AutoCloner

Multiple sequence alignment - TraesCS5A01G182700

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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	TraesCS5A01G182700	chr5A	100.000	2339	0	0	1	2339	382330000	382327662	0.000000e+00	4320.0
1	TraesCS5A01G182700	chr5A	71.143	1050	250	46	427	1451	442504607	442505628	6.550000e-51	211.0
2	TraesCS5A01G182700	chr5A	77.341	331	61	12	427	750	442290827	442291150	1.430000e-42	183.0
3	TraesCS5A01G182700	chr5D	94.657	1909	60	14	2	1875	289074953	289073052	0.000000e+00	2922.0
4	TraesCS5A01G182700	chr5D	82.407	432	24	28	1913	2339	289073056	289072672	1.730000e-86	329.0
5	TraesCS5A01G182700	chr5D	71.985	1053	236	53	427	1451	556721195	556722216	2.980000e-64	255.0
6	TraesCS5A01G182700	chr5D	80.159	378	35	18	1524	1894	15547853	15547509	1.800000e-61	246.0
7	TraesCS5A01G182700	chr5D	82.184	174	20	2	1131	1304	15553318	15553156	3.130000e-29	139.0
8	TraesCS5A01G182700	chr5D	83.673	98	7	2	1317	1414	15548000	15547912	1.490000e-12	84.2
9	TraesCS5A01G182700	chr5D	80.469	128	10	4	974	1101	15553436	15553324	1.490000e-12	84.2
10	TraesCS5A01G182700	chr5B	92.614	2058	96	27	1	2037	328367911	328365889	0.000000e+00	2907.0
11	TraesCS5A01G182700	chr5B	93.289	298	13	3	2039	2336	328365702	328365412	1.280000e-117	433.0
12	TraesCS5A01G182700	chr5B	73.040	1046	227	47	427	1446	400562817	400563833	3.750000e-83	318.0
13	TraesCS5A01G182700	chr3D	83.212	411	46	11	974	1384	18501171	18501558	2.860000e-94	355.0
14	TraesCS5A01G182700	chr3D	82.620	374	37	9	1524	1891	18501628	18501979	2.920000e-79	305.0
15	TraesCS5A01G182700	chr3D	85.034	147	14	2	1697	1843	18445154	18445292	2.420000e-30	143.0
16	TraesCS5A01G182700	chr4A	72.000	1050	241	49	427	1451	605085451	605086472	6.410000e-66	261.0
17	TraesCS5A01G182700	chr4A	75.849	265	60	4	466	728	662326565	662326303	5.240000e-27	132.0
18	TraesCS5A01G182700	chr7D	77.239	268	57	4	463	728	47402008	47402273	1.120000e-33	154.0
19	TraesCS5A01G182700	chr7A	76.604	265	58	4	466	728	50115347	50115085	2.420000e-30	143.0
20	TraesCS5A01G182700	chr2D	88.608	79	9	0	637	715	407981841	407981763	1.910000e-16	97.1

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	TraesCS5A01G182700	chr5A	382327662	382330000	2338	True	4320.0	4320	100.0000	1	2339	1	chr5A.!!$R1	2338
1	TraesCS5A01G182700	chr5A	442504607	442505628	1021	False	211.0	211	71.1430	427	1451	1	chr5A.!!$F2	1024
