AutoCloner

Multiple sequence alignment - TraesCS4B01G180900

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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	TraesCS4B01G180900	chr4B	100.000	2594	0	0	1	2594	395911659	395909066	0.000000e+00	4791.0
1	TraesCS4B01G180900	chr4D	93.652	2237	78	26	214	2411	318607308	318605097	0.000000e+00	3286.0
2	TraesCS4B01G180900	chr4D	75.000	676	109	44	1955	2590	426216520	426215865	9.210000e-65	257.0
3	TraesCS4B01G180900	chr4D	79.404	403	45	28	2221	2594	318605376	318604983	1.540000e-62	250.0
4	TraesCS4B01G180900	chr4D	94.304	158	8	1	1	158	318607777	318607621	9.280000e-60	241.0
5	TraesCS4B01G180900	chr4D	92.623	122	7	2	2474	2594	318603728	318603608	9.540000e-40	174.0
6	TraesCS4B01G180900	chr4D	96.429	56	2	0	154	209	318607529	318607474	2.750000e-15	93.5
7	TraesCS4B01G180900	chr4A	90.004	2501	129	60	1	2411	155592935	155595404	0.000000e+00	3121.0
8	TraesCS4B01G180900	chr6A	73.082	717	108	48	1924	2594	513355212	513355889	2.650000e-40	176.0
9	TraesCS4B01G180900	chr6A	82.967	182	25	6	2415	2594	15790743	15790566	2.670000e-35	159.0
10	TraesCS4B01G180900	chr3D	83.333	192	26	4	2403	2592	151849680	151849867	3.430000e-39	172.0
11	TraesCS4B01G180900	chr3D	87.681	138	16	1	2457	2593	599530677	599530540	2.670000e-35	159.0
12	TraesCS4B01G180900	chr1D	83.696	184	23	6	2412	2592	422858031	422858210	1.600000e-37	167.0
13	TraesCS4B01G180900	chr1D	79.394	165	28	5	2247	2411	40910177	40910019	7.590000e-21	111.0
14	TraesCS4B01G180900	chr2A	82.286	175	28	3	2422	2594	751395673	751395500	5.780000e-32	148.0

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	TraesCS4B01G180900	chr4B	395909066	395911659	2593	True	4791.0	4791	100.0000	1	2594	1	chr4B.!!$R1	2593
1	TraesCS4B01G180900	chr4D	318603608	318607777	4169	True	808.9	3286	91.2824	1	2594	5	chr4D.!!$R2	2593
2	TraesCS4B01G180900	chr4D	426215865	426216520	655	True	257.0	257	75.0000	1955	2590	1	chr4D.!!$R1	635
3	TraesCS4B01G180900	chr4A	155592935	155595404	2469	False	3121.0	3121	90.0040	1	2411	1	chr4A.!!$F1	2410

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
274	531	0.037419	TTTCCTAACGTACGTGCCCC	60.037	55.0	23.57	0.0	0.00	5.80	F
337	594	0.179134	GGAGTCGTGTCGAGGGAATG	60.179	60.0	0.00	0.0	36.23	2.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1290	1562	1.022735	GCAGCATCCTCATGACCTTG	58.977	55.0	0.0	0.00	30.57	3.61	R
