AutoCloner

Multiple sequence alignment - TraesCS1D01G427000

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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	TraesCS1D01G427000	chr1D	100.000	2370	0	0	1	2370	479760391	479758022	0.000000e+00	4377.0
1	TraesCS1D01G427000	chr1D	88.336	2392	183	44	1	2370	479751797	479749480	0.000000e+00	2784.0
2	TraesCS1D01G427000	chr1D	93.238	281	16	1	2093	2370	479722102	479721822	6.100000e-111	411.0
3	TraesCS1D01G427000	chr1D	87.739	261	29	1	1018	1278	479737852	479737595	3.830000e-78	302.0
4	TraesCS1D01G427000	chr1D	91.892	148	10	1	1920	2065	479722323	479722176	3.090000e-49	206.0
5	TraesCS1D01G427000	chr1D	79.661	236	16	12	1531	1761	479737354	479737146	8.830000e-30	141.0
6	TraesCS1D01G427000	chr1A	91.277	1777	111	23	1	1760	576204541	576202792	0.000000e+00	2383.0
7	TraesCS1D01G427000	chr1A	88.790	1686	120	20	23	1660	576140157	576138493	0.000000e+00	2002.0
8	TraesCS1D01G427000	chr1A	90.772	596	48	6	1777	2370	576138448	576137858	0.000000e+00	789.0
9	TraesCS1D01G427000	chr1A	89.570	604	52	3	1777	2370	576202806	576202204	0.000000e+00	756.0
10	TraesCS1D01G427000	chr1A	81.316	471	61	15	1018	1478	576078231	576077778	8.060000e-95	357.0
11	TraesCS1D01G427000	chr1A	79.237	236	17	12	1531	1761	576077757	576077549	4.110000e-28	135.0
12	TraesCS1D01G427000	chr1B	91.134	1252	65	14	539	1761	667930469	667931703	0.000000e+00	1655.0
13	TraesCS1D01G427000	chr1B	94.098	881	28	9	984	1840	667997262	667996382	0.000000e+00	1317.0
14	TraesCS1D01G427000	chr1B	94.293	806	32	1	970	1761	667975788	667974983	0.000000e+00	1221.0
15	TraesCS1D01G427000	chr1B	89.217	881	39	19	986	1846	668031093	668030249	0.000000e+00	1050.0
16	TraesCS1D01G427000	chr1B	84.558	939	100	21	1	932	668031997	668031097	0.000000e+00	889.0
17	TraesCS1D01G427000	chr1B	92.965	597	32	6	1777	2370	667974998	667974409	0.000000e+00	861.0
18	TraesCS1D01G427000	chr1B	89.051	685	48	15	1	676	667976847	667976181	0.000000e+00	824.0
19	TraesCS1D01G427000	chr1B	91.188	522	42	3	1853	2370	668029994	668029473	0.000000e+00	706.0
20	TraesCS1D01G427000	chr1B	89.700	534	41	6	1849	2370	667932022	667932553	0.000000e+00	669.0
21	TraesCS1D01G427000	chr1B	91.224	490	31	7	1	478	667929977	667930466	0.000000e+00	656.0
22	TraesCS1D01G427000	chr1B	90.300	433	37	2	1843	2273	667996255	667995826	1.590000e-156	562.0
23	TraesCS1D01G427000	chr1B	83.710	620	65	13	319	932	667997851	667997262	9.570000e-154	553.0
24	TraesCS1D01G427000	chr1B	86.747	332	32	7	1	332	667998688	667998369	2.240000e-95	359.0
25	TraesCS1D01G427000	chr1B	93.860	114	6	1	799	911	667975901	667975788	1.130000e-38	171.0
26	TraesCS1D01G427000	chr1B	94.118	68	4	0	2303	2370	667995560	667995493	1.160000e-18	104.0
27	TraesCS1D01G427000	chr1B	96.429	56	2	0	1780	1835	667931691	667931746	2.510000e-15	93.5

