AutoCloner

Multiple sequence alignment - TraesCS2D01G364200

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	TraesCS2D01G364200	chr2D	100.000	4523	0	0	1	4523	469983040	469987562	0.000000e+00	8353
1	TraesCS2D01G364200	chr2D	88.806	2823	276	27	814	3617	599926241	599929042	0.000000e+00	3426
2	TraesCS2D01G364200	chr2B	96.788	2366	70	5	489	2849	548608998	548611362	0.000000e+00	3943
3	TraesCS2D01G364200	chr2B	88.186	2844	291	27	796	3617	729766393	729769213	0.000000e+00	3349
4	TraesCS2D01G364200	chr2B	97.273	1687	45	1	2837	4523	548619285	548620970	0.000000e+00	2859
5	TraesCS2D01G364200	chr2B	84.153	2644	342	38	939	3535	548623930	548626543	0.000000e+00	2490
6	TraesCS2D01G364200	chr2B	85.614	285	20	6	166	429	548608685	548608969	3.450000e-71	279
7	TraesCS2D01G364200	chr2B	89.655	174	16	2	3	175	548608491	548608663	2.120000e-53	220
8	TraesCS2D01G364200	chr2A	95.382	2317	74	6	166	2470	611295334	611297629	0.000000e+00	3655
9	TraesCS2D01G364200	chr2A	96.849	2063	62	3	2461	4523	611297823	611299882	0.000000e+00	3446
10	TraesCS2D01G364200	chr2A	88.877	2823	281	20	815	3617	733628714	733631523	0.000000e+00	3443
11	TraesCS2D01G364200	chr2A	97.143	175	5	0	1	175	611295138	611295312	3.420000e-76	296
12	TraesCS2D01G364200	chr1D	84.559	2720	326	59	985	3655	407672559	407669885	0.000000e+00	2610
13	TraesCS2D01G364200	chr1D	83.900	2733	364	40	935	3625	6714673	6711975	0.000000e+00	2540
14	TraesCS2D01G364200	chr1D	82.555	2740	384	52	951	3638	6913119	6915816	0.000000e+00	2326
15	TraesCS2D01G364200	chr1D	82.586	2676	356	52	920	3539	6898375	6900996	0.000000e+00	2259
16	TraesCS2D01G364200	chr1A	83.351	2757	384	44	939	3652	8144561	8141837	0.000000e+00	2479
17	TraesCS2D01G364200	chr1A	83.464	2679	353	48	900	3528	8331858	8334496	0.000000e+00	2410
18	TraesCS2D01G364200	chr1A	83.315	2667	358	59	999	3621	7834683	7837306	0.000000e+00	2379
19	TraesCS2D01G364200	chr1B	77.030	862	126	35	920	1744	9281195	9282021	3.230000e-116	429

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	TraesCS2D01G364200	chr2D	469983040	469987562	4522	False	8353.000000	8353	100.000000	1	4523	1	chr2D.!!$F1	4522
1	TraesCS2D01G364200	chr2D	599926241	599929042	2801	False	3426.000000	3426	88.806000	814	3617	1	chr2D.!!$F2	2803
2	TraesCS2D01G364200	chr2B	729766393	729769213	2820	False	3349.000000	3349	88.186000	796	3617	1	chr2B.!!$F1	2821
