AutoCloner

Multiple sequence alignment - TraesCS6A01G213800

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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	TraesCS6A01G213800	chr6A	100.000	3503	0	0	1	3503	389243761	389247263	0.000000e+00	6469.0
1	TraesCS6A01G213800	chr6A	87.500	472	57	2	2987	3456	155748670	155748199	8.550000e-151	544.0
2	TraesCS6A01G213800	chr6B	96.476	3008	86	19	503	3503	433707899	433710893	0.000000e+00	4950.0
3	TraesCS6A01G213800	chr6B	96.939	490	12	3	21	507	433707308	433707797	0.000000e+00	819.0
4	TraesCS6A01G213800	chr6D	97.174	2760	41	12	1	2742	272645989	272648729	0.000000e+00	4630.0
5	TraesCS6A01G213800	chr6D	91.930	570	44	2	2935	3503	272649554	272650122	0.000000e+00	797.0
6	TraesCS6A01G213800	chr6D	94.715	246	11	2	2740	2984	272649314	272649558	7.100000e-102	381.0
7	TraesCS6A01G213800	chr6D	90.741	162	13	1	2821	2982	431160670	431160829	7.620000e-52	215.0
8	TraesCS6A01G213800	chr2B	86.752	468	57	4	2989	3454	310850687	310851151	1.860000e-142	516.0
9	TraesCS6A01G213800	chr2B	86.308	409	49	5	3050	3456	338774817	338775220	4.150000e-119	438.0
10	TraesCS6A01G213800	chr2A	86.374	455	59	3	2988	3440	348048630	348049083	8.730000e-136	494.0
11	TraesCS6A01G213800	chr2A	88.172	372	41	3	3086	3456	550180571	550180940	1.150000e-119	440.0
12	TraesCS6A01G213800	chr2A	90.683	161	14	1	2821	2981	342647401	342647560	2.740000e-51	213.0
13	TraesCS6A01G213800	chr2A	89.222	167	18	0	2821	2987	70985744	70985578	3.540000e-50	209.0
14	TraesCS6A01G213800	chr2A	83.810	105	16	1	2987	3090	550171689	550171793	8.000000e-17	99.0
15	TraesCS6A01G213800	chr2D	85.870	460	61	4	2999	3456	460571052	460571509	1.460000e-133	486.0
16	TraesCS6A01G213800	chr7A	81.435	474	73	11	2988	3456	419564516	419564053	1.190000e-99	374.0
17	TraesCS6A01G213800	chr7A	94.737	38	2	0	1568	1605	704907640	704907677	3.780000e-05	60.2
18	TraesCS6A01G213800	chr1B	94.444	162	8	1	2821	2982	673969369	673969209	7.510000e-62	248.0
19	TraesCS6A01G213800	chr1B	90.123	162	16	0	2821	2982	533863223	533863062	9.850000e-51	211.0
20	TraesCS6A01G213800	chr4B	91.358	162	14	0	2821	2982	178081104	178081265	4.550000e-54	222.0
21	TraesCS6A01G213800	chr4D	89.697	165	15	2	2818	2981	34661690	34661527	3.540000e-50	209.0

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	TraesCS6A01G213800	chr6A	389243761	389247263	3502	False	6469.0	6469	100.000000	1	3503	1	chr6A.!!$F1	3502
1	TraesCS6A01G213800	chr6B	433707308	433710893	3585	False	2884.5	4950	96.707500	21	3503	2	chr6B.!!$F1	3482
2	TraesCS6A01G213800	chr6D	272645989	272650122	4133	False	1936.0	4630	94.606333	1	3503	3	chr6D.!!$F2	3502

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
818	933	0.673022	CTCTGTGTTGAGCTGGCTCC	60.673	60.0	18.3	6.1	42.09	4.70	F
1647	1762	0.250252	TGCTCAGTCCGCACATTCAA	60.250	50.0	0.0	0.0	31.40	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2328	2443	0.833834	AGTCAGTCTCACCCACCCTG	60.834	60.0	0.0	0.0	0.0	4.45	R
3100	3862	0.602638	CCTGGCACAAACGCACTCTA	60.603	55.0	0.0	0.0	38.7	2.43	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
