AutoCloner

Multiple sequence alignment - TraesCS4B01G276100

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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	TraesCS4B01G276100	chr4B	100.000	2459	0	0	1	2459	555215570	555213112	0.000000e+00	4542
1	TraesCS4B01G276100	chr4B	93.311	1510	93	7	2	1506	555540090	555538584	0.000000e+00	2222
2	TraesCS4B01G276100	chr4B	91.805	903	62	8	1506	2401	555515808	555514911	0.000000e+00	1247
3	TraesCS4B01G276100	chr4B	92.384	302	19	4	2138	2435	555514994	555514693	6.280000e-116	427
4	TraesCS4B01G276100	chr4B	90.291	103	10	0	1869	1971	555514911	555514809	4.270000e-28	135
5	TraesCS4B01G276100	chr4B	90.291	103	10	0	1869	1971	555515094	555514992	4.270000e-28	135
6	TraesCS4B01G276100	chr4B	88.462	104	10	1	1869	1972	555213351	555213250	9.230000e-25	124
7	TraesCS4B01G276100	chr4B	88.462	104	10	1	2220	2321	555213702	555213599	9.230000e-25	124
8	TraesCS4B01G276100	chr4D	94.197	2068	95	12	400	2457	444884864	444886916	0.000000e+00	3131
9	TraesCS4B01G276100	chr4D	90.291	103	10	0	1869	1971	444886676	444886778	4.270000e-28	135
10	TraesCS4B01G276100	chr4D	88.660	97	9	1	2220	2316	444886322	444886416	1.540000e-22	117
11	TraesCS4B01G276100	chr4A	94.365	1118	50	3	494	1608	22082535	22083642	0.000000e+00	1703
12	TraesCS4B01G276100	chr4A	89.249	679	50	10	1802	2458	22085463	22086140	0.000000e+00	828
13	TraesCS4B01G276100	chr4A	95.266	169	6	2	1643	1811	22083639	22083805	1.450000e-67	267
14	TraesCS4B01G276100	chr4A	93.407	91	4	2	423	511	22081939	22082029	1.530000e-27	134
15	TraesCS4B01G276100	chr4A	86.000	100	12	2	1992	2090	609917693	609917791	3.340000e-19	106
16	TraesCS4B01G276100	chr2D	90.099	404	33	2	1	401	422511625	422511226	3.620000e-143	518
17	TraesCS4B01G276100	chr2D	82.979	141	21	3	1992	2131	646299254	646299116	9.230000e-25	124
18	TraesCS4B01G276100	chr6D	89.604	404	35	2	1	401	163829499	163829100	7.850000e-140	507
19	TraesCS4B01G276100	chr3D	89.474	399	30	6	9	401	582177244	582176852	6.110000e-136	494
20	TraesCS4B01G276100	chr5A	87.745	408	39	5	1	401	426309056	426308653	1.330000e-127	466
21	TraesCS4B01G276100	chr7D	87.500	408	40	5	1	401	135939394	135939797	6.200000e-126	460
22	TraesCS4B01G276100	chr3B	87.407	405	41	4	1	401	1384202	1383804	8.010000e-125	457
23	TraesCS4B01G276100	chr3B	87.032	401	40	3	9	401	798619800	798619404	2.240000e-120	442
24	TraesCS4B01G276100	chr5B	85.859	396	49	2	9	401	437726523	437726914	4.890000e-112	414
25	TraesCS4B01G276100	chr5B	84.887	397	50	6	9	401	437782380	437782770	2.290000e-105	392
26	TraesCS4B01G276100	chr5B	82.517	143	22	2	1992	2134	278442546	278442407	3.320000e-24	122

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	TraesCS4B01G276100	chr4B	555213112	555215570	2458	True	1596.666667	4542	92.308000	1	2459	3	chr4B.!!$R2	2458
