AutoCloner

Multiple sequence alignment - TraesCS3D01G378600

Loading Multiple Alignment...

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	TraesCS3D01G378600	chr3D	100.000	3078	0	0	1	3078	495809498	495806421	0.000000e+00	5685.0
1	TraesCS3D01G378600	chr3D	98.092	2359	42	3	1	2357	539239548	539241905	0.000000e+00	4104.0
2	TraesCS3D01G378600	chr3D	79.252	294	41	9	1	292	608568827	608569102	1.460000e-43	187.0
3	TraesCS3D01G378600	chr3D	88.235	136	12	4	2808	2941	601236380	601236513	3.180000e-35	159.0
4	TraesCS3D01G378600	chr3D	82.727	110	16	3	2830	2938	584976868	584976761	9.090000e-16	95.3
5	TraesCS3D01G378600	chr3D	96.970	33	0	1	67	99	178025796	178025765	2.000000e-03	54.7
6	TraesCS3D01G378600	chr3B	93.157	1739	91	13	1342	3075	811751497	811753212	0.000000e+00	2527.0
7	TraesCS3D01G378600	chr3B	91.091	1403	110	8	967	2359	714915997	714917394	0.000000e+00	1884.0
8	TraesCS3D01G378600	chr3B	93.706	286	17	1	1060	1345	811748712	811748996	7.890000e-116	427.0
9	TraesCS3D01G378600	chr3B	86.099	223	23	3	842	1056	811743034	811743256	1.850000e-57	233.0
10	TraesCS3D01G378600	chr3B	80.000	135	20	6	1	131	222796075	222796206	3.270000e-15	93.5
11	TraesCS3D01G378600	chr3A	95.866	1524	57	4	838	2359	674459659	674461178	0.000000e+00	2460.0
12	TraesCS3D01G378600	chr2D	89.020	255	23	5	2828	3078	642507859	642507606	8.290000e-81	311.0
13	TraesCS3D01G378600	chr2D	89.300	243	25	1	2834	3075	583831468	583831710	1.390000e-78	303.0
14	TraesCS3D01G378600	chr2D	84.106	151	22	2	291	439	351065007	351064857	8.900000e-31	145.0
15	TraesCS3D01G378600	chr2D	82.432	148	21	4	148	292	360994011	360993866	1.160000e-24	124.0
16	TraesCS3D01G378600	chr2D	87.500	48	3	3	69	114	411388028	411388074	6.000000e-03	52.8
17	TraesCS3D01G378600	chr6A	86.730	211	23	5	602	810	169514999	169514792	2.390000e-56	230.0
18	TraesCS3D01G378600	chr6A	96.970	33	1	0	2808	2840	87535702	87535670	4.290000e-04	56.5
19	TraesCS3D01G378600	chr6A	100.000	28	0	0	2810	2837	87535694	87535667	6.000000e-03	52.8
20	TraesCS3D01G378600	chr2B	83.810	210	31	3	602	810	667259421	667259214	2.420000e-46	196.0
21	TraesCS3D01G378600	chr2B	82.667	150	25	1	291	439	110428305	110428454	6.930000e-27	132.0
22	TraesCS3D01G378600	chr2B	82.000	150	25	2	291	439	651366691	651366543	3.220000e-25	126.0
23	TraesCS3D01G378600	chr5B	78.689	305	50	15	1	301	391130579	391130872	4.050000e-44	189.0
24	TraesCS3D01G378600	chr5B	79.545	176	31	5	291	462	497381819	497381645	1.500000e-23	121.0
25	TraesCS3D01G378600	chr5B	86.111	108	15	0	2834	2941	478129960	478130067	1.940000e-22	117.0
26	TraesCS3D01G378600	chr5B	100.000	30	0	0	2810	2839	489813971	489814000	4.290000e-04	56.5
27	TraesCS3D01G378600	chr7D	82.381	210	35	2	602	810	26835496	26835704	6.780000e-42	182.0
28	TraesCS3D01G378600	chr7D	81.281	203	31	6	611	810	428711584	428711386	1.140000e-34	158.0
