AutoCloner

Multiple sequence alignment - TraesCS6D01G076500

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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	TraesCS6D01G076500	chr6D	100.000	3445	0	0	1	3445	41232814	41236258	0.000000e+00	6362.0
1	TraesCS6D01G076500	chr6D	83.896	2043	316	11	1215	3249	22182653	22184690	0.000000e+00	1938.0
2	TraesCS6D01G076500	chr6A	96.994	1896	41	5	1556	3445	51879802	51881687	0.000000e+00	3171.0
3	TraesCS6D01G076500	chr6A	84.962	1709	246	5	1226	2928	7186768	7185065	0.000000e+00	1722.0
4	TraesCS6D01G076500	chr6A	84.084	1709	258	11	1228	2928	7175931	7174229	0.000000e+00	1637.0
5	TraesCS6D01G076500	chr6A	89.848	788	37	5	801	1565	51851532	51852299	0.000000e+00	972.0
6	TraesCS6D01G076500	chr6A	90.028	361	34	2	1	359	51838481	51838841	1.870000e-127	466.0
7	TraesCS6D01G076500	chr6A	88.934	244	12	4	577	805	51847847	51848090	1.560000e-73	287.0
8	TraesCS6D01G076500	chr6A	84.249	273	34	5	421	690	51847569	51847835	1.230000e-64	257.0
9	TraesCS6D01G076500	chr7D	85.564	1711	236	7	1226	2928	597677104	597675397	0.000000e+00	1781.0
10	TraesCS6D01G076500	chr6B	94.223	1177	48	4	209	1370	96644296	96643125	0.000000e+00	1779.0
11	TraesCS6D01G076500	chr6B	84.226	1756	260	8	1188	2928	12886567	12888320	0.000000e+00	1692.0
12	TraesCS6D01G076500	chr6B	82.958	1907	291	24	1047	2928	26861644	26863541	0.000000e+00	1690.0
13	TraesCS6D01G076500	chr6B	97.664	428	9	1	3019	3445	96638827	96638400	0.000000e+00	734.0
14	TraesCS6D01G076500	chr6B	92.040	201	16	0	1	201	96644721	96644521	2.020000e-72	283.0
15	TraesCS6D01G076500	chr5B	84.755	1758	247	12	1188	2928	432982668	432984421	0.000000e+00	1742.0
16	TraesCS6D01G076500	chr5B	94.595	37	1	1	510	546	710360270	710360235	4.800000e-04	56.5
17	TraesCS6D01G076500	chrUn	83.603	1854	270	16	1090	2924	79936998	79938836	0.000000e+00	1709.0
18	TraesCS6D01G076500	chr7B	94.595	37	1	1	510	546	543189493	543189458	4.800000e-04	56.5
19	TraesCS6D01G076500	chr3B	94.595	37	1	1	510	546	377115039	377115004	4.800000e-04	56.5
20	TraesCS6D01G076500	chr2B	94.595	37	1	1	510	546	11451647	11451682	4.800000e-04	56.5
21	TraesCS6D01G076500	chr2B	94.595	37	1	1	510	546	494858585	494858620	4.800000e-04	56.5

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	TraesCS6D01G076500	chr6D	41232814	41236258	3444	False	6362.000000	6362	100.0000	1	3445	1	chr6D.!!$F2	3444
1	TraesCS6D01G076500	chr6D	22182653	22184690	2037	False	1938.000000	1938	83.8960	1215	3249	1	chr6D.!!$F1	2034
2	TraesCS6D01G076500	chr6A	51879802	51881687	1885	False	3171.000000	3171	96.9940	1556	3445	1	chr6A.!!$F2	1889
3	TraesCS6D01G076500	chr6A	7185065	7186768	1703	True	1722.000000	1722	84.9620	1226	2928	1	chr6A.!!$R2	1702
4	TraesCS6D01G076500	chr6A	7174229	7175931	1702	True	1637.000000	1637	84.0840	1228	2928	1	chr6A.!!$R1	1700
