AutoCloner

Multiple sequence alignment - TraesCS5D01G030100

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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	TraesCS5D01G030100	chr5D	100.000	2528	0	0	1	2528	27690504	27693031	0.000000e+00	4669.0
1	TraesCS5D01G030100	chr5D	88.834	1218	88	13	787	2000	27681815	27682988	0.000000e+00	1452.0
2	TraesCS5D01G030100	chr5D	88.352	807	53	14	1731	2528	27682786	27683560	0.000000e+00	931.0
3	TraesCS5D01G030100	chr5D	92.692	260	19	0	1782	2041	27692228	27692487	2.370000e-100	375.0
4	TraesCS5D01G030100	chr5D	92.692	260	19	0	1725	1984	27692285	27692544	2.370000e-100	375.0
5	TraesCS5D01G030100	chr5D	93.750	160	6	2	411	566	27681193	27681352	1.170000e-58	237.0
6	TraesCS5D01G030100	chr5A	92.040	1922	86	26	1	1863	18949838	18951751	0.000000e+00	2639.0
7	TraesCS5D01G030100	chr5A	87.645	688	61	11	1845	2528	18951618	18952285	0.000000e+00	778.0
8	TraesCS5D01G030100	chr5A	88.153	498	38	5	1316	1813	18920700	18921176	7.840000e-160	573.0
9	TraesCS5D01G030100	chr5A	89.676	339	24	4	1959	2295	18921094	18921423	3.010000e-114	422.0
10	TraesCS5D01G030100	chr5A	90.476	231	16	4	2295	2522	18940377	18940604	1.470000e-77	300.0
11	TraesCS5D01G030100	chr5A	95.556	180	8	0	160	339	18920328	18920507	3.180000e-74	289.0
12	TraesCS5D01G030100	chr5A	79.832	119	21	3	168	283	475310587	475310705	1.610000e-12	84.2
13	TraesCS5D01G030100	chr5B	92.368	1271	65	17	615	1858	20688480	20689745	0.000000e+00	1781.0
14	TraesCS5D01G030100	chr5B	92.384	1208	59	18	615	1794	20672270	20673472	0.000000e+00	1690.0
15	TraesCS5D01G030100	chr5B	93.711	1113	65	5	788	1898	20013381	20012272	0.000000e+00	1663.0
16	TraesCS5D01G030100	chr5B	90.221	1268	105	6	783	2041	20066159	20064902	0.000000e+00	1637.0
17	TraesCS5D01G030100	chr5B	86.897	1244	112	12	761	2000	20036164	20034968	0.000000e+00	1347.0
18	TraesCS5D01G030100	chr5B	89.359	780	73	8	1731	2504	20064984	20064209	0.000000e+00	972.0
19	TraesCS5D01G030100	chr5B	84.768	755	64	16	1731	2479	20035170	20034461	0.000000e+00	710.0
20	TraesCS5D01G030100	chr5B	90.875	526	33	6	104	618	20671531	20672052	0.000000e+00	691.0
21	TraesCS5D01G030100	chr5B	90.875	526	33	6	104	618	20687741	20688262	0.000000e+00	691.0
22	TraesCS5D01G030100	chr5B	93.018	444	30	1	1904	2346	20689620	20690063	0.000000e+00	647.0
23	TraesCS5D01G030100	chr5B	83.359	655	58	22	1881	2528	20067722	20067112	2.200000e-155	558.0
