AutoCloner

Multiple sequence alignment - TraesCS3D01G425700

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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	TraesCS3D01G425700	chr3D	100.000	2780	0	0	1	2780	538179883	538177104	0.000000e+00	5134.0
1	TraesCS3D01G425700	chr3D	89.971	349	32	2	1653	2000	532808552	532808898	5.460000e-122	448.0
2	TraesCS3D01G425700	chr3D	83.073	384	32	14	2372	2723	538085239	538084857	4.470000e-83	318.0
3	TraesCS3D01G425700	chr3D	90.991	111	4	4	2114	2218	538121678	538121568	8.020000e-31	145.0
4	TraesCS3D01G425700	chr1D	99.151	2002	17	0	1	2002	463533179	463531178	0.000000e+00	3603.0
5	TraesCS3D01G425700	chr1D	98.603	2005	26	2	1	2003	47641028	47639024	0.000000e+00	3546.0
6	TraesCS3D01G425700	chr5D	99.050	2001	19	0	1	2001	322187733	322189733	0.000000e+00	3591.0
7	TraesCS3D01G425700	chr5B	94.605	2002	93	4	1	2002	448041234	448039248	0.000000e+00	3085.0
8	TraesCS3D01G425700	chr2D	93.666	2005	120	5	1	2001	628169296	628171297	0.000000e+00	2992.0
9	TraesCS3D01G425700	chr4D	93.566	2005	122	5	1	2001	389490678	389492679	0.000000e+00	2981.0
10	TraesCS3D01G425700	chr7A	93.263	2004	129	4	1	2001	711168954	711170954	0.000000e+00	2948.0
11	TraesCS3D01G425700	chr7A	86.185	2005	264	13	1	2001	109451694	109453689	0.000000e+00	2156.0
12	TraesCS3D01G425700	chr7D	98.864	1585	16	2	216	1799	574676019	574674436	0.000000e+00	2826.0
13	TraesCS3D01G425700	chr3A	87.935	804	48	28	2002	2778	673602539	673601758	0.000000e+00	902.0
14	TraesCS3D01G425700	chr3A	85.028	354	32	10	2382	2716	673588004	673587653	9.540000e-90	340.0
15	TraesCS3D01G425700	chr3A	89.474	114	3	3	2114	2218	673588882	673588769	4.830000e-28	135.0
16	TraesCS3D01G425700	chr3A	100.000	29	0	0	2305	2333	673588615	673588587	1.000000e-03	54.7
17	TraesCS3D01G425700	chr3B	86.006	343	26	9	2382	2702	712990775	712990433	5.700000e-92	348.0
18	TraesCS3D01G425700	chr3B	93.333	165	10	1	2135	2298	712991791	712991627	2.770000e-60	243.0

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	TraesCS3D01G425700	chr3D	538177104	538179883	2779	True	5134.0	5134	100.0000	1	2780	1	chr3D.!!$R3	2779
1	TraesCS3D01G425700	chr1D	463531178	463533179	2001	True	3603.0	3603	99.1510	1	2002	1	chr1D.!!$R2	2001
2	TraesCS3D01G425700	chr1D	47639024	47641028	2004	True	3546.0	3546	98.6030	1	2003	1	chr1D.!!$R1	2002
3	TraesCS3D01G425700	chr5D	322187733	322189733	2000	False	3591.0	3591	99.0500	1	2001	1	chr5D.!!$F1	2000
4	TraesCS3D01G425700	chr5B	448039248	448041234	1986	True	3085.0	3085	94.6050	1	2002	1	chr5B.!!$R1	2001
5	TraesCS3D01G425700	chr2D	628169296	628171297	2001	False	2992.0	2992	93.6660	1	2001	1	chr2D.!!$F1	2000
6	TraesCS3D01G425700	chr4D	389490678	389492679	2001	False	2981.0	2981	93.5660	1	2001	1	chr4D.!!$F1	2000
7	TraesCS3D01G425700	chr7A	711168954	711170954	2000	False	2948.0	2948	93.2630	1	2001	1	chr7A.!!$F2	2000
