AutoCloner

Multiple sequence alignment - TraesCS2A01G547200

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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	TraesCS2A01G547200	chr2A	100.000	3530	0	0	1	3530	755478557	755482086	0.000000e+00	6519
1	TraesCS2A01G547200	chr2A	98.556	277	4	0	3193	3469	444312972	444312696	1.140000e-134	490
2	TraesCS2A01G547200	chr7B	98.962	3469	35	1	1	3469	742950729	742947262	0.000000e+00	6205
3	TraesCS2A01G547200	chr7B	98.645	3469	46	1	1	3469	716782616	716786083	0.000000e+00	6144
4	TraesCS2A01G547200	chr7A	98.905	3469	37	1	1	3469	60170758	60167291	0.000000e+00	6194
5	TraesCS2A01G547200	chr7A	98.907	3295	33	3	175	3469	60083121	60086412	0.000000e+00	5882
6	TraesCS2A01G547200	chr5A	98.732	3469	42	2	1	3469	420183712	420187178	0.000000e+00	6161
7	TraesCS2A01G547200	chr5A	98.950	3428	35	1	42	3469	16542604	16546030	0.000000e+00	6130
8	TraesCS2A01G547200	chr6B	97.579	3469	81	3	1	3469	388289027	388285562	0.000000e+00	5938
9	TraesCS2A01G547200	chr6B	97.059	68	2	0	3463	3530	264947062	264946995	8.010000e-22	115
10	TraesCS2A01G547200	chr6B	97.059	68	2	0	3463	3530	596602050	596601983	8.010000e-22	115
11	TraesCS2A01G547200	chr6B	97.059	68	2	0	3463	3530	715991263	715991196	8.010000e-22	115
12	TraesCS2A01G547200	chr4D	98.667	3300	41	3	1	3299	123348131	123351428	0.000000e+00	5847
13	TraesCS2A01G547200	chr4D	97.059	68	2	0	3463	3530	123401327	123401394	8.010000e-22	115
14	TraesCS2A01G547200	chr2D	96.570	3469	103	12	1	3469	291771629	291775081	0.000000e+00	5733
15	TraesCS2A01G547200	chrUn	97.059	68	2	0	3463	3530	432742162	432742229	8.010000e-22	115
16	TraesCS2A01G547200	chr7D	97.059	68	2	0	3463	3530	382089607	382089674	8.010000e-22	115
17	TraesCS2A01G547200	chr5B	97.059	68	2	0	3463	3530	169062607	169062674	8.010000e-22	115
18	TraesCS2A01G547200	chr1D	97.059	68	2	0	3463	3530	212444897	212444830	8.010000e-22	115
19	TraesCS2A01G547200	chr1A	97.059	68	2	0	3463	3530	94664133	94664066	8.010000e-22	115

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	TraesCS2A01G547200	chr2A	755478557	755482086	3529	False	6519	6519	100.000	1	3530	1	chr2A.!!$F1	3529
1	TraesCS2A01G547200	chr7B	742947262	742950729	3467	True	6205	6205	98.962	1	3469	1	chr7B.!!$R1	3468
2	TraesCS2A01G547200	chr7B	716782616	716786083	3467	False	6144	6144	98.645	1	3469	1	chr7B.!!$F1	3468
3	TraesCS2A01G547200	chr7A	60167291	60170758	3467	True	6194	6194	98.905	1	3469	1	chr7A.!!$R1	3468
4	TraesCS2A01G547200	chr7A	60083121	60086412	3291	False	5882	5882	98.907	175	3469	1	chr7A.!!$F1	3294
