AutoCloner

Multiple sequence alignment - TraesCS5B01G477500

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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	TraesCS5B01G477500	chr5B	100.000	2557	0	0	1	2557	649728714	649731270	0.000000e+00	4723.0
1	TraesCS5B01G477500	chr5B	91.834	796	46	3	562	1354	649540051	649540830	0.000000e+00	1092.0
2	TraesCS5B01G477500	chr5B	85.330	743	54	17	710	1448	649859562	649858871	0.000000e+00	717.0
3	TraesCS5B01G477500	chr5B	80.912	702	58	28	742	1443	649829156	649828531	3.820000e-133	484.0
4	TraesCS5B01G477500	chr5B	94.915	236	8	2	182	414	649539622	649539856	1.450000e-97	366.0
5	TraesCS5B01G477500	chr5B	97.297	111	3	0	449	559	649539855	649539965	3.360000e-44	189.0
6	TraesCS5B01G477500	chr5B	91.473	129	8	2	1	129	649537244	649537369	9.400000e-40	174.0
7	TraesCS5B01G477500	chr5B	87.931	58	2	4	130	186	649539558	649539611	2.120000e-06	63.9
8	TraesCS5B01G477500	chr5D	94.323	1004	50	6	1556	2557	517281165	517282163	0.000000e+00	1531.0
9	TraesCS5B01G477500	chr5D	91.717	990	53	8	562	1539	517317367	517318339	0.000000e+00	1347.0
10	TraesCS5B01G477500	chr5D	90.010	1001	53	21	562	1538	517270191	517271168	0.000000e+00	1251.0
11	TraesCS5B01G477500	chr5D	90.843	688	48	11	1591	2272	517319042	517319720	0.000000e+00	907.0
12	TraesCS5B01G477500	chr5D	89.579	451	44	2	693	1143	517360493	517360046	1.030000e-158	569.0
13	TraesCS5B01G477500	chr5D	89.858	424	16	10	1	401	517269583	517270002	1.050000e-143	520.0
14	TraesCS5B01G477500	chr5D	90.541	296	21	2	2264	2557	517337497	517337787	3.990000e-103	385.0
15	TraesCS5B01G477500	chr5D	91.870	246	7	4	181	414	517316930	517317174	5.270000e-87	331.0
16	TraesCS5B01G477500	chr5D	83.696	368	31	12	1179	1532	517360046	517359694	1.140000e-83	320.0
17	TraesCS5B01G477500	chr5D	76.904	407	56	26	1711	2095	486247931	486248321	2.010000e-46	196.0
18	TraesCS5B01G477500	chr5D	92.437	119	7	1	449	567	517317173	517317289	4.380000e-38	169.0
19	TraesCS5B01G477500	chr5D	84.091	132	14	4	1	129	517362398	517362271	1.240000e-23	121.0
20	TraesCS5B01G477500	chr5D	95.833	48	2	0	520	567	517270070	517270117	7.590000e-11	78.7
21	TraesCS5B01G477500	chr5D	85.714	63	5	3	359	420	517360859	517360800	2.120000e-06	63.9
22	TraesCS5B01G477500	chr5A	92.077	934	50	9	1525	2456	644359311	644360222	0.000000e+00	1293.0
23	TraesCS5B01G477500	chr5A	89.301	916	44	19	652	1538	644358383	644359273	0.000000e+00	1099.0
24	TraesCS5B01G477500	chr5A	87.386	658	40	13	710	1352	644456299	644455670	0.000000e+00	715.0
25	TraesCS5B01G477500	chr5A	83.489	642	63	20	714	1354	644445324	644444725	2.220000e-155	558.0
26	TraesCS5B01G477500	chr5A	88.596	456	25	10	904	1352	644501720	644501285	1.740000e-146	529.0
27	TraesCS5B01G477500	chr5A	88.542	384	21	4	187	567	644357629	644357992	6.490000e-121	444.0
