AutoCloner

Multiple sequence alignment - TraesCS6A01G295900

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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	TraesCS6A01G295900	chr6A	100.000	3459	0	0	1	3459	529558486	529561944	0.000000e+00	6388.0
1	TraesCS6A01G295900	chr6A	93.923	3439	146	18	1	3402	529484382	529487794	0.000000e+00	5134.0
2	TraesCS6A01G295900	chr6A	86.237	3117	263	74	1	3017	529286281	529289331	0.000000e+00	3227.0
3	TraesCS6A01G295900	chr6A	91.248	1234	92	5	2173	3404	529374996	529376215	0.000000e+00	1666.0
4	TraesCS6A01G295900	chr6A	74.335	1691	269	93	698	2288	536024983	536023358	1.800000e-157	566.0
5	TraesCS6A01G295900	chr6A	94.949	99	4	1	1	99	529374903	529375000	1.660000e-33	154.0
6	TraesCS6A01G295900	chr6A	96.154	52	2	0	3408	3459	64910090	64910141	6.150000e-13	86.1
7	TraesCS6A01G295900	chr6D	93.663	3440	155	22	1	3404	385221792	385225204	0.000000e+00	5086.0
8	TraesCS6A01G295900	chr6D	84.427	3108	311	68	1	3017	385164376	385167401	0.000000e+00	2898.0
9	TraesCS6A01G295900	chr6D	84.220	2896	294	81	474	3260	385164835	385167676	0.000000e+00	2665.0
10	TraesCS6A01G295900	chr6D	92.079	202	13	3	1	200	385164006	385164206	7.310000e-72	281.0
11	TraesCS6A01G295900	chr6D	78.947	437	53	21	1857	2288	389652161	389651759	9.520000e-66	261.0
12	TraesCS6A01G295900	chr6D	91.781	73	6	0	3332	3404	385167677	385167749	6.110000e-18	102.0
13	TraesCS6A01G295900	chr6B	92.368	2660	127	22	547	3166	575320828	575323451	0.000000e+00	3718.0
14	TraesCS6A01G295900	chr6B	85.462	3109	302	68	1	3017	575313754	575316804	0.000000e+00	3099.0
15	TraesCS6A01G295900	chr6B	75.467	750	89	46	1577	2288	583335472	583334780	9.450000e-71	278.0
16	TraesCS6A01G295900	chr6B	88.584	219	21	4	3187	3404	575324010	575324225	2.650000e-66	263.0
17	TraesCS6A01G295900	chr6B	96.226	53	2	0	3407	3459	196149728	196149676	1.710000e-13	87.9
18	TraesCS6A01G295900	chr6B	96.154	52	2	0	3408	3459	176545573	176545624	6.150000e-13	86.1
19	TraesCS6A01G295900	chr7D	96.154	52	2	0	3408	3459	358233855	358233906	6.150000e-13	86.1
20	TraesCS6A01G295900	chr4D	96.154	52	2	0	3408	3459	475398204	475398255	6.150000e-13	86.1
21	TraesCS6A01G295900	chr4D	96.154	52	2	0	3408	3459	475434633	475434684	6.150000e-13	86.1
22	TraesCS6A01G295900	chr4D	95.918	49	2	0	3411	3459	143022914	143022962	2.860000e-11	80.5
23	TraesCS6A01G295900	chr4A	97.959	49	1	0	3411	3459	167981780	167981732	6.150000e-13	86.1
24	TraesCS6A01G295900	chr5B	92.453	53	4	0	3407	3459	263229702	263229650	3.700000e-10	76.8

