AutoCloner

Multiple sequence alignment - TraesCS2A01G049300

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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	TraesCS2A01G049300	chr2A	100.000	2318	0	0	1	2318	19054898	19052581	0.000000e+00	4281
1	TraesCS2A01G049300	chr2A	82.177	836	119	17	1	826	19035102	19034287	0.000000e+00	691
2	TraesCS2A01G049300	chr2B	87.957	1204	101	24	829	2009	29319124	29320306	0.000000e+00	1380
3	TraesCS2A01G049300	chr2B	87.625	1204	105	24	829	2009	29263887	29265069	0.000000e+00	1358
4	TraesCS2A01G049300	chr2B	87.469	1205	106	21	829	2009	29350242	29351425	0.000000e+00	1347
5	TraesCS2A01G049300	chr2B	89.916	833	71	7	5	830	29263096	29263922	0.000000e+00	1061
6	TraesCS2A01G049300	chr2B	89.676	833	73	7	5	830	29318333	29319159	0.000000e+00	1050
7	TraesCS2A01G049300	chr2B	89.556	833	73	7	5	830	29349452	29350277	0.000000e+00	1044
8	TraesCS2A01G049300	chr2B	94.069	607	30	4	224	827	29218472	29219075	0.000000e+00	917
9	TraesCS2A01G049300	chr2B	83.094	834	112	17	1	826	29549217	29550029	0.000000e+00	732
10	TraesCS2A01G049300	chr2B	82.789	796	102	15	829	1604	29549998	29550778	0.000000e+00	678
11	TraesCS2A01G049300	chr2B	92.157	357	11	4	1348	1700	29219531	29219874	2.680000e-134	488
12	TraesCS2A01G049300	chr2B	94.403	268	10	4	1686	1949	29221213	29221479	7.710000e-110	407
13	TraesCS2A01G049300	chr2B	94.758	248	11	2	1	248	29218223	29218468	3.610000e-103	385
14	TraesCS2A01G049300	chr2B	86.471	340	15	12	1979	2318	29221479	29221787	6.130000e-91	344
15	TraesCS2A01G049300	chr2D	95.349	817	22	7	1508	2318	17772462	17771656	0.000000e+00	1284
16	TraesCS2A01G049300	chr2D	93.357	828	48	5	1	825	17775263	17774440	0.000000e+00	1218
17	TraesCS2A01G049300	chr2D	94.714	681	35	1	828	1508	17774471	17773792	0.000000e+00	1057
18	TraesCS2A01G049300	chr2D	82.833	833	114	18	1	824	17640262	17639450	0.000000e+00	719
19	TraesCS2A01G049300	chr2D	82.713	833	115	18	1	824	17612891	17612079	0.000000e+00	713
20	TraesCS2A01G049300	chr2D	83.269	783	93	18	835	1596	17612102	17611337	0.000000e+00	686
21	TraesCS2A01G049300	chr2D	82.680	791	99	18	835	1604	17639473	17638700	0.000000e+00	667
22	TraesCS2A01G049300	chr7B	93.203	765	40	6	1006	1766	745128183	745128939	0.000000e+00	1114
23	TraesCS2A01G049300	chr1B	92.810	765	47	6	1006	1766	651061658	651060898	0.000000e+00	1101

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	TraesCS2A01G049300	chr2A	19052581	19054898	2317	True	4281.000000	4281	100.000000	1	2318	1	chr2A.!!$R2	2317
1	TraesCS2A01G049300	chr2A	19034287	19035102	815	True	691.000000	691	82.177000	1	826	1	chr2A.!!$R1	825
2	TraesCS2A01G049300	chr2B	29318333	29320306	1973	False	1215.000000	1380	88.816500	5	2009	2	chr2B.!!$F3	2004
