AutoCloner

Multiple sequence alignment - TraesCS1D01G426500

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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	TraesCS1D01G426500	chr1D	100.000	2788	0	0	1	2788	479595531	479598318	0.000000e+00	5149.0
1	TraesCS1D01G426500	chr1D	80.806	1042	159	20	1742	2761	401437475	401438497	0.000000e+00	778.0
2	TraesCS1D01G426500	chr1B	90.980	1796	97	32	1	1753	667823511	667825284	0.000000e+00	2359.0
3	TraesCS1D01G426500	chr1A	92.727	935	55	5	1240	2169	575872983	575873909	0.000000e+00	1338.0
4	TraesCS1D01G426500	chr1A	92.038	628	44	4	2164	2785	575893181	575893808	0.000000e+00	878.0
5	TraesCS1D01G426500	chr1A	92.895	563	32	5	60	616	575871826	575872386	0.000000e+00	811.0
6	TraesCS1D01G426500	chr1A	90.017	591	32	11	603	1187	575872412	575872981	0.000000e+00	739.0
7	TraesCS1D01G426500	chr1A	100.000	41	0	0	1187	1227	121110748	121110708	2.980000e-10	76.8
8	TraesCS1D01G426500	chr3B	82.803	942	114	20	1754	2690	512798393	512797495	0.000000e+00	798.0
9	TraesCS1D01G426500	chr3B	82.332	832	117	22	1760	2580	704295540	704294728	0.000000e+00	695.0
10	TraesCS1D01G426500	chr3B	81.119	143	25	2	1749	1890	758415785	758415926	2.270000e-21	113.0
11	TraesCS1D01G426500	chr3B	80.420	143	26	2	1749	1890	758259127	758259268	1.060000e-19	108.0
12	TraesCS1D01G426500	chr3D	83.816	828	97	14	1754	2577	393010451	393009657	0.000000e+00	752.0
13	TraesCS1D01G426500	chr3D	78.618	926	174	20	1829	2744	9462014	9462925	2.390000e-165	592.0
14	TraesCS1D01G426500	chr7B	80.283	1060	152	25	1756	2788	384202897	384201868	0.000000e+00	747.0
15	TraesCS1D01G426500	chr7B	79.103	847	141	26	1838	2656	510763526	510762688	4.060000e-153	551.0
16	TraesCS1D01G426500	chr7D	79.849	1057	159	26	1758	2788	388999208	388998180	0.000000e+00	723.0
17	TraesCS1D01G426500	chr7D	90.385	52	4	1	222	273	5355889	5355839	1.790000e-07	67.6
18	TraesCS1D01G426500	chr7A	81.210	942	121	29	1758	2674	439634967	439634057	0.000000e+00	708.0
19	TraesCS1D01G426500	chr7A	78.685	821	157	11	1977	2788	726741145	726741956	5.290000e-147	531.0
20	TraesCS1D01G426500	chr7A	89.764	127	13	0	1756	1882	202520391	202520517	2.220000e-36	163.0
21	TraesCS1D01G426500	chr7A	97.619	42	1	0	1187	1228	29481402	29481443	3.850000e-09	73.1
22	TraesCS1D01G426500	chr7A	97.561	41	1	0	1187	1227	30863900	30863860	1.390000e-08	71.3
23	TraesCS1D01G426500	chrUn	81.178	781	131	11	1756	2525	24941387	24940612	5.100000e-172	614.0
24	TraesCS1D01G426500	chr5D	82.931	580	68	12	1759	2331	11211378	11210823	6.940000e-136	494.0
25	TraesCS1D01G426500	chr2D	81.901	547	76	10	1826	2356	423613090	423612551	9.170000e-120	440.0
