AutoCloner

Multiple sequence alignment - TraesCS2D01G439600

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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	TraesCS2D01G439600	chr2D	100.000	4383	0	0	1	4383	548973572	548977954	0.000000e+00	8094.0
1	TraesCS2D01G439600	chr2D	91.111	45	4	0	3150	3194	569184651	569184695	1.320000e-05	62.1
2	TraesCS2D01G439600	chr2A	89.572	1285	119	9	2712	3986	764771595	764770316	0.000000e+00	1616.0
3	TraesCS2D01G439600	chr7A	84.644	1335	192	9	2778	4102	693207238	693205907	0.000000e+00	1317.0
4	TraesCS2D01G439600	chr7A	89.637	193	18	2	4099	4291	112453353	112453543	1.220000e-60	244.0
5	TraesCS2D01G439600	chr5D	95.796	666	23	5	1	663	495289341	495290004	0.000000e+00	1070.0
6	TraesCS2D01G439600	chr5D	94.595	666	30	4	1	663	555506283	555505621	0.000000e+00	1026.0
7	TraesCS2D01G439600	chr5D	91.005	189	16	1	4099	4287	377148042	377147855	2.020000e-63	254.0
8	TraesCS2D01G439600	chr3D	95.789	665	23	4	1	663	121907492	121908153	0.000000e+00	1068.0
9	TraesCS2D01G439600	chr3D	94.753	667	23	5	1	662	191574626	191573967	0.000000e+00	1027.0
10	TraesCS2D01G439600	chr7D	94.864	662	30	4	3	662	35812746	35813405	0.000000e+00	1031.0
11	TraesCS2D01G439600	chr7D	95.186	644	29	2	22	663	597509134	597508491	0.000000e+00	1016.0
12	TraesCS2D01G439600	chr7D	74.324	888	199	22	2946	3815	205949595	205950471	2.510000e-92	350.0
13	TraesCS2D01G439600	chr3A	94.225	658	34	4	1	656	434007172	434006517	0.000000e+00	1002.0
14	TraesCS2D01G439600	chr6A	92.868	659	43	4	4	659	5075769	5075112	0.000000e+00	953.0
15	TraesCS2D01G439600	chr6A	92.632	190	13	1	4099	4288	335743488	335743300	5.590000e-69	272.0
16	TraesCS2D01G439600	chr7B	92.504	667	45	4	4	666	99110107	99109442	0.000000e+00	950.0
17	TraesCS2D01G439600	chr7B	90.576	191	14	4	4099	4289	334460230	334460416	2.620000e-62	250.0
18	TraesCS2D01G439600	chr6D	93.085	188	10	3	4099	4286	9899561	9899377	5.590000e-69	272.0
19	TraesCS2D01G439600	chr4A	91.398	186	15	1	4100	4285	647135034	647135218	2.020000e-63	254.0
20	TraesCS2D01G439600	chr5B	91.005	189	14	3	4099	4287	61200006	61200191	7.280000e-63	252.0
21	TraesCS2D01G439600	chr4D	90.526	190	14	2	4099	4287	93350903	93350717	9.410000e-62	248.0
22	TraesCS2D01G439600	chr2B	89.947	189	18	1	4099	4287	152752173	152751986	4.380000e-60	243.0

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	TraesCS2D01G439600	chr2D	548973572	548977954	4382	False	8094	8094	100.000	1	4383	1	chr2D.!!$F1	4382
1	TraesCS2D01G439600	chr2A	764770316	764771595	1279	True	1616	1616	89.572	2712	3986	1	chr2A.!!$R1	1274
2	TraesCS2D01G439600	chr7A	693205907	693207238	1331	True	1317	1317	84.644	2778	4102	1	chr7A.!!$R1	1324
3	TraesCS2D01G439600	chr5D	495289341	495290004	663	False	1070	1070	95.796	1	663	1	chr5D.!!$F1	662
4	TraesCS2D01G439600	chr5D	555505621	555506283	662	True	1026	1026	94.595	1	663	1	chr5D.!!$R2	662
5	TraesCS2D01G439600	chr3D	121907492	121908153	661	False	1068	1068	95.789	1	663	1	chr3D.!!$F1	662
6	TraesCS2D01G439600	chr3D	191573967	191574626	659	True	1027	1027	94.753	1	662	1	chr3D.!!$R1	661
7	TraesCS2D01G439600	chr7D	35812746	35813405	659	False	1031	1031	94.864	3	662	1	chr7D.!!$F1	659
8	TraesCS2D01G439600	chr7D	597508491	597509134	643	True	1016	1016	95.186	22	663	1	chr7D.!!$R1	641
9	TraesCS2D01G439600	chr7D	205949595	205950471	876	False	350	350	74.324	2946	3815	1	chr7D.!!$F2	869
10	TraesCS2D01G439600	chr3A	434006517	434007172	655	True	1002	1002	94.225	1	656	1	chr3A.!!$R1	655
11	TraesCS2D01G439600	chr6A	5075112	5075769	657	True	953	953	92.868	4	659	1	chr6A.!!$R1	655
12	TraesCS2D01G439600	chr7B	99109442	99110107	665	True	950	950	92.504	4	666	1	chr7B.!!$R1	662