5	TraesCS6D01G076500	chr6A	51847569	51852299	4730	False	505.333333	972	87.6770	421	1565	3	chr6A.!!$F3	1144
6	TraesCS6D01G076500	chr7D	597675397	597677104	1707	True	1781.000000	1781	85.5640	1226	2928	1	chr7D.!!$R1	1702
7	TraesCS6D01G076500	chr6B	12886567	12888320	1753	False	1692.000000	1692	84.2260	1188	2928	1	chr6B.!!$F1	1740
8	TraesCS6D01G076500	chr6B	26861644	26863541	1897	False	1690.000000	1690	82.9580	1047	2928	1	chr6B.!!$F2	1881
9	TraesCS6D01G076500	chr6B	96643125	96644721	1596	True	1031.000000	1779	93.1315	1	1370	2	chr6B.!!$R2	1369
10	TraesCS6D01G076500	chr5B	432982668	432984421	1753	False	1742.000000	1742	84.7550	1188	2928	1	chr5B.!!$F1	1740
11	TraesCS6D01G076500	chrUn	79936998	79938836	1838	False	1709.000000	1709	83.6030	1090	2924	1	chrUn.!!$F1	1834

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
185	186	1.427819	CGCCGTTGCACCCTATTTC	59.572	57.895	0.00	0.0	37.32	2.17	F
1096	4905	1.339929	GCTAGCCTCCTAACTCTGCTC	59.660	57.143	2.29	0.0	33.63	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1896	5752	0.316204	GCTTGAACCTTGCACATGCT	59.684	50.0	5.31	0.0	42.66	3.79	R
2804	6665	5.012664	AGTGTGTTATAGGTGACAACATCCA	59.987	40.0	0.00	0.0	34.89	3.41	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
32	33	2.224354	CCATGAGTTGCCAAAGCCTTTT	60.224	45.455	0.00	0.00	38.69	2.27
43	44	2.126850	GCCTTTTGCGCGGAGAAC	60.127	61.111	8.83	0.00	0.00	3.01
55	56	2.159787	CGCGGAGAACTTCAAACATGAG	60.160	50.000	0.00	0.00	0.00	2.90
56	57	2.808543	GCGGAGAACTTCAAACATGAGT	59.191	45.455	0.00	0.00	0.00	3.41
64	65	6.830838	AGAACTTCAAACATGAGTTCTTCCTT	59.169	34.615	16.88	0.86	44.39	3.36
103	104	2.293122	CACCTGTCGCATCAAAAGGAAA	59.707	45.455	0.00	0.00	0.00	3.13
109	110	4.037327	TGTCGCATCAAAAGGAAATTGTCA	59.963	37.500	0.00	0.00	0.00	3.58
114	115	6.183360	CGCATCAAAAGGAAATTGTCATGAAG	60.183	38.462	0.00	0.00	0.00	3.02
122	123	4.560035	GGAAATTGTCATGAAGATTGCACG	59.440	41.667	0.00	0.00	0.00	5.34
125	126	2.153645	TGTCATGAAGATTGCACGCTT	58.846	42.857	0.00	0.12	0.00	4.68
168	169	1.994779	GGCAACAATTTCCTTCATGCG	59.005	47.619	0.00	0.00	33.30	4.73
185	186	1.427819	CGCCGTTGCACCCTATTTC	59.572	57.895	0.00	0.00	37.32	2.17
189	190	2.942306	GCCGTTGCACCCTATTTCCTAA	60.942	50.000	0.00	0.00	37.47	2.69
191	192	3.340034	CGTTGCACCCTATTTCCTAACA	58.660	45.455	0.00	0.00	0.00	2.41
195	196	4.780815	TGCACCCTATTTCCTAACATCTG	58.219	43.478	0.00	0.00	0.00	2.90
201	202	4.335315	CCTATTTCCTAACATCTGCGCAAA	59.665	41.667	13.05	0.00	0.00	3.68
203	204	2.177394	TCCTAACATCTGCGCAAACA	57.823	45.000	13.05	0.00	0.00	2.83
204	205	2.499197	TCCTAACATCTGCGCAAACAA	58.501	42.857	13.05	0.00	0.00	2.83
207	425	2.869233	AACATCTGCGCAAACAACTT	57.131	40.000	13.05	0.00	0.00	2.66
225	443	5.046304	ACAACTTAGAGAAGCTATGAGGCAA	60.046	40.000	0.00	0.00	35.97	4.52
237	455	1.921982	TGAGGCAAGCTTATTGGCAA	58.078	45.000	15.31	0.68	46.01	4.52
259	477	4.697756	CGCCAACCTCCTCCGCAA	62.698	66.667	0.00	0.00	0.00	4.85
