AutoCloner

Multiple sequence alignment - TraesCS7B01G206800

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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	TraesCS7B01G206800	chr7B	100.000	2552	0	0	1	2552	378391553	378389002	0.000000e+00	4713.0
1	TraesCS7B01G206800	chr7B	84.375	256	33	4	2155	2405	163488637	163488384	7.050000e-61	244.0
2	TraesCS7B01G206800	chr7B	93.711	159	10	0	626	784	378390839	378390681	3.280000e-59	239.0
3	TraesCS7B01G206800	chr7B	93.711	159	10	0	715	873	378390928	378390770	3.280000e-59	239.0
4	TraesCS7B01G206800	chr7B	93.506	77	5	0	626	702	378390750	378390674	5.770000e-22	115.0
5	TraesCS7B01G206800	chr7B	93.506	77	5	0	804	880	378390928	378390852	5.770000e-22	115.0
6	TraesCS7B01G206800	chr7B	77.473	182	23	12	236	409	316405034	316404863	2.700000e-15	93.5
7	TraesCS7B01G206800	chr7A	91.616	2624	144	22	1	2552	432695732	432693113	0.000000e+00	3557.0
8	TraesCS7B01G206800	chr7A	95.597	159	7	0	626	784	432695005	432694847	3.260000e-64	255.0
9	TraesCS7B01G206800	chr7A	84.436	257	30	7	2155	2405	209155814	209155562	7.050000e-61	244.0
10	TraesCS7B01G206800	chr7A	94.340	159	9	0	715	873	432695094	432694936	7.050000e-61	244.0
11	TraesCS7B01G206800	chr7A	94.805	77	4	0	626	702	432694916	432694840	1.240000e-23	121.0
12	TraesCS7B01G206800	chr7A	95.714	70	3	0	804	873	432695094	432695025	2.080000e-21	113.0
13	TraesCS7B01G206800	chr7A	84.091	88	10	4	355	441	486240097	486240013	5.850000e-12	82.4
14	TraesCS7B01G206800	chr7D	91.475	2604	157	23	1	2552	383975651	383973061	0.000000e+00	3518.0
15	TraesCS7B01G206800	chr7D	81.308	428	73	6	1	424	376327093	376326669	8.740000e-90	340.0
16	TraesCS7B01G206800	chr7D	84.884	258	32	4	2155	2407	199355913	199355658	1.170000e-63	254.0
17	TraesCS7B01G206800	chr7D	94.340	159	9	0	626	784	383974926	383974768	7.050000e-61	244.0
18	TraesCS7B01G206800	chr7D	93.082	159	11	0	715	873	383975015	383974857	1.530000e-57	233.0
19	TraesCS7B01G206800	chr7D	94.805	77	4	0	626	702	383974837	383974761	1.240000e-23	121.0
20	TraesCS7B01G206800	chr7D	95.714	70	3	0	804	873	383975015	383974946	2.080000e-21	113.0
21	TraesCS7B01G206800	chr5D	82.558	258	39	4	2153	2406	460939879	460939624	3.300000e-54	222.0
22	TraesCS7B01G206800	chr2D	82.222	270	37	9	2155	2418	73591148	73590884	3.300000e-54	222.0
23	TraesCS7B01G206800	chr5A	81.919	271	39	9	160	425	292735582	292735847	1.190000e-53	220.0
24	TraesCS7B01G206800	chr1B	82.000	250	35	7	2175	2418	112191845	112192090	1.200000e-48	204.0
25	TraesCS7B01G206800	chr1B	87.755	49	6	0	1629	1677	628119158	628119206	9.860000e-05	58.4
26	TraesCS7B01G206800	chr1D	81.423	253	30	11	2150	2398	331188798	331189037	9.320000e-45	191.0
27	TraesCS7B01G206800	chr6D	88.750	80	4	5	348	425	112822493	112822569	2.700000e-15	93.5
