AutoCloner

Multiple sequence alignment - TraesCS6B01G307500

Loading Multiple Alignment...

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	TraesCS6B01G307500	chr6B	100.000	2321	0	0	1	2321	551036636	551034316	0.000000e+00	4287.0
1	TraesCS6B01G307500	chr5A	99.089	988	8	1	520	1507	353597462	353598448	0.000000e+00	1773.0
2	TraesCS6B01G307500	chr5A	83.590	390	43	5	1934	2321	622987000	622987370	1.710000e-91	346.0
3	TraesCS6B01G307500	chr5A	96.947	131	4	0	1697	1827	622986282	622986412	1.080000e-53	220.0
4	TraesCS6B01G307500	chr5A	100.000	30	0	0	505	534	36322168	36322139	3.220000e-04	56.5
5	TraesCS6B01G307500	chr4A	98.499	933	10	2	575	1507	10534977	10534049	0.000000e+00	1642.0
6	TraesCS6B01G307500	chr4A	90.840	786	52	7	1550	2321	542020170	542020949	0.000000e+00	1035.0
7	TraesCS6B01G307500	chr4A	90.686	204	14	3	324	524	542019914	542020115	1.370000e-67	267.0
8	TraesCS6B01G307500	chr3A	92.714	851	60	1	657	1507	642168525	642169373	0.000000e+00	1227.0
9	TraesCS6B01G307500	chr4B	90.975	831	44	15	1509	2321	82022396	82021579	0.000000e+00	1090.0
10	TraesCS6B01G307500	chr4B	83.304	563	48	29	1	550	82022909	82022380	5.800000e-131	477.0
11	TraesCS6B01G307500	chr4D	92.558	430	26	3	1898	2321	55068063	55067634	1.520000e-171	612.0
12	TraesCS6B01G307500	chr4D	88.328	317	20	2	1509	1825	55068486	55068187	4.710000e-97	364.0
13	TraesCS6B01G307500	chr3B	94.881	293	11	2	586	877	293752708	293752419	2.720000e-124	455.0
14	TraesCS6B01G307500	chr3B	83.333	168	14	8	1333	1493	169694142	169693982	2.400000e-30	143.0
15	TraesCS6B01G307500	chr5B	86.316	380	44	4	1934	2311	618121101	618121474	7.720000e-110	407.0
16	TraesCS6B01G307500	chr5B	93.431	137	8	1	1697	1832	618120477	618120613	3.910000e-48	202.0
17	TraesCS6B01G307500	chr5D	83.777	413	51	10	1913	2318	498622281	498622684	6.050000e-101	377.0
18	TraesCS6B01G307500	chr5D	96.124	129	5	0	1697	1825	498621662	498621790	6.500000e-51	211.0
19	TraesCS6B01G307500	chr2B	85.836	353	43	5	1163	1511	638764465	638764116	3.640000e-98	368.0
20	TraesCS6B01G307500	chr2A	83.520	358	47	4	1133	1480	679270551	679270196	8.000000e-85	324.0

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	TraesCS6B01G307500	chr6B	551034316	551036636	2320	True	4287.0	4287	100.0000	1	2321	1	chr6B.!!$R1	2320
1	TraesCS6B01G307500	chr5A	353597462	353598448	986	False	1773.0	1773	99.0890	520	1507	1	chr5A.!!$F1	987
2	TraesCS6B01G307500	chr5A	622986282	622987370	1088	False	283.0	346	90.2685	1697	2321	2	chr5A.!!$F2	624
3	TraesCS6B01G307500	chr4A	10534049	10534977	928	True	1642.0	1642	98.4990	575	1507	1	chr4A.!!$R1	932
4	TraesCS6B01G307500	chr4A	542019914	542020949	1035	False	651.0	1035	90.7630	324	2321	2	chr4A.!!$F1	1997
5	TraesCS6B01G307500	chr3A	642168525	642169373	848	False	1227.0	1227	92.7140	657	1507	1	chr3A.!!$F1	850
6	TraesCS6B01G307500	chr4B	82021579	82022909	1330	True	783.5	1090	87.1395	1	2321	2	chr4B.!!$R1	2320