1	TraesCS4B01G276100	chr4B	555538584	555540090	1506	True	2222.000000	2222	93.311000	2	1506	1	chr4B.!!$R1	1504
2	TraesCS4B01G276100	chr4B	555514693	555515808	1115	True	486.000000	1247	91.192750	1506	2435	4	chr4B.!!$R3	929
3	TraesCS4B01G276100	chr4D	444884864	444886916	2052	False	1127.666667	3131	91.049333	400	2457	3	chr4D.!!$F1	2057
4	TraesCS4B01G276100	chr4A	22081939	22086140	4201	False	733.000000	1703	93.071750	423	2458	4	chr4A.!!$F2	2035

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
196	200	0.036952	CCACAGAGTACCAGCCACAG	60.037	60.0	0.00	0.0	0.0	3.66	F
838	1369	0.462759	CACCTCGATCCTTTGGCCTC	60.463	60.0	3.32	0.0	0.0	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1194	1725	0.621609	CCCCGGGGTAAATCTTCACA	59.378	55.000	33.25	0.0	0.0	3.58	R
1752	2286	1.202915	TCCAAGCTGCATCAAGGAACA	60.203	47.619	1.02	0.0	0.0	3.18	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
41	42	1.221840	CGCCTGAGCCACCAACTAT	59.778	57.895	0.00	0.00	34.57	2.12
46	47	2.421529	CCTGAGCCACCAACTATTACCC	60.422	54.545	0.00	0.00	0.00	3.69
53	54	1.761198	ACCAACTATTACCCCTCTCGC	59.239	52.381	0.00	0.00	0.00	5.03
55	56	1.038280	AACTATTACCCCTCTCGCCG	58.962	55.000	0.00	0.00	0.00	6.46
82	86	3.579302	CCAAGGGAGCCACCACCA	61.579	66.667	0.00	0.00	41.20	4.17
84	88	3.953775	AAGGGAGCCACCACCACG	61.954	66.667	0.00	0.00	41.20	4.94
127	131	0.038166	AACCATGCGAACCACCATCT	59.962	50.000	0.00	0.00	0.00	2.90
133	137	0.674895	GCGAACCACCATCTGAAGCT	60.675	55.000	0.00	0.00	0.00	3.74
153	157	2.892425	CGCTCCGGCATCCAAGTC	60.892	66.667	0.00	0.00	38.60	3.01
171	175	2.516888	CCAAGACCTCACCCACCGT	61.517	63.158	0.00	0.00	0.00	4.83
174	178	2.920912	GACCTCACCCACCGTCCA	60.921	66.667	0.00	0.00	0.00	4.02
182	186	2.280797	CCACCGTCCACACCACAG	60.281	66.667	0.00	0.00	0.00	3.66
195	199	0.762842	ACCACAGAGTACCAGCCACA	60.763	55.000	0.00	0.00	0.00	4.17
196	200	0.036952	CCACAGAGTACCAGCCACAG	60.037	60.000	0.00	0.00	0.00	3.66
211	215	2.870435	GCCACAGTAGGAAGAGCGAAAA	60.870	50.000	0.00	0.00	0.00	2.29
214	218	4.499183	CACAGTAGGAAGAGCGAAAATCT	58.501	43.478	0.00	0.00	0.00	2.40
227	231	6.876257	AGAGCGAAAATCTACATCTTTCACTT	59.124	34.615	0.00	0.00	0.00	3.16
236	240	2.093447	ACATCTTTCACTTCTAGCCCGG	60.093	50.000	0.00	0.00	0.00	5.73
251	255	2.584418	CGGCATGAGCGACTCAGG	60.584	66.667	14.38	14.38	44.08	3.86
277	281	2.663852	GCGCCACCACAGTACGTT	60.664	61.111	0.00	0.00	0.00	3.99
311	315	4.506255	GTCCCCAGCCAATCCCGG	62.506	72.222	0.00	0.00	0.00	5.73
316	320	2.124570	CAGCCAATCCCGGTGGAG	60.125	66.667	13.59	1.40	46.08	3.86
346	350	1.345715	ACCCCTCCATGATTCCCGAC	61.346	60.000	0.00	0.00	0.00	4.79
395	399	4.988716	TGTCCGTGGCCCTCGACT	62.989	66.667	17.09	0.00	0.00	4.18
654	1184	1.556373	TAGCAGCACACCAGGCAGAT	61.556	55.000	0.00	0.00	0.00	2.90
838	1369	0.462759	CACCTCGATCCTTTGGCCTC	60.463	60.000	3.32	0.00	0.00	4.70