3	TraesCS2D01G364200	chr2B	548619285	548626543	7258	False	2674.500000	2859	90.713000	939	4523	2	chr2B.!!$F3	3584
4	TraesCS2D01G364200	chr2B	548608491	548611362	2871	False	1480.666667	3943	90.685667	3	2849	3	chr2B.!!$F2	2846
5	TraesCS2D01G364200	chr2A	733628714	733631523	2809	False	3443.000000	3443	88.877000	815	3617	1	chr2A.!!$F1	2802
6	TraesCS2D01G364200	chr2A	611295138	611299882	4744	False	2465.666667	3655	96.458000	1	4523	3	chr2A.!!$F2	4522
7	TraesCS2D01G364200	chr1D	407669885	407672559	2674	True	2610.000000	2610	84.559000	985	3655	1	chr1D.!!$R2	2670
8	TraesCS2D01G364200	chr1D	6711975	6714673	2698	True	2540.000000	2540	83.900000	935	3625	1	chr1D.!!$R1	2690
9	TraesCS2D01G364200	chr1D	6913119	6915816	2697	False	2326.000000	2326	82.555000	951	3638	1	chr1D.!!$F2	2687
10	TraesCS2D01G364200	chr1D	6898375	6900996	2621	False	2259.000000	2259	82.586000	920	3539	1	chr1D.!!$F1	2619
11	TraesCS2D01G364200	chr1A	8141837	8144561	2724	True	2479.000000	2479	83.351000	939	3652	1	chr1A.!!$R1	2713
12	TraesCS2D01G364200	chr1A	8331858	8334496	2638	False	2410.000000	2410	83.464000	900	3528	1	chr1A.!!$F2	2628
13	TraesCS2D01G364200	chr1A	7834683	7837306	2623	False	2379.000000	2379	83.315000	999	3621	1	chr1A.!!$F1	2622
14	TraesCS2D01G364200	chr1B	9281195	9282021	826	False	429.000000	429	77.030000	920	1744	1	chr1B.!!$F1	824

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
672	728	0.247736	AAGTGGCTCCAGTCGATCAC	59.752	55.000	0.00	0.00	0.00	3.06	F
916	994	2.497138	CTCCATGCTTGTTCACACTCA	58.503	47.619	0.00	0.00	0.00	3.41	F
1704	5485	2.365582	CCCTTGGTAGTGTATTGGCAC	58.634	52.381	0.00	0.00	39.51	5.01	F
2454	6240	0.250038	GAGTGGTCACTGCTGCAAGA	60.250	55.000	8.49	1.76	42.66	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1704	5485	1.753073	GATGTTTTGGAGGATGCCCAG	59.247	52.381	0.00	0.00	34.77	4.45	R
2099	5883	2.033492	GTGTTGCAGTGTAACGGTGTAC	60.033	50.000	17.65	7.51	45.86	2.90	R
2923	6927	1.351017	CAACCCTCTGGCAACTCCTAA	59.649	52.381	0.00	0.00	35.26	2.69	R
4228	8250	1.135575	CATCTGCGGTTGCTTTCTTCC	60.136	52.381	0.00	0.00	43.34	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
192	225	2.179517	CTGCCGAGTCTCCGTCAC	59.820	66.667	0.00	0.00	0.00	3.67
210	243	0.322187	ACGCGGGCTCCATTTACTTT	60.322	50.000	12.47	0.00	0.00	2.66
220	260	4.879545	GCTCCATTTACTTTCATTCCGGTA	59.120	41.667	0.00	0.00	0.00	4.02
