AutoCloner

Multiple sequence alignment - TraesCS7D01G135800

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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	TraesCS7D01G135800	chr7D	100.000	3210	0	0	1	3210	87219529	87222738	0.000000e+00	5928.0
1	TraesCS7D01G135800	chr7D	95.328	899	36	5	947	1842	87206445	87207340	0.000000e+00	1423.0
2	TraesCS7D01G135800	chr7D	100.000	457	0	0	3645	4101	87223173	87223629	0.000000e+00	845.0
3	TraesCS7D01G135800	chr7D	92.056	428	32	2	1416	1842	86919030	86919456	5.870000e-168	601.0
4	TraesCS7D01G135800	chr7D	91.355	428	34	3	1416	1842	86755540	86755965	2.120000e-162	582.0
5	TraesCS7D01G135800	chr7D	88.981	481	33	9	1371	1842	86292328	86292797	9.880000e-161	577.0
6	TraesCS7D01G135800	chr7D	90.789	380	21	8	789	1162	86754993	86755364	2.850000e-136	496.0
7	TraesCS7D01G135800	chr7D	90.000	380	25	7	789	1162	86918482	86918854	2.870000e-131	479.0
8	TraesCS7D01G135800	chr7D	85.613	424	44	6	1	409	91778983	91779404	2.930000e-116	429.0
9	TraesCS7D01G135800	chr7D	85.142	424	44	6	1	409	91748651	91749070	2.280000e-112	416.0
10	TraesCS7D01G135800	chr7D	96.316	190	7	0	1203	1392	86918849	86919038	3.080000e-81	313.0
11	TraesCS7D01G135800	chr7D	86.809	235	28	3	2091	2325	86292911	86293142	4.070000e-65	259.0
12	TraesCS7D01G135800	chr7D	91.803	183	14	1	2091	2272	87207453	87207635	1.890000e-63	254.0
13	TraesCS7D01G135800	chr7D	84.082	245	33	5	485	727	86753556	86753796	8.870000e-57	231.0
14	TraesCS7D01G135800	chr7D	100.000	28	0	0	924	951	87206170	87206197	7.000000e-03	52.8
15	TraesCS7D01G135800	chr7A	96.007	1177	36	7	762	1931	88500082	88501254	0.000000e+00	1903.0
16	TraesCS7D01G135800	chr7A	95.688	1090	33	11	762	1842	88435713	88436797	0.000000e+00	1740.0
17	TraesCS7D01G135800	chr7A	96.169	1018	30	5	2200	3209	88501276	88502292	0.000000e+00	1655.0
18	TraesCS7D01G135800	chr7A	92.779	914	58	7	933	1842	88315480	88316389	0.000000e+00	1315.0
19	TraesCS7D01G135800	chr7A	88.622	791	69	6	1	778	88188139	88188921	0.000000e+00	942.0
20	TraesCS7D01G135800	chr7A	82.677	1143	99	50	731	1842	87451043	87452117	0.000000e+00	922.0
21	TraesCS7D01G135800	chr7A	87.990	791	73	6	1	778	88144209	88144990	0.000000e+00	915.0
22	TraesCS7D01G135800	chr7A	93.729	606	31	3	189	790	88435110	88435712	0.000000e+00	902.0
23	TraesCS7D01G135800	chr7A	93.698	603	34	2	189	790	88499482	88500081	0.000000e+00	900.0
24	TraesCS7D01G135800	chr7A	89.327	609	34	14	789	1392	88008334	88008916	0.000000e+00	736.0
25	TraesCS7D01G135800	chr7A	94.588	425	22	1	3663	4086	88502294	88502718	0.000000e+00	656.0
26	TraesCS7D01G135800	chr7A	88.462	520	29	11	878	1392	88172469	88172962	2.110000e-167	599.0
27	TraesCS7D01G135800	chr7A	89.027	401	32	3	1	389	88035307	88035707	1.710000e-133	486.0
28	TraesCS7D01G135800	chr7A	88.342	386	37	4	393	778	88047215	88047592	1.340000e-124	457.0
29	TraesCS7D01G135800	chr7A	85.804	317	40	3	412	727	88119764	88120076	8.500000e-87	331.0
30	TraesCS7D01G135800	chr7A	89.524	210	10	1	1	198	88429757	88429966	5.260000e-64	255.0
31	TraesCS7D01G135800	chr7A	89.048	210	11	1	1	198	88494102	88494311	2.450000e-62	250.0
