AutoCloner

Multiple sequence alignment - TraesCS5D01G541800

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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	TraesCS5D01G541800	chr5D	100.000	3968	0	0	1	3968	552445237	552441270	0.000000e+00	7328.0
1	TraesCS5D01G541800	chr5D	86.777	242	28	4	3089	3327	552420419	552420179	2.350000e-67	267.0
2	TraesCS5D01G541800	chr5D	77.184	412	81	12	1973	2374	537216839	537217247	1.110000e-55	228.0
3	TraesCS5D01G541800	chr5D	87.179	195	21	3	2827	3018	552420821	552420628	6.680000e-53	219.0
4	TraesCS5D01G541800	chr5D	97.059	102	1	1	3326	3427	30613906	30614005	1.900000e-38	171.0
5	TraesCS5D01G541800	chr5D	75.487	359	73	11	1077	1429	552422797	552422448	1.140000e-35	161.0
6	TraesCS5D01G541800	chr5D	86.466	133	12	3	3428	3555	478461247	478461116	1.490000e-29	141.0
7	TraesCS5D01G541800	chr5D	80.851	141	23	3	1043	1182	543503748	543503611	1.510000e-19	108.0
8	TraesCS5D01G541800	chr1B	85.097	2429	306	35	779	3174	327487059	327489464	0.000000e+00	2429.0
9	TraesCS5D01G541800	chr1B	83.542	559	72	12	3	553	327486154	327486700	4.580000e-139	505.0
10	TraesCS5D01G541800	chr1D	86.000	1950	240	20	779	2708	227867094	227869030	0.000000e+00	2058.0
11	TraesCS5D01G541800	chr1D	86.727	1213	156	4	779	1988	208239528	208238318	0.000000e+00	1343.0
12	TraesCS5D01G541800	chr1D	82.988	1205	164	25	1993	3174	208202660	208201474	0.000000e+00	1051.0
13	TraesCS5D01G541800	chr1D	84.838	554	66	11	6	553	208240169	208239628	3.490000e-150	542.0
14	TraesCS5D01G541800	chr1D	84.324	555	62	14	7	553	227866171	227866708	1.630000e-143	520.0
15	TraesCS5D01G541800	chr1D	95.238	105	5	0	2747	2851	227869032	227869136	2.450000e-37	167.0
16	TraesCS5D01G541800	chr1A	87.411	1676	207	4	779	2453	295465840	295467512	0.000000e+00	1923.0
17	TraesCS5D01G541800	chr1A	85.766	555	64	9	3	553	295464912	295465455	1.240000e-159	573.0
18	TraesCS5D01G541800	chr1A	79.238	761	110	28	2443	3174	295517172	295517913	1.660000e-133	486.0
19	TraesCS5D01G541800	chr1A	100.000	94	0	0	3335	3428	445930225	445930132	1.470000e-39	174.0
20	TraesCS5D01G541800	chr1A	97.959	98	2	0	3330	3427	549119553	549119650	1.900000e-38	171.0
21	TraesCS5D01G541800	chr5A	94.343	548	24	3	3428	3968	536286492	536287039	0.000000e+00	833.0
22	TraesCS5D01G541800	chr5A	91.058	548	35	7	3431	3968	534584427	534584970	0.000000e+00	728.0
23	TraesCS5D01G541800	chr3A	91.978	536	36	3	3440	3968	158167026	158166491	0.000000e+00	745.0
24	TraesCS5D01G541800	chr4D	91.408	547	40	4	3428	3968	251423489	251424034	0.000000e+00	743.0
25	TraesCS5D01G541800	chr4D	81.921	354	51	9	3428	3773	440385381	440385033	1.800000e-73	287.0
26	TraesCS5D01G541800	chr4D	85.075	67	9	1	473	538	506346931	506346997	2.560000e-07	67.6
27	TraesCS5D01G541800	chr3B	93.439	503	27	5	3468	3968	810545350	810544852	0.000000e+00	741.0
28	TraesCS5D01G541800	chr3B	91.650	503	41	1	3464	3965	734477930	734477428	0.000000e+00	695.0
29	TraesCS5D01G541800	chr3B	84.746	59	9	0	476	534	477364270	477364328	4.280000e-05	60.2
30	TraesCS5D01G541800	chr6A	91.865	504	38	1	3468	3968	234173142	234172639	0.000000e+00	701.0