28	TraesCS7B01G206800	chr6D	80.328	122	12	6	306	424	156733903	156733791	5.850000e-12	82.4
29	TraesCS7B01G206800	chr2B	86.585	82	9	2	349	428	647590234	647590153	3.500000e-14	89.8
30	TraesCS7B01G206800	chr2B	89.091	55	6	0	1625	1679	263078895	263078949	4.560000e-08	69.4
31	TraesCS7B01G206800	chr4A	87.097	62	6	1	1628	1689	118633690	118633749	4.560000e-08	69.4
32	TraesCS7B01G206800	chrUn	87.719	57	6	1	1629	1684	23538144	23538200	5.890000e-07	65.8
33	TraesCS7B01G206800	chr4B	89.796	49	5	0	1629	1677	26807875	26807923	2.120000e-06	63.9
34	TraesCS7B01G206800	chr4B	85.000	60	7	2	1629	1687	45787595	45787537	2.740000e-05	60.2
35	TraesCS7B01G206800	chr6A	84.127	63	10	0	1630	1692	13346871	13346809	7.620000e-06	62.1

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	TraesCS7B01G206800	chr7B	378389002	378391553	2551	True	1084.2	4713	94.8868	1	2552	5	chr7B.!!$R3	2551
1	TraesCS7B01G206800	chr7A	432693113	432695732	2619	True	858.0	3557	94.4144	1	2552	5	chr7A.!!$R3	2551
2	TraesCS7B01G206800	chr7D	383973061	383975651	2590	True	845.8	3518	93.8832	1	2552	5	chr7D.!!$R3	2551

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
417	419	0.17576	GTTCTATGGTCTGCGGCTCA	59.824	55.0	0.0	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1753	1770	0.250989	CCCAGTTTGCCTCCGGTTTA	60.251	55.0	0.0	0.0	0.0	2.01	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
39	40	3.622206	GCTGGGACAACATCATTCCACTA	60.622	47.826	0.00	0.00	38.70	2.74
131	132	5.936187	TTGGACATTGTAACTACGGGATA	57.064	39.130	0.00	0.00	0.00	2.59
170	171	9.376075	GTCTATCAGAAATGACAAGATCTTCAA	57.624	33.333	4.57	0.00	0.00	2.69
197	198	3.643237	CTCCTCCTCACATACCTGGTTA	58.357	50.000	3.84	0.00	0.00	2.85
220	221	6.313519	AGATGCATTACTTACAGGAAGGAA	57.686	37.500	0.00	0.00	42.43	3.36
256	257	5.237779	CAGATCAAAGCAAAGCAAACCAAAT	59.762	36.000	0.00	0.00	0.00	2.32
417	419	0.175760	GTTCTATGGTCTGCGGCTCA	59.824	55.000	0.00	0.00	0.00	4.26
451	453	3.206150	GCTGGCCAAATCTAAATCGAGA	58.794	45.455	7.01	0.00	0.00	4.04
472	474	6.931281	CGAGACATATTAACCATTGGATCAGT	59.069	38.462	10.37	0.00	0.00	3.41
563	565	2.787625	TCTAGGATCTTCGGGTCCCTTA	59.212	50.000	6.29	0.00	35.00	2.69
759	774	4.075963	ACAAGCAAGATTGGCATTTTGT	57.924	36.364	2.95	0.00	34.36	2.83
784	799	8.839343	GTCAATTGTCCACATATATGTCATCAA	58.161	33.333	15.60	17.93	39.39	2.57
867	882	4.520111	TCTGCCAATTGTCCATATACATGC	59.480	41.667	4.43	0.00	0.00	4.06
890	905	0.301687	CATTTGTGTAGGCGCGCTAG	59.698	55.000	32.29	4.83	0.00	3.42
921	936	2.978978	TCCATCTCCAGTTCTCAACCAA	59.021	45.455	0.00	0.00	0.00	3.67
1185	1200	1.956629	CTAGCCCGTCCGTCCACATT	61.957	60.000	0.00	0.00	0.00	2.71
1560	1575	4.556233	TCGGTAGCATATGAGCATTACAC	58.444	43.478	6.97	0.00	36.85	2.90
1639	1654	7.988028	ACTAATAAGAACTTGTAAGGGCATCTC	59.012	37.037	0.00	0.00	0.00	2.75
