AutoCloner

Multiple sequence alignment - TraesCS2B01G548900

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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	TraesCS2B01G548900	chr2B	100.000	3083	0	0	1	3083	744858194	744855112	0.000000e+00	5694
1	TraesCS2B01G548900	chr2B	85.250	2183	205	65	641	2775	744826612	744824499	0.000000e+00	2139
2	TraesCS2B01G548900	chr2B	96.223	1059	19	6	1	1042	744839904	744838850	0.000000e+00	1714
3	TraesCS2B01G548900	chr2B	88.509	1288	103	15	727	2004	744483058	744481806	0.000000e+00	1517
4	TraesCS2B01G548900	chr2B	85.234	1429	144	27	899	2286	745034124	745035526	0.000000e+00	1408
5	TraesCS2B01G548900	chr2B	89.256	1089	78	18	1276	2353	744553585	744552525	0.000000e+00	1327
6	TraesCS2B01G548900	chr2B	87.633	752	67	8	2349	3081	744552487	744551743	0.000000e+00	850
7	TraesCS2B01G548900	chr2B	88.177	609	44	14	676	1273	744554637	744554046	0.000000e+00	701
8	TraesCS2B01G548900	chr2B	99.338	302	2	0	2782	3083	744838856	744838555	5.810000e-152	547
9	TraesCS2B01G548900	chr2B	89.328	253	25	2	2022	2272	744480725	744480473	1.780000e-82	316
10	TraesCS2B01G548900	chr2A	88.629	2779	204	45	1	2718	742773511	742770784	0.000000e+00	3278
11	TraesCS2B01G548900	chr2A	78.990	614	120	7	1	611	86289008	86288401	7.960000e-111	411
12	TraesCS2B01G548900	chr2D	89.468	1785	106	28	731	2481	609959096	609957360	0.000000e+00	2180
13	TraesCS2B01G548900	chr2D	90.776	1225	71	11	1887	3083	609913377	609912167	0.000000e+00	1598
14	TraesCS2B01G548900	chr2D	73.935	1009	198	40	962	1950	611244689	611245652	2.280000e-91	346
15	TraesCS2B01G548900	chr2D	90.123	243	22	1	2841	3083	609957304	609957064	6.420000e-82	315
16	TraesCS2B01G548900	chr2D	89.147	129	14	0	1001	1129	609893274	609893146	8.850000e-36	161
17	TraesCS2B01G548900	chr2D	93.939	66	4	0	57	122	609980926	609980861	1.960000e-17	100
18	TraesCS2B01G548900	chr7B	79.800	599	109	11	1	596	696890255	696889666	2.840000e-115	425
19	TraesCS2B01G548900	chr7B	76.877	826	135	32	1288	2082	632966250	632965450	1.710000e-112	416
20	TraesCS2B01G548900	chrUn	76.877	826	135	32	1288	2082	289619316	289620116	1.710000e-112	416
21	TraesCS2B01G548900	chrUn	76.877	826	135	32	1288	2082	299515962	299515162	1.710000e-112	416
22	TraesCS2B01G548900	chr4D	76.049	906	155	36	1214	2082	6462505	6461625	6.150000e-112	414
23	TraesCS2B01G548900	chr6D	80.998	521	93	4	90	608	327608919	327608403	2.860000e-110	409
24	TraesCS2B01G548900	chr6D	78.510	577	110	12	24	595	378432448	378431881	1.750000e-97	366
25	TraesCS2B01G548900	chr7A	81.139	509	90	5	90	597	20429793	20430296	1.330000e-108	403
26	TraesCS2B01G548900	chr5A	81.139	509	90	5	90	597	632193137	632193640	1.330000e-108	403

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	TraesCS2B01G548900	chr2B	744855112	744858194	3082	True	5694.000000	5694	100.000000	1	3083	1	chr2B.!!$R2	3082
