AutoCloner

Multiple sequence alignment - TraesCS3D01G218500

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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	TraesCS3D01G218500	chr3D	100.000	2671	0	0	1	2671	297676820	297679490	0.000000e+00	4933.0
1	TraesCS3D01G218500	chr3A	95.541	1839	43	19	1	1810	394647866	394649694	0.000000e+00	2905.0
2	TraesCS3D01G218500	chr3A	90.144	416	31	5	2248	2654	394650125	394650539	1.410000e-147	532.0
3	TraesCS3D01G218500	chr3A	96.000	225	7	2	2040	2264	394649888	394650110	5.430000e-97	364.0
4	TraesCS3D01G218500	chr3A	93.706	143	9	0	1901	2043	394649711	394649853	5.790000e-52	215.0
5	TraesCS3D01G218500	chr3A	100.000	36	0	0	1846	1881	394649682	394649717	1.720000e-07	67.6
6	TraesCS3D01G218500	chr3B	96.244	772	20	6	1272	2039	392809441	392810207	0.000000e+00	1256.0
7	TraesCS3D01G218500	chr3B	97.162	599	13	3	679	1275	392797602	392798198	0.000000e+00	1009.0
8	TraesCS3D01G218500	chr3B	91.135	643	44	8	2040	2671	392810246	392810886	0.000000e+00	859.0
9	TraesCS3D01G218500	chr3B	98.551	207	3	0	1	207	392797124	392797330	1.510000e-97	366.0
10	TraesCS3D01G218500	chr3B	95.862	145	4	1	537	681	392797337	392797479	1.600000e-57	233.0
11	TraesCS3D01G218500	chr2A	81.967	488	73	13	840	1317	715813324	715813806	1.490000e-107	399.0
12	TraesCS3D01G218500	chr2A	80.863	371	40	20	1360	1705	715813905	715814269	2.040000e-66	263.0
13	TraesCS3D01G218500	chr2D	78.493	637	106	22	706	1317	577602803	577602173	3.220000e-104	388.0
14	TraesCS3D01G218500	chr2D	81.132	371	39	20	1360	1705	577602074	577601710	4.380000e-68	268.0
15	TraesCS3D01G218500	chr2B	81.276	486	76	13	840	1314	694990986	694991467	1.940000e-101	379.0
16	TraesCS3D01G218500	chr2B	82.102	352	32	20	1379	1705	694991588	694991933	3.390000e-69	272.0
17	TraesCS3D01G218500	chr7A	91.071	168	11	1	2340	2503	60114581	60114414	9.620000e-55	224.0

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	TraesCS3D01G218500	chr3D	297676820	297679490	2670	False	4933.00	4933	100.000000	1	2671	1	chr3D.!!$F1	2670
1	TraesCS3D01G218500	chr3A	394647866	394650539	2673	False	816.72	2905	95.078200	1	2654	5	chr3A.!!$F1	2653
2	TraesCS3D01G218500	chr3B	392809441	392810886	1445	False	1057.50	1256	93.689500	1272	2671	2	chr3B.!!$F2	1399
3	TraesCS3D01G218500	chr3B	392797124	392798198	1074	False	536.00	1009	97.191667	1	1275	3	chr3B.!!$F1	1274
4	TraesCS3D01G218500	chr2A	715813324	715814269	945	False	331.00	399	81.415000	840	1705	2	chr2A.!!$F1	865
5	TraesCS3D01G218500	chr2D	577601710	577602803	1093	True	328.00	388	79.812500	706	1705	2	chr2D.!!$R1	999
6	TraesCS3D01G218500	chr2B	694990986	694991933	947	False	325.50	379	81.689000	840	1705	2	chr2B.!!$F1	865

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
249	275	0.105778	GCACTCCAGCATCCTCCTAC	59.894	60.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1838	2094	0.674581	TGAAGTGGCTCATGGCTTCG	60.675	55.0	6.2	0.0	39.91	3.79	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
249	275	0.105778	GCACTCCAGCATCCTCCTAC	59.894	60.000	0.00	0.00	0.00	3.18
