AutoCloner

Multiple sequence alignment - TraesCS3D01G118800

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	TraesCS3D01G118800	chr3D	100.000	2909	0	0	1	2909	73393018	73395926	0.000000e+00	5373.0
1	TraesCS3D01G118800	chr3A	90.723	2544	144	44	24	2512	86372815	86375321	0.000000e+00	3306.0
2	TraesCS3D01G118800	chr3A	89.493	276	20	7	2636	2909	86375795	86376063	9.980000e-90	340.0
3	TraesCS3D01G118800	chr3B	91.107	2249	115	38	331	2516	118759179	118761405	0.000000e+00	2966.0
4	TraesCS3D01G118800	chr3B	92.118	406	27	4	2504	2909	118761451	118761851	4.210000e-158	568.0
5	TraesCS3D01G118800	chr3B	93.586	343	16	5	7	347	118758824	118759162	9.300000e-140	507.0
6	TraesCS3D01G118800	chr2D	93.661	773	28	12	1460	2230	66077207	66076454	0.000000e+00	1136.0
7	TraesCS3D01G118800	chrUn	92.975	726	29	13	1509	2232	105815339	105816044	0.000000e+00	1038.0
8	TraesCS3D01G118800	chrUn	92.975	726	30	12	1509	2232	106336592	106337298	0.000000e+00	1038.0
9	TraesCS3D01G118800	chrUn	100.000	29	0	0	2514	2542	83395538	83395510	1.000000e-03	54.7
10	TraesCS3D01G118800	chrUn	96.875	32	1	0	2514	2545	304748271	304748302	1.000000e-03	54.7
11	TraesCS3D01G118800	chr5D	92.562	726	33	12	1509	2232	187522747	187523453	0.000000e+00	1022.0
12	TraesCS3D01G118800	chr5D	92.435	727	33	13	1509	2232	180244278	180244985	0.000000e+00	1018.0
13	TraesCS3D01G118800	chr4D	100.000	32	0	0	2511	2542	67186589	67186558	3.130000e-05	60.2
14	TraesCS3D01G118800	chr7D	94.286	35	2	0	2508	2542	610222483	610222517	1.000000e-03	54.7

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	TraesCS3D01G118800	chr3D	73393018	73395926	2908	False	5373	5373	100.000000	1	2909	1	chr3D.!!$F1	2908
1	TraesCS3D01G118800	chr3A	86372815	86376063	3248	False	1823	3306	90.108000	24	2909	2	chr3A.!!$F1	2885
2	TraesCS3D01G118800	chr3B	118758824	118761851	3027	False	1347	2966	92.270333	7	2909	3	chr3B.!!$F1	2902
3	TraesCS3D01G118800	chr2D	66076454	66077207	753	True	1136	1136	93.661000	1460	2230	1	chr2D.!!$R1	770
4	TraesCS3D01G118800	chrUn	105815339	105816044	705	False	1038	1038	92.975000	1509	2232	1	chrUn.!!$F1	723
5	TraesCS3D01G118800	chrUn	106336592	106337298	706	False	1038	1038	92.975000	1509	2232	1	chrUn.!!$F2	723
6	TraesCS3D01G118800	chr5D	187522747	187523453	706	False	1022	1022	92.562000	1509	2232	1	chr5D.!!$F2	723
7	TraesCS3D01G118800	chr5D	180244278	180244985	707	False	1018	1018	92.435000	1509	2232	1	chr5D.!!$F1	723

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
358	396	0.59531	GCTACGATCCTTCACTCCGC	60.595	60.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2288	2404	1.136305	CCTCCGTCCTAATTCTCGCAA	59.864	52.381	0.0	0.0	0.0	4.85	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
136	137	7.923461	ACTCTAGACTCTGGCTGTATATATCA	58.077	38.462	0.00	0.00	0.00	2.15