28	TraesCS5B01G477500	chr5A	90.196	153	8	4	1	149	644357366	644357515	2.600000e-45	193.0
29	TraesCS5B01G477500	chr5A	91.919	99	2	2	562	655	644358070	644358167	1.600000e-27	134.0
30	TraesCS5B01G477500	chr3D	80.412	291	45	10	1814	2098	346642823	346643107	7.170000e-51	211.0
31	TraesCS5B01G477500	chr3D	88.571	70	8	0	2031	2100	596881603	596881534	4.530000e-13	86.1
32	TraesCS5B01G477500	chr3B	75.836	269	51	11	1829	2093	734164130	734164388	9.610000e-25	124.0
33	TraesCS5B01G477500	chr4A	88.462	104	9	2	1	104	388678697	388678797	3.450000e-24	122.0
34	TraesCS5B01G477500	chr4A	77.512	209	31	14	1897	2096	618563415	618563616	7.480000e-21	111.0
35	TraesCS5B01G477500	chr3A	87.850	107	10	2	1	107	435387213	435387110	3.450000e-24	122.0
36	TraesCS5B01G477500	chr3A	90.541	74	4	2	1	74	338475779	338475709	7.530000e-16	95.3
37	TraesCS5B01G477500	chr2A	86.916	107	11	2	1	107	69376122	69376019	1.610000e-22	117.0
38	TraesCS5B01G477500	chr7A	91.892	74	3	2	1	74	29047218	29047148	1.620000e-17	100.0

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	TraesCS5B01G477500	chr5B	649728714	649731270	2556	False	4723.000000	4723	100.000000	1	2557	1	chr5B.!!$F1	2556
1	TraesCS5B01G477500	chr5B	649858871	649859562	691	True	717.000000	717	85.330000	710	1448	1	chr5B.!!$R2	738
2	TraesCS5B01G477500	chr5B	649828531	649829156	625	True	484.000000	484	80.912000	742	1443	1	chr5B.!!$R1	701
3	TraesCS5B01G477500	chr5B	649537244	649540830	3586	False	376.980000	1092	92.690000	1	1354	5	chr5B.!!$F2	1353
4	TraesCS5B01G477500	chr5D	517281165	517282163	998	False	1531.000000	1531	94.323000	1556	2557	1	chr5D.!!$F2	1001
5	TraesCS5B01G477500	chr5D	517316930	517319720	2790	False	688.500000	1347	91.716750	181	2272	4	chr5D.!!$F5	2091
6	TraesCS5B01G477500	chr5D	517269583	517271168	1585	False	616.566667	1251	91.900333	1	1538	3	chr5D.!!$F4	1537
7	TraesCS5B01G477500	chr5D	517359694	517362398	2704	True	268.475000	569	85.770000	1	1532	4	chr5D.!!$R1	1531
8	TraesCS5B01G477500	chr5A	644455670	644456299	629	True	715.000000	715	87.386000	710	1352	1	chr5A.!!$R2	642
9	TraesCS5B01G477500	chr5A	644357366	644360222	2856	False	632.600000	1293	90.407000	1	2456	5	chr5A.!!$F1	2455
10	TraesCS5B01G477500	chr5A	644444725	644445324	599	True	558.000000	558	83.489000	714	1354	1	chr5A.!!$R1	640

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
90	91	0.173255	GGTGACATGGCAATTTCCCG	59.827	55.0	0.58	0.0	0.0	5.14	F
1390	4607	0.036952	CAGCTGTGTGGGTGGTCTAG	60.037	60.0	5.25	0.0	0.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1482	4720	1.134340	AGCACGTACCCAGTCAAAACA	60.134	47.619	0.00	0.00	0.00	2.83	R
2503	6406	1.030457	GCAATGGATCAGCTTCCCTG	58.970	55.000	1.91	1.42	43.17	4.45	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
77	78	2.932855	TACCAATCCAAACGGTGACA	57.067	45.000	0.00	0.00	34.12	3.58
