AutoCloner

Multiple sequence alignment - TraesCS3D01G428100

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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	TraesCS3D01G428100	chr3D	100.000	2537	0	0	1	2537	542378785	542381321	0.000000e+00	4686.0
1	TraesCS3D01G428100	chr3D	91.902	778	53	7	1	768	461442480	461441703	0.000000e+00	1079.0
2	TraesCS3D01G428100	chr3A	94.849	1495	51	8	769	2256	678497798	678499273	0.000000e+00	2311.0
3	TraesCS3D01G428100	chr3B	91.363	1563	79	25	769	2305	718286816	718288348	0.000000e+00	2087.0
4	TraesCS3D01G428100	chr3B	91.850	773	59	2	1	769	547176791	547176019	0.000000e+00	1075.0
5	TraesCS3D01G428100	chr3B	95.783	166	7	0	2372	2537	718288733	718288898	4.160000e-68	268.0
6	TraesCS3D01G428100	chr3B	98.462	65	1	0	2310	2374	718288646	718288710	5.740000e-22	115.0
7	TraesCS3D01G428100	chr3B	85.714	56	7	1	1640	1695	717695807	717695861	9.800000e-05	58.4
8	TraesCS3D01G428100	chr7D	94.171	772	39	6	1	768	190126301	190127070	0.000000e+00	1171.0
9	TraesCS3D01G428100	chr4D	93.273	773	42	4	1	769	375376882	375377648	0.000000e+00	1131.0
10	TraesCS3D01G428100	chr1D	92.626	773	51	4	1	768	447440411	447441182	0.000000e+00	1107.0
11	TraesCS3D01G428100	chr1D	92.074	757	50	6	22	768	411272247	411273003	0.000000e+00	1057.0
12	TraesCS3D01G428100	chr7A	92.257	762	55	2	11	768	131961632	131960871	0.000000e+00	1077.0
13	TraesCS3D01G428100	chr7A	91.864	762	58	3	11	768	132003876	132003115	0.000000e+00	1061.0
14	TraesCS3D01G428100	chr6A	91.451	772	62	4	1	768	89300208	89299437	0.000000e+00	1057.0

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	TraesCS3D01G428100	chr3D	542378785	542381321	2536	False	4686.000000	4686	100.000000	1	2537	1	chr3D.!!$F1	2536
1	TraesCS3D01G428100	chr3D	461441703	461442480	777	True	1079.000000	1079	91.902000	1	768	1	chr3D.!!$R1	767
2	TraesCS3D01G428100	chr3A	678497798	678499273	1475	False	2311.000000	2311	94.849000	769	2256	1	chr3A.!!$F1	1487
3	TraesCS3D01G428100	chr3B	547176019	547176791	772	True	1075.000000	1075	91.850000	1	769	1	chr3B.!!$R1	768
4	TraesCS3D01G428100	chr3B	718286816	718288898	2082	False	823.333333	2087	95.202667	769	2537	3	chr3B.!!$F2	1768
5	TraesCS3D01G428100	chr7D	190126301	190127070	769	False	1171.000000	1171	94.171000	1	768	1	chr7D.!!$F1	767
6	TraesCS3D01G428100	chr4D	375376882	375377648	766	False	1131.000000	1131	93.273000	1	769	1	chr4D.!!$F1	768
7	TraesCS3D01G428100	chr1D	447440411	447441182	771	False	1107.000000	1107	92.626000	1	768	1	chr1D.!!$F2	767
8	TraesCS3D01G428100	chr1D	411272247	411273003	756	False	1057.000000	1057	92.074000	22	768	1	chr1D.!!$F1	746
