AutoCloner

Multiple sequence alignment - TraesCS1A01G055700

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	TraesCS1A01G055700	chr1A	100.000	2380	0	0	1	2380	36607873	36605494	0.000000e+00	4396.0
1	TraesCS1A01G055700	chr1A	88.639	1778	190	11	334	2105	36172122	36173893	0.000000e+00	2154.0
2	TraesCS1A01G055700	chr1A	88.182	1777	191	13	334	2105	36185633	36187395	0.000000e+00	2100.0
3	TraesCS1A01G055700	chr1A	89.148	1585	166	6	522	2105	36615691	36614112	0.000000e+00	1969.0
4	TraesCS1A01G055700	chr1A	91.418	268	21	2	2114	2380	36261201	36261467	1.340000e-97	366.0
5	TraesCS1A01G055700	chr1A	90.262	267	26	0	2114	2380	36174207	36174473	1.350000e-92	350.0
6	TraesCS1A01G055700	chr1A	90.262	267	26	0	2114	2380	36187709	36187975	1.350000e-92	350.0
7	TraesCS1A01G055700	chr1D	93.883	2109	121	8	1	2105	36621577	36623681	0.000000e+00	3173.0
8	TraesCS1A01G055700	chr1D	89.708	1778	174	9	333	2105	36615497	36617270	0.000000e+00	2261.0
9	TraesCS1A01G055700	chr1D	87.827	1569	191	0	537	2105	37426330	37424762	0.000000e+00	1840.0
10	TraesCS1A01G055700	chr1D	91.386	267	23	0	2114	2380	38583399	38583665	1.340000e-97	366.0
11	TraesCS1A01G055700	chr1D	91.011	267	24	0	2114	2380	37430794	37430528	6.250000e-96	361.0
12	TraesCS1A01G055700	chr1D	90.698	258	24	0	2123	2380	38559667	38559924	6.300000e-91	344.0
13	TraesCS1A01G055700	chr1D	93.023	43	1	2	261	302	36615493	36615534	7.100000e-06	62.1
14	TraesCS1A01G055700	chr1B	89.494	1818	164	12	297	2105	56499075	56500874	0.000000e+00	2274.0
15	TraesCS1A01G055700	chr1B	89.189	1776	182	8	334	2105	56490922	56492691	0.000000e+00	2207.0
16	TraesCS1A01G055700	chr1B	88.802	1786	179	12	334	2105	56617822	56619600	0.000000e+00	2170.0
17	TraesCS1A01G055700	chr1B	94.382	267	15	0	2114	2380	56501186	56501452	6.120000e-111	411.0
18	TraesCS1A01G055700	chr1B	92.135	267	21	0	2114	2380	56493005	56493271	6.210000e-101	377.0
19	TraesCS1A01G055700	chr1B	90.262	267	26	0	2114	2380	56619914	56620180	1.350000e-92	350.0
20	TraesCS1A01G055700	chr1B	95.349	43	1	1	261	302	56490917	56490959	1.530000e-07	67.6

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	TraesCS1A01G055700	chr1A	36605494	36607873	2379	True	4396.000000	4396	100.000000	1	2380	1	chr1A.!!$R1	2379
1	TraesCS1A01G055700	chr1A	36614112	36615691	1579	True	1969.000000	1969	89.148000	522	2105	1	chr1A.!!$R2	1583
2	TraesCS1A01G055700	chr1A	36172122	36174473	2351	False	1252.000000	2154	89.450500	334	2380	2	chr1A.!!$F2	2046
