AutoCloner

Multiple sequence alignment - TraesCS2D01G436600

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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	TraesCS2D01G436600	chr2D	100.000	2548	0	0	1	2548	547243333	547240786	0.000000e+00	4706
1	TraesCS2D01G436600	chr2D	95.576	1989	51	11	591	2548	498471644	498469662	0.000000e+00	3151
2	TraesCS2D01G436600	chr2D	94.633	354	17	1	591	942	16065486	16065839	4.790000e-152	547
3	TraesCS2D01G436600	chr2D	87.784	352	34	5	239	586	555110043	555109697	1.100000e-108	403
4	TraesCS2D01G436600	chr2D	91.129	248	16	5	234	476	555110632	555110386	5.250000e-87	331
5	TraesCS2D01G436600	chr2D	85.887	248	33	2	339	586	547203488	547203243	1.940000e-66	263
6	TraesCS2D01G436600	chr1A	94.700	1981	77	13	591	2548	71245439	71243464	0.000000e+00	3051
7	TraesCS2D01G436600	chr3D	94.615	1987	74	17	590	2548	410899594	410901575	0.000000e+00	3046
8	TraesCS2D01G436600	chr6A	94.450	2000	74	13	581	2548	57901151	57903145	0.000000e+00	3044
9	TraesCS2D01G436600	chr6A	93.882	1994	82	12	591	2548	203520912	203518923	0.000000e+00	2970
10	TraesCS2D01G436600	chr3A	94.361	1986	79	12	591	2548	696312540	696310560	0.000000e+00	3016
11	TraesCS2D01G436600	chr2A	94.322	1990	76	12	591	2548	233255261	233257245	0.000000e+00	3014
12	TraesCS2D01G436600	chr2A	93.725	1992	86	13	591	2548	611725136	611723150	0.000000e+00	2950
13	TraesCS2D01G436600	chr2A	93.471	1991	92	10	591	2548	674415062	674413077	0.000000e+00	2922
14	TraesCS2D01G436600	chr2A	96.102	590	11	1	1	590	690733204	690732627	0.000000e+00	952
15	TraesCS2D01G436600	chr2A	88.081	344	35	4	239	577	690523762	690523420	1.100000e-108	403
16	TraesCS2D01G436600	chr2A	91.638	287	19	4	234	516	690524376	690524091	2.380000e-105	392
17	TraesCS2D01G436600	chr2A	86.072	359	37	9	238	585	690724035	690723679	8.610000e-100	374
18	TraesCS2D01G436600	chr2A	87.967	241	28	1	346	586	690732108	690731869	1.490000e-72	283
19	TraesCS2D01G436600	chr5A	91.922	359	24	4	589	944	689409580	689409224	4.900000e-137	497
20	TraesCS2D01G436600	chr1B	91.549	355	27	2	591	942	645321437	645321791	1.060000e-133	486
21	TraesCS2D01G436600	chr2B	85.675	363	38	10	238	589	653670521	653670162	1.110000e-98	370
22	TraesCS2D01G436600	chr2B	86.290	248	32	2	339	586	653689702	653689457	4.180000e-68	268
23	TraesCS2D01G436600	chr2B	86.441	177	12	6	2	169	653690680	653690507	1.560000e-42	183
24	TraesCS2D01G436600	chr2B	87.931	116	10	2	236	347	653689937	653689822	1.590000e-27	134
25	TraesCS2D01G436600	chrUn	85.338	266	17	8	2298	2548	302375549	302375807	3.250000e-64	255