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	TraesCS6A01G295900	chr6A	529558486	529561944	3458	False	6388.0	6388	100.00000	1	3459	1	chr6A.!!$F4	3458
1	TraesCS6A01G295900	chr6A	529484382	529487794	3412	False	5134.0	5134	93.92300	1	3402	1	chr6A.!!$F3	3401
2	TraesCS6A01G295900	chr6A	529286281	529289331	3050	False	3227.0	3227	86.23700	1	3017	1	chr6A.!!$F2	3016
3	TraesCS6A01G295900	chr6A	529374903	529376215	1312	False	910.0	1666	93.09850	1	3404	2	chr6A.!!$F5	3403
4	TraesCS6A01G295900	chr6A	536023358	536024983	1625	True	566.0	566	74.33500	698	2288	1	chr6A.!!$R1	1590
5	TraesCS6A01G295900	chr6D	385221792	385225204	3412	False	5086.0	5086	93.66300	1	3404	1	chr6D.!!$F1	3403
6	TraesCS6A01G295900	chr6D	385164006	385167749	3743	False	1486.5	2898	88.12675	1	3404	4	chr6D.!!$F2	3403
7	TraesCS6A01G295900	chr6B	575313754	575316804	3050	False	3099.0	3099	85.46200	1	3017	1	chr6B.!!$F2	3016
8	TraesCS6A01G295900	chr6B	575320828	575324225	3397	False	1990.5	3718	90.47600	547	3404	2	chr6B.!!$F3	2857
9	TraesCS6A01G295900	chr6B	583334780	583335472	692	True	278.0	278	75.46700	1577	2288	1	chr6B.!!$R2	711

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
676	1076	1.070786	TGGAACAACAGAGACCGGC	59.929	57.895	0.0	0.0	31.92	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2674	3334	1.074775	GCATGAGGGTGGGTTGTCA	59.925	57.895	0.0	0.0	0.0	3.58	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
112	114	4.324267	CCCTATATTAAAAGTGCTCCCGG	58.676	47.826	0.00	0.00	0.00	5.73
164	537	3.429822	CCGCTACGGTTTCCTTGATCTAA	60.430	47.826	0.00	0.00	42.73	2.10
246	620	1.341209	TGATCTAGGCCAGTGCATACG	59.659	52.381	5.01	0.00	40.13	3.06
271	645	3.851897	TTCCGCGGCCCACAAATCA	62.852	57.895	23.51	0.00	0.00	2.57
279	653	2.223923	CGGCCCACAAATCAGTCAAAAA	60.224	45.455	0.00	0.00	0.00	1.94
312	686	2.832838	TCCTTGATCTAGGCCAGTCAA	58.167	47.619	17.41	8.64	35.15	3.18
451	849	1.879380	CGAAACTTTCATGCCACCAGA	59.121	47.619	2.49	0.00	0.00	3.86
452	850	2.489329	CGAAACTTTCATGCCACCAGAT	59.511	45.455	2.49	0.00	0.00	2.90
676	1076	1.070786	TGGAACAACAGAGACCGGC	59.929	57.895	0.00	0.00	31.92	6.13
749	1156	6.467723	AACTGCCTTAATCGCTATAATTCG	57.532	37.500	0.00	0.00	0.00	3.34
801	1209	1.272536	GGTGTCTAGAGTGGGGAGTGA	60.273	57.143	0.00	0.00	0.00	3.41
1808	2365	2.955660	TGTTCGATGCAAACCTTTTCCT	59.044	40.909	0.00	0.00	0.00	3.36
2093	2696	9.243637	GCAATAAATAAAGAACATTAATCGCCA	57.756	29.630	0.00	0.00	0.00	5.69