31	TraesCS5D01G541800	chr4A	76.857	579	114	14	1809	2374	616839988	616839417	3.850000e-80	309.0
32	TraesCS5D01G541800	chr4A	75.891	589	118	18	1803	2374	616885286	616884705	3.020000e-71	279.0
33	TraesCS5D01G541800	chr4A	74.727	550	120	17	1748	2286	616229932	616229391	1.110000e-55	228.0
34	TraesCS5D01G541800	chr4A	80.214	187	37	0	1093	1279	616897505	616897319	1.490000e-29	141.0
35	TraesCS5D01G541800	chr5B	76.967	521	108	11	1864	2374	677812796	677813314	1.800000e-73	287.0
36	TraesCS5D01G541800	chr5B	76.259	556	107	19	1791	2340	685504419	685504955	5.050000e-69	272.0
37	TraesCS5D01G541800	chr5B	75.507	592	114	22	1803	2374	699354723	699355303	1.090000e-65	261.0
38	TraesCS5D01G541800	chr5B	76.626	492	104	9	1799	2286	703716856	703717340	1.090000e-65	261.0
39	TraesCS5D01G541800	chr5B	76.096	502	105	12	1791	2286	685322424	685321932	8.510000e-62	248.0
40	TraesCS5D01G541800	chr5B	75.233	537	108	20	1748	2270	700229028	700228503	8.580000e-57	231.0
41	TraesCS5D01G541800	chr5B	76.038	313	60	9	1042	1352	685323111	685322812	8.880000e-32	148.0
42	TraesCS5D01G541800	chr5B	78.333	240	40	7	1042	1279	685503732	685503961	1.150000e-30	145.0
43	TraesCS5D01G541800	chr2D	89.831	177	17	1	3661	3836	2567158	2566982	3.990000e-55	226.0
44	TraesCS5D01G541800	chr6B	100.000	94	0	0	3334	3427	706995395	706995302	1.470000e-39	174.0
45	TraesCS5D01G541800	chr6B	93.103	58	4	0	3911	3968	719748492	719748549	7.070000e-13	86.1
46	TraesCS5D01G541800	chr2B	98.980	98	0	1	3331	3427	57884578	57884481	1.470000e-39	174.0
47	TraesCS5D01G541800	chr2B	98.958	96	1	0	3332	3427	653671191	653671286	5.270000e-39	172.0
48	TraesCS5D01G541800	chrUn	98.958	96	1	0	3332	3427	79765330	79765425	5.270000e-39	172.0
49	TraesCS5D01G541800	chrUn	96.970	33	1	0	503	535	282486920	282486888	5.540000e-04	56.5
50	TraesCS5D01G541800	chrUn	96.970	33	1	0	503	535	307153120	307153088	5.540000e-04	56.5
51	TraesCS5D01G541800	chr7B	98.969	97	0	1	3332	3427	704405836	704405740	5.270000e-39	172.0
52	TraesCS5D01G541800	chr7B	78.912	147	19	7	475	612	186819135	186819278	5.460000e-14	89.8
53	TraesCS5D01G541800	chr7D	93.578	109	5	2	3318	3426	561540616	561540722	1.140000e-35	161.0
54	TraesCS5D01G541800	chr3D	93.103	58	4	0	3911	3968	601183283	601183226	7.070000e-13	86.1
55	TraesCS5D01G541800	chr6D	89.655	58	5	1	479	535	450126285	450126342	5.500000e-09	73.1

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	TraesCS5D01G541800	chr5D	552441270	552445237	3967	True	7328.000000	7328	100.000000	1	3968	1	chr5D.!!$R3	3967
1	TraesCS5D01G541800	chr5D	552420179	552422797	2618	True	215.666667	267	83.147667	1077	3327	3	chr5D.!!$R4	2250
2	TraesCS5D01G541800	chr1B	327486154	327489464	3310	False	1467.000000	2429	84.319500	3	3174	2	chr1B.!!$F1	3171
3	TraesCS5D01G541800	chr1D	208201474	208202660	1186	True	1051.000000	1051	82.988000	1993	3174	1	chr1D.!!$R1	1181
4	TraesCS5D01G541800	chr1D	208238318	208240169	1851	True	942.500000	1343	85.782500	6	1988	2	chr1D.!!$R2	1982
5	TraesCS5D01G541800	chr1D	227866171	227869136	2965	False	915.000000	2058	88.520667	7	2851	3	chr1D.!!$F1	2844