1	TraesCS2B01G548900	chr2B	744824499	744826612	2113	True	2139.000000	2139	85.250000	641	2775	1	chr2B.!!$R1	2134
2	TraesCS2B01G548900	chr2B	745034124	745035526	1402	False	1408.000000	1408	85.234000	899	2286	1	chr2B.!!$F1	1387
3	TraesCS2B01G548900	chr2B	744838555	744839904	1349	True	1130.500000	1714	97.780500	1	3083	2	chr2B.!!$R5	3082
4	TraesCS2B01G548900	chr2B	744551743	744554637	2894	True	959.333333	1327	88.355333	676	3081	3	chr2B.!!$R4	2405
5	TraesCS2B01G548900	chr2B	744480473	744483058	2585	True	916.500000	1517	88.918500	727	2272	2	chr2B.!!$R3	1545
6	TraesCS2B01G548900	chr2A	742770784	742773511	2727	True	3278.000000	3278	88.629000	1	2718	1	chr2A.!!$R2	2717
7	TraesCS2B01G548900	chr2A	86288401	86289008	607	True	411.000000	411	78.990000	1	611	1	chr2A.!!$R1	610
8	TraesCS2B01G548900	chr2D	609912167	609913377	1210	True	1598.000000	1598	90.776000	1887	3083	1	chr2D.!!$R2	1196
9	TraesCS2B01G548900	chr2D	609957064	609959096	2032	True	1247.500000	2180	89.795500	731	3083	2	chr2D.!!$R4	2352
10	TraesCS2B01G548900	chr2D	611244689	611245652	963	False	346.000000	346	73.935000	962	1950	1	chr2D.!!$F1	988
11	TraesCS2B01G548900	chr7B	696889666	696890255	589	True	425.000000	425	79.800000	1	596	1	chr7B.!!$R2	595
12	TraesCS2B01G548900	chr7B	632965450	632966250	800	True	416.000000	416	76.877000	1288	2082	1	chr7B.!!$R1	794
13	TraesCS2B01G548900	chrUn	289619316	289620116	800	False	416.000000	416	76.877000	1288	2082	1	chrUn.!!$F1	794
14	TraesCS2B01G548900	chrUn	299515162	299515962	800	True	416.000000	416	76.877000	1288	2082	1	chrUn.!!$R1	794
15	TraesCS2B01G548900	chr4D	6461625	6462505	880	True	414.000000	414	76.049000	1214	2082	1	chr4D.!!$R1	868
16	TraesCS2B01G548900	chr6D	327608403	327608919	516	True	409.000000	409	80.998000	90	608	1	chr6D.!!$R1	518
17	TraesCS2B01G548900	chr6D	378431881	378432448	567	True	366.000000	366	78.510000	24	595	1	chr6D.!!$R2	571
18	TraesCS2B01G548900	chr7A	20429793	20430296	503	False	403.000000	403	81.139000	90	597	1	chr7A.!!$F1	507
19	TraesCS2B01G548900	chr5A	632193137	632193640	503	False	403.000000	403	81.139000	90	597	1	chr5A.!!$F1	507

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
291	292	1.032114	GCATGCCGGGAAGCTTTAGT	61.032	55.0	16.47	0.0	0.0	2.24	F
1773	2326	1.104630	TGACCGGAAACAACCCAAAC	58.895	50.0	9.46	0.0	0.0	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1778	2331	0.098552	CAGTGCGCACAAGTTGTTGA	59.901	50.000	39.21	0.0	37.1	3.18	R
2697	4451	3.499048	CGCAGAACTCTCTAAACGCTAA	58.501	45.455	0.00	0.0	0.0	3.09	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
205	206	1.065701	GTATGTCATGACGAGCGAGGT	59.934	52.381	20.54	2.48	0.00	3.85
291	292	1.032114	GCATGCCGGGAAGCTTTAGT	61.032	55.000	16.47	0.00	0.00	2.24