2433	3065	2.979676	CAAGTCCGGCAGCAGCAA	60.980	61.111	2.65	0.00	44.61	3.91
2463	3095	4.041762	CGGGCCAGGCTAACCCAA	62.042	66.667	20.61	0.00	44.49	4.12
2515	3157	8.382405	TGCCATACATATATGTGGTACAATCTT	58.618	33.333	25.48	0.00	44.16	2.40
2583	3243	4.710324	GAATAATGGTCGGTTACATCCCA	58.290	43.478	0.00	0.00	0.00	4.37
2592	3252	4.638421	GTCGGTTACATCCCATTTCATGAA	59.362	41.667	3.38	3.38	0.00	2.57
2650	3310	5.123502	GCGAGATATTTACCTCCATAGTCGA	59.876	44.000	0.00	0.00	0.00	4.20
2655	3315	4.713824	TTTACCTCCATAGTCGACAGTG	57.286	45.455	19.50	15.05	0.00	3.66
2775	3435	1.987855	CTTGGCCTCGACCACCCTA	60.988	63.158	3.32	0.00	40.19	3.53
2906	3577	0.761802	GGATTCCGAGGAGCCAGATT	59.238	55.000	7.85	0.00	0.00	2.40
2914	3585	0.032615	AGGAGCCAGATTCGGACTCT	60.033	55.000	0.77	0.00	32.81	3.24
2937	3608	5.762825	TTTTATCGTATCTACTCACGCCT	57.237	39.130	0.00	0.00	38.05	5.52
2938	3609	5.354054	TTTATCGTATCTACTCACGCCTC	57.646	43.478	0.00	0.00	38.05	4.70
2939	3610	2.320745	TCGTATCTACTCACGCCTCA	57.679	50.000	0.00	0.00	38.05	3.86
2940	3611	2.635714	TCGTATCTACTCACGCCTCAA	58.364	47.619	0.00	0.00	38.05	3.02
2941	3612	2.612672	TCGTATCTACTCACGCCTCAAG	59.387	50.000	0.00	0.00	38.05	3.02
2942	3613	2.355132	CGTATCTACTCACGCCTCAAGT	59.645	50.000	0.00	0.00	0.00	3.16
2943	3614	3.558829	CGTATCTACTCACGCCTCAAGTA	59.441	47.826	0.00	0.00	0.00	2.24
2944	3615	4.318903	CGTATCTACTCACGCCTCAAGTAG	60.319	50.000	3.01	3.01	42.43	2.57
2996	3667	2.447887	GCACACGCTCCATCGACAG	61.448	63.158	0.00	0.00	34.30	3.51
3117	3820	3.114606	TCCCTTGAGCATTCCATCACTA	58.885	45.455	0.00	0.00	0.00	2.74
3124	3827	4.020307	TGAGCATTCCATCACTAGACAACA	60.020	41.667	0.00	0.00	0.00	3.33
3145	3848	0.321919	GTGCACTTCTCATGGCTCCA	60.322	55.000	10.32	0.00	0.00	3.86
3150	3856	2.842394	CTTCTCATGGCTCCACGCGT	62.842	60.000	5.58	5.58	40.44	6.01
3191	4444	7.095355	GGACACTATAACTTTGCTTTCTTCGAA	60.095	37.037	0.00	0.00	0.00	3.71
3241	4495	5.741388	AACCATATCTTTCAGATTCGTGC	57.259	39.130	0.00	0.00	36.20	5.34
3268	4522	0.908198	GAGGTCATCTCTGGCAAGGT	59.092	55.000	0.00	0.00	39.38	3.50
3271	4525	0.326264	GTCATCTCTGGCAAGGTGGT	59.674	55.000	9.15	0.00	0.00	4.16
3279	4533	1.302949	GGCAAGGTGGTGATGGCTA	59.697	57.895	0.00	0.00	36.76	3.93
3383	4637	4.627467	CCTTGATACTTGAGAGAACCAACG	59.373	45.833	0.00	0.00	0.00	4.10
3404	4658	0.250381	TCGCGGAAACCAAAAGGCTA	60.250	50.000	6.13	0.00	0.00	3.93
3405	4659	0.808755	CGCGGAAACCAAAAGGCTAT	59.191	50.000	0.00	0.00	0.00	2.97
3406	4660	2.011222	CGCGGAAACCAAAAGGCTATA	58.989	47.619	0.00	0.00	0.00	1.31
