AutoCloner

Multiple sequence alignment - TraesCS7A01G290600

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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	TraesCS7A01G290600	chr7A	100.000	2297	0	0	1	2297	352676717	352674421	0.000000e+00	4242.0
1	TraesCS7A01G290600	chr7A	92.500	520	38	1	1432	1951	591996637	591996119	0.000000e+00	743.0
2	TraesCS7A01G290600	chr7A	93.435	457	26	4	1	454	650019361	650018906	0.000000e+00	675.0
3	TraesCS7A01G290600	chr7A	100.000	42	0	0	451	492	352676166	352676125	6.800000e-11	78.7
4	TraesCS7A01G290600	chr5B	92.373	1993	98	22	1	1951	413608167	413610147	0.000000e+00	2789.0
5	TraesCS7A01G290600	chr5B	90.996	1988	115	25	1	1951	432877456	432879416	0.000000e+00	2621.0
6	TraesCS7A01G290600	chr5B	90.183	1752	93	35	220	1951	429037648	429039340	0.000000e+00	2209.0
7	TraesCS7A01G290600	chr2D	92.158	2002	94	20	1	1951	630271025	630273014	0.000000e+00	2769.0
8	TraesCS7A01G290600	chr2D	92.020	2005	94	19	1	1951	33934548	33936540	0.000000e+00	2756.0
9	TraesCS7A01G290600	chr2D	94.721	341	17	1	1957	2297	272809715	272810054	1.560000e-146	529.0
10	TraesCS7A01G290600	chr2D	94.721	341	17	1	1957	2297	591987140	591986801	1.560000e-146	529.0
11	TraesCS7A01G290600	chr4D	91.600	1988	118	20	1	1953	245649415	245651388	0.000000e+00	2700.0
12	TraesCS7A01G290600	chr3B	91.562	1991	99	27	1	1951	201560042	201558081	0.000000e+00	2682.0
13	TraesCS7A01G290600	chrUn	92.295	1817	81	15	95	1864	371049286	371051090	0.000000e+00	2525.0
14	TraesCS7A01G290600	chrUn	95.308	341	15	1	1957	2297	428084361	428084700	7.220000e-150	540.0
15	TraesCS7A01G290600	chr3A	92.005	1776	87	19	4	1738	672877697	672875936	0.000000e+00	2442.0
16	TraesCS7A01G290600	chr1A	91.681	1707	110	21	263	1951	371922144	371923836	0.000000e+00	2337.0
17	TraesCS7A01G290600	chr1A	87.189	281	20	4	1	265	371832143	371832423	2.870000e-79	305.0
18	TraesCS7A01G290600	chr1A	93.939	66	2	2	1	65	340428989	340429053	5.220000e-17	99.0
19	TraesCS7A01G290600	chr5D	91.732	1403	79	18	1	1379	432291988	432290599	0.000000e+00	1914.0
20	TraesCS7A01G290600	chr1B	92.006	1326	72	17	1	1304	633728132	633726819	0.000000e+00	1831.0
21	TraesCS7A01G290600	chr4A	90.851	1093	74	19	1	1084	219339138	219338063	0.000000e+00	1441.0
22	TraesCS7A01G290600	chr5A	92.950	695	33	3	1272	1951	482027372	482026679	0.000000e+00	998.0
23	TraesCS7A01G290600	chr5A	89.916	595	30	16	1	576	442271111	442271694	0.000000e+00	739.0
24	TraesCS7A01G290600	chr7D	95.015	341	16	1	1957	2297	231605386	231605725	3.360000e-148	534.0
