AutoCloner

Multiple sequence alignment - TraesCS7B01G349200

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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	TraesCS7B01G349200	chr7B	100.000	2540	0	0	1	2540	606135345	606137884	0.000000e+00	4691.0
1	TraesCS7B01G349200	chr7B	92.531	2584	118	33	1	2540	606185087	606187639	0.000000e+00	3633.0
2	TraesCS7B01G349200	chr7B	79.401	267	48	6	1044	1308	605874158	605874419	5.580000e-42	182.0
3	TraesCS7B01G349200	chr7B	90.299	134	13	0	483	616	1062824	1062691	2.600000e-40	176.0
4	TraesCS7B01G349200	chr7B	74.423	477	84	26	1049	1500	606039373	606039836	1.210000e-38	171.0
5	TraesCS7B01G349200	chr7B	85.217	115	15	2	1387	1500	605969349	605969462	1.600000e-22	117.0
6	TraesCS7B01G349200	chr7B	90.588	85	8	0	615	699	31131666	31131750	2.070000e-21	113.0
7	TraesCS7B01G349200	chr7B	81.301	123	23	0	1082	1204	606533579	606533701	1.610000e-17	100.0
8	TraesCS7B01G349200	chr7D	87.007	1801	137	49	822	2540	558161104	558162889	0.000000e+00	1940.0
9	TraesCS7B01G349200	chr7D	76.007	571	101	16	1000	1547	558009707	558010264	1.940000e-66	263.0
10	TraesCS7B01G349200	chr7D	74.739	479	89	24	1044	1500	557893125	557893593	4.320000e-43	185.0
11	TraesCS7B01G349200	chr7D	78.022	273	42	11	943	1204	558168495	558168760	3.380000e-34	156.0
12	TraesCS7B01G349200	chr7A	89.469	1016	81	17	822	1831	643634552	643635547	0.000000e+00	1260.0
13	TraesCS7B01G349200	chr7A	79.268	246	41	7	973	1209	643603146	643603390	2.020000e-36	163.0
14	TraesCS7B01G349200	chr7A	84.049	163	23	3	1043	1204	643645174	643645334	1.220000e-33	154.0
15	TraesCS7B01G349200	chr4B	93.023	86	6	0	615	700	308049641	308049726	2.650000e-25	126.0
16	TraesCS7B01G349200	chr4B	91.954	87	7	0	615	701	519258920	519259006	3.430000e-24	122.0
17	TraesCS7B01G349200	chr6A	89.247	93	10	0	615	707	66089054	66089146	1.600000e-22	117.0
18	TraesCS7B01G349200	chr2D	90.000	90	9	0	612	701	204417081	204417170	1.600000e-22	117.0
19	TraesCS7B01G349200	chr2D	89.130	46	4	1	2065	2109	640978557	640978602	3.530000e-04	56.5
20	TraesCS7B01G349200	chr5A	90.110	91	6	3	610	699	339739853	339739765	5.740000e-22	115.0
21	TraesCS7B01G349200	chr5A	88.172	93	11	0	614	706	564177723	564177631	7.430000e-21	111.0
22	TraesCS7B01G349200	chr1D	89.888	89	9	0	615	703	415987227	415987139	5.740000e-22	115.0
23	TraesCS7B01G349200	chr1D	84.507	71	10	1	2065	2134	446701398	446701468	4.530000e-08	69.4
24	TraesCS7B01G349200	chr2B	86.567	67	8	1	2069	2134	791470156	791470222	3.510000e-09	73.1
