AutoCloner

Multiple sequence alignment - TraesCS1B01G062100

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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	TraesCS1B01G062100	chr1B	100.000	3545	0	0	1	3545	47172030	47175574	0.000000e+00	6547.0
1	TraesCS1B01G062100	chr1B	91.892	185	9	5	360	543	47166989	47167168	1.630000e-63	254.0
2	TraesCS1B01G062100	chr1A	88.780	3173	199	64	360	3432	29786796	29789911	0.000000e+00	3742.0
3	TraesCS1B01G062100	chr1A	92.073	164	8	1	199	362	29786537	29786695	3.560000e-55	226.0
4	TraesCS1B01G062100	chr1A	91.150	113	9	1	3432	3544	29789956	29790067	6.130000e-33	152.0
5	TraesCS1B01G062100	chr1A	78.924	223	23	13	1	205	29786293	29786509	2.870000e-26	130.0
6	TraesCS1B01G062100	chr1D	90.720	2360	139	32	360	2677	28564198	28566519	0.000000e+00	3072.0
7	TraesCS1B01G062100	chr1D	86.364	704	38	13	2733	3432	28566609	28567258	0.000000e+00	715.0
8	TraesCS1B01G062100	chr1D	90.566	159	9	2	204	362	28563947	28564099	4.640000e-49	206.0
9	TraesCS1B01G062100	chr1D	85.052	194	3	4	1	168	28563649	28563842	1.310000e-39	174.0
10	TraesCS1B01G062100	chr1D	93.333	45	2	1	1092	1135	54927198	54927154	8.210000e-07	65.8
11	TraesCS1B01G062100	chr5D	75.956	549	108	18	1733	2275	469245439	469245969	9.760000e-66	261.0
12	TraesCS1B01G062100	chr5D	95.556	45	1	1	1092	1135	495290612	495290656	1.770000e-08	71.3
13	TraesCS1B01G062100	chr5B	75.862	551	105	21	1733	2275	576055149	576055679	4.540000e-64	255.0
14	TraesCS1B01G062100	chr5B	74.790	476	89	18	1849	2313	576260681	576261136	6.040000e-43	185.0
15	TraesCS1B01G062100	chr5B	75.972	283	63	3	1733	2014	576257393	576257671	1.330000e-29	141.0
16	TraesCS1B01G062100	chr5B	95.556	45	1	1	1092	1135	611868621	611868665	1.770000e-08	71.3
17	TraesCS1B01G062100	chr5A	75.862	551	105	21	1733	2275	589329025	589329555	4.540000e-64	255.0
18	TraesCS1B01G062100	chr5A	87.671	146	16	2	2098	2242	590453210	590453354	6.090000e-38	169.0
19	TraesCS1B01G062100	chr5A	87.671	146	16	2	2098	2242	590527395	590527539	6.090000e-38	169.0
20	TraesCS1B01G062100	chr5A	88.806	134	14	1	3298	3430	4705016	4704883	2.830000e-36	163.0
21	TraesCS1B01G062100	chr5A	81.633	196	34	2	2098	2292	589585149	589585343	1.020000e-35	161.0
22	TraesCS1B01G062100	chr5A	95.556	45	1	1	1092	1135	619359906	619359950	1.770000e-08	71.3
23	TraesCS1B01G062100	chr6D	89.542	153	14	2	3281	3432	470858580	470858429	3.610000e-45	193.0
24	TraesCS1B01G062100	chr2D	80.952	126	19	5	1013	1135	337923093	337923216	1.050000e-15	95.3
25	TraesCS1B01G062100	chr2B	85.106	94	12	2	3451	3544	47757529	47757620	1.050000e-15	95.3
26	TraesCS1B01G062100	chr2B	80.952	126	19	5	1013	1135	405262351	405262474	1.050000e-15	95.3
27	TraesCS1B01G062100	chr2A	81.102	127	17	7	1013	1135	448153121	448153244	1.050000e-15	95.3

