AutoCloner

Multiple sequence alignment - TraesCS4D01G330800

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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	TraesCS4D01G330800	chr4D	100.000	2943	0	0	1	2943	488820299	488817357	0.000000e+00	5435
1	TraesCS4D01G330800	chr4D	82.458	1237	118	55	1738	2913	348365382	348364184	0.000000e+00	990
2	TraesCS4D01G330800	chr4D	86.750	800	78	22	953	1739	348366215	348365431	0.000000e+00	865
3	TraesCS4D01G330800	chr4D	88.889	666	57	11	1	658	348378577	348377921	0.000000e+00	804
4	TraesCS4D01G330800	chr5D	91.113	2993	161	55	1	2943	556337361	556340298	0.000000e+00	3956
5	TraesCS4D01G330800	chr2D	90.718	2995	162	49	1	2914	562772506	562769547	0.000000e+00	3884
6	TraesCS4D01G330800	chr1D	80.295	1629	243	53	1	1607	364209890	364211462	0.000000e+00	1158
7	TraesCS4D01G330800	chr1D	79.128	1744	279	59	1	1720	364189396	364191078	0.000000e+00	1125
8	TraesCS4D01G330800	chr7D	80.578	1488	217	46	1	1453	69842404	69840954	0.000000e+00	1081
9	TraesCS4D01G330800	chr3D	80.704	1477	210	46	12	1450	22151972	22153411	0.000000e+00	1079
10	TraesCS4D01G330800	chr3D	78.737	1726	243	85	7	1707	361846498	361844872	0.000000e+00	1040
11	TraesCS4D01G330800	chr3D	81.774	823	108	22	17	824	418832882	418833677	0.000000e+00	651
12	TraesCS4D01G330800	chr3D	77.534	730	119	30	909	1614	418856854	418857562	5.910000e-107	398
13	TraesCS4D01G330800	chr4A	80.934	1327	200	33	1	1312	45452000	45450712	0.000000e+00	1000
14	TraesCS4D01G330800	chr7B	77.072	1291	233	45	23	1298	63222693	63221451	0.000000e+00	686
15	TraesCS4D01G330800	chr2B	75.403	1179	212	49	388	1554	544089799	544088687	1.570000e-137	499
16	TraesCS4D01G330800	chr2B	86.885	183	24	0	1761	1943	544088633	544088451	3.840000e-49	206

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	TraesCS4D01G330800	chr4D	488817357	488820299	2942	True	5435.0	5435	100.000	1	2943	1	chr4D.!!$R2	2942
1	TraesCS4D01G330800	chr4D	348364184	348366215	2031	True	927.5	990	84.604	953	2913	2	chr4D.!!$R3	1960
2	TraesCS4D01G330800	chr4D	348377921	348378577	656	True	804.0	804	88.889	1	658	1	chr4D.!!$R1	657
3	TraesCS4D01G330800	chr5D	556337361	556340298	2937	False	3956.0	3956	91.113	1	2943	1	chr5D.!!$F1	2942
4	TraesCS4D01G330800	chr2D	562769547	562772506	2959	True	3884.0	3884	90.718	1	2914	1	chr2D.!!$R1	2913
5	TraesCS4D01G330800	chr1D	364209890	364211462	1572	False	1158.0	1158	80.295	1	1607	1	chr1D.!!$F2	1606
6	TraesCS4D01G330800	chr1D	364189396	364191078	1682	False	1125.0	1125	79.128	1	1720	1	chr1D.!!$F1	1719
7	TraesCS4D01G330800	chr7D	69840954	69842404	1450	True	1081.0	1081	80.578	1	1453	1	chr7D.!!$R1	1452