29	TraesCS3D01G378600	chr7D	83.007	153	25	1	148	299	483874102	483873950	1.490000e-28	137.0
30	TraesCS3D01G378600	chr7D	82.394	142	22	3	151	290	413108796	413108656	1.500000e-23	121.0
31	TraesCS3D01G378600	chr7D	78.689	122	16	6	10	130	505578592	505578704	4.260000e-09	73.1
32	TraesCS3D01G378600	chr7D	78.571	98	17	4	34	130	450273160	450273254	9.220000e-06	62.1
33	TraesCS3D01G378600	chr1B	80.357	224	38	4	590	810	513475682	513475902	6.830000e-37	165.0
34	TraesCS3D01G378600	chr1B	83.962	106	15	2	2833	2938	16432864	16432761	1.950000e-17	100.0
35	TraesCS3D01G378600	chr1B	97.500	40	0	1	2810	2849	598294254	598294292	1.980000e-07	67.6
36	TraesCS3D01G378600	chr1B	93.182	44	3	0	2810	2853	307155619	307155576	7.120000e-07	65.8
37	TraesCS3D01G378600	chr1B	83.333	66	10	1	66	131	545434860	545434796	3.310000e-05	60.2
38	TraesCS3D01G378600	chr4B	80.556	216	34	7	595	807	89455034	89454824	3.180000e-35	159.0
39	TraesCS3D01G378600	chr4B	83.562	146	21	3	151	295	618070752	618070609	1.930000e-27	134.0
40	TraesCS3D01G378600	chrUn	80.597	201	36	2	602	802	290640424	290640621	5.320000e-33	152.0
41	TraesCS3D01G378600	chrUn	80.597	201	36	2	602	802	290646149	290646346	5.320000e-33	152.0
42	TraesCS3D01G378600	chrUn	82.386	176	28	3	291	464	126962941	126962767	1.910000e-32	150.0
43	TraesCS3D01G378600	chr5A	84.106	151	22	2	291	439	510547031	510547181	8.900000e-31	145.0
44	TraesCS3D01G378600	chr5A	85.047	107	11	4	2837	2941	345570118	345570015	1.510000e-18	104.0
45	TraesCS3D01G378600	chr7A	84.058	138	21	1	151	287	261688242	261688379	6.930000e-27	132.0
46	TraesCS3D01G378600	chr5D	81.875	160	23	6	294	449	264075580	264075423	2.490000e-26	130.0
47	TraesCS3D01G378600	chr1D	77.193	228	47	4	291	514	468694599	468694373	8.960000e-26	128.0
48	TraesCS3D01G378600	chr1A	85.345	116	15	2	2825	2939	31949562	31949676	5.390000e-23	119.0
49	TraesCS3D01G378600	chr7B	75.833	240	42	12	1	235	657370777	657370549	1.170000e-19	108.0

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	TraesCS3D01G378600	chr3D	495806421	495809498	3077	True	5685	5685	100.0000	1	3078	1	chr3D.!!$R2	3077
1	TraesCS3D01G378600	chr3D	539239548	539241905	2357	False	4104	4104	98.0920	1	2357	1	chr3D.!!$F1	2356
2	TraesCS3D01G378600	chr3B	714915997	714917394	1397	False	1884	1884	91.0910	967	2359	1	chr3B.!!$F2	1392
3	TraesCS3D01G378600	chr3B	811748712	811753212	4500	False	1477	2527	93.4315	1060	3075	2	chr3B.!!$F4	2015
4	TraesCS3D01G378600	chr3A	674459659	674461178	1519	False	2460	2460	95.8660	838	2359	1	chr3A.!!$F1	1521

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
641	643	0.719465	GTGGCACGAAGTAACATCGG	59.281	55.000	0.0	0.0	41.61	4.18	F
1058	1062	8.553696	CAAAAAGAAAAAGATCAAACATGGAGG	58.446	33.333	0.0	0.0	0.00	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1460	3968	0.255604	ATGTGGACCGATTCATGGCA	59.744	50.0	0.00	0.00	0.00	4.92	R