263	289	0.811915	TCCTACTCAAGCTCGAGTGC	59.188	55.000	17.75	0.56	45.79	4.40
302	329	6.806739	CGTGAGTTAAATTTGAATCCCCTTTC	59.193	38.462	7.79	0.00	0.00	2.62
303	330	6.806739	GTGAGTTAAATTTGAATCCCCTTTCG	59.193	38.462	7.79	0.00	0.00	3.46
304	331	6.071616	TGAGTTAAATTTGAATCCCCTTTCGG	60.072	38.462	7.79	0.00	0.00	4.30
305	332	5.778241	AGTTAAATTTGAATCCCCTTTCGGT	59.222	36.000	0.00	0.00	0.00	4.69
306	333	6.269077	AGTTAAATTTGAATCCCCTTTCGGTT	59.731	34.615	0.00	0.00	0.00	4.44
342	369	2.690786	CAACCCAGATGCCACAATTTG	58.309	47.619	0.00	0.00	0.00	2.32
396	423	5.395768	CCGGAAGAGTACCAAATTGAGAGAT	60.396	44.000	0.00	0.00	0.00	2.75
417	444	8.989980	AGAGATAACTTAAAACCGAACTTCTTG	58.010	33.333	0.00	0.00	0.00	3.02
560	588	4.669206	ACTGTTCAGATCAGGCTCTATG	57.331	45.455	12.31	0.00	37.25	2.23
665	693	5.178061	TGTACAACCTCTAAGCATGTGATG	58.822	41.667	0.00	0.00	0.00	3.07
1376	1608	1.902508	CCCACTTGCTTCAGAGAGGTA	59.097	52.381	0.00	0.00	0.00	3.08
1536	1769	6.148811	GCTTACCATGCTGTAAGTGTCTTAAA	59.851	38.462	17.75	0.00	46.08	1.52
1603	1853	5.034797	GGTTTGCAAGTTTTATATCGGCTC	58.965	41.667	0.00	0.00	0.00	4.70
1605	1855	6.037830	GGTTTGCAAGTTTTATATCGGCTCTA	59.962	38.462	0.00	0.00	0.00	2.43
1981	2237	4.154195	ACTTCGTGAATGCCAATGTTAGTC	59.846	41.667	0.00	0.00	0.00	2.59
2005	2261	5.332581	CCGTGTGCTCTTATCATATTGTTCG	60.333	44.000	0.00	0.00	0.00	3.95
2023	2279	2.283298	TCGCTTGATCCAGCAAAGATC	58.717	47.619	18.05	4.24	40.09	2.75
2089	2383	1.300311	CACCGCCGTGTGTTCAGTA	60.300	57.895	0.00	0.00	35.10	2.74
2115	2409	3.635373	TGTACTCAGGTCGTCAAAGTCTT	59.365	43.478	0.00	0.00	0.00	3.01
2219	2513	3.388024	ACGGTGATCCACTAAGTGCATAT	59.612	43.478	0.00	0.00	34.40	1.78
2308	2638	2.806608	TTTTACTCGCTCCGTTGACT	57.193	45.000	0.00	0.00	0.00	3.41
2385	2717	1.134491	GTCCGCCTTAGCATACAAGGT	60.134	52.381	3.27	0.00	43.83	3.50
2387	2719	1.299541	CGCCTTAGCATACAAGGTGG	58.700	55.000	6.76	0.00	45.78	4.61
2388	2720	1.025041	GCCTTAGCATACAAGGTGGC	58.975	55.000	3.27	0.00	43.83	5.01
2390	2722	2.565841	CCTTAGCATACAAGGTGGCTC	58.434	52.381	0.00	0.00	38.21	4.70
2393	2725	2.813179	GCATACAAGGTGGCTCGCG	61.813	63.158	0.00	0.00	0.00	5.87
2410	2746	1.885157	CGGCAGGTAGTTACGGTGA	59.115	57.895	0.00	0.00	0.00	4.02
2436	2772	1.371558	GAGACCCGCTCAAGGTTGT	59.628	57.895	0.00	0.00	43.38	3.32
2489	2825	2.415759	CGCCAAGCTCAATACATGCAAA	60.416	45.455	0.00	0.00	0.00	3.68
2553	2889	0.178068	GCGGAAAGCTAGGATGGACA	59.822	55.000	0.00	0.00	44.04	4.02
2587	2923	0.097674	GCTGCGTTGATGCTACAAGG	59.902	55.000	10.18	10.18	38.26	3.61
2617	2954	3.124297	GCTAATGCTGGAATCGACTATGC	59.876	47.826	0.00	0.00	36.03	3.14
2656	2994	3.854669	CCGCGGAAGATGGGAGCT	61.855	66.667	24.07	0.00	0.00	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
249	275	2.507992	CGGGCACTCGAGCTTGAG	60.508	66.667	26.64	26.64	41.86	3.02
263	289	2.184322	CACGGTGATCAGGTCGGG	59.816	66.667	0.74	8.81	0.00	5.14
302	329	5.151389	GTTGCAGGTATGAAAACTAAACCG	58.849	41.667	0.00	0.00	35.32	4.44
303	330	5.466819	GGTTGCAGGTATGAAAACTAAACC	58.533	41.667	0.00	0.00	27.78	3.27