8	TraesCS4D01G330800	chr3D	22151972	22153411	1439	False	1079.0	1079	80.704	12	1450	1	chr3D.!!$F1	1438
9	TraesCS4D01G330800	chr3D	361844872	361846498	1626	True	1040.0	1040	78.737	7	1707	1	chr3D.!!$R1	1700
10	TraesCS4D01G330800	chr3D	418832882	418833677	795	False	651.0	651	81.774	17	824	1	chr3D.!!$F2	807
11	TraesCS4D01G330800	chr3D	418856854	418857562	708	False	398.0	398	77.534	909	1614	1	chr3D.!!$F3	705
12	TraesCS4D01G330800	chr4A	45450712	45452000	1288	True	1000.0	1000	80.934	1	1312	1	chr4A.!!$R1	1311
13	TraesCS4D01G330800	chr7B	63221451	63222693	1242	True	686.0	686	77.072	23	1298	1	chr7B.!!$R1	1275
14	TraesCS4D01G330800	chr2B	544088451	544089799	1348	True	352.5	499	81.144	388	1943	2	chr2B.!!$R1	1555

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
798	837	2.559440	TGTTTTCAGTTGGCAAATGGC	58.441	42.857	25.30	14.32	43.74	4.40	F
1555	1661	4.070009	TGCATGGCATGTGCATTTTTAAA	58.930	34.783	26.94	0.00	46.76	1.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1754	1909	0.307760	CAGTCAACCCTGCAACGAAC	59.692	55.000	0.0	0.0	0.00	3.95	R
2904	3124	4.020039	TGGCAACCGAATAGAAAGGAACTA	60.020	41.667	0.0	0.0	38.49	2.24	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
120	122	9.965824	GAAGAAGTTTACAATGAAAAGATCCAA	57.034	29.630	0.00	0.00	0.00	3.53
165	167	3.853355	AGAGAGGCAAACAGATATGGG	57.147	47.619	0.00	0.00	0.00	4.00
219	221	6.703607	ACAATGCGTCTCCTTATCTAAATGAG	59.296	38.462	0.00	0.00	0.00	2.90
316	324	8.763049	TGAGAACTTCAAATAGTGAGTACATG	57.237	34.615	0.00	0.00	37.61	3.21
317	325	7.331934	TGAGAACTTCAAATAGTGAGTACATGC	59.668	37.037	0.00	0.00	37.61	4.06
324	332	6.378280	TCAAATAGTGAGTACATGCTCTCTGA	59.622	38.462	15.48	8.98	39.01	3.27
328	336	3.636300	GTGAGTACATGCTCTCTGATCCT	59.364	47.826	15.48	0.00	36.51	3.24
329	337	4.099266	GTGAGTACATGCTCTCTGATCCTT	59.901	45.833	15.48	0.00	36.51	3.36
340	348	5.566230	GCTCTCTGATCCTTTTTGTGCAAAT	60.566	40.000	0.00	0.00	0.00	2.32
353	361	9.635632	CTTTTTGTGCAAATAGTTGTTATGTTG	57.364	29.630	4.65	0.00	37.06	3.33
359	367	8.849490	GTGCAAATAGTTGTTATGTTGTACATG	58.151	33.333	4.65	0.00	36.93	3.21
726	765	4.755629	CAGGAGCATCTTATGAACATGGAG	59.244	45.833	0.00	0.00	33.73	3.86
798	837	2.559440	TGTTTTCAGTTGGCAAATGGC	58.441	42.857	25.30	14.32	43.74	4.40
951	997	8.195436	GTGCACTTTCCTACATTATACACTCTA	58.805	37.037	10.32	0.00	0.00	2.43
966	1013	5.051891	ACACTCTAAATCAATGCAAGCAC	57.948	39.130	0.00	0.00	0.00	4.40
984	1031	4.432712	AGCACTGGTTTGATTTTGTTGTC	58.567	39.130	0.00	0.00	0.00	3.18
1248	1312	4.703897	TCGCGGAATCTTAATTGGAGAAT	58.296	39.130	6.13	0.00	0.00	2.40
1526	1632	7.744087	ATATGCTACTGTGTGAACTTTTTGA	57.256	32.000	0.00	0.00	0.00	2.69
1529	1635	5.356751	TGCTACTGTGTGAACTTTTTGATGT	59.643	36.000	0.00	0.00	0.00	3.06