3	TraesCS2A01G049300	chr2B	29263096	29265069	1973	False	1209.500000	1358	88.770500	5	2009	2	chr2B.!!$F2	2004
4	TraesCS2A01G049300	chr2B	29349452	29351425	1973	False	1195.500000	1347	88.512500	5	2009	2	chr2B.!!$F4	2004
5	TraesCS2A01G049300	chr2B	29549217	29550778	1561	False	705.000000	732	82.941500	1	1604	2	chr2B.!!$F5	1603
6	TraesCS2A01G049300	chr2B	29218223	29221787	3564	False	508.200000	917	92.371600	1	2318	5	chr2B.!!$F1	2317
7	TraesCS2A01G049300	chr2D	17771656	17775263	3607	True	1186.333333	1284	94.473333	1	2318	3	chr2D.!!$R3	2317
8	TraesCS2A01G049300	chr2D	17611337	17612891	1554	True	699.500000	713	82.991000	1	1596	2	chr2D.!!$R1	1595
9	TraesCS2A01G049300	chr2D	17638700	17640262	1562	True	693.000000	719	82.756500	1	1604	2	chr2D.!!$R2	1603
10	TraesCS2A01G049300	chr7B	745128183	745128939	756	False	1114.000000	1114	93.203000	1006	1766	1	chr7B.!!$F1	760
11	TraesCS2A01G049300	chr1B	651060898	651061658	760	True	1101.000000	1101	92.810000	1006	1766	1	chr1B.!!$R1	760

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
833	877	0.316204	TTCAACCCTTCCTCGTCGAC	59.684	55.0	5.18	5.18	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2114	4891	0.173481	TCCCATCTCTCGCTTCGTTG	59.827	55.0	0.0	0.0	0.0	4.1	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
52	58	6.547930	AGTTATACCTTGAGTCTTTCTCCC	57.452	41.667	0.00	0.00	42.12	4.30
63	69	7.782897	TGAGTCTTTCTCCCATATATAGGTG	57.217	40.000	0.00	0.00	42.12	4.00
83	89	2.059541	GTGTTAACTGCTCCGAGTGTC	58.940	52.381	7.22	0.00	0.00	3.67
160	167	7.415592	TCCCATGTTTGATTTAATGCATGTA	57.584	32.000	0.00	0.00	33.70	2.29
299	335	8.746922	AGAAACAAACTAATACATGCATGTTG	57.253	30.769	35.45	26.23	41.97	3.33
307	343	9.709495	AACTAATACATGCATGTTGACAAAAAT	57.291	25.926	35.45	18.22	41.97	1.82
320	356	8.057536	TGTTGACAAAAATTAGGTAGTTGTGT	57.942	30.769	0.00	0.00	32.75	3.72
330	366	8.788325	AATTAGGTAGTTGTGTGAGGTATTTC	57.212	34.615	0.00	0.00	0.00	2.17
491	528	9.472361	AATATTTGTCATTCTATGCAAATGCTC	57.528	29.630	20.00	2.56	41.92	4.26
550	587	8.947055	AATTTGAACTTGCACAATTTACTTCT	57.053	26.923	0.00	0.00	0.00	2.85
554	591	7.129622	TGAACTTGCACAATTTACTTCTAACG	58.870	34.615	0.00	0.00	0.00	3.18
625	662	6.202954	CCATTAACTAGGTTTCTAGAATGCGG	59.797	42.308	5.89	0.00	44.35	5.69
675	712	8.652810	TCCGAAAGCCACTTTATTATAGTTAC	57.347	34.615	0.00	0.00	33.49	2.50
826	870	3.371380	GCTCATGATCTTCAACCCTTCCT	60.371	47.826	0.00	0.00	0.00	3.36
827	871	4.450053	CTCATGATCTTCAACCCTTCCTC	58.550	47.826	0.00	0.00	0.00	3.71
831	875	0.601558	TCTTCAACCCTTCCTCGTCG	59.398	55.000	0.00	0.00	0.00	5.12
833	877	0.316204	TTCAACCCTTCCTCGTCGAC	59.684	55.000	5.18	5.18	0.00	4.20