7	TraesCS6B01G307500	chr4D	55067634	55068486	852	True	488.0	612	90.4430	1509	2321	2	chr4D.!!$R1	812
8	TraesCS6B01G307500	chr5B	618120477	618121474	997	False	304.5	407	89.8735	1697	2311	2	chr5B.!!$F1	614
9	TraesCS6B01G307500	chr5D	498621662	498622684	1022	False	294.0	377	89.9505	1697	2318	2	chr5D.!!$F1	621

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
206	218	0.033228	TTGCGCAGGACAAATTTGGG	59.967	50.0	21.74	9.53	0.0	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2085	2741	0.537371	AAGCCCACCTTCCTTTCACG	60.537	55.0	0.0	0.0	0.0	4.35	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
43	51	6.442487	TTTAAGATGTTCGTGTTAGTGACG	57.558	37.500	0.00	0.00	38.20	4.35
46	54	1.923899	TGTTCGTGTTAGTGACGCAA	58.076	45.000	0.00	0.00	38.71	4.85
47	55	2.269172	TGTTCGTGTTAGTGACGCAAA	58.731	42.857	0.00	0.00	38.71	3.68
51	59	2.219903	TCGTGTTAGTGACGCAAACATG	59.780	45.455	11.77	11.77	40.08	3.21
52	60	2.307049	GTGTTAGTGACGCAAACATGC	58.693	47.619	0.00	0.00	38.64	4.06
64	72	6.089283	TGACGCAAACATGCTTGATAATTTTC	59.911	34.615	12.98	0.00	0.00	2.29
68	76	7.201453	CGCAAACATGCTTGATAATTTTCATGA	60.201	33.333	12.98	0.00	36.23	3.07
82	90	0.321346	TCATGAGAAACGGAGCAGCA	59.679	50.000	0.00	0.00	0.00	4.41
84	92	1.329906	CATGAGAAACGGAGCAGCATC	59.670	52.381	0.00	0.00	0.00	3.91
85	93	0.737367	TGAGAAACGGAGCAGCATCG	60.737	55.000	0.00	0.00	0.00	3.84
162	174	1.725641	GCAGGCCAAAATGCTTAACC	58.274	50.000	5.01	0.00	39.38	2.85
163	175	1.001860	GCAGGCCAAAATGCTTAACCA	59.998	47.619	5.01	0.00	39.38	3.67
175	187	2.094957	TGCTTAACCATTTTACGCAGCC	60.095	45.455	0.00	0.00	0.00	4.85
178	190	4.201970	GCTTAACCATTTTACGCAGCCATA	60.202	41.667	0.00	0.00	0.00	2.74
179	191	5.677598	GCTTAACCATTTTACGCAGCCATAA	60.678	40.000	0.00	0.00	0.00	1.90
180	192	6.458232	TTAACCATTTTACGCAGCCATAAT	57.542	33.333	0.00	0.00	0.00	1.28
181	193	5.337578	AACCATTTTACGCAGCCATAATT	57.662	34.783	0.00	0.00	0.00	1.40
182	194	5.337578	ACCATTTTACGCAGCCATAATTT	57.662	34.783	0.00	0.00	0.00	1.82
183	195	5.729510	ACCATTTTACGCAGCCATAATTTT	58.270	33.333	0.00	0.00	0.00	1.82
184	196	6.169800	ACCATTTTACGCAGCCATAATTTTT	58.830	32.000	0.00	0.00	0.00	1.94
205	217	1.863267	TTTGCGCAGGACAAATTTGG	58.137	45.000	21.74	5.55	32.27	3.28
206	218	0.033228	TTGCGCAGGACAAATTTGGG	59.967	50.000	21.74	9.53	0.00	4.12
208	220	0.885196	GCGCAGGACAAATTTGGGTA	59.115	50.000	21.74	0.00	0.00	3.69
209	221	1.135402	GCGCAGGACAAATTTGGGTAG	60.135	52.381	21.74	10.17	0.00	3.18
210	222	1.135402	CGCAGGACAAATTTGGGTAGC	60.135	52.381	21.74	17.37	0.00	3.58
212	224	2.497273	GCAGGACAAATTTGGGTAGCAT	59.503	45.455	21.74	0.00	0.00	3.79
214	226	4.497300	CAGGACAAATTTGGGTAGCATTG	58.503	43.478	21.74	5.49	0.00	2.82
219	231	6.112927	ACAAATTTGGGTAGCATTGTGAAT	57.887	33.333	21.74	0.00	30.46	2.57
221	233	7.850193	ACAAATTTGGGTAGCATTGTGAATAT	58.150	30.769	21.74	0.00	30.46	1.28
228	240	9.634021	TTGGGTAGCATTGTGAATATATAAACA	57.366	29.630	0.00	0.00	0.00	2.83
