AutoCloner

Multiple sequence alignment - TraesCS5D01G526200

Loading Multiple Alignment...

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	TraesCS5D01G526200	chr5D	100.000	3296	0	0	1	3296	544147968	544151263	0.000000e+00	6087.0
1	TraesCS5D01G526200	chr5D	85.206	2109	239	35	437	2492	544230877	544232965	0.000000e+00	2098.0
2	TraesCS5D01G526200	chr5D	79.654	1273	240	15	999	2263	544481609	544482870	0.000000e+00	898.0
3	TraesCS5D01G526200	chr5D	78.852	1272	252	13	999	2263	544459877	544461138	0.000000e+00	843.0
4	TraesCS5D01G526200	chr5D	81.688	557	91	6	1723	2277	543830902	543831449	1.390000e-123	453.0
5	TraesCS5D01G526200	chr5D	82.857	175	16	4	271	440	544213737	544213902	9.530000e-31	145.0
6	TraesCS5D01G526200	chr5D	81.366	161	10	5	445	605	544213961	544214101	2.690000e-21	113.0
7	TraesCS5D01G526200	chr5D	94.737	57	2	1	10	66	544230504	544230559	1.630000e-13	87.9
8	TraesCS5D01G526200	chr4A	93.401	2349	94	16	606	2917	625166661	625164337	0.000000e+00	3422.0
9	TraesCS5D01G526200	chr4A	85.701	2098	230	37	437	2492	625078200	625076131	0.000000e+00	2148.0
10	TraesCS5D01G526200	chr4A	79.826	1264	237	15	999	2253	624369657	624370911	0.000000e+00	905.0
11	TraesCS5D01G526200	chr4A	86.250	400	29	9	221	612	625167280	625166899	8.510000e-111	411.0
12	TraesCS5D01G526200	chr4A	92.754	276	9	6	3023	3296	625127560	625127294	3.990000e-104	388.0
13	TraesCS5D01G526200	chr4A	76.418	335	40	24	2785	3097	625075937	625075620	9.530000e-31	145.0
14	TraesCS5D01G526200	chr4A	89.583	96	10	0	2919	3014	625164225	625164130	4.470000e-24	122.0
15	TraesCS5D01G526200	chr5B	92.988	2125	121	10	843	2957	686200952	686203058	0.000000e+00	3073.0
16	TraesCS5D01G526200	chr5B	90.124	1367	101	14	1599	2952	686342922	686344267	0.000000e+00	1746.0
17	TraesCS5D01G526200	chr5B	86.424	1510	176	16	998	2490	686432236	686433733	0.000000e+00	1626.0
18	TraesCS5D01G526200	chr5B	82.411	1211	130	45	458	1594	686333366	686334567	0.000000e+00	979.0
19	TraesCS5D01G526200	chr5B	81.291	604	101	9	1723	2323	685657478	685656884	2.300000e-131	479.0
20	TraesCS5D01G526200	chr5B	89.180	305	7	12	3014	3296	686203545	686203845	1.120000e-94	357.0
21	TraesCS5D01G526200	chr5B	88.852	305	10	10	3014	3296	686344839	686345141	1.450000e-93	353.0
22	TraesCS5D01G526200	chr5B	83.891	329	27	11	285	605	686199946	686200256	1.160000e-74	291.0
23	TraesCS5D01G526200	chr5B	81.081	370	43	17	458	806	686430548	686430911	1.510000e-68	270.0
24	TraesCS5D01G526200	chr5B	86.335	161	18	4	65	224	605487799	605487956	4.370000e-39	172.0
25	TraesCS5D01G526200	chr5B	88.095	126	8	2	2782	2906	686433923	686434042	3.430000e-30	143.0
26	TraesCS5D01G526200	chr5B	87.500	72	7	2	2500	2570	291999079	291999149	7.580000e-12	82.4
27	TraesCS5D01G526200	chr2A	87.349	166	18	3	65	227	688585346	688585511	1.560000e-43	187.0
28	TraesCS5D01G526200	chr2A	86.420	162	20	2	65	224	722749013	722748852	3.380000e-40	176.0
29	TraesCS5D01G526200	chr6B	84.211	133	19	2	92	224	29371337	29371207	9.600000e-26	128.0
30	TraesCS5D01G526200	chr7B	93.846	65	2	2	3	66	213247965	213248028	2.710000e-16	97.1
31	TraesCS5D01G526200	chr7B	92.063	63	2	3	3	64	313691418	313691358	5.860000e-13	86.1
32	TraesCS5D01G526200	chr7A	92.308	65	3	2	3	66	251743400	251743463	1.260000e-14	91.6
33	TraesCS5D01G526200	chr7A	86.111	72	10	0	2500	2571	179531454	179531525	9.810000e-11	78.7
34	TraesCS5D01G526200	chr7D	94.737	57	2	1	9	64	13688581	13688637	1.630000e-13	87.9
35	TraesCS5D01G526200	chr7D	94.737	57	2	1	9	64	13689851	13689907	1.630000e-13	87.9
36	TraesCS5D01G526200	chr7D	94.737	57	2	1	9	64	13692393	13692449	1.630000e-13	87.9
37	TraesCS5D01G526200	chr7D	90.769	65	4	2	3	66	236640481	236640544	5.860000e-13	86.1
38	TraesCS5D01G526200	chr1B	92.063	63	3	2	3	64	636315870	636315809	1.630000e-13	87.9

