AutoCloner

Multiple sequence alignment - TraesCS4B01G289800

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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	TraesCS4B01G289800	chr4B	100.000	2859	0	0	1	2859	574531446	574528588	0.000000e+00	5280.0
1	TraesCS4B01G289800	chr4D	92.134	1373	77	13	930	2284	459589632	459588273	0.000000e+00	1908.0
2	TraesCS4B01G289800	chr4A	94.409	1091	42	5	530	1613	8581989	8583067	0.000000e+00	1659.0
3	TraesCS4B01G289800	chr4A	93.520	679	29	8	1611	2281	8583148	8583819	0.000000e+00	996.0
4	TraesCS4B01G289800	chr4A	92.667	300	18	4	2562	2858	8584392	8584690	2.040000e-116	429.0
5	TraesCS4B01G289800	chr4A	90.234	256	9	6	247	498	8581751	8581994	1.280000e-83	320.0
6	TraesCS4B01G289800	chr4A	92.661	218	15	1	2352	2569	8583826	8584042	2.140000e-81	313.0
7	TraesCS4B01G289800	chr4A	87.149	249	30	2	1	248	8581247	8581494	6.030000e-72	281.0
8	TraesCS4B01G289800	chr6A	92.537	67	3	2	2271	2336	565317055	565317120	8.430000e-16	95.3
9	TraesCS4B01G289800	chr3D	98.148	54	1	0	2283	2336	11592260	11592207	8.430000e-16	95.3
10	TraesCS4B01G289800	chr3D	98.148	54	1	0	2283	2336	610359389	610359336	8.430000e-16	95.3
11	TraesCS4B01G289800	chr2B	98.148	54	1	0	2283	2336	121512049	121512102	8.430000e-16	95.3
12	TraesCS4B01G289800	chr1D	98.148	54	1	0	2283	2336	285371888	285371835	8.430000e-16	95.3
13	TraesCS4B01G289800	chr1A	98.148	54	1	0	2283	2336	493207984	493208037	8.430000e-16	95.3
14	TraesCS4B01G289800	chr7B	96.491	57	1	1	2277	2333	733361483	733361538	3.030000e-15	93.5
15	TraesCS4B01G289800	chr5B	98.113	53	1	0	2282	2334	544518988	544519040	3.030000e-15	93.5
16	TraesCS4B01G289800	chr6B	89.552	67	5	2	2278	2342	52217884	52217818	1.830000e-12	84.2

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	TraesCS4B01G289800	chr4B	574528588	574531446	2858	True	5280.000000	5280	100.000000	1	2859	1	chr4B.!!$R1	2858
1	TraesCS4B01G289800	chr4D	459588273	459589632	1359	True	1908.000000	1908	92.134000	930	2284	1	chr4D.!!$R1	1354
2	TraesCS4B01G289800	chr4A	8581247	8584690	3443	False	666.333333	1659	91.773333	1	2858	6	chr4A.!!$F1	2857

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
465	729	0.105778	TTTTGCTTTTGCCCCTTCCG	59.894	50.0	0.0	0.0	46.87	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2332	2704	0.683412	GGTGTACTCCCTCCGTTTGT	59.317	55.0	2.33	0.0	0.0	2.83	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	1.068250	CAGGGCGCTAGTCTTAGGC	59.932	63.158	7.64	0.00	0.00	3.93
32	33	1.589196	GGCGCTAGTCTTAGGCACG	60.589	63.158	7.64	0.00	0.00	5.34
36	37	1.140407	GCTAGTCTTAGGCACGCGTG	61.140	60.000	34.01	34.01	0.00	5.34
46	47	2.356313	CACGCGTGCAGGAAGACT	60.356	61.111	28.16	0.00	0.00	3.24
59	61	2.779506	GGAAGACTTCCCGTTGTCATT	58.220	47.619	21.88	0.00	44.30	2.57
96	98	3.016997	TCGATAGAGGAACGGCGAT	57.983	52.632	16.62	0.00	42.67	4.58
100	102	2.582687	GATAGAGGAACGGCGATAACG	58.417	52.381	16.62	0.00	42.93	3.18
133	135	2.661566	CGTTCTGACGGCAGCAGTG	61.662	63.158	15.33	0.00	45.32	3.66
147	149	1.782028	GCAGTGGTCGTTTGGTGGTC	61.782	60.000	0.00	0.00	0.00	4.02
149	151	0.179056	AGTGGTCGTTTGGTGGTCTG	60.179	55.000	0.00	0.00	0.00	3.51
158	160	5.411669	GTCGTTTGGTGGTCTGAGAATTAAT	59.588	40.000	0.00	0.00	0.00	1.40
265	525	4.065088	GCCCATTCTTTCCTTGGTTTTTC	58.935	43.478	0.00	0.00	0.00	2.29
269	529	4.400529	TTCTTTCCTTGGTTTTTCCTGC	57.599	40.909	0.00	0.00	37.07	4.85
345	608	3.322828	GGCCTTAGTTACCGGTGATATGA	59.677	47.826	19.93	0.00	0.00	2.15
354	617	2.028839	ACCGGTGATATGAACGAACACA	60.029	45.455	6.12	0.00	33.82	3.72
414	678	4.285863	CTGCAATTCCCATTTTACCCCTA	58.714	43.478	0.00	0.00	0.00	3.53
428	692	2.231529	ACCCCTAGACAGAATCGATCG	58.768	52.381	9.36	9.36	0.00	3.69
429	693	2.158652	ACCCCTAGACAGAATCGATCGA	60.159	50.000	21.86	21.86	0.00	3.59
462	726	3.402186	GCTTTTGCTTTTGCCCCTT	57.598	47.368	0.00	0.00	46.87	3.95
463	727	1.229428	GCTTTTGCTTTTGCCCCTTC	58.771	50.000	0.00	0.00	46.87	3.46
464	728	1.882912	CTTTTGCTTTTGCCCCTTCC	58.117	50.000	0.00	0.00	46.87	3.46
465	729	0.105778	TTTTGCTTTTGCCCCTTCCG	59.894	50.000	0.00	0.00	46.87	4.30
466	730	1.045911	TTTGCTTTTGCCCCTTCCGT	61.046	50.000	0.00	0.00	46.87	4.69
467	731	1.045911	TTGCTTTTGCCCCTTCCGTT	61.046	50.000	0.00	0.00	46.87	4.44
468	732	1.289066	GCTTTTGCCCCTTCCGTTC	59.711	57.895	0.00	0.00	40.15	3.95