8	TraesCS3D01G425700	chr7A	109451694	109453689	1995	False	2156.0	2156	86.1850	1	2001	1	chr7A.!!$F1	2000
9	TraesCS3D01G425700	chr7D	574674436	574676019	1583	True	2826.0	2826	98.8640	216	1799	1	chr7D.!!$R1	1583
10	TraesCS3D01G425700	chr3A	673601758	673602539	781	True	902.0	902	87.9350	2002	2778	1	chr3A.!!$R1	776
11	TraesCS3D01G425700	chr3B	712990433	712991791	1358	True	295.5	348	89.6695	2135	2702	2	chr3B.!!$R1	567

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
485	486	8.46393	TTGAAAAGTCTTGACCTTGATATTGT	57.536	30.769	0.0	0.0	0.0	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2370	2446	1.015109	GCAGATGCATCACTGACAGG	58.985	55.0	27.81	8.06	41.59	4.0	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
485	486	8.463930	TTGAAAAGTCTTGACCTTGATATTGT	57.536	30.769	0.00	0.00	0.00	2.71
1916	1920	8.723942	AAGGAGAGTATGCTTTACTTACATTG	57.276	34.615	0.00	0.00	35.84	2.82
1977	1985	0.178947	TTGATTTTTGTCCCGGGCCT	60.179	50.000	18.49	0.00	0.00	5.19
2004	2012	0.755698	TCTGGAGACGGCCCTGATAC	60.756	60.000	0.00	0.00	36.33	2.24
2008	2016	0.601311	GAGACGGCCCTGATACATGC	60.601	60.000	0.00	0.00	0.00	4.06
2047	2055	6.897986	AGAATCCAAAGAGATACATCAGCTT	58.102	36.000	0.00	0.00	0.00	3.74
2049	2057	8.149647	AGAATCCAAAGAGATACATCAGCTTAG	58.850	37.037	0.00	0.00	0.00	2.18
2066	2074	6.556495	TCAGCTTAGATATGAGGATCCAAAGT	59.444	38.462	15.82	0.00	0.00	2.66
2067	2075	6.649973	CAGCTTAGATATGAGGATCCAAAGTG	59.350	42.308	15.82	2.78	0.00	3.16
2068	2076	6.328672	AGCTTAGATATGAGGATCCAAAGTGT	59.671	38.462	15.82	0.00	0.00	3.55
2069	2077	7.510685	AGCTTAGATATGAGGATCCAAAGTGTA	59.489	37.037	15.82	0.00	0.00	2.90
2070	2078	8.317679	GCTTAGATATGAGGATCCAAAGTGTAT	58.682	37.037	15.82	3.40	0.00	2.29
2071	2079	9.650539	CTTAGATATGAGGATCCAAAGTGTATG	57.349	37.037	15.82	0.00	0.00	2.39
2072	2080	6.471146	AGATATGAGGATCCAAAGTGTATGC	58.529	40.000	15.82	0.00	0.00	3.14
2073	2081	3.998913	TGAGGATCCAAAGTGTATGCA	57.001	42.857	15.82	0.00	0.00	3.96
2074	2082	3.877559	TGAGGATCCAAAGTGTATGCAG	58.122	45.455	15.82	0.00	0.00	4.41
2075	2083	3.264193	TGAGGATCCAAAGTGTATGCAGT	59.736	43.478	15.82	0.00	0.00	4.40
2076	2084	4.263462	TGAGGATCCAAAGTGTATGCAGTT	60.263	41.667	15.82	0.00	39.76	3.16
2077	2085	4.666512	AGGATCCAAAGTGTATGCAGTTT	58.333	39.130	15.82	10.46	46.01	2.66
2078	2086	4.702131	AGGATCCAAAGTGTATGCAGTTTC	59.298	41.667	15.82	3.42	44.00	2.78
2079	2087	4.458989	GGATCCAAAGTGTATGCAGTTTCA	59.541	41.667	13.02	4.56	44.00	2.69
2080	2088	5.126061	GGATCCAAAGTGTATGCAGTTTCAT	59.874	40.000	13.02	8.69	44.00	2.57
2081	2089	6.318648	GGATCCAAAGTGTATGCAGTTTCATA	59.681	38.462	13.02	3.50	44.00	2.15
2082	2090	7.013655	GGATCCAAAGTGTATGCAGTTTCATAT	59.986	37.037	13.02	7.58	44.00	1.78
2083	2091	8.978874	ATCCAAAGTGTATGCAGTTTCATATA	57.021	30.769	13.02	0.00	44.00	0.86
