AutoCloner

Multiple sequence alignment - TraesCS3A01G079600

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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	TraesCS3A01G079600	chr3A	100.000	5648	0	0	1	5648	51474712	51469065	0.000000e+00	10430.0
1	TraesCS3A01G079600	chr3A	86.957	138	16	2	157	294	719641060	719640925	2.720000e-33	154.0
2	TraesCS3A01G079600	chr3B	96.368	5672	151	27	1	5646	63413152	63407510	0.000000e+00	9282.0
3	TraesCS3A01G079600	chr3B	93.197	147	9	1	4674	4819	63400132	63399986	1.230000e-51	215.0
4	TraesCS3A01G079600	chr3B	97.222	36	1	0	2121	2156	63411092	63411057	1.700000e-05	62.1
5	TraesCS3A01G079600	chr3D	96.415	3738	94	9	1946	5648	40010237	40006505	0.000000e+00	6124.0
6	TraesCS3A01G079600	chr3D	96.341	1968	51	9	1	1953	40012362	40010401	0.000000e+00	3216.0
7	TraesCS3A01G079600	chr3D	86.990	2306	269	20	2538	4841	25397179	25394903	0.000000e+00	2567.0
8	TraesCS3A01G079600	chr3D	86.144	599	68	7	962	1547	25398681	25398085	2.870000e-177	632.0
9	TraesCS3A01G079600	chr3D	89.928	139	12	2	156	294	589759274	589759138	1.620000e-40	178.0
10	TraesCS3A01G079600	chr3D	93.478	92	4	2	1962	2053	420315597	420315686	9.870000e-28	135.0
11	TraesCS3A01G079600	chr3D	89.855	69	2	4	4952	5020	40007298	40007235	3.630000e-12	84.2
12	TraesCS3A01G079600	chr7D	86.834	2309	271	21	2535	4841	37801888	37804165	0.000000e+00	2549.0
13	TraesCS3A01G079600	chr7D	83.266	741	89	14	956	1663	37800387	37801125	0.000000e+00	649.0
14	TraesCS3A01G079600	chr7D	93.137	102	5	2	1952	2053	66526370	66526271	1.270000e-31	148.0
15	TraesCS3A01G079600	chr4A	87.580	2198	249	15	2538	4726	687180957	687178775	0.000000e+00	2525.0
16	TraesCS3A01G079600	chr4A	85.828	628	72	10	936	1547	687182451	687181825	0.000000e+00	651.0
17	TraesCS3A01G079600	chr7A	86.554	2298	271	21	2553	4841	37113835	37116103	0.000000e+00	2497.0
18	TraesCS3A01G079600	chr7A	85.875	623	73	7	935	1544	37112277	37112897	0.000000e+00	649.0
19	TraesCS3A01G079600	chr7A	90.323	93	6	2	1961	2053	220987390	220987479	9.940000e-23	119.0
20	TraesCS3A01G079600	chr5B	94.118	102	4	2	1952	2053	639280700	639280799	2.720000e-33	154.0
21	TraesCS3A01G079600	chr7B	91.176	102	6	3	1952	2053	681240160	681240258	9.870000e-28	135.0
22	TraesCS3A01G079600	chr5D	93.478	92	5	1	1960	2051	161443765	161443675	9.870000e-28	135.0
23	TraesCS3A01G079600	chr5D	91.489	94	6	2	1960	2053	20302688	20302597	1.650000e-25	128.0

