AutoCloner

Multiple sequence alignment - TraesCS5D01G543500

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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	TraesCS5D01G543500	chr5D	100.000	7064	0	0	1	7064	553678093	553671030	0.000000e+00	13045.0
1	TraesCS5D01G543500	chr5D	94.286	105	5	1	1	104	553658544	553658440	7.330000e-35	159.0
2	TraesCS5D01G543500	chr4A	84.098	1635	223	23	3843	5460	615039703	615041317	0.000000e+00	1544.0
3	TraesCS5D01G543500	chr4A	80.352	341	46	12	5979	6314	615042127	615042451	9.160000e-59	239.0
4	TraesCS5D01G543500	chr4A	85.484	186	19	6	1	179	614871131	614871315	3.360000e-43	187.0
5	TraesCS5D01G543500	chr5B	84.137	1431	169	34	4020	5440	697293924	697295306	0.000000e+00	1332.0
6	TraesCS5D01G543500	chr5B	84.661	1017	131	17	4564	5566	697125070	697126075	0.000000e+00	990.0
7	TraesCS5D01G543500	chr5B	81.989	1066	155	25	1481	2531	697287694	697288737	0.000000e+00	870.0
8	TraesCS5D01G543500	chr5B	89.509	591	43	10	1	577	697118035	697118620	0.000000e+00	730.0
9	TraesCS5D01G543500	chr5B	83.714	700	94	15	3800	4490	697124024	697124712	1.660000e-180	643.0
10	TraesCS5D01G543500	chr5B	78.554	401	72	12	3630	4021	697290036	697290431	1.180000e-62	252.0
11	TraesCS5D01G543500	chr5B	82.979	188	23	7	6435	6620	577082583	577082763	2.040000e-35	161.0
12	TraesCS5D01G543500	chr7B	76.043	1749	313	71	3868	5576	709559127	709560809	0.000000e+00	811.0
13	TraesCS5D01G543500	chr7B	81.732	843	131	12	4559	5383	709524952	709525789	0.000000e+00	682.0
14	TraesCS5D01G543500	chr7B	75.517	1499	293	55	3894	5349	746051886	746053353	0.000000e+00	667.0
15	TraesCS5D01G543500	chr7D	76.000	1750	287	78	3898	5587	616310755	616312431	0.000000e+00	782.0
16	TraesCS5D01G543500	chr7D	93.258	178	11	1	6426	6603	381000225	381000401	1.950000e-65	261.0
17	TraesCS5D01G543500	chr7D	95.890	146	5	1	6888	7033	71982515	71982371	1.180000e-57	235.0
18	TraesCS5D01G543500	chr7D	93.631	157	8	2	6877	7033	570276796	570276642	4.260000e-57	233.0
19	TraesCS5D01G543500	chr7D	87.709	179	21	1	6445	6622	483890736	483890558	2.580000e-49	207.0
20	TraesCS5D01G543500	chr7D	82.857	70	10	2	1426	1495	520390475	520390408	2.130000e-05	62.1
21	TraesCS5D01G543500	chr2B	79.134	1016	185	20	4556	5553	17594574	17593568	0.000000e+00	676.0
22	TraesCS5D01G543500	chr2B	79.395	859	141	25	4549	5387	17396122	17395280	2.210000e-159	573.0
23	TraesCS5D01G543500	chr2B	78.978	509	90	14	3854	4352	17595255	17594754	1.470000e-86	331.0
