AutoCloner

Multiple sequence alignment - TraesCS2A01G309500

Loading Multiple Alignment...

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	TraesCS2A01G309500	chr2A	100.000	3589	0	0	1	3589	532853936	532857524	0.000000e+00	6628
1	TraesCS2A01G309500	chr2A	86.166	253	31	4	3224	3473	606574487	606574236	1.640000e-68	270
2	TraesCS2A01G309500	chr2D	95.665	3345	77	18	296	3589	394786706	394790033	0.000000e+00	5312
3	TraesCS2A01G309500	chr2D	91.547	627	28	6	1	607	394786059	394786680	0.000000e+00	841
4	TraesCS2A01G309500	chr2D	86.111	252	31	4	3224	3472	329951825	329952075	5.910000e-68	268
5	TraesCS2A01G309500	chr2B	96.074	2853	84	10	1	2837	467790304	467793144	0.000000e+00	4623
6	TraesCS2A01G309500	chr2B	92.661	763	43	10	2836	3589	467797176	467797934	0.000000e+00	1086
7	TraesCS2A01G309500	chr5B	93.056	216	15	0	2096	2311	75339557	75339342	2.080000e-82	316
8	TraesCS2A01G309500	chr6A	86.614	254	29	5	3224	3474	595480305	595480556	3.530000e-70	276
9	TraesCS2A01G309500	chr6A	86.220	254	29	6	3224	3473	109177965	109177714	1.640000e-68	270
10	TraesCS2A01G309500	chr3A	86.800	250	27	5	3224	3470	475281060	475281306	1.270000e-69	274
11	TraesCS2A01G309500	chr4A	86.400	250	30	4	3224	3470	165816543	165816295	1.640000e-68	270
12	TraesCS2A01G309500	chr1A	86.220	254	25	10	3224	3470	434422678	434422928	2.120000e-67	267

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	TraesCS2A01G309500	chr2A	532853936	532857524	3588	False	6628.0	6628	100.000	1	3589	1	chr2A.!!$F1	3588
1	TraesCS2A01G309500	chr2D	394786059	394790033	3974	False	3076.5	5312	93.606	1	3589	2	chr2D.!!$F2	3588
2	TraesCS2A01G309500	chr2B	467790304	467793144	2840	False	4623.0	4623	96.074	1	2837	1	chr2B.!!$F1	2836
3	TraesCS2A01G309500	chr2B	467797176	467797934	758	False	1086.0	1086	92.661	2836	3589	1	chr2B.!!$F2	753

