AutoCloner

Multiple sequence alignment - TraesCS1D01G051700

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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	TraesCS1D01G051700	chr1D	100.000	4582	0	0	1	4582	32478445	32483026	0.000000e+00	8462.0
1	TraesCS1D01G051700	chr1D	77.904	353	65	9	2259	2605	14484317	14483972	1.670000e-49	207.0
2	TraesCS1D01G051700	chr1D	74.317	366	64	17	2254	2615	210477520	210477859	1.340000e-25	128.0
3	TraesCS1D01G051700	chr1B	95.869	1743	56	10	528	2264	49933110	49934842	0.000000e+00	2806.0
4	TraesCS1D01G051700	chr1B	90.919	936	60	12	3404	4319	49937206	49938136	0.000000e+00	1234.0
5	TraesCS1D01G051700	chr1B	91.709	796	44	5	2603	3396	49934838	49935613	0.000000e+00	1085.0
6	TraesCS1D01G051700	chr1B	83.422	561	87	3	739	1293	685366084	685365524	2.440000e-142	516.0
7	TraesCS1D01G051700	chr1B	93.609	266	7	5	1	257	49932554	49932818	5.560000e-104	388.0
8	TraesCS1D01G051700	chr1B	84.030	263	13	13	290	524	49932818	49933079	4.610000e-55	226.0
9	TraesCS1D01G051700	chr1B	90.526	95	8	1	4356	4450	49938222	49938315	1.730000e-24	124.0
10	TraesCS1D01G051700	chr1A	92.428	1215	43	12	311	1478	31161080	31162292	0.000000e+00	1688.0
11	TraesCS1D01G051700	chr1A	94.480	942	43	3	2460	3396	31174660	31175597	0.000000e+00	1443.0
12	TraesCS1D01G051700	chr1A	93.496	492	23	4	3404	3893	31176044	31176528	0.000000e+00	723.0
13	TraesCS1D01G051700	chr1A	91.076	381	26	6	3942	4319	31176528	31176903	4.090000e-140	508.0
14	TraesCS1D01G051700	chr1A	95.349	258	8	1	1476	1733	31174412	31174665	1.530000e-109	407.0
15	TraesCS1D01G051700	chr1A	90.323	310	16	7	1	306	31160619	31160918	1.190000e-105	394.0
16	TraesCS1D01G051700	chr1A	92.135	267	19	1	4318	4582	31176965	31177231	4.330000e-100	375.0
17	TraesCS1D01G051700	chr1A	79.885	174	33	2	2312	2483	15433218	15433391	4.810000e-25	126.0
18	TraesCS1D01G051700	chr5B	81.720	558	93	5	739	1290	61369162	61369716	1.500000e-124	457.0
19	TraesCS1D01G051700	chr4B	82.184	348	60	2	2258	2604	486624536	486624190	9.640000e-77	298.0
20	TraesCS1D01G051700	chr4B	94.118	85	4	1	1363	1446	447451794	447451710	1.340000e-25	128.0
21	TraesCS1D01G051700	chr7D	78.857	350	63	10	2259	2604	24116185	24116527	4.610000e-55	226.0
22	TraesCS1D01G051700	chr3D	75.637	353	76	8	2256	2605	582229316	582228971	2.840000e-37	167.0
23	TraesCS1D01G051700	chr4D	75.482	363	62	13	2246	2604	38525499	38525838	7.940000e-33	152.0
24	TraesCS1D01G051700	chr3B	76.027	292	59	9	2256	2544	779196932	779197215	1.720000e-29	141.0
25	TraesCS1D01G051700	chr2D	74.862	362	64	13	2246	2604	452994109	452993772	6.180000e-29	139.0
26	TraesCS1D01G051700	chr7A	95.294	85	3	1	1363	1446	181833294	181833210	2.880000e-27	134.0
27	TraesCS1D01G051700	chr4A	82.667	150	25	1	2341	2489	697989543	697989394	1.030000e-26	132.0
28	TraesCS1D01G051700	chr4A	93.182	44	3	0	2440	2483	86703053	86703010	1.060000e-06	65.8
29	TraesCS1D01G051700	chr3A	91.489	94	6	2	1358	1449	57262242	57262149	1.340000e-25	128.0
30	TraesCS1D01G051700	chr2B	93.182	88	5	1	1360	1446	483452950	483453037	1.340000e-25	128.0
31	TraesCS1D01G051700	chr2B	92.857	42	2	1	2257	2298	414804100	414804140	4.950000e-05	60.2
32	TraesCS1D01G051700	chrUn	92.941	85	5	1	1363	1446	31863630	31863546	6.230000e-24	122.0
33	TraesCS1D01G051700	chr2A	91.954	87	6	1	1363	1448	96074910	96074996	2.240000e-23	121.0
34	TraesCS1D01G051700	chr2A	91.860	86	6	1	1362	1446	650624329	650624414	8.050000e-23	119.0
35	TraesCS1D01G051700	chr6A	100.000	50	0	0	3288	3337	490323130	490323081	4.880000e-15	93.5