24	TraesCS5D01G030100	chr5B	92.021	376	11	4	166	533	20037004	20036640	6.240000e-141	510.0
25	TraesCS5D01G030100	chr5B	92.429	317	23	1	1946	2261	20012254	20011938	3.830000e-123	451.0
26	TraesCS5D01G030100	chr5B	92.763	304	18	2	104	403	20014111	20013808	1.070000e-118	436.0
27	TraesCS5D01G030100	chr5B	91.961	311	24	1	1731	2041	20065155	20064846	3.860000e-118	435.0
28	TraesCS5D01G030100	chr5B	91.640	311	25	1	1731	2041	20065098	20064789	1.800000e-116	429.0
29	TraesCS5D01G030100	chr5B	91.318	311	26	1	1731	2041	20065041	20064732	8.360000e-115	424.0
30	TraesCS5D01G030100	chr5B	84.173	417	35	17	1	404	20072640	20072242	2.370000e-100	375.0
31	TraesCS5D01G030100	chr5B	91.732	254	21	0	1788	2041	20065212	20064959	1.110000e-93	353.0
32	TraesCS5D01G030100	chr5B	88.433	268	28	1	2264	2528	19995274	19995007	1.130000e-83	320.0
33	TraesCS5D01G030100	chr5B	93.401	197	13	0	1845	2041	20065212	20065016	2.460000e-75	292.0
34	TraesCS5D01G030100	chr5B	90.155	193	16	1	2339	2528	20690613	20690805	5.400000e-62	248.0
35	TraesCS5D01G030100	chr5B	89.340	197	19	2	137	333	684384149	684383955	1.940000e-61	246.0
36	TraesCS5D01G030100	chr5B	82.796	279	18	9	497	750	20013792	20013519	3.270000e-54	222.0
37	TraesCS5D01G030100	chr1A	80.220	91	16	2	237	326	61713762	61713673	1.620000e-07	67.6

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	TraesCS5D01G030100	chr5D	27690504	27693031	2527	False	1806.333333	4669	95.128000	1	2528	3	chr5D.!!$F2	2527
1	TraesCS5D01G030100	chr5D	27681193	27683560	2367	False	873.333333	1452	90.312000	411	2528	3	chr5D.!!$F1	2117
2	TraesCS5D01G030100	chr5A	18949838	18952285	2447	False	1708.500000	2639	89.842500	1	2528	2	chr5A.!!$F4	2527
3	TraesCS5D01G030100	chr5A	18920328	18921423	1095	False	428.000000	573	91.128333	160	2295	3	chr5A.!!$F3	2135
4	TraesCS5D01G030100	chr5B	20671531	20673472	1941	False	1190.500000	1690	91.629500	104	1794	2	chr5B.!!$F1	1690
5	TraesCS5D01G030100	chr5B	20034461	20037004	2543	True	855.666667	1347	87.895333	166	2479	3	chr5B.!!$R5	2313
6	TraesCS5D01G030100	chr5B	20687741	20690805	3064	False	841.750000	1781	91.604000	104	2528	4	chr5B.!!$F2	2424
7	TraesCS5D01G030100	chr5B	20011938	20014111	2173	True	693.000000	1663	90.424750	104	2261	4	chr5B.!!$R4	2157
8	TraesCS5D01G030100	chr5B	20064209	20067722	3513	True	637.500000	1637	90.373875	783	2528	8	chr5B.!!$R6	1745

