AutoCloner

Multiple sequence alignment - TraesCS6A01G040800

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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	TraesCS6A01G040800	chr6A	100.000	2095	0	0	1	2095	21160070	21162164	0.000000e+00	3869.0
1	TraesCS6A01G040800	chr6A	100.000	71	0	0	2524	2594	21162593	21162663	5.820000e-27	132.0
2	TraesCS6A01G040800	chr6A	88.406	69	6	2	1873	1940	569404768	569404835	5.950000e-12	82.4
3	TraesCS6A01G040800	chr7D	95.000	1980	57	14	1	1945	36515156	36517128	0.000000e+00	3070.0
4	TraesCS6A01G040800	chr7D	88.889	72	6	2	1873	1943	135778565	135778495	1.280000e-13	87.9
5	TraesCS6A01G040800	chr5A	96.076	1682	51	11	273	1944	298258990	298260666	0.000000e+00	2726.0
6	TraesCS6A01G040800	chr5A	92.481	399	26	2	1	396	298258641	298259038	3.750000e-158	568.0
7	TraesCS6A01G040800	chr5A	82.181	651	95	19	1227	1866	491689088	491689728	8.170000e-150	540.0
8	TraesCS6A01G040800	chr5A	80.444	225	21	8	1022	1224	491686237	491686460	1.610000e-32	150.0
9	TraesCS6A01G040800	chr3A	96.004	951	33	5	1	947	159346674	159345725	0.000000e+00	1541.0
10	TraesCS6A01G040800	chr3A	97.541	610	10	3	1335	1942	159345730	159345124	0.000000e+00	1038.0
11	TraesCS6A01G040800	chr3A	97.500	40	1	0	2555	2594	159344405	159344366	4.630000e-08	69.4
12	TraesCS6A01G040800	chr6B	83.533	668	77	10	1227	1864	507364360	507365024	6.180000e-166	593.0
13	TraesCS6A01G040800	chr6B	77.689	753	120	25	1227	1940	602479519	602480262	1.440000e-112	416.0
14	TraesCS6A01G040800	chr5D	83.308	653	82	23	1227	1866	388778398	388777760	6.220000e-161	577.0
15	TraesCS6A01G040800	chr5D	90.278	72	5	2	1873	1943	125659977	125659907	2.750000e-15	93.5
16	TraesCS6A01G040800	chr4D	82.949	651	82	25	1227	1866	19057980	19058612	6.270000e-156	560.0
17	TraesCS6A01G040800	chr4D	89.216	102	11	0	1123	1224	485090109	485090210	7.530000e-26	128.0
18	TraesCS6A01G040800	chr4D	90.278	72	5	2	1873	1943	152888907	152888837	2.750000e-15	93.5
19	TraesCS6A01G040800	chr4D	87.500	72	8	1	1873	1943	353864428	353864357	5.950000e-12	82.4
20	TraesCS6A01G040800	chr4D	78.523	149	12	12	946	1077	485089894	485090039	2.140000e-11	80.5
21	TraesCS6A01G040800	chr7B	82.764	644	90	19	1235	1866	608231024	608231658	2.920000e-154	555.0
22	TraesCS6A01G040800	chr7B	81.442	652	94	22	1227	1865	20506407	20505770	2.300000e-140	508.0
23	TraesCS6A01G040800	chr7B	83.489	321	25	9	506	814	368154021	368153717	9.150000e-70	274.0
24	TraesCS6A01G040800	chr7B	75.645	349	50	15	909	1224	20509791	20509445	9.680000e-30	141.0
25	TraesCS6A01G040800	chr4A	82.515	652	90	21	1227	1866	581338233	581337594	3.770000e-153	551.0
26	TraesCS6A01G040800	chr4A	79.592	147	18	8	1721	1866	607384758	607384623	7.640000e-16	95.3
27	TraesCS6A01G040800	chr4A	85.714	84	8	3	242	325	607414889	607414810	4.600000e-13	86.1