5	TraesCS2A01G547200	chr5A	420183712	420187178	3466	False	6161	6161	98.732	1	3469	1	chr5A.!!$F2	3468
6	TraesCS2A01G547200	chr5A	16542604	16546030	3426	False	6130	6130	98.950	42	3469	1	chr5A.!!$F1	3427
7	TraesCS2A01G547200	chr6B	388285562	388289027	3465	True	5938	5938	97.579	1	3469	1	chr6B.!!$R2	3468
8	TraesCS2A01G547200	chr4D	123348131	123351428	3297	False	5847	5847	98.667	1	3299	1	chr4D.!!$F1	3298
9	TraesCS2A01G547200	chr2D	291771629	291775081	3452	False	5733	5733	96.570	1	3469	1	chr2D.!!$F1	3468

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
1103	1106	1.096416	GAGATCGGTCGAGTGGTCTT	58.904	55.0	1.45	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2740	2743	0.187851	ATAGGTAGGGGGTCCGTCAG	59.812	60.0	0.0	0.0	38.33	3.51	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
1103	1106	1.096416	GAGATCGGTCGAGTGGTCTT	58.904	55.000	1.45	0.00	0.00	3.01
1384	1387	2.367772	CTCTAAGCGATCACGAACGAG	58.632	52.381	0.50	0.00	42.66	4.18
1427	1430	5.596772	CCCCAGGGATTATTGAACGTAAATT	59.403	40.000	7.25	0.00	37.50	1.82
2025	2028	2.241685	AGACGTATCGGCCTATATCCCT	59.758	50.000	0.00	0.00	34.11	4.20
2585	2588	1.349357	AGGAAGAAGGCTTTTCTCGCT	59.651	47.619	0.00	0.00	33.61	4.93
2697	2700	3.589542	CCCAGCCACAAGGGGGAA	61.590	66.667	0.00	0.00	41.58	3.97
2728	2731	0.996583	GTTCAGGATACCCCACCCAA	59.003	55.000	0.00	0.00	37.41	4.12
2805	2808	9.293404	CTATACCTGATGATTTTCAATCCACAT	57.707	33.333	0.00	0.00	0.00	3.21
3118	3122	1.066002	CGCGAAATCCATCATTGGCTT	59.934	47.619	0.00	0.00	43.29	4.35
3413	3417	4.819105	TTATTTCTGTGTCCTCATCCGT	57.181	40.909	0.00	0.00	0.00	4.69
3469	3473	5.396101	GCCTTACTTTACTAACAGGTAGGGG	60.396	48.000	0.00	0.00	33.68	4.79
3470	3474	5.960202	CCTTACTTTACTAACAGGTAGGGGA	59.040	44.000	0.00	0.00	33.68	4.81
3471	3475	6.097981	CCTTACTTTACTAACAGGTAGGGGAG	59.902	46.154	0.00	0.00	33.68	4.30
3472	3476	5.280998	ACTTTACTAACAGGTAGGGGAGA	57.719	43.478	0.00	0.00	33.68	3.71
3473	3477	5.658474	ACTTTACTAACAGGTAGGGGAGAA	58.342	41.667	0.00	0.00	33.68	2.87
3474	3478	5.720520	ACTTTACTAACAGGTAGGGGAGAAG	59.279	44.000	0.00	0.00	33.68	2.85
3475	3479	2.468915	ACTAACAGGTAGGGGAGAAGC	58.531	52.381	0.00	0.00	33.68	3.86
3476	3480	2.225547	ACTAACAGGTAGGGGAGAAGCA	60.226	50.000	0.00	0.00	33.68	3.91
3477	3481	1.742308	AACAGGTAGGGGAGAAGCAA	58.258	50.000	0.00	0.00	0.00	3.91
3478	3482	1.280457	ACAGGTAGGGGAGAAGCAAG	58.720	55.000	0.00	0.00	0.00	4.01
3479	3483	0.107459	CAGGTAGGGGAGAAGCAAGC	60.107	60.000	0.00	0.00	0.00	4.01
3480	3484	1.224870	GGTAGGGGAGAAGCAAGCC	59.775	63.158	0.00	0.00	0.00	4.35
