AutoCloner

Multiple sequence alignment - TraesCS5A01G107400

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	TraesCS5A01G107400	chr5A	100.000	3568	0	0	1	3568	183437919	183434352	0.000000e+00	6589.0
1	TraesCS5A01G107400	chr5A	85.124	121	16	2	587	705	635494694	635494814	4.840000e-24	122.0
2	TraesCS5A01G107400	chr5A	82.443	131	15	4	2934	3056	452434648	452434778	1.350000e-19	108.0
3	TraesCS5A01G107400	chr5B	95.876	2158	66	10	848	2991	155279883	155282031	0.000000e+00	3470.0
4	TraesCS5A01G107400	chr5B	84.426	122	13	5	588	705	604866635	604866516	8.090000e-22	115.0
5	TraesCS5A01G107400	chr5B	85.714	105	10	5	2904	3007	405561961	405561861	4.870000e-19	106.0
6	TraesCS5A01G107400	chr5D	95.915	1787	55	6	590	2364	173095631	173093851	0.000000e+00	2880.0
7	TraesCS5A01G107400	chr5D	97.440	586	14	1	2367	2952	173091560	173090976	0.000000e+00	998.0
8	TraesCS5A01G107400	chr5D	88.702	593	45	15	1	587	173096263	173095687	0.000000e+00	704.0
9	TraesCS5A01G107400	chr5D	94.697	264	14	0	3257	3520	173089635	173089372	9.220000e-111	411.0
10	TraesCS5A01G107400	chr5D	85.345	116	13	3	592	705	377311767	377311880	2.250000e-22	117.0
11	TraesCS5A01G107400	chr5D	100.000	47	0	0	3522	3568	173089330	173089284	1.760000e-13	87.9
12	TraesCS5A01G107400	chr1D	88.718	390	35	7	96	477	39864703	39864315	5.390000e-128	468.0
13	TraesCS5A01G107400	chr2D	87.532	385	45	3	96	477	430224880	430225264	3.270000e-120	442.0
14	TraesCS5A01G107400	chr2D	87.147	389	40	10	96	477	627039149	627038764	1.970000e-117	433.0
15	TraesCS5A01G107400	chr3B	86.634	404	34	15	94	483	606379563	606379166	2.550000e-116	429.0
16	TraesCS5A01G107400	chr3B	82.993	147	16	8	2914	3056	475993837	475993696	1.340000e-24	124.0
17	TraesCS5A01G107400	chr3D	86.445	391	42	8	96	482	58397539	58397922	5.510000e-113	418.0
18	TraesCS5A01G107400	chr2A	86.445	391	42	9	96	477	44757376	44757764	5.510000e-113	418.0
19	TraesCS5A01G107400	chr2A	85.345	116	12	3	475	589	696313695	696313584	8.090000e-22	115.0
20	TraesCS5A01G107400	chr3A	85.714	385	45	8	96	477	175363189	175363566	7.180000e-107	398.0
21	TraesCS5A01G107400	chr3A	86.179	123	14	2	587	706	69171556	69171434	2.890000e-26	130.0
22	TraesCS5A01G107400	chr3A	82.308	130	14	5	2925	3045	686140844	686140973	1.750000e-18	104.0
23	TraesCS5A01G107400	chr1B	84.872	390	41	11	93	477	550923039	550923415	9.350000e-101	377.0
24	TraesCS5A01G107400	chr6A	86.777	121	14	2	587	705	521859548	521859668	2.230000e-27	134.0
25	TraesCS5A01G107400	chr6A	79.021	143	28	2	2914	3056	243958290	243958430	2.930000e-16	97.1
26	TraesCS5A01G107400	chr7D	86.325	117	14	2	592	706	139303306	139303422	3.740000e-25	126.0
27	TraesCS5A01G107400	chr7D	85.185	108	14	2	601	706	602823821	602823714	3.770000e-20	110.0
28	TraesCS5A01G107400	chr4B	84.746	118	15	3	592	706	498442897	498443014	8.090000e-22	115.0
29	TraesCS5A01G107400	chr4B	79.592	147	18	6	2914	3056	423773450	423773312	1.050000e-15	95.3
30	TraesCS5A01G107400	chr7B	80.921	152	19	3	2914	3056	211374196	211374046	1.050000e-20	111.0
31	TraesCS5A01G107400	chr4A	83.065	124	18	3	2934	3056	543368315	543368436	3.770000e-20	110.0
32	TraesCS5A01G107400	chr4D	82.258	124	19	3	2934	3056	53760116	53759995	1.750000e-18	104.0
33	TraesCS5A01G107400	chr6D	80.576	139	19	5	2914	3051	153810792	153810661	2.270000e-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	TraesCS5A01G107400	chr5A	183434352	183437919	3567	True	6589.00	6589	100.0000	1	3568	1	chr5A.!!$R1	3567
1	TraesCS5A01G107400	chr5B	155279883	155282031	2148	False	3470.00	3470	95.8760	848	2991	1	chr5B.!!$F1	2143
2	TraesCS5A01G107400	chr5D	173089284	173096263	6979	True	1016.18	2880	95.3508	1	3568	5	chr5D.!!$R1	3567