6	TraesCS5D01G541800	chr1A	295464912	295467512	2600	False	1248.000000	1923	86.588500	3	2453	2	chr1A.!!$F3	2450
7	TraesCS5D01G541800	chr1A	295517172	295517913	741	False	486.000000	486	79.238000	2443	3174	1	chr1A.!!$F1	731
8	TraesCS5D01G541800	chr5A	536286492	536287039	547	False	833.000000	833	94.343000	3428	3968	1	chr5A.!!$F2	540
9	TraesCS5D01G541800	chr5A	534584427	534584970	543	False	728.000000	728	91.058000	3431	3968	1	chr5A.!!$F1	537
10	TraesCS5D01G541800	chr3A	158166491	158167026	535	True	745.000000	745	91.978000	3440	3968	1	chr3A.!!$R1	528
11	TraesCS5D01G541800	chr4D	251423489	251424034	545	False	743.000000	743	91.408000	3428	3968	1	chr4D.!!$F1	540
12	TraesCS5D01G541800	chr3B	734477428	734477930	502	True	695.000000	695	91.650000	3464	3965	1	chr3B.!!$R1	501
13	TraesCS5D01G541800	chr6A	234172639	234173142	503	True	701.000000	701	91.865000	3468	3968	1	chr6A.!!$R1	500
14	TraesCS5D01G541800	chr4A	616839417	616839988	571	True	309.000000	309	76.857000	1809	2374	1	chr4A.!!$R2	565
15	TraesCS5D01G541800	chr4A	616884705	616885286	581	True	279.000000	279	75.891000	1803	2374	1	chr4A.!!$R3	571
16	TraesCS5D01G541800	chr4A	616229391	616229932	541	True	228.000000	228	74.727000	1748	2286	1	chr4A.!!$R1	538
17	TraesCS5D01G541800	chr5B	677812796	677813314	518	False	287.000000	287	76.967000	1864	2374	1	chr5B.!!$F1	510
18	TraesCS5D01G541800	chr5B	699354723	699355303	580	False	261.000000	261	75.507000	1803	2374	1	chr5B.!!$F2	571
19	TraesCS5D01G541800	chr5B	700228503	700229028	525	True	231.000000	231	75.233000	1748	2270	1	chr5B.!!$R1	522
20	TraesCS5D01G541800	chr5B	685503732	685504955	1223	False	208.500000	272	77.296000	1042	2340	2	chr5B.!!$F4	1298

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
758	940	0.108804	GAGTCGAATGCGGTGGAGAA	60.109	55.0	0.0	0.0	38.28	2.87	F
1465	1656	0.109458	CCACGGAGTTCATCGTTCGA	60.109	55.0	0.0	0.0	41.61	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1653	1844	0.173935	CAAGGACACACCCGCGTATA	59.826	55.0	4.92	0.0	40.05	1.47	R
3417	4201	0.107654	CTCCGCCCCTCTTTGTAAGG	60.108	60.0	0.00	0.0	0.00	2.69	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
48	50	1.878102	GCATGAAGACCGTGGTCACTT	60.878	52.381	20.51	7.46	46.76	3.16
61	63	2.105128	CACTTCCGCCTAGCCTCG	59.895	66.667	0.00	0.00	0.00	4.63
64	66	2.361992	TTCCGCCTAGCCTCGTCA	60.362	61.111	0.00	0.00	0.00	4.35
65	67	1.945354	CTTCCGCCTAGCCTCGTCAA	61.945	60.000	0.00	0.00	0.00	3.18
73	75	2.288702	CCTAGCCTCGTCAATCCATCTG	60.289	54.545	0.00	0.00	0.00	2.90
86	88	7.359849	CGTCAATCCATCTGTAGCATTGATTAG	60.360	40.741	0.00	0.00	36.22	1.73
96	98	7.011389	TCTGTAGCATTGATTAGTGTTGTATGC	59.989	37.037	0.00	0.00	37.70	3.14
114	116	6.804677	TGTATGCTGTCTGTTGTTTGATTTT	58.195	32.000	0.00	0.00	0.00	1.82
119	121	7.319646	TGCTGTCTGTTGTTTGATTTTAACTT	58.680	30.769	0.00	0.00	0.00	2.66
120	122	7.275341	TGCTGTCTGTTGTTTGATTTTAACTTG	59.725	33.333	0.00	0.00	0.00	3.16
121	123	7.487829	GCTGTCTGTTGTTTGATTTTAACTTGA	59.512	33.333	0.00	0.00	0.00	3.02
122	124	9.352784	CTGTCTGTTGTTTGATTTTAACTTGAA	57.647	29.630	0.00	0.00	0.00	2.69