32	TraesCS7D01G135800	chr7A	90.164	183	17	1	2091	2272	88316502	88316684	1.910000e-58	237.0
33	TraesCS7D01G135800	chr7A	90.164	183	15	3	2091	2272	88436910	88437090	6.850000e-58	235.0
34	TraesCS7D01G135800	chr7A	84.375	160	19	5	789	947	88121353	88121507	7.100000e-33	152.0
35	TraesCS7D01G135800	chr7B	96.338	1147	38	4	2065	3209	35638327	35639471	0.000000e+00	1882.0
36	TraesCS7D01G135800	chr7B	92.736	1239	56	10	721	1931	35637095	35638327	0.000000e+00	1759.0
37	TraesCS7D01G135800	chr7B	85.730	904	61	22	947	1842	35307638	35308481	0.000000e+00	893.0
38	TraesCS7D01G135800	chr7B	90.539	687	43	11	721	1395	35507037	35507713	0.000000e+00	889.0
39	TraesCS7D01G135800	chr7B	88.529	741	63	6	1	727	35636338	35637070	0.000000e+00	878.0
40	TraesCS7D01G135800	chr7B	96.073	331	13	0	3663	3993	35639473	35639803	1.300000e-149	540.0
41	TraesCS7D01G135800	chr7B	89.019	428	43	4	1416	1842	35507702	35508126	1.010000e-145	527.0
42	TraesCS7D01G135800	chr7B	88.050	318	34	3	412	728	35506699	35507013	1.390000e-99	374.0
43	TraesCS7D01G135800	chr7B	95.556	225	9	1	3862	4086	35639802	35640025	3.900000e-95	359.0
44	TraesCS7D01G135800	chr7B	89.677	155	12	2	809	963	35301965	35302115	1.160000e-45	195.0
45	TraesCS7D01G135800	chr1D	86.588	425	45	3	1	413	439108547	439108971	3.740000e-125	459.0
46	TraesCS7D01G135800	chr1D	86.260	393	41	2	2	381	293617395	293617003	8.200000e-112	414.0
47	TraesCS7D01G135800	chr3D	86.667	420	43	4	1	408	123618627	123619045	1.740000e-123	453.0
48	TraesCS7D01G135800	chr2B	84.186	430	39	9	1	410	741122198	741121778	1.380000e-104	390.0
49	TraesCS7D01G135800	chr1B	84.635	384	57	2	11	393	532405962	532406344	8.320000e-102	381.0
50	TraesCS7D01G135800	chr2D	83.092	414	57	10	1	408	645994568	645994974	8.380000e-97	364.0
51	TraesCS7D01G135800	chr2D	98.519	135	2	0	1931	2065	33935356	33935490	5.300000e-59	239.0
52	TraesCS7D01G135800	chr2D	98.519	135	2	0	1931	2065	630271832	630271966	5.300000e-59	239.0
53	TraesCS7D01G135800	chr4A	99.259	135	1	0	1931	2065	310763952	310764086	1.140000e-60	244.0
54	TraesCS7D01G135800	chrUn	98.519	135	2	0	1931	2065	371049993	371050127	5.300000e-59	239.0
55	TraesCS7D01G135800	chr5B	98.519	135	2	0	1931	2065	429038227	429038361	5.300000e-59	239.0
56	TraesCS7D01G135800	chr5B	98.519	135	2	0	1931	2065	432878267	432878401	5.300000e-59	239.0
57	TraesCS7D01G135800	chr5B	86.765	136	6	4	1	124	387146022	387145887	1.540000e-29	141.0
58	TraesCS7D01G135800	chr3B	97.183	142	2	1	1931	2072	201559228	201559089	5.300000e-59	239.0
59	TraesCS7D01G135800	chr1A	98.519	135	2	0	1931	2065	371922680	371922814	5.300000e-59	239.0
60	TraesCS7D01G135800	chr3A	97.183	142	1	2	1931	2072	672876888	672876750	1.910000e-58	237.0

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	TraesCS7D01G135800	chr7D	87219529	87223629	4100	False	3386.500000	5928	100.000000	1	4101	2	chr7D.!!$F7	4100
1	TraesCS7D01G135800	chr7D	87206170	87207635	1465	False	576.600000	1423	95.710333	924	2272	3	chr7D.!!$F6	1348
2	TraesCS7D01G135800	chr7D	86918482	86919456	974	False	464.333333	601	92.790667	789	1842	3	chr7D.!!$F5	1053
3	TraesCS7D01G135800	chr7D	86753556	86755965	2409	False	436.333333	582	88.742000	485	1842	3	chr7D.!!$F4	1357