842	886	3.250744	CTTCCTCGTCGACAAATGCTTA	58.749	45.455	17.16	0.00	0.00	3.09
855	899	6.212888	ACAAATGCTTATGATCTTCAACCC	57.787	37.500	0.00	0.00	0.00	4.11
1011	1062	1.065126	AGAGGGAAAATGGCGAAGAGG	60.065	52.381	0.00	0.00	0.00	3.69
1065	1116	9.109393	GCAATTATGTTCTCCTACAATGTCTTA	57.891	33.333	0.00	0.00	0.00	2.10
1084	1135	4.962836	AGGGCAGTGCACACCAGC	62.963	66.667	21.75	19.15	32.33	4.85
1194	1245	1.745115	TGCGACCAATGCAGTAGGC	60.745	57.895	0.00	0.00	45.13	3.93
1345	1397	3.256704	ACCTAAGACAAAGGACCATGGA	58.743	45.455	21.47	0.00	37.57	3.41
1494	1557	9.021863	GTGTCAAGCTATTTACTGATGTACTAC	57.978	37.037	0.00	0.00	0.00	2.73
1604	3019	9.997482	TTTGTTGTTCTACAAATAGACAAACTC	57.003	29.630	8.05	0.00	41.65	3.01
1605	3020	8.958119	TGTTGTTCTACAAATAGACAAACTCT	57.042	30.769	0.00	0.00	40.15	3.24
1998	4773	9.753674	AACAGATGTAATAATTTTCCTTCCTCA	57.246	29.630	0.00	0.00	0.00	3.86
2010	4787	2.163509	CCTTCCTCAGACGTCTCTTCA	58.836	52.381	16.96	0.00	0.00	3.02
2030	4807	3.704566	TCATCCTATTACGAGTTGGCTGT	59.295	43.478	0.00	0.00	0.00	4.40
2034	4811	2.981859	ATTACGAGTTGGCTGTAGGG	57.018	50.000	0.00	0.00	0.00	3.53
2074	4851	2.480419	CGAAGCGGAGAGACAAACAATT	59.520	45.455	0.00	0.00	0.00	2.32
2114	4891	1.668419	ATGGCTAGCATGGAACGAAC	58.332	50.000	18.24	0.00	0.00	3.95
2115	4892	0.323302	TGGCTAGCATGGAACGAACA	59.677	50.000	18.24	0.00	0.00	3.18
2116	4893	1.271108	TGGCTAGCATGGAACGAACAA	60.271	47.619	18.24	0.00	0.00	2.83
2117	4894	1.130561	GGCTAGCATGGAACGAACAAC	59.869	52.381	18.24	0.00	0.00	3.32
2119	4896	2.333926	CTAGCATGGAACGAACAACGA	58.666	47.619	0.00	0.00	45.77	3.85
2120	4897	1.588674	AGCATGGAACGAACAACGAA	58.411	45.000	0.00	0.00	45.77	3.85
2285	5062	6.387220	AGCTGGGATGGATAAAAGTTAGTACT	59.613	38.462	0.00	0.00	35.68	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	8.648557	TGACAATAAAGATAACCATCTCTTCG	57.351	34.615	0.00	0.00	40.81	3.79
52	58	6.586463	CGGAGCAGTTAACACACCTATATATG	59.414	42.308	8.61	0.00	0.00	1.78
63	69	2.059541	GACACTCGGAGCAGTTAACAC	58.940	52.381	8.61	0.00	0.00	3.32
83	89	0.035152	TCCCTGCTGGCAAGTATGTG	60.035	55.000	3.63	0.00	0.00	3.21
109	115	6.321717	ACATTATGGCAACTTACATGTTTCG	58.678	36.000	2.30	0.00	30.91	3.46
299	335	7.012989	ACCTCACACAACTACCTAATTTTTGTC	59.987	37.037	0.00	0.00	0.00	3.18
307	343	7.383687	CAGAAATACCTCACACAACTACCTAA	58.616	38.462	0.00	0.00	0.00	2.69
330	366	6.209192	TGGCCATTGGTCATAATTATAAGCAG	59.791	38.462	5.72	0.00	29.54	4.24
550	587	9.340695	CAAGATAAATTTCAAGCATGTTCGTTA	57.659	29.630	0.00	0.00	0.00	3.18
606	643	5.416271	TTTCCGCATTCTAGAAACCTAGT	57.584	39.130	9.71	0.00	36.05	2.57
651	688	8.333186	GTGTAACTATAATAAAGTGGCTTTCGG	58.667	37.037	0.00	0.00	35.21	4.30
652	689	8.875803	TGTGTAACTATAATAAAGTGGCTTTCG	58.124	33.333	0.00	0.00	38.04	3.46