28	TraesCS6A01G040800	chr4A	83.908	87	13	1	1858	1943	617109926	617110012	5.950000e-12	82.4
29	TraesCS6A01G040800	chr2D	90.681	279	26	0	874	1152	438293009	438293287	3.150000e-99	372.0
30	TraesCS6A01G040800	chr2B	90.681	279	25	1	874	1152	516080762	516081039	1.130000e-98	370.0
31	TraesCS6A01G040800	chr7A	90.667	225	13	4	506	723	418112730	418112507	2.520000e-75	292.0
32	TraesCS6A01G040800	chr5B	84.106	151	18	6	1721	1866	643903399	643903250	9.680000e-30	141.0
33	TraesCS6A01G040800	chr5B	83.444	151	19	6	1721	1866	643798340	643798191	4.500000e-28	135.0
34	TraesCS6A01G040800	chr5B	83.553	152	17	8	1721	1866	643833736	643833587	4.500000e-28	135.0
35	TraesCS6A01G040800	chr5B	86.154	65	8	1	242	305	643801090	643801026	4.630000e-08	69.4
36	TraesCS6A01G040800	chr5B	86.154	65	8	1	242	305	643906137	643906073	4.630000e-08	69.4
37	TraesCS6A01G040800	chr3D	81.457	151	22	5	1721	1866	66896098	66895949	4.530000e-23	119.0
38	TraesCS6A01G040800	chr3D	77.056	231	37	12	1721	1942	101658953	101658730	4.530000e-23	119.0
39	TraesCS6A01G040800	chr1A	78.462	130	25	2	177	305	537057720	537057593	5.950000e-12	82.4
40	TraesCS6A01G040800	chr6D	84.524	84	9	2	242	325	29986870	29986949	2.140000e-11	80.5
41	TraesCS6A01G040800	chr6D	87.500	64	8	0	1657	1720	30003833	30003896	9.960000e-10	75.0

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	TraesCS6A01G040800	chr6A	21160070	21162663	2593	False	2000.5	3869	100.0000	1	2594	2	chr6A.!!$F2	2593
1	TraesCS6A01G040800	chr7D	36515156	36517128	1972	False	3070.0	3070	95.0000	1	1945	1	chr7D.!!$F1	1944
2	TraesCS6A01G040800	chr5A	298258641	298260666	2025	False	1647.0	2726	94.2785	1	1944	2	chr5A.!!$F1	1943
3	TraesCS6A01G040800	chr5A	491686237	491689728	3491	False	345.0	540	81.3125	1022	1866	2	chr5A.!!$F2	844
4	TraesCS6A01G040800	chr3A	159344366	159346674	2308	True	882.8	1541	97.0150	1	2594	3	chr3A.!!$R1	2593
5	TraesCS6A01G040800	chr6B	507364360	507365024	664	False	593.0	593	83.5330	1227	1864	1	chr6B.!!$F1	637
6	TraesCS6A01G040800	chr6B	602479519	602480262	743	False	416.0	416	77.6890	1227	1940	1	chr6B.!!$F2	713
7	TraesCS6A01G040800	chr5D	388777760	388778398	638	True	577.0	577	83.3080	1227	1866	1	chr5D.!!$R2	639
8	TraesCS6A01G040800	chr4D	19057980	19058612	632	False	560.0	560	82.9490	1227	1866	1	chr4D.!!$F1	639
9	TraesCS6A01G040800	chr7B	608231024	608231658	634	False	555.0	555	82.7640	1235	1866	1	chr7B.!!$F1	631
10	TraesCS6A01G040800	chr7B	20505770	20509791	4021	True	324.5	508	78.5435	909	1865	2	chr7B.!!$R2	956
11	TraesCS6A01G040800	chr4A	581337594	581338233	639	True	551.0	551	82.5150	1227	1866	1	chr4A.!!$R1	639

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