252	292	3.154473	CGGCCTCCCTGATTCGGA	61.154	66.667	0.00	0.00	0.00	4.55
345	397	5.354842	AAACTACCCAGGCTCTTACATAC	57.645	43.478	0.00	0.00	0.00	2.39
348	400	1.838077	ACCCAGGCTCTTACATACCAC	59.162	52.381	0.00	0.00	0.00	4.16
388	443	8.740906	AGACTGTCGATTGTTATTTCTTCTCTA	58.259	33.333	1.52	0.00	0.00	2.43
436	491	8.711457	GTTTATTATTTGCTGCTTCATGTGTTT	58.289	29.630	0.00	0.00	0.00	2.83
467	522	8.370940	TCTTCCTATTCTGCCAATATACAAGAG	58.629	37.037	0.00	0.00	0.00	2.85
470	525	7.038729	TCCTATTCTGCCAATATACAAGAGGAG	60.039	40.741	0.00	0.00	0.00	3.69
471	526	4.963318	TCTGCCAATATACAAGAGGAGG	57.037	45.455	0.00	0.00	0.00	4.30
475	530	3.406764	CCAATATACAAGAGGAGGCAGC	58.593	50.000	0.00	0.00	0.00	5.25
479	534	2.478872	TACAAGAGGAGGCAGCCTAT	57.521	50.000	16.16	6.06	38.73	2.57
480	535	1.589414	ACAAGAGGAGGCAGCCTATT	58.411	50.000	16.16	5.22	39.94	1.73
481	536	1.488393	ACAAGAGGAGGCAGCCTATTC	59.512	52.381	16.16	15.04	37.38	1.75
482	537	1.767681	CAAGAGGAGGCAGCCTATTCT	59.232	52.381	16.16	17.18	37.38	2.40
487	542	4.102367	AGAGGAGGCAGCCTATTCTTTTAG	59.898	45.833	16.16	0.00	38.73	1.85
489	544	4.662650	AGGAGGCAGCCTATTCTTTTAGAT	59.337	41.667	16.16	0.00	36.22	1.98
490	545	5.846714	AGGAGGCAGCCTATTCTTTTAGATA	59.153	40.000	16.16	0.00	36.22	1.98
492	547	7.680310	AGGAGGCAGCCTATTCTTTTAGATATA	59.320	37.037	16.16	0.00	36.22	0.86
493	548	8.490311	GGAGGCAGCCTATTCTTTTAGATATAT	58.510	37.037	16.16	0.00	31.76	0.86
518	573	6.363577	TCGATGTATGCTTCATTTCCTTTC	57.636	37.500	0.00	0.00	0.00	2.62
575	630	3.330267	CCTGCAGTTAGGTTTCTGAGTC	58.670	50.000	13.81	0.00	34.02	3.36
672	728	0.247736	AAGTGGCTCCAGTCGATCAC	59.752	55.000	0.00	0.00	0.00	3.06
718	774	2.693762	CCTTGGTGTGCCTCATGCG	61.694	63.158	0.00	0.00	45.60	4.73
916	994	2.497138	CTCCATGCTTGTTCACACTCA	58.503	47.619	0.00	0.00	0.00	3.41
930	1009	3.055602	TCACACTCATGTCCTCTTCCATG	60.056	47.826	0.00	0.00	36.72	3.66
942	1022	7.952671	TGTCCTCTTCCATGTTATCTGTATAC	58.047	38.462	0.00	0.00	0.00	1.47
956	4664	6.875972	ATCTGTATACACACCCTCTTCTTT	57.124	37.500	0.08	0.00	0.00	2.52
1385	5154	3.131396	CTGTAGTTTGGTCCACTCACAC	58.869	50.000	0.00	0.00	0.00	3.82
1704	5485	2.365582	CCCTTGGTAGTGTATTGGCAC	58.634	52.381	0.00	0.00	39.51	5.01
2099	5883	3.204526	GAACAGGAGGATGCATCAGAAG	58.795	50.000	27.25	14.78	0.00	2.85
2340	6124	6.543465	TGCTTAGTGTAAATCTGAATGATGGG	59.457	38.462	0.00	0.00	35.21	4.00
