AutoCloner

Multiple sequence alignment - TraesCS3D01G440300

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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	TraesCS3D01G440300	chr3D	100.000	4724	0	0	1	4724	550659189	550663912	0.000000e+00	8724.0
1	TraesCS3D01G440300	chr3D	85.817	2919	365	27	925	3812	550668147	550671047	0.000000e+00	3051.0
2	TraesCS3D01G440300	chr3D	84.028	288	35	8	3811	4093	550671141	550671422	2.800000e-67	267.0
3	TraesCS3D01G440300	chr3D	78.067	269	37	12	4459	4718	338314917	338314662	2.940000e-32	150.0
4	TraesCS3D01G440300	chr3B	96.225	4397	126	15	1	4393	730282420	730286780	0.000000e+00	7164.0
5	TraesCS3D01G440300	chr3B	85.929	2857	357	32	925	3757	730309400	730312235	0.000000e+00	3007.0
6	TraesCS3D01G440300	chr3B	89.759	332	24	5	3922	4246	730312330	730312658	2.630000e-112	416.0
7	TraesCS3D01G440300	chr3B	96.622	148	4	1	4552	4699	730288440	730288586	1.310000e-60	244.0
8	TraesCS3D01G440300	chr3B	81.768	181	22	6	4549	4718	436558472	436558292	1.770000e-29	141.0
9	TraesCS3D01G440300	chr3B	93.750	80	5	0	3790	3869	730312236	730312315	2.310000e-23	121.0
10	TraesCS3D01G440300	chr3B	100.000	39	0	0	4685	4723	730288605	730288643	6.560000e-09	73.1
11	TraesCS3D01G440300	chr3A	96.729	3118	87	3	906	4019	687592790	687595896	0.000000e+00	5179.0
12	TraesCS3D01G440300	chr3A	89.312	1600	124	16	2818	4396	687614129	687615702	0.000000e+00	1964.0
13	TraesCS3D01G440300	chr3A	86.316	665	55	15	1	652	687592016	687592657	0.000000e+00	691.0
14	TraesCS3D01G440300	chr3A	88.791	339	28	3	4104	4432	687595895	687596233	1.580000e-109	407.0
15	TraesCS3D01G440300	chr3A	94.643	224	9	3	4501	4722	687596383	687596605	1.260000e-90	344.0
16	TraesCS3D01G440300	chr3A	94.857	175	7	1	4466	4638	687616272	687616446	6.020000e-69	272.0
17	TraesCS3D01G440300	chr3A	93.478	138	5	2	741	878	687592657	687592790	8.020000e-48	202.0
18	TraesCS3D01G440300	chr3A	82.653	196	20	8	4537	4718	456443119	456442924	1.360000e-35	161.0
19	TraesCS3D01G440300	chr3A	93.182	44	3	0	4389	4432	456443357	456443314	1.100000e-06	65.8
20	TraesCS3D01G440300	chr4A	77.728	1787	343	38	2012	3781	532216194	532217942	0.000000e+00	1044.0
21	TraesCS3D01G440300	chr2D	84.752	282	25	11	4454	4718	584841343	584841623	2.800000e-67	267.0
22	TraesCS3D01G440300	chr2B	83.273	275	24	13	4462	4718	705222576	705222846	2.840000e-57	233.0

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	TraesCS3D01G440300	chr3D	550659189	550663912	4723	False	8724.000000	8724	100.000000	1	4724	1	chr3D.!!$F1	4723
1	TraesCS3D01G440300	chr3D	550668147	550671422	3275	False	1659.000000	3051	84.922500	925	4093	2	chr3D.!!$F2	3168
2	TraesCS3D01G440300	chr3B	730282420	730288643	6223	False	2493.700000	7164	97.615667	1	4723	3	chr3B.!!$F1	4722
3	TraesCS3D01G440300	chr3B	730309400	730312658	3258	False	1181.333333	3007	89.812667	925	4246	3	chr3B.!!$F2	3321