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
975	985	0.036294	AGGGGAGCAAAAGACGTAGC	60.036	55.0	0.00	0.00	0.00	3.58	F
1748	1758	0.031585	GAAAAACCAGTGGTTCCGGC	59.968	55.0	27.53	13.53	46.20	6.13	F
2264	2274	0.030705	TCCCTGGGAGGAGATTCCAG	60.031	60.0	12.53	0.00	45.57	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	2255	0.030705	CTGGAATCTCCTCCCAGGGA	60.031	60.0	8.35	8.35	42.75	4.20	R
3335	3346	0.250467	AGAGCACTTGCGGTGTCAAT	60.250	50.0	10.54	0.00	46.86	2.57	R
4249	4267	0.036294	GGATTATACCCGCCCTCTGC	60.036	60.0	0.00	0.00	0.00	4.26	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
212	215	0.747255	CCGGAGAGGTTGATCACGAT	59.253	55.000	0.00	0.00	34.51	3.73
441	444	4.483243	GGGGAAAGGCGGCGATCA	62.483	66.667	12.98	0.00	0.00	2.92
596	606	0.469331	TCGGCTCTACCTGTATGGGG	60.469	60.000	0.00	0.00	41.11	4.96
650	660	2.223711	CGTATGCCCAAAATGCCCTTAC	60.224	50.000	0.00	0.00	0.00	2.34
666	676	4.332428	CCTTACACGTTAAGGGGGATAG	57.668	50.000	20.16	0.00	40.20	2.08
667	677	3.708121	CCTTACACGTTAAGGGGGATAGT	59.292	47.826	20.16	1.56	40.20	2.12
668	678	4.202192	CCTTACACGTTAAGGGGGATAGTC	60.202	50.000	20.16	0.00	40.20	2.59
669	679	2.823959	ACACGTTAAGGGGGATAGTCA	58.176	47.619	1.98	0.00	0.00	3.41
670	680	3.381335	ACACGTTAAGGGGGATAGTCAT	58.619	45.455	1.98	0.00	0.00	3.06
671	681	3.134081	ACACGTTAAGGGGGATAGTCATG	59.866	47.826	1.98	0.00	0.00	3.07
672	682	3.134081	CACGTTAAGGGGGATAGTCATGT	59.866	47.826	0.00	0.00	0.00	3.21
673	683	3.387050	ACGTTAAGGGGGATAGTCATGTC	59.613	47.826	0.00	0.00	0.00	3.06
674	684	3.386726	CGTTAAGGGGGATAGTCATGTCA	59.613	47.826	0.00	0.00	0.00	3.58
675	685	4.040461	CGTTAAGGGGGATAGTCATGTCAT	59.960	45.833	0.00	0.00	0.00	3.06
676	686	5.552178	GTTAAGGGGGATAGTCATGTCATC	58.448	45.833	0.00	0.00	0.00	2.92
677	687	3.350992	AGGGGGATAGTCATGTCATCA	57.649	47.619	0.00	0.00	0.00	3.07
678	688	3.879346	AGGGGGATAGTCATGTCATCAT	58.121	45.455	0.00	0.00	34.21	2.45
679	689	5.028678	AGGGGGATAGTCATGTCATCATA	57.971	43.478	0.00	0.00	32.47	2.15
680	690	4.780021	AGGGGGATAGTCATGTCATCATAC	59.220	45.833	0.00	0.00	32.47	2.39
681	691	4.780021	GGGGGATAGTCATGTCATCATACT	59.220	45.833	0.00	0.00	32.47	2.12
682	692	5.337894	GGGGGATAGTCATGTCATCATACTG	60.338	48.000	0.00	0.00	32.47	2.74
683	693	5.247110	GGGGATAGTCATGTCATCATACTGT	59.753	44.000	0.00	0.00	32.47	3.55
684	694	6.437477	GGGGATAGTCATGTCATCATACTGTA	59.563	42.308	0.00	0.00	32.47	2.74
685	695	7.316640	GGGATAGTCATGTCATCATACTGTAC	58.683	42.308	0.00	0.00	32.47	2.90
686	696	7.177568	GGGATAGTCATGTCATCATACTGTACT	59.822	40.741	0.00	0.00	32.47	2.73

