AutoCloner

Multiple sequence alignment - TraesCS2D01G234300

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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	TraesCS2D01G234300	chr2D	100.000	2414	0	0	1	2414	215733173	215730760	0.000000e+00	4458
1	TraesCS2D01G234300	chr2D	95.318	1794	73	8	35	1820	423361692	423359902	0.000000e+00	2837
2	TraesCS2D01G234300	chr2D	91.872	1870	115	12	480	2331	439509429	439507579	0.000000e+00	2577
3	TraesCS2D01G234300	chr2D	91.313	495	23	7	1857	2331	423359903	423359409	0.000000e+00	658
4	TraesCS2D01G234300	chr3D	93.307	2316	121	11	35	2331	365091791	365094091	0.000000e+00	3387
5	TraesCS2D01G234300	chr3D	93.635	1791	102	7	35	1820	437449715	437447932	0.000000e+00	2665
6	TraesCS2D01G234300	chr3D	94.033	1743	77	4	604	2328	418259609	418257876	0.000000e+00	2617
7	TraesCS2D01G234300	chr3D	100.000	83	0	0	2332	2414	220117952	220118034	1.160000e-33	154
8	TraesCS2D01G234300	chr4D	92.746	2316	120	22	35	2331	253646389	253648675	0.000000e+00	3302
9	TraesCS2D01G234300	chr4D	92.819	1128	61	3	35	1145	30247167	30248291	0.000000e+00	1616
10	TraesCS2D01G234300	chr5D	92.743	2136	137	9	35	2168	311825308	311827427	0.000000e+00	3070
11	TraesCS2D01G234300	chr5D	92.909	1791	92	9	35	1820	317933315	317931555	0.000000e+00	2571
12	TraesCS2D01G234300	chr7D	93.475	1793	95	10	35	1820	85641303	85643080	0.000000e+00	2643
13	TraesCS2D01G234300	chr7D	93.091	1708	92	10	649	2332	188533190	188534895	0.000000e+00	2477
14	TraesCS2D01G234300	chr6B	91.893	1690	123	8	35	1719	137852336	137850656	0.000000e+00	2350
15	TraesCS2D01G234300	chr6B	100.000	83	0	0	2332	2414	60559383	60559301	1.160000e-33	154
16	TraesCS2D01G234300	chr6B	98.810	84	1	0	2331	2414	368673012	368672929	1.500000e-32	150
17	TraesCS2D01G234300	chr2B	90.892	1043	75	10	1307	2330	573234933	573233892	0.000000e+00	1382
18	TraesCS2D01G234300	chr3A	89.303	1047	86	4	1296	2332	477692015	477690985	0.000000e+00	1290
19	TraesCS2D01G234300	chr3A	98.810	84	1	0	2331	2414	495087405	495087488	1.500000e-32	150
20	TraesCS2D01G234300	chr7B	88.968	698	65	3	1644	2331	526008788	526009483	0.000000e+00	852
21	TraesCS2D01G234300	chr7A	91.075	493	42	2	1840	2331	49468531	49469022	0.000000e+00	665
22	TraesCS2D01G234300	chr7A	96.341	82	3	0	2329	2410	215473637	215473556	4.190000e-28	135
23	TraesCS2D01G234300	chr1D	100.000	83	0	0	2332	2414	336664850	336664768	1.160000e-33	154
24	TraesCS2D01G234300	chr2A	98.810	84	1	0	2331	2414	338484592	338484509	1.500000e-32	150
25	TraesCS2D01G234300	chr6D	98.795	83	1	0	2332	2414	101906613	101906695	5.380000e-32	148
26	TraesCS2D01G234300	chr6D	97.674	86	2	0	2329	2414	360912127	360912042	5.380000e-32	148