1789	2064	1.102222	CCTTCTAGTAGACCGCGCCT	61.102	60.0	0.0	1.95	0.00	5.52	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
51	52	7.080099	CCTTATATCTTTGCCGATGTTTGATG	58.920	38.462	0.00	0.00	0.00	3.07
73	74	4.082625	TGTTGCTGTGCTGATCATTTTAGG	60.083	41.667	0.00	0.00	0.00	2.69
116	117	1.811266	CCGTGACAAGCTGATCCGG	60.811	63.158	0.00	0.00	0.00	5.14
138	139	2.626266	TCTCTGTACTCTCGGTGCAAAA	59.374	45.455	0.00	0.00	39.86	2.44
139	140	3.069016	TCTCTGTACTCTCGGTGCAAAAA	59.931	43.478	0.00	0.00	39.86	1.94
187	283	1.477553	AATGGACCGCATGCATTCTT	58.522	45.000	19.57	0.00	45.52	2.52
188	284	1.477553	ATGGACCGCATGCATTCTTT	58.522	45.000	19.57	2.20	35.46	2.52
210	306	5.536497	TCCTGGAGGAGTCTGCATATATA	57.464	43.478	0.00	0.00	40.54	0.86
212	308	7.226059	TCCTGGAGGAGTCTGCATATATATA	57.774	40.000	0.00	0.00	40.54	0.86
262	519	7.751646	TGGGAGTCTATGAAAAGTTTTCCTAA	58.248	34.615	22.47	7.48	0.00	2.69
263	520	7.664318	TGGGAGTCTATGAAAAGTTTTCCTAAC	59.336	37.037	22.47	15.48	0.00	2.34
264	521	7.148457	GGGAGTCTATGAAAAGTTTTCCTAACG	60.148	40.741	22.47	8.96	0.00	3.18
265	522	7.387122	GGAGTCTATGAAAAGTTTTCCTAACGT	59.613	37.037	22.47	6.48	0.00	3.99
274	531	0.037419	TTTCCTAACGTACGTGCCCC	60.037	55.000	23.57	0.00	0.00	5.80
337	594	0.179134	GGAGTCGTGTCGAGGGAATG	60.179	60.000	0.00	0.00	36.23	2.67
573	831	8.885494	TCTCTCTTCTCTCTGAAAAAGAAAAG	57.115	34.615	0.00	0.00	33.37	2.27
574	832	8.700051	TCTCTCTTCTCTCTGAAAAAGAAAAGA	58.300	33.333	0.00	0.00	33.37	2.52
575	833	8.885494	TCTCTTCTCTCTGAAAAAGAAAAGAG	57.115	34.615	9.06	9.06	41.73	2.85
576	834	7.930865	TCTCTTCTCTCTGAAAAAGAAAAGAGG	59.069	37.037	13.45	2.54	41.29	3.69
616	875	1.338674	TGGCGCCTACCATATGCATAC	60.339	52.381	29.70	0.00	33.75	2.39
617	876	1.338674	GGCGCCTACCATATGCATACA	60.339	52.381	22.15	0.00	0.00	2.29
618	877	1.732259	GCGCCTACCATATGCATACAC	59.268	52.381	8.99	0.00	0.00	2.90
619	878	2.870035	GCGCCTACCATATGCATACACA	60.870	50.000	8.99	0.00	0.00	3.72
620	879	3.599343	CGCCTACCATATGCATACACAT	58.401	45.455	8.99	0.00	0.00	3.21
621	880	4.754322	CGCCTACCATATGCATACACATA	58.246	43.478	8.99	0.00	36.96	2.29
681	940	0.690762	AAGCTAAGCTCCCCGTCAAA	59.309	50.000	0.00	0.00	38.25	2.69
804	1063	4.289245	GAATACGCCGCGCCCCTA	62.289	66.667	13.88	0.00	0.00	3.53
805	1064	3.584868	GAATACGCCGCGCCCCTAT	62.585	63.158	13.88	0.00	0.00	2.57
806	1065	2.216750	GAATACGCCGCGCCCCTATA	62.217	60.000	13.88	0.00	0.00	1.31