25	TraesCS7A01G290600	chr7D	95.015	341	16	1	1957	2297	606923632	606923293	3.360000e-148	534.0
26	TraesCS7A01G290600	chr7D	94.721	341	17	1	1957	2297	231551341	231551002	1.560000e-146	529.0
27	TraesCS7A01G290600	chr7D	94.721	341	17	1	1957	2297	231606969	231607308	1.560000e-146	529.0
28	TraesCS7A01G290600	chr6D	95.015	341	16	1	1957	2297	389243291	389243630	3.360000e-148	534.0
29	TraesCS7A01G290600	chr7B	94.721	341	18	0	1957	2297	662729445	662729105	4.350000e-147	531.0

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	TraesCS7A01G290600	chr7A	352674421	352676717	2296	True	2160.35	4242	100.000	1	2297	2	chr7A.!!$R3	2296
1	TraesCS7A01G290600	chr7A	591996119	591996637	518	True	743.00	743	92.500	1432	1951	1	chr7A.!!$R1	519
2	TraesCS7A01G290600	chr5B	413608167	413610147	1980	False	2789.00	2789	92.373	1	1951	1	chr5B.!!$F1	1950
3	TraesCS7A01G290600	chr5B	432877456	432879416	1960	False	2621.00	2621	90.996	1	1951	1	chr5B.!!$F3	1950
4	TraesCS7A01G290600	chr5B	429037648	429039340	1692	False	2209.00	2209	90.183	220	1951	1	chr5B.!!$F2	1731
5	TraesCS7A01G290600	chr2D	630271025	630273014	1989	False	2769.00	2769	92.158	1	1951	1	chr2D.!!$F3	1950
6	TraesCS7A01G290600	chr2D	33934548	33936540	1992	False	2756.00	2756	92.020	1	1951	1	chr2D.!!$F1	1950
7	TraesCS7A01G290600	chr4D	245649415	245651388	1973	False	2700.00	2700	91.600	1	1953	1	chr4D.!!$F1	1952
8	TraesCS7A01G290600	chr3B	201558081	201560042	1961	True	2682.00	2682	91.562	1	1951	1	chr3B.!!$R1	1950
9	TraesCS7A01G290600	chrUn	371049286	371051090	1804	False	2525.00	2525	92.295	95	1864	1	chrUn.!!$F1	1769
10	TraesCS7A01G290600	chr3A	672875936	672877697	1761	True	2442.00	2442	92.005	4	1738	1	chr3A.!!$R1	1734
11	TraesCS7A01G290600	chr1A	371922144	371923836	1692	False	2337.00	2337	91.681	263	1951	1	chr1A.!!$F3	1688
12	TraesCS7A01G290600	chr5D	432290599	432291988	1389	True	1914.00	1914	91.732	1	1379	1	chr5D.!!$R1	1378
13	TraesCS7A01G290600	chr1B	633726819	633728132	1313	True	1831.00	1831	92.006	1	1304	1	chr1B.!!$R1	1303
14	TraesCS7A01G290600	chr4A	219338063	219339138	1075	True	1441.00	1441	90.851	1	1084	1	chr4A.!!$R1	1083
15	TraesCS7A01G290600	chr5A	482026679	482027372	693	True	998.00	998	92.950	1272	1951	1	chr5A.!!$R1	679
16	TraesCS7A01G290600	chr5A	442271111	442271694	583	False	739.00	739	89.916	1	576	1	chr5A.!!$F1	575
17	TraesCS7A01G290600	chr7D	231605386	231607308	1922	False	531.50	534	94.868	1957	2297	2	chr7D.!!$F1	340

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