212	214	7.539712	TCACGTTCTCTTCATTTCCATTATC	57.460	36.000	0.00	0.00	0.00	1.75
213	215	6.538742	TCACGTTCTCTTCATTTCCATTATCC	59.461	38.462	0.00	0.00	0.00	2.59
243	247	0.780637	TGCATGGTCTTGGGGGTTTA	59.219	50.000	0.00	0.00	0.00	2.01
356	394	1.067821	CCAGCTACGATCCTTCACTCC	59.932	57.143	0.00	0.00	0.00	3.85
358	396	0.595310	GCTACGATCCTTCACTCCGC	60.595	60.000	0.00	0.00	0.00	5.54
385	423	4.395854	TGCAACGAGATATTCTGCAATTGT	59.604	37.500	7.40	0.00	0.00	2.71
386	424	4.966366	GCAACGAGATATTCTGCAATTGTC	59.034	41.667	7.40	0.07	0.00	3.18
389	427	4.504461	ACGAGATATTCTGCAATTGTCGTC	59.496	41.667	7.40	0.00	30.50	4.20
397	435	3.743911	TCTGCAATTGTCGTCGTGTTTAT	59.256	39.130	7.40	0.00	0.00	1.40
400	438	3.838550	GCAATTGTCGTCGTGTTTATCAC	59.161	43.478	7.40	0.00	43.03	3.06
440	481	5.774690	ACATGTAGGTGGTTGATGAAACATT	59.225	36.000	0.00	0.00	40.86	2.71
448	489	7.392113	AGGTGGTTGATGAAACATTAATACGAA	59.608	33.333	0.00	0.00	40.86	3.85
710	763	6.109320	ACGATTAAATTATTTCCGCGTGAA	57.891	33.333	4.92	5.58	0.00	3.18
713	766	7.795272	ACGATTAAATTATTTCCGCGTGAATAC	59.205	33.333	4.92	0.00	31.67	1.89
739	793	5.013391	TCGGTTTAATTTTCCAGGGTACTCT	59.987	40.000	0.00	0.00	0.00	3.24
770	824	8.945758	GCTATGTGCTGTTAGATGATTAATTG	57.054	34.615	0.00	0.00	38.95	2.32
971	1034	5.031066	TCCATCCTAACCCACGATAAAAG	57.969	43.478	0.00	0.00	0.00	2.27
972	1035	4.717778	TCCATCCTAACCCACGATAAAAGA	59.282	41.667	0.00	0.00	0.00	2.52
1092	1155	0.321564	TGATTCTTGCCACTGTCCGG	60.322	55.000	0.00	0.00	0.00	5.14
1553	1631	2.646719	GGTCGCCGTGTAGACACA	59.353	61.111	12.98	0.00	46.75	3.72
1611	1697	3.761657	ACCGTCGTTTCTTTTGTTTTCC	58.238	40.909	0.00	0.00	0.00	3.13
1709	1796	1.564348	CACCTGTAAATGGTAGCCCCT	59.436	52.381	0.00	0.00	35.80	4.79
1710	1797	1.844497	ACCTGTAAATGGTAGCCCCTC	59.156	52.381	0.00	0.00	35.80	4.30
1711	1798	1.202651	CCTGTAAATGGTAGCCCCTCG	60.203	57.143	0.00	0.00	0.00	4.63
1712	1799	1.760613	CTGTAAATGGTAGCCCCTCGA	59.239	52.381	0.00	0.00	0.00	4.04
1743	1830	5.163713	CCAATATCATGATCAGCATCTGCAG	60.164	44.000	12.53	7.63	45.16	4.41
1751	1838	2.443416	TCAGCATCTGCAGCAATCTTT	58.557	42.857	9.47	0.00	45.16	2.52
1837	1925	9.346005	TGTCTTGCAATGTTGAATCAGATATAT	57.654	29.630	0.00	0.00	0.00	0.86
1930	2027	4.396166	AGAATCCAAGTGCAAATCTTACCG	59.604	41.667	0.00	0.00	0.00	4.02
2075	2175	3.745799	TGTTTCTTGGTGATTAGGCGAA	58.254	40.909	0.00	0.00	0.00	4.70
2135	2235	4.524316	TCCTCATTTTTCAATGCACCAG	57.476	40.909	0.00	0.00	39.90	4.00
2147	2247	1.065600	GCACCAGACGCTTGCAAAA	59.934	52.632	0.00	0.00	36.22	2.44
2163	2263	3.198635	TGCAAAATTGACCACCAAAAGGA	59.801	39.130	0.00	0.00	38.43	3.36
2197	2299	3.735208	CGTGACAGCGAAATATCTGACCT	60.735	47.826	0.00	0.00	34.57	3.85
2360	2480	3.854809	CGACCTCATCTCTCTTTCGAAAC	59.145	47.826	6.47	0.00	0.00	2.78