2781	5303	0.320073	CCAAACCCAACTGCAGCATG	60.320	55.0	15.27	13.35	40.87	4.06	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
238	240	2.162754	GCATAACACGTCCGGACCG	61.163	63.158	28.52	23.77	0.00	4.79
411	413	7.870826	TGAAATCCGGCATAAAATGTATACAG	58.129	34.615	11.91	0.00	0.00	2.74
444	446	3.282157	CGCCTCCCGCATTCATGG	61.282	66.667	0.00	0.00	37.30	3.66
518	520	2.500098	AGCGTTCAAGATGCCCTAACTA	59.500	45.455	0.00	0.00	41.38	2.24
597	599	5.774690	AGAAGATGTGGTGGCATTTTCTTTA	59.225	36.000	6.17	0.00	43.37	1.85
641	643	0.719465	GTGGCACGAAGTAACATCGG	59.281	55.000	0.00	0.00	41.61	4.18
767	770	8.600449	TGCCATTTTTGAATAACTAAACTTGG	57.400	30.769	0.00	0.00	33.89	3.61
1058	1062	8.553696	CAAAAAGAAAAAGATCAAACATGGAGG	58.446	33.333	0.00	0.00	0.00	4.30
1856	4365	0.961753	CTTGGAGGAGCCCACAAAAC	59.038	55.000	0.00	0.00	35.62	2.43
1903	4412	0.602905	CCGGACACACTTCCTTGACC	60.603	60.000	0.00	0.00	32.88	4.02
2061	4572	3.858129	GCGGGGAAACGATGTCGATAATA	60.858	47.826	9.67	0.00	43.02	0.98
2110	4627	2.921538	CTACCGAGCCAGACGAAGCG	62.922	65.000	0.00	0.00	0.00	4.68
2359	4876	7.945033	AAAAACCAGTTGTTAGTTGCATATG	57.055	32.000	0.00	0.00	35.67	1.78
2364	4881	5.880332	CCAGTTGTTAGTTGCATATGTAGGT	59.120	40.000	4.29	0.00	0.00	3.08
2409	4927	3.168963	CGTTGCTGAGATTTGATGCAAG	58.831	45.455	0.00	0.00	43.00	4.01
2455	4973	7.769044	TCCTTAACAGTATCTGAACTAATTGCC	59.231	37.037	3.70	0.00	35.18	4.52
2457	4975	5.339008	ACAGTATCTGAACTAATTGCCGA	57.661	39.130	3.70	0.00	35.18	5.54
2489	5007	8.723942	TTAATAGAAGCAATTCTCTTGGAGAC	57.276	34.615	0.00	0.00	38.51	3.36
2535	5054	4.944962	TCTGGCTGATTTATGTCGTTTG	57.055	40.909	0.00	0.00	0.00	2.93
2589	5108	7.592885	AAATATCTACGCCTACTTCTGGTAA	57.407	36.000	0.00	0.00	0.00	2.85
2709	5231	3.101019	GGCAAAACCGATTGGAACG	57.899	52.632	5.81	0.00	39.21	3.95
2720	5242	0.937304	ATTGGAACGAATCGGCATCG	59.063	50.000	7.80	3.21	45.47	3.84
2770	5292	1.522668	CAAAGCCGATTGGTCTGTCA	58.477	50.000	0.00	0.00	37.67	3.58
2781	5303	1.003580	TGGTCTGTCAGCTTGGAATCC	59.996	52.381	0.00	0.00	0.00	3.01
2825	5347	9.875691	GGCAAAACCAATCTTTATCTTTATCTT	57.124	29.630	0.00	0.00	38.86	2.40
2872	5394	5.351948	AAGAGAGGAGGCTTTCATAGTTC	57.648	43.478	0.00	0.00	0.00	3.01
2879	5401	7.292120	AGAGGAGGCTTTCATAGTTCTTCATAT	59.708	37.037	0.00	0.00	0.00	1.78
2904	5426	7.881142	TGTCATCCTTTTACATTCGTTGATTT	58.119	30.769	0.00	0.00	0.00	2.17
2957	5479	7.445945	AGATTTAAATAGAGGAAGATGACGGG	58.554	38.462	0.00	0.00	0.00	5.28
2999	5521	1.448540	AGCCAATGAAGCGACGGAG	60.449	57.895	0.00	0.00	34.64	4.63
3052	5574	1.073025	TGCCTGTTTCGGTGCTGAT	59.927	52.632	0.00	0.00	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	0.909610	AACCATTCTCCCTCGCTGGA	60.910	55.000	0.00	0.00	38.35	3.86