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	TraesCS1B01G062100	chr1B	47172030	47175574	3544	False	6547.00	6547	100.00000	1	3545	1	chr1B.!!$F2	3544
1	TraesCS1B01G062100	chr1A	29786293	29790067	3774	False	1062.50	3742	87.73175	1	3544	4	chr1A.!!$F1	3543
2	TraesCS1B01G062100	chr1D	28563649	28567258	3609	False	1041.75	3072	88.17550	1	3432	4	chr1D.!!$F1	3431
3	TraesCS1B01G062100	chr5D	469245439	469245969	530	False	261.00	261	75.95600	1733	2275	1	chr5D.!!$F1	542
4	TraesCS1B01G062100	chr5B	576055149	576055679	530	False	255.00	255	75.86200	1733	2275	1	chr5B.!!$F1	542
5	TraesCS1B01G062100	chr5A	589329025	589329555	530	False	255.00	255	75.86200	1733	2275	1	chr5A.!!$F1	542

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	Hairpin	End Stability	Orientation
211	314	0.108615	AGAACCATCGCCTTGAGACG	60.109	55.0	0.00	4.18	F
793	1019	0.530431	GCTGTGCAAACCCCAACAAG	60.530	55.0	0.00	3.16	F
1590	1870	0.246635	CTACAGTGGGTGAGGGAACG	59.753	60.0	0.00	3.95	F
2412	2692	0.622665	ACCAGAGCATTCAGGAAGGG	59.377	55.0	34.29	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
1086	1348	1.070786	GACGTTGAAGCCCCTGTCA	59.929	57.895	3.58	R
2469	2749	0.034059	CCTGAACGCTCACTTCCTGT	59.966	55.000	4.00	R
2470	2750	0.318441	TCCTGAACGCTCACTTCCTG	59.682	55.000	3.86	R
3472	3876	0.612453	GCCCCGACCTCCCTATAGAG	60.612	65.000	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	2.642171	TCCATTAGGGTGGTCTCACT	57.358	50.000	0.00	0.00	43.17	3.41
89	116	7.282224	GTGAATCCAACATAAGTATACCAGCAA	59.718	37.037	0.00	0.00	0.00	3.91
120	147	1.580942	GTCAAAGCTCGCATTGGCA	59.419	52.632	6.59	0.00	41.24	4.92
162	189	5.979288	TTTCAGAACAGAGGGAGTAGTAC	57.021	43.478	0.00	0.00	0.00	2.73
168	195	5.839606	AGAACAGAGGGAGTAGTACTGTTTT	59.160	40.000	7.76	0.00	46.81	2.43
169	196	5.725325	ACAGAGGGAGTAGTACTGTTTTC	57.275	43.478	7.76	0.53	38.41	2.29
170	197	5.145564	ACAGAGGGAGTAGTACTGTTTTCA	58.854	41.667	7.76	0.00	38.41	2.69
171	198	5.601313	ACAGAGGGAGTAGTACTGTTTTCAA	59.399	40.000	7.76	0.00	38.41	2.69
172	199	6.159988	CAGAGGGAGTAGTACTGTTTTCAAG	58.840	44.000	7.76	0.00	0.00	3.02
173	200	4.895961	AGGGAGTAGTACTGTTTTCAAGC	58.104	43.478	7.76	0.00	0.00	4.01
178	205	6.292919	GGAGTAGTACTGTTTTCAAGCAAGTG	60.293	42.308	7.76	0.00	0.00	3.16
198	225	0.473694	TGGAGGGAGCAGAAGAACCA	60.474	55.000	0.00	0.00	0.00	3.67
211	314	0.108615	AGAACCATCGCCTTGAGACG	60.109	55.000	0.00	0.00	0.00	4.18
218	321	3.185188	CCATCGCCTTGAGACGATAAATG	59.815	47.826	1.95	0.00	46.63	2.32
233	336	8.132995	AGACGATAAATGATGATACACGTAACA	58.867	33.333	0.00	0.00	0.00	2.41
234	337	8.812147	ACGATAAATGATGATACACGTAACAT	57.188	30.769	0.10	0.10	32.31	2.71
235	338	9.902196	ACGATAAATGATGATACACGTAACATA	57.098	29.630	0.51	0.00	30.21	2.29
318	421	1.084370	GGTCGAATGTTCCGAGCTGG	61.084	60.000	0.00	0.00	46.92	4.85
319	422	3.426126	GGTCGAATGTTCCGAGCTGGA	62.426	57.143	0.00	0.00	46.92	3.86
338	441	5.386924	CTGGATAGGCTAGGTAGTGTTACT	58.613	45.833	0.00	0.00	0.00	2.24
462	668	7.065120	TGTCAAAAATGACAAAAGATGGGAT	57.935	32.000	9.07	0.00	44.73	3.85
518	734	1.607225	TGGGAGCCAGGTTCCATTAT	58.393	50.000	23.14	0.00	34.53	1.28
537	753	3.627395	ATGTCATCTTGGGCGAAGTTA	57.373	42.857	9.15	0.00	32.90	2.24
664	890	6.375455	CCAAGTGTGTTTATCTCCTATGCTTT	59.625	38.462	0.00	0.00	0.00	3.51
745	971	8.297470	ACAATGCCTGATCATAAAATACAAGT	57.703	30.769	0.00	0.00	0.00	3.16