4	TraesCS7D01G135800	chr7D	86292328	86293142	814	False	418.000000	577	87.895000	1371	2325	2	chr7D.!!$F3	954
5	TraesCS7D01G135800	chr7A	88499482	88502718	3236	False	1278.500000	1903	95.115500	189	4086	4	chr7A.!!$F13	3897
6	TraesCS7D01G135800	chr7A	88435110	88437090	1980	False	959.000000	1740	93.193667	189	2272	3	chr7A.!!$F12	2083
7	TraesCS7D01G135800	chr7A	88188139	88188921	782	False	942.000000	942	88.622000	1	778	1	chr7A.!!$F7	777
8	TraesCS7D01G135800	chr7A	87451043	87452117	1074	False	922.000000	922	82.677000	731	1842	1	chr7A.!!$F1	1111
9	TraesCS7D01G135800	chr7A	88144209	88144990	781	False	915.000000	915	87.990000	1	778	1	chr7A.!!$F5	777
10	TraesCS7D01G135800	chr7A	88315480	88316684	1204	False	776.000000	1315	91.471500	933	2272	2	chr7A.!!$F11	1339
11	TraesCS7D01G135800	chr7A	88008334	88008916	582	False	736.000000	736	89.327000	789	1392	1	chr7A.!!$F2	603
12	TraesCS7D01G135800	chr7A	88119764	88121507	1743	False	241.500000	331	85.089500	412	947	2	chr7A.!!$F10	535
13	TraesCS7D01G135800	chr7B	35636338	35640025	3687	False	1083.600000	1882	93.846400	1	4086	5	chr7B.!!$F4	4085
14	TraesCS7D01G135800	chr7B	35307638	35308481	843	False	893.000000	893	85.730000	947	1842	1	chr7B.!!$F2	895
15	TraesCS7D01G135800	chr7B	35506699	35508126	1427	False	596.666667	889	89.202667	412	1842	3	chr7B.!!$F3	1430

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	Hairpin	End Stability	Orientation
88	101	0.180406	ACGGCTTGCACTTATAGGGG	59.820	55.000	0.00	4.79	F
191	204	1.071542	TCATGCGGGTGAAAGAGTGAA	59.928	47.619	0.00	3.18	F
1772	3384	1.737793	GTACCTGTGGGCATCTTTTCG	59.262	52.381	35.63	3.46	F
2212	3885	0.684535	TTGTCCACGAGATCTGGCAA	59.315	50.000	0.00	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1614	3226	1.000955	GCCTTTCTTCTCCGAGTCACA	59.999	52.381	0.00	0.00	3.58	R
2073	3746	1.619827	ACCAACGTCCTACCATTCGAA	59.380	47.619	0.00	0.00	3.71	R
2926	4609	1.070445	GCGCTGGTGAGCCTCATAT	59.930	57.895	0.00	42.91	1.78	R
3809	5493	0.252148	TCAGGGGGCAATGCATTTCA	60.252	50.000	9.83	0.00	2.69	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	101	0.180406	ACGGCTTGCACTTATAGGGG	59.820	55.000	0.00	0.00	0.00	4.79
126	139	3.077484	TCAAGGCTTCCCATCTTTCTG	57.923	47.619	0.00	0.00	0.00	3.02
129	142	1.283321	AGGCTTCCCATCTTTCTGGAC	59.717	52.381	0.00	0.00	38.69	4.02
155	168	4.060205	CCACTCAAGGCATTTTGAAAAGG	58.940	43.478	0.00	0.00	36.69	3.11
191	204	1.071542	TCATGCGGGTGAAAGAGTGAA	59.928	47.619	0.00	0.00	0.00	3.18
368	382	6.801862	GTCAAAATCACTGTACCTGTAATTGC	59.198	38.462	0.00	0.00	0.00	3.56
516	531	5.408356	TCATACTCGAAGAACAAACCTAGC	58.592	41.667	0.00	0.00	34.09	3.42
528	543	4.523083	ACAAACCTAGCTTGAACAGTTCA	58.477	39.130	12.24	12.24	38.04	3.18
529	544	5.133221	ACAAACCTAGCTTGAACAGTTCAT	58.867	37.500	16.89	5.03	39.84	2.57
559	579	3.518634	TTTTTGTTCTGGGTCAACTGC	57.481	42.857	0.00	0.00	0.00	4.40
1387	2998	5.573337	AGCTGGCAAAATTAGAGATCAAC	57.427	39.130	0.00	0.00	0.00	3.18
1406	3018	2.051804	CTTGGACGGGAATCGCATGC	62.052	60.000	7.91	7.91	43.89	4.06
1527	3139	3.961480	TGGGTGTCTAGTTCTGATGTG	57.039	47.619	0.00	0.00	0.00	3.21