249	251	2.466520	CTTAAACCGCCCACAACCGC	62.467	60.000	0.00	0.00	0.00	5.68
411	413	1.290009	GCGGCCATCCAATAATGCC	59.710	57.895	2.24	0.00	0.00	4.40
444	446	1.898330	ATGGGGGAACAATTTGCGGC	61.898	55.000	0.00	0.00	0.00	6.53
449	451	1.555967	CACGGATGGGGGAACAATTT	58.444	50.000	0.00	0.00	0.00	1.82
492	494	1.661341	GGCATCTTGAACGCTGATCT	58.339	50.000	0.00	0.00	0.00	2.75
597	599	5.048083	ACGTGTGGCACTGATTATTTGAAAT	60.048	36.000	19.83	0.00	31.34	2.17
693	696	3.318839	TCTGTTTGGATGGCAAGTTTCAG	59.681	43.478	0.00	0.00	0.00	3.02
767	770	1.529438	TGTTCGGACGTTTTCTGATGC	59.471	47.619	0.00	0.00	39.52	3.91
1460	3968	0.255604	ATGTGGACCGATTCATGGCA	59.744	50.000	0.00	0.00	0.00	4.92
1856	4365	1.732259	GCTCACGTCCAAGGTGTAATG	59.268	52.381	0.00	0.00	35.64	1.90
2020	4531	1.476891	GCTTCCACACGTCTATCCTCA	59.523	52.381	0.00	0.00	0.00	3.86
2061	4572	2.039084	CCCTTGAGTGTAGCCAGACTTT	59.961	50.000	0.00	0.00	0.00	2.66
2110	4627	8.630054	ATGTACACCAGAGAGATAATAGAGAC	57.370	38.462	0.00	0.00	0.00	3.36
2118	4635	7.255139	CGACAACATATGTACACCAGAGAGATA	60.255	40.741	9.21	0.00	44.12	1.98
2381	4899	2.487762	CAAATCTCAGCAACGCCCTAAA	59.512	45.455	0.00	0.00	0.00	1.85
2475	4993	8.792830	TTGAAATATTCGTCTCCAAGAGAATT	57.207	30.769	0.00	0.00	40.59	2.17
2515	5033	4.154015	TCACAAACGACATAAATCAGCCAG	59.846	41.667	0.00	0.00	0.00	4.85
2561	5080	7.287235	ACCAGAAGTAGGCGTAGATATTTTACT	59.713	37.037	0.00	0.00	0.00	2.24
2720	5242	1.600916	GGGACTAATCGGCATGGCC	60.601	63.158	14.46	0.00	46.75	5.36
2781	5303	0.320073	CCAAACCCAACTGCAGCATG	60.320	55.000	15.27	13.35	40.87	4.06
2836	5358	9.448587	AGCCTCCTCTCTTTAATATTAGGTAAA	57.551	33.333	0.00	0.00	0.00	2.01
2837	5359	9.448587	AAGCCTCCTCTCTTTAATATTAGGTAA	57.551	33.333	0.00	0.00	0.00	2.85
2838	5360	9.448587	AAAGCCTCCTCTCTTTAATATTAGGTA	57.551	33.333	0.00	0.00	31.39	3.08
2853	5375	4.780021	TGAAGAACTATGAAAGCCTCCTCT	59.220	41.667	0.00	0.00	0.00	3.69
2854	5376	5.091261	TGAAGAACTATGAAAGCCTCCTC	57.909	43.478	0.00	0.00	0.00	3.71
2872	5394	8.830580	ACGAATGTAAAAGGATGACATATGAAG	58.169	33.333	10.38	0.00	33.48	3.02
2879	5401	7.447374	AATCAACGAATGTAAAAGGATGACA	57.553	32.000	0.00	0.00	0.00	3.58
2892	5414	9.553418	TTGTGATGTACATAAAATCAACGAATG	57.447	29.630	8.71	0.00	39.48	2.67
2895	5417	8.994170	TCTTTGTGATGTACATAAAATCAACGA	58.006	29.630	8.71	9.72	38.66	3.85
2904	5426	5.065859	CCGCCAATCTTTGTGATGTACATAA	59.934	40.000	8.71	0.00	39.48	1.90
2911	5433	2.228582	TCAACCGCCAATCTTTGTGATG	59.771	45.455	0.00	0.00	35.21	3.07
2915	5437	2.270352	TCTCAACCGCCAATCTTTGT	57.730	45.000	0.00	0.00	0.00	2.83
2924	5446	5.365619	TCCTCTATTTAAATCTCAACCGCC	58.634	41.667	3.39	0.00	0.00	6.13
2957	5479	4.275689	GCCCAATATAATTTTTGGCCTTGC	59.724	41.667	3.32	4.41	40.89	4.01
2999	5521	2.032204	GCAGCGATCATGAATTCAGGTC	60.032	50.000	18.78	14.08	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.