2	TraesCS5A01G182700	chr5D	289072672	289074953	2281	True	1625.5	2922	88.5320	2	2339	2	chr5D.!!$R3	2337
3	TraesCS5A01G182700	chr5D	556721195	556722216	1021	False	255.0	255	71.9850	427	1451	1	chr5D.!!$F1	1024
4	TraesCS5A01G182700	chr5B	328365412	328367911	2499	True	1670.0	2907	92.9515	1	2336	2	chr5B.!!$R1	2335
5	TraesCS5A01G182700	chr5B	400562817	400563833	1016	False	318.0	318	73.0400	427	1446	1	chr5B.!!$F1	1019
6	TraesCS5A01G182700	chr3D	18501171	18501979	808	False	330.0	355	82.9160	974	1891	2	chr3D.!!$F2	917
7	TraesCS5A01G182700	chr4A	605085451	605086472	1021	False	261.0	261	72.0000	427	1451	1	chr4A.!!$F1	1024

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
280	311	0.459899	TAGCACGACCTATGCACCTG	59.54	55.0	0.0	0.0	45.92	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1704	1739	1.957186	GTACAACCGGAAGCACGCA	60.957	57.895	9.46	0.0	0.0	5.24	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
50	51	6.902224	TCATTACGTTACCATGACATTCAG	57.098	37.500	0.00	0.00	0.00	3.02
69	85	2.866156	CAGAACGAGACAACACACACAT	59.134	45.455	0.00	0.00	0.00	3.21
71	87	3.555956	AGAACGAGACAACACACACATTC	59.444	43.478	0.00	0.00	0.00	2.67
115	137	1.525197	AGCACAACGTAATGTCACACG	59.475	47.619	7.15	7.15	43.63	4.49
250	277	5.065988	GTCTTGGACAAGTTAACACACACAT	59.934	40.000	8.61	0.00	39.38	3.21
259	286	2.057137	AACACACACATGCAGTTCCT	57.943	45.000	0.00	0.00	0.00	3.36
260	287	2.928801	ACACACACATGCAGTTCCTA	57.071	45.000	0.00	0.00	0.00	2.94
279	310	1.414158	ATAGCACGACCTATGCACCT	58.586	50.000	0.00	0.00	45.92	4.00
280	311	0.459899	TAGCACGACCTATGCACCTG	59.540	55.000	0.00	0.00	45.92	4.00
301	336	9.669353	CACCTGCATTGTAATGTAAATCTTATC	57.331	33.333	6.48	0.00	38.65	1.75
302	337	8.559536	ACCTGCATTGTAATGTAAATCTTATCG	58.440	33.333	6.48	0.00	38.65	2.92
336	371	3.667360	TGGATCGATCTATTCCGACGTA	58.333	45.455	23.96	0.00	37.64	3.57
936	971	1.227263	CGACCCCGTGATGATGGAC	60.227	63.158	0.00	0.00	0.00	4.02
951	986	4.908877	GACGAGTAGAGCGCCGCC	62.909	72.222	4.98	0.00	0.00	6.13
1512	1547	1.430632	GATGAGCATGGCCACGTTG	59.569	57.895	8.16	3.33	0.00	4.10
1704	1739	2.910479	TCCGTCTCGTGCAGGTGT	60.910	61.111	6.26	0.00	0.00	4.16
1798	1833	1.374252	ATCGTTCACCACCAGCGTC	60.374	57.895	0.00	0.00	0.00	5.19
1800	1835	2.110213	GTTCACCACCAGCGTCCA	59.890	61.111	0.00	0.00	0.00	4.02
