AutoCloner

Multiple sequence alignment - TraesCS4D01G230300

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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	TraesCS4D01G230300	chr4D	100.000	2723	0	0	1	2723	390272595	390275317	0.000000e+00	5029
1	TraesCS4D01G230300	chr4D	83.445	447	33	21	1225	1667	93448543	93448134	7.120000e-101	377
2	TraesCS4D01G230300	chr4D	90.789	152	11	1	994	1145	93448734	93448586	1.650000e-47	200
3	TraesCS4D01G230300	chr4A	93.128	2794	102	31	1	2723	72025473	72028247	0.000000e+00	4013
4	TraesCS4D01G230300	chr4B	91.596	2356	79	29	1	2272	480058457	480060777	0.000000e+00	3144
5	TraesCS4D01G230300	chr4B	91.844	1925	62	34	856	2723	480059358	480061244	0.000000e+00	2597
6	TraesCS4D01G230300	chr4B	83.458	671	59	18	978	1648	339262973	339262355	6.540000e-161	577
7	TraesCS4D01G230300	chr7B	85.714	637	81	8	795	1431	366668203	366668829	0.000000e+00	664
8	TraesCS4D01G230300	chr7B	82.336	685	60	26	972	1648	375392469	375393100	3.090000e-149	538
9	TraesCS4D01G230300	chr2D	84.490	677	53	16	972	1648	118534389	118535013	2.980000e-174	621
10	TraesCS4D01G230300	chr2D	90.526	190	13	4	1480	1669	11560028	11559844	2.090000e-61	246
11	TraesCS4D01G230300	chr5D	85.810	599	41	22	880	1469	472426993	472427556	1.810000e-166	595
12	TraesCS4D01G230300	chr3A	83.010	671	58	30	978	1648	431136229	431136843	8.520000e-155	556
13	TraesCS4D01G230300	chr1D	81.221	655	49	34	994	1648	212526495	212527075	6.870000e-126	460
14	TraesCS4D01G230300	chr1D	86.730	422	31	10	1227	1648	239620972	239620576	1.920000e-121	446
15	TraesCS4D01G230300	chrUn	85.263	190	23	4	1480	1669	369331010	369330826	9.950000e-45	191
16	TraesCS4D01G230300	chr2A	82.895	152	8	1	1518	1669	12174705	12174572	1.320000e-23	121

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	TraesCS4D01G230300	chr4D	390272595	390275317	2722	False	5029.0	5029	100.000	1	2723	1	chr4D.!!$F1	2722
1	TraesCS4D01G230300	chr4D	93448134	93448734	600	True	288.5	377	87.117	994	1667	2	chr4D.!!$R1	673
2	TraesCS4D01G230300	chr4A	72025473	72028247	2774	False	4013.0	4013	93.128	1	2723	1	chr4A.!!$F1	2722
3	TraesCS4D01G230300	chr4B	480058457	480061244	2787	False	2870.5	3144	91.720	1	2723	2	chr4B.!!$F1	2722
4	TraesCS4D01G230300	chr4B	339262355	339262973	618	True	577.0	577	83.458	978	1648	1	chr4B.!!$R1	670
5	TraesCS4D01G230300	chr7B	366668203	366668829	626	False	664.0	664	85.714	795	1431	1	chr7B.!!$F1	636
6	TraesCS4D01G230300	chr7B	375392469	375393100	631	False	538.0	538	82.336	972	1648	1	chr7B.!!$F2	676
7	TraesCS4D01G230300	chr2D	118534389	118535013	624	False	621.0	621	84.490	972	1648	1	chr2D.!!$F1	676
8	TraesCS4D01G230300	chr5D	472426993	472427556	563	False	595.0	595	85.810	880	1469	1	chr5D.!!$F1	589
9	TraesCS4D01G230300	chr3A	431136229	431136843	614	False	556.0	556	83.010	978	1648	1	chr3A.!!$F1	670
10	TraesCS4D01G230300	chr1D	212526495	212527075	580	False	460.0	460	81.221	994	1648	1	chr1D.!!$F1	654

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