24	TraesCS5D01G543500	chr2B	73.684	513	112	15	4556	5051	787800957	787800451	2.020000e-40	178.0
25	TraesCS5D01G543500	chr2B	82.514	183	20	10	6435	6611	94807985	94808161	4.410000e-32	150.0
26	TraesCS5D01G543500	chr2B	82.243	107	15	2	1371	1477	418269890	418269788	9.760000e-14	89.8
27	TraesCS5D01G543500	chr3D	78.049	1066	165	41	1500	2546	539909599	539908584	6.060000e-170	608.0
28	TraesCS5D01G543500	chr3D	95.376	173	7	1	6427	6599	472443017	472442846	2.510000e-69	274.0
29	TraesCS5D01G543500	chr3D	96.364	165	6	0	6435	6599	2350724	2350560	9.030000e-69	272.0
30	TraesCS5D01G543500	chr3D	94.253	174	8	2	6431	6604	250054187	250054016	1.510000e-66	265.0
31	TraesCS5D01G543500	chr3D	96.479	142	4	1	6888	7029	604800440	604800300	4.260000e-57	233.0
32	TraesCS5D01G543500	chr3D	83.333	210	29	6	6434	6641	59924215	59924420	9.350000e-44	189.0
33	TraesCS5D01G543500	chr3D	97.297	37	1	0	1426	1462	236232984	236232948	5.920000e-06	63.9
34	TraesCS5D01G543500	chr2D	76.775	831	147	31	4572	5370	11257567	11258383	2.360000e-114	424.0
35	TraesCS5D01G543500	chr2D	77.279	691	123	26	4753	5426	11292141	11292814	6.690000e-100	375.0
36	TraesCS5D01G543500	chr2D	95.238	168	8	0	6435	6602	120100091	120099924	4.200000e-67	267.0
37	TraesCS5D01G543500	chr2D	95.775	142	5	1	6888	7029	136380372	136380512	1.980000e-55	228.0
38	TraesCS5D01G543500	chr2D	90.654	107	8	2	3261	3366	622352010	622351905	2.660000e-29	141.0
39	TraesCS5D01G543500	chr7A	82.150	493	76	9	4556	5042	709296236	709296722	5.100000e-111	412.0
40	TraesCS5D01G543500	chr7A	87.295	244	29	2	5139	5380	709296795	709297038	1.940000e-70	278.0
41	TraesCS5D01G543500	chr7A	95.105	143	7	0	6888	7030	495505227	495505369	7.130000e-55	226.0
42	TraesCS5D01G543500	chr7A	77.679	112	23	2	1370	1480	315296362	315296252	4.570000e-07	67.6
43	TraesCS5D01G543500	chr4B	95.455	176	8	0	6434	6609	97895048	97894873	1.500000e-71	281.0
44	TraesCS5D01G543500	chr1D	95.833	168	7	0	6435	6602	403044476	403044309	9.030000e-69	272.0
45	TraesCS5D01G543500	chr1D	82.857	210	31	4	6435	6641	315034929	315035136	4.350000e-42	183.0
46	TraesCS5D01G543500	chr1D	91.262	103	9	0	3269	3371	31154862	31154760	2.660000e-29	141.0
47	TraesCS5D01G543500	chr1D	89.720	107	9	2	3270	3375	258092058	258091953	1.240000e-27	135.0
48	TraesCS5D01G543500	chr6D	93.889	180	10	1	6424	6602	119803528	119803707	3.250000e-68	270.0
49	TraesCS5D01G543500	chr6D	95.804	143	6	0	6888	7030	426639432	426639290	1.530000e-56	231.0
50	TraesCS5D01G543500	chr6D	78.723	94	17	3	1370	1462	223454552	223454461	7.650000e-05	60.2