Showing 1 to 25 of 104 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	7.815840	TCACATTTTTCTCACCTTGATACAA	57.184	32.000	0.00	0.00	0.00	2.41
59	60	9.693739	TGGTATACTTATGTTGGATTCACATTT	57.306	29.630	2.25	0.00	0.00	2.32
89	116	3.826729	GAGCTTTGACCAACAATTACCCT	59.173	43.478	0.00	0.00	38.36	4.34
120	147	3.560636	ATACCTTGCAGATTACGCCTT	57.439	42.857	0.00	0.00	0.00	4.35
162	189	3.489738	CCTCCACACTTGCTTGAAAACAG	60.490	47.826	0.00	0.00	0.00	3.16
168	195	0.397941	CTCCCTCCACACTTGCTTGA	59.602	55.000	0.00	0.00	0.00	3.02
169	196	1.239968	GCTCCCTCCACACTTGCTTG	61.240	60.000	0.00	0.00	0.00	4.01
170	197	1.073897	GCTCCCTCCACACTTGCTT	59.926	57.895	0.00	0.00	0.00	3.91
171	198	2.121992	CTGCTCCCTCCACACTTGCT	62.122	60.000	0.00	0.00	0.00	3.91
172	199	1.673665	CTGCTCCCTCCACACTTGC	60.674	63.158	0.00	0.00	0.00	4.01
173	200	0.397941	TTCTGCTCCCTCCACACTTG	59.602	55.000	0.00	0.00	0.00	3.16
178	205	0.035915	GGTTCTTCTGCTCCCTCCAC	60.036	60.000	0.00	0.00	0.00	4.02
218	321	9.244799	TCAAGATGTTATGTTACGTGTATCATC	57.755	33.333	0.00	6.67	30.62	2.92
233	336	6.822667	TCATGTGTTTGCTCAAGATGTTAT	57.177	33.333	0.00	0.00	0.00	1.89
234	337	6.822667	ATCATGTGTTTGCTCAAGATGTTA	57.177	33.333	0.00	0.00	29.17	2.41
235	338	5.717078	ATCATGTGTTTGCTCAAGATGTT	57.283	34.783	0.00	0.00	29.17	2.71
236	339	5.242171	TGAATCATGTGTTTGCTCAAGATGT	59.758	36.000	0.00	0.00	30.28	3.06
237	340	5.705902	TGAATCATGTGTTTGCTCAAGATG	58.294	37.500	0.00	0.00	30.28	2.90
318	421	6.016108	CCTTGAGTAACACTACCTAGCCTATC	60.016	46.154	0.00	0.00	0.00	2.08
319	422	5.834204	CCTTGAGTAACACTACCTAGCCTAT	59.166	44.000	0.00	0.00	0.00	2.57
419	625	4.018506	TGACAGGGATTGCCTCATTTAAGA	60.019	41.667	0.00	0.00	0.00	2.10
518	734	3.410631	TTAACTTCGCCCAAGATGACA	57.589	42.857	0.00	0.00	35.82	3.58
537	753	4.935352	TGCCAAGTAAGAAGCAACAATT	57.065	36.364	0.00	0.00	30.97	2.32
577	793	5.522824	AGTTCTTTTACCAAGTCTTCACGAC	59.477	40.000	0.00	0.00	43.17	4.34
745	971	7.618019	AGAATAGTTATGGTCTGGCATTCTA	57.382	36.000	0.00	0.00	31.52	2.10

Showing 1 to 25 of 118 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.