9	TraesCS3D01G428100	chr7A	131960871	131961632	761	True	1077.000000	1077	92.257000	11	768	1	chr7A.!!$R1	757
10	TraesCS3D01G428100	chr7A	132003115	132003876	761	True	1061.000000	1061	91.864000	11	768	1	chr7A.!!$R2	757
11	TraesCS3D01G428100	chr6A	89299437	89300208	771	True	1057.000000	1057	91.451000	1	768	1	chr6A.!!$R1	767

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
481	484	0.106967	GTGAAGGAGATGGAAGGGGC	60.107	60.0	0.0	0.0	0.0	5.8	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2027	2077	0.036875	GGAAGACCAGTGTTCCCAGG	59.963	60.0	14.26	0.0	44.57	4.45	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
58	59	0.249120	ATCGGATCACCAAGTTCGCA	59.751	50.000	0.00	0.00	35.59	5.10
128	129	3.190535	GTGAATCACCTTGCACCGTATTT	59.809	43.478	1.10	0.00	0.00	1.40
139	140	2.343101	CACCGTATTTCAAAGCTCGGA	58.657	47.619	12.57	0.00	40.90	4.55
250	251	3.181482	TGGACGAGATTGAAGATCTCTGC	60.181	47.826	12.62	7.05	41.68	4.26
416	418	2.918712	AGTAGTTGTGAGCAGCAAGT	57.081	45.000	0.00	0.00	34.34	3.16
481	484	0.106967	GTGAAGGAGATGGAAGGGGC	60.107	60.000	0.00	0.00	0.00	5.80
517	520	5.720486	AAAGCTAGAGTAGAGGTAGAGGT	57.280	43.478	0.00	0.00	0.00	3.85
805	830	2.189499	GCCAGATGCCGATCCAACC	61.189	63.158	0.00	0.00	0.00	3.77
938	966	1.135689	GTGCGCTGTCCGATCATTTTT	60.136	47.619	9.73	0.00	40.02	1.94
1019	1047	0.461693	GCCAGCAGCACAAAACCAAA	60.462	50.000	0.00	0.00	42.97	3.28
1023	1051	2.740981	CAGCAGCACAAAACCAAACAAA	59.259	40.909	0.00	0.00	0.00	2.83
1339	1370	3.080765	ATGGATCGACCCGTGCCA	61.081	61.111	0.00	0.00	38.00	4.92
1369	1405	4.421952	GGGCTAGTTGCTCGCTAC	57.578	61.111	0.00	0.00	42.39	3.58
1897	1947	9.034544	GTCCCTGAAATAAAAACATTGCATATC	57.965	33.333	0.00	0.00	0.00	1.63
1898	1948	8.980596	TCCCTGAAATAAAAACATTGCATATCT	58.019	29.630	0.00	0.00	0.00	1.98
1899	1949	9.252962	CCCTGAAATAAAAACATTGCATATCTC	57.747	33.333	0.00	0.00	0.00	2.75
1948	1998	5.991328	AACATGTGTCTTGTGTAGAGTTG	57.009	39.130	0.00	0.00	32.23	3.16
1993	2043	4.202030	GGTACCTAGAGTCACCTGAATTCG	60.202	50.000	4.06	0.00	0.00	3.34
2027	2077	1.404391	CTGCACCCAGATGATTGCTTC	59.596	52.381	7.03	0.00	41.77	3.86
2052	2102	0.179018	AACACTGGTCTTCCACTGGC	60.179	55.000	0.00	0.00	39.03	4.85
2084	2134	8.838649	AATACCTTTGATTTAGCCCTGTATTT	57.161	30.769	0.00	0.00	0.00	1.40
2178	2232	1.479323	GGGTATACTGGAAGCGTGACA	59.521	52.381	2.25	0.00	37.60	3.58
2261	2316	1.811778	AGAATCTGCCATGGGAGCTA	58.188	50.000	27.43	12.72	33.42	3.32
2269	2324	2.777114	TGCCATGGGAGCTATTACTTGA	59.223	45.455	15.13	0.00	0.00	3.02
2289	2344	7.791029	ACTTGATTTAAGAACCCACACAAAAT	58.209	30.769	0.00	0.00	39.76	1.82