51	TraesCS5D01G543500	chr5A	93.785	177	11	0	6434	6610	436260735	436260559	4.200000e-67	267.0
52	TraesCS5D01G543500	chr5A	83.684	190	26	4	6435	6623	37590761	37590946	2.620000e-39	174.0
53	TraesCS5D01G543500	chr5A	80.000	95	12	7	1370	1461	95672442	95672352	5.920000e-06	63.9
54	TraesCS5D01G543500	chr4D	97.183	142	4	0	6888	7029	17560313	17560454	2.550000e-59	241.0
55	TraesCS5D01G543500	chr4D	97.183	142	3	1	6888	7029	507858228	507858368	9.160000e-59	239.0
56	TraesCS5D01G543500	chr4D	79.787	94	16	3	1370	1462	152155305	152155214	1.640000e-06	65.8
57	TraesCS5D01G543500	chr3A	85.586	222	24	5	2683	2902	674755095	674754880	7.130000e-55	226.0
58	TraesCS5D01G543500	chr3A	89.720	107	10	1	3262	3367	7126828	7126934	1.240000e-27	135.0
59	TraesCS5D01G543500	chr2A	95.105	143	6	1	6888	7030	207465078	207465219	2.560000e-54	224.0
60	TraesCS5D01G543500	chr2A	72.745	510	113	20	4556	5051	771805383	771804886	1.590000e-31	148.0
61	TraesCS5D01G543500	chr2A	97.297	37	1	0	1426	1462	106518122	106518086	5.920000e-06	63.9
62	TraesCS5D01G543500	chr3B	75.000	464	93	17	3895	4350	1372869	1373317	7.230000e-45	193.0
63	TraesCS5D01G543500	chr3B	89.286	140	15	0	2578	2717	715890897	715890758	7.280000e-40	176.0
64	TraesCS5D01G543500	chr3B	90.566	106	9	1	3262	3366	4219307	4219202	9.550000e-29	139.0
65	TraesCS5D01G543500	chr3B	89.623	106	10	1	3262	3366	5074752	5074647	4.450000e-27	134.0
66	TraesCS5D01G543500	chr3B	83.133	83	6	7	6539	6620	524326234	524326309	1.270000e-07	69.4
67	TraesCS5D01G543500	chr1B	82.857	210	31	4	6435	6641	426855320	426855527	4.350000e-42	183.0
68	TraesCS5D01G543500	chr1B	90.654	107	9	1	3270	3375	354987434	354987540	2.660000e-29	141.0
69	TraesCS5D01G543500	chr1A	92.784	97	7	0	3270	3366	489239018	489238922	2.660000e-29	141.0
70	TraesCS5D01G543500	chr1A	90.476	105	9	1	3267	3370	385895955	385896059	3.440000e-28	137.0
71	TraesCS5D01G543500	chr1A	81.111	90	13	4	1374	1461	478551102	478551015	1.270000e-07	69.4

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	TraesCS5D01G543500	chr5D	553671030	553678093	7063	True	13045.0	13045	100.0000	1	7064	1	chr5D.!!$R2	7063
1	TraesCS5D01G543500	chr4A	615039703	615042451	2748	False	891.5	1544	82.2250	3843	6314	2	chr4A.!!$F2	2471
2	TraesCS5D01G543500	chr5B	697287694	697295306	7612	False	818.0	1332	81.5600	1481	5440	3	chr5B.!!$F4	3959
3	TraesCS5D01G543500	chr5B	697124024	697126075	2051	False	816.5	990	84.1875	3800	5566	2	chr5B.!!$F3	1766