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
697	1252	0.702316	AGGCGTAGGATTTTTGGGGT	59.298	50.0	0.0	0.0	0.0	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2125	3479	1.804748	CCAGCCGGAAACACTTAAGTC	59.195	52.381	5.05	0.0	0.0	3.01	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
36	37	1.270550	CGAAGGGCTGCAGAATTGTTT	59.729	47.619	20.43	1.88	0.00	2.83
56	57	3.928727	TGACGGGAACAGTGTTAGTAG	57.071	47.619	8.88	3.78	0.00	2.57
57	58	3.225104	TGACGGGAACAGTGTTAGTAGT	58.775	45.455	8.88	7.02	0.00	2.73
58	59	4.397420	TGACGGGAACAGTGTTAGTAGTA	58.603	43.478	8.88	0.00	0.00	1.82
352	374	1.722034	TCTTCTCCCTCTGTGCTTGT	58.278	50.000	0.00	0.00	0.00	3.16
405	431	3.565902	TCATCATCGAGCACTAGTAGTGG	59.434	47.826	27.48	13.94	46.01	4.00
406	432	2.298610	TCATCGAGCACTAGTAGTGGG	58.701	52.381	27.48	7.74	46.01	4.61
697	1252	0.702316	AGGCGTAGGATTTTTGGGGT	59.298	50.000	0.00	0.00	0.00	4.95
744	1299	9.914131	AAAAATTGAGTAACTCATAGCCTTTTC	57.086	29.630	0.00	0.00	40.39	2.29
753	1308	7.913674	AACTCATAGCCTTTTCTACAAGAAG	57.086	36.000	0.00	0.00	35.37	2.85
923	1827	3.718723	AGACATCCTGTAGGCTTTCTCT	58.281	45.455	0.00	0.00	34.44	3.10
1053	1963	0.314302	CCGTCCTTCTCGTGTTGTCT	59.686	55.000	0.00	0.00	0.00	3.41
1062	1972	0.671796	TCGTGTTGTCTGGTGTCGAT	59.328	50.000	0.00	0.00	0.00	3.59
1080	1990	0.534203	ATGCGACCGTGGAAACAACT	60.534	50.000	0.00	0.00	46.06	3.16
1197	2107	1.527844	CCTGGCCAAGATAGCAGCC	60.528	63.158	7.01	0.20	45.96	4.85
1359	2269	0.731417	CCTACGACGAGATCAACGGT	59.269	55.000	0.00	7.87	34.93	4.83
1388	2298	2.685380	CGCAGGGAAGGAGGAGGT	60.685	66.667	0.00	0.00	0.00	3.85
1701	2612	6.460781	TCAATGCATCTTGATTTGCTTTCTT	58.539	32.000	0.00	0.00	39.60	2.52
1707	2618	7.175467	TGCATCTTGATTTGCTTTCTTCTCTTA	59.825	33.333	0.00	0.00	39.60	2.10
1739	2713	6.811170	CACACATTAATTTCGCATACCCTTTT	59.189	34.615	0.00	0.00	0.00	2.27
1782	2756	5.009210	TGCTTGTAACGTAGCCAAAGAATTT	59.991	36.000	5.63	0.00	35.28	1.82
1787	2761	8.380743	TGTAACGTAGCCAAAGAATTTTCTTA	57.619	30.769	6.01	0.00	46.22	2.10
1788	2762	9.005777	TGTAACGTAGCCAAAGAATTTTCTTAT	57.994	29.630	6.01	0.00	46.22	1.73
1898	3101	6.347888	GCTTGTAACGTAGCCAAAGAATTGTA	60.348	38.462	0.00	0.00	34.60	2.41
1956	3303	5.302360	TGTAACGTAGCCAAAGAATTGTCT	58.698	37.500	0.00	0.00	34.60	3.41
1957	3304	5.761234	TGTAACGTAGCCAAAGAATTGTCTT	59.239	36.000	0.00	0.00	46.47	3.01