2292	2347	9.454859	TTGATTTAAGAACCCACACAAAATTTT	57.545	25.926	0.00	0.00	0.00	1.82
2295	2350	8.485976	TTTAAGAACCCACACAAAATTTTCAG	57.514	30.769	0.00	0.00	0.00	3.02
2296	2351	5.675684	AGAACCCACACAAAATTTTCAGT	57.324	34.783	0.00	0.00	0.00	3.41
2297	2352	5.418676	AGAACCCACACAAAATTTTCAGTG	58.581	37.500	18.63	18.63	37.95	3.66
2298	2353	4.817318	ACCCACACAAAATTTTCAGTGT	57.183	36.364	21.57	19.48	45.29	3.55
2299	2354	5.159273	ACCCACACAAAATTTTCAGTGTT	57.841	34.783	19.11	7.49	42.79	3.32
2300	2355	5.175127	ACCCACACAAAATTTTCAGTGTTC	58.825	37.500	19.11	0.00	42.79	3.18
2301	2356	5.174395	CCCACACAAAATTTTCAGTGTTCA	58.826	37.500	19.11	0.00	42.79	3.18
2302	2357	5.291614	CCCACACAAAATTTTCAGTGTTCAG	59.708	40.000	19.11	12.95	42.79	3.02
2303	2358	5.220453	CCACACAAAATTTTCAGTGTTCAGC	60.220	40.000	19.11	0.00	42.79	4.26
2304	2359	5.348179	CACACAAAATTTTCAGTGTTCAGCA	59.652	36.000	19.11	0.00	42.79	4.41
2306	2361	4.567959	ACAAAATTTTCAGTGTTCAGCAGC	59.432	37.500	0.00	0.00	0.00	5.25
2317	2664	0.323087	TTCAGCAGCATGTCCAGCAT	60.323	50.000	0.00	0.00	39.31	3.79
2398	2770	1.003118	CTCCAAACCTCCCGTCATCAA	59.997	52.381	0.00	0.00	0.00	2.57
2402	2774	0.321653	AACCTCCCGTCATCAAGCAC	60.322	55.000	0.00	0.00	0.00	4.40
2410	2782	3.068165	CCCGTCATCAAGCACTAGTATCA	59.932	47.826	0.00	0.00	0.00	2.15
2439	2811	3.253955	GACATTGTTGTCGCGCCT	58.746	55.556	0.00	0.00	42.66	5.52
2466	2838	6.548441	AAAATCTTGTGCCATGTTGATTTG	57.452	33.333	0.00	0.00	35.28	2.32
2497	2869	7.175119	AGGGACACTTCTTTTGCTTAGATTTAC	59.825	37.037	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	1.299468	GCGATCGCGGATGAACTCT	60.299	57.895	26.12	0.00	38.16	3.24
92	93	0.892755	ATTCACCAGTCGGCGTCTAA	59.107	50.000	6.85	0.00	34.57	2.10
128	129	1.561643	ATCTCCACTCCGAGCTTTGA	58.438	50.000	0.00	0.00	0.00	2.69
139	140	0.530744	TCGCGCTAACAATCTCCACT	59.469	50.000	5.56	0.00	0.00	4.00
250	251	2.952310	TGGATCTACATGTGAGTCTCCG	59.048	50.000	9.11	0.00	0.00	4.63
416	418	4.499472	CCTACATCCCCATAACCCTAGAA	58.501	47.826	0.00	0.00	0.00	2.10
481	484	3.714798	TCTAGCTTTACCCCCACCAATAG	59.285	47.826	0.00	0.00	0.00	1.73
810	835	0.984109	GTGTTTGATTTGGATGCGCG	59.016	50.000	0.00	0.00	0.00	6.86
881	906	0.321653	AGAAACGTGATGTCCCTGGC	60.322	55.000	0.00	0.00	0.00	4.85
938	966	0.099968	CGTCGCTCTATCCACGGAAA	59.900	55.000	0.00	0.00	0.00	3.13
1130	1158	2.406401	CGTAGTAGGTGGACGCCG	59.594	66.667	0.00	0.00	0.00	6.46
1133	1161	1.061570	GACGCGTAGTAGGTGGACG	59.938	63.158	13.97	0.00	39.55	4.79
1137	1165	0.797249	GTGCTGACGCGTAGTAGGTG	60.797	60.000	13.97	1.94	39.65	4.00
1178	1209	2.653115	CTCTGCTCGCACCTCACA	59.347	61.111	0.00	0.00	0.00	3.58