1643	1658	3.073274	ACTTGTAAGGGCATCTCCAAC	57.927	47.619	0.00	0.00	36.21	3.77
1646	1661	0.107654	GTAAGGGCATCTCCAACGCT	60.108	55.000	0.00	0.00	36.21	5.07
1662	1677	0.962356	CGCTGACCCTCAAAATGCCT	60.962	55.000	0.00	0.00	0.00	4.75
1671	1686	2.161609	CCTCAAAATGCCTGTAACCGTC	59.838	50.000	0.00	0.00	0.00	4.79
1676	1691	2.125793	GCCTGTAACCGTCCGGAC	60.126	66.667	25.28	25.28	38.96	4.79
1685	1700	4.052229	CGTCCGGACCGAGCAGTT	62.052	66.667	28.52	0.00	0.00	3.16
1686	1701	2.126031	GTCCGGACCGAGCAGTTC	60.126	66.667	24.75	0.00	0.00	3.01
1687	1702	2.599281	TCCGGACCGAGCAGTTCA	60.599	61.111	17.49	0.00	0.00	3.18
1696	1711	1.869767	CCGAGCAGTTCAGGCATAATC	59.130	52.381	0.00	0.00	0.00	1.75
1698	1713	3.243873	CCGAGCAGTTCAGGCATAATCTA	60.244	47.826	0.00	0.00	0.00	1.98
1708	1725	3.869832	CAGGCATAATCTATCATCCAGCG	59.130	47.826	0.00	0.00	0.00	5.18
1713	1730	5.163509	GCATAATCTATCATCCAGCGGTAGA	60.164	44.000	0.00	0.00	0.00	2.59
1757	1774	4.326413	GGTTGTCCGAATTACCGTAAAC	57.674	45.455	0.00	0.00	0.00	2.01
1758	1775	3.125146	GGTTGTCCGAATTACCGTAAACC	59.875	47.826	0.00	0.00	31.88	3.27
1844	1862	0.332632	CCAGCTCAAATCCCCTTCCA	59.667	55.000	0.00	0.00	0.00	3.53
1847	1865	1.713078	AGCTCAAATCCCCTTCCAGTT	59.287	47.619	0.00	0.00	0.00	3.16
1888	1907	2.887360	CCCCCTGCTTTGCATTCG	59.113	61.111	0.00	0.00	38.13	3.34
1903	1922	0.250513	ATTCGCACCCTCCTTGTCTC	59.749	55.000	0.00	0.00	0.00	3.36
1905	1924	0.904865	TCGCACCCTCCTTGTCTCAT	60.905	55.000	0.00	0.00	0.00	2.90
1949	1968	2.225791	CTCCCACGCATTCTCGGACA	62.226	60.000	0.00	0.00	0.00	4.02
1958	1977	0.829333	ATTCTCGGACATCTGCAGCT	59.171	50.000	9.47	0.00	0.00	4.24
1990	2009	1.005037	CTGCACGCCTTGGACTACA	60.005	57.895	0.00	0.00	0.00	2.74
2024	2043	0.674895	GGATTCGTCTGCAGCCAAGT	60.675	55.000	9.47	0.00	0.00	3.16
2030	2049	1.406069	CGTCTGCAGCCAAGTATCCTT	60.406	52.381	9.47	0.00	0.00	3.36
2040	2059	3.646637	GCCAAGTATCCTTAGCCTTCCTA	59.353	47.826	0.00	0.00	30.18	2.94
2050	2069	2.183555	CCTTCCTACCGACGCCAC	59.816	66.667	0.00	0.00	0.00	5.01
2104	2123	4.511082	CGGTCAAATGCCATTCAACTTTTT	59.489	37.500	0.00	0.00	0.00	1.94
2128	2174	1.952102	GACGATGGCGGGGTACTCAA	61.952	60.000	0.00	0.00	43.17	3.02
2135	2181	0.535102	GCGGGGTACTCAATGATGGG	60.535	60.000	0.00	0.00	0.00	4.00
2151	2197	2.750888	GGGGAATGAGTGCGAACGC	61.751	63.158	12.33	12.33	42.35	4.84
2168	2214	1.070105	GCGTTGTACCACAGGACCA	59.930	57.895	0.00	0.00	0.00	4.02
2308	2357	8.617290	AACTTATTGAACATATCCGGTTATCC	57.383	34.615	0.00	0.00	0.00	2.59
2422	2471	7.542534	TTAAGTGTTGCGACTTAAAAGAAGA	57.457	32.000	5.50	0.00	42.68	2.87
2424	2473	6.049263	AGTGTTGCGACTTAAAAGAAGAAG	57.951	37.500	5.50	0.00	0.00	2.85
2428	2477	7.483691	GTGTTGCGACTTAAAAGAAGAAGAAAA	59.516	33.333	5.50	0.00	0.00	2.29
2455	2526	1.001120	TGGCCGACTCCAGTATCCA	59.999	57.895	0.00	0.00	0.00	3.41