864	1395	4.248842	CCGACCCACCAGCACACA	62.249	66.667	0.00	0.00	0.00	3.72
920	1451	2.330372	CGTCGACAGAGGAACCGGA	61.330	63.158	17.16	0.00	34.40	5.14
1021	1552	2.100631	GGGATGCAACAGTCGACGG	61.101	63.158	14.42	14.42	0.00	4.79
1022	1553	2.740714	GGATGCAACAGTCGACGGC	61.741	63.158	15.92	15.18	0.00	5.68
1237	1768	2.689691	AAGGTGGTGGTGGTGCACT	61.690	57.895	17.98	0.00	34.40	4.40
1281	1812	1.687494	GCGACGACATGGAGCTTGAC	61.687	60.000	0.00	0.00	0.00	3.18
1458	1989	3.883462	CTCGTGGCCGTGCAATAA	58.117	55.556	0.00	0.00	35.01	1.40
1625	2159	6.114187	TGAGGAAGAGAACTGCTTCATAAA	57.886	37.500	0.00	0.00	42.68	1.40
1718	2252	4.082081	GTGAATGCAGATGAAATTGTGGGA	60.082	41.667	0.00	0.00	0.00	4.37
1752	2286	5.506708	ACTGGAACTCTGTTTACTTGGTTT	58.493	37.500	0.00	0.00	0.00	3.27
1811	4012	2.688507	TGCCAGATTTCGTCAGTCTTC	58.311	47.619	0.00	0.00	0.00	2.87
1812	4013	1.656095	GCCAGATTTCGTCAGTCTTCG	59.344	52.381	0.00	0.00	0.00	3.79
1832	4033	5.356882	TCGTTCCTAAAGTTCAATTGCAG	57.643	39.130	0.00	0.00	0.00	4.41
1906	4107	1.443802	GTCTTAGGTCTGCAGCCAAC	58.556	55.000	23.46	11.76	0.00	3.77
1925	4126	1.071071	ACTGCACGTTGGCCTTTACTA	59.929	47.619	3.32	0.00	0.00	1.82
1953	4155	4.691216	CCTACAACTCTGTTCTTGGTTAGC	59.309	45.833	0.00	0.00	36.96	3.09
1955	4157	4.781934	ACAACTCTGTTCTTGGTTAGCTT	58.218	39.130	0.00	0.00	28.57	3.74
1997	4199	3.960102	AGATCTGAGCCTCTTACCTCTTG	59.040	47.826	0.00	0.00	0.00	3.02
2005	4207	1.760029	CTCTTACCTCTTGCCTCCTCC	59.240	57.143	0.00	0.00	0.00	4.30
2023	4225	4.223032	TCCTCCTTTCACATGAGAGGTAAC	59.777	45.833	15.95	0.00	44.34	2.50
2055	4257	2.100584	AGATCTGAGCCGTTGATCTCAC	59.899	50.000	0.00	0.00	41.95	3.51
2059	4261	3.509967	TCTGAGCCGTTGATCTCACTAAA	59.490	43.478	0.00	0.00	35.66	1.85
2104	4306	6.833342	TCTTCTTACCTCACACGTAAAAAC	57.167	37.500	0.00	0.00	0.00	2.43
2218	4425	4.867608	CCCAAGTTCAAACACACGAAATTT	59.132	37.500	0.00	0.00	27.73	1.82
2310	4517	3.674997	TCTGTTCTTGGATAGTTGTGCC	58.325	45.455	0.00	0.00	0.00	5.01
2315	4524	4.365514	TCTTGGATAGTTGTGCCAGAAA	57.634	40.909	0.00	0.00	32.47	2.52
2394	4786	4.098960	TGAGACTCAAGTTCAAACCTACGT	59.901	41.667	1.64	0.00	0.00	3.57
2424	4826	2.631160	TATAGCCAAATGACCCCACG	57.369	50.000	0.00	0.00	0.00	4.94
2458	4860	2.568090	CGGCTGGAATGCACAACC	59.432	61.111	0.00	0.00	34.04	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	0.392998	AATAGTTGGTGGCTCAGGCG	60.393	55.000	0.00	0.00	39.81	5.52
27	28	1.562475	GGGGTAATAGTTGGTGGCTCA	59.438	52.381	0.00	0.00	0.00	4.26
62	63	3.636231	TGGTGGCTCCCTTGGTCG	61.636	66.667	2.66	0.00	34.77	4.79
70	71	2.764637	ATTTCCGTGGTGGTGGCTCC	62.765	60.000	0.00	0.00	39.52	4.70
143	147	1.003580	TGAGGTCTTGGACTTGGATGC	59.996	52.381	0.00	0.00	32.47	3.91
153	157	2.347490	CGGTGGGTGAGGTCTTGG	59.653	66.667	0.00	0.00	0.00	3.61