304	331	5.010213	TGGGTTGCAGGTATGAAAACTAAAC	59.990	40.000	0.00	0.00	31.54	2.01
305	332	5.141182	TGGGTTGCAGGTATGAAAACTAAA	58.859	37.500	0.00	0.00	31.54	1.85
306	333	4.730966	TGGGTTGCAGGTATGAAAACTAA	58.269	39.130	0.00	0.00	31.54	2.24
342	369	4.586001	ACATGCCAAATCCATCAGTAATCC	59.414	41.667	0.00	0.00	0.00	3.01
396	423	7.862512	TTCCAAGAAGTTCGGTTTTAAGTTA	57.137	32.000	0.00	0.00	0.00	2.24
417	444	3.296854	AGGTTTTGGACAGAGGTTTTCC	58.703	45.455	0.00	0.00	41.05	3.13
455	482	0.037975	CAACATGGCAAGGTTGGAGC	60.038	55.000	21.09	0.00	42.87	4.70
486	514	5.782893	TGTTTTCCATTTCGATTTCCTGT	57.217	34.783	0.00	0.00	0.00	4.00
560	588	1.341209	CAGAAACAGGAGGGGCAAAAC	59.659	52.381	0.00	0.00	0.00	2.43
623	651	4.602340	ACAGTACTACAGTGGTGGAAAG	57.398	45.455	0.00	0.00	31.20	2.62
796	952	2.745968	TGGGAAAGGCAAAGTTTCTGT	58.254	42.857	0.00	0.00	34.81	3.41
1329	1559	3.319405	TGGCACGGTACACAAAATGAAAT	59.681	39.130	0.00	0.00	0.00	2.17
1603	1853	7.862372	ACATGTATTGCTGAACAACAAAGTTAG	59.138	33.333	0.00	0.00	42.27	2.34
1605	1855	6.572519	ACATGTATTGCTGAACAACAAAGTT	58.427	32.000	0.00	0.00	42.27	2.66
1749	2005	5.419788	CCAGGATTCCAATCAAAACATCTCA	59.580	40.000	5.29	0.00	37.15	3.27
1838	2094	0.674581	TGAAGTGGCTCATGGCTTCG	60.675	55.000	6.20	0.00	39.91	3.79
1906	2162	5.771666	CCATGCTTCAATAAGGTACCATCAT	59.228	40.000	15.94	0.54	32.98	2.45
1981	2237	5.332581	CGAACAATATGATAAGAGCACACGG	60.333	44.000	0.00	0.00	0.00	4.94
2005	2261	2.358267	CCTGATCTTTGCTGGATCAAGC	59.642	50.000	15.73	15.73	45.67	4.01
2023	2279	6.049955	TCTTGTGTAAAATAGAGGTCCCTG	57.950	41.667	0.00	0.00	0.00	4.45
2089	2383	4.202223	ACTTTGACGACCTGAGTACACAAT	60.202	41.667	0.00	0.00	0.00	2.71
2219	2513	2.701951	ACTTTCGTACCTTGGGAAGTCA	59.298	45.455	0.00	0.00	0.00	3.41
2317	2648	7.824289	CAGGCCTATTTTGGATCGATAAATCTA	59.176	37.037	3.98	0.00	0.00	1.98
2365	2697	1.134491	ACCTTGTATGCTAAGGCGGAC	60.134	52.381	10.43	0.00	46.89	4.79
2386	2718	3.072486	TAACTACCTGCCGCGAGCC	62.072	63.158	8.23	0.00	42.71	4.70
2387	2719	1.877165	GTAACTACCTGCCGCGAGC	60.877	63.158	8.23	10.56	44.14	5.03
2388	2720	1.585521	CGTAACTACCTGCCGCGAG	60.586	63.158	8.23	0.00	0.00	5.03
2390	2722	2.581409	CCGTAACTACCTGCCGCG	60.581	66.667	0.00	0.00	0.00	6.46
2393	2725	2.685850	AATCACCGTAACTACCTGCC	57.314	50.000	0.00	0.00	0.00	4.85
2396	2732	4.529377	TCCTCAAAATCACCGTAACTACCT	59.471	41.667	0.00	0.00	0.00	3.08
2410	2746	0.984230	TGAGCGGGTCTCCTCAAAAT	59.016	50.000	8.82	0.00	41.18	1.82
2436	2772	2.494471	TCTCGGAATAGCTTCGAACCAA	59.506	45.455	0.00	0.00	31.75	3.67
2483	2819	2.038952	GGGCCTTTCTTTCCTTTTGCAT	59.961	45.455	0.84	0.00	0.00	3.96
2489	2825	5.013079	CCTTATTTTGGGCCTTTCTTTCCTT	59.987	40.000	4.53	0.00	0.00	3.36
2535	2871	1.757118	TCTGTCCATCCTAGCTTTCCG	59.243	52.381	0.00	0.00	0.00	4.30
2553	2889	1.743321	GCAGCTCTAGCCGACCATCT	61.743	60.000	0.00	0.00	43.38	2.90
2587	2923	1.953559	TCCAGCATTAGCCATCGTTC	58.046	50.000	0.00	0.00	43.56	3.95
2617	2954	2.281761	AGCTGCCACAACTTCCCG	60.282	61.111	0.00	0.00	0.00	5.14
2642	2979	1.078214	TTGCAGCTCCCATCTTCCG	60.078	57.895	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.