1339	1370	1.980784	CTAGCCCAGCAGAGCATGGT	61.981	60.000	0.00	0.00	41.36	3.55
1369	1405	2.085262	CACGTCAGAGCGCTGTCAG	61.085	63.158	18.48	6.78	42.84	3.51
1897	1947	8.915654	GTCCATTTGCATGTTTTAGTTTTAGAG	58.084	33.333	0.00	0.00	0.00	2.43
1898	1948	7.593273	CGTCCATTTGCATGTTTTAGTTTTAGA	59.407	33.333	0.00	0.00	0.00	2.10
1899	1949	7.593273	TCGTCCATTTGCATGTTTTAGTTTTAG	59.407	33.333	0.00	0.00	0.00	1.85
1905	1955	5.689514	TGTTTCGTCCATTTGCATGTTTTAG	59.310	36.000	0.00	0.00	0.00	1.85
1948	1998	0.309612	CAACGTTTACCCAGGCACAC	59.690	55.000	0.00	0.00	0.00	3.82
1993	2043	2.424956	GGGTGCAGAAGAAATCCATCAC	59.575	50.000	0.00	0.00	0.00	3.06
2027	2077	0.036875	GGAAGACCAGTGTTCCCAGG	59.963	60.000	14.26	0.00	44.57	4.45
2052	2102	6.430451	GGCTAAATCAAAGGTATTCATGTCG	58.570	40.000	0.00	0.00	0.00	4.35
2084	2134	8.000127	TGTGAGTGTACCTACCACATACATATA	59.000	37.037	0.00	0.00	33.42	0.86
2156	2210	1.754803	TCACGCTTCCAGTATACCCTG	59.245	52.381	0.00	0.00	0.00	4.45
2200	2254	4.489771	AGGGAAATCGCCAGGCCG	62.490	66.667	5.63	0.84	0.00	6.13
2221	2275	1.198759	TTCCCCCTTCTCAACTCCGG	61.199	60.000	0.00	0.00	0.00	5.14
2261	2316	8.472007	TTGTGTGGGTTCTTAAATCAAGTAAT	57.528	30.769	0.00	0.00	35.58	1.89
2269	2324	9.108284	CTGAAAATTTTGTGTGGGTTCTTAAAT	57.892	29.630	8.47	0.00	0.00	1.40
2289	2344	2.689471	ACATGCTGCTGAACACTGAAAA	59.311	40.909	0.00	0.00	0.00	2.29
2292	2347	1.516161	GACATGCTGCTGAACACTGA	58.484	50.000	0.00	0.00	0.00	3.41
2295	2350	0.520404	CTGGACATGCTGCTGAACAC	59.480	55.000	0.00	0.00	0.00	3.32
2296	2351	1.239296	GCTGGACATGCTGCTGAACA	61.239	55.000	0.00	1.79	0.00	3.18
2297	2352	1.239296	TGCTGGACATGCTGCTGAAC	61.239	55.000	0.00	0.00	0.00	3.18
2298	2353	0.323087	ATGCTGGACATGCTGCTGAA	60.323	50.000	0.00	0.00	37.70	3.02
2299	2354	0.746923	GATGCTGGACATGCTGCTGA	60.747	55.000	0.00	0.00	39.84	4.26
2300	2355	0.748367	AGATGCTGGACATGCTGCTG	60.748	55.000	0.00	0.00	39.84	4.41
2301	2356	0.748367	CAGATGCTGGACATGCTGCT	60.748	55.000	0.00	0.00	39.84	4.24
2302	2357	1.728069	CAGATGCTGGACATGCTGC	59.272	57.895	0.00	0.00	39.84	5.25
2303	2358	1.728069	GCAGATGCTGGACATGCTG	59.272	57.895	0.00	0.00	39.84	4.41
2304	2359	4.237445	GCAGATGCTGGACATGCT	57.763	55.556	0.00	0.00	39.84	3.79
2317	2664	2.163509	GTCTGTCTACACTCCAGCAGA	58.836	52.381	0.00	0.00	0.00	4.26
2402	2774	3.664486	GTCGTGTAATGCGCTGATACTAG	59.336	47.826	9.73	7.63	0.00	2.57
2410	2782	1.438651	ACAATGTCGTGTAATGCGCT	58.561	45.000	9.73	0.00	0.00	5.92
2433	2805	0.802494	ACAAGATTTTACCAGGCGCG	59.198	50.000	0.00	0.00	0.00	6.86
2466	2838	2.287849	GCAAAAGAAGTGTCCCTGAAGC	60.288	50.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.