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	TraesCS3A01G079600	chr3A	51469065	51474712	5647	True	10430.00	10430	100.000000	1	5648	1	chr3A.!!$R1	5647
1	TraesCS3A01G079600	chr3B	63407510	63413152	5642	True	4672.05	9282	96.795000	1	5646	2	chr3B.!!$R2	5645
2	TraesCS3A01G079600	chr3D	40006505	40012362	5857	True	3141.40	6124	94.203667	1	5648	3	chr3D.!!$R3	5647
3	TraesCS3A01G079600	chr3D	25394903	25398681	3778	True	1599.50	2567	86.567000	962	4841	2	chr3D.!!$R2	3879
4	TraesCS3A01G079600	chr7D	37800387	37804165	3778	False	1599.00	2549	85.050000	956	4841	2	chr7D.!!$F1	3885
5	TraesCS3A01G079600	chr4A	687178775	687182451	3676	True	1588.00	2525	86.704000	936	4726	2	chr4A.!!$R1	3790
6	TraesCS3A01G079600	chr7A	37112277	37116103	3826	False	1573.00	2497	86.214500	935	4841	2	chr7A.!!$F2	3906

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
837	848	1.275657	GGTCTGTCGTTTGTGCGTG	59.724	57.895	0.00	0.00	0.00	5.34	F
1098	1115	0.326264	ACAAAGGAGGAGAAGCGCAT	59.674	50.000	11.47	0.00	0.00	4.73	F
1115	1132	1.936656	GCATGCTGTTGACGTCTCTCA	60.937	52.381	17.92	11.64	0.00	3.27	F
2955	3344	3.763897	AGGACATTATCAAAGGTGTTGGC	59.236	43.478	0.00	0.00	27.75	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2465	2726	6.622549	TGTAAGAGAGAACTAAAGTAGCAGC	58.377	40.000	0.00	5.25	R
2955	3344	9.880157	AAATCCTTCACATTATCAAATTCTTGG	57.120	29.630	33.01	3.61	R
3270	3659	6.234177	CCCATACTCCTCATGTATTTCCTTC	58.766	44.000	0.00	3.46	R
4926	5325	3.330701	AGGCAACCAAAAGTAGATCTCCA	59.669	43.478	37.17	3.86	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
76	77	6.367969	GGTAACATAACAGAGGCCATTATACG	59.632	42.308	5.01	0.00	0.00	3.06
88	89	7.549488	AGAGGCCATTATACGTATGCTTATTTC	59.451	37.037	18.37	8.40	0.00	2.17
313	314	9.463443	CGGTTCTTGAATTTTATTTTCAACTCT	57.537	29.630	0.00	0.00	37.97	3.24
449	450	5.144832	TGCTATATCTGTACTGGTAAGCCA	58.855	41.667	16.73	5.75	43.73	4.75
495	496	7.090808	GTGTCGGCATATATGTAGAATCTTGA	58.909	38.462	14.14	0.00	0.00	3.02
552	553	1.483827	CACAGGAGCAATCTAGAGGCA	59.516	52.381	18.25	0.00	0.00	4.75
598	599	6.152638	TGAGTAAAATCAGAATTTCCCCCT	57.847	37.500	0.00	0.00	33.93	4.79
732	734	6.969043	TGGTATACTTGATTGGAAGGTTGAT	58.031	36.000	2.25	0.00	0.00	2.57
819	830	7.307219	GGAGGAATATCGAAAGTAAATGGTTCG	60.307	40.741	0.00	0.00	44.18	3.95
837	848	1.275657	GGTCTGTCGTTTGTGCGTG	59.724	57.895	0.00	0.00	0.00	5.34
1098	1115	0.326264	ACAAAGGAGGAGAAGCGCAT	59.674	50.000	11.47	0.00	0.00	4.73
1115	1132	1.936656	GCATGCTGTTGACGTCTCTCA	60.937	52.381	17.92	11.64	0.00	3.27