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	TraesCS1D01G427000	chr1D	479758022	479760391	2369	True	4377.000000	4377	100.00000	1	2370	1	chr1D.!!$R2	2369
1	TraesCS1D01G427000	chr1D	479749480	479751797	2317	True	2784.000000	2784	88.33600	1	2370	1	chr1D.!!$R1	2369
2	TraesCS1D01G427000	chr1D	479721822	479722323	501	True	308.500000	411	92.56500	1920	2370	2	chr1D.!!$R3	450
3	TraesCS1D01G427000	chr1D	479737146	479737852	706	True	221.500000	302	83.70000	1018	1761	2	chr1D.!!$R4	743
4	TraesCS1D01G427000	chr1A	576202204	576204541	2337	True	1569.500000	2383	90.42350	1	2370	2	chr1A.!!$R3	2369
5	TraesCS1D01G427000	chr1A	576137858	576140157	2299	True	1395.500000	2002	89.78100	23	2370	2	chr1A.!!$R2	2347
6	TraesCS1D01G427000	chr1A	576077549	576078231	682	True	246.000000	357	80.27650	1018	1761	2	chr1A.!!$R1	743
7	TraesCS1D01G427000	chr1B	668029473	668031997	2524	True	881.666667	1050	88.32100	1	2370	3	chr1B.!!$R3	2369
8	TraesCS1D01G427000	chr1B	667974409	667976847	2438	True	769.250000	1221	92.54225	1	2370	4	chr1B.!!$R1	2369
9	TraesCS1D01G427000	chr1B	667929977	667932553	2576	False	768.375000	1655	92.12175	1	2370	4	chr1B.!!$F1	2369
10	TraesCS1D01G427000	chr1B	667995493	667998688	3195	True	579.000000	1317	89.79460	1	2370	5	chr1B.!!$R2	2369

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
336	907	1.156736	CCGCAAGAAGTTGGTCGAAT	58.843	50.0	0.0	0.0	43.02	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1502	2346	0.685097	ACTTTTCTGCCCGCTAGTCA	59.315	50.0	0.0	0.0	0.0	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
73	75	9.778741	AAAAGTAAGATATATTCTGGATCGCAA	57.221	29.630	0.00	0.00	33.93	4.85
117	119	2.363359	GGTGATGGCATCCCAATCTTTC	59.637	50.000	23.92	0.00	46.14	2.62
146	148	8.082852	ACTAACTATTTGTAGATAGCGACATGG	58.917	37.037	0.00	0.00	33.77	3.66
147	149	5.230942	ACTATTTGTAGATAGCGACATGGC	58.769	41.667	0.00	0.00	33.77	4.40
203	215	8.806429	TCACATGTATGAAGATTATGTTTGGT	57.194	30.769	0.00	0.00	30.15	3.67
204	216	8.676401	TCACATGTATGAAGATTATGTTTGGTG	58.324	33.333	0.00	0.00	30.15	4.17
212	224	8.506168	TGAAGATTATGTTTGGTGTTATCCTC	57.494	34.615	0.00	0.00	0.00	3.71
213	225	8.328758	TGAAGATTATGTTTGGTGTTATCCTCT	58.671	33.333	0.00	0.00	0.00	3.69
214	226	8.738645	AAGATTATGTTTGGTGTTATCCTCTC	57.261	34.615	0.00	0.00	0.00	3.20
215	227	7.283329	AGATTATGTTTGGTGTTATCCTCTCC	58.717	38.462	0.00	0.00	0.00	3.71
216	228	3.328382	TGTTTGGTGTTATCCTCTCCG	57.672	47.619	0.00	0.00	0.00	4.63
226	260	6.535508	GGTGTTATCCTCTCCGAATATTATGC	59.464	42.308	0.00	0.00	0.00	3.14
232	266	7.718334	TCCTCTCCGAATATTATGCAGATTA	57.282	36.000	0.00	0.00	0.00	1.75
332	903	2.954611	GCCCGCAAGAAGTTGGTC	59.045	61.111	0.00	0.00	43.02	4.02
336	907	1.156736	CCGCAAGAAGTTGGTCGAAT	58.843	50.000	0.00	0.00	43.02	3.34
349	920	4.330944	TGGTCGAATCACAACACTAGTT	57.669	40.909	0.00	0.00	38.88	2.24