264	284	0.76489	CTCCAGAAACACCACAGGGA	59.235	55.0	0.0	0.0	38.05	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2176	2353	0.322008	AGGCTGCAACTCCTGTTAGC	60.322	55.0	0.5	0.0	36.93	3.09	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
49	53	4.588951	TGGTAGTGGTGATCTGGTGATATC	59.411	45.833	0.00	0.00	32.19	1.63
129	138	2.099141	TCACTTGTAGCAGGCACATC	57.901	50.000	0.00	0.00	0.00	3.06
264	284	0.764890	CTCCAGAAACACCACAGGGA	59.235	55.000	0.00	0.00	38.05	4.20
334	354	2.026262	TGTGCTATTCCTGGACCCTTTC	60.026	50.000	0.00	0.00	0.00	2.62
370	394	2.429610	TCCGTTTTAGAGATTCCCGGAG	59.570	50.000	0.73	0.00	38.02	4.63
422	446	2.941720	GTCCTCTGATTTGGCATCAGAC	59.058	50.000	15.09	5.28	46.66	3.51
470	494	4.046938	TCGGATACTTGTCTTGATCTGC	57.953	45.455	0.00	0.00	0.00	4.26
503	527	7.025365	CCACATTCAGACACATTCAGTTATTG	58.975	38.462	0.00	0.00	0.00	1.90
700	727	1.879575	AGTGCTTATCCACAGGGCTA	58.120	50.000	0.00	0.00	38.18	3.93
704	731	2.369860	TGCTTATCCACAGGGCTATCTG	59.630	50.000	0.00	0.00	40.40	2.90
706	733	3.262915	GCTTATCCACAGGGCTATCTGAT	59.737	47.826	8.72	0.00	38.11	2.90
724	751	2.028839	TGATTGCAAGCACTCCCATTTG	60.029	45.455	14.49	0.00	0.00	2.32
739	766	6.024552	TCCCATTTGTAAGATTCAGTTTGC	57.975	37.500	0.00	0.00	0.00	3.68
748	775	6.604396	TGTAAGATTCAGTTTGCCATGATCAT	59.396	34.615	1.18	1.18	0.00	2.45
835	882	2.414825	GCAGCTGAGACTAGAAACAAGC	59.585	50.000	20.43	0.00	0.00	4.01
851	898	4.228912	ACAAGCGATCCTTTTCAGTTTG	57.771	40.909	0.00	0.00	0.00	2.93
961	1043	7.281999	AGAGATAGATAAAGGAGCAAACAAAGC	59.718	37.037	0.00	0.00	0.00	3.51
1193	1311	2.477176	GCACCACCGACAGCAACAA	61.477	57.895	0.00	0.00	0.00	2.83
1194	1312	1.355210	CACCACCGACAGCAACAAC	59.645	57.895	0.00	0.00	0.00	3.32
1749	1908	2.954868	GTACGCCGTCCATCGCTG	60.955	66.667	0.00	0.00	38.35	5.18
1759	1918	0.673985	TCCATCGCTGCGCTTATACT	59.326	50.000	18.65	0.00	0.00	2.12
1760	1919	1.883926	TCCATCGCTGCGCTTATACTA	59.116	47.619	18.65	0.00	0.00	1.82
1761	1920	1.986378	CCATCGCTGCGCTTATACTAC	59.014	52.381	18.65	0.00	0.00	2.73
1762	1921	1.644295	CATCGCTGCGCTTATACTACG	59.356	52.381	18.65	0.72	0.00	3.51
1764	1923	1.866601	TCGCTGCGCTTATACTACGTA	59.133	47.619	18.65	0.00	0.00	3.57
1806	1965	3.350909	CTCCCGACGCCGATCAACA	62.351	63.158	0.00	0.00	38.22	3.33
1818	1980	2.420547	CCGATCAACAGATCATGGTGGT	60.421	50.000	9.42	3.65	44.98	4.16
1819	1981	3.181466	CCGATCAACAGATCATGGTGGTA	60.181	47.826	9.42	0.00	41.22	3.25
1850	2012	0.593518	TTTGTTTCATGCGTGCGTGG	60.594	50.000	13.66	0.00	33.99	4.94
1851	2013	2.126888	GTTTCATGCGTGCGTGGG	60.127	61.111	13.66	0.00	33.99	4.61
1852	2014	2.593148	TTTCATGCGTGCGTGGGT	60.593	55.556	13.66	0.00	33.99	4.51
1853	2015	1.301795	TTTCATGCGTGCGTGGGTA	60.302	52.632	13.66	0.00	33.99	3.69
1950	2116	2.298163	CCTACAACTTCCCGCGGTATAT	59.702	50.000	26.12	3.56	0.00	0.86
1951	2117	2.994186	ACAACTTCCCGCGGTATATT	57.006	45.000	26.12	10.31	0.00	1.28
1952	2118	4.022068	CCTACAACTTCCCGCGGTATATTA	60.022	45.833	26.12	5.24	0.00	0.98
2047	2224	6.090898	GCTAATAATGTTGTCGTGTGAGACTT	59.909	38.462	0.00	0.00	41.47	3.01
2176	2353	0.391528	TGCTGTCGGACCATGATGTG	60.392	55.000	5.55	0.00	0.00	3.21
2305	2511	6.765989	TCGAAAAAGAGAGGAGAAAATGACAA	59.234	34.615	0.00	0.00	0.00	3.18