3481	3485	1.153349	GTAGGGGAGAAGCAAGCCG	60.153	63.158	0.00	0.00	0.00	5.52
3482	3486	1.305802	TAGGGGAGAAGCAAGCCGA	60.306	57.895	0.00	0.00	0.00	5.54
3483	3487	0.907704	TAGGGGAGAAGCAAGCCGAA	60.908	55.000	0.00	0.00	0.00	4.30
3484	3488	2.041115	GGGGAGAAGCAAGCCGAAC	61.041	63.158	0.00	0.00	0.00	3.95
3485	3489	2.041115	GGGAGAAGCAAGCCGAACC	61.041	63.158	0.00	0.00	0.00	3.62
3486	3490	1.003233	GGAGAAGCAAGCCGAACCT	60.003	57.895	0.00	0.00	0.00	3.50
3487	3491	1.021920	GGAGAAGCAAGCCGAACCTC	61.022	60.000	0.00	0.00	0.00	3.85
3488	3492	0.036858	GAGAAGCAAGCCGAACCTCT	60.037	55.000	0.00	0.00	0.00	3.69
3489	3493	0.321122	AGAAGCAAGCCGAACCTCTG	60.321	55.000	0.00	0.00	0.00	3.35
3490	3494	0.320771	GAAGCAAGCCGAACCTCTGA	60.321	55.000	0.00	0.00	0.00	3.27
3491	3495	0.326264	AAGCAAGCCGAACCTCTGAT	59.674	50.000	0.00	0.00	0.00	2.90
3492	3496	0.107945	AGCAAGCCGAACCTCTGATC	60.108	55.000	0.00	0.00	0.00	2.92
3493	3497	1.424493	GCAAGCCGAACCTCTGATCG	61.424	60.000	0.00	0.00	38.74	3.69
3494	3498	0.173481	CAAGCCGAACCTCTGATCGA	59.827	55.000	1.01	0.00	41.43	3.59
3495	3499	0.173708	AAGCCGAACCTCTGATCGAC	59.826	55.000	1.01	0.00	41.43	4.20
3496	3500	1.227002	GCCGAACCTCTGATCGACC	60.227	63.158	1.01	0.00	41.43	4.79
3497	3501	1.437986	CCGAACCTCTGATCGACCC	59.562	63.158	1.01	0.00	41.43	4.46
3498	3502	1.064296	CGAACCTCTGATCGACCCG	59.936	63.158	0.00	0.00	41.43	5.28
3499	3503	1.437986	GAACCTCTGATCGACCCGG	59.562	63.158	0.00	0.00	0.00	5.73
3500	3504	1.000019	AACCTCTGATCGACCCGGA	60.000	57.895	0.73	0.00	0.00	5.14
3501	3505	1.321074	AACCTCTGATCGACCCGGAC	61.321	60.000	0.73	0.00	0.00	4.79
3502	3506	1.753078	CCTCTGATCGACCCGGACA	60.753	63.158	0.73	0.00	0.00	4.02
3503	3507	1.433879	CTCTGATCGACCCGGACAC	59.566	63.158	0.73	0.00	0.00	3.67
3504	3508	2.102357	CTGATCGACCCGGACACG	59.898	66.667	0.73	5.72	40.55	4.49
3505	3509	2.674033	TGATCGACCCGGACACGT	60.674	61.111	0.73	0.00	38.78	4.49
3506	3510	1.371337	CTGATCGACCCGGACACGTA	61.371	60.000	0.73	0.00	38.78	3.57
3507	3511	0.959867	TGATCGACCCGGACACGTAA	60.960	55.000	0.73	0.00	38.78	3.18
3508	3512	0.171007	GATCGACCCGGACACGTAAA	59.829	55.000	0.73	0.00	38.78	2.01
3509	3513	0.602562	ATCGACCCGGACACGTAAAA	59.397	50.000	0.73	0.00	38.78	1.52
3510	3514	0.387202	TCGACCCGGACACGTAAAAA	59.613	50.000	0.73	0.00	38.78	1.94
3524	3528	3.975246	AAAAATTCTCGGCGCCGA	58.025	50.000	45.07	45.07	46.87	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
690	693	0.248012	TTCCCGCGAGAATTGCTACA	59.752	50.000	8.23	0.00	45.68	2.74
994	997	5.745227	TCTGGGTGAGAATTCCATACTTTC	58.255	41.667	0.65	0.00	0.00	2.62