308	309	5.583457	GCTTTAGTACTTGCCGAGGATTTAA	59.417	40.000	0.00	0.00	0.00	1.52
314	315	3.502211	ACTTGCCGAGGATTTAACTGTTG	59.498	43.478	2.69	0.00	0.00	3.33
374	375	4.142337	TGCAAGACATATCCAGCAACAATG	60.142	41.667	0.00	0.00	33.58	2.82
375	376	4.096833	GCAAGACATATCCAGCAACAATGA	59.903	41.667	0.00	0.00	0.00	2.57
376	377	5.575957	CAAGACATATCCAGCAACAATGAC	58.424	41.667	0.00	0.00	0.00	3.06
377	378	4.847198	AGACATATCCAGCAACAATGACA	58.153	39.130	0.00	0.00	0.00	3.58
381	382	2.363306	TCCAGCAACAATGACAAGGT	57.637	45.000	0.00	0.00	0.00	3.50
499	500	6.354622	GCTCATAGTTTAGCTAAATTTTCGCG	59.645	38.462	21.28	0.00	35.80	5.87
512	513	3.515071	TTTTCGCGTTCTTTAGCTCAC	57.485	42.857	5.77	0.00	0.00	3.51
1024	1069	1.244019	GGCACGGCAGTTCCTGAATT	61.244	55.000	0.00	0.00	32.44	2.17
1149	1197	2.267961	GCGGAACCCAAGGACGAT	59.732	61.111	0.00	0.00	0.00	3.73
1265	1334	1.601419	TTGCCCTTCTACGGACGAGG	61.601	60.000	0.00	0.00	0.00	4.63
1266	1335	2.806237	CCCTTCTACGGACGAGGC	59.194	66.667	0.00	0.00	0.00	4.70
1267	1336	2.050350	CCCTTCTACGGACGAGGCA	61.050	63.158	0.00	0.00	0.00	4.75
1416	1946	3.699955	CTCCATCACTCGCGCGGAA	62.700	63.158	31.69	11.04	0.00	4.30
1418	1948	2.395690	CATCACTCGCGCGGAAAC	59.604	61.111	31.69	0.00	0.00	2.78
1770	2323	1.175983	GCATGACCGGAAACAACCCA	61.176	55.000	9.46	0.00	0.00	4.51
1771	2324	1.323412	CATGACCGGAAACAACCCAA	58.677	50.000	9.46	0.00	0.00	4.12
1772	2325	1.683917	CATGACCGGAAACAACCCAAA	59.316	47.619	9.46	0.00	0.00	3.28
1773	2326	1.104630	TGACCGGAAACAACCCAAAC	58.895	50.000	9.46	0.00	0.00	2.93
1774	2327	1.104630	GACCGGAAACAACCCAAACA	58.895	50.000	9.46	0.00	0.00	2.83
1775	2328	1.477295	GACCGGAAACAACCCAAACAA	59.523	47.619	9.46	0.00	0.00	2.83
1776	2329	1.205179	ACCGGAAACAACCCAAACAAC	59.795	47.619	9.46	0.00	0.00	3.32
1777	2330	1.478916	CCGGAAACAACCCAAACAACT	59.521	47.619	0.00	0.00	0.00	3.16
1778	2331	2.093921	CCGGAAACAACCCAAACAACTT	60.094	45.455	0.00	0.00	0.00	2.66
1810	2363	1.821061	CGCACTGGACCTCTCCAACT	61.821	60.000	0.00	0.00	46.63	3.16
1959	2518	2.683465	GGAGCAAGATGCCCAGGGA	61.683	63.158	10.89	0.00	46.52	4.20
2160	3786	3.226347	GAGTTTTGACTTGCGGATTTCG	58.774	45.455	0.00	0.00	42.76	3.46
2190	3816	1.355720	ACCCCTTTCAATCTCCACCAG	59.644	52.381	0.00	0.00	0.00	4.00
2385	4105	2.270352	TTTGGTGCACCTGGTCTAAG	57.730	50.000	34.75	0.00	36.82	2.18
2535	4277	7.220491	CACATCAAAATTAATACATCGCTGCAA	59.780	33.333	0.00	0.00	0.00	4.08
2621	4374	7.008628	CCAAATCATACAAGAGAAACGCAATTC	59.991	37.037	0.00	0.00	0.00	2.17
2635	4388	2.541346	CGCAATTCAGTCATATCGCAGT	59.459	45.455	0.00	0.00	0.00	4.40
2636	4389	3.001634	CGCAATTCAGTCATATCGCAGTT	59.998	43.478	0.00	0.00	0.00	3.16
2667	4421	5.116180	TCTAAACCATACAAGAGGATTGCG	58.884	41.667	0.00	0.00	0.00	4.85
2670	4424	3.733337	ACCATACAAGAGGATTGCGATC	58.267	45.455	5.25	5.25	0.00	3.69