1614	3226	2.270205	CTGGGCTCTCCGCATTGT	59.730	61.111	0.00	0.00	41.67	2.71
1772	3384	1.737793	GTACCTGTGGGCATCTTTTCG	59.262	52.381	0.00	0.00	35.63	3.46
1850	3523	4.396166	CAGAACTAGAATTTTGTGGCCGAT	59.604	41.667	0.00	0.00	0.00	4.18
1865	3538	2.035961	GGCCGATCACTGCTACTGAATA	59.964	50.000	0.00	0.00	0.00	1.75
1894	3567	7.768120	GTGATCTCCAAACAGTTATCTGAGAAT	59.232	37.037	7.81	0.00	43.76	2.40
1920	3593	9.208022	TGTTTGTGTTATTGTTCATTGTTTTCA	57.792	25.926	0.00	0.00	0.00	2.69
1930	3603	7.509141	TGTTCATTGTTTTCAAGATAGCTGA	57.491	32.000	0.00	0.00	43.41	4.26
1931	3604	7.587629	TGTTCATTGTTTTCAAGATAGCTGAG	58.412	34.615	0.00	0.00	43.41	3.35
1932	3605	7.229306	TGTTCATTGTTTTCAAGATAGCTGAGT	59.771	33.333	0.00	0.00	43.41	3.41
1933	3606	8.721478	GTTCATTGTTTTCAAGATAGCTGAGTA	58.279	33.333	0.00	0.00	43.41	2.59
1934	3607	8.256611	TCATTGTTTTCAAGATAGCTGAGTAC	57.743	34.615	0.00	0.00	43.41	2.73
1935	3608	7.877612	TCATTGTTTTCAAGATAGCTGAGTACA	59.122	33.333	0.00	0.00	43.41	2.90

Showing 1 to 25 of 97 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	45	5.349817	CGAATCACTATATCTTCACCATGGC	59.650	44.000	13.04	0.00	0.00	4.40
88	101	2.536365	TGATCGATGAACGTACTTGGC	58.464	47.619	0.54	0.00	43.13	4.52
191	204	3.678056	TGGACTAGAGCAACGATGTTT	57.322	42.857	0.00	0.00	0.00	2.83
404	418	7.015584	ACTCATACAAAGGAATGGCTTCTTTTT	59.984	33.333	4.78	0.00	38.27	1.94
405	419	6.494835	ACTCATACAAAGGAATGGCTTCTTTT	59.505	34.615	0.00	2.55	40.23	2.27
409	424	5.904362	AACTCATACAAAGGAATGGCTTC	57.096	39.130	0.00	0.00	0.00	3.86
540	558	1.403679	CGCAGTTGACCCAGAACAAAA	59.596	47.619	0.00	0.00	0.00	2.44
541	559	1.021202	CGCAGTTGACCCAGAACAAA	58.979	50.000	0.00	0.00	0.00	2.83
559	579	4.621034	GGTATGTTTCAAAGTGAAATGGCG	59.379	41.667	6.69	0.00	46.55	5.69
1387	2998	2.016961	CATGCGATTCCCGTCCAAG	58.983	57.895	0.00	0.00	41.15	3.61
1406	3018	1.672441	CGCCCAATTGGACACCATTTG	60.672	52.381	26.60	14.54	41.65	2.32
1527	3139	5.127693	TCAAGAGCAGAGACTGAACTTAC	57.872	43.478	2.81	0.00	32.44	2.34
1614	3226	1.000955	GCCTTTCTTCTCCGAGTCACA	59.999	52.381	0.00	0.00	0.00	3.58
1865	3538	6.014242	TCAGATAACTGTTTGGAGATCACTGT	60.014	38.462	0.00	0.00	43.81	3.55
1894	3567	9.208022	TGAAAACAATGAACAATAACACAAACA	57.792	25.926	0.00	0.00	0.00	2.83
1986	3659	8.677148	TGGCAGTAGATGGATTTTACTAAATC	57.323	34.615	0.00	0.00	45.81	2.17
1987	3660	8.903820	GTTGGCAGTAGATGGATTTTACTAAAT	58.096	33.333	0.00	0.00	36.68	1.40
1988	3661	7.885922	TGTTGGCAGTAGATGGATTTTACTAAA	59.114	33.333	0.00	0.00	0.00	1.85
1989	3662	7.398829	TGTTGGCAGTAGATGGATTTTACTAA	58.601	34.615	0.00	0.00	0.00	2.24
1990	3663	6.953101	TGTTGGCAGTAGATGGATTTTACTA	58.047	36.000	0.00	0.00	0.00	1.82
1991	3664	5.815581	TGTTGGCAGTAGATGGATTTTACT	58.184	37.500	0.00	0.00	0.00	2.24
1992	3665	6.509418	TTGTTGGCAGTAGATGGATTTTAC	57.491	37.500	0.00	0.00	0.00	2.01
1993	3666	7.716799	ATTTGTTGGCAGTAGATGGATTTTA	57.283	32.000	0.00	0.00	0.00	1.52
1994	3667	6.610075	ATTTGTTGGCAGTAGATGGATTTT	57.390	33.333	0.00	0.00	0.00	1.82
1995	3668	6.096846	GGTATTTGTTGGCAGTAGATGGATTT	59.903	38.462	0.00	0.00	0.00	2.17

Showing 1 to 25 of 81 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.