AutoCloner

Multiple sequence alignment - TraesCS1A01G177300

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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	TraesCS1A01G177300	chr1A	100.000	3527	0	0	1	3527	319890390	319886864	0.000000e+00	6514.0
1	TraesCS1A01G177300	chr1A	87.275	1556	176	13	984	2521	319447514	319445963	0.000000e+00	1757.0
2	TraesCS1A01G177300	chr1A	79.466	1461	218	50	1087	2496	320155973	320154544	0.000000e+00	961.0
3	TraesCS1A01G177300	chr1A	87.500	56	7	0	3205	3260	285042734	285042789	8.170000e-07	65.8
4	TraesCS1A01G177300	chr1A	90.385	52	2	3	3211	3261	321282513	321282464	8.170000e-07	65.8
5	TraesCS1A01G177300	chr1D	95.032	2214	78	13	490	2688	250071304	250069108	0.000000e+00	3450.0
6	TraesCS1A01G177300	chr1D	87.444	1553	176	11	984	2521	249755646	249754098	0.000000e+00	1770.0
7	TraesCS1A01G177300	chr1D	81.584	1477	219	30	1079	2519	442798159	442799618	0.000000e+00	1171.0
8	TraesCS1A01G177300	chr1D	79.932	1460	240	28	1087	2500	250139011	250137559	0.000000e+00	1024.0
9	TraesCS1A01G177300	chr1D	91.912	272	19	3	2718	2986	194200505	194200776	9.240000e-101	377.0
10	TraesCS1A01G177300	chr1D	93.119	218	9	6	2987	3201	250069041	250068827	7.350000e-82	315.0
11	TraesCS1A01G177300	chr1D	91.534	189	3	5	1	189	250071463	250071288	7.560000e-62	248.0
12	TraesCS1A01G177300	chr1D	83.146	267	20	10	3277	3525	250068810	250068551	1.650000e-53	220.0
13	TraesCS1A01G177300	chr1B	95.088	2056	84	9	643	2687	364504550	364506599	0.000000e+00	3221.0
14	TraesCS1A01G177300	chr1B	80.645	1457	236	35	1087	2514	522744770	522743331	0.000000e+00	1086.0
15	TraesCS1A01G177300	chr1B	80.515	1437	230	29	1092	2485	364423143	364424572	0.000000e+00	1057.0
16	TraesCS1A01G177300	chr1B	91.186	590	52	0	1932	2521	364812164	364812753	0.000000e+00	802.0
17	TraesCS1A01G177300	chr1B	83.464	768	110	9	984	1737	364811187	364811951	0.000000e+00	699.0
18	TraesCS1A01G177300	chr1B	94.340	318	16	2	179	494	588322729	588322412	1.470000e-133	486.0
19	TraesCS1A01G177300	chr1B	92.884	267	16	3	2718	2981	555256827	555256561	5.520000e-103	385.0
20	TraesCS1A01G177300	chr1B	91.617	167	5	6	2988	3147	364506645	364506809	4.580000e-54	222.0
21	TraesCS1A01G177300	chr1B	86.082	194	15	6	1	189	364504282	364504468	7.720000e-47	198.0
22	TraesCS1A01G177300	chr1B	97.143	35	1	0	3211	3245	48253484	48253450	3.800000e-05	60.2
23	TraesCS1A01G177300	chrUn	78.159	1456	251	50	1092	2500	28754123	28752688	0.000000e+00	865.0
24	TraesCS1A01G177300	chr3A	95.752	306	12	1	194	499	444716755	444716451	3.160000e-135	492.0