1020	1279	3.567797	GCATGCGAGCTTCCGTCC	61.568	66.667	0.00	0.00	0.00	4.79
1329	1601	0.517755	TCGACAAGCTCTCAGACGAC	59.482	55.000	0.00	0.00	0.00	4.34
1502	1774	5.473796	TTACGTTCGATAGGGCAAATTTC	57.526	39.130	0.00	0.00	0.00	2.17
1687	1961	4.943093	GCAATGAAGGCCCAATTATTTTGT	59.057	37.500	0.00	0.00	0.00	2.83
1789	2064	3.193903	TCGAGTTCCGGTACAATTCATCA	59.806	43.478	14.14	0.00	39.14	3.07
1811	2086	1.337387	GCGCGGTCTACTAGAAGGAAT	59.663	52.381	8.83	0.00	0.00	3.01
1831	2106	1.975660	AGAGCCGGCTTTTACACAAA	58.024	45.000	33.34	0.00	0.00	2.83
1832	2107	2.303175	AGAGCCGGCTTTTACACAAAA	58.697	42.857	33.34	0.00	32.73	2.44
1842	2117	9.376171	CCGGCTTTTACACAAAATTTTTATTTC	57.624	29.630	0.00	0.00	33.27	2.17
1922	2202	9.069082	TCCATTTCTTCTGTTTTATTCGGTTTA	57.931	29.630	0.00	0.00	0.00	2.01
1923	2203	9.855021	CCATTTCTTCTGTTTTATTCGGTTTAT	57.145	29.630	0.00	0.00	0.00	1.40
2413	2846	9.793252	AACACATCTATCATCTTTAAAATGTGC	57.207	29.630	18.52	0.00	43.98	4.57
2414	2847	8.959548	ACACATCTATCATCTTTAAAATGTGCA	58.040	29.630	18.52	0.00	43.98	4.57
2452	3077	9.617975	TTTTTGAACACATGGTTGAAATTTTTC	57.382	25.926	10.64	0.00	41.23	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
51	52	4.082571	ACCTAAAATGATCAGCACAGCAAC	60.083	41.667	0.09	0.00	0.00	4.17
73	74	6.346359	GGGTAAATTGCTAACGATCGATGTAC	60.346	42.308	24.34	12.40	0.00	2.90
116	117	1.166129	TGCACCGAGAGTACAGAGAC	58.834	55.000	0.00	0.00	0.00	3.36
138	139	0.695347	AGCTAGCTTGCAGGTTCCTT	59.305	50.000	22.05	0.00	34.99	3.36
139	140	1.484240	CTAGCTAGCTTGCAGGTTCCT	59.516	52.381	24.88	2.09	34.99	3.36
187	283	2.550277	TATGCAGACTCCTCCAGGAA	57.450	50.000	0.00	0.00	44.91	3.36
188	284	2.783379	ATATGCAGACTCCTCCAGGA	57.217	50.000	0.00	0.00	43.08	3.86
210	306	9.624373	ATCACCGACGTTAAGTAGGATATATAT	57.376	33.333	4.42	0.00	46.99	0.86
212	308	7.934855	ATCACCGACGTTAAGTAGGATATAT	57.065	36.000	4.42	0.00	46.99	0.86
262	519	2.181954	TATTTTTGGGGCACGTACGT	57.818	45.000	16.72	16.72	0.00	3.57
263	520	4.121317	TCTATATTTTTGGGGCACGTACG	58.879	43.478	15.01	15.01	0.00	3.67
264	521	6.435428	CAATCTATATTTTTGGGGCACGTAC	58.565	40.000	0.00	0.00	0.00	3.67
265	522	5.009210	GCAATCTATATTTTTGGGGCACGTA	59.991	40.000	0.00	0.00	0.00	3.57
274	531	7.011773	CACCGATCGAGCAATCTATATTTTTG	58.988	38.462	18.66	0.00	0.00	2.44
337	594	3.914426	ATCACTACAACACCCTGGATC	57.086	47.619	0.00	0.00	0.00	3.36
573	831	0.604578	ATTGTTGCACACATGGCCTC	59.395	50.000	3.32	0.00	34.43	4.70