3407	4661	2.031683	CGCGGAAACCAAAAGGCTATAG	59.968	50.000	0.00	0.00	0.00	1.31
3408	4662	3.014623	GCGGAAACCAAAAGGCTATAGT	58.985	45.455	0.84	0.00	0.00	2.12
3409	4663	3.064958	GCGGAAACCAAAAGGCTATAGTC	59.935	47.826	0.00	0.00	0.00	2.59
3410	4664	3.626217	CGGAAACCAAAAGGCTATAGTCC	59.374	47.826	0.00	2.95	0.00	3.85
3411	4665	4.625564	CGGAAACCAAAAGGCTATAGTCCT	60.626	45.833	0.00	5.35	34.90	3.85
3412	4666	5.262009	GGAAACCAAAAGGCTATAGTCCTT	58.738	41.667	17.66	17.66	45.31	3.36
3422	4676	7.392494	AAGGCTATAGTCCTTTTTAGTTTGC	57.608	36.000	17.66	0.00	40.87	3.68
3423	4677	6.481643	AGGCTATAGTCCTTTTTAGTTTGCA	58.518	36.000	0.00	0.00	0.00	4.08
3424	4678	7.119387	AGGCTATAGTCCTTTTTAGTTTGCAT	58.881	34.615	0.00	0.00	0.00	3.96
3425	4679	8.272173	AGGCTATAGTCCTTTTTAGTTTGCATA	58.728	33.333	0.00	0.00	0.00	3.14
3426	4680	9.067986	GGCTATAGTCCTTTTTAGTTTGCATAT	57.932	33.333	0.84	0.00	0.00	1.78
3452	4706	8.926092	AAGATTTTTCTAAAGTCAAGCCTAGT	57.074	30.769	0.00	0.00	0.00	2.57
3457	4711	9.623000	TTTTTCTAAAGTCAAGCCTAGTAAAGT	57.377	29.630	0.00	0.00	0.00	2.66
3458	4712	9.623000	TTTTCTAAAGTCAAGCCTAGTAAAGTT	57.377	29.630	0.00	0.00	0.00	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	114	5.205565	GGTTGTGTTCACTCGAATCTTTTC	58.794	41.667	4.59	0.00	32.61	2.29
164	537	1.605058	AACCGTCGCTATGACTGGCT	61.605	55.000	6.04	0.00	45.87	4.75
188	562	5.428253	GACTTTTGACAGATATGTGGGCTA	58.572	41.667	0.00	0.00	0.00	3.93
259	633	3.467374	TTTTTGACTGATTTGTGGGCC	57.533	42.857	0.00	0.00	0.00	5.80
271	645	4.306600	GAAACGGCAATGGATTTTTGACT	58.693	39.130	0.00	0.00	29.49	3.41
279	653	2.214376	TCAAGGAAACGGCAATGGAT	57.786	45.000	0.00	0.00	0.00	3.41
312	686	1.206578	CGAAAACCGTCAATGCGCT	59.793	52.632	9.73	0.00	0.00	5.92
328	702	1.725557	GACTATCGACAGGGCTGCGA	61.726	60.000	0.00	0.00	40.90	5.10
402	784	5.422145	CCACATTATCATGCGAGATATGGA	58.578	41.667	9.21	0.00	33.17	3.41
636	1036	0.687757	TCGGGCAATGGCTACTCTCT	60.688	55.000	6.78	0.00	40.87	3.10
637	1037	0.394565	ATCGGGCAATGGCTACTCTC	59.605	55.000	6.78	0.00	40.87	3.20
676	1076	2.809119	TGTATGTGTGCGGTAAAACCAG	59.191	45.455	0.00	0.00	38.47	4.00
749	1156	9.752274	GCTTTTGATCTCGTGATTTATCATATC	57.248	33.333	0.87	0.00	39.30	1.63
821	1245	3.877735	GCAGGGGCATAAAAAGAGGAAGA	60.878	47.826	0.00	0.00	40.72	2.87
822	1246	2.428530	GCAGGGGCATAAAAAGAGGAAG	59.571	50.000	0.00	0.00	40.72	3.46
823	1247	2.456577	GCAGGGGCATAAAAAGAGGAA	58.543	47.619	0.00	0.00	40.72	3.36
1808	2365	3.641437	GGCAACAAGTAACATGCTGAA	57.359	42.857	0.00	0.00	38.79	3.02