871	986	0.107993	CTGATCATGGCTGTGACCGT	60.108	55.0	0.0	0.0	0.0	4.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2028	5546	1.37825	CCTCCTGCTTCCCTTGCTG	60.378	63.158	0.0	0.0	0.0	4.41	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
39	40	2.733218	CACGACAGCGAAGGCGAA	60.733	61.111	9.83	0.00	46.35	4.70
117	119	2.358737	CCCCTCGCGTTTTGCTCT	60.359	61.111	5.77	0.00	43.27	4.09
175	177	3.150949	CCACTGCCTCCACTCACA	58.849	61.111	0.00	0.00	0.00	3.58
240	273	1.934459	ATCTGCTGCTCCTGGCCATT	61.934	55.000	5.51	0.00	40.92	3.16
360	471	0.395311	CTCATGGCCTCCATTGCTGT	60.395	55.000	3.32	0.00	42.23	4.40
380	491	4.651008	GTCGCCCGTGTTGTCCGA	62.651	66.667	0.00	0.00	0.00	4.55
473	584	5.685728	ACTATTCCTATTTGTTGCTCCCTC	58.314	41.667	0.00	0.00	0.00	4.30
564	675	6.339587	TGGTCCAAGAAAATAAATGGTGTC	57.660	37.500	0.00	0.00	34.50	3.67
713	827	9.466497	ACCTACATATGCATATATCCTTTTTGG	57.534	33.333	18.70	12.17	37.10	3.28
855	970	8.899427	TTGAAATGAAAATAATTTGGTGCTGA	57.101	26.923	0.00	0.00	0.00	4.26
863	978	2.154567	ATTTGGTGCTGATCATGGCT	57.845	45.000	8.27	0.00	0.00	4.75
871	986	0.107993	CTGATCATGGCTGTGACCGT	60.108	55.000	0.00	0.00	0.00	4.83
1457	4652	2.862541	CAGTCCCAATCCTGTGACAAA	58.137	47.619	0.00	0.00	0.00	2.83
1664	4906	4.323485	CCAGACTTGCCATCCTACTTTGTA	60.323	45.833	0.00	0.00	0.00	2.41
1668	4910	3.576078	TGCCATCCTACTTTGTATGGG	57.424	47.619	0.00	0.00	39.45	4.00
1963	5481	8.851960	AATTTGACCGAAGTTTAAAAGTTCTC	57.148	30.769	0.00	0.00	38.42	2.87
1971	5489	9.010366	CCGAAGTTTAAAAGTTCTCAGAAAAAG	57.990	33.333	0.00	0.00	38.42	2.27
2007	5525	7.369803	ACAGAAAATCACTCATGTATGTGTC	57.630	36.000	12.95	6.42	35.82	3.67
2023	5541	4.220693	TGTGTCACTAATCTGGGAATGG	57.779	45.455	4.27	0.00	0.00	3.16
2024	5542	3.054434	TGTGTCACTAATCTGGGAATGGG	60.054	47.826	4.27	0.00	0.00	4.00
2025	5543	2.509548	TGTCACTAATCTGGGAATGGGG	59.490	50.000	0.00	0.00	0.00	4.96
2026	5544	2.135189	TCACTAATCTGGGAATGGGGG	58.865	52.381	0.00	0.00	0.00	5.40
2041	5559	4.684134	GGGGCAGCAAGGGAAGCA	62.684	66.667	0.00	0.00	0.00	3.91
2042	5560	3.066814	GGGCAGCAAGGGAAGCAG	61.067	66.667	0.00	0.00	0.00	4.24
2043	5561	3.066814	GGCAGCAAGGGAAGCAGG	61.067	66.667	0.00	0.00	0.00	4.85
2044	5562	2.034687	GCAGCAAGGGAAGCAGGA	59.965	61.111	0.00	0.00	0.00	3.86
2045	5563	2.045131	GCAGCAAGGGAAGCAGGAG	61.045	63.158	0.00	0.00	0.00	3.69
2046	5564	1.378250	CAGCAAGGGAAGCAGGAGG	60.378	63.158	0.00	0.00	0.00	4.30
2047	5565	2.044551	GCAAGGGAAGCAGGAGGG	60.045	66.667	0.00	0.00	0.00	4.30
2048	5566	2.679716	CAAGGGAAGCAGGAGGGG	59.320	66.667	0.00	0.00	0.00	4.79
2049	5567	2.615288	AAGGGAAGCAGGAGGGGG	60.615	66.667	0.00	0.00	0.00	5.40
2053	5571	4.785453	GAAGCAGGAGGGGGCGTG	62.785	72.222	0.00	0.00	34.54	5.34
2060	5578	4.162690	GAGGGGGCGTGGCAGTAG	62.163	72.222	0.00	0.00	0.00	2.57
2070	5588	4.496336	GGCAGTAGGGCAGCAGGG	62.496	72.222	0.00	0.00	42.77	4.45
2087	5605	4.577246	GCCGCCGGAGAGCAGTAG	62.577	72.222	7.68	0.00	0.00	2.57
