AutoCloner

Multiple sequence alignment - TraesCS3B01G284200

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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	TraesCS3B01G284200	chr3B	100.000	2258	0	0	1	2258	455066131	455063874	0.000000e+00	4170.0
1	TraesCS3B01G284200	chr5B	98.099	789	11	2	1473	2258	658766752	658765965	0.000000e+00	1371.0
2	TraesCS3B01G284200	chr2B	97.719	789	15	1	1473	2258	91052874	91053662	0.000000e+00	1354.0
3	TraesCS3B01G284200	chr2B	97.338	789	18	1	1473	2258	91062538	91063326	0.000000e+00	1338.0
4	TraesCS3B01G284200	chr2B	97.085	789	19	2	1473	2257	91056062	91056850	0.000000e+00	1327.0
5	TraesCS3B01G284200	chr2B	96.701	788	23	1	1473	2257	91059351	91060138	0.000000e+00	1308.0
6	TraesCS3B01G284200	chr6B	96.578	789	24	1	1473	2258	462170873	462171661	0.000000e+00	1304.0
7	TraesCS3B01G284200	chrUn	96.914	713	19	1	1473	2182	411185830	411185118	0.000000e+00	1192.0
8	TraesCS3B01G284200	chrUn	96.634	713	21	1	1473	2182	411184402	411183690	0.000000e+00	1181.0
9	TraesCS3B01G284200	chr3D	91.197	852	50	9	1	832	354621066	354620220	0.000000e+00	1134.0
10	TraesCS3B01G284200	chr3D	94.028	653	28	3	831	1473	354620178	354619527	0.000000e+00	979.0
11	TraesCS3B01G284200	chr3A	93.529	680	42	2	616	1294	473213393	473212715	0.000000e+00	1011.0
12	TraesCS3B01G284200	chr3A	91.795	585	25	11	48	612	473216720	473216139	0.000000e+00	793.0
13	TraesCS3B01G284200	chr3A	96.053	76	3	0	1337	1412	473212718	473212643	8.470000e-25	124.0
14	TraesCS3B01G284200	chr3A	90.909	55	0	3	1419	1473	473212465	473212416	4.020000e-08	69.4
15	TraesCS3B01G284200	chr7D	88.619	782	86	1	1480	2258	131448184	131448965	0.000000e+00	948.0

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	TraesCS3B01G284200	chr3B	455063874	455066131	2257	True	4170.00	4170	100.00000	1	2258	1	chr3B.!!$R1	2257
1	TraesCS3B01G284200	chr5B	658765965	658766752	787	True	1371.00	1371	98.09900	1473	2258	1	chr5B.!!$R1	785
2	TraesCS3B01G284200	chr2B	91052874	91063326	10452	False	1331.75	1354	97.21075	1473	2258	4	chr2B.!!$F1	785
3	TraesCS3B01G284200	chr6B	462170873	462171661	788	False	1304.00	1304	96.57800	1473	2258	1	chr6B.!!$F1	785
4	TraesCS3B01G284200	chrUn	411183690	411185830	2140	True	1186.50	1192	96.77400	1473	2182	2	chrUn.!!$R1	709
5	TraesCS3B01G284200	chr3D	354619527	354621066	1539	True	1056.50	1134	92.61250	1	1473	2	chr3D.!!$R1	1472
6	TraesCS3B01G284200	chr3A	473212416	473216720	4304	True	499.35	1011	93.07150	48	1473	4	chr3A.!!$R1	1425
7	TraesCS3B01G284200	chr7D	131448184	131448965	781	False	948.00	948	88.61900	1480	2258	1	chr7D.!!$F1	778

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
898	3724	0.178992	TGGAGCCAAACCCACTCTTG	60.179	55.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1738	11214	2.418197	CGCGAAAACTCATTCCTCCCTA	60.418	50.0	0.0	0.0	0.0	3.53	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
40	41	9.877178	TGTGGAAAAAGCTTTAATTCAGTAAAA	57.123	25.926	20.02	1.78	0.00	1.52
64	65	3.153919	TGGAATGCCTGTCTTGTAAACC	58.846	45.455	0.00	0.00	34.31	3.27
92	93	2.676463	GCCTGTTTGTGCTTGGTTTTCA	60.676	45.455	0.00	0.00	0.00	2.69