2326	2532	5.185828	ACAAGCTGGGAAGTTGAAATATTCC	59.814	40.000	0.00	0.00	41.51	3.01
2362	2571	7.943079	TGCCAATTATAGCATAGCATAACAT	57.057	32.000	0.00	0.00	33.08	2.71
2363	2572	7.764331	TGCCAATTATAGCATAGCATAACATG	58.236	34.615	0.00	0.00	33.08	3.21
2373	2582	1.661480	CATAACATGGCATGGGGCG	59.339	57.895	29.49	12.71	46.16	6.13
2501	2714	2.470821	CCTCCTCCGCTTATAACAACG	58.529	52.381	0.00	0.00	0.00	4.10
2624	2837	2.772691	GCATTCAGGAGCAGCAGGC	61.773	63.158	0.00	0.00	45.30	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
129	138	1.681264	GACTTCCCTGGTGGTGTTTTG	59.319	52.381	0.00	0.00	34.77	2.44
194	204	1.518572	AGCTACGCCGAATTCACCG	60.519	57.895	6.22	9.48	0.00	4.94
264	284	1.273211	CCCTGGTGTTCCCATCCAAAT	60.273	52.381	0.00	0.00	44.15	2.32
370	394	1.518903	AAGCGTGGCCTCTTTTCTGC	61.519	55.000	3.32	0.00	0.00	4.26
422	446	2.029020	TGCTAAGCCTGGATATGCTACG	60.029	50.000	0.00	0.00	36.66	3.51
470	494	1.271001	TGTCTGAATGTGGAGTGCAGG	60.271	52.381	0.00	0.00	0.00	4.85
503	527	3.631145	TTTCAAGCTTCATGTGTGCTC	57.369	42.857	0.00	0.00	35.85	4.26
700	727	1.005097	TGGGAGTGCTTGCAATCAGAT	59.995	47.619	21.59	0.00	0.00	2.90
704	731	2.028748	ACAAATGGGAGTGCTTGCAATC	60.029	45.455	13.70	13.70	0.00	2.67
706	733	1.412079	ACAAATGGGAGTGCTTGCAA	58.588	45.000	0.00	0.00	0.00	4.08
724	751	6.441093	TGATCATGGCAAACTGAATCTTAC	57.559	37.500	0.00	0.00	0.00	2.34
739	766	4.510571	TCTTGTCAGTGTGATGATCATGG	58.489	43.478	14.30	0.00	0.00	3.66
748	775	2.279741	GTGTTGCTCTTGTCAGTGTGA	58.720	47.619	0.00	0.00	0.00	3.58
835	882	3.624326	TGCACAAACTGAAAAGGATCG	57.376	42.857	0.00	0.00	0.00	3.69
851	898	4.157289	ACTTGGTGAGATGATTTGATGCAC	59.843	41.667	0.00	0.00	0.00	4.57
961	1043	3.029074	CTGTCTGTTTTCTTTCGTTGCG	58.971	45.455	0.00	0.00	0.00	4.85
1759	1918	2.892852	AGTTGCACCAACCTAGTACGTA	59.107	45.455	4.60	0.00	44.49	3.57
1760	1919	1.690352	AGTTGCACCAACCTAGTACGT	59.310	47.619	4.60	0.00	44.49	3.57
1761	1920	2.334838	GAGTTGCACCAACCTAGTACG	58.665	52.381	4.60	0.00	44.49	3.67
1762	1921	2.288640	ACGAGTTGCACCAACCTAGTAC	60.289	50.000	4.60	0.00	44.49	2.73
1764	1923	0.756903	ACGAGTTGCACCAACCTAGT	59.243	50.000	4.60	0.89	44.49	2.57
1818	1980	4.517952	TGAAACAAATACGGGTCGTCTA	57.482	40.909	0.00	0.00	41.54	2.59
1819	1981	3.389925	TGAAACAAATACGGGTCGTCT	57.610	42.857	0.00	0.00	41.54	4.18
1952	2118	9.750125	CATGATTGATTGATCACATGAATCTTT	57.250	29.630	19.81	11.54	40.71	2.52
2176	2353	0.322008	AGGCTGCAACTCCTGTTAGC	60.322	55.000	0.50	0.00	36.93	3.09
2326	2532	1.016627	AATTGGCATCGTCGTCATGG	58.983	50.000	0.00	0.00	0.00	3.66
2359	2568	1.381599	ATTTCGCCCCATGCCATGT	60.382	52.632	3.63	0.00	36.24	3.21
2362	2571	3.459965	GCATTTCGCCCCATGCCA	61.460	61.111	0.00	0.00	40.04	4.92
2363	2572	3.459965	TGCATTTCGCCCCATGCC	61.460	61.111	6.26	0.00	44.49	4.40
2435	2644	4.214980	ACTTGACAGCATTTTCAGTTCG	57.785	40.909	0.00	0.00	0.00	3.95
2526	2739	5.527951	TGTTGTGTTCCATCTGTAATTTGC	58.472	37.500	0.00	0.00	0.00	3.68
2650	2865	3.791320	AGATGTGGGTGTAGAGAGGAAA	58.209	45.455	0.00	0.00	0.00	3.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.