86	87	2.547642	CCAAACGGTGACATGGCAATTT	60.548	45.455	0.58	1.31	0.00	1.82
90	91	0.173255	GGTGACATGGCAATTTCCCG	59.827	55.000	0.58	0.00	0.00	5.14
318	3138	1.859080	GCGTTTTCTCGACTGACTGTT	59.141	47.619	0.00	0.00	0.00	3.16
331	3151	7.151976	TCGACTGACTGTTGATTTCAAGATTA	58.848	34.615	0.00	0.00	36.39	1.75
403	3236	2.349886	CGTCTCATTTAAGCCAGCTGTC	59.650	50.000	13.81	0.00	0.00	3.51
420	3253	0.391130	GTCTGTAGGCATTGGCGTCA	60.391	55.000	4.38	7.28	42.47	4.35
441	3274	6.128282	CGTCACATTTAAGCTGTTTGTAGGAT	60.128	38.462	0.00	0.00	0.00	3.24
442	3275	7.573096	CGTCACATTTAAGCTGTTTGTAGGATT	60.573	37.037	0.00	0.00	0.00	3.01
443	3276	8.082242	GTCACATTTAAGCTGTTTGTAGGATTT	58.918	33.333	0.00	0.00	0.00	2.17
444	3277	8.081633	TCACATTTAAGCTGTTTGTAGGATTTG	58.918	33.333	0.00	0.00	0.00	2.32
445	3278	8.081633	CACATTTAAGCTGTTTGTAGGATTTGA	58.918	33.333	0.00	0.00	0.00	2.69
446	3279	8.637986	ACATTTAAGCTGTTTGTAGGATTTGAA	58.362	29.630	0.00	0.00	0.00	2.69
447	3280	9.643693	CATTTAAGCTGTTTGTAGGATTTGAAT	57.356	29.630	0.00	0.00	0.00	2.57
681	3851	3.706594	ACAGTATCATCGACCAGGTCAAT	59.293	43.478	20.13	3.35	32.09	2.57
708	3880	2.073816	CACCTTTTGTCGTCCGCTTAT	58.926	47.619	0.00	0.00	0.00	1.73
806	3978	4.856801	ATGGATCACACGGCCCGC	62.857	66.667	1.23	0.00	0.00	6.13
832	4011	1.408702	GAGTGGCCAGTCAAAAAGCAA	59.591	47.619	31.78	0.00	0.00	3.91
875	4063	6.510799	GCACCGTCTCTAATCATTCAAATCAG	60.511	42.308	0.00	0.00	0.00	2.90
897	4089	1.082117	GCCTAACCATCCACACGACG	61.082	60.000	0.00	0.00	0.00	5.12
930	4122	4.093556	GTCGCCTTAATCAAACTCTCAAGG	59.906	45.833	0.00	0.00	36.45	3.61
979	4173	5.640189	TCTCTAGCCGCTATAAATACACC	57.360	43.478	0.00	0.00	0.00	4.16
980	4174	5.322754	TCTCTAGCCGCTATAAATACACCT	58.677	41.667	0.00	0.00	0.00	4.00
989	4184	5.172591	CGCTATAAATACACCTACACACACG	59.827	44.000	0.00	0.00	0.00	4.49
1053	4252	3.836949	CACATTTTGCAACGGAGCTAAT	58.163	40.909	0.00	0.00	34.99	1.73
1101	4309	1.566231	GATGGGGTGTGGGAAGAAGAT	59.434	52.381	0.00	0.00	0.00	2.40
1134	4342	1.871676	GTCCTTGTTCGGGTTCAAGAC	59.128	52.381	6.50	0.97	42.22	3.01
1266	4483	4.388499	CTACGCCCGGCACTGGTT	62.388	66.667	10.77	0.00	34.22	3.67
1390	4607	0.036952	CAGCTGTGTGGGTGGTCTAG	60.037	60.000	5.25	0.00	0.00	2.43
1432	4649	3.857854	CGTCGTGCATGCAGGCTC	61.858	66.667	30.59	23.67	34.04	4.70
1482	4720	1.405469	GCGCGCGATCAATTGCTTTT	61.405	50.000	37.18	0.00	34.99	2.27
1498	4736	3.181495	TGCTTTTGTTTTGACTGGGTACG	60.181	43.478	0.00	0.00	0.00	3.67
1528	4772	4.545208	TGTTTCCATCTTGTCGGATGTA	57.455	40.909	0.00	0.00	40.85	2.29
1576	4876	7.682021	GCAATATTTTTACCCTTAGTGAGCCAG	60.682	40.741	0.00	0.00	0.00	4.85
1618	5516	3.056304	CCGGTGGTGCAAATAACAAAAG	58.944	45.455	0.00	0.00	0.00	2.27
1687	5585	4.715527	ACCACTCTTACTATCACCGAAC	57.284	45.455	0.00	0.00	0.00	3.95