1958	3305	6.930164	TGTAACGTAGCCAAAGAATTGTCTTA	59.070	34.615	0.00	0.00	43.59	2.10
1959	3306	7.604927	TGTAACGTAGCCAAAGAATTGTCTTAT	59.395	33.333	0.00	0.00	43.59	1.73
1960	3307	9.090692	GTAACGTAGCCAAAGAATTGTCTTATA	57.909	33.333	0.00	0.00	43.59	0.98
1961	3308	7.535489	ACGTAGCCAAAGAATTGTCTTATAC	57.465	36.000	0.00	0.00	43.59	1.47
1962	3309	6.537660	ACGTAGCCAAAGAATTGTCTTATACC	59.462	38.462	0.00	0.00	43.59	2.73
1963	3310	6.018180	CGTAGCCAAAGAATTGTCTTATACCC	60.018	42.308	0.00	0.00	43.59	3.69
1964	3311	6.079712	AGCCAAAGAATTGTCTTATACCCT	57.920	37.500	0.00	0.00	43.59	4.34
1965	3312	6.494059	AGCCAAAGAATTGTCTTATACCCTT	58.506	36.000	0.00	0.00	43.59	3.95
1966	3313	6.954102	AGCCAAAGAATTGTCTTATACCCTTT	59.046	34.615	0.00	0.00	43.59	3.11
1967	3314	7.122799	AGCCAAAGAATTGTCTTATACCCTTTC	59.877	37.037	0.00	0.00	43.59	2.62
1968	3315	7.093945	GCCAAAGAATTGTCTTATACCCTTTCA	60.094	37.037	0.00	0.00	43.59	2.69
1969	3316	8.802267	CCAAAGAATTGTCTTATACCCTTTCAA	58.198	33.333	0.00	0.00	43.59	2.69
1972	3319	9.533831	AAGAATTGTCTTATACCCTTTCAATGT	57.466	29.630	0.00	0.00	42.53	2.71
1973	3320	8.960591	AGAATTGTCTTATACCCTTTCAATGTG	58.039	33.333	0.00	0.00	0.00	3.21
1974	3321	6.509418	TTGTCTTATACCCTTTCAATGTGC	57.491	37.500	0.00	0.00	0.00	4.57
1975	3322	5.815581	TGTCTTATACCCTTTCAATGTGCT	58.184	37.500	0.00	0.00	0.00	4.40
1976	3323	6.953101	TGTCTTATACCCTTTCAATGTGCTA	58.047	36.000	0.00	0.00	0.00	3.49
1977	3324	7.573710	TGTCTTATACCCTTTCAATGTGCTAT	58.426	34.615	0.00	0.00	0.00	2.97
1978	3325	8.710239	TGTCTTATACCCTTTCAATGTGCTATA	58.290	33.333	0.00	0.00	0.00	1.31
1979	3326	9.726438	GTCTTATACCCTTTCAATGTGCTATAT	57.274	33.333	0.00	0.00	0.00	0.86
2002	3349	7.954666	ATTTATTTTGCTTCTAAGGTAGCCA	57.045	32.000	0.00	0.00	35.42	4.75
2003	3350	7.768807	TTTATTTTGCTTCTAAGGTAGCCAA	57.231	32.000	0.00	0.00	35.42	4.52
2004	3351	7.768807	TTATTTTGCTTCTAAGGTAGCCAAA	57.231	32.000	0.00	0.00	35.92	3.28
2005	3352	5.705609	TTTTGCTTCTAAGGTAGCCAAAG	57.294	39.130	0.00	0.00	35.42	2.77
2006	3353	4.634012	TTGCTTCTAAGGTAGCCAAAGA	57.366	40.909	0.00	0.00	35.42	2.52
2007	3354	4.634012	TGCTTCTAAGGTAGCCAAAGAA	57.366	40.909	0.00	0.00	35.42	2.52
2008	3355	5.179452	TGCTTCTAAGGTAGCCAAAGAAT	57.821	39.130	0.00	0.00	35.42	2.40
2009	3356	5.570320	TGCTTCTAAGGTAGCCAAAGAATT	58.430	37.500	0.00	0.00	35.42	2.17
2010	3357	5.415701	TGCTTCTAAGGTAGCCAAAGAATTG	59.584	40.000	0.00	0.00	35.42	2.32