26	TraesCS1D01G426500	chr2D	100.000	38	0	0	1187	1224	22789330	22789293	1.390000e-08	71.3
27	TraesCS1D01G426500	chr2D	100.000	38	0	0	1187	1224	40785167	40785130	1.390000e-08	71.3
28	TraesCS1D01G426500	chr6B	82.500	520	72	6	1758	2273	715801582	715801078	3.300000e-119	438.0
29	TraesCS1D01G426500	chr6A	100.000	40	0	0	1188	1227	16617261	16617222	1.070000e-09	75.0
30	TraesCS1D01G426500	chr6D	100.000	38	0	0	1187	1224	119162856	119162893	1.390000e-08	71.3
31	TraesCS1D01G426500	chr4D	97.500	40	1	0	1188	1227	71415859	71415820	4.980000e-08	69.4

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	TraesCS1D01G426500	chr1D	479595531	479598318	2787	False	5149.000000	5149	100.000000	1	2788	1	chr1D.!!$F2	2787
1	TraesCS1D01G426500	chr1D	401437475	401438497	1022	False	778.000000	778	80.806000	1742	2761	1	chr1D.!!$F1	1019
2	TraesCS1D01G426500	chr1B	667823511	667825284	1773	False	2359.000000	2359	90.980000	1	1753	1	chr1B.!!$F1	1752
3	TraesCS1D01G426500	chr1A	575871826	575873909	2083	False	962.666667	1338	91.879667	60	2169	3	chr1A.!!$F2	2109
4	TraesCS1D01G426500	chr1A	575893181	575893808	627	False	878.000000	878	92.038000	2164	2785	1	chr1A.!!$F1	621
5	TraesCS1D01G426500	chr3B	512797495	512798393	898	True	798.000000	798	82.803000	1754	2690	1	chr3B.!!$R1	936
6	TraesCS1D01G426500	chr3B	704294728	704295540	812	True	695.000000	695	82.332000	1760	2580	1	chr3B.!!$R2	820
7	TraesCS1D01G426500	chr3D	393009657	393010451	794	True	752.000000	752	83.816000	1754	2577	1	chr3D.!!$R1	823
8	TraesCS1D01G426500	chr3D	9462014	9462925	911	False	592.000000	592	78.618000	1829	2744	1	chr3D.!!$F1	915
9	TraesCS1D01G426500	chr7B	384201868	384202897	1029	True	747.000000	747	80.283000	1756	2788	1	chr7B.!!$R1	1032
10	TraesCS1D01G426500	chr7B	510762688	510763526	838	True	551.000000	551	79.103000	1838	2656	1	chr7B.!!$R2	818
11	TraesCS1D01G426500	chr7D	388998180	388999208	1028	True	723.000000	723	79.849000	1758	2788	1	chr7D.!!$R2	1030
12	TraesCS1D01G426500	chr7A	439634057	439634967	910	True	708.000000	708	81.210000	1758	2674	1	chr7A.!!$R2	916
13	TraesCS1D01G426500	chr7A	726741145	726741956	811	False	531.000000	531	78.685000	1977	2788	1	chr7A.!!$F3	811
14	TraesCS1D01G426500	chrUn	24940612	24941387	775	True	614.000000	614	81.178000	1756	2525	1	chrUn.!!$R1	769
15	TraesCS1D01G426500	chr5D	11210823	11211378	555	True	494.000000	494	82.931000	1759	2331	1	chr5D.!!$R1	572
16	TraesCS1D01G426500	chr2D	423612551	423613090	539	True	440.000000	440	81.901000	1826	2356	1	chr2D.!!$R3	530
17	TraesCS1D01G426500	chr6B	715801078	715801582	504	True	438.000000	438	82.500000	1758	2273	1	chr6B.!!$R1	515

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