1821	5721	4.300457	TTTTTGCGCGCTCACAAG	57.700	50.000	33.29	0.00	0.00	3.16
1893	5793	9.305925	GGATGCTCCAAAAGTTATTATTTTCAG	57.694	33.333	0.00	0.00	36.28	3.02
1921	5821	7.413877	GCATTTTGGAGTGTTGATTTTGTTTGA	60.414	33.333	0.00	0.00	0.00	2.69
1940	5840	3.205338	TGATTTGCCACGACTATCATGG	58.795	45.455	0.00	0.00	36.51	3.66
1993	5893	8.077836	TCACTGAAAACGTTTGTCAAAATTTT	57.922	26.923	15.46	16.09	0.00	1.82
1998	5898	5.788055	AACGTTTGTCAAAATTTTCCACC	57.212	34.783	0.00	0.00	0.00	4.61
1999	5899	4.822026	ACGTTTGTCAAAATTTTCCACCA	58.178	34.783	0.00	0.00	0.00	4.17
2000	5900	5.238583	ACGTTTGTCAAAATTTTCCACCAA	58.761	33.333	0.00	0.00	0.00	3.67
2072	5975	3.874392	TCATCACGAGCTCAAATGAGA	57.126	42.857	15.40	10.09	44.74	3.27
2105	6008	7.224753	GCAGAAGATGACTTTCGGTAAATATGA	59.775	37.037	0.00	0.00	36.39	2.15
2308	6211	8.408043	TGAGGCTTTGAATTCTCTTCAATTTA	57.592	30.769	7.05	0.00	38.12	1.40
2469	6372	1.658968	CAAAAAGCGCACGTGTCTAC	58.341	50.000	18.38	4.31	0.00	2.59
2482	6385	3.172050	CGTGTCTACCACAATCTTCTCG	58.828	50.000	0.00	0.00	44.78	4.04
2485	6388	4.989168	GTGTCTACCACAATCTTCTCGTTT	59.011	41.667	0.00	0.00	43.92	3.60
2503	6406	4.024048	TCGTTTCCATGTTGCTTCTTTCTC	60.024	41.667	0.00	0.00	0.00	2.87
2546	6449	3.523157	TCATGGAGGACTTGGCATCTTTA	59.477	43.478	0.00	0.00	0.00	1.85
2552	6455	7.453393	TGGAGGACTTGGCATCTTTATATTAG	58.547	38.462	0.00	0.00	0.00	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	5.533154	GCAGAAAGGAGCTAGTAGATCAGTA	59.467	44.000	16.84	0.00	30.96	2.74
14	15	1.981495	AGTTGGCAGAAAGGAGCTAGT	59.019	47.619	0.00	0.00	0.00	2.57
15	16	2.027745	TGAGTTGGCAGAAAGGAGCTAG	60.028	50.000	0.00	0.00	0.00	3.42
16	17	1.977854	TGAGTTGGCAGAAAGGAGCTA	59.022	47.619	0.00	0.00	0.00	3.32
17	18	0.767375	TGAGTTGGCAGAAAGGAGCT	59.233	50.000	0.00	0.00	0.00	4.09
77	78	0.324645	AAGCTCCGGGAAATTGCCAT	60.325	50.000	4.40	0.00	0.00	4.40
86	87	1.789523	ATTACTAGCAAGCTCCGGGA	58.210	50.000	0.00	0.00	0.00	5.14
90	91	5.859495	ACCAATCTATTACTAGCAAGCTCC	58.141	41.667	0.00	0.00	0.00	4.70
318	3138	8.239314	GCAACATCTTGTCTAATCTTGAAATCA	58.761	33.333	0.00	0.00	0.00	2.57
331	3151	7.573843	GCAAATTGTAGTAGCAACATCTTGTCT	60.574	37.037	0.00	0.00	0.00	3.41
403	3236	0.673333	TGTGACGCCAATGCCTACAG	60.673	55.000	0.00	0.00	0.00	2.74
420	3253	8.177119	TCAAATCCTACAAACAGCTTAAATGT	57.823	30.769	0.00	0.00	0.00	2.71
446	3279	9.781834	CCAACGTGTACACATATATTTCAAAAT	57.218	29.630	24.98	0.00	0.00	1.82
447	3280	9.000486	TCCAACGTGTACACATATATTTCAAAA	58.000	29.630	24.98	0.00	0.00	2.44
491	3324	6.128902	CGTTCTTGAACACTATCAACTGTACC	60.129	42.308	13.05	0.00	35.55	3.34
508	3341	4.574892	TGTCAAATCTATGGCGTTCTTGA	58.425	39.130	0.00	0.00	0.00	3.02
681	3851	2.224354	GGACGACAAAAGGTGGGAACTA	60.224	50.000	0.00	0.00	0.00	2.24
708	3880	2.682856	ACTCGAGCAAGCAAACAGAAAA	59.317	40.909	13.61	0.00	0.00	2.29