2088	5606	3.905678	CCGCCGGAGAGCAGTAGG	61.906	72.222	5.05	0.00	0.00	3.18
2089	5607	3.905678	CGCCGGAGAGCAGTAGGG	61.906	72.222	5.05	0.00	0.00	3.53
2090	5608	3.541713	GCCGGAGAGCAGTAGGGG	61.542	72.222	5.05	0.00	0.00	4.79
2091	5609	2.042843	CCGGAGAGCAGTAGGGGT	60.043	66.667	0.00	0.00	0.00	4.95
2092	5610	2.427245	CCGGAGAGCAGTAGGGGTG	61.427	68.421	0.00	0.00	0.00	4.61
2093	5611	2.427245	CGGAGAGCAGTAGGGGTGG	61.427	68.421	0.00	0.00	0.00	4.61
2094	5612	2.066999	GGAGAGCAGTAGGGGTGGG	61.067	68.421	0.00	0.00	0.00	4.61
2543	6061	2.845659	TGGGGTGAGGTTGATCTATGT	58.154	47.619	0.00	0.00	0.00	2.29
2548	6066	4.878397	GGGTGAGGTTGATCTATGTTTCAG	59.122	45.833	0.00	0.00	0.00	3.02
2549	6067	5.491982	GGTGAGGTTGATCTATGTTTCAGT	58.508	41.667	0.00	0.00	0.00	3.41
2550	6068	5.582665	GGTGAGGTTGATCTATGTTTCAGTC	59.417	44.000	0.00	0.00	0.00	3.51
2551	6069	6.166279	GTGAGGTTGATCTATGTTTCAGTCA	58.834	40.000	0.00	0.00	0.00	3.41
2552	6070	6.650807	GTGAGGTTGATCTATGTTTCAGTCAA	59.349	38.462	0.00	0.00	0.00	3.18
2553	6071	7.173218	GTGAGGTTGATCTATGTTTCAGTCAAA	59.827	37.037	0.00	0.00	0.00	2.69
2586	6473	4.816925	GGGTATACTTGTCCTCTGATTTGC	59.183	45.833	2.25	0.00	0.00	3.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	0.820871	AGAGAAGATTCGCCTTCGCT	59.179	50.000	10.60	10.60	44.60	4.93
39	40	2.840102	CGGGGCGGGAGAGAAGAT	60.840	66.667	0.00	0.00	0.00	2.40
69	71	3.133542	GCGACAAGTAACCCTAACCCTAT	59.866	47.826	0.00	0.00	0.00	2.57
162	164	0.961019	GCAAAATGTGAGTGGAGGCA	59.039	50.000	0.00	0.00	0.00	4.75
352	463	2.480555	GGGCGACGAACAGCAATG	59.519	61.111	0.00	0.00	34.54	2.82
473	584	4.201589	CCTTGACGTATTCGCAAGTACAAG	60.202	45.833	19.23	0.00	42.95	3.16
564	675	9.459640	CTGAAAGCACATGAATAAATAATCAGG	57.540	33.333	0.00	0.00	33.80	3.86
855	970	1.153568	CGACGGTCACAGCCATGAT	60.154	57.895	9.10	0.00	0.00	2.45
1309	4504	4.906065	TCCTGCATGTATTGAGAAATGC	57.094	40.909	0.00	0.00	44.49	3.56
1457	4652	1.340991	ACGCCATAGCCAACATCCTTT	60.341	47.619	0.00	0.00	34.57	3.11
1522	4717	4.482386	GACATGTCATATGCAATCATGGC	58.518	43.478	21.07	18.44	39.76	4.40
1640	4835	1.958288	AGTAGGATGGCAAGTCTGGT	58.042	50.000	0.00	0.00	0.00	4.00
1664	4906	6.328148	AGGAAATATTTGATGCATTGTCCCAT	59.672	34.615	5.17	0.00	0.00	4.00
1668	4910	9.754382	ACATAAGGAAATATTTGATGCATTGTC	57.246	29.630	5.17	0.00	0.00	3.18
2007	5525	2.664402	CCCCCATTCCCAGATTAGTG	57.336	55.000	0.00	0.00	0.00	2.74
2024	5542	4.684134	TGCTTCCCTTGCTGCCCC	62.684	66.667	0.00	0.00	0.00	5.80
2025	5543	3.066814	CTGCTTCCCTTGCTGCCC	61.067	66.667	0.00	0.00	0.00	5.36
2026	5544	3.066814	CCTGCTTCCCTTGCTGCC	61.067	66.667	0.00	0.00	0.00	4.85
2027	5545	2.034687	TCCTGCTTCCCTTGCTGC	59.965	61.111	0.00	0.00	0.00	5.25
2028	5546	1.378250	CCTCCTGCTTCCCTTGCTG	60.378	63.158	0.00	0.00	0.00	4.41
2029	5547	2.610519	CCCTCCTGCTTCCCTTGCT	61.611	63.158	0.00	0.00	0.00	3.91
