AutoCloner

Multiple sequence alignment - TraesCS3B01G327200

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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	TraesCS3B01G327200	chr3B	100.000	3304	0	0	1	3304	527898873	527902176	0.000000e+00	6102
1	TraesCS3B01G327200	chr3D	96.505	2575	56	14	756	3304	402463300	402465866	0.000000e+00	4226
2	TraesCS3B01G327200	chr3D	88.329	814	50	27	1	798	402462530	402463314	0.000000e+00	935
3	TraesCS3B01G327200	chr3D	80.000	300	34	14	343	621	7178904	7179198	7.230000e-47	198
4	TraesCS3B01G327200	chr3D	77.846	325	51	10	281	592	572636103	572636419	7.280000e-42	182
5	TraesCS3B01G327200	chr3A	94.367	2237	80	16	521	2730	523315343	523317560	0.000000e+00	3391
6	TraesCS3B01G327200	chr3A	97.628	548	9	3	2758	3304	523317557	523318101	0.000000e+00	937
7	TraesCS3B01G327200	chr3A	85.206	534	50	14	1	522	523309643	523310159	3.780000e-144	521
8	TraesCS3B01G327200	chr3A	77.778	189	26	11	364	549	28901531	28901706	5.830000e-18	102
9	TraesCS3B01G327200	chr7B	82.422	256	28	10	350	592	745225496	745225747	1.200000e-49	207
10	TraesCS3B01G327200	chr7B	79.851	268	27	17	342	592	745225755	745225498	1.580000e-38	171
11	TraesCS3B01G327200	chr7B	79.297	256	32	14	352	592	48966516	48966765	3.410000e-35	159
12	TraesCS3B01G327200	chr6D	78.354	328	53	11	281	592	4637002	4636677	2.600000e-46	196
13	TraesCS3B01G327200	chr2D	97.727	88	2	0	2794	2881	588164126	588164213	5.710000e-33	152
14	TraesCS3B01G327200	chr2D	95.699	93	3	1	2794	2885	382456024	382455932	7.390000e-32	148
15	TraesCS3B01G327200	chr5D	94.624	93	4	1	2790	2881	8408140	8408048	3.440000e-30	143
16	TraesCS3B01G327200	chr5D	88.034	117	11	3	2765	2878	225584046	225584162	5.750000e-28	135
17	TraesCS3B01G327200	chr4B	94.565	92	5	0	2790	2881	648544279	648544188	3.440000e-30	143
18	TraesCS3B01G327200	chr6B	91.262	103	6	3	2786	2887	646750152	646750052	1.600000e-28	137
19	TraesCS3B01G327200	chr6B	81.618	136	13	8	453	578	114267783	114267650	5.830000e-18	102
20	TraesCS3B01G327200	chr1B	91.089	101	7	2	2790	2888	586056804	586056704	5.750000e-28	135
21	TraesCS3B01G327200	chr5B	80.240	167	24	7	363	522	253135532	253135368	2.080000e-22	117
22	TraesCS3B01G327200	chr2A	79.762	168	24	7	363	522	41215627	41215462	2.690000e-21	113
23	TraesCS3B01G327200	chr2A	83.471	121	14	3	335	449	707262377	707262497	1.250000e-19	108

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	TraesCS3B01G327200	chr3B	527898873	527902176	3303	False	6102.0	6102	100.0000	1	3304	1	chr3B.!!$F1	3303
1	TraesCS3B01G327200	chr3D	402462530	402465866	3336	False	2580.5	4226	92.4170	1	3304	2	chr3D.!!$F3	3303