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	TraesCS5D01G526200	chr5D	544147968	544151263	3295	False	6087.000000	6087	100.000000	1	3296	1	chr5D.!!$F2	3295
1	TraesCS5D01G526200	chr5D	544230504	544232965	2461	False	1092.950000	2098	89.971500	10	2492	2	chr5D.!!$F6	2482
2	TraesCS5D01G526200	chr5D	544481609	544482870	1261	False	898.000000	898	79.654000	999	2263	1	chr5D.!!$F4	1264
3	TraesCS5D01G526200	chr5D	544459877	544461138	1261	False	843.000000	843	78.852000	999	2263	1	chr5D.!!$F3	1264
4	TraesCS5D01G526200	chr5D	543830902	543831449	547	False	453.000000	453	81.688000	1723	2277	1	chr5D.!!$F1	554
5	TraesCS5D01G526200	chr4A	625164130	625167280	3150	True	1318.333333	3422	89.744667	221	3014	3	chr4A.!!$R3	2793
6	TraesCS5D01G526200	chr4A	625075620	625078200	2580	True	1146.500000	2148	81.059500	437	3097	2	chr4A.!!$R2	2660
7	TraesCS5D01G526200	chr4A	624369657	624370911	1254	False	905.000000	905	79.826000	999	2253	1	chr4A.!!$F1	1254
8	TraesCS5D01G526200	chr5B	686199946	686203845	3899	False	1240.333333	3073	88.686333	285	3296	3	chr5B.!!$F4	3011
9	TraesCS5D01G526200	chr5B	686342922	686345141	2219	False	1049.500000	1746	89.488000	1599	3296	2	chr5B.!!$F5	1697
10	TraesCS5D01G526200	chr5B	686333366	686334567	1201	False	979.000000	979	82.411000	458	1594	1	chr5B.!!$F3	1136
11	TraesCS5D01G526200	chr5B	686430548	686434042	3494	False	679.666667	1626	85.200000	458	2906	3	chr5B.!!$F6	2448
12	TraesCS5D01G526200	chr5B	685656884	685657478	594	True	479.000000	479	81.291000	1723	2323	1	chr5B.!!$R1	600

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	Hairpin	End Stability	Orientation
389	415	0.171007	CACATCATCCCGGTTTGTGC	59.829	55.0	32.24	4.57	F
426	459	0.673333	CGCCACAGTGCATCCTAACA	60.673	55.0	0.00	2.41	F
719	1258	0.949105	GCCGAACTGTCCACGACAAT	60.949	55.0	42.26	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1242	2997	0.105760	GAGAGGCTCCTGGGATGAGA	60.106	60.000	11.71	31.26	3.27	R
1301	3056	0.599204	GACGCCCACGAAAGAGTTCA	60.599	55.000	0.00	43.93	3.18	R
2624	4461	1.634753	TCGATAGACGACGAGTGCG	59.365	57.895	0.00	46.45	5.34	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
71	97	6.554334	TGTGGTCAAACTTAGAAATGCTAC	57.446	37.500	0.00	0.00	0.00	3.58
73	99	6.017440	TGTGGTCAAACTTAGAAATGCTACAC	60.017	38.462	0.00	0.00	0.00	2.90
74	100	5.472137	TGGTCAAACTTAGAAATGCTACACC	59.528	40.000	0.00	0.00	0.00	4.16
76	102	6.877322	GGTCAAACTTAGAAATGCTACACCTA	59.123	38.462	0.00	0.00	0.00	3.08
77	103	7.148457	GGTCAAACTTAGAAATGCTACACCTAC	60.148	40.741	0.00	0.00	0.00	3.18
78	104	6.588756	TCAAACTTAGAAATGCTACACCTACG	59.411	38.462	0.00	0.00	0.00	3.51
79	105	5.909621	ACTTAGAAATGCTACACCTACGA	57.090	39.130	0.00	0.00	0.00	3.43
81	107	6.875076	ACTTAGAAATGCTACACCTACGAAT	58.125	36.000	0.00	0.00	0.00	3.34
82	108	6.757010	ACTTAGAAATGCTACACCTACGAATG	59.243	38.462	0.00	0.00	0.00	2.67
83	109	4.442706	AGAAATGCTACACCTACGAATGG	58.557	43.478	0.00	0.00	0.00	3.16
84	110	3.906720	AATGCTACACCTACGAATGGT	57.093	42.857	0.00	0.00	38.53	3.55
87	113	4.804868	TGCTACACCTACGAATGGTTTA	57.195	40.909	0.00	0.00	35.28	2.01
88	114	5.149973	TGCTACACCTACGAATGGTTTAA	57.850	39.130	0.00	0.00	35.28	1.52
90	116	5.640357	TGCTACACCTACGAATGGTTTAAAG	59.360	40.000	0.00	0.00	35.28	1.85
91	117	5.640783	GCTACACCTACGAATGGTTTAAAGT	59.359	40.000	0.00	0.00	35.28	2.66
92	118	6.813152	GCTACACCTACGAATGGTTTAAAGTA	59.187	38.462	0.00	0.00	35.28	2.24
93	119	7.331687	GCTACACCTACGAATGGTTTAAAGTAA	59.668	37.037	0.00	0.00	35.28	2.24
94	120	9.374838	CTACACCTACGAATGGTTTAAAGTAAT	57.625	33.333	0.00	0.00	35.28	1.89
96	122	7.335171	ACACCTACGAATGGTTTAAAGTAATCC	59.665	37.037	0.00	0.00	35.28	3.01
97	123	7.334921	CACCTACGAATGGTTTAAAGTAATCCA	59.665	37.037	0.00	0.00	40.65	3.41
98	124	8.050930	ACCTACGAATGGTTTAAAGTAATCCAT	58.949	33.333	2.27	2.27	45.51	3.41
101	127	7.912383	ACGAATGGTTTAAAGTAATCCATACG	58.088	34.615	7.50	0.00	43.79	3.06
102	128	7.550196	ACGAATGGTTTAAAGTAATCCATACGT	59.450	33.333	7.50	0.00	43.79	3.57
103	129	7.849026	CGAATGGTTTAAAGTAATCCATACGTG	59.151	37.037	0.00	0.00	43.79	4.49
107	133	9.887629	TGGTTTAAAGTAATCCATACGTGATTA	57.112	29.630	0.00	0.02	39.62	1.75