4	TraesCS3D01G440300	chr3A	687592016	687596605	4589	False	1364.600000	5179	91.991400	1	4722	5	chr3A.!!$F1	4721
5	TraesCS3D01G440300	chr3A	687614129	687616446	2317	False	1118.000000	1964	92.084500	2818	4638	2	chr3A.!!$F2	1820
6	TraesCS3D01G440300	chr4A	532216194	532217942	1748	False	1044.000000	1044	77.728000	2012	3781	1	chr4A.!!$F1	1769

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
584	597	0.260816	ATGAGGCCCATGAGCACAAT	59.739	50.0	0.27	0.0	33.39	2.71	F
895	910	0.871057	CACACACACACACACACACA	59.129	50.0	0.00	0.0	0.00	3.72	F
2827	2867	0.406750	TAAGGTCAGGTCACTCCCGA	59.593	55.0	0.00	0.0	36.75	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1401	1417	1.201429	ACCACCCCTTGAGCTCGATT	61.201	55.000	9.64	0.0	0.00	3.34	R
2883	2923	0.843309	TCCCACTTGGCAGTTTCTCA	59.157	50.000	0.00	0.0	0.00	3.27	R
4081	4235	1.067776	GGACACGGAAATCAGTCTCGT	60.068	52.381	0.00	0.0	34.19	4.18	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
124	125	1.762419	TGTCGGAAGAACGAGAAACG	58.238	50.000	0.00	0.00	44.42	3.60
128	129	1.525619	CGGAAGAACGAGAAACGCTTT	59.474	47.619	0.00	0.00	46.94	3.51
183	184	1.069227	GTGTTCGGCTGCAAAGTTAGG	60.069	52.381	0.50	0.00	0.00	2.69
190	191	0.598065	CTGCAAAGTTAGGCACCACC	59.402	55.000	0.00	0.00	35.86	4.61
302	315	4.811024	GCATATGAGGTTCGACATCTTTGA	59.189	41.667	6.97	0.00	29.01	2.69
303	316	5.468072	GCATATGAGGTTCGACATCTTTGAT	59.532	40.000	6.97	0.00	29.01	2.57
386	399	5.525378	CCCTCCTTCATAGAAGAACATTTCG	59.475	44.000	8.26	0.00	34.02	3.46
402	415	8.134895	AGAACATTTCGATTTTGCTGACTTTTA	58.865	29.630	0.00	0.00	34.02	1.52
429	442	3.902261	TTGCAGCTATTTATGCCATCG	57.098	42.857	0.00	0.00	41.85	3.84
450	463	7.226720	CCATCGTAAGCATTAAAGTTCCATAGT	59.773	37.037	0.00	0.00	28.70	2.12
488	501	2.622436	AGCGATTAAGTCAAGTCAGGC	58.378	47.619	0.00	0.00	0.00	4.85
489	502	2.028112	AGCGATTAAGTCAAGTCAGGCA	60.028	45.455	0.00	0.00	0.00	4.75
490	503	2.742053	GCGATTAAGTCAAGTCAGGCAA	59.258	45.455	0.00	0.00	0.00	4.52
491	504	3.188460	GCGATTAAGTCAAGTCAGGCAAA	59.812	43.478	0.00	0.00	0.00	3.68
492	505	4.142600	GCGATTAAGTCAAGTCAGGCAAAT	60.143	41.667	0.00	0.00	0.00	2.32
502	515	5.048083	TCAAGTCAGGCAAATCAAATGTACC	60.048	40.000	0.00	0.00	0.00	3.34
584	597	0.260816	ATGAGGCCCATGAGCACAAT	59.739	50.000	0.27	0.00	33.39	2.71
626	640	6.737254	ATGTAATATACGCACCCAATTAGC	57.263	37.500	0.00	0.00	0.00	3.09
674	689	6.712095	TCAGCTGACAAAGAGTGATAATTGTT	59.288	34.615	13.74	0.00	36.22	2.83
718	733	8.083828	ACATTGACATAAGGTATCTTCACTCT	57.916	34.615	0.00	0.00	34.59	3.24
720	735	9.039870	CATTGACATAAGGTATCTTCACTCTTC	57.960	37.037	0.00	0.00	34.59	2.87
769	784	2.217750	TCAACAGAACCACACATTCCG	58.782	47.619	0.00	0.00	0.00	4.30
777	792	0.959867	CCACACATTCCGTCCATGCA	60.960	55.000	0.00	0.00	0.00	3.96