2	TraesCS3B01G327200	chr3A	523315343	523318101	2758	False	2164.0	3391	95.9975	521	3304	2	chr3A.!!$F3	2783
3	TraesCS3B01G327200	chr3A	523309643	523310159	516	False	521.0	521	85.2060	1	522	1	chr3A.!!$F2	521

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
873	929	0.725117	GTTGTAAACGGGCCGATCAG	59.275	55.0	35.78	2.65	36.92	2.90	F
1363	1422	1.685355	GCACTGGGTTTGGTTGGCTT	61.685	55.0	0.00	0.00	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2030	2111	1.067916	CAACACACTTTGCAGGGCC	59.932	57.895	0.0	0.0	0.0	5.80	R
2734	2817	1.134521	TGTGTTGCAAGAGGTCGAAGT	60.135	47.619	0.0	0.0	0.0	3.01	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
27	28	3.677190	AGAGAGTACGTTCGCATACTG	57.323	47.619	0.00	0.00	31.69	2.74
303	308	2.330216	AGTACCCTTGTGAGCTTGAGT	58.670	47.619	0.00	0.00	0.00	3.41
317	322	2.555757	GCTTGAGTCCAAATGAGCTTGT	59.444	45.455	0.00	0.00	0.00	3.16
334	339	8.039603	TGAGCTTGTATGAACAATAAAATCGT	57.960	30.769	0.00	0.00	44.43	3.73
404	412	8.871686	AATTTGACAATTCTAAGTGTTTGGAC	57.128	30.769	0.00	0.00	37.34	4.02
409	417	9.126151	TGACAATTCTAAGTGTTTGGACATTTA	57.874	29.630	0.00	0.00	37.34	1.40
417	425	7.523293	AAGTGTTTGGACATTTACATCATGA	57.477	32.000	0.00	0.00	38.23	3.07
429	437	7.712205	ACATTTACATCATGAGATCACATTCGA	59.288	33.333	2.55	0.00	30.20	3.71
493	506	5.990120	AAGTAGCATTTTTGGAGCATCTT	57.010	34.783	0.00	0.00	33.73	2.40
613	630	8.691661	TTTTATTCTACTGTTCTTCCAAGCTT	57.308	30.769	0.00	0.00	0.00	3.74
621	638	6.064717	ACTGTTCTTCCAAGCTTATTTGAGT	58.935	36.000	0.00	0.00	0.00	3.41
636	653	1.746470	TGAGTTCGAGCGATACTCCA	58.254	50.000	21.07	12.79	43.01	3.86
690	707	1.981254	CGAAACGGCTACTTCGGTTA	58.019	50.000	6.68	0.00	40.52	2.85
705	722	9.382244	CTACTTCGGTTATCAAACTTCAAAAAG	57.618	33.333	0.00	0.00	38.54	2.27
716	733	6.989169	TCAAACTTCAAAAAGAGAGAGAGAGG	59.011	38.462	0.00	0.00	36.30	3.69
722	739	2.736670	AAGAGAGAGAGAGGGAGAGC	57.263	55.000	0.00	0.00	0.00	4.09
764	782	9.609346	TTTTGTTAGAGATAAGTATGGGTAAGC	57.391	33.333	0.00	0.00	0.00	3.09
765	783	7.907841	TGTTAGAGATAAGTATGGGTAAGCA	57.092	36.000	0.00	0.00	0.00	3.91
766	784	7.952671	TGTTAGAGATAAGTATGGGTAAGCAG	58.047	38.462	0.00	0.00	0.00	4.24
767	785	5.476091	AGAGATAAGTATGGGTAAGCAGC	57.524	43.478	0.00	0.00	0.00	5.25
768	786	5.151454	AGAGATAAGTATGGGTAAGCAGCT	58.849	41.667	0.00	0.00	0.00	4.24
769	787	5.604650	AGAGATAAGTATGGGTAAGCAGCTT	59.395	40.000	13.46	13.46	0.00	3.74
773	791	8.272173	AGATAAGTATGGGTAAGCAGCTTTTTA	58.728	33.333	14.29	0.00	0.00	1.52
873	929	0.725117	GTTGTAAACGGGCCGATCAG	59.275	55.000	35.78	2.65	36.92	2.90
903	962	2.178273	GCGGCGTTCCATTCCAAC	59.822	61.111	9.37	0.00	0.00	3.77
943	1002	3.055385	CCAGCTAAGCAGTGTAGGGTTTA	60.055	47.826	0.00	0.00	0.00	2.01