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
93	96	0.608308	ACCACGGGGAAAGCTTAAGC	60.608	55.000	20.09	20.09	38.58	3.09	F
591	968	1.153823	CAGGGCTTACTGTCGGACG	60.154	63.158	3.34	1.29	33.81	4.79	F
1429	1834	1.207089	CCATGGTCGCTCCTGACTTTA	59.793	52.381	2.57	0.00	38.91	1.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2008	2418	1.484038	AACTTTTCAGCAGCCAACCA	58.516	45.0	0.00	0.0	3.67	R
2238	2648	1.239968	CCACCACTTTCTCTGCTGCC	61.240	60.0	0.00	0.0	4.85	R
2681	3091	2.032030	CACGAACTACAAGTTGCCCAAG	60.032	50.0	1.81	38.8	3.61	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
90	93	0.611714	GAGACCACGGGGAAAGCTTA	59.388	55.000	12.96	0.00	38.05	3.09
92	95	1.003233	AGACCACGGGGAAAGCTTAAG	59.997	52.381	12.96	0.00	38.05	1.85
93	96	0.608308	ACCACGGGGAAAGCTTAAGC	60.608	55.000	20.09	20.09	38.58	3.09
175	179	7.624360	TCTATTGGATCGCTGTTAAATTTGT	57.376	32.000	0.00	0.00	0.00	2.83
176	180	8.725405	TCTATTGGATCGCTGTTAAATTTGTA	57.275	30.769	0.00	0.00	0.00	2.41
309	314	5.954296	AGTGAATGTTGTGAAAGAGGATG	57.046	39.130	0.00	0.00	0.00	3.51
433	806	7.687941	AAGTGGTGGAAACAATCATTAGTAG	57.312	36.000	0.00	0.00	46.06	2.57
506	880	4.282068	GTTTGTATTGTGCAGTGTGACAG	58.718	43.478	0.00	0.00	0.00	3.51
523	900	5.065474	TGTGACAGTTGCCTTAAACAGTTAC	59.935	40.000	0.00	0.00	36.91	2.50
530	907	7.225931	CAGTTGCCTTAAACAGTTACTACAAGA	59.774	37.037	0.00	0.00	32.21	3.02
591	968	1.153823	CAGGGCTTACTGTCGGACG	60.154	63.158	3.34	1.29	33.81	4.79
662	1065	7.690256	ACTAATGGAAAGACTCATTGGTACTT	58.310	34.615	3.46	0.00	41.19	2.24
690	1093	6.349300	AGGTTTAATGCGAGAACATATCAGT	58.651	36.000	0.00	0.00	0.00	3.41
752	1155	5.888724	TGGACCATGTTGTTCTTGAACTTAA	59.111	36.000	13.65	0.00	0.00	1.85
1018	1423	5.552870	AAACATGTATAGGCCGAAGATCT	57.447	39.130	0.00	0.00	0.00	2.75
1070	1475	4.471726	GCGTGGCACAGCTGATGC	62.472	66.667	23.35	23.98	41.80	3.91
1429	1834	1.207089	CCATGGTCGCTCCTGACTTTA	59.793	52.381	2.57	0.00	38.91	1.85
1439	1844	1.284785	TCCTGACTTTATGCCAAGGGG	59.715	52.381	0.00	0.00	37.18	4.79
1659	2064	8.158169	TGAAGATGATGAGGTATATTGCAAAC	57.842	34.615	1.71	0.00	0.00	2.93
1664	2069	6.905736	TGATGAGGTATATTGCAAACCCTTA	58.094	36.000	13.95	8.94	33.53	2.69
1668	2073	9.875708	ATGAGGTATATTGCAAACCCTTATTTA	57.124	29.630	13.95	0.00	33.53	1.40
1783	2188	6.974932	AGCAACATACTTCTGTAACTCATG	57.025	37.500	0.00	0.00	31.80	3.07
2008	2418	2.178580	CCCTCAGAGCTCAAGAAGAGT	58.821	52.381	17.77	0.00	46.47	3.24
2238	2648	1.619654	TTGCTGTCCCAAATGAGGTG	58.380	50.000	0.00	0.00	0.00	4.00
2564	2974	1.202818	AGGCCTGGTGTTTTCTCTGTC	60.203	52.381	3.11	0.00	0.00	3.51
2674	3084	3.183574	TGTGCTGTCAACGAAATAGAACG	59.816	43.478	0.00	0.00	0.00	3.95
2681	3091	7.097342	TGTCAACGAAATAGAACGTAGAAAC	57.903	36.000	0.00	0.00	41.87	2.78
2692	3102	2.927028	ACGTAGAAACTTGGGCAACTT	58.073	42.857	0.00	0.00	0.00	2.66
2755	3165	1.326951	TGGCTAGTGATGCGCTACCA	61.327	55.000	9.73	0.21	31.00	3.25
2999	3412	6.664428	AGGCCACAATGTACTGTTATTTTT	57.336	33.333	5.01	0.00	0.00	1.94
3020	3433	0.242017	CTTACTGCTGCAACCAAGGC	59.758	55.000	3.02	0.00	0.00	4.35
3022	3435	0.606401	TACTGCTGCAACCAAGGCTC	60.606	55.000	3.02	0.00	0.00	4.70
3058	3471	5.643664	TGATTTGAATGCCTCAGAATTTCG	58.356	37.500	0.00	0.00	34.81	3.46
3160	3577	8.341903	GGAGAAGAAAAGAAGTGAAAGAAGAAG	58.658	37.037	0.00	0.00	0.00	2.85
3161	3578	9.103861	GAGAAGAAAAGAAGTGAAAGAAGAAGA	57.896	33.333	0.00	0.00	0.00	2.87