675	712	3.663995	TGCATCAATTTGGAGGTTGTG	57.336	42.857	0.00	0.00	0.00	3.33
690	727	4.157656	TGCTTAGTTGGTTAACCATGCATC	59.842	41.667	27.57	15.14	46.97	3.91
826	870	4.682787	AGATCATAAGCATTTGTCGACGA	58.317	39.130	11.62	6.16	0.00	4.20
827	871	5.005682	TGAAGATCATAAGCATTTGTCGACG	59.994	40.000	11.62	0.00	0.00	5.12
831	875	6.096001	AGGGTTGAAGATCATAAGCATTTGTC	59.904	38.462	0.00	0.00	0.00	3.18
833	877	6.461110	AGGGTTGAAGATCATAAGCATTTG	57.539	37.500	0.00	0.00	0.00	2.32
842	886	2.840651	ACGAGGAAGGGTTGAAGATCAT	59.159	45.455	0.00	0.00	0.00	2.45
855	899	7.861630	TGAAAATAGAAAGTCAAACGAGGAAG	58.138	34.615	0.00	0.00	0.00	3.46
908	952	9.438163	AAGGGAAATAATTTCATGGATATGTGT	57.562	29.630	0.00	0.00	41.43	3.72
910	954	9.659135	TCAAGGGAAATAATTTCATGGATATGT	57.341	29.630	0.00	0.00	41.43	2.29
916	960	9.538508	GAGAAATCAAGGGAAATAATTTCATGG	57.461	33.333	8.36	0.00	41.43	3.66
976	1027	5.779241	TTCCCTCTGGATGAGTTAACAAT	57.221	39.130	8.61	0.70	41.40	2.71
1011	1062	3.679824	AGTAGTAGGCCAACAGTGTTC	57.320	47.619	5.01	0.00	0.00	3.18
1065	1116	3.170672	TGGTGTGCACTGCCCTCT	61.171	61.111	19.41	0.00	0.00	3.69
1084	1135	1.324736	GCGAGAGAATACAACTTGGCG	59.675	52.381	0.00	0.00	0.00	5.69
1190	1241	3.867857	TCAGCATTATTGTTCACGCCTA	58.132	40.909	0.00	0.00	0.00	3.93
1345	1397	1.136305	CCACGGATATCGAGTTGGTGT	59.864	52.381	0.00	0.00	42.43	4.16
1542	2937	7.669722	GGAACATATAAATACCATGGACCACAT	59.330	37.037	21.47	8.34	41.57	3.21
1604	3019	8.466617	TCCTTGCTACCTCTTTATAGTCTAAG	57.533	38.462	0.00	0.00	0.00	2.18
1605	3020	8.834004	TTCCTTGCTACCTCTTTATAGTCTAA	57.166	34.615	0.00	0.00	0.00	2.10
1998	4773	5.366460	TCGTAATAGGATGAAGAGACGTCT	58.634	41.667	20.18	20.18	32.81	4.18
2010	4787	4.281182	CCTACAGCCAACTCGTAATAGGAT	59.719	45.833	0.00	0.00	31.37	3.24
2030	4807	0.680921	GCATCAGCAAACCAGCCCTA	60.681	55.000	0.00	0.00	41.58	3.53
2074	4851	1.834301	GCCGTAAAGCCCCTGGATA	59.166	57.895	0.00	0.00	0.00	2.59
2105	4882	0.528033	TCGCTTCGTTGTTCGTTCCA	60.528	50.000	0.00	0.00	40.80	3.53
2114	4891	0.173481	TCCCATCTCTCGCTTCGTTG	59.827	55.000	0.00	0.00	0.00	4.10
2115	4892	0.895530	TTCCCATCTCTCGCTTCGTT	59.104	50.000	0.00	0.00	0.00	3.85
2116	4893	0.457851	CTTCCCATCTCTCGCTTCGT	59.542	55.000	0.00	0.00	0.00	3.85
2117	4894	0.741326	TCTTCCCATCTCTCGCTTCG	59.259	55.000	0.00	0.00	0.00	3.79
2118	4895	1.068434	CCTCTTCCCATCTCTCGCTTC	59.932	57.143	0.00	0.00	0.00	3.86
2119	4896	1.118838	CCTCTTCCCATCTCTCGCTT	58.881	55.000	0.00	0.00	0.00	4.68
2120	4897	0.260230	TCCTCTTCCCATCTCTCGCT	59.740	55.000	0.00	0.00	0.00	4.93
2153	4930	1.067565	TGAACCTTCTCTGCTACAGCG	60.068	52.381	0.00	0.00	45.83	5.18
2285	5062	2.076100	GCCTTCGACATCACACAATCA	58.924	47.619	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.