4	TraesCS5D01G543500	chr5B	697118035	697118620	585	False	730.0	730	89.5090	1	577	1	chr5B.!!$F2	576
5	TraesCS5D01G543500	chr7B	709559127	709560809	1682	False	811.0	811	76.0430	3868	5576	1	chr7B.!!$F2	1708
6	TraesCS5D01G543500	chr7B	709524952	709525789	837	False	682.0	682	81.7320	4559	5383	1	chr7B.!!$F1	824
7	TraesCS5D01G543500	chr7B	746051886	746053353	1467	False	667.0	667	75.5170	3894	5349	1	chr7B.!!$F3	1455
8	TraesCS5D01G543500	chr7D	616310755	616312431	1676	False	782.0	782	76.0000	3898	5587	1	chr7D.!!$F2	1689
9	TraesCS5D01G543500	chr2B	17395280	17396122	842	True	573.0	573	79.3950	4549	5387	1	chr2B.!!$R1	838
10	TraesCS5D01G543500	chr2B	17593568	17595255	1687	True	503.5	676	79.0560	3854	5553	2	chr2B.!!$R4	1699
11	TraesCS5D01G543500	chr3D	539908584	539909599	1015	True	608.0	608	78.0490	1500	2546	1	chr3D.!!$R5	1046
12	TraesCS5D01G543500	chr2D	11257567	11258383	816	False	424.0	424	76.7750	4572	5370	1	chr2D.!!$F1	798
13	TraesCS5D01G543500	chr2D	11292141	11292814	673	False	375.0	375	77.2790	4753	5426	1	chr2D.!!$F2	673
14	TraesCS5D01G543500	chr7A	709296236	709297038	802	False	345.0	412	84.7225	4556	5380	2	chr7A.!!$F2	824

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	Hairpin	End Stability	Orientation
717	729	0.039911	AGCCGAGTAGAGTGGACCTT	59.960	55.000	0.00	0.00	3.50	F
953	965	0.040058	TCCCTTGCTTGCATCCACAT	59.960	50.000	0.00	0.00	3.21	F
963	975	0.099436	GCATCCACATCTTGTTCCGC	59.901	55.000	0.00	0.00	5.54	F
966	978	0.109532	TCCACATCTTGTTCCGCCAA	59.890	50.000	0.00	0.00	4.52	F
970	982	0.109597	CATCTTGTTCCGCCAACTGC	60.110	55.000	0.00	35.79	4.40	F
2840	3065	0.178992	CTGGGGCAAAGAACCAGTGA	60.179	55.000	0.00	45.21	3.41	F
2936	3161	0.030773	TCACGTGCTCACTCACACTC	59.969	55.000	11.67	36.80	3.51	F
2937	3162	0.031314	CACGTGCTCACTCACACTCT	59.969	55.000	0.82	36.80	3.24	F
2938	3163	0.031314	ACGTGCTCACTCACACTCTG	59.969	55.000	0.00	36.80	3.35	F
2940	3165	0.033228	GTGCTCACTCACACTCTGCT	59.967	55.000	0.00	36.97	4.24	F
3384	3609	0.038744	ACATGTTCTTCAGCCCCAGG	59.961	55.000	0.00	0.00	4.45	F
3892	4761	0.463654	TGCAGACAACACCCACACTC	60.464	55.000	0.00	0.00	3.51	F
3893	4762	0.463654	GCAGACAACACCCACACTCA	60.464	55.000	0.00	0.00	3.41	F
5266	10053	1.446792	CTGCGTGAATCCTGAGCGT	60.447	57.895	0.00	0.00	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2004	2032	0.251354	TCCAGCTCACCTGATTCAGC	59.749	55.000	8.23	0.00	44.64	4.26	R
2917	3142	0.030773	GAGTGTGAGTGAGCACGTGA	59.969	55.000	22.23	0.00	41.63	4.35	R
2918	3143	0.031314	AGAGTGTGAGTGAGCACGTG	59.969	55.000	12.28	12.28	41.63	4.49	R