2367	2487	3.147629	TCTCTCTTTCGAAACGGAGAGT	58.852	45.455	33.72	0.00	46.76	3.24
2370	2490	3.317149	TCTCTTTCGAAACGGAGAGTTCA	59.683	43.478	20.13	3.89	43.37	3.18
2383	2503	7.920639	AACGGAGAGTTCACAGTTAATCTGGA	61.921	42.308	9.05	2.87	42.92	3.86
2454	2581	3.751698	GGCTGTTCTTTTCGTAGGTTCAT	59.248	43.478	0.00	0.00	0.00	2.57
2501	2628	4.154015	TGTCTGTTTGCAAGTGGATTATCG	59.846	41.667	0.00	0.00	0.00	2.92
2579	2764	8.155510	AGTCTCTAAAACGAACCTAAAATTCCT	58.844	33.333	0.00	0.00	0.00	3.36
2580	2765	8.228464	GTCTCTAAAACGAACCTAAAATTCCTG	58.772	37.037	0.00	0.00	0.00	3.86
2589	2774	7.881232	ACGAACCTAAAATTCCTGAATCTAACA	59.119	33.333	0.00	0.00	0.00	2.41
2601	2786	7.685481	TCCTGAATCTAACAAATGGTTCTACA	58.315	34.615	0.00	0.00	40.96	2.74
2637	3117	1.135859	GCGGCGGATCATGAATTCATC	60.136	52.381	18.16	8.39	33.61	2.92
2664	3144	2.425668	CCAGTTCCGTTTGTTCCAAAGT	59.574	45.455	0.00	0.00	0.00	2.66
2689	3169	3.369546	TTTTCCTGTTTTAGCTGCTGC	57.630	42.857	13.43	7.62	40.05	5.25
2736	3217	7.608761	ACTTTTGTGACTAACTTTCTACACCAA	59.391	33.333	0.00	0.00	0.00	3.67
2739	3220	8.514330	TTGTGACTAACTTTCTACACCAATTT	57.486	30.769	0.00	0.00	0.00	1.82
2740	3221	8.514330	TGTGACTAACTTTCTACACCAATTTT	57.486	30.769	0.00	0.00	0.00	1.82
2785	3266	2.332063	ATCATTCGACAATTCCCGCT	57.668	45.000	0.00	0.00	0.00	5.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	9.014297	TGTTTATGTTTTCCCAACAAACAAATT	57.986	25.926	2.56	0.00	45.02	1.82
136	137	9.722056	GCAGAAGATATGTTTTGATACGATTTT	57.278	29.630	7.26	0.00	0.00	1.82
212	214	1.031571	ACCATGCATACAACTGGCGG	61.032	55.000	0.00	0.00	31.72	6.13
213	215	0.378257	GACCATGCATACAACTGGCG	59.622	55.000	0.00	0.00	31.72	5.69
243	247	7.582667	AAGCCAAGTGTGTCTTTACTATTTT	57.417	32.000	0.00	0.00	33.63	1.82
269	273	5.366829	TGTCAATCAATTCTTGCTGTCAG	57.633	39.130	0.00	0.00	0.00	3.51
461	502	1.969256	GCATTGCTAAACACAACGTCG	59.031	47.619	0.16	0.00	0.00	5.12
541	584	4.750098	CGCGGGGCTTATGATATAATTAGG	59.250	45.833	0.00	0.00	0.00	2.69
542	585	4.211374	GCGCGGGGCTTATGATATAATTAG	59.789	45.833	8.83	0.00	39.11	1.73
543	586	4.124238	GCGCGGGGCTTATGATATAATTA	58.876	43.478	8.83	0.00	39.11	1.40
544	587	2.943033	GCGCGGGGCTTATGATATAATT	59.057	45.455	8.83	0.00	39.11	1.40
554	601	2.360600	ATGTTTGCGCGGGGCTTA	60.361	55.556	18.19	3.60	44.05	3.09
710	763	6.250711	ACCCTGGAAAATTAAACCGAAGTAT	58.749	36.000	0.00	0.00	0.00	2.12
713	766	5.708697	AGTACCCTGGAAAATTAAACCGAAG	59.291	40.000	0.00	0.00	0.00	3.79
770	824	4.392921	TGAAGTGAGAATAGCTGGCTAC	57.607	45.455	4.33	0.00	0.00	3.58
811	865	2.596346	TGGCACCAACACATTTCTGAT	58.404	42.857	0.00	0.00	0.00	2.90
979	1042	2.123468	GGTGGCAGGTGGGTGTTT	60.123	61.111	0.00	0.00	0.00	2.83
990	1053	2.611800	ATGGGCAGAGAGGTGGCA	60.612	61.111	0.00	0.00	44.72	4.92
1067	1130	3.152341	ACAGTGGCAAGAATCAAGAAGG	58.848	45.455	0.00	0.00	0.00	3.46