171	175	1.338107	CTGGTACTCTGTGGTGTGGA	58.662	55.000	0.00	0.00	0.00	4.02
174	178	0.762842	TGGCTGGTACTCTGTGGTGT	60.763	55.000	0.00	0.00	0.00	4.16
182	186	1.848652	TCCTACTGTGGCTGGTACTC	58.151	55.000	0.00	0.00	0.00	2.59
195	199	5.916661	TGTAGATTTTCGCTCTTCCTACT	57.083	39.130	0.00	0.00	0.00	2.57
196	200	6.508777	AGATGTAGATTTTCGCTCTTCCTAC	58.491	40.000	0.00	0.00	0.00	3.18
211	215	5.221342	CGGGCTAGAAGTGAAAGATGTAGAT	60.221	44.000	0.00	0.00	0.00	1.98
214	218	3.132289	CCGGGCTAGAAGTGAAAGATGTA	59.868	47.826	0.00	0.00	0.00	2.29
227	231	3.916544	CGCTCATGCCGGGCTAGA	61.917	66.667	21.46	16.14	35.36	2.43
236	240	2.172372	CAGCCTGAGTCGCTCATGC	61.172	63.158	20.74	20.74	47.00	4.06
291	295	2.763215	GGATTGGCTGGGGACACA	59.237	61.111	0.00	0.00	35.60	3.72
311	315	2.430367	GTGTGTCCCCCACTCCAC	59.570	66.667	0.00	0.00	44.81	4.02
324	328	0.106519	GGGAATCATGGAGGGGTGTG	60.107	60.000	0.00	0.00	0.00	3.82
395	399	2.224892	TGTGAATCCCAAAATCCACGGA	60.225	45.455	0.00	0.00	0.00	4.69
397	401	2.819608	ACTGTGAATCCCAAAATCCACG	59.180	45.455	0.00	0.00	0.00	4.94
654	1184	1.954146	GCGACGGCAGTGAGTTTGA	60.954	57.895	0.00	0.00	39.62	2.69
838	1369	1.043116	TGGTGGGTCGGAGATGCTAG	61.043	60.000	0.00	0.00	40.67	3.42
864	1395	0.734942	CCGGGCGACGCGATTTATAT	60.735	55.000	15.93	0.00	42.31	0.86
920	1451	2.110899	TCTCACCTCTGTCCCTCTCTTT	59.889	50.000	0.00	0.00	0.00	2.52
1194	1725	0.621609	CCCCGGGGTAAATCTTCACA	59.378	55.000	33.25	0.00	0.00	3.58
1237	1768	2.360852	GTCGTCTCCGGTCCCAGA	60.361	66.667	0.00	0.00	33.95	3.86
1281	1812	2.683933	AGCCGGTACCTCCACCTG	60.684	66.667	10.90	0.00	36.35	4.00
1479	2010	2.868583	CAATTATGGAGCTCACACTCGG	59.131	50.000	17.19	0.00	37.57	4.63
1625	2159	1.203313	TCCTTCAGCAGGGAGGTAGTT	60.203	52.381	2.92	0.00	44.12	2.24
1752	2286	1.202915	TCCAAGCTGCATCAAGGAACA	60.203	47.619	1.02	0.00	0.00	3.18
1811	4012	5.356882	TCTGCAATTGAACTTTAGGAACG	57.643	39.130	10.34	0.00	0.00	3.95
1812	4013	7.336931	TCCTATCTGCAATTGAACTTTAGGAAC	59.663	37.037	10.34	0.00	32.02	3.62
1832	4033	5.091431	GCGAAATGCTGCATAATTCCTATC	58.909	41.667	16.58	4.07	41.73	2.08
1864	4065	8.043710	AGACGAATGAAAGAGGTTAGATTTGAT	58.956	33.333	0.00	0.00	0.00	2.57
1906	4107	1.463444	GTAGTAAAGGCCAACGTGCAG	59.537	52.381	5.01	0.00	0.00	4.41
1925	4126	2.690840	AGAACAGAGTTGTAGGTGGGT	58.309	47.619	0.00	0.00	36.23	4.51
1997	4199	1.556911	TCTCATGTGAAAGGAGGAGGC	59.443	52.381	0.00	0.00	37.31	4.70
2023	4225	9.208022	TCAACGGCTCAGATCTATTTTATATTG	57.792	33.333	0.00	0.00	0.00	1.90
2096	4298	6.310711	GGTCTCTCTTACCTCATGTTTTTACG	59.689	42.308	0.00	0.00	33.97	3.18
2104	4306	5.350504	AACATGGTCTCTCTTACCTCATG	57.649	43.478	0.00	0.00	37.91	3.07
2320	4529	2.285868	CCTCCCCCGGTGGTCTAT	59.714	66.667	1.78	0.00	32.24	1.98
2394	4786	6.265196	GGTCATTTGGCTATATTGGTCAATCA	59.735	38.462	0.00	0.00	32.50	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.