25	TraesCS7B01G349200	chr5D	92.157	51	0	4	2074	2122	14127009	14127057	4.530000e-08	69.4

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	TraesCS7B01G349200	chr7B	606135345	606137884	2539	False	4691	4691	100.000	1	2540	1	chr7B.!!$F5	2539
1	TraesCS7B01G349200	chr7B	606185087	606187639	2552	False	3633	3633	92.531	1	2540	1	chr7B.!!$F6	2539
2	TraesCS7B01G349200	chr7D	558161104	558162889	1785	False	1940	1940	87.007	822	2540	1	chr7D.!!$F3	1718
3	TraesCS7B01G349200	chr7D	558009707	558010264	557	False	263	263	76.007	1000	1547	1	chr7D.!!$F2	547
4	TraesCS7B01G349200	chr7A	643634552	643635547	995	False	1260	1260	89.469	822	1831	1	chr7A.!!$F2	1009

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
166	167	0.098552	TGCATCAAATTGCTACGGCG	59.901	50.0	4.8	4.8	43.18	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1575	1595	0.304705	CGATTCTTGATTTCCGGCGG	59.695	55.0	22.51	22.51	0.0	6.13	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
56	57	4.376413	CGAGCGACATAAATTGCTACATCC	60.376	45.833	0.00	0.00	39.57	3.51
165	166	1.919918	GTTGCATCAAATTGCTACGGC	59.080	47.619	0.00	0.00	43.18	5.68
166	167	0.098552	TGCATCAAATTGCTACGGCG	59.901	50.000	4.80	4.80	43.18	6.46
307	308	1.741770	CACCAGAGTTGCTACCGGC	60.742	63.158	0.00	0.00	42.22	6.13
603	604	2.237066	AACGCAAGCGCTTTTTGCC	61.237	52.632	22.51	5.97	46.20	4.52
619	620	1.192146	TGCCGGAACCAAGCTACTCT	61.192	55.000	5.05	0.00	0.00	3.24
620	621	0.460459	GCCGGAACCAAGCTACTCTC	60.460	60.000	5.05	0.00	0.00	3.20
722	723	2.483877	TGTGAAACGAGGCATGCTAAAG	59.516	45.455	18.92	9.35	42.39	1.85
728	729	0.375106	GAGGCATGCTAAAGACGTGC	59.625	55.000	18.92	0.00	46.94	5.34
1575	1595	3.195610	GGGATGGATTTGGTTCTTGAACC	59.804	47.826	21.83	21.83	43.12	3.62
1591	1611	0.250989	AACCCGCCGGAAATCAAGAA	60.251	50.000	5.05	0.00	0.00	2.52
1679	1725	8.398665	GGTTCACCTTTCATGATAACTTATGTC	58.601	37.037	0.00	0.00	0.00	3.06
1819	1872	2.420372	TGTGCTGCAGACGTTTGTAAAA	59.580	40.909	20.43	0.00	0.00	1.52
1832	1885	4.675671	CGTTTGTAAAACAAGGTGGCTTGA	60.676	41.667	0.00	0.00	39.53	3.02
1833	1886	5.356426	GTTTGTAAAACAAGGTGGCTTGAT	58.644	37.500	0.00	0.00	39.53	2.57
1834	1887	5.606348	TTGTAAAACAAGGTGGCTTGATT	57.394	34.783	0.00	0.00	37.72	2.57
1835	1888	5.606348	TGTAAAACAAGGTGGCTTGATTT	57.394	34.783	0.00	0.00	40.60	2.17
1836	1889	5.355596	TGTAAAACAAGGTGGCTTGATTTG	58.644	37.500	2.37	0.00	38.89	2.32
1837	1890	4.751767	AAAACAAGGTGGCTTGATTTGA	57.248	36.364	0.00	0.00	37.72	2.69
1883	1938	3.536956	TCGACCAGAAAAGTGACTGTT	57.463	42.857	0.00	0.00	32.93	3.16