3	TraesCS1A01G055700	chr1A	36185633	36187975	2342	False	1225.000000	2100	89.222000	334	2380	2	chr1A.!!$F3	2046
4	TraesCS1A01G055700	chr1D	36621577	36623681	2104	False	3173.000000	3173	93.883000	1	2105	1	chr1D.!!$F1	2104
5	TraesCS1A01G055700	chr1D	37424762	37426330	1568	True	1840.000000	1840	87.827000	537	2105	1	chr1D.!!$R1	1568
6	TraesCS1A01G055700	chr1D	36615493	36617270	1777	False	1161.550000	2261	91.365500	261	2105	2	chr1D.!!$F4	1844
7	TraesCS1A01G055700	chr1B	56499075	56501452	2377	False	1342.500000	2274	91.938000	297	2380	2	chr1B.!!$F2	2083
8	TraesCS1A01G055700	chr1B	56617822	56620180	2358	False	1260.000000	2170	89.532000	334	2380	2	chr1B.!!$F3	2046
9	TraesCS1A01G055700	chr1B	56490917	56493271	2354	False	883.866667	2207	92.224333	261	2380	3	chr1B.!!$F1	2119

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
416	421	0.830648	CTACCTTTCCTCGCCCATCA	59.169	55.0	0.0	0.0	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2109	2131	0.835276	CCTGCTCCAGATGATGACCA	59.165	55.0	0.0	0.0	32.44	4.02	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
105	106	4.381411	GAGGTAAGTTGTGCAAGAAGACT	58.619	43.478	0.00	0.00	0.00	3.24
124	125	9.384764	AGAAGACTAACACTTATTATGAAAGGC	57.615	33.333	0.00	0.00	0.00	4.35
194	195	1.740025	CCGCCATGGTTCTTCTTCTTC	59.260	52.381	14.67	0.00	0.00	2.87
225	226	4.911514	TCACCTGAAAAAGTTACAAGCC	57.088	40.909	0.00	0.00	0.00	4.35
285	286	4.228210	TCTTTCCCAATAGCCATCAGAAGT	59.772	41.667	0.00	0.00	0.00	3.01
288	289	5.912149	TCCCAATAGCCATCAGAAGTAAT	57.088	39.130	0.00	0.00	0.00	1.89
361	365	5.760253	CCAATCGCCATCAGAAGTAATTACT	59.240	40.000	12.50	12.50	38.39	2.24
416	421	0.830648	CTACCTTTCCTCGCCCATCA	59.169	55.000	0.00	0.00	0.00	3.07
459	464	2.076100	TGTCACTTTCATGTGATCCGC	58.924	47.619	0.64	0.00	46.77	5.54
1100	1119	7.665559	TGCACAATTATTTCTACAAAGACCTCT	59.334	33.333	0.00	0.00	0.00	3.69
1205	1224	0.673437	CCAGCACGAAACAACCCATT	59.327	50.000	0.00	0.00	0.00	3.16
1208	1227	2.030007	CAGCACGAAACAACCCATTCAT	60.030	45.455	0.00	0.00	0.00	2.57
1212	1231	5.047377	AGCACGAAACAACCCATTCATTATT	60.047	36.000	0.00	0.00	0.00	1.40
1217	1236	6.977502	CGAAACAACCCATTCATTATTATGCA	59.022	34.615	0.00	0.00	0.00	3.96
1257	1276	4.515432	GTTTAATTCTCTTACGCGGCATC	58.485	43.478	12.47	0.00	0.00	3.91
1297	1316	7.442364	TCAAACTATCATCGATCCTTCCATTTC	59.558	37.037	0.00	0.00	0.00	2.17
1377	1396	7.667219	ACTGATTCCATGACATCAAGTACTTTT	59.333	33.333	5.07	0.00	0.00	2.27