34	35	4.247380	GCCAGGATCCAGGAGCCG	62.247	72.222	26.62	12.72	43.66	5.52
164	165	4.035112	CCCCCTCTGTACCACAATACTTA	58.965	47.826	0.00	0.00	0.00	2.24
377	378	5.250774	AGCTGTCCCAGTTAAGGATTTAGAA	59.749	40.000	0.00	0.00	35.38	2.10
510	625	8.943085	ACAGGATCCAGAGATAATGAGTATTTT	58.057	33.333	15.82	0.00	30.90	1.82
511	626	9.434420	CAGGATCCAGAGATAATGAGTATTTTC	57.566	37.037	15.82	0.00	30.90	2.29
512	627	9.391227	AGGATCCAGAGATAATGAGTATTTTCT	57.609	33.333	15.82	0.00	37.32	2.52
775	890	4.897051	ACTAGGGAATGTAGGAACCAGAT	58.103	43.478	0.00	0.00	0.00	2.90
818	933	0.673022	CTCTGTGTTGAGCTGGCTCC	60.673	60.000	18.30	6.10	42.09	4.70
851	966	2.241176	GGGTGGATGTTGGTAGATTCCA	59.759	50.000	0.00	0.00	35.49	3.53
873	988	1.134729	GCTTTGGCAATACATGGGTGG	60.135	52.381	0.00	0.00	38.54	4.61
1178	1293	3.117888	AGGAGTTCTCTTTTGAAGGCACA	60.118	43.478	0.00	0.00	0.00	4.57
1400	1515	2.092753	GGAAGATGAGGCAGATTGACCA	60.093	50.000	0.00	0.00	0.00	4.02
1614	1729	3.470645	AAGAAGGTTGAAGTAGCACGT	57.529	42.857	0.00	0.00	0.00	4.49
1647	1762	0.250252	TGCTCAGTCCGCACATTCAA	60.250	50.000	0.00	0.00	31.40	2.69
1874	1989	3.823873	TGCCATCCAAACGTCATTACTTT	59.176	39.130	0.00	0.00	0.00	2.66
1896	2011	7.343057	ACTTTCACTATGATCATGACCTCACTA	59.657	37.037	18.72	0.00	0.00	2.74
1936	2051	5.429130	TCGAAGAAGCTCTGAGTGTATCTA	58.571	41.667	6.53	0.00	0.00	1.98
2037	2152	0.397941	TGTCTGAAGCTTCCCAGGTG	59.602	55.000	23.42	7.08	0.00	4.00
2328	2443	3.376546	GTCTTCTGATCCATGGTCTTTGC	59.623	47.826	12.58	0.00	0.00	3.68
2358	2473	2.697229	TGAGACTGACTGGGCATATCAG	59.303	50.000	8.94	8.94	44.49	2.90
2496	2611	9.705290	AATTACATGACTTGTTTTGGTATTTCC	57.295	29.630	0.00	0.00	39.87	3.13
2696	2827	2.741517	TGCATTGGTATGTCGTCACTTG	59.258	45.455	0.00	0.00	34.12	3.16
2755	3473	5.201243	TCTCCGAGTAAAAGATCAGGATCA	58.799	41.667	11.55	0.00	40.22	2.92
2827	3546	1.783979	TCATCTACTCCCTCTCCCTCC	59.216	57.143	0.00	0.00	0.00	4.30
2831	3550	0.708802	TACTCCCTCTCCCTCCGTTT	59.291	55.000	0.00	0.00	0.00	3.60
2984	3746	6.809976	ATTTAGAAACGGAGGGAGTATCTT	57.190	37.500	0.00	0.00	33.73	2.40
3028	3790	4.745125	CGACCAATTAGTCTATGCGATGTT	59.255	41.667	2.54	0.00	34.46	2.71
3100	3862	9.391006	TCCTTTTAGATATTATCAACGCAACTT	57.609	29.630	6.46	0.00	0.00	2.66
3239	4001	7.739825	ACTGGATATGCACAAAGTATATGACT	58.260	34.615	0.00	0.00	41.56	3.41
3263	4025	5.833667	TGAGTAGAGTGGTCTTTTCTGAAGA	59.166	40.000	0.00	0.00	33.84	2.87
3355	4118	5.546526	AGTACCGGGTTCGTTTTAATACAA	58.453	37.500	4.31	0.00	33.95	2.41
3364	4127	9.949174	GGGTTCGTTTTAATACAAAAGAAACTA	57.051	29.630	8.93	0.00	40.01	2.24
3447	4210	7.013220	TCTTGCTATGTATAGAGGGATTGACT	58.987	38.462	3.15	0.00	32.05	3.41
3454	4217	6.556639	TGTATAGAGGGATTGACTGCTCTAT	58.443	40.000	0.00	0.00	37.70	1.98
3462	4225	7.577303	AGGGATTGACTGCTCTATTTCAAATA	58.423	34.615	0.00	0.00	31.96	1.40
3465	4228	9.060347	GGATTGACTGCTCTATTTCAAATATGA	57.940	33.333	0.00	0.00	31.96	2.15
3489	4252	7.284261	TGAGTATGGACAAAAGTGATTGTTTCA	59.716	33.333	0.00	0.00	43.31	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	4.247380	CGGCTCCTGGATCCTGGC	62.247	72.222	28.49	19.00	35.38	4.85
143	144	5.888982	ATAAGTATTGTGGTACAGAGGGG	57.111	43.478	0.00	0.00	41.80	4.79