2084	2092	8.208718	TCCAAAGTGTATGCAGTTTCATATAC	57.791	34.615	13.02	0.00	44.00	1.47
2085	2093	7.826744	TCCAAAGTGTATGCAGTTTCATATACA	59.173	33.333	13.02	0.00	44.00	2.29
2086	2094	8.623903	CCAAAGTGTATGCAGTTTCATATACAT	58.376	33.333	13.02	0.04	44.00	2.29
2087	2095	9.442033	CAAAGTGTATGCAGTTTCATATACATG	57.558	33.333	13.02	0.00	44.00	3.21
2088	2096	8.737168	AAGTGTATGCAGTTTCATATACATGT	57.263	30.769	2.69	2.69	40.95	3.21
2193	2214	7.426929	ACAAGTTGTGACTATTCAACAGATC	57.573	36.000	7.96	0.00	44.08	2.75
2199	2220	8.436200	GTTGTGACTATTCAACAGATCAAGTAC	58.564	37.037	0.00	0.00	42.10	2.73
2229	2250	2.282180	GGCTTTCGGGCTGGTTCA	60.282	61.111	0.00	0.00	37.53	3.18
2283	2304	6.292168	GGAAACACGGAGATATGTACAAATCG	60.292	42.308	0.00	1.48	0.00	3.34
2285	2306	4.098960	ACACGGAGATATGTACAAATCGGT	59.901	41.667	0.00	3.78	0.00	4.69
2340	2381	0.173708	CGTTAGCTCCACCTCCACTC	59.826	60.000	0.00	0.00	0.00	3.51
2352	2393	1.609501	TCCACTCGGGAGGAAGGTG	60.610	63.158	0.00	0.00	42.15	4.00
2368	2444	3.482156	AGGTGGTATGCTATGCTGAAG	57.518	47.619	0.00	0.00	0.00	3.02
2370	2446	3.134458	GGTGGTATGCTATGCTGAAGAC	58.866	50.000	0.00	0.00	0.00	3.01
2371	2447	3.134458	GTGGTATGCTATGCTGAAGACC	58.866	50.000	0.00	0.00	0.00	3.85
2372	2448	3.041211	TGGTATGCTATGCTGAAGACCT	58.959	45.455	0.00	0.00	0.00	3.85
2373	2449	3.181462	TGGTATGCTATGCTGAAGACCTG	60.181	47.826	0.00	0.00	0.00	4.00
2377	2453	2.093816	TGCTATGCTGAAGACCTGTCAG	60.094	50.000	0.00	0.00	44.48	3.51
2378	2454	2.093764	GCTATGCTGAAGACCTGTCAGT	60.094	50.000	0.00	0.00	43.71	3.41
2409	3202	1.064758	CATTAGGTGCTACAGGCCCAA	60.065	52.381	0.00	0.00	40.92	4.12
2410	3203	1.068948	TTAGGTGCTACAGGCCCAAA	58.931	50.000	0.00	0.00	40.92	3.28
2512	3322	2.169789	CCGTTCGCCTGATGAGCAG	61.170	63.158	0.00	0.00	44.49	4.24
2591	3401	1.962822	CGTGACCTGTGCATGCACT	60.963	57.895	41.43	27.66	46.30	4.40
2599	3416	1.934525	CTGTGCATGCACTGAGATCTC	59.065	52.381	41.43	19.87	46.30	2.75
2615	3432	0.681733	TCTCCTAATCCTGGCGCATC	59.318	55.000	10.83	0.00	0.00	3.91
2616	3433	0.668706	CTCCTAATCCTGGCGCATCG	60.669	60.000	10.83	0.00	0.00	3.84
2649	3466	5.238868	ACATGTCGCTATAACTCTGACGTAT	59.761	40.000	0.00	0.00	32.32	3.06
2669	3486	1.979155	TGCTCTGAGTCCGGTCCAG	60.979	63.158	0.00	7.73	0.00	3.86
2704	3521	2.368875	GACGGGATCTCTCTCTCTCTCT	59.631	54.545	0.00	0.00	0.00	3.10
2744	3566	6.351711	TCTCTCTCTCTCTCTCTCTTCATTG	58.648	44.000	0.00	0.00	0.00	2.82
2755	3577	4.527509	TCTCTTCATTGAGAGTGTGGTC	57.472	45.455	10.78	0.00	42.96	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
485	486	2.568546	TCCCTGCCCTCTCAGATTAA	57.431	50.000	0.00	0.00	36.19	1.40
740	743	5.237344	GCTGACAATGACTTGAGTGTTACTT	59.763	40.000	0.00	0.00	36.20	2.24
811	814	5.286221	AGCCTCCCTTATTTCTGGTAGTTA	58.714	41.667	0.00	0.00	0.00	2.24
1328	1331	1.342819	AGGATCGCAGCCTATCTGAAC	59.657	52.381	0.00	0.00	45.72	3.18