2384	6168	1.071699	TCTTTACCTTCGCCTTGCTGT	59.928	47.619	0.00	0.00	0.00	4.40
2454	6240	0.250038	GAGTGGTCACTGCTGCAAGA	60.250	55.000	8.49	1.76	42.66	3.02
2643	6644	1.133606	GGAGGAGGTGGTTTTGGTTCA	60.134	52.381	0.00	0.00	0.00	3.18
2669	6670	4.772886	ACAAGGGAGTGTTAAGTGACTT	57.227	40.909	2.37	2.37	0.00	3.01
2850	6854	5.473504	ACACATGTTAAATGGGTCTCTTGAC	59.526	40.000	0.00	0.00	42.22	3.18
2923	6927	5.604231	TGGAACAGCAGATATCAGATAACCT	59.396	40.000	5.32	0.00	0.00	3.50
3093	7097	6.073927	GGGATTTTAGCCGAATTCTAACTACG	60.074	42.308	3.52	0.00	0.00	3.51
3148	7152	1.940613	GGCTTACCGGAGTTGCTATTG	59.059	52.381	9.46	0.00	0.00	1.90
3193	7197	3.138798	GCATGGTGCTGCTGGAGG	61.139	66.667	0.00	0.00	40.96	4.30
3308	7324	1.476471	GCTTCATGGGGGAGATGTGAG	60.476	57.143	0.00	0.00	0.00	3.51
3429	7445	1.810030	GCCGACGATGGGTGAAGTC	60.810	63.158	0.00	0.00	0.00	3.01
3673	7695	2.935849	CAGTGCCGTATGTAATCAAGCA	59.064	45.455	0.00	0.00	0.00	3.91
3833	7855	1.211457	GGTCATCCCTCATGCTCACTT	59.789	52.381	0.00	0.00	31.70	3.16
3843	7865	2.156917	CATGCTCACTTGATGGTGTGT	58.843	47.619	0.00	0.00	38.28	3.72
3855	7877	1.942677	TGGTGTGTTGTTCTGGTACG	58.057	50.000	0.00	0.00	0.00	3.67
3871	7893	2.162338	TACGAAACCGAGTGGCCTGG	62.162	60.000	3.32	3.04	39.70	4.45
3895	7917	1.206578	CACCTGCGCGACGAAATTT	59.793	52.632	12.10	0.00	0.00	1.82
4010	8032	7.386848	ACGGTATGTAATATGTTGACTATTGCC	59.613	37.037	0.00	0.00	0.00	4.52
4025	8047	7.334858	TGACTATTGCCACATATAAACTCACA	58.665	34.615	0.00	0.00	0.00	3.58
4048	8070	6.656693	ACATAATGTCTGCTAAACTTTCTGCT	59.343	34.615	0.00	0.00	0.00	4.24
4058	8080	3.550437	AACTTTCTGCTATCGCCATCT	57.450	42.857	0.00	0.00	34.43	2.90
4090	8112	7.178983	TGAGGATATGATTGCCTTTTGAGTTTT	59.821	33.333	0.00	0.00	30.70	2.43
4228	8250	3.392616	AGGCTATTACATTCAGTCCCCTG	59.607	47.826	0.00	0.00	40.25	4.45
4231	8253	4.141482	GCTATTACATTCAGTCCCCTGGAA	60.141	45.833	0.00	0.00	39.31	3.53
4324	8346	4.998671	TGGTGACAAAGCAATGAAGAAA	57.001	36.364	0.00	0.00	37.44	2.52
4360	8382	4.382147	GGACAACACCTTTGGTTTTAAGCA	60.382	41.667	0.00	0.00	31.02	3.91
4381	8403	7.148355	AGCATCCTAAATTTTGCAAATTTGG	57.852	32.000	19.47	14.88	37.56	3.28
4395	8417	5.250313	TGCAAATTTGGTAAAGATTCCCCAT	59.750	36.000	19.47	0.00	0.00	4.00
4401	8423	3.011144	TGGTAAAGATTCCCCATCAGCAA	59.989	43.478	0.00	0.00	33.75	3.91