470	500	3.066064	TGTGGGTTCACTTCATTCGTTTG	59.934	43.478	0.0	0.0	43.94	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2254	3433	0.109827	CGGAATGCGTTGATGTGCAA	60.11	50.0	0.0	0.0	45.45	4.08	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
201	226	7.955750	TCCTTTTTCCTTCCTTGAATCCTTTAT	59.044	33.333	0.00	0.00	0.00	1.40
202	227	8.253810	CCTTTTTCCTTCCTTGAATCCTTTATC	58.746	37.037	0.00	0.00	0.00	1.75
345	370	9.413734	GGTCTAGGAGTAGTATTACTTACCAAA	57.586	37.037	0.85	0.00	40.21	3.28
382	407	5.413523	GCCTTTTCGTTGGGATTAGTTCTTA	59.586	40.000	0.00	0.00	0.00	2.10
454	484	6.600032	TCGCACAACTTATTATTTATGTGGGT	59.400	34.615	16.68	0.00	45.91	4.51
457	487	8.247562	GCACAACTTATTATTTATGTGGGTTCA	58.752	33.333	5.93	0.00	38.78	3.18
458	488	9.567848	CACAACTTATTATTTATGTGGGTTCAC	57.432	33.333	0.00	0.00	43.87	3.18
466	496	5.621197	TTTATGTGGGTTCACTTCATTCG	57.379	39.130	0.00	0.00	43.94	3.34
469	499	3.283751	TGTGGGTTCACTTCATTCGTTT	58.716	40.909	0.00	0.00	43.94	3.60
470	500	3.066064	TGTGGGTTCACTTCATTCGTTTG	59.934	43.478	0.00	0.00	43.94	2.93
472	502	4.273969	GTGGGTTCACTTCATTCGTTTGTA	59.726	41.667	0.00	0.00	40.58	2.41
473	503	5.048991	GTGGGTTCACTTCATTCGTTTGTAT	60.049	40.000	0.00	0.00	40.58	2.29
474	504	6.148150	GTGGGTTCACTTCATTCGTTTGTATA	59.852	38.462	0.00	0.00	40.58	1.47
476	506	7.019418	GGGTTCACTTCATTCGTTTGTATAAC	58.981	38.462	0.00	0.00	0.00	1.89
477	507	7.094933	GGGTTCACTTCATTCGTTTGTATAACT	60.095	37.037	0.00	0.00	0.00	2.24
478	508	8.928733	GGTTCACTTCATTCGTTTGTATAACTA	58.071	33.333	0.00	0.00	0.00	2.24
564	594	4.598036	ATTGGAGATGGGTTCACTTCAT	57.402	40.909	0.00	0.00	0.00	2.57
646	676	9.832445	GTATGGAATTCTTTGGACTACAAGATA	57.168	33.333	5.23	0.00	40.82	1.98
710	740	8.557864	CAACAAATTGGAATTCATTTAGCAACA	58.442	29.630	7.93	0.00	31.63	3.33
729	759	7.433680	AGCAACAAATATTTCTCTTCCGTTTT	58.566	30.769	0.00	0.00	0.00	2.43
977	1011	7.664552	TCTTGCCCTCATATTGAAATGAATT	57.335	32.000	0.00	0.00	35.51	2.17
1073	1107	4.729227	TCTACGTATTGATCACAAGCCA	57.271	40.909	0.00	0.00	39.46	4.75
1080	1114	6.150307	ACGTATTGATCACAAGCCAAAACATA	59.850	34.615	0.00	0.00	39.46	2.29
1175	1209	8.413229	TCTATTTGATAGTGGCCAATTAAAAGC	58.587	33.333	12.70	0.00	34.47	3.51
1187	1221	6.756542	GGCCAATTAAAAGCAGATATTTTCGT	59.243	34.615	0.00	0.00	32.38	3.85
1255	1289	7.589993	ACTATCCATTCTTTCTTCCATCCATT	58.410	34.615	0.00	0.00	0.00	3.16
1349	1417	4.038642	AGAATCCTTTAAACAAAGGCGCAA	59.961	37.500	10.83	0.00	46.89	4.85
1687	1797	9.175060	CATTGATTCGTCTAGTGTCTACAATAG	57.825	37.037	10.53	10.53	43.57	1.73