260	478	2.044946	GCCAACCTCCTCCGCAAT	60.045	61.111	0.00	0.00	0.00	3.56
334	552	4.298626	TCTGCTATCCTCCCATTACAACT	58.701	43.478	0.00	0.00	0.00	3.16
344	562	5.323371	TCCCATTACAACTTAAGCAATGC	57.677	39.130	1.29	0.00	0.00	3.56
374	592	4.553330	TGTCAACTACTTTCTCCATCCC	57.447	45.455	0.00	0.00	0.00	3.85
415	633	8.888836	TTTGATACTATCACCGAGGGAATATA	57.111	34.615	0.00	0.00	39.39	0.86
521	739	6.621316	TTTGTCGCTTTTATCTAAACACCA	57.379	33.333	0.00	0.00	0.00	4.17
528	746	8.784994	TCGCTTTTATCTAAACACCAAAATACA	58.215	29.630	0.00	0.00	0.00	2.29
567	785	2.209838	ACGATAAGCAGACACATCCG	57.790	50.000	0.00	0.00	0.00	4.18
571	789	4.109766	CGATAAGCAGACACATCCGTTTA	58.890	43.478	0.00	0.00	0.00	2.01
596	939	3.228453	GACAGGTAATATGGGTCGGAGA	58.772	50.000	0.00	0.00	0.00	3.71
715	1076	7.153315	AGTGTAAAAGACTTGGCTCTAGTTAC	58.847	38.462	0.00	0.00	0.00	2.50
1011	4819	2.261361	CTCGCCATGTCGGTGTCA	59.739	61.111	0.00	0.00	46.24	3.58
1096	4905	1.339929	GCTAGCCTCCTAACTCTGCTC	59.660	57.143	2.29	0.00	33.63	4.26
1458	5310	1.937191	TGTCACCTACAGCATCCTCA	58.063	50.000	0.00	0.00	33.01	3.86
1623	5478	3.740128	ATGGACATCGCACTCCGGC	62.740	63.158	0.00	0.00	37.59	6.13
1736	5591	5.819379	TCTTGAGCTTATTCACATGATGGTC	59.181	40.000	0.00	0.00	0.00	4.02
1894	5750	6.149129	TGTGACGTATAGCTCAATCATCTT	57.851	37.500	0.00	0.00	0.00	2.40
1896	5752	7.712797	TGTGACGTATAGCTCAATCATCTTTA	58.287	34.615	0.00	0.00	0.00	1.85
2035	5891	1.367840	GACAGTGCGAAGAGGTGGT	59.632	57.895	0.00	0.00	0.00	4.16
2194	6050	5.048991	ACCAAAAACCGAATGTTACTAGCTG	60.049	40.000	0.00	0.00	35.67	4.24
2804	6665	2.225091	TGGTCTCAATTGGCATGGAACT	60.225	45.455	5.42	0.00	0.00	3.01
2915	6776	2.287608	ACAAGAAAGTTAAGCCTTGCGC	60.288	45.455	0.00	0.00	39.51	6.09
3125	6986	8.958043	GTGTTCAACAAATTATCAACTTGAGAC	58.042	33.333	0.00	0.00	0.00	3.36
3297	7158	0.319405	GCAAGAATGGTTTGCTGCCT	59.681	50.000	0.00	0.00	45.64	4.75
3329	7191	7.535258	CGTATGTTAAATGCCATCTTAGAATGC	59.465	37.037	0.27	0.27	0.00	3.56
3388	7250	1.206849	GAGAGGAGCTTCACCCTTGAG	59.793	57.143	0.00	0.00	31.71	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	0.812014	TGTTTGAAGTTCTCCGCGCA	60.812	50.000	8.75	0.00	0.00	6.09
36	37	4.752101	AGAACTCATGTTTGAAGTTCTCCG	59.248	41.667	16.88	0.00	41.39	4.63
43	44	5.218139	GCAAGGAAGAACTCATGTTTGAAG	58.782	41.667	0.00	0.00	36.39	3.02
55	56	3.692791	AAAACTCACGCAAGGAAGAAC	57.307	42.857	0.00	0.00	46.39	3.01
56	57	3.945285	AGAAAAACTCACGCAAGGAAGAA	59.055	39.130	0.00	0.00	46.39	2.52
64	65	0.749818	TGGCCAGAAAAACTCACGCA	60.750	50.000	0.00	0.00	0.00	5.24
103	104	2.751259	AGCGTGCAATCTTCATGACAAT	59.249	40.909	0.00	0.00	0.00	2.71
109	110	1.825090	TCCAAGCGTGCAATCTTCAT	58.175	45.000	0.00	0.00	0.00	2.57
114	115	1.199789	TGTTCATCCAAGCGTGCAATC	59.800	47.619	0.00	0.00	0.00	2.67
122	123	5.927689	TGAATCAATTTGTGTTCATCCAAGC	59.072	36.000	12.59	0.00	0.00	4.01