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	TraesCS1D01G051700	chr1D	32478445	32483026	4581	False	8462.000000	8462	100.000000	1	4582	1	chr1D.!!$F1	4581
1	TraesCS1D01G051700	chr1B	49932554	49938315	5761	False	977.166667	2806	91.110333	1	4450	6	chr1B.!!$F1	4449
2	TraesCS1D01G051700	chr1B	685365524	685366084	560	True	516.000000	516	83.422000	739	1293	1	chr1B.!!$R1	554
3	TraesCS1D01G051700	chr1A	31160619	31162292	1673	False	1041.000000	1688	91.375500	1	1478	2	chr1A.!!$F2	1477
4	TraesCS1D01G051700	chr1A	31174412	31177231	2819	False	691.200000	1443	93.307200	1476	4582	5	chr1A.!!$F3	3106
5	TraesCS1D01G051700	chr5B	61369162	61369716	554	False	457.000000	457	81.720000	739	1290	1	chr5B.!!$F1	551

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	Hairpin	End Stability	Orientation
841	1086	0.113972	TGGGGAAACATGTGATGGCA	59.886	50.000	33.6	4.92	F
2078	2327	1.343142	AGTAACGATGCTGTGTGTCCA	59.657	47.619	0.0	4.02	F
2407	2656	0.106918	AGAGAAAACCCACCAACGCA	60.107	50.000	0.0	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2388	2637	0.106918	TGCGTTGGTGGGTTTTCTCT	60.107	50.0	0.00	0.00	0.00	3.10	R
3563	5476	0.098905	GTCAGTCGCGATCTGCAGTA	59.901	55.0	24.59	11.57	46.97	2.74	R
3923	5853	0.535335	TAGCCCAACGATGACACCTC	59.465	55.0	0.00	0.00	0.00	3.85	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	65	2.939103	CGTGGAGGAAGAAATAGCAAGG	59.061	50.000	0.00	0.00	0.00	3.61
211	224	3.131223	TGCTCTTCAGTACTGTAGATGGC	59.869	47.826	26.51	25.49	36.61	4.40
221	234	3.209410	ACTGTAGATGGCAAAGCATAGC	58.791	45.455	0.00	0.00	0.00	2.97
388	562	1.051812	AGCTGGCCTACGCTCATAAT	58.948	50.000	3.32	0.00	34.44	1.28
422	603	1.748493	TGTTTTGCACACCCAGAGAAC	59.252	47.619	0.00	0.00	0.00	3.01
425	606	0.546122	TTGCACACCCAGAGAACAGT	59.454	50.000	0.00	0.00	0.00	3.55
428	609	2.171659	TGCACACCCAGAGAACAGTTAA	59.828	45.455	0.00	0.00	0.00	2.01
429	610	3.211045	GCACACCCAGAGAACAGTTAAA	58.789	45.455	0.00	0.00	0.00	1.52
491	693	5.008415	TGCTGTTGTTTTTAAATTGGGCATG	59.992	36.000	0.00	0.00	0.00	4.06
706	941	7.453393	CCATATTAATTCTTGCTAGTGAGGGA	58.547	38.462	0.00	0.00	0.00	4.20
719	954	6.780522	TGCTAGTGAGGGAAATTAAGGTTTTT	59.219	34.615	0.00	0.00	0.00	1.94
765	1004	5.106948	GGTTCATGTGCATATTGAGATACCG	60.107	44.000	0.00	0.00	0.00	4.02
807	1046	1.538419	GCAAGGCTCGACTATGGTACC	60.538	57.143	4.43	4.43	0.00	3.34
841	1086	0.113972	TGGGGAAACATGTGATGGCA	59.886	50.000	0.00	0.00	33.60	4.92
1176	1421	1.590238	CGTGCTTGTCGAGATGATTCC	59.410	52.381	0.00	0.00	0.00	3.01
1377	1622	6.212791	AGCTGTGTTATACTCCCTCTGTAAAA	59.787	38.462	0.00	0.00	0.00	1.52
1447	1692	9.597681	TCTTATATTTCTTACGGAGGGAGTAAT	57.402	33.333	0.00	0.00	34.10	1.89
1680	1928	2.212812	TGCATGCCATGTCCAACTTA	57.787	45.000	16.68	0.00	0.00	2.24
1722	1970	5.192927	TGCTAACCCTTGGTATCTCAATTG	58.807	41.667	0.00	0.00	33.12	2.32
1838	2087	3.399440	TTCTTTTGCCGGAAATGCATT	57.601	38.095	5.05	5.99	38.76	3.56
1856	2105	8.774890	AATGCATTCAAACATACTGCAAAATA	57.225	26.923	5.99	0.00	45.03	1.40
1907	2156	3.435327	TGACGTGTCCTGATACAAAATGC	59.565	43.478	0.00	0.00	0.00	3.56
1926	2175	1.947456	GCGAAGGTGTTGTTTCTCCTT	59.053	47.619	0.00	0.00	41.87	3.36
1928	2177	3.059120	GCGAAGGTGTTGTTTCTCCTTAC	60.059	47.826	0.00	0.00	40.11	2.34
2069	2318	3.197766	TGGAGGATGAAAGTAACGATGCT	59.802	43.478	0.00	0.00	0.00	3.79