2471	2542	1.592669	CCATGTCCGCGGATCAGTC	60.593	63.158	33.58	18.74	0.00	3.51
2492	2563	2.416296	CCGCGGACAAATAGTGTGTCTA	60.416	50.000	24.07	0.00	44.02	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
131	132	9.359653	CATTTCTGATAGACTAAATTCCCCAAT	57.640	33.333	0.00	0.00	0.00	3.16
170	171	0.259065	TATGTGAGGAGGAGCCGACT	59.741	55.000	0.00	0.00	43.43	4.18
197	198	5.957771	TCCTTCCTGTAAGTAATGCATCT	57.042	39.130	0.00	0.00	32.89	2.90
220	221	3.752665	CTTTGATCTGAGCAGCCCATAT	58.247	45.455	0.00	0.00	0.00	1.78
429	431	2.945008	CTCGATTTAGATTTGGCCAGCA	59.055	45.455	5.11	0.00	0.00	4.41
430	432	3.002759	GTCTCGATTTAGATTTGGCCAGC	59.997	47.826	5.11	0.00	0.00	4.85
563	565	6.930731	TGTTTTCTTTTCTTTGTTAGCAGGT	58.069	32.000	0.00	0.00	0.00	4.00
697	712	1.623311	TCTCTCGCCATTTTCCACTCA	59.377	47.619	0.00	0.00	0.00	3.41
759	774	8.977267	TTGATGACATATATGTGGACAATTGA	57.023	30.769	22.93	2.85	41.95	2.57
784	799	6.909550	ATCTCTCGCTATTTTCCACTCTAT	57.090	37.500	0.00	0.00	0.00	1.98
786	801	5.606348	AATCTCTCGCTATTTTCCACTCT	57.394	39.130	0.00	0.00	0.00	3.24
867	882	0.027979	CGCGCCTACACAAATGATGG	59.972	55.000	0.00	0.00	0.00	3.51
890	905	0.888619	TGGAGATGGAGTGACACGTC	59.111	55.000	0.00	0.00	0.00	4.34
899	914	2.568956	TGGTTGAGAACTGGAGATGGAG	59.431	50.000	0.00	0.00	0.00	3.86
1185	1200	1.807226	CGCATACTCGGTGACCTCA	59.193	57.895	0.00	0.00	0.00	3.86
1286	1301	4.803426	CAGCCCTCTCGTCGCCAC	62.803	72.222	0.00	0.00	0.00	5.01
1302	1317	1.879380	GTCAAGCATGTGTTGTAGGCA	59.121	47.619	9.06	0.00	0.00	4.75
1518	1533	1.482593	AGCAATTGACCGAGGGAGTAG	59.517	52.381	10.34	0.00	0.00	2.57
1639	1654	1.068333	CATTTTGAGGGTCAGCGTTGG	60.068	52.381	0.00	0.00	0.00	3.77
1643	1658	0.962356	AGGCATTTTGAGGGTCAGCG	60.962	55.000	0.00	0.00	0.00	5.18
1646	1661	3.153919	GTTACAGGCATTTTGAGGGTCA	58.846	45.455	0.00	0.00	0.00	4.02
1662	1677	2.282110	TCGGTCCGGACGGTTACA	60.282	61.111	33.31	17.32	36.47	2.41
1671	1686	2.125912	CTGAACTGCTCGGTCCGG	60.126	66.667	12.29	0.00	0.00	5.14
1676	1691	1.869767	GATTATGCCTGAACTGCTCGG	59.130	52.381	0.00	0.00	0.00	4.63
1685	1700	4.382362	CGCTGGATGATAGATTATGCCTGA	60.382	45.833	0.00	0.00	0.00	3.86
1686	1701	3.869832	CGCTGGATGATAGATTATGCCTG	59.130	47.826	0.00	0.00	0.00	4.85
1687	1702	3.118482	CCGCTGGATGATAGATTATGCCT	60.118	47.826	0.00	0.00	0.00	4.75
1696	1711	4.497173	CGATGATCTACCGCTGGATGATAG	60.497	50.000	1.50	0.00	0.00	2.08
1698	1713	2.165234	CGATGATCTACCGCTGGATGAT	59.835	50.000	1.50	4.71	0.00	2.45
1708	1725	2.034812	GTCTGTGGACCGATGATCTACC	59.965	54.545	0.00	0.00	36.53	3.18
1753	1770	0.250989	CCCAGTTTGCCTCCGGTTTA	60.251	55.000	0.00	0.00	0.00	2.01
1757	1774	2.045926	CTCCCAGTTTGCCTCCGG	60.046	66.667	0.00	0.00	0.00	5.14
1758	1775	2.045926	CCTCCCAGTTTGCCTCCG	60.046	66.667	0.00	0.00	0.00	4.63