103	104	4.217550	TGCTTGGTTTTCAATGGTACTAGC	59.782	41.667	0.00	0.00	34.45	3.42
160	182	4.036144	GGAGAAATGCTGCTTAAGATGTCC	59.964	45.833	6.67	0.00	31.32	4.02
173	195	3.611766	AGATGTCCTCCTGTTAAACCG	57.388	47.619	0.00	0.00	0.00	4.44
178	200	1.000060	TCCTCCTGTTAAACCGTGTCG	60.000	52.381	0.00	0.00	0.00	4.35
179	201	1.000060	CCTCCTGTTAAACCGTGTCGA	60.000	52.381	0.00	0.00	0.00	4.20
181	203	1.142474	CCTGTTAAACCGTGTCGACC	58.858	55.000	14.12	3.43	0.00	4.79
462	484	1.078214	TGTGCTCTGCATACTGGCC	60.078	57.895	0.00	0.00	41.91	5.36
543	565	6.822676	TGAAATCATTTCCACAATTATTGGCC	59.177	34.615	7.68	0.00	38.90	5.36
553	575	5.490159	CACAATTATTGGCCTTCCACATTT	58.510	37.500	3.32	0.00	43.33	2.32
583	605	1.242076	CTGAGTTGCTTGGAGTTGGG	58.758	55.000	0.00	0.00	0.00	4.12
584	606	0.843309	TGAGTTGCTTGGAGTTGGGA	59.157	50.000	0.00	0.00	0.00	4.37
585	607	1.239347	GAGTTGCTTGGAGTTGGGAC	58.761	55.000	0.00	0.00	0.00	4.46
591	613	0.607489	CTTGGAGTTGGGACTGCTGG	60.607	60.000	0.00	0.00	43.87	4.85
612	634	4.277174	TGGTGATGCGTGTTTTTCTGTTAT	59.723	37.500	0.00	0.00	0.00	1.89
613	635	4.616802	GGTGATGCGTGTTTTTCTGTTATG	59.383	41.667	0.00	0.00	0.00	1.90
626	3390	3.073678	TCTGTTATGCATGTGCTCGTTT	58.926	40.909	10.16	0.00	42.66	3.60
666	3431	3.161866	ACTTGGTATTTTGCGTGGGAAT	58.838	40.909	0.00	0.00	0.00	3.01
778	3561	3.627395	AGTATTCCGTGAGCATCCAAA	57.373	42.857	0.00	0.00	0.00	3.28
799	3582	2.879646	AGAAATTTAACGCCACGGAACA	59.120	40.909	0.00	0.00	0.00	3.18
824	3607	6.811253	ATTTAACAGTCAAAATCTACGCCA	57.189	33.333	0.00	0.00	0.00	5.69
898	3724	0.178992	TGGAGCCAAACCCACTCTTG	60.179	55.000	0.00	0.00	0.00	3.02
903	3729	1.754226	GCCAAACCCACTCTTGACAAA	59.246	47.619	0.00	0.00	0.00	2.83
952	3778	2.413310	ACCGGTATAAAACCCAGCTG	57.587	50.000	4.49	6.78	46.62	4.24
995	3823	1.574702	CGAAGAAACCAAGACCCCGC	61.575	60.000	0.00	0.00	0.00	6.13
996	3824	0.250770	GAAGAAACCAAGACCCCGCT	60.251	55.000	0.00	0.00	0.00	5.52
1018	3846	2.362369	ATGTCAGTCGGCCAGAGGG	61.362	63.158	2.24	0.00	37.18	4.30
1029	3857	3.003173	CAGAGGGCCACCGAGGAA	61.003	66.667	6.18	0.00	43.47	3.36
1095	3923	2.359169	CCGCCTCTTGTCTGGCCTA	61.359	63.158	3.32	0.00	45.90	3.93
1098	3926	1.903877	GCCTCTTGTCTGGCCTAGCA	61.904	60.000	3.32	0.00	43.11	3.49
1276	4104	0.400213	ATTCGGCTTGGACTGGACAA	59.600	50.000	0.00	0.00	0.00	3.18
1405	4233	9.864034	CATTCATTAATTCGTTGTATGTACTCC	57.136	33.333	0.00	0.00	0.00	3.85
1437	4436	7.685481	TGTCTCTCCCATTCTTAACAAATACA	58.315	34.615	0.00	0.00	0.00	2.29
1442	4441	7.769044	TCTCCCATTCTTAACAAATACAGTAGC	59.231	37.037	0.00	0.00	0.00	3.58
1648	7835	1.398958	GGTTTGCAAAGGCCTCACCA	61.399	55.000	13.26	0.00	43.14	4.17
1738	11214	1.967319	ACTTGCATCACCGAAGTGTT	58.033	45.000	0.00	0.00	44.83	3.32
1750	11226	2.500098	CCGAAGTGTTAGGGAGGAATGA	59.500	50.000	0.00	0.00	0.00	2.57
1785	11261	3.411446	TGAGTTATTCAACCTGGCACTG	58.589	45.455	0.00	0.00	35.05	3.66
2171	14837	0.257328	TTGAATATCCCCTTGCGCCA	59.743	50.000	4.18	0.00	0.00	5.69
2173	14839	0.465460	GAATATCCCCTTGCGCCACA	60.465	55.000	4.18	0.00	0.00	4.17