778	793	1.097232	CACACATTCCGTCCATGCAT	58.903	50.000	0.00	0.00	0.00	3.96
779	794	1.097232	ACACATTCCGTCCATGCATG	58.903	50.000	20.19	20.19	0.00	4.06
882	897	7.020914	AGAAATTTTCTCTCTGAACACACAC	57.979	36.000	5.82	0.00	34.07	3.82
884	899	5.741388	ATTTTCTCTCTGAACACACACAC	57.259	39.130	0.00	0.00	33.88	3.82
886	901	3.165058	TCTCTCTGAACACACACACAC	57.835	47.619	0.00	0.00	0.00	3.82
887	902	2.495669	TCTCTCTGAACACACACACACA	59.504	45.455	0.00	0.00	0.00	3.72
888	903	2.604914	CTCTCTGAACACACACACACAC	59.395	50.000	0.00	0.00	0.00	3.82
889	904	2.028567	TCTCTGAACACACACACACACA	60.029	45.455	0.00	0.00	0.00	3.72
890	905	2.073056	TCTGAACACACACACACACAC	58.927	47.619	0.00	0.00	0.00	3.82
891	906	1.803555	CTGAACACACACACACACACA	59.196	47.619	0.00	0.00	0.00	3.72
892	907	1.533299	TGAACACACACACACACACAC	59.467	47.619	0.00	0.00	0.00	3.82
893	908	1.533299	GAACACACACACACACACACA	59.467	47.619	0.00	0.00	0.00	3.72
894	909	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
895	910	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
896	911	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
897	912	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
898	913	0.871722	ACACACACACACACACACAC	59.128	50.000	0.00	0.00	0.00	3.82
1365	1381	5.009210	CCTGGTTTTCAGTCAAATTACCGAA	59.991	40.000	0.00	0.00	41.83	4.30
1401	1417	6.609212	AGATAGAGAAGGACATCAAGCAAGTA	59.391	38.462	0.00	0.00	0.00	2.24
1422	1441	2.583441	CGAGCTCAAGGGGTGGTCA	61.583	63.158	15.40	0.00	37.36	4.02
2301	2326	7.036220	GCTTCTTGTACTGTAGCTTATTCTCA	58.964	38.462	0.00	0.00	0.00	3.27
2827	2867	0.406750	TAAGGTCAGGTCACTCCCGA	59.593	55.000	0.00	0.00	36.75	5.14
2883	2923	7.014615	ACTCTGGACATCAAGCAAACTAAAATT	59.985	33.333	0.00	0.00	0.00	1.82
2952	2992	6.261826	ACCTATTTGCTGATAGATTTGCTGAC	59.738	38.462	8.05	0.00	32.48	3.51
3048	3088	1.066573	ACTCTTGAGACCATCCAAGCG	60.067	52.381	4.49	0.00	39.53	4.68
3461	3501	0.600057	GCCTTGGTTCTTTCTGCAGG	59.400	55.000	15.13	0.00	0.00	4.85
3519	3559	0.671472	TGCCTCATGTCAACGAGCTG	60.671	55.000	0.00	0.00	0.00	4.24
3880	4029	4.638421	ACGGTTTCTGTTCTGAAAATGTCA	59.362	37.500	6.47	0.00	37.63	3.58
4025	4178	3.830755	ACCTTGTTGTCAGTAGATACCGT	59.169	43.478	0.00	0.00	0.00	4.83
4060	4214	1.238439	CTGCATCCTGGTTGTCGTTT	58.762	50.000	6.62	0.00	0.00	3.60
4180	4341	6.094186	TCAACAACTGCAGTGTTTAATGTGTA	59.906	34.615	22.49	8.60	0.00	2.90
4210	4371	5.728351	TGTTGTGTTTCAGTAACAGTAGC	57.272	39.130	0.00	0.00	46.95	3.58
4221	4382	6.993079	TCAGTAACAGTAGCTTTGATTCTGA	58.007	36.000	10.87	10.87	0.00	3.27
4416	4592	3.009714	AGGGTCCCCTTCTTCCGC	61.010	66.667	3.51	0.00	45.70	5.54
4422	4598	4.840005	CCCTTCTTCCGCGCCTCC	62.840	72.222	0.00	0.00	0.00	4.30
4439	4615	2.895372	CGGCCTTGGCACCGTATC	60.895	66.667	14.04	0.00	44.46	2.24
4441	4617	1.523938	GGCCTTGGCACCGTATCTC	60.524	63.158	14.04	0.00	0.00	2.75