1802	1837	1.302431	TTCACCACCAGCGTCCATG	60.302	57.895	0.00	0.00	0.00	3.66
1803	1838	1.763546	TTCACCACCAGCGTCCATGA	61.764	55.000	0.00	0.00	0.00	3.07
1805	1840	0.888736	CACCACCAGCGTCCATGAAA	60.889	55.000	0.00	0.00	0.00	2.69
1851	1904	3.987868	TCTCGTGTCAAGTAAATCAGTGC	59.012	43.478	0.00	0.00	0.00	4.40
1855	1908	4.641954	GTGTCAAGTAAATCAGTGCGATG	58.358	43.478	0.00	0.00	33.40	3.84
1874	1927	8.855279	GTGCGATGAAGAAATATACTCTACATC	58.145	37.037	0.00	0.00	0.00	3.06
1898	1951	8.025243	TCACATTTCGGTGAAAGATAACTAAC	57.975	34.615	0.00	0.00	44.34	2.34
1900	1953	7.957484	CACATTTCGGTGAAAGATAACTAACTG	59.043	37.037	0.00	0.00	41.32	3.16
1906	1959	7.929785	TCGGTGAAAGATAACTAACTGAAAACT	59.070	33.333	0.00	0.00	0.00	2.66
1910	1963	9.199982	TGAAAGATAACTAACTGAAAACTACCG	57.800	33.333	0.00	0.00	0.00	4.02
1911	1964	8.543862	AAAGATAACTAACTGAAAACTACCGG	57.456	34.615	0.00	0.00	0.00	5.28
1939	1992	7.189079	TCCAGGAAAATTGGTTTTGTTACTT	57.811	32.000	0.00	0.00	37.65	2.24
1940	1993	7.044798	TCCAGGAAAATTGGTTTTGTTACTTG	58.955	34.615	0.00	0.00	37.65	3.16
1991	2046	3.436700	GTGTGGACACTTCCCTTTTTG	57.563	47.619	2.53	0.00	42.01	2.44
1997	2052	3.005791	GGACACTTCCCTTTTTGTCATGG	59.994	47.826	3.23	0.00	40.18	3.66
1999	2054	2.364970	CACTTCCCTTTTTGTCATGGCA	59.635	45.455	0.00	0.00	0.00	4.92
2013	2069	7.558161	TTGTCATGGCAATCTACTAATCTTG	57.442	36.000	9.09	0.00	0.00	3.02
2018	2074	2.808543	GCAATCTACTAATCTTGGGCGG	59.191	50.000	0.00	0.00	0.00	6.13
2037	2093	3.455619	GGAAACGAGTTGTGCATACTG	57.544	47.619	8.93	5.03	0.00	2.74
2137	2378	5.086058	CACAATCGTTAGAAATGGTTTCCG	58.914	41.667	0.00	0.00	40.54	4.30
2183	2424	6.535508	CAGTAGGTAAAGGAAGCAGTATTGAC	59.464	42.308	0.00	0.00	0.00	3.18
2226	2467	8.170553	CACTCCAAACAAAACAAAAAGAAGATG	58.829	33.333	0.00	0.00	0.00	2.90
2258	2500	6.760770	CCATAATGGCCATTACGTTTTCATTT	59.239	34.615	35.00	16.06	36.24	2.32
2259	2501	7.254387	CCATAATGGCCATTACGTTTTCATTTG	60.254	37.037	35.00	24.50	36.24	2.32
2260	2502	3.919216	TGGCCATTACGTTTTCATTTGG	58.081	40.909	0.00	0.00	0.00	3.28
2261	2503	3.322254	TGGCCATTACGTTTTCATTTGGT	59.678	39.130	0.00	0.00	0.00	3.67
2274	2516	4.112634	TCATTTGGTACTCTTTTGGCCT	57.887	40.909	3.32	0.00	0.00	5.19
2275	2517	5.249780	TCATTTGGTACTCTTTTGGCCTA	57.750	39.130	3.32	0.00	0.00	3.93
2293	2535	3.248602	GCCTATAGACAATGCGTCCTTTG	59.751	47.826	0.00	0.00	46.69	2.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	7.732025	TGGTAACGTAATGATCATACCTTCAT	58.268	34.615	19.17	2.58	42.51	2.57