25	TraesCS1A01G177300	chr3A	92.857	42	3	0	3205	3246	95939510	95939551	1.060000e-05	62.1
26	TraesCS1A01G177300	chr7A	95.724	304	13	0	189	492	633395992	633396295	1.140000e-134	490.0
27	TraesCS1A01G177300	chr7A	92.620	271	16	4	2713	2979	715247961	715247691	1.540000e-103	387.0
28	TraesCS1A01G177300	chr7A	92.884	267	16	3	2718	2981	635698497	635698763	5.520000e-103	385.0
29	TraesCS1A01G177300	chr4A	95.425	306	14	0	189	494	12206912	12206607	4.090000e-134	488.0
30	TraesCS1A01G177300	chr4A	95.710	303	13	0	189	491	365619633	365619935	4.090000e-134	488.0
31	TraesCS1A01G177300	chr4A	92.285	337	19	6	171	505	641405204	641405535	4.120000e-129	472.0
32	TraesCS1A01G177300	chr7B	94.286	315	16	2	184	497	633031183	633030870	6.850000e-132	481.0
33	TraesCS1A01G177300	chr2A	93.009	329	23	0	176	504	126470973	126471301	6.850000e-132	481.0
34	TraesCS1A01G177300	chr6B	93.478	322	19	2	171	491	634640307	634640627	8.860000e-131	477.0
35	TraesCS1A01G177300	chr2B	93.182	264	15	3	2719	2979	666724540	666724803	5.520000e-103	385.0
36	TraesCS1A01G177300	chr2B	89.796	49	5	0	3211	3259	799446707	799446755	2.940000e-06	63.9
37	TraesCS1A01G177300	chr7D	92.509	267	17	3	2718	2981	294050201	294049935	2.570000e-101	379.0
38	TraesCS1A01G177300	chr6A	92.509	267	17	3	2718	2981	421221587	421221321	2.570000e-101	379.0
39	TraesCS1A01G177300	chr4B	91.882	271	18	4	2718	2985	115413824	115414093	3.320000e-100	375.0
40	TraesCS1A01G177300	chr5A	92.164	268	16	5	2718	2981	591530059	591530325	1.200000e-99	374.0
41	TraesCS1A01G177300	chr5A	87.963	108	12	1	1345	1452	708528374	708528268	3.700000e-25	126.0
42	TraesCS1A01G177300	chr5A	94.872	39	2	0	3211	3249	586314398	586314360	1.060000e-05	62.1
43	TraesCS1A01G177300	chr5A	100.000	28	0	0	3221	3248	128425945	128425972	6.000000e-03	52.8
44	TraesCS1A01G177300	chr3B	85.714	56	7	1	3205	3260	765885967	765886021	1.370000e-04	58.4

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	TraesCS1A01G177300	chr1A	319886864	319890390	3526	True	6514.000000	6514	100.00000	1	3527	1	chr1A.!!$R2	3526
1	TraesCS1A01G177300	chr1A	319445963	319447514	1551	True	1757.000000	1757	87.27500	984	2521	1	chr1A.!!$R1	1537
2	TraesCS1A01G177300	chr1A	320154544	320155973	1429	True	961.000000	961	79.46600	1087	2496	1	chr1A.!!$R3	1409
3	TraesCS1A01G177300	chr1D	249754098	249755646	1548	True	1770.000000	1770	87.44400	984	2521	1	chr1D.!!$R1	1537
4	TraesCS1A01G177300	chr1D	442798159	442799618	1459	False	1171.000000	1171	81.58400	1079	2519	1	chr1D.!!$F2	1440
5	TraesCS1A01G177300	chr1D	250068551	250071463	2912	True	1058.250000	3450	90.70775	1	3525	4	chr1D.!!$R3	3524