4408	8430	1.619654	TCCCCATCAGCAACAAACAG	58.380	50.000	0.00	0.00	0.00	3.16
4432	8454	1.730501	TTCTCTTCTGATTGCCGCAG	58.269	50.000	0.00	0.00	34.71	5.18
4482	8504	9.037737	GCAAATGTTTTGATGAATATATGTGCT	57.962	29.630	4.24	0.00	0.00	4.40
4498	8520	2.166007	GTGCTGCGTTTAGTATTTGCG	58.834	47.619	0.00	0.00	0.00	4.85
4499	8521	1.180166	GCTGCGTTTAGTATTTGCGC	58.820	50.000	0.00	0.00	47.00	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
178	211	4.813526	CGCGTGACGGAGACTCGG	62.814	72.222	7.25	8.39	39.23	4.63
192	225	0.377203	GAAAGTAAATGGAGCCCGCG	59.623	55.000	0.00	0.00	0.00	6.46
252	292	3.693085	CAGCCATTGTTCAGCTTGTAGAT	59.307	43.478	0.00	0.00	33.70	1.98
345	397	2.834549	AGTCTGATGTAGAACAGGGTGG	59.165	50.000	0.00	0.00	37.12	4.61
348	400	3.428180	CGACAGTCTGATGTAGAACAGGG	60.428	52.174	6.91	0.00	37.12	4.45
418	473	2.429971	TGGAAACACATGAAGCAGCAAA	59.570	40.909	0.00	0.00	33.40	3.68
436	491	4.860802	TTGGCAGAATAGGAAGAATGGA	57.139	40.909	0.00	0.00	0.00	3.41
467	522	4.423625	TCTAAAAGAATAGGCTGCCTCC	57.576	45.455	27.16	15.44	34.61	4.30
490	545	9.896645	AAGGAAATGAAGCATACATCGATATAT	57.103	29.630	0.00	0.00	0.00	0.86
492	547	8.627208	AAAGGAAATGAAGCATACATCGATAT	57.373	30.769	0.00	0.00	0.00	1.63
493	548	7.173218	GGAAAGGAAATGAAGCATACATCGATA	59.827	37.037	0.00	0.00	0.00	2.92
518	573	1.928868	AGCATTTCCAAGTTCAGGGG	58.071	50.000	0.00	0.00	0.00	4.79
575	630	0.514691	GTGCAGAAGGTCAGAAAGCG	59.485	55.000	0.00	0.00	0.00	4.68
672	728	3.877559	TCCAATGAAGCATCCACTACAG	58.122	45.455	0.00	0.00	0.00	2.74
718	774	3.207547	GAAAACCGTGTGCTGCCCC	62.208	63.158	0.00	0.00	0.00	5.80
916	994	5.965033	ACAGATAACATGGAAGAGGACAT	57.035	39.130	0.00	0.00	0.00	3.06
930	1009	7.349412	AGAAGAGGGTGTGTATACAGATAAC	57.651	40.000	5.62	2.87	37.52	1.89
942	1022	3.071602	TGGAGAAGAAAGAAGAGGGTGTG	59.928	47.826	0.00	0.00	0.00	3.82
956	4664	3.771479	TCTGCTCTGCTATTTGGAGAAGA	59.229	43.478	0.00	0.00	42.56	2.87
1184	4917	1.697432	TGGTGTTCTGGGACTTACTGG	59.303	52.381	0.00	0.00	0.00	4.00
1333	5084	4.135747	TCACGATGACAAGATTGCCATA	57.864	40.909	0.00	0.00	31.20	2.74
1365	5134	2.769663	AGTGTGAGTGGACCAAACTACA	59.230	45.455	0.00	0.00	30.73	2.74
1385	5154	6.403636	GCTGGTTTGTGTCCTATTATTGACAG	60.404	42.308	0.00	0.00	41.82	3.51
1704	5485	1.753073	GATGTTTTGGAGGATGCCCAG	59.247	52.381	0.00	0.00	34.77	4.45
2099	5883	2.033492	GTGTTGCAGTGTAACGGTGTAC	60.033	50.000	17.65	7.51	45.86	2.90