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
833	902	0.107268	GGTTTGGTGTGGTCCTACGT	59.893	55.0	0.0	0.0	0.0	3.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2578	4950	0.903942	GAATGCCCAAATGCTCCCAA	59.096	50.0	0.0	0.0	0.0	4.12	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
55	56	7.649715	AGGTGATCCTAATATAATAGGGACGA	58.350	38.462	13.00	0.00	43.12	4.20
68	69	2.913060	GACGATCGGAGGGAGGGG	60.913	72.222	20.98	0.00	0.00	4.79
92	93	1.395608	TCCGAATTGGATTTCGCGAAC	59.604	47.619	23.33	11.23	45.42	3.95
94	95	1.129624	CGAATTGGATTTCGCGAACCA	59.870	47.619	23.33	23.15	41.61	3.67
101	102	3.894547	TTTCGCGAACCAGGAGGGC	62.895	63.158	23.33	0.00	42.05	5.19
136	137	3.423539	GGTGCATATGCTCCCTAATGA	57.576	47.619	30.27	6.05	46.01	2.57
241	242	4.661402	GCTTGTCAAATTTCATGCGAAACG	60.661	41.667	0.00	0.00	43.75	3.60
242	243	4.216366	TGTCAAATTTCATGCGAAACGA	57.784	36.364	0.00	0.00	43.75	3.85
257	258	2.086054	AACGAGATGACTGTGCTTCC	57.914	50.000	0.00	0.00	0.00	3.46
377	378	5.351948	AAAATTGCAGGTAGTGTTTTGGT	57.648	34.783	0.00	0.00	0.00	3.67
391	392	5.302568	AGTGTTTTGGTGTGACAATGATCAT	59.697	36.000	1.18	1.18	0.00	2.45
399	402	8.352137	TGGTGTGACAATGATCATATCTTTTT	57.648	30.769	9.04	0.00	0.00	1.94
492	497	1.872388	TTTCGCGAATCAACCTGTGA	58.128	45.000	24.05	0.00	41.67	3.58
519	524	4.713321	GGTTAGATGGTTACAGGGACAGTA	59.287	45.833	0.00	0.00	0.00	2.74
520	525	5.163437	GGTTAGATGGTTACAGGGACAGTAG	60.163	48.000	0.00	0.00	30.53	2.57
537	543	3.711704	CAGTAGTATCCCAACCCATCAGT	59.288	47.826	0.00	0.00	0.00	3.41
544	550	2.091610	TCCCAACCCATCAGTGTTCAAA	60.092	45.455	0.00	0.00	0.00	2.69
549	555	5.165676	CAACCCATCAGTGTTCAAATCATG	58.834	41.667	0.00	0.00	0.00	3.07
564	570	6.376177	TCAAATCATGATGCTCGCATTATTC	58.624	36.000	9.46	0.00	36.70	1.75
565	571	4.959596	ATCATGATGCTCGCATTATTCC	57.040	40.909	7.59	0.00	36.70	3.01
568	574	2.497138	TGATGCTCGCATTATTCCTGG	58.503	47.619	5.79	0.00	36.70	4.45
587	593	6.291377	TCCTGGATTTATCTCAGGATTTTCG	58.709	40.000	18.26	0.00	43.26	3.46
588	594	5.471456	CCTGGATTTATCTCAGGATTTTCGG	59.529	44.000	16.16	0.00	42.71	4.30
630	689	0.461961	GTATGCCGGCTCAGTCTCTT	59.538	55.000	29.70	3.51	0.00	2.85
631	690	1.681793	GTATGCCGGCTCAGTCTCTTA	59.318	52.381	29.70	2.45	0.00	2.10