590	616	0.886563	GCTGAACTCATGCTTTGCCT	59.113	50.0	0.0	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2045	2217	0.179073	CGATGGCCTGTCGAGGAATT	60.179	55.0	21.6	0.0	42.93	2.17	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
41	43	4.142609	TGAGTGAATATGACTCCTTGGC	57.857	45.455	11.03	0.00	39.36	4.52
99	120	8.394971	TCTTTGTCTTGCTAATGAAATGAGAA	57.605	30.769	0.00	0.00	0.00	2.87
100	121	8.509690	TCTTTGTCTTGCTAATGAAATGAGAAG	58.490	33.333	0.00	0.00	0.00	2.85
135	156	1.238439	CCACACGTGGCTCATTTCTT	58.762	50.000	21.57	0.00	44.73	2.52
137	158	1.872952	CACACGTGGCTCATTTCTTCA	59.127	47.619	21.57	0.00	0.00	3.02
147	168	3.770666	CTCATTTCTTCAGGCATGCTTG	58.229	45.455	22.93	22.93	0.00	4.01
269	295	3.264964	TCCACCATAAGGAACCTAACCAC	59.735	47.826	0.00	0.00	38.69	4.16
380	406	8.195165	TCTGAAGGAGAGTAAGAAAGATTCAA	57.805	34.615	0.00	0.00	0.00	2.69
381	407	8.820831	TCTGAAGGAGAGTAAGAAAGATTCAAT	58.179	33.333	0.00	0.00	0.00	2.57
404	430	6.860790	TCATTCCAATTAAAACCCCCTAAC	57.139	37.500	0.00	0.00	0.00	2.34
422	448	3.669251	AACGAACTCTCTTCCTCCTTG	57.331	47.619	0.00	0.00	0.00	3.61
465	491	2.634453	TCTCACACTTGCTCATCCTTCA	59.366	45.455	0.00	0.00	0.00	3.02
466	492	3.001414	CTCACACTTGCTCATCCTTCAG	58.999	50.000	0.00	0.00	0.00	3.02
473	499	3.430042	TGCTCATCCTTCAGAAAAGCT	57.570	42.857	0.00	0.00	37.14	3.74
590	616	0.886563	GCTGAACTCATGCTTTGCCT	59.113	50.000	0.00	0.00	0.00	4.75
669	734	5.347342	TGTGTTCAAGATTTTGTTGCGAAT	58.653	33.333	0.00	0.00	35.73	3.34
753	818	2.032681	GGAGTTTGACGCAGGGCT	59.967	61.111	0.00	0.00	0.00	5.19
819	884	2.290071	ACCTCCGTCACAGGTAAATTGG	60.290	50.000	0.00	0.00	42.91	3.16
922	988	5.641636	TGCTCGTTCAAATTCTAACAGCATA	59.358	36.000	16.71	5.49	36.13	3.14
1073	1144	1.439543	AAGCTCCCACTTCTCCTTGT	58.560	50.000	0.00	0.00	0.00	3.16
1117	1188	1.384989	CGTCTCCCAGGATGTAGCGT	61.385	60.000	0.00	0.00	0.00	5.07
1147	1218	2.890945	GGTGGTTTGCAAACTGATACCT	59.109	45.455	34.39	0.00	38.89	3.08
1224	1296	1.603455	CCACTTTCGGTGCACCCAT	60.603	57.895	29.95	8.21	44.08	4.00
1336	1414	5.578005	CATCCATGCAGAAGAAAAGATGT	57.422	39.130	0.00	0.00	0.00	3.06
1339	1417	6.053632	TCCATGCAGAAGAAAAGATGTCTA	57.946	37.500	0.00	0.00	0.00	2.59
1382	1460	1.053424	GGATATGGGCCTGGTTACGA	58.947	55.000	4.53	0.00	0.00	3.43
1425	1503	0.253327	GAGGAGGAGCCGGTCAAAAT	59.747	55.000	1.90	0.00	43.43	1.82
1426	1504	0.035056	AGGAGGAGCCGGTCAAAATG	60.035	55.000	1.90	0.00	43.43	2.32
1427	1505	1.032114	GGAGGAGCCGGTCAAAATGG	61.032	60.000	1.90	0.00	0.00	3.16
1436	1514	0.678950	GGTCAAAATGGTGGTGGTGG	59.321	55.000	0.00	0.00	0.00	4.61
1492	1570	1.175983	GGTGGCGGTCAAAATGGTGA	61.176	55.000	0.00	0.00	0.00	4.02
1493	1571	0.671251	GTGGCGGTCAAAATGGTGAA	59.329	50.000	0.00	0.00	0.00	3.18