229	241	9.062524	TGGGTAGCATTGTGAATATATAAACAC	57.937	33.333	12.66	12.66	0.00	3.32
230	242	9.062524	GGGTAGCATTGTGAATATATAAACACA	57.937	33.333	16.19	16.19	40.66	3.72
280	293	7.692088	ACATTTCAAAAATCATTTTTCGCACA	58.308	26.923	5.04	0.00	40.65	4.57
288	301	0.598065	ATTTTTCGCACAGTGGGAGC	59.402	50.000	18.83	0.00	40.47	4.70
294	307	2.109126	GCACAGTGGGAGCGGAATC	61.109	63.158	0.00	0.00	0.00	2.52
303	316	0.179056	GGAGCGGAATCGGATTTCCA	60.179	55.000	12.27	0.00	44.58	3.53
345	358	2.376109	GAATCGATATAGCTCCGGGGA	58.624	52.381	4.80	0.00	0.00	4.81
347	361	2.526888	TCGATATAGCTCCGGGGATT	57.473	50.000	4.80	0.00	0.00	3.01
420	434	0.599728	ACCCGCGCTTAAACAACGTA	60.600	50.000	5.56	0.00	0.00	3.57
478	492	3.299977	TCACGCGTGCTACTGGGT	61.300	61.111	33.63	0.00	0.00	4.51
572	586	0.586256	CACACAGCACACGAACGTTG	60.586	55.000	5.00	0.24	0.00	4.10
601	615	0.992695	TCTCTTCCCGTCCTCTCTCA	59.007	55.000	0.00	0.00	0.00	3.27
938	955	1.280746	GAGTTGGTCGTCGTCGTCA	59.719	57.895	1.33	0.00	38.33	4.35
1118	1135	2.642254	CGGGAGGTGGCTACGACAA	61.642	63.158	0.00	0.00	0.00	3.18
1329	1346	0.544697	TCCGGATCTAAAGGGGTTGC	59.455	55.000	0.00	0.00	0.00	4.17
1528	1545	5.622346	AAGAATCCTAAACCCTAGAGCTG	57.378	43.478	0.00	0.00	0.00	4.24
1529	1546	4.884961	AGAATCCTAAACCCTAGAGCTGA	58.115	43.478	0.00	0.00	0.00	4.26
1725	1798	3.201290	CGCTAGCAATCTTGATGGAAGT	58.799	45.455	16.45	0.00	32.90	3.01
1729	1802	5.298777	GCTAGCAATCTTGATGGAAGTCATT	59.701	40.000	10.63	0.00	35.97	2.57
1868	2307	1.455849	CACCTCCTTCCCACAAGCA	59.544	57.895	0.00	0.00	0.00	3.91
1870	2309	1.676967	CCTCCTTCCCACAAGCAGC	60.677	63.158	0.00	0.00	0.00	5.25
1892	2543	1.093159	AAGTAGGTAGGAGTCGCGTG	58.907	55.000	5.77	0.00	0.00	5.34
1907	2558	1.577134	CGCGTGTTTGTTGACTTTGTG	59.423	47.619	0.00	0.00	0.00	3.33
1930	2581	2.355197	TCATGTTGCCGTTCGATCATT	58.645	42.857	0.00	0.00	0.00	2.57
2019	2674	0.888736	TTGTGGTGGACAATCTGCCG	60.889	55.000	0.00	0.00	39.78	5.69
2030	2686	3.622060	ATCTGCCGGTTGTTCCCCG	62.622	63.158	1.90	0.00	45.07	5.73
2064	2720	1.896220	AGCTGGAGAATGTTTTGCGA	58.104	45.000	0.00	0.00	0.00	5.10
2085	2741	4.153117	CGAAAGATATATGGTCAGCTTGGC	59.847	45.833	0.00	0.00	0.00	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	30	3.916172	GCGTCACTAACACGAACATCTTA	59.084	43.478	0.00	0.00	39.75	2.10
23	31	2.729882	GCGTCACTAACACGAACATCTT	59.270	45.455	0.00	0.00	39.75	2.40
31	39	2.559872	CATGTTTGCGTCACTAACACG	58.440	47.619	0.00	0.00	44.80	4.49
46	54	9.932207	TTTCTCATGAAAATTATCAAGCATGTT	57.068	25.926	0.00	0.00	39.02	2.71
47	55	9.362539	GTTTCTCATGAAAATTATCAAGCATGT	57.637	29.630	0.00	0.00	42.94	3.21
51	59	7.250569	TCCGTTTCTCATGAAAATTATCAAGC	58.749	34.615	0.00	0.00	42.94	4.01
52	60	7.430502	GCTCCGTTTCTCATGAAAATTATCAAG	59.569	37.037	0.00	0.00	42.94	3.02
64	72	1.329906	GATGCTGCTCCGTTTCTCATG	59.670	52.381	0.00	0.00	0.00	3.07
68	76	0.320771	AACGATGCTGCTCCGTTTCT	60.321	50.000	20.47	5.80	42.90	2.52