2174	14840	0.033601	AATATCCCCTTGCGCCACAA	60.034	50.000	4.18	0.00	36.62	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	5.279456	GGTTTACAAGACAGGCATTCCATTT	60.279	40.000	0.00	0.00	33.74	2.32
42	43	3.763897	GGTTTACAAGACAGGCATTCCAT	59.236	43.478	0.00	0.00	33.74	3.41
64	65	3.673484	CACAAACAGGCAGGGGCG	61.673	66.667	0.00	0.00	42.47	6.13
92	93	4.385310	GGACCATTTCCAGCTAGTACCATT	60.385	45.833	0.00	0.00	45.10	3.16
160	182	2.056577	GTCGACACGGTTTAACAGGAG	58.943	52.381	11.55	0.00	0.00	3.69
173	195	4.813296	AGAAAACAAATGAGGTCGACAC	57.187	40.909	18.91	11.25	0.00	3.67
178	200	9.565213	CATTAGATCAAGAAAACAAATGAGGTC	57.435	33.333	0.00	0.00	0.00	3.85
179	201	8.526147	CCATTAGATCAAGAAAACAAATGAGGT	58.474	33.333	0.00	0.00	0.00	3.85
181	203	9.918630	AACCATTAGATCAAGAAAACAAATGAG	57.081	29.630	0.00	0.00	0.00	2.90
208	230	4.473444	TGACCTGGAAAGCAAGAAGAATT	58.527	39.130	0.00	0.00	0.00	2.17
462	484	9.535878	GATATAGAACCTACTGAGAAAACTTGG	57.464	37.037	0.00	0.00	0.00	3.61
543	565	7.439056	ACTCAGCAAAAACAATAAATGTGGAAG	59.561	33.333	0.00	0.00	42.99	3.46
553	575	5.049167	CCAAGCAACTCAGCAAAAACAATA	58.951	37.500	0.00	0.00	36.85	1.90
583	605	1.230635	AACACGCATCACCAGCAGTC	61.231	55.000	0.00	0.00	0.00	3.51
584	606	0.819259	AAACACGCATCACCAGCAGT	60.819	50.000	0.00	0.00	0.00	4.40
585	607	0.311790	AAAACACGCATCACCAGCAG	59.688	50.000	0.00	0.00	0.00	4.24
591	613	4.088496	GCATAACAGAAAAACACGCATCAC	59.912	41.667	0.00	0.00	0.00	3.06
612	634	1.069296	GCACTTAAACGAGCACATGCA	60.069	47.619	6.64	0.00	45.16	3.96
613	635	1.197721	AGCACTTAAACGAGCACATGC	59.802	47.619	0.00	0.00	42.49	4.06
648	3413	5.244178	ACTTAAATTCCCACGCAAAATACCA	59.756	36.000	0.00	0.00	0.00	3.25
655	3420	3.759086	TGCATACTTAAATTCCCACGCAA	59.241	39.130	0.00	0.00	0.00	4.85
778	3561	2.879646	TGTTCCGTGGCGTTAAATTTCT	59.120	40.909	0.00	0.00	0.00	2.52
799	3582	7.653647	TGGCGTAGATTTTGACTGTTAAATTT	58.346	30.769	0.00	0.00	0.00	1.82
824	3607	5.368989	GTCCAAGGAATCGACTTTCCATAT	58.631	41.667	17.84	3.50	46.40	1.78
898	3724	2.589442	TGTCCCGCACGGTTTGTC	60.589	61.111	8.49	0.00	0.00	3.18
952	3778	5.221244	GGTGAAATTGTGGATTATAGGTGGC	60.221	44.000	0.00	0.00	0.00	5.01
995	3823	2.821366	GGCCGACTGACATGCCAG	60.821	66.667	7.56	7.56	43.46	4.85
1069	3897	0.824759	GACAAGAGGCGGTCATACCT	59.175	55.000	0.00	0.00	39.65	3.08
1276	4104	2.938354	GCTGTGAAGTGCCATCAGT	58.062	52.632	0.00	0.00	0.00	3.41
1349	4177	4.521639	TGAAATCTTCAGCAGCATCTTGTT	59.478	37.500	0.00	0.00	34.08	2.83
1388	4216	5.769484	AGATCGGAGTACATACAACGAAT	57.231	39.130	10.65	3.03	39.02	3.34
1405	4233	5.720371	AAGAATGGGAGAGACATAGATCG	57.280	43.478	0.00	0.00	0.00	3.69
1437	4436	3.768757	TGCTGCCCAAATTTTATGCTACT	59.231	39.130	0.00	0.00	0.00	2.57
1738	11214	2.418197	CGCGAAAACTCATTCCTCCCTA	60.418	50.000	0.00	0.00	0.00	3.53
1750	11226	5.637810	TGAATAACTCAAGATCGCGAAAACT	59.362	36.000	15.24	10.56	0.00	2.66
1979	11455	5.878406	ATCTTCCCAAATCGAGATAGTGT	57.122	39.130	0.00	0.00	0.00	3.55
2171	14837	2.760092	CGAAAATCATCACCCCCATTGT	59.240	45.455	0.00	0.00	0.00	2.71
2173	14839	3.290710	CTCGAAAATCATCACCCCCATT	58.709	45.455	0.00	0.00	0.00	3.16
2174	14840	2.936202	CTCGAAAATCATCACCCCCAT	58.064	47.619	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.