1498	1576	2.850321	CGGTCAAAATGGTGAATGTCG	58.150	47.619	0.00	0.00	0.00	4.35
1570	1648	0.919981	CTTCATCTGCTCGAGCGTTC	59.080	55.000	30.75	6.88	45.83	3.95
1582	1660	1.363744	GAGCGTTCACTTGCTAGCAT	58.636	50.000	20.13	0.51	42.60	3.79
1613	1691	9.658475	GATATGATAGTATTGCGAGCTAGTAAG	57.342	37.037	3.54	0.00	0.00	2.34
1624	1705	5.241728	TGCGAGCTAGTAAGTGTATGATCAT	59.758	40.000	13.81	13.81	0.00	2.45
1630	1711	8.478066	AGCTAGTAAGTGTATGATCATTTGTGA	58.522	33.333	14.65	0.00	0.00	3.58
1683	1774	1.282817	GCAACGGTCATGCGTACATA	58.717	50.000	0.00	0.00	33.67	2.29
1684	1775	1.864711	GCAACGGTCATGCGTACATAT	59.135	47.619	0.00	0.00	33.67	1.78
1858	1955	3.695830	TTTGGTCGGTTCTAGCTGATT	57.304	42.857	0.00	0.00	0.00	2.57
2045	2217	3.136443	CCATAGTGGAGGTTGAGCCAATA	59.864	47.826	0.00	0.00	40.96	1.90
2152	2327	1.655885	GACGTCGAACTCCTCCTCCC	61.656	65.000	0.00	0.00	0.00	4.30
2219	2455	1.757118	GGAGATGACGATGACCTTCCA	59.243	52.381	0.00	0.00	0.00	3.53
2388	2627	3.838271	GCTGGCGGATCGAGGTGA	61.838	66.667	0.00	0.00	0.00	4.02
2679	2920	1.642037	GCTTGAAGATGCGCTGCTCA	61.642	55.000	9.73	3.30	0.00	4.26
2692	2933	0.249868	CTGCTCAAGGACGAACCACA	60.250	55.000	0.00	0.00	42.04	4.17
2750	2994	4.148825	GCTCCGACCACCGCATCT	62.149	66.667	0.00	0.00	36.84	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	7.275183	CCAAGGAGTCATATTCACTCATACAA	58.725	38.462	11.91	0.00	41.94	2.41
72	93	6.615088	TCATTTCATTAGCAAGACAAAGAGC	58.385	36.000	0.00	0.00	0.00	4.09
99	120	4.681781	CGTGTGGAAGGAAAGATATGCTCT	60.682	45.833	0.00	0.00	34.96	4.09
100	121	3.557595	CGTGTGGAAGGAAAGATATGCTC	59.442	47.826	0.00	0.00	0.00	4.26
189	213	8.154856	ACATGGGTACTAGCATATTTCGTAAAT	58.845	33.333	0.00	0.00	34.90	1.40
191	215	7.058023	ACATGGGTACTAGCATATTTCGTAA	57.942	36.000	0.00	0.00	0.00	3.18
193	217	5.069914	TGACATGGGTACTAGCATATTTCGT	59.930	40.000	0.00	0.00	0.00	3.85
194	218	5.405571	GTGACATGGGTACTAGCATATTTCG	59.594	44.000	0.00	0.00	0.00	3.46
380	406	6.097696	CGTTAGGGGGTTTTAATTGGAATGAT	59.902	38.462	0.00	0.00	0.00	2.45
381	407	5.419471	CGTTAGGGGGTTTTAATTGGAATGA	59.581	40.000	0.00	0.00	0.00	2.57
404	430	2.094442	GGTCAAGGAGGAAGAGAGTTCG	60.094	54.545	0.00	0.00	0.00	3.95
422	448	2.438434	CAAGCCGGTGATGGGGTC	60.438	66.667	1.90	0.00	33.29	4.46
465	491	3.432378	TCTAGGACTTCGGAGCTTTTCT	58.568	45.455	0.00	0.00	0.00	2.52
466	492	3.870633	TCTAGGACTTCGGAGCTTTTC	57.129	47.619	0.00	0.00	0.00	2.29
473	499	1.476471	GGGTCGATCTAGGACTTCGGA	60.476	57.143	0.00	0.00	34.82	4.55
556	582	7.151999	TGAGTTCAGCACTAGTTTTTCAAAA	57.848	32.000	0.00	0.00	35.01	2.44
590	616	5.802465	AGAGAGAGCAGAAAATCACATTGA	58.198	37.500	0.00	0.00	0.00	2.57
706	771	6.053632	ACAACATTGTCTGTCAGGATCATA	57.946	37.500	0.00	0.00	36.50	2.15