Showing 1 to 25 of 162 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.755698	TAAGACTAGCGCCCTGGAGG	60.756	60.000	2.29	0.00	39.47	4.30
18	19	2.945315	CACGCGTGCCTAAGACTAG	58.055	57.895	28.16	0.00	0.00	2.57
29	30	1.891060	GAAGTCTTCCTGCACGCGTG	61.891	60.000	34.01	34.01	0.00	5.34
32	33	3.567473	GGAAGTCTTCCTGCACGC	58.433	61.111	22.42	0.00	46.57	5.34
46	47	2.226330	CCTTGTCAATGACAACGGGAA	58.774	47.619	23.28	3.96	45.88	3.97
59	61	2.557317	GAAACCGACTTGACCTTGTCA	58.443	47.619	0.00	0.00	41.09	3.58
76	78	1.097232	TCGCCGTTCCTCTATCGAAA	58.903	50.000	0.00	0.00	0.00	3.46
103	105	2.813908	AGAACGATCCGCCAACGC	60.814	61.111	0.00	0.00	38.22	4.84
116	118	2.320587	CCACTGCTGCCGTCAGAAC	61.321	63.158	0.00	0.00	42.95	3.01
128	130	1.782028	GACCACCAAACGACCACTGC	61.782	60.000	0.00	0.00	0.00	4.40
129	131	0.179056	AGACCACCAAACGACCACTG	60.179	55.000	0.00	0.00	0.00	3.66
133	135	0.391597	TCTCAGACCACCAAACGACC	59.608	55.000	0.00	0.00	0.00	4.79
168	170	8.472007	AAGTTCATGTACAAACCCTATCAAAA	57.528	30.769	0.00	0.00	0.00	2.44
208	210	4.927978	TTTCTTTTGCGAAAGGGATCAA	57.072	36.364	23.38	9.47	42.05	2.57
209	211	4.927978	TTTTCTTTTGCGAAAGGGATCA	57.072	36.364	23.38	3.87	42.05	2.92
219	221	3.487574	TGCACGGTTATTTTTCTTTTGCG	59.512	39.130	0.00	0.00	0.00	4.85
265	525	3.042887	GCACGTTAAGAAAACTTGCAGG	58.957	45.455	12.68	0.00	42.63	4.85
345	608	1.027792	AAAGTGCCCGTGTGTTCGTT	61.028	50.000	0.00	0.00	0.00	3.85
414	678	4.338400	TGGTGTATTCGATCGATTCTGTCT	59.662	41.667	20.18	0.96	0.00	3.41
428	692	1.826385	AAGCTGCTGGTGGTGTATTC	58.174	50.000	1.35	0.00	0.00	1.75
429	693	2.292828	AAAGCTGCTGGTGGTGTATT	57.707	45.000	1.35	0.00	0.00	1.89
452	716	4.184439	GGAACGGAAGGGGCAAAA	57.816	55.556	0.00	0.00	0.00	2.44
465	729	1.154073	CGGGAGAGACGAACGGAAC	60.154	63.158	0.00	0.00	0.00	3.62
466	730	1.601759	ACGGGAGAGACGAACGGAA	60.602	57.895	0.00	0.00	34.93	4.30
467	731	2.033141	ACGGGAGAGACGAACGGA	59.967	61.111	0.00	0.00	34.93	4.69

Showing 1 to 25 of 158 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.