3162	3579	9.454859	AGAAGAAAAGAAGTGAAAGAAGAAGAA	57.545	29.630	0.00	0.00	0.00	2.52
3165	3582	8.187480	AGAAAAGAAGTGAAAGAAGAAGAAAGC	58.813	33.333	0.00	0.00	0.00	3.51
3166	3583	7.396540	AAAGAAGTGAAAGAAGAAGAAAGCA	57.603	32.000	0.00	0.00	0.00	3.91
3221	3643	6.138761	GTCATCATGGCTTAGCTTTATTTCG	58.861	40.000	3.59	0.00	0.00	3.46
3500	3922	9.169592	GCAAACTAGGGTACATCATTTAAGTTA	57.830	33.333	0.00	0.00	0.00	2.24
3580	4006	5.181009	GTCCACAAACCCTAACCATACTAC	58.819	45.833	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
175	179	3.750221	TCCCCCAAATACTAAGCCCTTA	58.250	45.455	0.00	0.00	0.00	2.69
176	180	2.580232	TCCCCCAAATACTAAGCCCTT	58.420	47.619	0.00	0.00	0.00	3.95
244	249	9.838339	ACAAATATTAAGCTACTATGCACTTCT	57.162	29.630	0.00	0.00	34.99	2.85
309	314	5.582665	AGTCGTTCTTCATCAATTTAGAGCC	59.417	40.000	0.00	0.00	0.00	4.70
378	751	8.851541	ATTAACAATTGCTGGAAACAATCATT	57.148	26.923	5.05	0.00	42.06	2.57
433	806	6.273071	AGGTTATTTTCTTTGTCACAGTTGC	58.727	36.000	0.00	0.00	0.00	4.17
506	880	7.486802	TCTTGTAGTAACTGTTTAAGGCAAC	57.513	36.000	0.00	0.00	0.00	4.17
523	900	8.064222	CCTATGATTATGCACGTTTTCTTGTAG	58.936	37.037	0.00	0.00	0.00	2.74
530	907	8.677148	AATAGACCTATGATTATGCACGTTTT	57.323	30.769	0.00	0.00	0.00	2.43
591	968	5.712152	ATGATTGGACCTTTGACTTGAAC	57.288	39.130	0.00	0.00	0.00	3.18
662	1065	9.990360	TGATATGTTCTCGCATTAAACCTTATA	57.010	29.630	0.00	0.00	0.00	0.98
726	1129	3.289407	TCAAGAACAACATGGTCCACA	57.711	42.857	0.00	0.00	33.71	4.17
1018	1423	2.938798	AGCCCACCCCGAATTGGA	60.939	61.111	0.00	0.00	42.00	3.53
1070	1475	2.282407	TGACATCAACATCATCGCCTG	58.718	47.619	0.00	0.00	0.00	4.85
1439	1844	3.009143	AGGTTGACCAGTTGTTCTATCCC	59.991	47.826	2.56	0.00	38.89	3.85
1442	1847	3.910627	AGGAGGTTGACCAGTTGTTCTAT	59.089	43.478	2.56	0.00	38.89	1.98
1659	2064	8.533569	AGTGAAACCCATAACATAAATAAGGG	57.466	34.615	0.00	0.00	37.80	3.95
1664	2069	8.823220	AAGCTAGTGAAACCCATAACATAAAT	57.177	30.769	0.00	0.00	37.80	1.40
1668	2073	6.263168	GCATAAGCTAGTGAAACCCATAACAT	59.737	38.462	2.66	0.00	35.72	2.71
2008	2418	1.484038	AACTTTTCAGCAGCCAACCA	58.516	45.000	0.00	0.00	0.00	3.67
2238	2648	1.239968	CCACCACTTTCTCTGCTGCC	61.240	60.000	0.00	0.00	0.00	4.85
2424	2834	5.627499	TGCAAAACAATAAGATCTCGCTT	57.373	34.783	0.00	0.00	0.00	4.68
2427	2837	8.390354	TGTAAGATGCAAAACAATAAGATCTCG	58.610	33.333	0.00	0.00	0.00	4.04
2564	2974	2.713154	CGGCGAAATTTAGGGCGG	59.287	61.111	22.27	12.95	44.69	6.13
2674	3084	4.820173	ACTACAAGTTGCCCAAGTTTCTAC	59.180	41.667	1.81	0.00	32.02	2.59
2681	3091	2.032030	CACGAACTACAAGTTGCCCAAG	60.032	50.000	1.81	0.00	38.80	3.61
2692	3102	5.867174	CCACATTCAAGATACACGAACTACA	59.133	40.000	0.00	0.00	0.00	2.74
2807	3217	8.742554	ATTAAGAAAAACTAAAATCAGGCACG	57.257	30.769	0.00	0.00	0.00	5.34
3020	3433	8.719648	GCATTCAAATCATAGAGTAATCAGGAG	58.280	37.037	0.00	0.00	0.00	3.69
3022	3435	7.664731	AGGCATTCAAATCATAGAGTAATCAGG	59.335	37.037	0.00	0.00	0.00	3.86
3178	3595	9.753674	ATGATGACATTTCCTAAAAGAACCTAA	57.246	29.630	0.00	0.00	32.21	2.69
3221	3643	2.396590	TTATGGAACGGAGGAAGTGC	57.603	50.000	0.00	0.00	0.00	4.40
3415	3837	9.248291	GAGAAGTCAACTTTGCAAATTTTGATA	57.752	29.630	26.69	12.32	36.11	2.15
3470	3892	1.562475	GATGTACCCTAGTTTGCCCCA	59.438	52.381	0.00	0.00	0.00	4.96
3500	3922	8.882736	GTTTTTGAATGATGTGTCCTTTTTCTT	58.117	29.630	0.00	0.00	0.00	2.52
3502	3924	7.279758	TGGTTTTTGAATGATGTGTCCTTTTTC	59.720	33.333	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.