1555	1661	4.070009	TGCATGGCATGTGCATTTTTAAA	58.930	34.783	26.94	0.00	46.76	1.52
1639	1747	7.412063	GCATTTTTGTTCTTGAAGCAATTCTT	58.588	30.769	0.00	0.00	37.83	2.52
1640	1748	7.911727	GCATTTTTGTTCTTGAAGCAATTCTTT	59.088	29.630	0.00	0.00	34.56	2.52
1765	1920	3.557577	TCATGATTTGTTCGTTGCAGG	57.442	42.857	0.00	0.00	0.00	4.85
1848	2003	7.514784	TGCATGACATTATTAAGGATGAAGG	57.485	36.000	0.00	0.69	0.00	3.46
1903	2058	5.046087	TGAGATGATGTTCACTGACCTCAAT	60.046	40.000	0.00	0.00	29.96	2.57
1912	2067	6.166279	GTTCACTGACCTCAATATTCTGACA	58.834	40.000	0.00	0.00	0.00	3.58
1945	2100	9.741647	AAGAACTTTGTTCTTGATTTCTGATTC	57.258	29.630	20.51	0.00	37.37	2.52
1946	2101	8.906867	AGAACTTTGTTCTTGATTTCTGATTCA	58.093	29.630	7.09	0.00	0.00	2.57
1979	2136	8.159344	AGTAAGCTTGCCATCTTATACATTTC	57.841	34.615	9.86	0.00	0.00	2.17
1983	2140	8.930846	AGCTTGCCATCTTATACATTTCTAAT	57.069	30.769	0.00	0.00	0.00	1.73
1984	2141	9.359653	AGCTTGCCATCTTATACATTTCTAATT	57.640	29.630	0.00	0.00	0.00	1.40
1985	2142	9.971922	GCTTGCCATCTTATACATTTCTAATTT	57.028	29.630	0.00	0.00	0.00	1.82
2011	2192	7.828717	TCTGATTCTTGTGCCATCTGTTTTATA	59.171	33.333	0.00	0.00	0.00	0.98
2124	2306	6.721318	AGCCATTTCAACAAGGAGATAACTA	58.279	36.000	0.00	0.00	0.00	2.24
2255	2443	7.114866	TGAATGATTGGAATGTTATGTGCAT	57.885	32.000	0.00	0.00	0.00	3.96
2437	2628	4.275810	AGTTTCATCCTGGATCATGTTGG	58.724	43.478	6.13	0.00	0.00	3.77
2441	2632	1.891933	TCCTGGATCATGTTGGGCTA	58.108	50.000	0.00	0.00	0.00	3.93
2931	3151	4.407621	TCCTTTCTATTCGGTTGCCATCTA	59.592	41.667	0.00	0.00	0.00	1.98
2936	3156	8.740123	TTTCTATTCGGTTGCCATCTATTTTA	57.260	30.769	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	6.264067	GGAATTAGCAAGCAAGATGTTATCCT	59.736	38.462	0.00	0.00	0.00	3.24
120	122	4.946157	CCAGAGTTACCAGCAGAATGATTT	59.054	41.667	0.00	0.00	39.69	2.17
165	167	5.643379	TTGGATGTACAATTCTCTTTGGC	57.357	39.130	0.00	0.00	0.00	4.52
219	221	8.965172	GTGCTGACATGATATTTTGATGATTTC	58.035	33.333	0.00	0.00	0.00	2.17
316	324	2.816087	TGCACAAAAAGGATCAGAGAGC	59.184	45.455	0.00	0.00	0.00	4.09
317	325	5.443185	TTTGCACAAAAAGGATCAGAGAG	57.557	39.130	0.00	0.00	0.00	3.20
324	332	9.206870	CATAACAACTATTTGCACAAAAAGGAT	57.793	29.630	0.00	0.00	36.00	3.24
328	336	9.155975	ACAACATAACAACTATTTGCACAAAAA	57.844	25.926	0.00	0.00	36.00	1.94
329	337	8.709386	ACAACATAACAACTATTTGCACAAAA	57.291	26.923	0.00	0.00	36.00	2.44
726	765	6.641314	CGTACAACTCTTGGGTATCATATGAC	59.359	42.308	7.78	0.00	34.12	3.06
798	837	5.361135	TGCATGTATGGATTAATCTTGCG	57.639	39.130	14.95	0.14	0.00	4.85
868	911	4.326009	ACACTCAAAACAATGCGTGAAAAC	59.674	37.500	4.61	0.00	38.07	2.43