2011	3358	5.416013	GCTTCTAAGGTAGCCAAAGAATTGT	59.584	40.000	2.76	0.00	34.60	2.71
2012	3359	6.403746	GCTTCTAAGGTAGCCAAAGAATTGTC	60.404	42.308	2.76	0.00	34.60	3.18
2046	3395	8.542497	TTTCAATGTACTACACTTATGTCACC	57.458	34.615	0.00	0.00	40.48	4.02
2089	3438	7.454694	AGCAAAGAAGAGGTAAACCCAATAAAT	59.545	33.333	0.00	0.00	36.42	1.40
2125	3479	5.505173	AATCGCTCTTTCAACATAATGGG	57.495	39.130	0.00	0.00	0.00	4.00
2254	3610	3.119459	GCAGTGTCGTCCTTCTTGATCTA	60.119	47.826	0.00	0.00	0.00	1.98
2261	3617	6.368791	TGTCGTCCTTCTTGATCTAAAATGTG	59.631	38.462	0.00	0.00	0.00	3.21
2262	3618	6.369065	GTCGTCCTTCTTGATCTAAAATGTGT	59.631	38.462	0.00	0.00	0.00	3.72
2324	3680	2.358957	TGGTGCTAGTCATCACAATGC	58.641	47.619	0.00	0.00	35.04	3.56
2368	4281	3.506067	ACAATAGTTTTCTTCCTTGCCGG	59.494	43.478	0.00	0.00	0.00	6.13
2395	4308	9.981460	AGGTTTAATTCCAGATTATTCTTGAGT	57.019	29.630	0.00	0.00	0.00	3.41
2467	4386	6.646267	TCAGAGTAACAGTTGTACCTTTGTT	58.354	36.000	0.00	9.82	37.51	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	3.225104	ACTACTAACACTGTTCCCGTCA	58.775	45.455	0.00	0.00	0.00	4.35
56	57	2.429971	GGCCAAGGTCACCTACTACTAC	59.570	54.545	0.00	0.00	31.13	2.73
57	58	2.043389	TGGCCAAGGTCACCTACTACTA	59.957	50.000	0.61	0.00	31.13	1.82
58	59	1.203262	TGGCCAAGGTCACCTACTACT	60.203	52.381	0.61	0.00	31.13	2.57
99	100	3.403038	TGTAGGAAGCAAGAAACAGAGC	58.597	45.455	0.00	0.00	0.00	4.09
352	374	2.371306	TGGACGCATAGTAGTGCACTA	58.629	47.619	22.67	22.67	45.30	2.74
404	430	1.402325	GCGTGCTAAATGAACAACCCC	60.402	52.381	0.00	0.00	0.00	4.95
405	431	1.402325	GGCGTGCTAAATGAACAACCC	60.402	52.381	0.00	0.00	0.00	4.11
406	432	1.727857	CGGCGTGCTAAATGAACAACC	60.728	52.381	0.00	0.00	0.00	3.77
923	1827	5.644206	TGTTTGCGCCTCACAATACTATTTA	59.356	36.000	4.18	0.00	0.00	1.40
937	1847	1.001520	GGGGTAATTTTGTTTGCGCCT	59.998	47.619	4.18	0.00	39.92	5.52
1062	1972	0.745128	AAGTTGTTTCCACGGTCGCA	60.745	50.000	0.00	0.00	0.00	5.10
1197	2107	0.660005	CGTTGTTGACGCCCATGTTG	60.660	55.000	0.00	0.00	45.86	3.33
1388	2298	4.388499	GGGAGACGGCCTTTGCGA	62.388	66.667	0.00	0.00	38.85	5.10
1502	2412	3.857157	TGATAAGGTTAGTGATGGCCC	57.143	47.619	0.00	0.00	0.00	5.80
1714	2625	5.499139	AGGGTATGCGAAATTAATGTGTG	57.501	39.130	0.00	0.00	0.00	3.82
1721	2633	6.975772	GCACATTAAAAGGGTATGCGAAATTA	59.024	34.615	0.00	0.00	0.00	1.40
1759	2733	4.680171	ATTCTTTGGCTACGTTACAAGC	57.320	40.909	0.00	0.00	38.03	4.01