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	TraesCS2D01G234300	chr2D	215730760	215733173	2413	True	4458.0	4458	100.0000	1	2414	1	chr2D.!!$R1	2413
1	TraesCS2D01G234300	chr2D	439507579	439509429	1850	True	2577.0	2577	91.8720	480	2331	1	chr2D.!!$R2	1851
2	TraesCS2D01G234300	chr2D	423359409	423361692	2283	True	1747.5	2837	93.3155	35	2331	2	chr2D.!!$R3	2296
3	TraesCS2D01G234300	chr3D	365091791	365094091	2300	False	3387.0	3387	93.3070	35	2331	1	chr3D.!!$F2	2296
4	TraesCS2D01G234300	chr3D	437447932	437449715	1783	True	2665.0	2665	93.6350	35	1820	1	chr3D.!!$R2	1785
5	TraesCS2D01G234300	chr3D	418257876	418259609	1733	True	2617.0	2617	94.0330	604	2328	1	chr3D.!!$R1	1724
6	TraesCS2D01G234300	chr4D	253646389	253648675	2286	False	3302.0	3302	92.7460	35	2331	1	chr4D.!!$F2	2296
7	TraesCS2D01G234300	chr4D	30247167	30248291	1124	False	1616.0	1616	92.8190	35	1145	1	chr4D.!!$F1	1110
8	TraesCS2D01G234300	chr5D	311825308	311827427	2119	False	3070.0	3070	92.7430	35	2168	1	chr5D.!!$F1	2133
9	TraesCS2D01G234300	chr5D	317931555	317933315	1760	True	2571.0	2571	92.9090	35	1820	1	chr5D.!!$R1	1785
10	TraesCS2D01G234300	chr7D	85641303	85643080	1777	False	2643.0	2643	93.4750	35	1820	1	chr7D.!!$F1	1785
11	TraesCS2D01G234300	chr7D	188533190	188534895	1705	False	2477.0	2477	93.0910	649	2332	1	chr7D.!!$F2	1683
12	TraesCS2D01G234300	chr6B	137850656	137852336	1680	True	2350.0	2350	91.8930	35	1719	1	chr6B.!!$R2	1684
13	TraesCS2D01G234300	chr2B	573233892	573234933	1041	True	1382.0	1382	90.8920	1307	2330	1	chr2B.!!$R1	1023
14	TraesCS2D01G234300	chr3A	477690985	477692015	1030	True	1290.0	1290	89.3030	1296	2332	1	chr3A.!!$R1	1036
15	TraesCS2D01G234300	chr7B	526008788	526009483	695	False	852.0	852	88.9680	1644	2331	1	chr7B.!!$F1	687

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
913	967	0.338467	TAAGCCACCCTCTGCCTCTA	59.662	55.0	0.0	0.0	0.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1894	1969	1.219393	CCGCTGGTTCCTCTCTTCC	59.781	63.158	0.0	0.0	0.0	3.46	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
17	18	3.369921	GCCTCAAGGGTTTGCTGG	58.630	61.111	0.00	0.00	37.43	4.85
18	19	1.228552	GCCTCAAGGGTTTGCTGGA	60.229	57.895	0.00	0.00	37.43	3.86
19	20	0.827507	GCCTCAAGGGTTTGCTGGAA	60.828	55.000	0.00	0.00	37.43	3.53
20	21	0.961753	CCTCAAGGGTTTGCTGGAAC	59.038	55.000	0.00	0.00	34.21	3.62
21	22	0.961753	CTCAAGGGTTTGCTGGAACC	59.038	55.000	8.21	8.21	46.70	3.62
25	26	3.351450	GGTTTGCTGGAACCCGTC	58.649	61.111	6.09	0.00	42.63	4.79
26	27	1.527380	GGTTTGCTGGAACCCGTCA	60.527	57.895	6.09	0.00	42.63	4.35
27	28	0.893727	GGTTTGCTGGAACCCGTCAT	60.894	55.000	6.09	0.00	42.63	3.06
28	29	0.521735	GTTTGCTGGAACCCGTCATC	59.478	55.000	0.00	0.00	0.00	2.92
29	30	0.608035	TTTGCTGGAACCCGTCATCC	60.608	55.000	0.00	0.00	36.21	3.51
30	31	2.511600	GCTGGAACCCGTCATCCG	60.512	66.667	0.00	0.00	38.63	4.18
31	32	3.014085	GCTGGAACCCGTCATCCGA	62.014	63.158	0.00	0.00	38.63	4.55
32	33	1.153628	CTGGAACCCGTCATCCGAC	60.154	63.158	0.00	0.00	38.63	4.79
33	34	1.884075	CTGGAACCCGTCATCCGACA	61.884	60.000	0.00	0.00	42.74	4.35
89	91	7.959658	TTTCATGAAAATGACCATAGACCAT	57.040	32.000	18.45	0.00	0.00	3.55
210	219	0.768622	TCGAAACCCCATTGACCAGT	59.231	50.000	0.00	0.00	0.00	4.00
224	233	2.230660	GACCAGTTCAAAACCCCTCTG	58.769	52.381	0.00	0.00	0.00	3.35
232	241	1.358051	AAAACCCCTCTGAACCCCGT	61.358	55.000	0.00	0.00	0.00	5.28
285	294	2.265904	CGCCCGATCATACCCTCGA	61.266	63.158	0.00	0.00	37.05	4.04
294	303	2.797278	ATACCCTCGAGCCAAGCGG	61.797	63.158	6.99	4.10	0.00	5.52
399	408	1.520192	CATCGTTGGATCGTGGGGA	59.480	57.895	0.00	0.00	0.00	4.81
451	460	4.082523	GCTGCTCGCCCACCACTA	62.083	66.667	0.00	0.00	0.00	2.74
462	476	0.736325	CCACCACTAACTCCGCGAAG	60.736	60.000	8.23	0.00	0.00	3.79
524	539	4.160635	GGCCGTCGAATTGCGTGG	62.161	66.667	0.00	0.00	41.80	4.94
525	540	3.419759	GCCGTCGAATTGCGTGGT	61.420	61.111	0.00	0.00	41.80	4.16