164	165	7.553504	AACTAATAAAAGTTTCCCCAGCAAT	57.446	32.000	0.00	0.00	36.26	3.56
210	211	7.472100	GCACATGAATTGTACTCCCTCTATACT	60.472	40.741	0.00	0.00	36.57	2.12
214	215	4.716784	AGCACATGAATTGTACTCCCTCTA	59.283	41.667	0.00	0.00	36.57	2.43
377	378	3.265995	CACATGTAGTTAAGGGAAGGGGT	59.734	47.826	0.00	0.00	0.00	4.95
510	625	5.585820	AACTAAACGCCCTTTTGAAAAGA	57.414	34.783	18.59	0.00	0.00	2.52
511	626	6.533723	AGAAAACTAAACGCCCTTTTGAAAAG	59.466	34.615	10.60	10.60	0.00	2.27
512	627	6.399743	AGAAAACTAAACGCCCTTTTGAAAA	58.600	32.000	0.00	0.00	0.00	2.29
516	631	4.738252	GTGAGAAAACTAAACGCCCTTTTG	59.262	41.667	0.00	0.00	0.00	2.44
517	632	4.643334	AGTGAGAAAACTAAACGCCCTTTT	59.357	37.500	0.00	0.00	0.00	2.27
521	636	2.350484	GCAGTGAGAAAACTAAACGCCC	60.350	50.000	0.00	0.00	0.00	6.13
775	890	4.471025	TCTCTTCTGATTGGTGCTAATGGA	59.529	41.667	0.00	0.00	0.00	3.41
851	966	1.273211	ACCCATGTATTGCCAAAGCCT	60.273	47.619	0.00	0.00	38.69	4.58
873	988	6.593268	ACTTCCTTGAGTTCCTTCTAGTAC	57.407	41.667	0.00	0.00	0.00	2.73
1178	1293	4.563993	CCAAATCCTGCACATTTCCATTGT	60.564	41.667	0.00	0.00	0.00	2.71
1400	1515	4.964897	TGTCAGACAATAGATCCCACATCT	59.035	41.667	0.00	0.00	0.00	2.90
1614	1729	2.891580	ACTGAGCACGAGAAAGACCTTA	59.108	45.455	0.00	0.00	0.00	2.69
1647	1762	4.334552	TGTTGAATGTGTATGCATCAGGT	58.665	39.130	0.19	0.00	0.00	4.00
1874	1989	7.006509	TGATAGTGAGGTCATGATCATAGTGA	58.993	38.462	8.15	0.00	30.10	3.41
1896	2011	6.698008	TCTTCGAACATATGGCATTTTGAT	57.302	33.333	4.78	0.00	0.00	2.57
1936	2051	4.472833	ACAGCCAGAGGACTTCATTCTATT	59.527	41.667	0.00	0.00	0.00	1.73
2037	2152	3.507233	TCATTGGCATCTCCACTTGAAAC	59.493	43.478	0.00	0.00	46.55	2.78
2328	2443	0.833834	AGTCAGTCTCACCCACCCTG	60.834	60.000	0.00	0.00	0.00	4.45
2358	2473	2.887152	ACCAACCATCTCTTCAAACAGC	59.113	45.455	0.00	0.00	0.00	4.40
2696	2827	5.897377	AACCTGTGGTTTTATATGCTGAC	57.103	39.130	0.00	0.00	44.33	3.51
2853	3572	7.788026	TCCGTATGTAGTCACTTATTGGAATT	58.212	34.615	0.00	0.00	0.00	2.17
2959	3678	7.287512	AGATACTCCCTCCGTTTCTAAATAC	57.712	40.000	0.00	0.00	0.00	1.89
2984	3746	4.512198	TCGAAATTGAGTTACCTTTTCGCA	59.488	37.500	10.30	0.00	44.87	5.10
3028	3790	7.276658	TCATTTCTGAAGTTACCTTGTACACA	58.723	34.615	0.00	0.00	0.00	3.72
3100	3862	0.602638	CCTGGCACAAACGCACTCTA	60.603	55.000	0.00	0.00	38.70	2.43
3239	4001	5.833667	TCTTCAGAAAAGACCACTCTACTCA	59.166	40.000	0.00	0.00	0.00	3.41
3263	4025	8.529424	TTGAAATCCAATCTGAGCATAATCTT	57.471	30.769	0.00	0.00	0.00	2.40
3364	4127	5.075493	TCCTCTAGTAGGTTTGAAACTCGT	58.925	41.667	8.09	0.00	46.62	4.18
3365	4128	5.640189	TCCTCTAGTAGGTTTGAAACTCG	57.360	43.478	8.09	0.00	46.62	4.18
3434	4197	5.899547	TGAAATAGAGCAGTCAATCCCTCTA	59.100	40.000	0.00	0.00	40.16	2.43
3435	4198	4.718774	TGAAATAGAGCAGTCAATCCCTCT	59.281	41.667	0.00	0.00	38.20	3.69
3447	4210	9.494271	GTCCATACTCATATTTGAAATAGAGCA	57.506	33.333	16.91	9.94	0.00	4.26
3462	4225	7.765695	AACAATCACTTTTGTCCATACTCAT	57.234	32.000	0.00	0.00	38.85	2.90
3465	4228	7.581213	TGAAACAATCACTTTTGTCCATACT	57.419	32.000	0.00	0.00	38.85	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.