2919	3144	0.031314	CAGAGTGTGAGTGAGCACGT	59.969	55.000	0.00	0.00	41.63	4.49	R
2921	3146	0.033228	AGCAGAGTGTGAGTGAGCAC	59.967	55.000	0.00	0.00	39.22	4.40	R
4609	9306	0.036875	GCCCATAGGAAATCCCCTCG	59.963	60.000	0.00	0.00	37.74	4.63	R
4627	9324	0.100861	GCTCGTGGAGGTACTGTAGC	59.899	60.000	8.91	8.91	41.55	3.58	R
4872	9601	5.662456	TGCATTAACATGAATGGGTGAATG	58.338	37.500	0.00	0.00	37.31	2.67	R
5053	9804	5.067805	GGGGCCTCAAAAGTTTATACAGATG	59.932	44.000	0.84	0.00	0.00	2.90	R
5075	9844	3.010138	TGACATGGTCTTTAGGAAAGGGG	59.990	47.826	0.00	0.00	39.01	4.79	R
5169	9953	3.525268	ACCTTGGTTCTTTTTGCAGTG	57.475	42.857	0.00	0.00	0.00	3.66	R
5648	10583	2.348472	TGGACTCTGAAACCATTCCCT	58.652	47.619	0.00	0.00	34.49	4.20	R
6028	11181	2.579873	CTGGATGTTGGGGCTTGATAG	58.420	52.381	0.00	0.00	0.00	2.08	R
6917	12073	0.033601	AATGGGACCATTTAGCGGCA	60.034	50.000	10.71	0.00	43.32	5.69	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
21	22	3.966026	CTCGTGGGCGTCGAACCTC	62.966	68.421	0.00	0.00	39.49	3.85
33	34	0.528470	CGAACCTCGAGAAGCTCCTT	59.472	55.000	15.71	0.00	43.74	3.36
122	123	4.051237	GCCTGAAGTGAACCATTTTGAAC	58.949	43.478	0.00	0.00	0.00	3.18
136	141	4.751767	TTTTGAACTGAATGGCCTTGTT	57.248	36.364	3.32	0.00	0.00	2.83
143	148	3.573967	ACTGAATGGCCTTGTTTAGGTTG	59.426	43.478	3.32	0.00	46.61	3.77
159	164	2.626743	AGGTTGTGTGCGTAGTAGACTT	59.373	45.455	0.00	0.00	37.29	3.01
161	166	3.427863	GGTTGTGTGCGTAGTAGACTTTC	59.572	47.826	0.00	0.00	37.29	2.62
162	167	3.293311	TGTGTGCGTAGTAGACTTTCC	57.707	47.619	0.00	0.00	37.29	3.13
163	168	2.624364	TGTGTGCGTAGTAGACTTTCCA	59.376	45.455	0.00	0.00	37.29	3.53
164	169	3.257375	TGTGTGCGTAGTAGACTTTCCAT	59.743	43.478	0.00	0.00	37.29	3.41
165	170	3.612860	GTGTGCGTAGTAGACTTTCCATG	59.387	47.826	0.00	0.00	32.90	3.66
166	171	3.187700	GTGCGTAGTAGACTTTCCATGG	58.812	50.000	4.97	4.97	0.00	3.66
167	172	3.093814	TGCGTAGTAGACTTTCCATGGA	58.906	45.455	11.44	11.44	0.00	3.41
173	178	6.183360	CGTAGTAGACTTTCCATGGATCTGAA	60.183	42.308	21.71	10.73	0.00	3.02
180	187	6.251471	ACTTTCCATGGATCTGAATTCACTT	58.749	36.000	17.06	0.00	0.00	3.16
187	194	5.624159	TGGATCTGAATTCACTTTCACTGT	58.376	37.500	3.38	0.00	32.39	3.55
189	196	6.650807	TGGATCTGAATTCACTTTCACTGTAC	59.349	38.462	3.38	0.00	32.39	2.90
191	198	4.988540	TCTGAATTCACTTTCACTGTACGG	59.011	41.667	3.38	0.00	32.39	4.02
207	214	6.750963	CACTGTACGGGTAAAACTATTCTCTC	59.249	42.308	6.65	0.00	0.00	3.20
208	215	6.662663	ACTGTACGGGTAAAACTATTCTCTCT	59.337	38.462	6.65	0.00	0.00	3.10