Showing 1 to 25 of 1,426 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
322	325	0.546747	ATTCTCCCCGTCTTCACCCA	60.547	55.000	0.00	0.00	0.00	4.51
465	468	2.890766	ATTCCAACGTCACCCGCCT	61.891	57.895	0.00	0.00	41.42	5.52
472	475	2.359354	CGGCCCATTCCAACGTCA	60.359	61.111	0.00	0.00	0.00	4.35
650	660	3.134081	ACATGACTATCCCCCTTAACGTG	59.866	47.826	0.00	0.00	0.00	4.49
663	673	7.869937	GCAAGTACAGTATGATGACATGACTAT	59.130	37.037	0.00	0.00	39.69	2.12
666	676	6.045318	AGCAAGTACAGTATGATGACATGAC	58.955	40.000	0.00	0.00	39.69	3.06
667	677	6.097412	AGAGCAAGTACAGTATGATGACATGA	59.903	38.462	0.00	0.00	39.69	3.07
668	678	6.279123	AGAGCAAGTACAGTATGATGACATG	58.721	40.000	0.00	0.00	39.69	3.21
669	679	6.477053	AGAGCAAGTACAGTATGATGACAT	57.523	37.500	0.00	0.00	39.69	3.06
670	680	5.921962	AGAGCAAGTACAGTATGATGACA	57.078	39.130	0.00	0.00	39.69	3.58
671	681	7.383572	CCATAAGAGCAAGTACAGTATGATGAC	59.616	40.741	0.00	0.00	39.69	3.06
672	682	7.287696	TCCATAAGAGCAAGTACAGTATGATGA	59.712	37.037	0.00	0.00	39.69	2.92
673	683	7.436933	TCCATAAGAGCAAGTACAGTATGATG	58.563	38.462	0.00	0.00	39.69	3.07
674	684	7.603180	TCCATAAGAGCAAGTACAGTATGAT	57.397	36.000	0.00	0.00	39.69	2.45
675	685	7.043961	CTCCATAAGAGCAAGTACAGTATGA	57.956	40.000	0.00	0.00	35.89	2.15
690	700	4.841813	TGTAGGTTGGTTGACTCCATAAGA	59.158	41.667	0.00	0.00	37.33	2.10
691	701	5.160607	TGTAGGTTGGTTGACTCCATAAG	57.839	43.478	0.00	0.00	37.33	1.73
692	702	4.595781	ACTGTAGGTTGGTTGACTCCATAA	59.404	41.667	0.00	0.00	37.33	1.90
693	703	4.020573	CACTGTAGGTTGGTTGACTCCATA	60.021	45.833	0.00	0.00	37.33	2.74
694	704	2.979678	ACTGTAGGTTGGTTGACTCCAT	59.020	45.455	0.00	0.00	37.33	3.41
695	705	2.104111	CACTGTAGGTTGGTTGACTCCA	59.896	50.000	0.00	0.00	35.49	3.86
696	706	2.367567	TCACTGTAGGTTGGTTGACTCC	59.632	50.000	0.00	0.00	0.00	3.85
697	707	3.746045	TCACTGTAGGTTGGTTGACTC	57.254	47.619	0.00	0.00	0.00	3.36
698	708	3.433173	GGTTCACTGTAGGTTGGTTGACT	60.433	47.826	0.00	0.00	0.00	3.41
699	709	2.876550	GGTTCACTGTAGGTTGGTTGAC	59.123	50.000	0.00	0.00	0.00	3.18

Showing 1 to 25 of 1,387 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.