6	TraesCS1A01G177300	chr1D	250137559	250139011	1452	True	1024.000000	1024	79.93200	1087	2500	1	chr1D.!!$R2	1413
7	TraesCS1A01G177300	chr1B	364504282	364506809	2527	False	1213.666667	3221	90.92900	1	3147	3	chr1B.!!$F2	3146
8	TraesCS1A01G177300	chr1B	522743331	522744770	1439	True	1086.000000	1086	80.64500	1087	2514	1	chr1B.!!$R2	1427
9	TraesCS1A01G177300	chr1B	364423143	364424572	1429	False	1057.000000	1057	80.51500	1092	2485	1	chr1B.!!$F1	1393
10	TraesCS1A01G177300	chr1B	364811187	364812753	1566	False	750.500000	802	87.32500	984	2521	2	chr1B.!!$F3	1537
11	TraesCS1A01G177300	chrUn	28752688	28754123	1435	True	865.000000	865	78.15900	1092	2500	1	chrUn.!!$R1	1408

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
403	417	0.033601	AGTCTCTCGGAGGTGCTCAT	60.034	55.0	4.96	0.0	31.08	2.90	F
451	465	0.179121	TAAGGGTGAGTGTATGCGCG	60.179	55.0	0.00	0.0	0.00	6.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2191	2462	0.327924	TCGGCCACCATGAAGTTCAT	59.672	50.000	12.75	12.75	37.65	2.57	R
2533	2807	3.972638	ACTACTTGCTGATGGAGATGGAT	59.027	43.478	0.00	0.00	0.00	3.41	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
69	83	7.654022	TTCCATGAAAACCAACTCTTTACTT	57.346	32.000	0.00	0.00	0.00	2.24
70	84	7.654022	TCCATGAAAACCAACTCTTTACTTT	57.346	32.000	0.00	0.00	0.00	2.66
71	85	7.712797	TCCATGAAAACCAACTCTTTACTTTC	58.287	34.615	0.00	0.00	0.00	2.62
72	86	6.923508	CCATGAAAACCAACTCTTTACTTTCC	59.076	38.462	0.00	0.00	0.00	3.13
73	87	7.201911	CCATGAAAACCAACTCTTTACTTTCCT	60.202	37.037	0.00	0.00	0.00	3.36
74	88	8.846211	CATGAAAACCAACTCTTTACTTTCCTA	58.154	33.333	0.00	0.00	0.00	2.94
75	89	8.217131	TGAAAACCAACTCTTTACTTTCCTAC	57.783	34.615	0.00	0.00	0.00	3.18
76	90	8.050930	TGAAAACCAACTCTTTACTTTCCTACT	58.949	33.333	0.00	0.00	0.00	2.57
77	91	8.818622	AAAACCAACTCTTTACTTTCCTACTT	57.181	30.769	0.00	0.00	0.00	2.24
78	92	7.803279	AACCAACTCTTTACTTTCCTACTTG	57.197	36.000	0.00	0.00	0.00	3.16
79	93	5.763698	ACCAACTCTTTACTTTCCTACTTGC	59.236	40.000	0.00	0.00	0.00	4.01
80	94	5.998363	CCAACTCTTTACTTTCCTACTTGCT	59.002	40.000	0.00	0.00	0.00	3.91
146	160	8.400947	TGCTCATTAATTGACAGCTAGATTTTC	58.599	33.333	0.00	0.00	0.00	2.29
147	161	8.619546	GCTCATTAATTGACAGCTAGATTTTCT	58.380	33.333	0.00	0.00	0.00	2.52
186	200	9.884636	ATAGTACACATTAACAATAAGCTGACA	57.115	29.630	0.00	0.00	0.00	3.58
187	201	8.256611	AGTACACATTAACAATAAGCTGACAG	57.743	34.615	0.00	0.00	0.00	3.51
188	202	6.500684	ACACATTAACAATAAGCTGACAGG	57.499	37.500	4.26	0.00	0.00	4.00
189	203	5.106157	ACACATTAACAATAAGCTGACAGGC	60.106	40.000	4.26	0.00	0.00	4.85