1772	1789	3.334054	ACTCCTGCAAGCCCCCTC	61.334	66.667	0.00	0.00	0.00	4.30
1827	1845	1.376649	ACTGGAAGGGGATTTGAGCT	58.623	50.000	0.00	0.00	39.30	4.09
1844	1862	5.367060	AGGTAGAGTGGAAGAAAAGTGAACT	59.633	40.000	0.00	0.00	0.00	3.01
1847	1865	5.611374	CAAGGTAGAGTGGAAGAAAAGTGA	58.389	41.667	0.00	0.00	0.00	3.41
1888	1907	1.028868	GCATGAGACAAGGAGGGTGC	61.029	60.000	0.00	0.00	0.00	5.01
1903	1922	0.392998	AGAGGTACAAAGGCGGCATG	60.393	55.000	13.08	12.60	0.00	4.06
1905	1924	1.295423	GAGAGGTACAAAGGCGGCA	59.705	57.895	13.08	0.00	0.00	5.69
1941	1960	1.670949	GGAGCTGCAGATGTCCGAGA	61.671	60.000	20.43	0.00	0.00	4.04
1949	1968	2.611800	TGGGTGGGAGCTGCAGAT	60.612	61.111	20.43	12.64	0.00	2.90
1975	1994	0.599204	ACGTTGTAGTCCAAGGCGTG	60.599	55.000	0.00	0.00	41.55	5.34
1976	1995	0.319297	GACGTTGTAGTCCAAGGCGT	60.319	55.000	0.00	0.00	41.55	5.68
1977	1996	0.319211	TGACGTTGTAGTCCAAGGCG	60.319	55.000	0.00	0.00	41.55	5.52
1990	2009	4.225860	TCCTGGGTGGATGACGTT	57.774	55.556	0.00	0.00	40.56	3.99
2024	2043	3.494332	GTCGGTAGGAAGGCTAAGGATA	58.506	50.000	0.00	0.00	0.00	2.59
2030	2049	2.123428	GGCGTCGGTAGGAAGGCTA	61.123	63.158	0.00	0.00	44.41	3.93
2077	2096	3.507103	TGAATGGCATTTGACCGAATG	57.493	42.857	14.93	5.77	39.47	2.67
2078	2097	3.511146	AGTTGAATGGCATTTGACCGAAT	59.489	39.130	14.93	0.00	0.00	3.34
2104	2123	1.828461	TACCCCGCCATCGTCAACAA	61.828	55.000	0.00	0.00	0.00	2.83
2106	2125	1.812507	GTACCCCGCCATCGTCAAC	60.813	63.158	0.00	0.00	0.00	3.18
2107	2126	1.952102	GAGTACCCCGCCATCGTCAA	61.952	60.000	0.00	0.00	0.00	3.18
2109	2128	1.952102	TTGAGTACCCCGCCATCGTC	61.952	60.000	0.00	0.00	0.00	4.20
2128	2174	0.839277	TCGCACTCATTCCCCATCAT	59.161	50.000	0.00	0.00	0.00	2.45
2135	2181	1.897398	AACGCGTTCGCACTCATTCC	61.897	55.000	20.79	0.00	39.84	3.01
2151	2197	1.508632	CTTGGTCCTGTGGTACAACG	58.491	55.000	0.00	0.00	44.16	4.10
2168	2214	7.861629	TGTATGAATGTAAATGACCTCTCCTT	58.138	34.615	0.00	0.00	0.00	3.36
2400	2449	6.315393	TCTTCTTCTTTTAAGTCGCAACACTT	59.685	34.615	0.00	0.00	39.94	3.16
2428	2477	1.228154	GAGTCGGCCACCCTTGTTT	60.228	57.895	2.24	0.00	0.00	2.83
2431	2480	3.612247	CTGGAGTCGGCCACCCTTG	62.612	68.421	2.24	0.00	33.52	3.61
2432	2481	2.741878	TACTGGAGTCGGCCACCCTT	62.742	60.000	2.24	0.00	33.52	3.95
2433	2482	2.531483	ATACTGGAGTCGGCCACCCT	62.531	60.000	2.24	0.00	33.52	4.34
2436	2507	1.327690	TGGATACTGGAGTCGGCCAC	61.328	60.000	2.24	0.00	33.52	5.01
2455	2526	2.815308	GGACTGATCCGCGGACAT	59.185	61.111	33.75	17.22	34.48	3.06
2471	2542	0.719465	GACACACTATTTGTCCGCGG	59.281	55.000	22.12	22.12	37.93	6.46
2500	2571	9.152327	TCTATGAAGACATCTCCAACATCTATT	57.848	33.333	0.00	0.00	37.87	1.73
2504	2575	7.048629	TCTCTATGAAGACATCTCCAACATC	57.951	40.000	0.00	0.00	37.87	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.