1931	2526	6.425735	ACATTTCATACATGATTCAGGGACA	58.574	36.000	0.00	0.00	36.56	4.02
2002	2603	9.379791	ACTAGAAAACTAAATCTTAATCCACCG	57.620	33.333	0.00	0.00	0.00	4.94
2040	2642	4.620803	GCTTCGGGGAGTATATATGGTGTG	60.621	50.000	0.00	0.00	0.00	3.82
2220	2837	4.512571	GCAGTGAAGAAACCATGCATTTTT	59.487	37.500	0.00	0.00	33.92	1.94
2515	3157	4.183101	GACGGACGGTTTAAATATGGTGA	58.817	43.478	0.00	0.00	0.00	4.02
2583	3243	4.460382	AGCGGTGAAACTGATTCATGAAAT	59.540	37.500	13.09	1.06	40.10	2.17
2650	3310	2.771089	TCGTTAGACCGAGTACACTGT	58.229	47.619	0.00	0.00	32.18	3.55
2674	3334	1.074775	GCATGAGGGTGGGTTGTCA	59.925	57.895	0.00	0.00	0.00	3.58
2773	3433	3.117738	ACAAGGAGGGAGGCAATGATTAG	60.118	47.826	0.00	0.00	0.00	1.73
2775	3435	1.642762	ACAAGGAGGGAGGCAATGATT	59.357	47.619	0.00	0.00	0.00	2.57
2906	3577	7.496920	TGAGTAGATACGATAAAAAGAGTCCGA	59.503	37.037	0.00	0.00	0.00	4.55
2914	3585	6.140303	AGGCGTGAGTAGATACGATAAAAA	57.860	37.500	0.00	0.00	42.54	1.94
2937	3608	4.065088	GTGCCATGAACTTGACTACTTGA	58.935	43.478	0.00	0.00	0.00	3.02
2938	3609	3.120546	CGTGCCATGAACTTGACTACTTG	60.121	47.826	0.00	0.00	0.00	3.16
2939	3610	3.067106	CGTGCCATGAACTTGACTACTT	58.933	45.455	0.00	0.00	0.00	2.24
2940	3611	2.688507	CGTGCCATGAACTTGACTACT	58.311	47.619	0.00	0.00	0.00	2.57
2941	3612	1.128692	GCGTGCCATGAACTTGACTAC	59.871	52.381	0.00	0.00	0.00	2.73
2942	3613	1.438651	GCGTGCCATGAACTTGACTA	58.561	50.000	0.00	0.00	0.00	2.59
2943	3614	1.237285	GGCGTGCCATGAACTTGACT	61.237	55.000	5.89	0.00	35.81	3.41
2944	3615	1.210155	GGCGTGCCATGAACTTGAC	59.790	57.895	5.89	0.00	35.81	3.18
2996	3667	3.307674	CGCAGCAGATGAAGAGAGATAC	58.692	50.000	0.00	0.00	0.00	2.24
3071	3774	2.391678	AGCCCCAAATAAGCCATCTTG	58.608	47.619	0.00	0.00	33.85	3.02
3117	3820	1.486310	TGAGAAGTGCACCTGTTGTCT	59.514	47.619	14.63	6.84	0.00	3.41
3124	3827	0.035630	GAGCCATGAGAAGTGCACCT	60.036	55.000	14.63	3.90	0.00	4.00
3150	3856	4.209620	TCCCCTTCCACCCACCCA	62.210	66.667	0.00	0.00	0.00	4.51
3191	4444	3.313526	GCTTACAATGAGACGCATGGATT	59.686	43.478	0.00	0.00	37.28	3.01
3279	4533	0.323725	AAGTGATGGAATGCGGCCTT	60.324	50.000	0.00	0.00	0.00	4.35
3383	4637	1.284715	CCTTTTGGTTTCCGCGACC	59.715	57.895	8.23	8.36	37.69	4.79
3427	4681	8.926092	ACTAGGCTTGACTTTAGAAAAATCTT	57.074	30.769	2.20	0.00	0.00	2.40
3431	4685	9.623000	ACTTTACTAGGCTTGACTTTAGAAAAA	57.377	29.630	2.20	0.00	0.00	1.94
3432	4686	9.623000	AACTTTACTAGGCTTGACTTTAGAAAA	57.377	29.630	2.20	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.