1611	1697	6.256757	AGACGAGAAAACAAGAAACAGAGAAG	59.743	38.462	0.00	0.00	0.00	2.85
1709	1796	6.949715	TGATCATGATATTGGGATTGATCGA	58.050	36.000	8.54	0.00	41.34	3.59
1710	1797	6.238402	GCTGATCATGATATTGGGATTGATCG	60.238	42.308	8.54	0.00	41.34	3.69
1711	1798	6.602009	TGCTGATCATGATATTGGGATTGATC	59.398	38.462	8.54	0.00	39.75	2.92
1712	1799	6.490492	TGCTGATCATGATATTGGGATTGAT	58.510	36.000	8.54	0.00	0.00	2.57
1743	1830	4.051237	GGGGCAAAATCGATAAAGATTGC	58.949	43.478	17.35	17.35	40.39	3.56
1751	1838	3.094484	AGGTTTGGGGCAAAATCGATA	57.906	42.857	0.00	0.00	35.03	2.92
1856	1944	5.941788	AGATGTTGGAAGTTGGAACTAAGT	58.058	37.500	0.00	0.00	38.57	2.24
1930	2027	8.478066	AGAGCATAAAAGGGATAAACATTTTCC	58.522	33.333	0.00	0.00	0.00	3.13
2020	2120	6.240549	AGCTAGGTTATCTGCACTTTACAT	57.759	37.500	0.00	0.00	0.00	2.29
2075	2175	2.029288	CTTCACATGTGCGGACGCT	61.029	57.895	21.38	0.00	42.51	5.07
2119	2219	2.297033	AGCGTCTGGTGCATTGAAAAAT	59.703	40.909	0.00	0.00	33.85	1.82
2135	2235	1.786579	GTGGTCAATTTTGCAAGCGTC	59.213	47.619	0.00	0.00	0.00	5.19
2147	2247	4.653341	TGTGAAATCCTTTTGGTGGTCAAT	59.347	37.500	0.00	0.00	41.38	2.57
2197	2299	7.384439	TGTTGTGTGTGAATTTTCTGTAGAA	57.616	32.000	0.00	0.00	0.00	2.10
2288	2404	1.136305	CCTCCGTCCTAATTCTCGCAA	59.864	52.381	0.00	0.00	0.00	4.85
2291	2407	2.029828	CCATCCTCCGTCCTAATTCTCG	60.030	54.545	0.00	0.00	0.00	4.04
2293	2409	2.330216	CCCATCCTCCGTCCTAATTCT	58.670	52.381	0.00	0.00	0.00	2.40
2360	2480	4.082190	TCCAGATTAACTGTGAACTCTCCG	60.082	45.833	0.00	0.00	44.40	4.63
2367	2487	8.717821	CGTTTAAAGATCCAGATTAACTGTGAA	58.282	33.333	0.00	0.00	44.40	3.18
2370	2490	8.842358	TTCGTTTAAAGATCCAGATTAACTGT	57.158	30.769	0.00	0.00	44.40	3.55
2383	2503	6.431234	ACAAGATTGCCTCTTCGTTTAAAGAT	59.569	34.615	0.00	0.00	42.48	2.40
2454	2581	2.779755	ATATCACGGTGCCAAAGTGA	57.220	45.000	2.51	6.05	46.99	3.41
2483	2610	4.419522	ACACGATAATCCACTTGCAAAC	57.580	40.909	0.00	0.00	0.00	2.93
2531	2716	8.211629	AGACTTAACACAGGTCTCTAAAACATT	58.788	33.333	0.00	0.00	35.72	2.71
2579	2764	7.119699	CAGCTGTAGAACCATTTGTTAGATTCA	59.880	37.037	5.25	0.00	37.29	2.57
2580	2765	7.467623	CAGCTGTAGAACCATTTGTTAGATTC	58.532	38.462	5.25	0.00	37.29	2.52
2589	2774	4.322198	CCAAATGCAGCTGTAGAACCATTT	60.322	41.667	16.64	16.86	34.35	2.32
2601	2786	1.308069	CCGCAGTACCAAATGCAGCT	61.308	55.000	5.76	0.00	42.68	4.24
2637	3117	4.457603	TGGAACAAACGGAACTGGATTATG	59.542	41.667	0.00	0.00	31.92	1.90
2689	3169	6.566197	AGTAGACAAAAATGGAAGAGCAAG	57.434	37.500	0.00	0.00	0.00	4.01
2763	3244	3.443681	AGCGGGAATTGTCGAATGATTTT	59.556	39.130	0.00	0.00	0.00	1.82
2792	3273	6.578919	GGTTGTTGTCGAATGATTTCTTCTTC	59.421	38.462	0.00	0.00	0.00	2.87
2795	3276	4.846137	CGGTTGTTGTCGAATGATTTCTTC	59.154	41.667	0.00	0.00	0.00	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.