215	222	6.314152	GGGTAAAACTATTCTCTCTGCTCAAC	59.686	42.308	0.00	0.00	0.00	3.18
218	225	4.734398	ACTATTCTCTCTGCTCAACTGG	57.266	45.455	0.00	0.00	0.00	4.00
221	228	0.833409	TCTCTCTGCTCAACTGGGCA	60.833	55.000	3.83	3.83	36.94	5.36
250	257	0.107410	TGCTTTGGGAACTCGTGTGT	60.107	50.000	0.00	0.00	0.00	3.72
258	265	1.828331	GAACTCGTGTGTGAACCGGC	61.828	60.000	0.00	0.00	0.00	6.13

Showing 1 to 25 of 2,079 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	0.108424	CCAGGTCAAGGAGCTTCTCG	60.108	60.000	0.00	0.00	38.40	4.04
33	34	0.178921	AGCTCTTCTCCACCAGGTCA	60.179	55.000	0.00	0.00	35.89	4.02
136	141	3.822735	AGTCTACTACGCACACAACCTAA	59.177	43.478	0.00	0.00	0.00	2.69
143	148	3.293311	TGGAAAGTCTACTACGCACAC	57.707	47.619	0.00	0.00	0.00	3.82
159	164	6.151648	GTGAAAGTGAATTCAGATCCATGGAA	59.848	38.462	20.67	1.11	39.84	3.53
161	166	5.651139	AGTGAAAGTGAATTCAGATCCATGG	59.349	40.000	8.80	4.97	39.84	3.66
162	167	6.150641	ACAGTGAAAGTGAATTCAGATCCATG	59.849	38.462	8.80	10.50	40.62	3.66
163	168	6.243900	ACAGTGAAAGTGAATTCAGATCCAT	58.756	36.000	8.80	0.00	40.62	3.41
164	169	5.624159	ACAGTGAAAGTGAATTCAGATCCA	58.376	37.500	8.80	2.56	40.62	3.41
165	170	6.183360	CGTACAGTGAAAGTGAATTCAGATCC	60.183	42.308	8.80	0.00	40.62	3.36
166	171	6.183360	CCGTACAGTGAAAGTGAATTCAGATC	60.183	42.308	8.80	8.11	40.62	2.75
167	172	5.639506	CCGTACAGTGAAAGTGAATTCAGAT	59.360	40.000	8.80	0.00	40.62	2.90
173	178	3.764237	ACCCGTACAGTGAAAGTGAAT	57.236	42.857	0.00	0.00	40.62	2.57
180	187	6.996509	AGAATAGTTTTACCCGTACAGTGAA	58.003	36.000	0.00	0.00	0.00	3.18
187	194	5.655532	AGCAGAGAGAATAGTTTTACCCGTA	59.344	40.000	0.00	0.00	0.00	4.02
189	196	5.012328	AGCAGAGAGAATAGTTTTACCCG	57.988	43.478	0.00	0.00	0.00	5.28
191	198	7.064016	CAGTTGAGCAGAGAGAATAGTTTTACC	59.936	40.741	0.00	0.00	0.00	2.85
207	214	2.758089	GCGATGCCCAGTTGAGCAG	61.758	63.158	0.00	0.00	43.38	4.24
208	215	2.747460	GCGATGCCCAGTTGAGCA	60.747	61.111	0.00	0.00	44.45	4.26
221	228	0.539438	TCCCAAAGCAAACAGGCGAT	60.539	50.000	0.00	0.00	39.27	4.58
250	257	0.899720	AGTATTTCGAGGCCGGTTCA	59.100	50.000	1.90	0.00	36.24	3.18
323	330	5.291858	CGCAAGAGCAGATAACAAGAATACA	59.708	40.000	0.00	0.00	42.27	2.29
324	331	5.520288	TCGCAAGAGCAGATAACAAGAATAC	59.480	40.000	0.00	0.00	45.01	1.89
325	332	5.660460	TCGCAAGAGCAGATAACAAGAATA	58.340	37.500	0.00	0.00	45.01	1.75
326	333	4.507710	TCGCAAGAGCAGATAACAAGAAT	58.492	39.130	0.00	0.00	45.01	2.40

Showing 1 to 25 of 2,025 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.