1771	2745	8.311109	TGAAAGGGTATAAGAAAATTCTTTGGC	58.689	33.333	13.18	4.76	44.70	4.52
1868	3071	3.889196	TGGCTACGTTACAAGCAAAAG	57.111	42.857	10.05	0.00	40.61	2.27
1976	3323	9.640952	TGGCTACCTTAGAAGCAAAATAAATAT	57.359	29.630	8.38	0.00	40.61	1.28
1977	3324	9.469097	TTGGCTACCTTAGAAGCAAAATAAATA	57.531	29.630	8.38	0.00	40.61	1.40
1978	3325	7.954666	TGGCTACCTTAGAAGCAAAATAAAT	57.045	32.000	8.38	0.00	40.61	1.40
1979	3326	7.768807	TTGGCTACCTTAGAAGCAAAATAAA	57.231	32.000	8.38	0.00	40.61	1.40
1980	3327	7.668052	TCTTTGGCTACCTTAGAAGCAAAATAA	59.332	33.333	8.73	1.12	40.08	1.40
1981	3328	7.172342	TCTTTGGCTACCTTAGAAGCAAAATA	58.828	34.615	8.73	1.82	40.08	1.40
1982	3329	6.010219	TCTTTGGCTACCTTAGAAGCAAAAT	58.990	36.000	8.73	0.00	40.08	1.82
1983	3330	5.381757	TCTTTGGCTACCTTAGAAGCAAAA	58.618	37.500	8.21	8.21	38.91	2.44
1984	3331	4.980573	TCTTTGGCTACCTTAGAAGCAAA	58.019	39.130	8.38	1.61	40.61	3.68
1985	3332	4.634012	TCTTTGGCTACCTTAGAAGCAA	57.366	40.909	8.38	0.00	40.61	3.91
1986	3333	4.634012	TTCTTTGGCTACCTTAGAAGCA	57.366	40.909	8.38	0.00	40.61	3.91
1987	3334	5.416013	ACAATTCTTTGGCTACCTTAGAAGC	59.584	40.000	0.00	0.00	37.15	3.86
1988	3335	7.078011	GACAATTCTTTGGCTACCTTAGAAG	57.922	40.000	0.00	0.00	37.91	2.85
1999	3346	6.775594	AAGGGTATAAGACAATTCTTTGGC	57.224	37.500	0.00	0.00	39.17	4.52
2000	3347	8.348285	TGAAAGGGTATAAGACAATTCTTTGG	57.652	34.615	0.00	0.00	39.17	3.28
2003	3350	9.533831	ACATTGAAAGGGTATAAGACAATTCTT	57.466	29.630	0.00	0.00	44.70	2.52
2006	3353	9.975218	AGTACATTGAAAGGGTATAAGACAATT	57.025	29.630	0.00	0.00	0.00	2.32
2008	3355	9.880157	GTAGTACATTGAAAGGGTATAAGACAA	57.120	33.333	0.00	0.00	0.00	3.18
2009	3356	9.038072	TGTAGTACATTGAAAGGGTATAAGACA	57.962	33.333	0.00	0.00	0.00	3.41
2010	3357	9.310716	GTGTAGTACATTGAAAGGGTATAAGAC	57.689	37.037	6.21	0.00	0.00	3.01
2011	3358	9.263446	AGTGTAGTACATTGAAAGGGTATAAGA	57.737	33.333	6.21	0.00	0.00	2.10
2012	3359	9.886132	AAGTGTAGTACATTGAAAGGGTATAAG	57.114	33.333	6.21	0.00	0.00	1.73
2046	3395	9.178427	CTTCTTTGCTCAACTCTTCTTATTTTG	57.822	33.333	0.00	0.00	0.00	2.44
2112	3466	8.472007	AAACACTTAAGTCCCATTATGTTGAA	57.528	30.769	4.77	0.00	0.00	2.69
2125	3479	1.804748	CCAGCCGGAAACACTTAAGTC	59.195	52.381	5.05	0.00	0.00	3.01
2415	4331	6.090358	CCAAAATGTCAATGCTCAATCTCAAC	59.910	38.462	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.