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	TraesCS2D01G436600	chr2D	547240786	547243333	2547	True	4706.0	4706	100.0000	1	2548	1	chr2D.!!$R3	2547
1	TraesCS2D01G436600	chr2D	498469662	498471644	1982	True	3151.0	3151	95.5760	591	2548	1	chr2D.!!$R1	1957
2	TraesCS2D01G436600	chr2D	555109697	555110632	935	True	367.0	403	89.4565	234	586	2	chr2D.!!$R4	352
3	TraesCS2D01G436600	chr1A	71243464	71245439	1975	True	3051.0	3051	94.7000	591	2548	1	chr1A.!!$R1	1957
4	TraesCS2D01G436600	chr3D	410899594	410901575	1981	False	3046.0	3046	94.6150	590	2548	1	chr3D.!!$F1	1958
5	TraesCS2D01G436600	chr6A	57901151	57903145	1994	False	3044.0	3044	94.4500	581	2548	1	chr6A.!!$F1	1967
6	TraesCS2D01G436600	chr6A	203518923	203520912	1989	True	2970.0	2970	93.8820	591	2548	1	chr6A.!!$R1	1957
7	TraesCS2D01G436600	chr3A	696310560	696312540	1980	True	3016.0	3016	94.3610	591	2548	1	chr3A.!!$R1	1957
8	TraesCS2D01G436600	chr2A	233255261	233257245	1984	False	3014.0	3014	94.3220	591	2548	1	chr2A.!!$F1	1957
9	TraesCS2D01G436600	chr2A	611723150	611725136	1986	True	2950.0	2950	93.7250	591	2548	1	chr2A.!!$R1	1957
10	TraesCS2D01G436600	chr2A	674413077	674415062	1985	True	2922.0	2922	93.4710	591	2548	1	chr2A.!!$R2	1957
11	TraesCS2D01G436600	chr2A	690731869	690733204	1335	True	617.5	952	92.0345	1	590	2	chr2A.!!$R5	589
12	TraesCS2D01G436600	chr2A	690523420	690524376	956	True	397.5	403	89.8595	234	577	2	chr2A.!!$R4	343

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
412	416	0.694771	TGCCTCTGCAATCAACTCCT	59.305	50.0	0.0	0.0	46.66	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2307	2703	0.590984	CGCGTGTGCAAACATTCACA	60.591	50.0	8.0	0.0	42.97	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
242	243	2.287308	TGTTCGTTGCATACAGGTTTGC	60.287	45.455	7.74	7.74	37.90	3.68
411	415	3.254629	TGCCTCTGCAATCAACTCC	57.745	52.632	0.00	0.00	46.66	3.85
412	416	0.694771	TGCCTCTGCAATCAACTCCT	59.305	50.000	0.00	0.00	46.66	3.69
413	417	1.093159	GCCTCTGCAATCAACTCCTG	58.907	55.000	0.00	0.00	37.47	3.86
414	418	1.093159	CCTCTGCAATCAACTCCTGC	58.907	55.000	0.00	0.00	36.60	4.85
415	419	1.612462	CCTCTGCAATCAACTCCTGCA	60.612	52.381	0.00	0.00	43.54	4.41
416	420	1.467734	CTCTGCAATCAACTCCTGCAC	59.532	52.381	0.00	0.00	41.01	4.57
417	421	1.072806	TCTGCAATCAACTCCTGCACT	59.927	47.619	0.00	0.00	41.01	4.40
418	422	1.884579	CTGCAATCAACTCCTGCACTT	59.115	47.619	0.00	0.00	41.01	3.16
419	423	2.295349	CTGCAATCAACTCCTGCACTTT	59.705	45.455	0.00	0.00	41.01	2.66
420	424	3.485394	TGCAATCAACTCCTGCACTTTA	58.515	40.909	0.00	0.00	41.01	1.85
520	536	8.551205	CCACATGCATATTACAGTACTTACTTG	58.449	37.037	0.00	0.00	33.46	3.16
521	537	8.551205	CACATGCATATTACAGTACTTACTTGG	58.449	37.037	0.00	0.00	33.46	3.61
610	626	5.043356	AGAGGGGTTAATTATCCTTTTGCCT	60.043	40.000	11.51	9.04	0.00	4.75
638	654	2.358898	GTGTCCATGTGCTCAGTTTTGT	59.641	45.455	0.00	0.00	0.00	2.83
677	693	1.351017	CTCAGTTTTGCCCCTAGTCCA	59.649	52.381	0.00	0.00	0.00	4.02
685	701	2.660064	CCCCTAGTCCAAGCGCACT	61.660	63.158	11.47	6.78	0.00	4.40
757	773	0.840722	CCTTACAGGTGGGACCAGGT	60.841	60.000	0.00	0.00	41.95	4.00
758	774	1.553884	CCTTACAGGTGGGACCAGGTA	60.554	57.143	0.00	0.00	41.95	3.08
905	956	3.404141	GACCACGGCGAGAGAGAGC	62.404	68.421	16.62	0.00	0.00	4.09
906	957	3.443925	CCACGGCGAGAGAGAGCA	61.444	66.667	16.62	0.00	34.54	4.26
907	958	2.202544	CACGGCGAGAGAGAGCAC	60.203	66.667	16.62	0.00	34.54	4.40
908	959	2.673341	ACGGCGAGAGAGAGCACA	60.673	61.111	16.62	0.00	34.54	4.57
953	1012	3.458163	CGGCGGTGGGAAGCTAGA	61.458	66.667	0.00	0.00	0.00	2.43
1213	1273	2.290896	TGGTCGGGATCTTTGAGCAATT	60.291	45.455	10.37	0.00	37.21	2.32