2030	5548	2.044551	CCCTCCTGCTTCCCTTGC	60.045	66.667	0.00	0.00	0.00	4.01
2031	5549	2.679716	CCCCTCCTGCTTCCCTTG	59.320	66.667	0.00	0.00	0.00	3.61
2032	5550	2.615288	CCCCCTCCTGCTTCCCTT	60.615	66.667	0.00	0.00	0.00	3.95
2036	5554	4.785453	CACGCCCCCTCCTGCTTC	62.785	72.222	0.00	0.00	0.00	3.86
2043	5561	4.162690	CTACTGCCACGCCCCCTC	62.163	72.222	0.00	0.00	0.00	4.30
2050	5568	4.393155	TGCTGCCCTACTGCCACG	62.393	66.667	0.00	0.00	42.24	4.94
2051	5569	2.437359	CTGCTGCCCTACTGCCAC	60.437	66.667	0.00	0.00	42.24	5.01
2052	5570	3.720601	CCTGCTGCCCTACTGCCA	61.721	66.667	0.00	0.00	42.24	4.92
2053	5571	4.496336	CCCTGCTGCCCTACTGCC	62.496	72.222	0.00	0.00	42.24	4.85
2055	5573	4.496336	GGCCCTGCTGCCCTACTG	62.496	72.222	0.00	0.00	46.11	2.74
2070	5588	4.577246	CTACTGCTCTCCGGCGGC	62.577	72.222	23.83	10.34	41.87	6.53
2071	5589	3.905678	CCTACTGCTCTCCGGCGG	61.906	72.222	22.51	22.51	43.58	6.13
2072	5590	3.905678	CCCTACTGCTCTCCGGCG	61.906	72.222	0.00	0.00	34.52	6.46
2073	5591	3.541713	CCCCTACTGCTCTCCGGC	61.542	72.222	0.00	0.00	0.00	6.13
2074	5592	2.042843	ACCCCTACTGCTCTCCGG	60.043	66.667	0.00	0.00	0.00	5.14
2075	5593	2.427245	CCACCCCTACTGCTCTCCG	61.427	68.421	0.00	0.00	0.00	4.63
2076	5594	2.066999	CCCACCCCTACTGCTCTCC	61.067	68.421	0.00	0.00	0.00	3.71
2077	5595	3.635510	CCCACCCCTACTGCTCTC	58.364	66.667	0.00	0.00	0.00	3.20
2523	6041	2.845659	ACATAGATCAACCTCACCCCA	58.154	47.619	0.00	0.00	0.00	4.96
2524	6042	3.933861	AACATAGATCAACCTCACCCC	57.066	47.619	0.00	0.00	0.00	4.95
2525	6043	4.843728	TGAAACATAGATCAACCTCACCC	58.156	43.478	0.00	0.00	0.00	4.61
2526	6044	5.491982	ACTGAAACATAGATCAACCTCACC	58.508	41.667	0.00	0.00	0.00	4.02
2527	6045	6.166279	TGACTGAAACATAGATCAACCTCAC	58.834	40.000	0.00	0.00	0.00	3.51
2528	6046	6.358974	TGACTGAAACATAGATCAACCTCA	57.641	37.500	0.00	0.00	0.00	3.86
2529	6047	7.604164	TCTTTGACTGAAACATAGATCAACCTC	59.396	37.037	0.00	0.00	0.00	3.85
2532	6050	7.389053	ACCTCTTTGACTGAAACATAGATCAAC	59.611	37.037	0.00	0.00	0.00	3.18
2534	6052	7.009179	ACCTCTTTGACTGAAACATAGATCA	57.991	36.000	0.00	0.00	0.00	2.92
2539	6057	8.265055	CCCTTATACCTCTTTGACTGAAACATA	58.735	37.037	0.00	0.00	0.00	2.29
2543	6061	6.697641	ACCCTTATACCTCTTTGACTGAAA	57.302	37.500	0.00	0.00	0.00	2.69
2548	6066	8.702819	ACAAGTATACCCTTATACCTCTTTGAC	58.297	37.037	0.00	0.00	40.74	3.18
2549	6067	8.849543	ACAAGTATACCCTTATACCTCTTTGA	57.150	34.615	0.00	0.00	40.74	2.69
2550	6068	8.148999	GGACAAGTATACCCTTATACCTCTTTG	58.851	40.741	0.00	0.00	40.74	2.77
2551	6069	8.072480	AGGACAAGTATACCCTTATACCTCTTT	58.928	37.037	0.00	0.00	40.74	2.52
2552	6070	7.602868	AGGACAAGTATACCCTTATACCTCTT	58.397	38.462	0.00	0.00	40.74	2.85
2553	6071	7.075267	AGAGGACAAGTATACCCTTATACCTCT	59.925	40.741	17.05	17.05	40.74	3.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.