1657	1721	6.318144	CAGTTCAAGCTGATACCAATGATCTT	59.682	38.462	0.00	0.00	38.70	2.40
2049	2301	6.483974	TGCCATCCATTTTCATTTATTCATGC	59.516	34.615	0.00	0.00	0.00	4.06
2054	2306	6.539464	TCCATTTTCATTTATTCATGCTTGGC	59.461	34.615	0.00	0.00	0.00	4.52
2264	2520	7.054751	GCATCTTCCTTACTTTGTTATACCCT	58.945	38.462	0.00	0.00	0.00	4.34
2955	3344	3.763897	AGGACATTATCAAAGGTGTTGGC	59.236	43.478	0.00	0.00	27.75	4.52
3270	3659	3.318839	TGCTCAAACCAAAGGATCTTGTG	59.681	43.478	0.00	0.00	0.00	3.33
3285	3674	7.052873	AGGATCTTGTGAAGGAAATACATGAG	58.947	38.462	0.00	0.00	33.74	2.90
3294	3683	5.832539	AGGAAATACATGAGGAGTATGGG	57.167	43.478	0.00	0.00	32.78	4.00
3375	3764	0.842635	ATGTTCAGAGGGAGGCATCC	59.157	55.000	9.46	9.46	45.85	3.51
3457	3846	5.734720	ACTTGTCTGAGTTCTCTGAAAACA	58.265	37.500	10.15	4.12	0.00	2.83
3465	3854	5.291128	TGAGTTCTCTGAAAACAGACGTTTC	59.709	40.000	0.00	0.00	44.65	2.78
3576	3965	4.286297	TGAGTATAAGTTGCTGGTTGCT	57.714	40.909	0.00	0.00	43.37	3.91
3765	4154	3.429141	GCTGCTGTCGCACATGCT	61.429	61.111	1.82	0.00	42.25	3.79
4398	4794	0.680618	TTGGGCGGTCTTTCTACGAA	59.319	50.000	0.00	0.00	0.00	3.85
4651	5047	4.060900	TGAAGCTGCTTTTCTGTAGACAG	58.939	43.478	17.10	3.12	45.08	3.51
4672	5068	5.035443	CAGAGCATTTTCTTTATCTGCAGC	58.965	41.667	9.47	0.00	35.32	5.25
4783	5182	9.109393	GCTAGGAATATGTAATGTTCAAACTCA	57.891	33.333	0.00	0.00	45.08	3.41
4996	5395	7.603404	TGCCTTCCATGAACAAGAAAATTAATG	59.397	33.333	0.00	0.00	0.00	1.90
5020	5419	2.711547	AGGAGGTCTACTTTTGGTTGCT	59.288	45.455	0.00	0.00	0.00	3.91
5143	5572	2.307686	GTCTTTGTTCCCTCCCATACCA	59.692	50.000	0.00	0.00	0.00	3.25
5157	5586	3.181438	CCCATACCAACCCCAAATCGATA	60.181	47.826	0.00	0.00	0.00	2.92
5158	5587	4.508405	CCCATACCAACCCCAAATCGATAT	60.508	45.833	0.00	0.00	0.00	1.63
5177	5606	7.952671	TCGATATTTTGCTACTCTCCATAGTT	58.047	34.615	0.00	0.00	0.00	2.24
5182	5611	2.619177	TGCTACTCTCCATAGTTCTCGC	59.381	50.000	0.00	0.00	0.00	5.03
5184	5613	1.404843	ACTCTCCATAGTTCTCGCCC	58.595	55.000	0.00	0.00	0.00	6.13
5262	5691	1.127567	TGGCTACTGGCAACTGAGGT	61.128	55.000	0.00	0.00	46.03	3.85
5309	5738	8.000127	AGGTGGAGGTCTTACTACTAGATTAAG	59.000	40.741	0.00	0.31	0.00	1.85
5403	5832	5.046591	TGAGTTCTTACTGTCCGATCCATTT	60.047	40.000	0.00	0.00	33.84	2.32
5452	5882	7.216494	ACATTTGATTTGGTTTCCTCGAATTT	58.784	30.769	0.00	0.00	0.00	1.82
5468	5898	5.234752	TCGAATTTGAAGTACTTGCTAGCA	58.765	37.500	14.93	14.93	0.00	3.49