Showing 1 to 25 of 57 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.827507	TTCCAGCAAACCCTTGAGGC	60.828	55.000	0.00	0.00	40.58	4.70
1	2	0.961753	GTTCCAGCAAACCCTTGAGG	59.038	55.000	0.00	0.00	43.78	3.86
2	3	0.961753	GGTTCCAGCAAACCCTTGAG	59.038	55.000	4.75	0.00	42.46	3.02
3	4	3.125520	GGTTCCAGCAAACCCTTGA	57.874	52.632	4.75	0.00	42.46	3.02
8	9	0.893727	ATGACGGGTTCCAGCAAACC	60.894	55.000	7.04	7.04	46.66	3.27
9	10	0.521735	GATGACGGGTTCCAGCAAAC	59.478	55.000	0.00	0.00	0.00	2.93
10	11	0.608035	GGATGACGGGTTCCAGCAAA	60.608	55.000	0.00	0.00	31.99	3.68
11	12	1.002624	GGATGACGGGTTCCAGCAA	60.003	57.895	0.00	0.00	31.99	3.91
12	13	2.668632	GGATGACGGGTTCCAGCA	59.331	61.111	0.00	0.00	31.99	4.41
13	14	2.511600	CGGATGACGGGTTCCAGC	60.512	66.667	0.00	0.00	39.42	4.85
14	15	1.153628	GTCGGATGACGGGTTCCAG	60.154	63.158	0.00	0.00	44.45	3.86
15	16	2.975536	GTCGGATGACGGGTTCCA	59.024	61.111	0.00	0.00	44.45	3.53
23	24	2.673368	GAGGTCAAATGTGTCGGATGAC	59.327	50.000	0.00	0.00	45.71	3.06
24	25	2.673893	CGAGGTCAAATGTGTCGGATGA	60.674	50.000	0.00	0.00	0.00	2.92
25	26	1.660607	CGAGGTCAAATGTGTCGGATG	59.339	52.381	0.00	0.00	0.00	3.51
26	27	1.548719	TCGAGGTCAAATGTGTCGGAT	59.451	47.619	0.00	0.00	0.00	4.18
27	28	0.963225	TCGAGGTCAAATGTGTCGGA	59.037	50.000	0.00	0.00	0.00	4.55
28	29	1.927174	GATCGAGGTCAAATGTGTCGG	59.073	52.381	0.00	0.00	0.00	4.79
29	30	1.583856	CGATCGAGGTCAAATGTGTCG	59.416	52.381	10.26	0.00	0.00	4.35
30	31	2.345641	CACGATCGAGGTCAAATGTGTC	59.654	50.000	24.34	0.00	0.00	3.67
31	32	2.337583	CACGATCGAGGTCAAATGTGT	58.662	47.619	24.34	0.00	0.00	3.72
32	33	1.061131	GCACGATCGAGGTCAAATGTG	59.939	52.381	24.34	6.39	0.00	3.21
33	34	1.359848	GCACGATCGAGGTCAAATGT	58.640	50.000	24.34	0.00	0.00	2.71
123	127	4.215399	TGAAACCTTCACCATTCGTCATTC	59.785	41.667	0.00	0.00	34.08	2.67
210	219	1.133294	GGGGTTCAGAGGGGTTTTGAA	60.133	52.381	0.00	0.00	0.00	2.69

Showing 1 to 25 of 72 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.