380	954	2.729360	GGTTTTCGCTATTTTGTGGTGC	59.271	45.455	0.00	0.00	0.00	5.01
433	1007	8.451908	AACACTTCAAAGCTAATAGAACTTGT	57.548	30.769	0.00	0.00	0.00	3.16
480	1054	4.843728	TGATTCACTGACCAAGGATTACC	58.156	43.478	0.00	0.00	0.00	2.85
647	1251	1.556911	GAGGTGAGGAAGGATGCTGAA	59.443	52.381	0.00	0.00	0.00	3.02
672	1276	4.084888	GCGACGCAAAAGGGACGG	62.085	66.667	16.42	0.00	0.00	4.79
697	1301	5.376653	AGATAGAAAGGTAGATCCCCCAT	57.623	43.478	1.44	0.00	36.75	4.00
846	1612	3.491598	CTCCGCCCCCACACAAAGT	62.492	63.158	0.00	0.00	0.00	2.66
953	1719	6.530534	CGTAGTTCAGGTCATAAGTTAAGGTG	59.469	42.308	0.00	0.00	0.00	4.00
959	1725	9.483489	TTCAGGTCATAAGTTAAGGTGTATAGA	57.517	33.333	0.00	0.00	0.00	1.98
1275	2043	2.478890	CGAGGCCGACAGGTACGAT	61.479	63.158	0.00	0.00	40.50	3.73
1282	2054	0.934901	CGACAGGTACGATCGCCATG	60.935	60.000	16.60	16.03	34.29	3.66
1289	2061	3.945434	CGATCGCCATGGCTGTGC	61.945	66.667	33.07	18.34	39.32	4.57
1510	2354	5.634859	TCAATGTATACATGCATGACTAGCG	59.365	40.000	32.75	13.24	36.56	4.26
1588	2434	6.718454	TGGCTAGTGGTCTATAAGTATGTACC	59.282	42.308	0.00	0.00	0.00	3.34
1754	2619	7.155655	TGTCAAATATGTTATGCACACACAT	57.844	32.000	11.02	11.02	38.61	3.21
1757	2622	8.397906	GTCAAATATGTTATGCACACACATACT	58.602	33.333	13.85	3.99	38.61	2.12
1758	2623	9.606631	TCAAATATGTTATGCACACACATACTA	57.393	29.630	13.85	0.37	38.61	1.82
1759	2624	9.650371	CAAATATGTTATGCACACACATACTAC	57.350	33.333	13.85	0.00	38.61	2.73
1762	2630	7.921786	ATGTTATGCACACACATACTACTTT	57.078	32.000	2.67	0.00	38.61	2.66
1795	2663	6.405508	CGAGGGACACACACATACTACTAATT	60.406	42.308	0.00	0.00	0.00	1.40
1865	3105	3.985019	TTTGGGGAGCATTTACGACTA	57.015	42.857	0.00	0.00	0.00	2.59
1888	3128	0.036952	ATCTCGTTGAGGTGCCACAG	60.037	55.000	0.00	0.00	0.00	3.66
1998	3240	4.402155	ACAGCAGAACCAAGAACAAATCAA	59.598	37.500	0.00	0.00	0.00	2.57
2080	3354	2.237392	GTTGTTGATAGTGGAGCTCCCT	59.763	50.000	29.95	25.58	35.38	4.20
2082	3356	2.292521	TGTTGATAGTGGAGCTCCCTCT	60.293	50.000	29.95	26.62	41.36	3.69
2206	3496	1.048160	TGATGATGGTGGAGCCGCTA	61.048	55.000	0.00	0.00	41.21	4.26
2207	3497	0.106708	GATGATGGTGGAGCCGCTAA	59.893	55.000	0.00	0.00	41.21	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
187	199	8.328758	AGAGGATAACACCAAACATAATCTTCA	58.671	33.333	0.00	0.00	0.00	3.02
188	200	8.738645	AGAGGATAACACCAAACATAATCTTC	57.261	34.615	0.00	0.00	0.00	2.87
191	203	6.202954	CGGAGAGGATAACACCAAACATAATC	59.797	42.308	0.00	0.00	0.00	1.75
193	205	5.188163	TCGGAGAGGATAACACCAAACATAA	59.812	40.000	0.00	0.00	0.00	1.90
194	206	4.712829	TCGGAGAGGATAACACCAAACATA	59.287	41.667	0.00	0.00	0.00	2.29
195	207	3.517901	TCGGAGAGGATAACACCAAACAT	59.482	43.478	0.00	0.00	0.00	2.71
197	209	3.604875	TCGGAGAGGATAACACCAAAC	57.395	47.619	0.00	0.00	0.00	2.93
201	213	6.535508	GCATAATATTCGGAGAGGATAACACC	59.464	42.308	0.00	0.00	38.43	4.16