Showing 1 to 25 of 30 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
409	413	2.551270	ACCAGAGGATAAAGTGCAGGA	58.449	47.619	0.00	0.00	0.00	3.86
410	414	3.432326	GGTACCAGAGGATAAAGTGCAGG	60.432	52.174	7.15	0.00	0.00	4.85
411	415	3.452627	AGGTACCAGAGGATAAAGTGCAG	59.547	47.826	15.94	0.00	0.00	4.41
412	416	3.197766	CAGGTACCAGAGGATAAAGTGCA	59.802	47.826	15.94	0.00	0.00	4.57
413	417	3.451178	TCAGGTACCAGAGGATAAAGTGC	59.549	47.826	15.94	0.00	0.00	4.40
414	418	5.269505	CTCAGGTACCAGAGGATAAAGTG	57.730	47.826	23.27	4.89	0.00	3.16
506	522	4.032960	TCCCGACCAAGTAAGTACTGTA	57.967	45.455	0.00	0.00	36.50	2.74
577	593	8.624670	AGGATAATTAACCCCTCTTCTTTTTCT	58.375	33.333	8.09	0.00	0.00	2.52
579	595	9.615660	AAAGGATAATTAACCCCTCTTCTTTTT	57.384	29.630	8.09	0.00	0.00	1.94
581	597	9.035890	CAAAAGGATAATTAACCCCTCTTCTTT	57.964	33.333	8.09	0.00	0.00	2.52
582	598	7.124298	GCAAAAGGATAATTAACCCCTCTTCTT	59.876	37.037	8.09	0.00	0.00	2.52
583	599	6.607600	GCAAAAGGATAATTAACCCCTCTTCT	59.392	38.462	8.09	0.00	0.00	2.85
584	600	6.183360	GGCAAAAGGATAATTAACCCCTCTTC	60.183	42.308	8.09	0.00	0.00	2.87
585	601	5.661312	GGCAAAAGGATAATTAACCCCTCTT	59.339	40.000	8.09	0.00	0.00	2.85
586	602	5.043356	AGGCAAAAGGATAATTAACCCCTCT	60.043	40.000	8.09	0.00	0.00	3.69
587	603	5.208890	AGGCAAAAGGATAATTAACCCCTC	58.791	41.667	8.09	0.00	0.00	4.30
588	604	5.220872	AGGCAAAAGGATAATTAACCCCT	57.779	39.130	8.09	4.74	0.00	4.79
610	626	0.473755	AGCACATGGACACCACTGAA	59.526	50.000	0.00	0.00	35.80	3.02
638	654	1.065926	AGCACAATTCGCATCTGAGGA	60.066	47.619	0.00	0.00	0.00	3.71
677	693	1.664965	GGAACGAGTCAGTGCGCTT	60.665	57.895	9.73	0.00	0.00	4.68
757	773	0.039035	AAAATTGGCCGTCCCTGCTA	59.961	50.000	0.00	0.00	0.00	3.49
758	774	0.039035	TAAAATTGGCCGTCCCTGCT	59.961	50.000	0.00	0.00	0.00	4.24
871	918	3.749064	TCACCGCCGTGCTCTCTC	61.749	66.667	0.00	0.00	40.04	3.20
905	956	1.448540	CTAGCTTCCCACCGCTGTG	60.449	63.158	0.56	0.56	42.39	3.66
906	957	2.982130	CTAGCTTCCCACCGCTGT	59.018	61.111	0.00	0.00	37.05	4.40

Showing 1 to 25 of 36 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.