944	1003	4.184629	CAGCTAAGCAGTGTAGGGTTTAG	58.815	47.826	0.00	0.00	32.86	1.85
945	1004	2.937149	GCTAAGCAGTGTAGGGTTTAGC	59.063	50.000	0.00	0.00	43.25	3.09
955	1014	2.588439	GGTTTAGCCCCCGTCTCC	59.412	66.667	0.00	0.00	0.00	3.71
956	1015	2.588439	GTTTAGCCCCCGTCTCCC	59.412	66.667	0.00	0.00	0.00	4.30
1221	1280	7.658575	CACTTGATCTGGATGAAAATTTTGGTT	59.341	33.333	8.47	0.00	0.00	3.67
1233	1292	5.416862	AAATTTTGGTTTCCATGTTTCGC	57.583	34.783	0.00	0.00	31.53	4.70
1363	1422	1.685355	GCACTGGGTTTGGTTGGCTT	61.685	55.000	0.00	0.00	0.00	4.35
1440	1506	3.658709	TGTCACGATGCATGTTTGTCTA	58.341	40.909	2.46	0.00	0.00	2.59
1520	1586	3.869272	GGGCTGATCACAAGCGCG	61.869	66.667	0.00	0.00	0.00	6.86
1522	1588	1.809619	GGCTGATCACAAGCGCGTA	60.810	57.895	8.43	0.00	0.00	4.42
1722	1790	8.421002	GCCCATTTCATAACCATACTGTAATTT	58.579	33.333	0.00	0.00	0.00	1.82
1740	1808	6.557633	TGTAATTTTATCTAGGGGGAGAGTCC	59.442	42.308	0.00	0.00	35.23	3.85
2081	2163	3.393089	AATGGTGCACGGCAATAAAAA	57.607	38.095	11.45	0.00	41.47	1.94
2254	2336	3.316029	TGAGTGACACATTTGAGGCAAAG	59.684	43.478	8.59	0.00	36.76	2.77
2592	2675	3.011032	ACTTCCCCATTCATCTGAAAGCT	59.989	43.478	0.00	0.00	37.61	3.74
2751	2834	6.478588	CAATTATACTTCGACCTCTTGCAAC	58.521	40.000	0.00	0.00	0.00	4.17
2756	2839	2.254546	TCGACCTCTTGCAACACAAT	57.745	45.000	0.00	0.00	37.72	2.71
2820	2903	9.495382	ACTCCCTCTGTAAAGAAATATAAGAGT	57.505	33.333	0.00	0.00	0.00	3.24
2951	3035	5.821995	CCAAAAGAATGTTTGTTTGACCCAT	59.178	36.000	0.00	0.00	36.87	4.00
2952	3036	6.318396	CCAAAAGAATGTTTGTTTGACCCATT	59.682	34.615	0.00	0.00	36.87	3.16
3096	3181	2.931969	GGCGCAAAGTAGTTATTACGGT	59.068	45.455	10.83	0.00	37.35	4.83
3248	3333	3.428532	AGTACTCTTTGGTCGCCTTCTA	58.571	45.455	0.00	0.00	0.00	2.10
3287	3372	8.342634	CCTGGGATTTTCGTTTGTATAAGTATG	58.657	37.037	0.00	0.00	0.00	2.39
3297	3382	7.648908	TCGTTTGTATAAGTATGTACGGGATTG	59.351	37.037	0.00	0.00	0.00	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
211	216	7.834881	TTATCACGAGGAAGGTGTATCTAAT	57.165	36.000	0.00	0.00	36.76	1.73
303	308	6.839124	ATTGTTCATACAAGCTCATTTGGA	57.161	33.333	0.00	0.00	46.71	3.53
370	375	9.965824	ACTTAGAATTGTCAAATTTTACCACAG	57.034	29.630	0.20	0.00	36.10	3.66
380	385	8.006298	TGTCCAAACACTTAGAATTGTCAAAT	57.994	30.769	0.00	0.00	0.00	2.32
404	412	8.080083	TCGAATGTGATCTCATGATGTAAATG	57.920	34.615	10.87	0.00	32.19	2.32
409	417	4.343239	TCCTCGAATGTGATCTCATGATGT	59.657	41.667	10.87	0.00	32.19	3.06
417	425	1.202463	CGCCTTCCTCGAATGTGATCT	60.202	52.381	0.00	0.00	0.00	2.75
539	556	8.411318	ACTTTGACAAATTTTCTAAGTGCTTG	57.589	30.769	18.95	0.00	37.56	4.01