125	126	5.459768	CGTGAATCAATTTGTGTTCATCCA	58.540	37.500	16.82	0.76	33.10	3.41
168	169	0.679960	AGGAAATAGGGTGCAACGGC	60.680	55.000	0.00	0.00	38.12	5.68
185	186	2.226437	AGTTGTTTGCGCAGATGTTAGG	59.774	45.455	11.31	0.00	0.00	2.69
189	190	3.138304	TCTAAGTTGTTTGCGCAGATGT	58.862	40.909	11.31	0.00	0.00	3.06
191	192	3.664107	TCTCTAAGTTGTTTGCGCAGAT	58.336	40.909	11.31	0.00	0.00	2.90
195	196	2.224314	AGCTTCTCTAAGTTGTTTGCGC	59.776	45.455	0.00	0.00	34.99	6.09
201	202	4.467795	TGCCTCATAGCTTCTCTAAGTTGT	59.532	41.667	0.00	0.00	34.99	3.32
203	204	5.669477	CTTGCCTCATAGCTTCTCTAAGTT	58.331	41.667	0.00	0.00	34.99	2.66
204	205	4.442753	GCTTGCCTCATAGCTTCTCTAAGT	60.443	45.833	0.00	0.00	34.99	2.24
207	425	3.303938	AGCTTGCCTCATAGCTTCTCTA	58.696	45.455	0.00	0.00	45.03	2.43
225	443	2.636768	GCGACTTTTGCCAATAAGCT	57.363	45.000	0.00	0.00	0.00	3.74
237	455	1.375326	GGAGGAGGTTGGCGACTTT	59.625	57.895	4.59	0.00	0.00	2.66
260	478	9.362151	ACATTGTCCTAATTTGGAAGAAAGTTA	57.638	29.630	10.35	0.00	37.93	2.24
324	542	5.713025	ACAGCATTGCTTAAGTTGTAATGG	58.287	37.500	8.83	0.00	36.40	3.16
334	552	4.701171	TGACATCATGACAGCATTGCTTAA	59.299	37.500	8.83	0.00	36.40	1.85
344	562	6.312426	GGAGAAAGTAGTTGACATCATGACAG	59.688	42.308	0.00	0.00	0.00	3.51
395	613	6.722590	TGCTTTATATTCCCTCGGTGATAGTA	59.277	38.462	0.00	0.00	0.00	1.82
415	633	9.435688	AAATTGAACTTCAAACTTAACTGCTTT	57.564	25.926	8.28	0.00	40.12	3.51
498	716	6.621316	TGGTGTTTAGATAAAAGCGACAAA	57.379	33.333	0.00	0.00	0.00	2.83
567	785	6.237915	CGACCCATATTACCTGTCGTTTAAAC	60.238	42.308	8.35	8.35	42.68	2.01
571	789	3.431207	CCGACCCATATTACCTGTCGTTT	60.431	47.826	9.16	0.00	45.29	3.60
579	922	4.586001	TGTACTTCTCCGACCCATATTACC	59.414	45.833	0.00	0.00	0.00	2.85
673	1019	0.899720	ACTAATCTTTGCCCGTCGGA	59.100	50.000	14.39	0.00	0.00	4.55
715	1076	1.375523	GGACCCACCTGTAAGCACG	60.376	63.158	0.00	0.00	35.41	5.34
1096	4905	3.939066	ACCTGGGATTAGAAACAACGAG	58.061	45.455	0.00	0.00	0.00	4.18
1623	5478	1.202031	GCAGTTAAACTCGGGCATTCG	60.202	52.381	0.00	0.00	0.00	3.34
1736	5591	1.593750	GCAGCTACCTCCAGCATCG	60.594	63.158	0.00	0.00	44.35	3.84
1894	5750	2.030007	GCTTGAACCTTGCACATGCTAA	60.030	45.455	5.31	0.00	42.66	3.09
1896	5752	0.316204	GCTTGAACCTTGCACATGCT	59.684	50.000	5.31	0.00	42.66	3.79
2035	5891	9.496873	TCCTAGACATTTTCTTGAAAATACGAA	57.503	29.630	17.54	9.89	35.55	3.85
2317	6173	6.916909	TCAACCATTTTCCCCTTAGCATATA	58.083	36.000	0.00	0.00	0.00	0.86
2804	6665	5.012664	AGTGTGTTATAGGTGACAACATCCA	59.987	40.000	0.00	0.00	34.89	3.41
2915	6776	5.812127	TGCAGCACTGTGTTATAAGTGATAG	59.188	40.000	9.86	0.00	45.43	2.08
3036	6897	6.911250	TTTCTACACAGACCACTGAGAATA	57.089	37.500	0.00	0.00	46.03	1.75
3329	7191	3.753797	GGCACCTCCTCTTTTTGAAGTAG	59.246	47.826	0.00	0.00	0.00	2.57
3365	7227	1.202330	AGGGTGAAGCTCCTCTCATG	58.798	55.000	0.00	0.00	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.