4442	4618	1.883084	GCCTTGGCACCGTATCTCG	60.883	63.158	6.79	0.00	39.52	4.04
4451	4948	2.802792	CGTATCTCGGGTTCGCCA	59.197	61.111	0.00	0.00	39.65	5.69
4456	4953	2.859273	ATCTCGGGTTCGCCAAGCAG	62.859	60.000	0.00	0.00	39.65	4.24
4457	4954	4.697756	TCGGGTTCGCCAAGCAGG	62.698	66.667	0.00	0.00	39.65	4.85
4490	6225	4.640364	AGAAGAAAGAAGCAGAGAAGTGG	58.360	43.478	0.00	0.00	0.00	4.00
4576	6400	1.362355	CTGGTTTTTGTGGGCCGTC	59.638	57.895	0.00	0.00	0.00	4.79
4662	6487	5.876357	TCTGTGCAGGGTTATCTTAGTTTT	58.124	37.500	0.00	0.00	0.00	2.43
4723	6581	2.100916	CCGGGTATAAGATGGGATAGCG	59.899	54.545	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
183	184	2.106683	GTCATAGCCACGGTGGTGC	61.107	63.158	26.86	14.40	43.00	5.01
190	191	6.036408	CCATATGTCAATATGTCATAGCCACG	59.964	42.308	1.24	0.00	42.85	4.94
196	197	6.179756	GTGCCCCATATGTCAATATGTCATA	58.820	40.000	1.24	0.00	42.85	2.15
256	269	5.390613	CCGGTACAGCAAAATTAGAACTTG	58.609	41.667	0.00	0.00	0.00	3.16
270	283	0.393077	ACCTCATATGCCGGTACAGC	59.607	55.000	13.00	0.00	0.00	4.40
322	335	1.882623	CAAGAGAACACCTTGAAGGGC	59.117	52.381	16.78	2.00	42.57	5.19
328	341	0.588252	CGCCACAAGAGAACACCTTG	59.412	55.000	0.00	0.00	44.75	3.61
386	399	9.745323	GCAATTGTTATAAAAGTCAGCAAAATC	57.255	29.630	7.40	0.00	0.00	2.17
402	415	7.053316	TGGCATAAATAGCTGCAATTGTTAT	57.947	32.000	7.40	0.00	40.18	1.89
423	436	4.095782	TGGAACTTTAATGCTTACGATGGC	59.904	41.667	0.00	0.00	0.00	4.40
429	442	7.859325	TCCACTATGGAACTTTAATGCTTAC	57.141	36.000	0.00	0.00	45.00	2.34
450	463	9.602568	TTAATCGCTTAAATATAGTTGTGTCCA	57.397	29.630	0.00	0.00	0.00	4.02
486	499	1.135517	ACGCGGTACATTTGATTTGCC	60.136	47.619	12.47	0.00	0.00	4.52
488	501	5.387279	ACTAAACGCGGTACATTTGATTTG	58.613	37.500	12.47	0.00	0.00	2.32
489	502	5.616488	ACTAAACGCGGTACATTTGATTT	57.384	34.783	12.47	0.00	0.00	2.17
490	503	5.410439	AGAACTAAACGCGGTACATTTGATT	59.590	36.000	12.47	0.47	0.00	2.57
491	504	4.933400	AGAACTAAACGCGGTACATTTGAT	59.067	37.500	12.47	0.00	0.00	2.57
492	505	4.150980	CAGAACTAAACGCGGTACATTTGA	59.849	41.667	12.47	0.00	0.00	2.69
567	580	2.012902	GCATTGTGCTCATGGGCCTC	62.013	60.000	16.70	9.04	40.96	4.70
615	629	6.949352	ATTGATAGAACTGCTAATTGGGTG	57.051	37.500	0.00	0.00	31.66	4.61
626	640	8.803201	TGACGCTAAGATAATTGATAGAACTG	57.197	34.615	0.00	0.00	0.00	3.16
644	659	1.613925	ACTCTTTGTCAGCTGACGCTA	59.386	47.619	35.00	22.91	46.99	4.26
688	703	7.985184	TGAAGATACCTTATGTCAATGTACCAC	59.015	37.037	0.00	0.00	31.62	4.16
689	704	7.985184	GTGAAGATACCTTATGTCAATGTACCA	59.015	37.037	0.00	0.00	31.62	3.25
743	758	7.378181	GGAATGTGTGGTTCTGTTGATATTTT	58.622	34.615	0.00	0.00	0.00	1.82
759	774	1.097232	ATGCATGGACGGAATGTGTG	58.903	50.000	0.00	0.00	0.00	3.82
769	784	2.756760	ACTGGTTTCATCATGCATGGAC	59.243	45.455	25.97	15.63	32.64	4.02
777	792	5.707298	CACTTAACTCCACTGGTTTCATCAT	59.293	40.000	0.00	0.00	0.00	2.45