708	773	4.356405	ACAACATTGTCTGTCAGGATCA	57.644	40.909	0.00	0.00	36.50	2.92
709	774	6.166279	TCTTACAACATTGTCTGTCAGGATC	58.834	40.000	0.00	0.00	42.35	3.36
710	775	6.114187	TCTTACAACATTGTCTGTCAGGAT	57.886	37.500	0.00	0.00	42.35	3.24
711	776	5.545063	TCTTACAACATTGTCTGTCAGGA	57.455	39.130	0.00	0.00	42.35	3.86
714	779	5.063204	CCCTTCTTACAACATTGTCTGTCA	58.937	41.667	0.00	0.00	42.35	3.58
819	884	2.149578	GCACTCCCATGCATCTATCAC	58.850	52.381	0.00	0.00	45.39	3.06
860	926	3.708890	TCGCTCTCAACTTTTCGTGTTA	58.291	40.909	0.00	0.00	0.00	2.41
887	953	1.937546	GAACGAGCAGGGCATTTGGG	61.938	60.000	0.00	0.00	0.00	4.12
888	954	1.243342	TGAACGAGCAGGGCATTTGG	61.243	55.000	0.00	0.00	0.00	3.28
922	988	2.189833	CATGCATGCAAGCTCACCT	58.810	52.632	26.68	1.67	34.99	4.00
1073	1144	0.454600	GAGAGCGACCAATACGACCA	59.545	55.000	0.00	0.00	0.00	4.02
1117	1188	2.195567	GCAAACCACCTGCTGCAGA	61.196	57.895	30.10	1.36	36.84	4.26
1147	1218	7.335924	AGCACTACTTGTTCTTAACAGTTTTGA	59.664	33.333	0.00	0.00	43.27	2.69
1224	1296	9.823647	CCTCTTCTATTAGAACTCAATTAAGCA	57.176	33.333	1.90	0.00	29.89	3.91
1336	1414	0.242825	CCGTCTGGAAGTTGCGTAGA	59.757	55.000	0.00	0.00	37.49	2.59
1339	1417	1.466025	TACCCGTCTGGAAGTTGCGT	61.466	55.000	0.00	0.00	37.49	5.24
1382	1460	1.519408	GTTGTTGTCGTAGCCACCAT	58.481	50.000	0.00	0.00	0.00	3.55
1425	1503	3.814906	CCACCACCACCACCACCA	61.815	66.667	0.00	0.00	0.00	4.17
1427	1505	4.514585	TGCCACCACCACCACCAC	62.515	66.667	0.00	0.00	0.00	4.16
1436	1514	2.897350	GATAGCCGCTGCCACCAC	60.897	66.667	2.16	0.00	38.69	4.16
1570	1648	0.816825	ATCGGCCATGCTAGCAAGTG	60.817	55.000	23.54	16.34	0.00	3.16
1582	1660	3.445805	TCGCAATACTATCATATCGGCCA	59.554	43.478	2.24	0.00	0.00	5.36
1613	1691	7.166970	GTCATGCATTCACAAATGATCATACAC	59.833	37.037	9.04	0.00	44.25	2.90
1624	1705	5.125739	TCAGCATATGTCATGCATTCACAAA	59.874	36.000	11.41	0.00	46.77	2.83
1630	1711	5.847111	AAAGTCAGCATATGTCATGCATT	57.153	34.783	11.46	0.00	46.77	3.56
1858	1955	5.422970	TGTTTTATTCCGCTAAGTCTAGGGA	59.577	40.000	0.00	0.00	39.82	4.20
1940	2046	5.547465	TCGGTTGTCAAGACTATGTTGAAT	58.453	37.500	1.53	0.00	35.71	2.57
2045	2217	0.179073	CGATGGCCTGTCGAGGAATT	60.179	55.000	21.60	0.00	42.93	2.17
2219	2455	3.214328	GCGATATTCCCTGACAATGGTT	58.786	45.455	0.00	0.00	0.00	3.67
2245	2481	2.515523	CAAGCTCATGGAGGCGGG	60.516	66.667	0.00	0.00	0.00	6.13
2388	2627	2.114411	ATTTGGGACGGCGTGGTT	59.886	55.556	21.19	0.00	0.00	3.67
2679	2920	2.030562	CGCCTGTGGTTCGTCCTT	59.969	61.111	1.80	0.00	37.07	3.36
2711	2952	1.402896	CCCCTCTAATCCGCAGCTCA	61.403	60.000	0.00	0.00	0.00	4.26
2739	2983	3.286694	AATGGCCAGATGCGGTGGT	62.287	57.895	13.05	0.00	42.61	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.