5478	5908	6.347859	AGTACTTGCTAGCAATAGTATCCC	57.652	41.667	29.40	16.33	35.20	3.85
5507	5938	4.744795	ACTAATCTTCCACTGGTAGCAG	57.255	45.455	20.16	20.16	0.00	4.24
5518	5949	2.670148	GGTAGCAGGGAGGGTGGTG	61.670	68.421	0.00	0.00	0.00	4.17
5546	5977	3.694043	TCGGTGGAATGAATTCTGACA	57.306	42.857	7.05	0.00	37.00	3.58
5627	6060	1.134848	GCGGCTGATGAAAGAGAGAGT	60.135	52.381	0.00	0.00	0.00	3.24
5632	6065	4.323409	GGCTGATGAAAGAGAGAGTTTCCT	60.323	45.833	0.00	0.00	33.67	3.36
5641	6074	6.869315	AAGAGAGAGTTTCCTAGCAAAAAC	57.131	37.500	5.82	5.82	35.97	2.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	5.758784	GCCTCTGTTATGTTACCATAAGGAC	59.241	44.000	1.08	0.00	42.66	3.85
76	77	8.925161	TGCATAACTTTTGGAAATAAGCATAC	57.075	30.769	0.00	0.00	0.00	2.39
140	141	7.064490	CCCCTTCAACGATGGATTTTTAAAATG	59.936	37.037	7.72	0.00	0.00	2.32
154	155	2.554564	GGAACTTTCCCCCTTCAACGAT	60.555	50.000	0.00	0.00	41.62	3.73
190	191	6.403878	GTGCCTCACTTCTACCTAACAAATA	58.596	40.000	0.00	0.00	0.00	1.40
259	260	0.250124	CCGGTTGGTTAGAGCACACA	60.250	55.000	0.00	0.00	0.00	3.72
469	470	6.590234	AGATTCTACATATATGCCGACACA	57.410	37.500	12.79	0.00	0.00	3.72
495	496	6.153340	ACCAGCTTATGTGATGCAACTAAAAT	59.847	34.615	0.00	0.00	0.00	1.82
501	502	2.159338	CCACCAGCTTATGTGATGCAAC	60.159	50.000	8.91	0.00	34.37	4.17
552	553	2.741878	CGCTGTTGGGATTCGATACCTT	60.742	50.000	8.03	0.00	32.98	3.50
598	599	4.893608	TCGATGTGGAAAACATTCTCTCA	58.106	39.130	0.00	0.00	44.51	3.27
635	636	2.035626	CCATTGGGAACGGCACCT	59.964	61.111	0.00	0.00	35.59	4.00
639	640	4.722361	TTTTATAACCATTGGGAACGGC	57.278	40.909	7.78	0.00	38.05	5.68
732	734	5.850557	TTCAATCTTTTGACTCCAAAGCA	57.149	34.783	0.00	0.00	41.50	3.91
804	815	4.143179	CGACAGACCGAACCATTTACTTTC	60.143	45.833	0.00	0.00	0.00	2.62
819	830	1.149361	TCACGCACAAACGACAGACC	61.149	55.000	0.00	0.00	36.70	3.85
837	848	5.752892	TCGTATGACAGGTAGACAGAATC	57.247	43.478	0.00	0.00	0.00	2.52
1098	1115	0.315251	CCTGAGAGACGTCAACAGCA	59.685	55.000	19.50	11.90	31.92	4.41
1657	1721	8.493607	TGATTGAGATCATTGGTAGGTTGATTA	58.506	33.333	0.00	0.00	37.37	1.75
2049	2301	9.226345	GATTTAAATTCTAGACATTTCGCCAAG	57.774	33.333	1.43	0.00	0.00	3.61
2054	2306	9.226345	GGCAAGATTTAAATTCTAGACATTTCG	57.774	33.333	1.43	0.00	0.00	3.46
2264	2520	6.828273	AGTGCAGATGCCTACAATGTAATAAA	59.172	34.615	1.72	0.00	41.18	1.40
2465	2726	6.622549	TGTAAGAGAGAACTAAAGTAGCAGC	58.377	40.000	0.00	0.00	0.00	5.25
2955	3344	9.880157	AAATCCTTCACATTATCAAATTCTTGG	57.120	29.630	0.00	0.00	33.01	3.61