1884	1939	3.194861	TCGACCAGAAAAGTGACTGTTG	58.805	45.455	0.00	0.00	32.93	3.33
1890	1945	2.870411	AGAAAAGTGACTGTTGTACGCC	59.130	45.455	0.00	0.00	0.00	5.68
1926	2024	3.084536	TGGCTTTCAATATGTCAGGCA	57.915	42.857	0.00	0.00	37.68	4.75
1945	2043	2.743183	GCATGATAGCCAACGAAGGAGT	60.743	50.000	0.00	0.00	0.00	3.85
1980	2078	7.981142	TGGATGGATCTGAATATCTGATTCAA	58.019	34.615	10.92	0.00	41.60	2.69
2000	2098	8.738645	ATTCAACAATAGGTGAAGGAGATAAC	57.261	34.615	2.26	0.00	0.00	1.89
2006	2104	4.067944	AGGTGAAGGAGATAACAGGAGT	57.932	45.455	0.00	0.00	0.00	3.85
2093	2194	3.480133	CGAAGGGGCTAGGTGGGG	61.480	72.222	0.00	0.00	0.00	4.96
2106	2207	0.474614	GGTGGGGAGAGCCTTATTCC	59.525	60.000	0.00	0.00	0.00	3.01
2114	2215	5.309638	GGGAGAGCCTTATTCCATCTTTAC	58.690	45.833	0.00	0.00	32.50	2.01
2142	2243	0.804544	CGTCGCCTCGCATTCCTAAA	60.805	55.000	0.00	0.00	0.00	1.85
2146	2247	4.491676	GTCGCCTCGCATTCCTAAATATA	58.508	43.478	0.00	0.00	0.00	0.86
2150	2251	5.163953	CGCCTCGCATTCCTAAATATAACTG	60.164	44.000	0.00	0.00	0.00	3.16
2154	2255	9.003658	CCTCGCATTCCTAAATATAACTGAAAT	57.996	33.333	0.00	0.00	0.00	2.17
2185	2286	9.781633	AATAAAATTAAAACAACTGGTAACCCC	57.218	29.630	0.00	0.00	0.00	4.95
2191	2292	1.232119	CAACTGGTAACCCCGTTGAC	58.768	55.000	14.57	0.00	43.93	3.18
2207	2309	5.505159	CCCGTTGACTAACTTGAAAAGGTTC	60.505	44.000	0.00	0.00	45.56	3.62
2434	2564	9.547279	AACTGGGAAAGTTCTATAAATTTGGAT	57.453	29.630	0.00	0.00	46.60	3.41
2510	2643	1.830477	TGGAACAAAAGCTGCAAACCT	59.170	42.857	1.02	0.00	31.92	3.50
2515	2648	1.615392	CAAAAGCTGCAAACCTAGCCT	59.385	47.619	1.02	0.00	40.76	4.58
2516	2649	2.001076	AAAGCTGCAAACCTAGCCTT	57.999	45.000	1.02	0.00	40.76	4.35
2523	2656	2.888414	TGCAAACCTAGCCTTGTAAACC	59.112	45.455	0.00	0.00	0.00	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	4.368315	TGTAGCAATTTATGTCGCTCGAT	58.632	39.130	0.00	0.00	35.93	3.59
56	57	2.425124	CAGCAAAACACGACGCCG	60.425	61.111	0.00	0.00	42.50	6.46
90	91	0.384477	CTATGCCGACGCTCGTAGAC	60.384	60.000	4.17	0.00	38.40	2.59
97	98	2.415010	CTCTGCTATGCCGACGCT	59.585	61.111	0.00	0.00	35.36	5.07
165	166	0.033228	TCCAGCAAAACAAATGCCCG	59.967	50.000	0.00	0.00	44.91	6.13
166	167	1.872952	GTTCCAGCAAAACAAATGCCC	59.127	47.619	0.00	0.00	44.91	5.36
203	204	2.815945	ATGGATGGAGCTCCGCCTG	61.816	63.158	32.46	0.00	38.21	4.85
204	205	2.447379	ATGGATGGAGCTCCGCCT	60.447	61.111	32.46	20.18	38.21	5.52
603	604	2.732597	CGAAGAGAGTAGCTTGGTTCCG	60.733	54.545	0.00	0.00	0.00	4.30