870	913	4.103365	ACACTCAAAACAATGCGTGAAA	57.897	36.364	4.61	0.00	38.07	2.69
873	916	6.509317	AATAAACACTCAAAACAATGCGTG	57.491	33.333	0.00	0.00	40.83	5.34
874	917	8.810652	ATAAATAAACACTCAAAACAATGCGT	57.189	26.923	0.00	0.00	0.00	5.24
951	997	3.756933	AACCAGTGCTTGCATTGATTT	57.243	38.095	17.60	8.74	0.00	2.17
966	1013	6.966435	AACAAGACAACAAAATCAAACCAG	57.034	33.333	0.00	0.00	0.00	4.00
1109	1166	3.480470	TGCAGAAGTGGAGAAAAAGAGG	58.520	45.455	0.00	0.00	0.00	3.69
1248	1312	7.356540	CACGTCAATAAAATGTGTAGACCAAA	58.643	34.615	0.00	0.00	0.00	3.28
1349	1431	8.507249	GCGTCCTCATAATTCTAAAAAGCATAT	58.493	33.333	0.00	0.00	0.00	1.78
1355	1437	7.681939	ACTTGCGTCCTCATAATTCTAAAAA	57.318	32.000	0.00	0.00	0.00	1.94
1365	1448	7.045416	ACACAAATATAACTTGCGTCCTCATA	58.955	34.615	0.00	0.00	0.00	2.15
1490	1595	6.863126	ACACAGTAGCATATTTGACAAAAAGC	59.137	34.615	4.41	9.22	0.00	3.51
1526	1632	1.807742	GCACATGCCATGCAAAAACAT	59.192	42.857	4.17	0.00	43.62	2.71
1597	1703	7.042119	ACAAAAATGCGAAAACTTAATTCCAGG	60.042	33.333	0.00	0.00	0.00	4.45
1607	1713	6.455513	GCTTCAAGAACAAAAATGCGAAAACT	60.456	34.615	0.00	0.00	0.00	2.66
1639	1747	5.633830	TGTTCAAAATGCAAAAAGCCAAA	57.366	30.435	0.00	0.00	44.83	3.28
1640	1748	5.125097	ACATGTTCAAAATGCAAAAAGCCAA	59.875	32.000	0.00	0.00	44.83	4.52
1740	1848	5.527033	TGCAACGAACAAATCATGATTGAA	58.473	33.333	21.39	0.00	34.96	2.69
1742	1850	4.325204	CCTGCAACGAACAAATCATGATTG	59.675	41.667	21.39	16.52	0.00	2.67
1746	1854	2.030007	ACCCTGCAACGAACAAATCATG	60.030	45.455	0.00	0.00	0.00	3.07
1747	1855	2.238521	ACCCTGCAACGAACAAATCAT	58.761	42.857	0.00	0.00	0.00	2.45
1748	1856	1.686355	ACCCTGCAACGAACAAATCA	58.314	45.000	0.00	0.00	0.00	2.57
1749	1857	2.034053	TCAACCCTGCAACGAACAAATC	59.966	45.455	0.00	0.00	0.00	2.17
1751	1859	1.133407	GTCAACCCTGCAACGAACAAA	59.867	47.619	0.00	0.00	0.00	2.83
1754	1909	0.307760	CAGTCAACCCTGCAACGAAC	59.692	55.000	0.00	0.00	0.00	3.95
1912	2067	5.431765	TCAAGAACAAAGTTCTTCTGCTCT	58.568	37.500	19.12	0.00	36.69	4.09
2011	2192	8.955388	ACAAAAAGTACTGAAATGGCAAAAATT	58.045	25.926	0.00	0.00	0.00	1.82
2060	2242	9.070149	GCAACAAAGCAAAACATCAAATAAAAA	57.930	25.926	0.00	0.00	0.00	1.94
2124	2306	6.703165	GCTTTGTTTGACTCCATCTTTTGAAT	59.297	34.615	0.00	0.00	0.00	2.57
2131	2313	5.809001	TCTATGCTTTGTTTGACTCCATCT	58.191	37.500	0.00	0.00	0.00	2.90
2276	2464	8.049117	ACAGTACACATGAGGAATCATTTACAT	58.951	33.333	0.00	0.00	0.00	2.29
2352	2543	7.310664	ACTCAAAGTAGCATCACATCAATTTG	58.689	34.615	0.00	0.00	0.00	2.32
2597	2792	9.308000	TCTTATTCCAATAACATCACAAAAGGT	57.692	29.630	0.00	0.00	0.00	3.50
2904	3124	4.020039	TGGCAACCGAATAGAAAGGAACTA	60.020	41.667	0.00	0.00	38.49	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.