806	3978	3.616956	TTTGACTGGCCACTCATCTAG	57.383	47.619	14.89	0.00	0.00	2.43
856	4035	5.755375	GGCGACTGATTTGAATGATTAGAGA	59.245	40.000	0.00	0.00	0.00	3.10
875	4063	1.082117	CGTGTGGATGGTTAGGCGAC	61.082	60.000	0.00	0.00	0.00	5.19
958	4152	5.646577	AGGTGTATTTATAGCGGCTAGAG	57.353	43.478	15.78	0.00	0.00	2.43
979	4173	0.512518	CATGGTGTGCGTGTGTGTAG	59.487	55.000	0.00	0.00	0.00	2.74
980	4174	0.179070	ACATGGTGTGCGTGTGTGTA	60.179	50.000	0.00	0.00	0.00	2.90
989	4184	3.566261	CACGGAGACATGGTGTGC	58.434	61.111	0.00	0.00	0.00	4.57
1053	4252	6.336566	CAAATCTGTCTTGCTCTAGCTAAGA	58.663	40.000	3.26	7.87	42.66	2.10
1070	4278	2.114670	ACCCCATCGCGCAAATCTG	61.115	57.895	8.75	0.00	0.00	2.90
1134	4342	1.830477	CTTCCTCCTCCAGTCTCTTGG	59.170	57.143	0.00	0.00	39.70	3.61
1143	4351	1.613630	GTGGCCTCTTCCTCCTCCA	60.614	63.158	3.32	0.00	0.00	3.86
1468	4706	6.349426	CAGTCAAAACAAAAGCAATTGATCG	58.651	36.000	10.34	0.00	33.12	3.69
1482	4720	1.134340	AGCACGTACCCAGTCAAAACA	60.134	47.619	0.00	0.00	0.00	2.83
1546	4846	8.506168	TCACTAAGGGTAAAAATATTGCTCAG	57.494	34.615	0.00	0.00	0.00	3.35
1553	4853	6.970191	ACTGGCTCACTAAGGGTAAAAATAT	58.030	36.000	0.00	0.00	0.00	1.28
1576	4876	5.809051	CCGGTGGTAAGAACATTAGTTAGAC	59.191	44.000	0.00	0.00	38.30	2.59
1618	5516	4.704965	AGGGACTAAAATATTGCTCGACC	58.295	43.478	0.00	0.00	36.02	4.79
1658	5556	7.861372	CGGTGATAGTAAGAGTGGTAATACTTG	59.139	40.741	0.00	0.00	31.46	3.16
1687	5585	3.120792	CCACGTCCCATATTGAAGTACG	58.879	50.000	0.00	0.00	35.17	3.67
1732	5630	8.080363	TGGATTTTACTGTTTACCCAAACTTT	57.920	30.769	2.33	0.00	43.73	2.66
1882	5782	9.023962	ACACTCCAAAATGCTCTGAAAATAATA	57.976	29.630	0.00	0.00	0.00	0.98
1883	5783	7.899973	ACACTCCAAAATGCTCTGAAAATAAT	58.100	30.769	0.00	0.00	0.00	1.28
1893	5793	5.754890	ACAAAATCAACACTCCAAAATGCTC	59.245	36.000	0.00	0.00	0.00	4.26
1968	5868	7.644986	AAATTTTGACAAACGTTTTCAGTGA	57.355	28.000	11.66	0.00	0.00	3.41
2072	5975	2.687700	AGTCATCTTCTGCTCGCAAT	57.312	45.000	0.00	0.00	0.00	3.56
2105	6008	5.239744	CGGTGTGCATTAGATAGAGTAGACT	59.760	44.000	0.00	0.00	0.00	3.24
2308	6211	6.544622	TCGTAACATCGTTTGTTTGAACTTT	58.455	32.000	10.80	0.00	46.51	2.66
2370	6273	5.310451	TGTCACATCCCCAGTTTACTAAAC	58.690	41.667	3.77	3.77	41.69	2.01
2375	6278	3.751518	AGTTGTCACATCCCCAGTTTAC	58.248	45.455	0.00	0.00	0.00	2.01
2432	6335	7.450627	GCTTTTTGCATTTTATCTGACATGTC	58.549	34.615	19.27	19.27	42.31	3.06
2436	6339	4.385447	GCGCTTTTTGCATTTTATCTGACA	59.615	37.500	0.00	0.00	43.06	3.58
2469	6372	3.753272	ACATGGAAACGAGAAGATTGTGG	59.247	43.478	0.00	0.00	0.00	4.17
2482	6385	5.186996	TGAGAAAGAAGCAACATGGAAAC	57.813	39.130	0.00	0.00	0.00	2.78
2485	6388	3.415212	CCTGAGAAAGAAGCAACATGGA	58.585	45.455	0.00	0.00	0.00	3.41
2503	6406	1.030457	GCAATGGATCAGCTTCCCTG	58.970	55.000	1.91	1.42	43.17	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.