669	670	8.998814	TCCTTTCTTCCCATAATGTAAGATGTA	58.001	33.333	0.00	0.00	0.00	2.29
672	673	8.107196	ACTCCTTTCTTCCCATAATGTAAGAT	57.893	34.615	0.00	0.00	0.00	2.40
688	689	5.336849	CCTCGTTTCACATCTACTCCTTTCT	60.337	44.000	0.00	0.00	0.00	2.52
690	691	4.822026	CCTCGTTTCACATCTACTCCTTT	58.178	43.478	0.00	0.00	0.00	3.11
1575	1595	0.304705	CGATTCTTGATTTCCGGCGG	59.695	55.000	22.51	22.51	0.00	6.13
1655	1701	7.822334	ACGACATAAGTTATCATGAAAGGTGAA	59.178	33.333	0.00	0.00	0.00	3.18
1670	1716	2.478894	CACGGCAAGAACGACATAAGTT	59.521	45.455	0.00	0.00	34.93	2.66
1679	1725	3.850207	CGTAATCACGGCAAGAACG	57.150	52.632	0.00	0.00	44.59	3.95
1767	1815	9.807649	GGTTCATATAAAGAATTCACAAGCAAT	57.192	29.630	8.44	0.00	0.00	3.56
1819	1872	4.961438	AATTCAAATCAAGCCACCTTGT	57.039	36.364	3.66	0.00	46.74	3.16
1832	1885	7.370383	ACGTGCTTCAGTATTCAAATTCAAAT	58.630	30.769	0.00	0.00	0.00	2.32
1833	1886	6.734137	ACGTGCTTCAGTATTCAAATTCAAA	58.266	32.000	0.00	0.00	0.00	2.69
1834	1887	6.017523	TGACGTGCTTCAGTATTCAAATTCAA	60.018	34.615	0.00	0.00	0.00	2.69
1835	1888	5.468409	TGACGTGCTTCAGTATTCAAATTCA	59.532	36.000	0.00	0.00	0.00	2.57
1836	1889	5.927030	TGACGTGCTTCAGTATTCAAATTC	58.073	37.500	0.00	0.00	0.00	2.17
1837	1890	5.940192	TGACGTGCTTCAGTATTCAAATT	57.060	34.783	0.00	0.00	0.00	1.82
1883	1938	1.061546	AAGAGAAAAGGGGGCGTACA	58.938	50.000	0.00	0.00	0.00	2.90
1884	1939	2.195741	AAAGAGAAAAGGGGGCGTAC	57.804	50.000	0.00	0.00	0.00	3.67
1926	2024	2.501723	ACACTCCTTCGTTGGCTATCAT	59.498	45.455	0.00	0.00	0.00	2.45
1980	2078	5.964477	TCCTGTTATCTCCTTCACCTATTGT	59.036	40.000	0.00	0.00	0.00	2.71
2037	2137	1.133606	TGTCAAACCCAAGGAAGACCC	60.134	52.381	0.00	0.00	36.73	4.46
2093	2194	6.821388	TCTGTAAAGATGGAATAAGGCTCTC	58.179	40.000	0.00	0.00	0.00	3.20
2106	2207	2.186076	GACGACGGCTCTGTAAAGATG	58.814	52.381	0.00	0.00	0.00	2.90
2165	2266	4.472496	ACGGGGTTACCAGTTGTTTTAAT	58.528	39.130	2.98	0.00	42.91	1.40
2185	2286	6.114221	TGAACCTTTTCAAGTTAGTCAACG	57.886	37.500	0.00	0.00	38.87	4.10
2491	2623	2.602257	AGGTTTGCAGCTTTTGTTCC	57.398	45.000	0.00	0.00	0.00	3.62
2500	2632	1.821216	TACAAGGCTAGGTTTGCAGC	58.179	50.000	0.00	0.00	37.05	5.25
2504	2637	3.404899	TCGGTTTACAAGGCTAGGTTTG	58.595	45.455	0.00	0.00	0.00	2.93
2510	2643	3.640029	CCTCCTATCGGTTTACAAGGCTA	59.360	47.826	0.00	0.00	0.00	3.93
2515	2648	3.452990	TGATGCCTCCTATCGGTTTACAA	59.547	43.478	0.00	0.00	0.00	2.41
2516	2649	3.035363	TGATGCCTCCTATCGGTTTACA	58.965	45.455	0.00	0.00	0.00	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.