574	832	1.820519	CTATTGTTGCACACATGGCCT	59.179	47.619	3.32	0.00	34.43	5.19
575	833	1.818060	TCTATTGTTGCACACATGGCC	59.182	47.619	0.00	0.00	34.43	5.36
576	834	3.441163	CATCTATTGTTGCACACATGGC	58.559	45.455	0.00	0.00	34.43	4.40
616	875	6.528072	AGATGTTCGTATCGTATGCATATGTG	59.472	38.462	22.30	10.64	32.33	3.21
617	876	6.528072	CAGATGTTCGTATCGTATGCATATGT	59.472	38.462	22.30	13.69	32.33	2.29
618	877	6.506984	GCAGATGTTCGTATCGTATGCATATG	60.507	42.308	18.27	18.27	38.43	1.78
619	878	5.516696	GCAGATGTTCGTATCGTATGCATAT	59.483	40.000	10.16	0.00	38.43	1.78
620	879	4.857037	GCAGATGTTCGTATCGTATGCATA	59.143	41.667	1.16	1.16	38.43	3.14
621	880	3.675225	GCAGATGTTCGTATCGTATGCAT	59.325	43.478	3.79	3.79	38.43	3.96
746	1005	2.105128	GCGAGACACTGCCGCTAT	59.895	61.111	0.00	0.00	44.83	2.97
803	1062	8.573885	CACGAACCACCTACAGAAAGATATATA	58.426	37.037	0.00	0.00	0.00	0.86
804	1063	7.434492	CACGAACCACCTACAGAAAGATATAT	58.566	38.462	0.00	0.00	0.00	0.86
805	1064	6.183360	CCACGAACCACCTACAGAAAGATATA	60.183	42.308	0.00	0.00	0.00	0.86
806	1065	5.395324	CCACGAACCACCTACAGAAAGATAT	60.395	44.000	0.00	0.00	0.00	1.63
994	1253	2.802667	GCTCGCATGCATCGTTCGT	61.803	57.895	19.57	0.00	0.00	3.85
1151	1420	6.819146	CAGTACCCTAGAATCTTCAAGGAAAC	59.181	42.308	0.00	0.00	0.00	2.78
1290	1562	1.022735	GCAGCATCCTCATGACCTTG	58.977	55.000	0.00	0.00	30.57	3.61
1388	1660	2.433970	TGTCGCTGTGGATCCATTCATA	59.566	45.455	19.62	1.06	0.00	2.15
1502	1774	6.971602	AGATGAATCAAAGAGCATAGCAATG	58.028	36.000	0.00	0.00	36.09	2.82
1507	1779	7.908827	AGCATAGATGAATCAAAGAGCATAG	57.091	36.000	0.00	0.00	0.00	2.23
1687	1961	4.715534	TGAACCCCTGTAATGAAGTCAA	57.284	40.909	0.00	0.00	0.00	3.18
1722	1997	1.136803	CGCGATGCAACGATGATACAG	60.137	52.381	21.39	0.00	35.09	2.74
1789	2064	1.102222	CCTTCTAGTAGACCGCGCCT	61.102	60.000	0.00	1.95	0.00	5.52
1811	2086	2.843401	TTGTGTAAAAGCCGGCTCTA	57.157	45.000	32.93	21.37	0.00	2.43
1842	2117	7.591426	CAGGAAAGATACAAAAACCGAAGAAAG	59.409	37.037	0.00	0.00	0.00	2.62
1952	2256	4.119136	ACCGAAGAAACAAATGCAAAAGG	58.881	39.130	0.00	0.00	0.00	3.11
2203	2628	8.975410	AAAAAGTTTAAAGTGTGTGTAGGAAC	57.025	30.769	0.00	0.00	0.00	3.62
2431	3056	9.914923	GTTTAGAAAAATTTCAACCATGTGTTC	57.085	29.630	8.47	0.00	39.61	3.18
2434	3059	8.877779	TGTGTTTAGAAAAATTTCAACCATGTG	58.122	29.630	8.47	0.00	39.61	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.