190	204	4.094887	ACATTAACAATAAGCTGACAGGCG	59.905	41.667	4.26	0.00	37.29	5.52
191	205	2.472695	AACAATAAGCTGACAGGCGA	57.527	45.000	4.26	0.00	37.29	5.54
192	206	2.472695	ACAATAAGCTGACAGGCGAA	57.527	45.000	4.26	0.00	37.29	4.70
193	207	2.991250	ACAATAAGCTGACAGGCGAAT	58.009	42.857	4.26	0.00	37.29	3.34
194	208	2.939103	ACAATAAGCTGACAGGCGAATC	59.061	45.455	4.26	0.00	37.29	2.52
195	209	2.938451	CAATAAGCTGACAGGCGAATCA	59.062	45.455	4.26	0.00	37.29	2.57
196	210	2.760634	TAAGCTGACAGGCGAATCAA	57.239	45.000	4.26	0.00	37.29	2.57

Showing 1 to 25 of 453 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	79	9.796180	TTATTTGGTAAAGCAAGTAGGAAAGTA	57.204	29.630	0.00	0.00	0.00	2.24
66	80	8.700439	TTATTTGGTAAAGCAAGTAGGAAAGT	57.300	30.769	0.00	0.00	0.00	2.66
67	81	9.974980	TTTTATTTGGTAAAGCAAGTAGGAAAG	57.025	29.630	0.00	0.00	33.99	2.62
70	84	9.528489	AGATTTTATTTGGTAAAGCAAGTAGGA	57.472	29.630	0.00	0.00	33.99	2.94
74	88	9.830975	AACAAGATTTTATTTGGTAAAGCAAGT	57.169	25.926	0.00	0.00	33.99	3.16
181	195	1.081892	CAGGTTGATTCGCCTGTCAG	58.918	55.000	15.13	0.00	45.28	3.51
182	196	3.231734	CAGGTTGATTCGCCTGTCA	57.768	52.632	15.13	0.00	45.28	3.58
186	200	0.110486	AACCACAGGTTGATTCGCCT	59.890	50.000	0.00	0.00	45.07	5.52
187	201	2.641197	AACCACAGGTTGATTCGCC	58.359	52.632	0.00	0.00	45.07	5.54
196	210	2.158667	CCTAACCAACTCAACCACAGGT	60.159	50.000	0.00	0.00	37.65	4.00
197	211	2.158667	ACCTAACCAACTCAACCACAGG	60.159	50.000	0.00	0.00	0.00	4.00
198	212	2.878406	CACCTAACCAACTCAACCACAG	59.122	50.000	0.00	0.00	0.00	3.66
199	213	2.422235	CCACCTAACCAACTCAACCACA	60.422	50.000	0.00	0.00	0.00	4.17
200	214	2.158726	TCCACCTAACCAACTCAACCAC	60.159	50.000	0.00	0.00	0.00	4.16
201	215	2.128535	TCCACCTAACCAACTCAACCA	58.871	47.619	0.00	0.00	0.00	3.67
202	216	2.158726	TGTCCACCTAACCAACTCAACC	60.159	50.000	0.00	0.00	0.00	3.77
203	217	3.139077	CTGTCCACCTAACCAACTCAAC	58.861	50.000	0.00	0.00	0.00	3.18
204	218	2.775384	ACTGTCCACCTAACCAACTCAA	59.225	45.455	0.00	0.00	0.00	3.02
205	219	2.104111	CACTGTCCACCTAACCAACTCA	59.896	50.000	0.00	0.00	0.00	3.41
206	220	2.550208	CCACTGTCCACCTAACCAACTC	60.550	54.545	0.00	0.00	0.00	3.01
207	221	1.420138	CCACTGTCCACCTAACCAACT	59.580	52.381	0.00	0.00	0.00	3.16
208	222	1.142262	ACCACTGTCCACCTAACCAAC	59.858	52.381	0.00	0.00	0.00	3.77
209	223	1.513858	ACCACTGTCCACCTAACCAA	58.486	50.000	0.00	0.00	0.00	3.67
210	224	2.402182	TACCACTGTCCACCTAACCA	57.598	50.000	0.00	0.00	0.00	3.67
211	225	2.169978	GGATACCACTGTCCACCTAACC	59.830	54.545	0.00	0.00	34.57	2.85

Showing 1 to 25 of 444 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.