2384	6168	4.121317	CAAACTTGGCAGCAAATCTTTGA	58.879	39.130	6.84	0.00	40.55	2.69
2454	6240	7.996066	AGCATTAGTAACCCAAAACCAAAAATT	59.004	29.630	0.00	0.00	0.00	1.82
2643	6644	6.724905	AGTCACTTAACACTCCCTTGTATACT	59.275	38.462	4.17	0.00	0.00	2.12
2669	6670	7.545965	GCTTTTTCACTGCTATAGTAGTCTTCA	59.454	37.037	19.34	3.46	38.95	3.02
2850	6854	7.721286	ATTGCTCTTCTTAAATAGATGACCG	57.279	36.000	0.00	0.00	34.41	4.79
2923	6927	1.351017	CAACCCTCTGGCAACTCCTAA	59.649	52.381	0.00	0.00	35.26	2.69
3148	7152	4.165779	CCATAAACATCAACTTTCGGTGC	58.834	43.478	0.00	0.00	0.00	5.01
3193	7197	6.052360	GTGAATTCCTCCTTCCTGATAAGAC	58.948	44.000	2.27	0.00	0.00	3.01
3254	7270	4.678509	TGCACCGAGAAATATTCAACAC	57.321	40.909	0.00	0.00	0.00	3.32
3429	7445	3.823330	CCCTCGAGAACCCGGACG	61.823	72.222	15.71	0.43	0.00	4.79
3652	7674	2.935849	TGCTTGATTACATACGGCACTG	59.064	45.455	0.00	0.00	0.00	3.66
3673	7695	5.203528	AGGTCTGCCATATTTTGCTACAAT	58.796	37.500	0.00	0.00	37.19	2.71
3684	7706	7.321717	ACACATATTTCTAGGTCTGCCATAT	57.678	36.000	0.00	0.00	37.19	1.78
3833	7855	2.727123	ACCAGAACAACACACCATCA	57.273	45.000	0.00	0.00	0.00	3.07
3855	7877	3.056328	GCCAGGCCACTCGGTTTC	61.056	66.667	5.01	0.00	33.28	2.78
3889	7911	1.153765	GGAGCCTGCCGCAAATTTC	60.154	57.895	0.00	0.00	41.38	2.17
4010	8032	9.049523	AGCAGACATTATGTGAGTTTATATGTG	57.950	33.333	1.24	0.00	0.00	3.21
4025	8047	8.970859	ATAGCAGAAAGTTTAGCAGACATTAT	57.029	30.769	13.20	1.52	0.00	1.28
4048	8070	3.566351	TCCTCAAGAGAAGATGGCGATA	58.434	45.455	0.00	0.00	0.00	2.92
4058	8080	5.901413	AGGCAATCATATCCTCAAGAGAA	57.099	39.130	0.00	0.00	0.00	2.87
4130	8152	9.209048	ACATTCCTTGTCTTACATAGTATGGTA	57.791	33.333	14.59	2.39	30.89	3.25
4228	8250	1.135575	CATCTGCGGTTGCTTTCTTCC	60.136	52.381	0.00	0.00	43.34	3.46
4231	8253	1.160137	GTCATCTGCGGTTGCTTTCT	58.840	50.000	0.00	0.00	43.34	2.52
4274	8296	4.937620	TGAATGTCACTTGTTATGCTCTCC	59.062	41.667	0.00	0.00	0.00	3.71
4324	8346	2.567615	GTGTTGTCCAGTAGGAGGATGT	59.432	50.000	0.00	0.00	46.92	3.06
4381	8403	4.016444	TGTTGCTGATGGGGAATCTTTAC	58.984	43.478	0.00	0.00	36.15	2.01
4408	8430	2.159599	CGGCAATCAGAAGAGAAACAGC	60.160	50.000	0.00	0.00	0.00	4.40
4498	8520	2.048444	TCATGCTCCTTTCCAGATGC	57.952	50.000	0.00	0.00	0.00	3.91
4499	8521	2.358267	GCTTCATGCTCCTTTCCAGATG	59.642	50.000	0.00	0.00	38.95	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.