1977	1985	1.613255	GGCCGTCTCCAGAAATTTGGA	60.613	52.381	0.00	0.00	44.84	3.53
2004	2012	8.729756	TGGATTCTCGTATATATTTTTGGCATG	58.270	33.333	0.00	0.00	0.00	4.06
2034	2042	9.135189	GATCCTCATATCTAAGCTGATGTATCT	57.865	37.037	0.00	0.00	0.00	1.98
2035	2043	8.359642	GGATCCTCATATCTAAGCTGATGTATC	58.640	40.741	3.84	0.00	0.00	2.24
2047	2055	7.235399	TGCATACACTTTGGATCCTCATATCTA	59.765	37.037	14.23	0.00	0.00	1.98
2049	2057	6.233434	TGCATACACTTTGGATCCTCATATC	58.767	40.000	14.23	0.00	0.00	1.63
2066	2074	9.777297	ATACACATGTATATGAAACTGCATACA	57.223	29.630	6.45	0.00	39.29	2.29
2068	2076	9.435688	GGATACACATGTATATGAAACTGCATA	57.564	33.333	0.25	0.00	40.99	3.14
2069	2077	7.938490	TGGATACACATGTATATGAAACTGCAT	59.062	33.333	0.25	0.00	46.17	3.96
2070	2078	7.278875	TGGATACACATGTATATGAAACTGCA	58.721	34.615	0.25	0.00	46.17	4.41
2071	2079	7.728847	TGGATACACATGTATATGAAACTGC	57.271	36.000	0.25	0.00	46.17	4.40
2143	2163	3.752747	TCACATGATGCCTGTACACTTTG	59.247	43.478	0.00	0.00	0.00	2.77
2193	2214	5.455056	AGCCCTAGATAATCGTGTACTTG	57.545	43.478	0.00	0.00	0.00	3.16
2199	2220	3.318017	CCGAAAGCCCTAGATAATCGTG	58.682	50.000	0.00	0.00	0.00	4.35
2229	2250	9.547753	CCTAAATGTAGCATAGTATGTCAACTT	57.452	33.333	11.73	8.88	0.00	2.66
2265	2286	4.447724	CCAACCGATTTGTACATATCTCCG	59.552	45.833	19.80	10.47	32.71	4.63
2283	2304	2.104253	CCGTGCCGTGATACCAACC	61.104	63.158	0.00	0.00	0.00	3.77
2285	2306	2.266372	CCCGTGCCGTGATACCAA	59.734	61.111	0.00	0.00	0.00	3.67
2340	2381	1.146263	GCATACCACCTTCCTCCCG	59.854	63.158	0.00	0.00	0.00	5.14
2346	2387	3.475566	TCAGCATAGCATACCACCTTC	57.524	47.619	0.00	0.00	0.00	3.46
2348	2389	3.041211	TCTTCAGCATAGCATACCACCT	58.959	45.455	0.00	0.00	0.00	4.00
2349	2390	3.134458	GTCTTCAGCATAGCATACCACC	58.866	50.000	0.00	0.00	0.00	4.61
2352	2393	3.181461	ACAGGTCTTCAGCATAGCATACC	60.181	47.826	0.00	0.00	0.00	2.73
2368	2444	2.277969	CAGATGCATCACTGACAGGTC	58.722	52.381	27.81	0.00	36.38	3.85
2370	2446	1.015109	GCAGATGCATCACTGACAGG	58.985	55.000	27.81	8.06	41.59	4.00
2457	3266	7.950684	AGACTTCCAGTAGGATGCACTATAATA	59.049	37.037	0.00	0.00	45.26	0.98
2512	3322	6.019075	GGTGTAAGAAACTCAACCAAATTTGC	60.019	38.462	12.92	0.00	0.00	3.68
2591	3401	2.242926	CGCCAGGATTAGGAGATCTCA	58.757	52.381	23.85	4.32	0.00	3.27
2599	3416	0.946221	GTCGATGCGCCAGGATTAGG	60.946	60.000	4.18	0.00	0.00	2.69
2616	3433	8.818057	AGAGTTATAGCGACATGTAAATTTGTC	58.182	33.333	0.00	0.00	0.00	3.18
2635	3452	4.640647	TCAGAGCACATACGTCAGAGTTAT	59.359	41.667	0.00	0.00	0.00	1.89
2649	3466	2.276116	GGACCGGACTCAGAGCACA	61.276	63.158	9.46	0.00	0.00	4.57
2669	3486	0.249489	CCCGTCGAATCCTGGTGATC	60.249	60.000	0.00	0.00	31.61	2.92
2704	3521	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
2744	3566	0.394565	AGCAACCAGACCACACTCTC	59.605	55.000	0.00	0.00	0.00	3.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.