTAGGGCATATTTCCTTCATAG	58.352	44.000	0.00	0.00	34.75	2.23
2402	3482	6.627087	CCTCTAGGGCATATTTCCTTCATA	57.373	41.667	0.00	0.00	34.75	2.15
2403	3483	5.511386	CCTCTAGGGCATATTTCCTTCAT	57.489	43.478	0.00	0.00	34.75	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.