123	125	9.868277	TGTCTGTTGTTTGATTTTAACTTGAAT	57.132	25.926	0.00	0.00	0.00	2.57
137	139	4.621068	ACTTGAATATCATGCGTGTTGG	57.379	40.909	5.68	0.00	0.00	3.77
139	141	4.458989	ACTTGAATATCATGCGTGTTGGTT	59.541	37.500	5.68	0.00	0.00	3.67
141	143	6.150307	ACTTGAATATCATGCGTGTTGGTTTA	59.850	34.615	5.68	0.00	0.00	2.01
144	146	7.192913	TGAATATCATGCGTGTTGGTTTATTC	58.807	34.615	5.68	10.24	0.00	1.75
147	149	3.818210	TCATGCGTGTTGGTTTATTCTGT	59.182	39.130	5.68	0.00	0.00	3.41
156	158	8.661257	CGTGTTGGTTTATTCTGTCATATGTAA	58.339	33.333	1.90	0.00	0.00	2.41
252	255	5.633830	ATTGTGTCTGGTTTATTCAGCAG	57.366	39.130	0.00	0.00	42.62	4.24
280	283	5.705609	TTGGTTACAAGAAAATGAGAGGC	57.294	39.130	0.00	0.00	31.73	4.70
492	498	8.697292	ACAACTATTTGGGTTTTGCTTTAGTAA	58.303	29.630	0.00	0.00	37.00	2.24
493	499	9.535878	CAACTATTTGGGTTTTGCTTTAGTAAA	57.464	29.630	0.00	0.00	0.00	2.01
501	507	5.539574	GGTTTTGCTTTAGTAAACCCCCTTA	59.460	40.000	13.26	0.00	43.09	2.69
502	508	6.041865	GGTTTTGCTTTAGTAAACCCCCTTAA	59.958	38.462	13.26	0.00	43.09	1.85

Showing 1 to 25 of 321 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.036105	CAGTGTACTGGGATGCTGCA	60.036	55.000	4.13	4.13	40.20	4.41
1	2	1.372087	GCAGTGTACTGGGATGCTGC	61.372	60.000	13.41	0.00	43.94	5.25
4	5	0.745845	CTGGCAGTGTACTGGGATGC	60.746	60.000	13.41	0.00	43.94	3.91
11	12	3.377656	CCGGACTGGCAGTGTACT	58.622	61.111	27.45	0.00	0.00	2.73
40	42	2.656069	GGCTAGGCGGAAGTGACCA	61.656	63.158	0.00	0.00	0.00	4.02
41	43	2.187163	GGCTAGGCGGAAGTGACC	59.813	66.667	0.00	0.00	0.00	4.02
48	50	1.735376	GATTGACGAGGCTAGGCGGA	61.735	60.000	11.10	0.00	0.00	5.54
64	66	7.285566	ACACTAATCAATGCTACAGATGGATT	58.714	34.615	0.00	0.00	0.00	3.01
65	67	6.835174	ACACTAATCAATGCTACAGATGGAT	58.165	36.000	0.00	0.00	0.00	3.41
73	75	7.128331	CAGCATACAACACTAATCAATGCTAC	58.872	38.462	6.59	0.00	44.88	3.58
86	88	4.552166	AACAACAGACAGCATACAACAC	57.448	40.909	0.00	0.00	0.00	3.32
96	98	8.909708	TCAAGTTAAAATCAAACAACAGACAG	57.090	30.769	0.00	0.00	0.00	3.51
114	116	5.645929	ACCAACACGCATGATATTCAAGTTA	59.354	36.000	0.00	0.00	0.00	2.24
119	121	6.691754	ATAAACCAACACGCATGATATTCA	57.308	33.333	0.00	0.00	0.00	2.57
120	122	7.376866	CAGAATAAACCAACACGCATGATATTC	59.623	37.037	0.00	0.00	0.00	1.75
121	123	7.148086	ACAGAATAAACCAACACGCATGATATT	60.148	33.333	0.00	0.00	0.00	1.28
122	124	6.318648	ACAGAATAAACCAACACGCATGATAT	59.681	34.615	0.00	0.00	0.00	1.63
123	125	5.645929	ACAGAATAAACCAACACGCATGATA	59.354	36.000	0.00	0.00	0.00	2.15
124	126	4.458989	ACAGAATAAACCAACACGCATGAT	59.541	37.500	0.00	0.00	0.00	2.45
125	127	3.818210	ACAGAATAAACCAACACGCATGA	59.182	39.130	0.00	0.00	0.00	3.07
127	129	3.818210	TGACAGAATAAACCAACACGCAT	59.182	39.130	0.00	0.00	0.00	4.73
202	205	9.567776	TTTACTACAACTGAATCTCATTTGGAA	57.432	29.630	10.36	0.24	40.14	3.53
231	234	4.713553	TCTGCTGAATAAACCAGACACAA	58.286	39.130	0.00	0.00	33.65	3.33
233	236	5.181748	AGATCTGCTGAATAAACCAGACAC	58.818	41.667	0.00	0.00	37.18	3.67
248	251	8.680903	CATTTTCTTGTAACCAATAGATCTGCT	58.319	33.333	5.18	0.00	0.00	4.24

Showing 1 to 25 of 345 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.