Showing 1 to 25 of 213 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	65	2.115291	GTGAATCCCCGCCAGCTTC	61.115	63.158	0.00	0.00	0.00	3.86
221	234	4.662468	TTCCATGAAGCTAGCTACTCAG	57.338	45.455	19.70	12.05	0.00	3.35
260	273	8.740906	ACTACGGTGATCTAATATGGAATGTAG	58.259	37.037	0.00	0.00	0.00	2.74
388	562	5.929697	TGCAAAACACAACAAAAATGTCA	57.070	30.435	0.00	0.00	0.00	3.58
429	610	1.117142	AGCACAAAAGCAGGCATGGT	61.117	50.000	0.00	0.00	39.32	3.55
599	834	6.092122	TGTTTAAAATGACTATGCTGTCTCCG	59.908	38.462	0.00	0.00	37.79	4.63
637	872	2.418334	GGACATACCTGGAAAGACCGTC	60.418	54.545	0.00	0.00	42.61	4.79
765	1004	4.440802	GCCGAGACATCTATACCATCATCC	60.441	50.000	0.00	0.00	0.00	3.51
807	1046	6.868622	TGTTTCCCCATAATTTAATGTTCCG	58.131	36.000	0.00	0.00	0.00	4.30
841	1086	6.119536	TGTAAACAAGATTATCCGAGGCATT	58.880	36.000	0.00	0.00	0.00	3.56
1176	1421	6.481976	TCCTTGTAATTATAACATCAGGTGCG	59.518	38.462	0.00	0.00	30.22	5.34
1583	1828	3.103742	ACCCTCAGAACAAAGGCAAAAA	58.896	40.909	0.00	0.00	0.00	1.94
1584	1829	2.745968	ACCCTCAGAACAAAGGCAAAA	58.254	42.857	0.00	0.00	0.00	2.44
1701	1949	6.659242	ACAACAATTGAGATACCAAGGGTTAG	59.341	38.462	13.59	0.00	37.09	2.34
1770	2018	4.813027	TCGACACCTGTGAAGTAATAACC	58.187	43.478	3.94	0.00	0.00	2.85
1779	2028	3.311322	GTGACAAAATCGACACCTGTGAA	59.689	43.478	3.94	0.00	0.00	3.18
1838	2087	7.880105	TGACATGTATTTTGCAGTATGTTTGA	58.120	30.769	0.00	0.00	39.31	2.69
1856	2105	3.864789	ACAGTTCCTTCCTTGACATGT	57.135	42.857	0.00	0.00	0.00	3.21
1907	2156	4.124238	TGTAAGGAGAAACAACACCTTCG	58.876	43.478	0.00	0.00	40.29	3.79
1926	2175	5.123186	CCGCCAGAAGTGTTTTCAATATGTA	59.877	40.000	0.00	0.00	0.00	2.29
1928	2177	4.155826	TCCGCCAGAAGTGTTTTCAATATG	59.844	41.667	0.00	0.00	0.00	1.78
2069	2318	5.029807	TGAATAGACAACTTGGACACACA	57.970	39.130	0.00	0.00	0.00	3.72
2078	2327	4.453819	GTGCAGAAGCTGAATAGACAACTT	59.546	41.667	0.00	0.00	42.74	2.66
2102	2351	4.245660	CATGACGGTGAGATGTACAAAGT	58.754	43.478	0.00	0.00	0.00	2.66
2114	2363	0.250553	GTTTCCCCACATGACGGTGA	60.251	55.000	0.00	0.00	41.32	4.02

Showing 1 to 25 of 230 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.