101	109	9.014297	TCAAATGTTACACCCAAATTTGTTTTT	57.986	25.926	16.73	1.74	38.66	1.94
102	110	8.567285	TCAAATGTTACACCCAAATTTGTTTT	57.433	26.923	16.73	1.41	38.66	2.43
103	111	8.619546	CATCAAATGTTACACCCAAATTTGTTT	58.380	29.630	16.73	4.88	38.66	2.83
142	150	1.349234	GTTAAGCATTTTGGCCTGCG	58.651	50.000	3.32	0.00	43.17	5.18
143	151	1.001860	TGGTTAAGCATTTTGGCCTGC	59.998	47.619	3.32	5.23	38.69	4.85
148	160	5.406780	TGCGTAAAATGGTTAAGCATTTTGG	59.593	36.000	41.38	35.39	40.10	3.28
155	167	2.094957	TGGCTGCGTAAAATGGTTAAGC	60.095	45.455	0.00	0.00	0.00	3.09
184	196	2.611292	CCAAATTTGTCCTGCGCAAAAA	59.389	40.909	13.05	10.44	38.98	1.94
185	197	2.208431	CCAAATTTGTCCTGCGCAAAA	58.792	42.857	13.05	9.74	38.98	2.44
186	198	1.539929	CCCAAATTTGTCCTGCGCAAA	60.540	47.619	13.05	1.92	39.69	3.68
187	199	0.033228	CCCAAATTTGTCCTGCGCAA	59.967	50.000	13.05	0.00	0.00	4.85
188	200	1.112315	ACCCAAATTTGTCCTGCGCA	61.112	50.000	10.98	10.98	0.00	6.09
189	201	0.885196	TACCCAAATTTGTCCTGCGC	59.115	50.000	16.73	0.00	0.00	6.09
190	202	1.135402	GCTACCCAAATTTGTCCTGCG	60.135	52.381	16.73	0.55	0.00	5.18
196	208	5.543507	TTCACAATGCTACCCAAATTTGT	57.456	34.783	16.73	2.12	0.00	2.83
197	209	9.985730	ATATATTCACAATGCTACCCAAATTTG	57.014	29.630	11.40	11.40	0.00	2.32
256	269	7.851963	ACTGTGCGAAAAATGATTTTTGAAATG	59.148	29.630	19.47	8.39	42.51	2.32
280	293	1.338136	AATCCGATTCCGCTCCCACT	61.338	55.000	0.00	0.00	0.00	4.00
368	382	2.187946	CAGATGGCCAGGTCCGTC	59.812	66.667	13.05	1.90	41.41	4.79
405	419	1.463528	CCAGCTACGTTGTTTAAGCGC	60.464	52.381	0.00	0.00	39.94	5.92
413	427	0.531090	TTTCGTGCCAGCTACGTTGT	60.531	50.000	7.35	0.00	41.91	3.32
478	492	0.395724	TGCTATGTGAGGAGAGCCGA	60.396	55.000	0.00	0.00	39.96	5.54
572	586	0.742635	CGGGAAGAGAGAGCCTTTGC	60.743	60.000	0.00	0.00	37.95	3.68
601	615	2.553247	GCCCTCTTCTGTAGGCAGTTTT	60.553	50.000	0.00	0.00	45.07	2.43
1118	1135	1.912043	CAACCTCCAGTCCTTCATCCT	59.088	52.381	0.00	0.00	0.00	3.24
1329	1346	2.525055	CGGAGAGAGAAGAAAAGCGAG	58.475	52.381	0.00	0.00	0.00	5.03
1507	1524	4.884961	TCAGCTCTAGGGTTTAGGATTCT	58.115	43.478	0.00	0.00	0.00	2.40
1716	1789	1.672363	GCGCATCAATGACTTCCATCA	59.328	47.619	0.30	0.00	33.53	3.07
1868	2307	2.100989	CGACTCCTACCTACTTTGGCT	58.899	52.381	0.00	0.00	0.00	4.75
1870	2309	1.202268	CGCGACTCCTACCTACTTTGG	60.202	57.143	0.00	0.00	0.00	3.28
1892	2543	7.393327	CAACATGAATCACAAAGTCAACAAAC	58.607	34.615	0.00	0.00	0.00	2.93
1907	2558	2.351418	TGATCGAACGGCAACATGAATC	59.649	45.455	0.00	0.00	0.00	2.52
1930	2581	0.806868	AAATCCTCGTCGTCGCTACA	59.193	50.000	0.00	0.00	36.96	2.74
2019	2674	0.685660	ACTTCTCTCGGGGAACAACC	59.314	55.000	0.00	0.00	38.08	3.77
2030	2686	3.011119	TCCAGCTTCTCGTACTTCTCTC	58.989	50.000	0.00	0.00	0.00	3.20
2064	2720	4.067896	CGCCAAGCTGACCATATATCTTT	58.932	43.478	0.00	0.00	0.00	2.52
2085	2741	0.537371	AAGCCCACCTTCCTTTCACG	60.537	55.000	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.