778	793	5.063204	CACTTAACTCCACTGGTTTCATCA	58.937	41.667	0.00	0.00	0.00	3.07
779	794	5.063880	ACACTTAACTCCACTGGTTTCATC	58.936	41.667	0.00	0.00	0.00	2.92
878	893	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
880	895	0.871057	TGTGTGTGTGTGTGTGTGTG	59.129	50.000	0.00	0.00	0.00	3.82
882	897	5.861222	ATATATGTGTGTGTGTGTGTGTG	57.139	39.130	0.00	0.00	0.00	3.82
912	927	5.959618	AAATTAGGTCGCAAACTAGCTTT	57.040	34.783	0.00	0.00	0.00	3.51
913	928	5.959618	AAAATTAGGTCGCAAACTAGCTT	57.040	34.783	0.00	0.00	0.00	3.74
1161	1177	2.969262	TGTGCCAATCTCCCGTATGATA	59.031	45.455	0.00	0.00	0.00	2.15
1365	1381	6.069323	TGTCCTTCTCTATCTTGACTACCTCT	60.069	42.308	0.00	0.00	0.00	3.69
1401	1417	1.201429	ACCACCCCTTGAGCTCGATT	61.201	55.000	9.64	0.00	0.00	3.34
1422	1441	1.777878	TGAACATACTGGGGTGGTTGT	59.222	47.619	0.00	0.00	0.00	3.32
2301	2326	2.897969	ACGTGACATTGGGTAGTCTTCT	59.102	45.455	0.00	0.00	35.81	2.85
2827	2867	6.439058	AGGTTAGATAGTTTCTCAACAGAGCT	59.561	38.462	0.00	0.00	35.79	4.09
2883	2923	0.843309	TCCCACTTGGCAGTTTCTCA	59.157	50.000	0.00	0.00	0.00	3.27
2952	2992	1.341606	GAAACTCCGTCTGCTTCTCG	58.658	55.000	0.00	0.00	0.00	4.04
3048	3088	1.743252	CTCGGCCAAGTCCTTGCTC	60.743	63.158	2.24	0.00	39.16	4.26
3461	3501	3.070748	GTCTTCAGCTGAGGAAAGGAAC	58.929	50.000	28.03	12.91	31.79	3.62
3519	3559	1.239968	GGGCGCCATCCATGATCTTC	61.240	60.000	30.85	0.98	0.00	2.87
3880	4029	2.553904	CCTCCTGAAGGCAATGAACACT	60.554	50.000	0.00	0.00	38.67	3.55
4025	4178	6.479990	CAGGATGCAGTAGAAACATAATCGAA	59.520	38.462	0.00	0.00	0.00	3.71
4060	4214	3.298958	AGGATGCGCCTCTTCGAA	58.701	55.556	12.54	0.00	46.97	3.71
4081	4235	1.067776	GGACACGGAAATCAGTCTCGT	60.068	52.381	0.00	0.00	34.19	4.18
4180	4341	9.139174	CTGTTACTGAAACACAACATTTTCTTT	57.861	29.630	0.00	0.00	43.22	2.52
4198	4359	7.840342	ATCAGAATCAAAGCTACTGTTACTG	57.160	36.000	0.00	0.00	0.00	2.74
4210	4371	3.629398	AGCGGCCTAAATCAGAATCAAAG	59.371	43.478	0.00	0.00	0.00	2.77
4221	4382	2.124151	CCCAGCAGCGGCCTAAAT	60.124	61.111	4.82	0.00	42.56	1.40
4370	4543	6.065976	ACCTCCATATGACACTTGAAATGA	57.934	37.500	3.65	0.00	0.00	2.57
4436	4612	1.143183	GCTTGGCGAACCCGAGATA	59.857	57.895	0.76	0.00	46.71	1.98
4438	4614	3.589654	CTGCTTGGCGAACCCGAGA	62.590	63.158	0.76	0.00	46.71	4.04
4439	4615	3.121030	CTGCTTGGCGAACCCGAG	61.121	66.667	0.00	0.00	46.52	4.63
4451	4948	1.617839	CTTCCTCCTCCCCCTGCTT	60.618	63.158	0.00	0.00	0.00	3.91
4456	4953	1.562008	CTTTCTTCTTCCTCCTCCCCC	59.438	57.143	0.00	0.00	0.00	5.40
4457	4954	2.552367	TCTTTCTTCTTCCTCCTCCCC	58.448	52.381	0.00	0.00	0.00	4.81
4459	4956	3.008485	TGCTTCTTTCTTCTTCCTCCTCC	59.992	47.826	0.00	0.00	0.00	4.30
4490	6225	2.880963	AATAACTCTCCTCTGCGCTC	57.119	50.000	9.73	0.00	0.00	5.03
4521	6281	1.142748	GATCTCCTCCTGTGCGTGG	59.857	63.158	0.00	0.00	0.00	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.