2697	4451	4.464597	TCCATTGTTTTAAATAGCGCCCTT	59.535	37.500	2.29	0.00	0.00	3.95
2767	4522	2.093152	CCGAGCGTTTTAAATAGCGTGT	59.907	45.455	8.98	0.00	34.34	4.49
2939	4696	5.408604	GGTTGAAGACGACACATTCATAAGT	59.591	40.000	0.00	0.00	33.26	2.24
3011	4768	0.972983	CACACCCCAGAGAGATCGGT	60.973	60.000	0.00	0.00	0.00	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	6.374417	TGCTCCTTTACTATTTTCAGGTCT	57.626	37.500	0.00	0.00	0.00	3.85
205	206	3.589641	TGTTGAACTCCCCAGGTAGTTA	58.410	45.455	4.73	0.00	36.10	2.24
291	292	4.546829	ACAGTTAAATCCTCGGCAAGTA	57.453	40.909	0.00	0.00	0.00	2.24
308	309	4.184629	GCCACGATAAGATTCTCAACAGT	58.815	43.478	0.00	0.00	0.00	3.55
314	315	4.876125	TCAGATGCCACGATAAGATTCTC	58.124	43.478	0.00	0.00	0.00	2.87
1024	1069	2.668632	GGACCTCCGCATCACCAA	59.331	61.111	0.00	0.00	0.00	3.67
1149	1197	0.595567	GTGATGGCGGCGTCGTATTA	60.596	55.000	24.19	5.42	38.89	0.98
1274	1343	0.959553	GAGGATCTTACCATCGCCGA	59.040	55.000	0.00	0.00	0.00	5.54
1419	1949	3.056328	GCTTGACGGGAGGTTGCC	61.056	66.667	0.00	0.00	0.00	4.52
1422	1952	2.529389	AGGGCTTGACGGGAGGTT	60.529	61.111	0.00	0.00	0.00	3.50
1773	2326	1.583404	GCGCACAAGTTGTTGAAGTTG	59.417	47.619	5.57	0.00	44.86	3.16
1774	2327	1.201181	TGCGCACAAGTTGTTGAAGTT	59.799	42.857	5.66	0.00	37.10	2.66
1775	2328	0.808125	TGCGCACAAGTTGTTGAAGT	59.192	45.000	5.66	0.00	37.10	3.01
1776	2329	1.191096	GTGCGCACAAGTTGTTGAAG	58.809	50.000	34.52	0.00	37.10	3.02
1777	2330	0.808125	AGTGCGCACAAGTTGTTGAA	59.192	45.000	39.21	0.00	37.10	2.69
1778	2331	0.098552	CAGTGCGCACAAGTTGTTGA	59.901	50.000	39.21	0.00	37.10	3.18
1992	2551	0.170561	CTTCGAGTACCACCTCCACG	59.829	60.000	0.00	0.00	0.00	4.94
2160	3786	1.886886	TGAAAGGGGTTGAGCGTAAC	58.113	50.000	0.00	0.00	0.00	2.50
2190	3816	0.667792	AGAGCTTGTTCGCTTCCGTC	60.668	55.000	0.00	0.00	41.08	4.79
2385	4105	6.293004	TCCAACAATCATAAATGGGGTTTC	57.707	37.500	0.00	0.00	0.00	2.78
2438	4161	6.862711	TTGTGGAACGATATGTTTGTGTTA	57.137	33.333	0.00	0.00	42.09	2.41
2535	4277	5.568620	TCTTTTTCTTGCTAGGTCCTCTT	57.431	39.130	0.00	0.00	0.00	2.85
2621	4374	6.150307	AGAGTCCTATAACTGCGATATGACTG	59.850	42.308	10.16	0.00	35.89	3.51
2635	4388	9.144298	CCTCTTGTATGGTTTAGAGTCCTATAA	57.856	37.037	0.00	0.00	33.83	0.98
2636	4389	8.508601	TCCTCTTGTATGGTTTAGAGTCCTATA	58.491	37.037	0.00	0.00	33.83	1.31
2667	4421	6.846283	CGCTATTTAAAACAATGGACTCGATC	59.154	38.462	0.00	0.00	0.00	3.69
2670	4424	4.728608	GCGCTATTTAAAACAATGGACTCG	59.271	41.667	0.00	0.00	0.00	4.18
2697	4451	3.499048	CGCAGAACTCTCTAAACGCTAA	58.501	45.455	0.00	0.00	0.00	3.09
2767	4522	5.067413	CAGTGGACCTCTCTAAACGCTATAA	59.933	44.000	0.00	0.00	0.00	0.98
2939	4696	8.587608	AGAAATTGCAGATCAACAAAGGAAATA	58.412	29.630	4.74	0.00	37.53	1.40
3011	4768	5.373222	CGGTATATTTCATTTCCACCTCCA	58.627	41.667	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.