1103	1106	2.419990	CGTGCAATCCCATCTCCAACTA	60.420	50.000	0.00	0.00	0.00	2.24
1384	1387	0.507358	GCTTTCACTTCGACACGTCC	59.493	55.000	0.00	0.00	0.00	4.79
2025	2028	6.806668	TCTGTAATGGAGATCACATTGGTA	57.193	37.500	19.83	9.27	38.84	3.25
2585	2588	5.987019	AATAGCCTATTGGGGTTCAGTTA	57.013	39.130	0.00	0.00	44.41	2.24
2697	2700	2.826488	ATCCTGAACTACTGGAGCAGT	58.174	47.619	0.00	0.00	46.78	4.40
2740	2743	0.187851	ATAGGTAGGGGGTCCGTCAG	59.812	60.000	0.00	0.00	38.33	3.51
3413	3417	5.656859	AGCCTATCTAACACAGACATACACA	59.343	40.000	0.00	0.00	35.62	3.72
3469	3473	0.036858	AGAGGTTCGGCTTGCTTCTC	60.037	55.000	0.00	0.00	0.00	2.87
3470	3474	0.321122	CAGAGGTTCGGCTTGCTTCT	60.321	55.000	0.00	0.00	0.00	2.85
3471	3475	0.320771	TCAGAGGTTCGGCTTGCTTC	60.321	55.000	0.00	0.00	0.00	3.86
3472	3476	0.326264	ATCAGAGGTTCGGCTTGCTT	59.674	50.000	0.00	0.00	0.00	3.91
3473	3477	0.107945	GATCAGAGGTTCGGCTTGCT	60.108	55.000	0.00	0.00	0.00	3.91
3474	3478	1.424493	CGATCAGAGGTTCGGCTTGC	61.424	60.000	0.00	0.00	33.64	4.01
3475	3479	0.173481	TCGATCAGAGGTTCGGCTTG	59.827	55.000	0.00	0.00	36.97	4.01
3476	3480	0.173708	GTCGATCAGAGGTTCGGCTT	59.826	55.000	0.00	0.00	37.74	4.35
3477	3481	1.668101	GGTCGATCAGAGGTTCGGCT	61.668	60.000	0.00	0.00	39.95	5.52
3478	3482	1.227002	GGTCGATCAGAGGTTCGGC	60.227	63.158	0.00	0.00	39.48	5.54
3479	3483	1.437986	GGGTCGATCAGAGGTTCGG	59.562	63.158	0.00	0.00	36.97	4.30
3480	3484	1.064296	CGGGTCGATCAGAGGTTCG	59.936	63.158	0.00	0.00	37.53	3.95
3481	3485	1.035932	TCCGGGTCGATCAGAGGTTC	61.036	60.000	0.00	0.00	0.00	3.62
3482	3486	1.000019	TCCGGGTCGATCAGAGGTT	60.000	57.895	0.00	0.00	0.00	3.50
3483	3487	1.753463	GTCCGGGTCGATCAGAGGT	60.753	63.158	0.00	0.00	0.00	3.85
3484	3488	1.753078	TGTCCGGGTCGATCAGAGG	60.753	63.158	0.00	0.00	0.00	3.69
3485	3489	1.433879	GTGTCCGGGTCGATCAGAG	59.566	63.158	0.00	0.00	0.00	3.35
3486	3490	2.404186	CGTGTCCGGGTCGATCAGA	61.404	63.158	0.00	0.00	0.00	3.27
3487	3491	1.371337	TACGTGTCCGGGTCGATCAG	61.371	60.000	17.39	0.00	38.78	2.90
3488	3492	0.959867	TTACGTGTCCGGGTCGATCA	60.960	55.000	17.39	0.00	38.78	2.92
3489	3493	0.171007	TTTACGTGTCCGGGTCGATC	59.829	55.000	17.39	0.00	38.78	3.69
3490	3494	0.602562	TTTTACGTGTCCGGGTCGAT	59.397	50.000	17.39	7.23	38.78	3.59
3491	3495	0.387202	TTTTTACGTGTCCGGGTCGA	59.613	50.000	17.39	0.00	38.78	4.20
3492	3496	2.897780	TTTTTACGTGTCCGGGTCG	58.102	52.632	0.00	6.97	38.78	4.79
3507	3511	3.975246	TCGGCGCCGAGAATTTTT	58.025	50.000	45.37	0.00	44.01	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.