595	612	7.389053	ACTCAAATAAGCTTGGAAGAACAGTAG	59.611	37.037	9.86	0.00	0.00	2.57
604	621	4.154195	GCTCGAACTCAAATAAGCTTGGAA	59.846	41.667	9.86	0.00	0.00	3.53
613	630	4.337274	TGGAGTATCGCTCGAACTCAAATA	59.663	41.667	22.73	11.83	45.03	1.40
621	638	0.376152	GACGTGGAGTATCGCTCGAA	59.624	55.000	0.00	0.00	45.03	3.71
636	653	1.045407	TGCAGTGTCTAAAGGGACGT	58.955	50.000	0.00	0.00	38.91	4.34
690	707	7.661027	CCTCTCTCTCTCTTTTTGAAGTTTGAT	59.339	37.037	0.00	0.00	0.00	2.57
705	722	0.550914	TGGCTCTCCCTCTCTCTCTC	59.449	60.000	0.00	0.00	0.00	3.20
760	778	8.934825	CCATTTGCTAAAATAAAAAGCTGCTTA	58.065	29.630	16.31	0.00	34.14	3.09
761	779	7.094677	CCCATTTGCTAAAATAAAAAGCTGCTT	60.095	33.333	9.53	9.53	34.14	3.91
763	781	6.149308	ACCCATTTGCTAAAATAAAAAGCTGC	59.851	34.615	0.00	0.00	34.14	5.25
764	782	7.671495	ACCCATTTGCTAAAATAAAAAGCTG	57.329	32.000	0.00	0.00	34.14	4.24
765	783	9.785982	TTAACCCATTTGCTAAAATAAAAAGCT	57.214	25.926	0.00	0.00	34.14	3.74
768	786	9.561069	TGCTTAACCCATTTGCTAAAATAAAAA	57.439	25.926	0.00	0.00	34.14	1.94
769	787	9.213799	CTGCTTAACCCATTTGCTAAAATAAAA	57.786	29.630	0.00	0.00	34.14	1.52
773	791	5.046376	AGCTGCTTAACCCATTTGCTAAAAT	60.046	36.000	0.00	0.00	36.39	1.82
869	924	0.807667	CGCAGCTTCGCCTTACTGAT	60.808	55.000	0.00	0.00	31.67	2.90
873	929	3.865830	GCCGCAGCTTCGCCTTAC	61.866	66.667	0.00	0.00	35.50	2.34
892	948	2.622011	GCGGCGTGTTGGAATGGAA	61.622	57.895	9.37	0.00	0.00	3.53
1221	1280	2.198827	ACAGATGGCGAAACATGGAA	57.801	45.000	0.00	0.00	0.00	3.53
1233	1292	0.175760	CACCGGTGACCTACAGATGG	59.824	60.000	31.31	0.00	0.00	3.51
1363	1422	9.739276	ATAGAAATGTGAAAATCACCTTCTGTA	57.261	29.630	22.41	12.22	46.40	2.74
1408	1474	2.874701	GCATCGTGACATAAGCCATCTT	59.125	45.455	0.00	0.00	36.35	2.40
1520	1586	3.972950	TGATCTAGCGCAGAGACTTAC	57.027	47.619	11.47	5.61	36.48	2.34
1522	1588	4.399004	AATTGATCTAGCGCAGAGACTT	57.601	40.909	11.47	0.00	36.48	3.01
1722	1790	2.863238	TGTGGACTCTCCCCCTAGATAA	59.137	50.000	0.00	0.00	35.03	1.75
1740	1808	5.003160	TGACTCCCATCACATAAGTTTGTG	58.997	41.667	10.24	10.24	46.70	3.33
2030	2111	1.067916	CAACACACTTTGCAGGGCC	59.932	57.895	0.00	0.00	0.00	5.80
2254	2336	5.710099	TCAATACAAAAGAATCAGTGACCCC	59.290	40.000	0.00	0.00	0.00	4.95
2592	2675	9.414295	CAAAAGAAACTTGATCAAGATGCAATA	57.586	29.630	36.15	0.00	40.79	1.90
2734	2817	1.134521	TGTGTTGCAAGAGGTCGAAGT	60.135	47.619	0.00	0.00	0.00	3.01
2756	2839	9.559732	AGCATATGTTAAGTATGTAGATTTGCA	57.440	29.630	4.29	0.00	33.19	4.08
2831	2914	5.706916	AGAGCGTTTCGATCACTAAAGTAA	58.293	37.500	9.83	0.00	45.07	2.24
3248	3333	6.407074	CGAAAATCCCAGGATAGTACAGACTT	60.407	42.308	0.00	0.00	37.10	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.