19	20	7.152645	GTCATGGTAACGTAATGATCATACCT	58.847	38.462	19.17	4.49	42.51	3.08
50	51	3.555956	AGAATGTGTGTGTTGTCTCGTTC	59.444	43.478	0.00	0.00	0.00	3.95
69	85	2.689983	TCTCGCTATGATGCACTGAGAA	59.310	45.455	0.00	0.00	28.95	2.87
71	87	2.392821	GTCTCGCTATGATGCACTGAG	58.607	52.381	0.00	0.00	0.00	3.35
136	158	4.087892	CTGGTGGCGGAGGTCAGG	62.088	72.222	0.00	0.00	0.00	3.86
207	229	3.760684	AGACCTCGTGTTCCTAATTACGT	59.239	43.478	0.00	0.00	37.74	3.57
208	230	4.367386	AGACCTCGTGTTCCTAATTACG	57.633	45.455	0.00	0.00	37.85	3.18
209	231	4.868734	CCAAGACCTCGTGTTCCTAATTAC	59.131	45.833	0.00	0.00	0.00	1.89
210	232	4.773674	TCCAAGACCTCGTGTTCCTAATTA	59.226	41.667	0.00	0.00	0.00	1.40
213	235	2.298163	GTCCAAGACCTCGTGTTCCTAA	59.702	50.000	0.00	0.00	0.00	2.69
216	238	0.391597	TGTCCAAGACCTCGTGTTCC	59.608	55.000	0.00	0.00	0.00	3.62
250	277	1.136305	GGTCGTGCTATAGGAACTGCA	59.864	52.381	1.04	0.00	41.52	4.41
259	286	2.296190	CAGGTGCATAGGTCGTGCTATA	59.704	50.000	0.00	0.00	42.92	1.31
260	287	1.069204	CAGGTGCATAGGTCGTGCTAT	59.931	52.381	0.00	0.00	42.92	2.97
283	314	9.961266	CGTGTTTCGATAAGATTTACATTACAA	57.039	29.630	0.00	0.00	42.86	2.41
286	317	8.187354	TGCGTGTTTCGATAAGATTTACATTA	57.813	30.769	0.00	0.00	42.86	1.90
301	336	1.332290	CGATCCATGATGCGTGTTTCG	60.332	52.381	0.00	0.00	43.12	3.46
302	337	1.933181	TCGATCCATGATGCGTGTTTC	59.067	47.619	0.00	0.00	0.00	2.78
375	410	4.704833	CACCACCACCGCCAGGAG	62.705	72.222	0.00	0.00	41.02	3.69
384	419	3.253838	TACCAGGGCCACCACCAC	61.254	66.667	6.18	0.00	40.13	4.16
503	538	0.797249	GGTCATGTCCGTCTTCGTCG	60.797	60.000	0.00	0.00	35.01	5.12
849	884	3.197790	CGGCGGGTGCTCTTCATG	61.198	66.667	0.00	0.00	42.25	3.07
951	986	4.194720	CTCGGGTTCGGCTCCTCG	62.195	72.222	0.00	0.00	36.95	4.63
966	1001	0.103937	CGGTCATCTTCCAGAGCCTC	59.896	60.000	0.00	0.00	0.00	4.70
1011	1046	4.020617	TTCCAGCAGCTGTCGGGG	62.021	66.667	21.26	13.89	0.00	5.73
1411	1446	2.279784	GGAGATCGCGCCCTTCAG	60.280	66.667	0.00	0.00	0.00	3.02
1704	1739	1.957186	GTACAACCGGAAGCACGCA	60.957	57.895	9.46	0.00	0.00	5.24
1798	1833	6.603201	AGTGGTAACTAATCATGGTTTCATGG	59.397	38.462	0.00	0.00	41.94	3.66
1800	1835	7.633789	AGAGTGGTAACTAATCATGGTTTCAT	58.366	34.615	0.00	0.00	36.52	2.57
1802	1837	7.390718	ACAAGAGTGGTAACTAATCATGGTTTC	59.609	37.037	0.00	0.00	36.52	2.78