3270	3659	6.234177	CCCATACTCCTCATGTATTTCCTTC	58.766	44.000	0.00	0.00	0.00	3.46
3285	3674	2.224548	GGTCAGCATAACCCCATACTCC	60.225	54.545	0.00	0.00	0.00	3.85
3294	3683	4.130118	CCTGTGAATAGGTCAGCATAACC	58.870	47.826	0.00	0.00	36.74	2.85
3457	3846	4.942852	TGGAATGCAAAAATGAAACGTCT	58.057	34.783	0.00	0.00	0.00	4.18
4398	4794	6.862209	TGTTGTGAAAAACTTTGAGCAGTAT	58.138	32.000	0.00	0.00	0.00	2.12
4651	5047	4.990257	TGCTGCAGATAAAGAAAATGCTC	58.010	39.130	20.43	0.00	37.76	4.26
4783	5182	3.624777	CCACTTATCCAGCAAGAATGGT	58.375	45.455	0.00	0.00	39.01	3.55
4821	5220	5.858581	GTCAAAACATCCTTGAGAAATTCCG	59.141	40.000	0.00	0.00	33.56	4.30
4861	5260	7.730364	AGATGTTTCAGTCGATGTAAAGTTT	57.270	32.000	0.00	0.00	0.00	2.66
4926	5325	3.330701	AGGCAACCAAAAGTAGATCTCCA	59.669	43.478	0.00	0.00	37.17	3.86
4996	5395	4.570930	CAACCAAAAGTAGACCTCCTCTC	58.429	47.826	0.00	0.00	0.00	3.20
5020	5419	7.776030	TGGAAACTAAACCTAGACAACAATTCA	59.224	33.333	0.00	0.00	0.00	2.57
5143	5572	5.891551	AGTAGCAAAATATCGATTTGGGGTT	59.108	36.000	1.71	0.00	38.04	4.11
5157	5586	6.276847	CGAGAACTATGGAGAGTAGCAAAAT	58.723	40.000	0.00	0.00	0.00	1.82
5158	5587	5.651530	CGAGAACTATGGAGAGTAGCAAAA	58.348	41.667	0.00	0.00	0.00	2.44
5177	5606	1.304962	TAGCTTGACAGGGGCGAGA	60.305	57.895	0.00	0.00	0.00	4.04
5182	5611	1.078143	GTGGCTAGCTTGACAGGGG	60.078	63.158	15.72	0.00	0.00	4.79
5184	5613	1.134670	GTAGGTGGCTAGCTTGACAGG	60.135	57.143	15.72	0.00	35.90	4.00
5257	5686	1.101635	CCGAGGCGACTATCACCTCA	61.102	60.000	12.22	0.00	44.00	3.86
5262	5691	2.520982	CCCCCGAGGCGACTATCA	60.521	66.667	0.00	0.00	44.43	2.15
5274	5703	4.740822	CCTCCACCTTTGCCCCCG	62.741	72.222	0.00	0.00	0.00	5.73
5309	5738	0.394565	AGCACCCAAGAGTCACAGAC	59.605	55.000	0.00	0.00	0.00	3.51
5361	5790	1.416030	TCAACCTAGTGCACAAGAGCA	59.584	47.619	21.04	0.00	43.35	4.26
5452	5882	7.434492	GGATACTATTGCTAGCAAGTACTTCA	58.566	38.462	31.88	12.73	39.47	3.02
5468	5898	9.440761	AAGATTAGTTCAGACTGGGATACTATT	57.559	33.333	1.81	3.24	36.60	1.73
5478	5908	5.174395	CCAGTGGAAGATTAGTTCAGACTG	58.826	45.833	1.68	0.00	37.77	3.51
5507	5938	0.763223	ATCGGTATCACCACCCTCCC	60.763	60.000	0.00	0.00	38.47	4.30
5518	5949	5.797042	AGAATTCATTCCACCGATCGGTATC	60.797	44.000	37.68	21.80	41.18	2.24
5532	5963	5.368256	ACAGCAACTGTCAGAATTCATTC	57.632	39.130	6.91	0.00	41.21	2.67
5546	5977	2.875296	TGGATTAGCCAAACAGCAACT	58.125	42.857	0.00	0.00	45.87	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.