202	214	7.097192	TGCATAATATTCGGAGAGGATAACAC	58.903	38.462	0.00	0.00	38.43	3.32
203	215	7.178451	TCTGCATAATATTCGGAGAGGATAACA	59.822	37.037	5.28	0.00	38.43	2.41
204	216	7.548097	TCTGCATAATATTCGGAGAGGATAAC	58.452	38.462	5.28	0.00	38.43	1.89
207	219	6.805016	ATCTGCATAATATTCGGAGAGGAT	57.195	37.500	12.51	0.00	38.43	3.24
208	220	6.611613	AATCTGCATAATATTCGGAGAGGA	57.388	37.500	12.51	0.00	38.43	3.71
209	221	7.776107	TCTAATCTGCATAATATTCGGAGAGG	58.224	38.462	12.51	7.34	38.43	3.69
210	222	8.681806	TCTCTAATCTGCATAATATTCGGAGAG	58.318	37.037	12.51	0.00	38.43	3.20
211	223	8.581253	TCTCTAATCTGCATAATATTCGGAGA	57.419	34.615	10.24	10.24	0.00	3.71
212	224	9.814899	AATCTCTAATCTGCATAATATTCGGAG	57.185	33.333	0.00	0.00	0.00	4.63
232	266	8.429641	TGTCTTGAGTGTACCTTAAAAATCTCT	58.570	33.333	0.00	0.00	0.00	3.10
360	933	3.376540	TGCACCACAAAATAGCGAAAAC	58.623	40.909	0.00	0.00	0.00	2.43
380	954	8.267620	TGTACATCCATGTTGACTCTTATTTG	57.732	34.615	0.00	0.00	41.97	2.32
454	1028	4.371624	TCCTTGGTCAGTGAATCAATGT	57.628	40.909	10.57	0.00	31.07	2.71
456	1030	5.888161	GGTAATCCTTGGTCAGTGAATCAAT	59.112	40.000	9.67	0.00	0.00	2.57
672	1276	5.607171	TGGGGGATCTACCTTTCTATCTTTC	59.393	44.000	7.55	0.00	38.98	2.62
697	1301	4.775236	CAAACATTTTTGTCCCCTGGAAA	58.225	39.130	0.00	0.00	37.85	3.13
846	1612	1.561643	AGCACTCGAGGAGGATTCAA	58.438	50.000	18.41	0.00	33.35	2.69
953	1719	7.804712	TCCTCGATCGACAATTACTTCTATAC	58.195	38.462	15.15	0.00	0.00	1.47
959	1725	4.081862	TGGTTCCTCGATCGACAATTACTT	60.082	41.667	15.15	0.00	0.00	2.24
1282	2054	4.260948	GCATAACTGATAAGAAGCACAGCC	60.261	45.833	0.00	0.00	34.25	4.85
1289	2061	5.068636	AGCCCATGCATAACTGATAAGAAG	58.931	41.667	0.00	0.00	41.13	2.85
1502	2346	0.685097	ACTTTTCTGCCCGCTAGTCA	59.315	50.000	0.00	0.00	0.00	3.41
1503	2347	1.360820	GACTTTTCTGCCCGCTAGTC	58.639	55.000	0.00	0.00	0.00	2.59
1510	2354	3.431725	CGGCCGACTTTTCTGCCC	61.432	66.667	24.07	0.00	46.75	5.36
1588	2434	4.638421	AGTAAGGAGACAAGTCGATCTCAG	59.362	45.833	14.09	2.35	42.73	3.35
1795	2663	2.490115	ACCGCAGTTGTTTTGTCTTTGA	59.510	40.909	0.00	0.00	0.00	2.69
1865	3105	2.846371	GCACCTCAACGAGATGCTT	58.154	52.632	2.97	0.00	45.15	3.91
1888	3128	6.588719	ACTCATGATCTCTAATGCCTCTAC	57.411	41.667	0.00	0.00	0.00	2.59
1945	3186	0.888736	CAATGGGTGCGTGTTCTCCA	60.889	55.000	0.00	0.00	0.00	3.86
1976	3218	4.572985	TGATTTGTTCTTGGTTCTGCTG	57.427	40.909	0.00	0.00	0.00	4.41
1998	3240	6.308015	TGATATGGGTGCTTTGTAGTAGTT	57.692	37.500	0.00	0.00	0.00	2.24
2080	3354	2.771943	GACCTGGTGTCCCAATATCAGA	59.228	50.000	2.82	0.00	41.27	3.27
2206	3496	4.669206	TGATCCAAGCACAACAACATTT	57.331	36.364	0.00	0.00	0.00	2.32
2207	3497	4.562082	CATGATCCAAGCACAACAACATT	58.438	39.130	0.00	0.00	0.00	2.71
2244	3534	1.321474	CCTTGCACTTGAGGAGCAAA	58.679	50.000	12.11	1.20	46.30	3.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.