1803	1838	7.231467	ACAAGAGTGGTAACTAATCATGGTTT	58.769	34.615	0.00	0.00	36.52	3.27
1805	1840	6.374417	ACAAGAGTGGTAACTAATCATGGT	57.626	37.500	0.00	0.00	36.52	3.55
1851	1904	9.899226	TGTGATGTAGAGTATATTTCTTCATCG	57.101	33.333	19.81	0.00	45.14	3.84
1874	1927	7.957484	CAGTTAGTTATCTTTCACCGAAATGTG	59.043	37.037	0.00	0.00	37.59	3.21
1891	1944	6.403866	TGACCGGTAGTTTTCAGTTAGTTA	57.596	37.500	7.34	0.00	0.00	2.24
1897	1950	2.635915	TGGATGACCGGTAGTTTTCAGT	59.364	45.455	7.34	0.00	39.42	3.41
1898	1951	3.262420	CTGGATGACCGGTAGTTTTCAG	58.738	50.000	7.34	7.41	39.42	3.02
1900	1953	2.235402	TCCTGGATGACCGGTAGTTTTC	59.765	50.000	7.34	0.00	40.75	2.29
1906	1959	3.616219	CAATTTTCCTGGATGACCGGTA	58.384	45.455	7.34	0.00	40.75	4.02
1910	1963	4.890158	AAACCAATTTTCCTGGATGACC	57.110	40.909	0.00	0.00	37.40	4.02
1911	1964	5.610398	ACAAAACCAATTTTCCTGGATGAC	58.390	37.500	0.00	0.00	35.79	3.06
1939	1992	8.927721	CACATAAAAGTTGAATTGCATGATTCA	58.072	29.630	9.30	9.30	42.58	2.57
1940	1993	8.385111	CCACATAAAAGTTGAATTGCATGATTC	58.615	33.333	0.00	4.46	36.73	2.52
1984	2037	5.649782	AGTAGATTGCCATGACAAAAAGG	57.350	39.130	0.00	0.00	32.27	3.11
1985	2038	8.680903	AGATTAGTAGATTGCCATGACAAAAAG	58.319	33.333	0.00	0.00	32.27	2.27
1991	2046	5.471456	CCCAAGATTAGTAGATTGCCATGAC	59.529	44.000	0.00	0.00	0.00	3.06
1997	2052	2.808543	CCGCCCAAGATTAGTAGATTGC	59.191	50.000	0.00	0.00	0.00	3.56
1999	2054	5.123936	GTTTCCGCCCAAGATTAGTAGATT	58.876	41.667	0.00	0.00	0.00	2.40
2013	2069	2.943653	CACAACTCGTTTCCGCCC	59.056	61.111	0.00	0.00	0.00	6.13
2018	2074	5.779806	ATACAGTATGCACAACTCGTTTC	57.220	39.130	0.57	0.00	42.53	2.78
2024	2080	7.555965	TCACATCTTATACAGTATGCACAACT	58.444	34.615	3.03	0.00	42.53	3.16
2030	2086	8.744652	AGAGGTATCACATCTTATACAGTATGC	58.255	37.037	3.03	0.00	35.48	3.14
2198	2439	5.241662	TCTTTTTGTTTTGTTTGGAGTGGG	58.758	37.500	0.00	0.00	0.00	4.61
2226	2467	2.664402	ATGGCCATTATGGTGTCTCC	57.336	50.000	14.09	5.55	40.46	3.71
2258	2500	5.027460	TGTCTATAGGCCAAAAGAGTACCA	58.973	41.667	5.01	0.00	0.00	3.25
2259	2501	5.609533	TGTCTATAGGCCAAAAGAGTACC	57.390	43.478	5.01	0.00	0.00	3.34
2260	2502	6.017852	GCATTGTCTATAGGCCAAAAGAGTAC	60.018	42.308	5.01	0.00	0.00	2.73
2261	2503	6.055588	GCATTGTCTATAGGCCAAAAGAGTA	58.944	40.000	5.01	0.00	0.00	2.59
2293	2535	8.250332	TCAATCATGGTTAATGCTTTCCTTTAC	58.750	33.333	0.00	0.00	36.11	2.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.