Showing 1 to 25 of 181 entries

Previous1 2 3 4 5…8Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	92	3.688694	AAACCATTCGTAGGTGTAGCA	57.311	42.857	0.00	0.00	39.86	3.49
67	93	5.640783	ACTTTAAACCATTCGTAGGTGTAGC	59.359	40.000	0.00	0.00	39.86	3.58
68	94	8.761575	TTACTTTAAACCATTCGTAGGTGTAG	57.238	34.615	0.00	0.00	39.86	2.74
70	96	7.335171	GGATTACTTTAAACCATTCGTAGGTGT	59.665	37.037	0.00	0.00	39.86	4.16
71	97	7.334921	TGGATTACTTTAAACCATTCGTAGGTG	59.665	37.037	0.00	0.00	39.86	4.00
73	99	7.852971	TGGATTACTTTAAACCATTCGTAGG	57.147	36.000	0.00	0.00	35.93	3.18
76	102	7.912383	CGTATGGATTACTTTAAACCATTCGT	58.088	34.615	18.09	4.07	45.57	3.85
78	104	8.885722	TCACGTATGGATTACTTTAAACCATTC	58.114	33.333	11.62	7.19	45.57	2.67
79	105	8.795842	TCACGTATGGATTACTTTAAACCATT	57.204	30.769	11.62	0.00	45.57	3.16
81	107	8.795842	AATCACGTATGGATTACTTTAAACCA	57.204	30.769	0.00	0.00	43.47	3.67
87	113	7.438459	GCTGTCTAATCACGTATGGATTACTTT	59.562	37.037	3.41	0.00	36.45	2.66
88	114	6.924060	GCTGTCTAATCACGTATGGATTACTT	59.076	38.462	3.41	0.00	36.45	2.24
90	116	6.363626	CAGCTGTCTAATCACGTATGGATTAC	59.636	42.308	5.25	0.00	36.45	1.89
91	117	6.447162	CAGCTGTCTAATCACGTATGGATTA	58.553	40.000	5.25	6.64	36.45	1.75
92	118	5.292765	CAGCTGTCTAATCACGTATGGATT	58.707	41.667	5.25	5.13	38.46	3.01
93	119	4.262207	CCAGCTGTCTAATCACGTATGGAT	60.262	45.833	13.81	0.00	0.00	3.41
94	120	3.068165	CCAGCTGTCTAATCACGTATGGA	59.932	47.826	13.81	0.00	0.00	3.41
96	122	2.797156	GCCAGCTGTCTAATCACGTATG	59.203	50.000	13.81	0.00	0.00	2.39
97	123	2.430694	TGCCAGCTGTCTAATCACGTAT	59.569	45.455	13.81	0.00	0.00	3.06
98	124	1.822371	TGCCAGCTGTCTAATCACGTA	59.178	47.619	13.81	0.00	0.00	3.57
100	126	1.284657	CTGCCAGCTGTCTAATCACG	58.715	55.000	13.81	0.00	0.00	4.35
101	127	1.065854	ACCTGCCAGCTGTCTAATCAC	60.066	52.381	13.81	0.00	0.00	3.06
102	128	1.279496	ACCTGCCAGCTGTCTAATCA	58.721	50.000	13.81	0.00	0.00	2.57
103	129	2.409948	AACCTGCCAGCTGTCTAATC	57.590	50.000	13.81	0.00	0.00	1.75
107	133	1.279496	TCATAACCTGCCAGCTGTCT	58.721	50.000	13.81	0.00	0.00	3.41

Showing 1 to 25 of 171 entries

Previous1 2 3 4 5 6 7Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.