1864	1975	7.515861	TGTATTAGAAATGATACCCTGGGATGA	59.484	37.037	22.23	4.31	0.00	2.92
1870	1981	6.725101	AATGATACCCTGGGATGAATGTAT	57.275	37.500	22.23	4.47	0.00	2.29
1872	1983	7.829224	ATGATACCCTGGGATGAATGTATAA	57.171	36.000	22.23	0.00	0.00	0.98
1895	2006	3.591979	GCAAATTGCTTCTGTGCCA	57.408	47.368	11.19	0.00	40.96	4.92
1900	2011	4.312443	CAAATTGCTTCTGTGCCAAGAAT	58.688	39.130	0.00	0.00	35.67	2.40
1935	2046	6.212589	TGTGGGTTGTAAGAGATGTGAATCTA	59.787	38.462	0.00	0.00	0.00	1.98
2028	2139	1.528129	CAAACCTCCTGGCTGTCTTC	58.472	55.000	0.00	0.00	36.63	2.87
2052	3231	1.063942	CCCCCAACCTCCTTTATCACC	60.064	57.143	0.00	0.00	0.00	4.02
2058	3237	0.744874	CCTCCTTTATCACCGAGCGA	59.255	55.000	0.00	0.00	0.00	4.93
2062	3241	2.128035	CCTTTATCACCGAGCGATCAC	58.872	52.381	0.00	0.00	0.00	3.06
2125	3304	2.038952	CGATGAAGCTTATCCCCCATCA	59.961	50.000	18.34	3.49	32.33	3.07
2192	3371	8.893219	TCTAGTATTCATAGTTTGCCTTGATG	57.107	34.615	0.00	0.00	0.00	3.07
2253	3432	3.012502	ACCCCTAGATGTCCAGTCAACTA	59.987	47.826	0.00	0.00	0.00	2.24
2254	3433	4.227197	CCCCTAGATGTCCAGTCAACTAT	58.773	47.826	0.00	0.00	0.00	2.12
2258	3437	4.558226	AGATGTCCAGTCAACTATTGCA	57.442	40.909	0.00	0.00	0.00	4.08
2260	3439	3.483808	TGTCCAGTCAACTATTGCACA	57.516	42.857	0.00	0.00	0.00	4.57
2271	3450	4.019919	ACTATTGCACATCAACGCATTC	57.980	40.909	0.00	0.00	38.10	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
248	273	4.469657	TGGTCCAGGTAAATCCATTATGC	58.530	43.478	0.00	0.00	39.02	3.14
345	370	5.222079	ACGAAAAGGCAAAATAAATGGGT	57.778	34.783	0.00	0.00	0.00	4.51
356	381	3.492337	ACTAATCCCAACGAAAAGGCAA	58.508	40.909	0.00	0.00	0.00	4.52
440	470	8.405531	CGAATGAAGTGAACCCACATAAATAAT	58.594	33.333	0.00	0.00	45.54	1.28
483	513	7.380065	GCCATTTACGAACATTACAGTGAAAAA	59.620	33.333	0.00	0.00	0.00	1.94
484	514	6.858993	GCCATTTACGAACATTACAGTGAAAA	59.141	34.615	0.00	0.00	0.00	2.29
485	515	6.205853	AGCCATTTACGAACATTACAGTGAAA	59.794	34.615	0.00	0.00	0.00	2.69
489	519	5.242434	TGAGCCATTTACGAACATTACAGT	58.758	37.500	0.00	0.00	0.00	3.55
599	629	2.031069	CCACGACGTATCTGGGATAGTG	60.031	54.545	0.00	0.00	0.00	2.74
714	744	9.067986	AGAAATGAGTTAAAACGGAAGAGAAAT	57.932	29.630	0.00	0.00	0.00	2.17
756	786	7.040409	AGCCATAGTAATTGCACCTATTAAAGC	60.040	37.037	0.00	0.00	0.00	3.51
1042	1076	8.082242	TGTGATCAATACGTAGATACCAATCAG	58.918	37.037	0.00	0.00	34.28	2.90
1056	1090	4.793071	TGTTTTGGCTTGTGATCAATACG	58.207	39.130	0.00	0.00	32.82	3.06
1058	1092	7.701539	ACTATGTTTTGGCTTGTGATCAATA	57.298	32.000	0.00	0.00	32.82	1.90