Showing 1 to 25 of 227 entries

Previous1 2 3 4 5…10Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	6.207025	CCCTCCGATCGTCCCTATTATATTAG	59.793	46.154	15.09	0.00	0.00	1.73
46	47	0.038455	CTCCCTCCGATCGTCCCTAT	59.962	60.000	15.09	0.00	0.00	2.57
55	56	4.798682	AACGCCCCTCCCTCCGAT	62.799	66.667	0.00	0.00	0.00	4.18
88	89	3.546714	AAACGGCCCTCCTGGTTCG	62.547	63.158	0.00	0.00	38.35	3.95
92	93	2.676471	CCAAAACGGCCCTCCTGG	60.676	66.667	0.00	0.00	37.09	4.45
101	102	1.659794	CACCCAAGAGCCAAAACGG	59.340	57.895	0.00	0.00	38.11	4.44
188	189	7.862741	TGTTACACTAACAAGAACATCTACG	57.137	36.000	0.00	0.00	44.95	3.51
200	201	5.478233	CAAGCACACTTGTTACACTAACA	57.522	39.130	0.00	0.00	46.84	2.41
223	224	4.740741	TCTCGTTTCGCATGAAATTTGA	57.259	36.364	0.00	0.00	45.31	2.69
241	242	1.470632	CCGAGGAAGCACAGTCATCTC	60.471	57.143	0.00	0.00	0.00	2.75
242	243	0.534412	CCGAGGAAGCACAGTCATCT	59.466	55.000	0.00	0.00	0.00	2.90
285	286	9.491675	TCGAACTACAAATGTTACCTCAAAATA	57.508	29.630	0.00	0.00	0.00	1.40
358	359	3.068024	CACACCAAAACACTACCTGCAAT	59.932	43.478	0.00	0.00	0.00	3.56
364	365	4.336993	TCATTGTCACACCAAAACACTACC	59.663	41.667	0.00	0.00	0.00	3.18
369	370	5.787953	ATGATCATTGTCACACCAAAACA	57.212	34.783	1.18	0.00	0.00	2.83
421	424	7.041167	GCTCTGCCCATTAAAAATGTTTTTCTT	60.041	33.333	6.73	0.00	40.53	2.52
423	426	6.204495	TGCTCTGCCCATTAAAAATGTTTTTC	59.796	34.615	6.73	0.00	40.53	2.29
430	433	5.544650	GCATATGCTCTGCCCATTAAAAAT	58.455	37.500	20.64	0.00	38.21	1.82
431	434	4.947645	GCATATGCTCTGCCCATTAAAAA	58.052	39.130	20.64	0.00	38.21	1.94
456	461	3.367292	GCGAAATCCAATTTGGCTCTTGA	60.367	43.478	10.76	0.00	46.29	3.02
492	497	5.968167	TGTCCCTGTAACCATCTAACCTAAT	59.032	40.000	0.00	0.00	0.00	1.73
493	498	5.343715	TGTCCCTGTAACCATCTAACCTAA	58.656	41.667	0.00	0.00	0.00	2.69
494	499	4.950361	TGTCCCTGTAACCATCTAACCTA	58.050	43.478	0.00	0.00	0.00	3.08
495	500	3.775316	CTGTCCCTGTAACCATCTAACCT	59.225	47.826	0.00	0.00	0.00	3.50
496	501	3.518303	ACTGTCCCTGTAACCATCTAACC	59.482	47.826	0.00	0.00	0.00	2.85

Showing 1 to 25 of 231 entries

Previous1 2 3 4 5…10Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.