1080	1114	9.196139	AGTTCAAGACATATTAGAGCTCTAACT	57.804	33.333	33.09	23.19	40.81	2.24
1162	1196	6.756542	ACGAAAATATCTGCTTTTAATTGGCC	59.243	34.615	0.00	0.00	0.00	5.36
1212	1246	1.009829	GTCCAATAGCGGCTTCAGTG	58.990	55.000	8.26	0.00	0.00	3.66
1213	1247	0.905357	AGTCCAATAGCGGCTTCAGT	59.095	50.000	8.26	0.00	0.00	3.41
1255	1289	7.591421	TGATACGAGTGGATTTCCTATTACA	57.409	36.000	0.00	0.00	36.82	2.41
1577	1687	8.470657	AAGAGAGCCAAGAGACTTTAATTTTT	57.529	30.769	0.00	0.00	0.00	1.94
1653	1763	7.327975	ACACTAGACGAATCAATGGTTTATCA	58.672	34.615	0.00	0.00	0.00	2.15
1754	1865	7.939039	ACGGAATGTGACATTGGATCTATAATT	59.061	33.333	16.52	0.00	0.00	1.40
1755	1866	7.453393	ACGGAATGTGACATTGGATCTATAAT	58.547	34.615	16.52	0.00	0.00	1.28
1822	1933	6.711277	TCTAATACATCTGTTGGACAAGCTT	58.289	36.000	0.00	0.00	0.00	3.74
1889	2000	3.189080	CACAATCTTCGATTCTTGGCACA	59.811	43.478	0.00	0.00	0.00	4.57
1891	2002	3.189080	CACACAATCTTCGATTCTTGGCA	59.811	43.478	0.00	0.00	0.00	4.92
1895	2006	4.021102	ACCCACACAATCTTCGATTCTT	57.979	40.909	0.00	0.00	0.00	2.52
1900	2011	2.631160	ACAACCCACACAATCTTCGA	57.369	45.000	0.00	0.00	0.00	3.71
1935	2046	1.003355	CACAATCTGTCGGGCAGGT	60.003	57.895	10.12	0.00	45.08	4.00
1955	2066	2.653448	CTCACTGATCGAGCGCCG	60.653	66.667	2.29	8.02	40.25	6.46
1980	2091	2.863809	CAGCCACCCTTTAAAGAGTGT	58.136	47.619	23.37	12.35	33.43	3.55
2028	2139	2.132089	TAAAGGAGGTTGGGGGTGCG	62.132	60.000	0.00	0.00	0.00	5.34
2052	3231	1.300233	GCCCCTAAGTGATCGCTCG	60.300	63.158	9.70	3.98	0.00	5.03
2058	3237	1.771255	CAGCTAAGGCCCCTAAGTGAT	59.229	52.381	0.00	0.00	39.73	3.06
2062	3241	0.181350	CACCAGCTAAGGCCCCTAAG	59.819	60.000	0.00	0.00	39.73	2.18
2089	3268	1.890489	TCATCGTCGAGAGGGAAACAA	59.110	47.619	0.00	0.00	0.00	2.83
2125	3304	0.904865	TCAAGGTCGGCCAGTGAGAT	60.905	55.000	9.71	0.00	37.19	2.75
2178	3357	3.681593	GGTACCACATCAAGGCAAACTA	58.318	45.455	7.15	0.00	0.00	2.24
2188	3367	2.183300	GCGAGCGGTACCACATCA	59.817	61.111	13.54	0.00	0.00	3.07
2213	3392	1.944709	GGTAAAGCACTGTTTCGGTGT	59.055	47.619	9.87	0.00	42.21	4.16
2253	3432	1.467883	CGGAATGCGTTGATGTGCAAT	60.468	47.619	0.00	0.00	45.45	3.56
2254	3433	0.109827	CGGAATGCGTTGATGTGCAA	60.110	50.000	0.00	0.00	45.45	4.08
2258	3437	1.748879	CCCCGGAATGCGTTGATGT	60.749	57.895	0.73	0.00	0.00	3.06
2260	3439	1.153168	CTCCCCGGAATGCGTTGAT	60.153	57.895	0.73	0.00	0.00	2.57
2271	3450	3.095347	GCTAGCTGGTTCTCCCCGG	62.095	68.421	7.70	0.00	0.00	5.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.