1428	1447	5.503031	GCAATATCCGTCAATCAGTGAACTG	60.503	44.000	3.98	3.98	45.08	3.16
1482	1501	9.698309	ATGTCTATAACCAAGTCAAAGATATCG	57.302	33.333	0.00	0.00	0.00	2.92
1496	1515	6.936335	TCAAAGATATCGTGTGCATCCATAAT	59.064	34.615	8.69	0.00	0.00	1.28
1579	1598	7.830739	AGGAATACCTTTGTTCATCATTTCAC	58.169	34.615	0.00	0.00	45.36	3.18
1661	1680	4.751098	GTGATAAACAGTTGTGTCCGGTTA	59.249	41.667	0.00	0.00	35.08	2.85
2070	2092	5.120830	AGTCATTAACGAGCTGCAAGTAAAG	59.879	40.000	1.02	0.00	35.30	1.85
2105	2127	3.008485	AGACCCTGACTTGTCATTTCTCC	59.992	47.826	3.79	0.00	33.89	3.71
2107	2129	3.331889	ACCCTGACTTGTCATTTCTCCAT	59.668	43.478	3.79	0.00	0.00	3.41
2108	2130	3.944015	CCCTGACTTGTCATTTCTCCATC	59.056	47.826	3.79	0.00	0.00	3.51
2109	2131	4.324099	CCCTGACTTGTCATTTCTCCATCT	60.324	45.833	3.79	0.00	0.00	2.90
2110	2132	4.634883	CCTGACTTGTCATTTCTCCATCTG	59.365	45.833	3.79	0.00	0.00	2.90
2111	2133	4.582869	TGACTTGTCATTTCTCCATCTGG	58.417	43.478	0.00	0.00	0.00	3.86
2245	2572	1.502163	GAAGCAGCACGTTCACAGCT	61.502	55.000	0.00	0.00	39.63	4.24
2266	2593	0.791422	CATCCGTCCGTTTTGCGTAA	59.209	50.000	0.00	0.00	39.32	3.18
2344	2671	4.803426	AGGCGAGCGAAGAAGGCG	62.803	66.667	0.00	0.00	35.00	5.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	7.008332	TCCAGAGAATAATATCCGAGGTTACA	58.992	38.462	0.00	0.00	0.00	2.41
124	125	3.433615	GCAAGTAGCTTGTGGTTCTACTG	59.566	47.826	10.10	0.00	42.77	2.74
220	221	1.395826	TTCGTTTTGGTGGGGGCTTG	61.396	55.000	0.00	0.00	0.00	4.01
224	225	1.184970	ATGCTTCGTTTTGGTGGGGG	61.185	55.000	0.00	0.00	0.00	5.40
225	226	0.038343	CATGCTTCGTTTTGGTGGGG	60.038	55.000	0.00	0.00	0.00	4.96
262	263	4.228210	ACTTCTGATGGCTATTGGGAAAGA	59.772	41.667	0.00	0.00	0.00	2.52
269	270	6.431234	GGGGTAATTACTTCTGATGGCTATTG	59.569	42.308	15.05	0.00	0.00	1.90
273	274	4.047883	AGGGGTAATTACTTCTGATGGCT	58.952	43.478	15.05	0.00	0.00	4.75
285	286	6.834969	GCCACCTGTAATTTTAGGGGTAATTA	59.165	38.462	11.15	0.00	35.65	1.40
288	289	4.292836	AGCCACCTGTAATTTTAGGGGTAA	59.707	41.667	11.15	0.00	35.65	2.85
361	365	7.513371	AACACGATTGGTTACAATTTTAGGA	57.487	32.000	0.00	0.00	46.89	2.94
459	464	4.104776	GTGAGTTCATTTTGTGGTGTGTG	58.895	43.478	0.00	0.00	0.00	3.82
467	472	9.436957	CCTACTTGTATAGTGAGTTCATTTTGT	57.563	33.333	0.00	0.00	37.73	2.83
805	824	1.201424	GGTATCGTTCCCAGTTCCCT	58.799	55.000	0.00	0.00	0.00	4.20
900	919	6.998074	TGGTGCCCAATGAATCTACTTATAAG	59.002	38.462	11.05	11.05	0.00	1.73
901	920	6.905736	TGGTGCCCAATGAATCTACTTATAA	58.094	36.000	0.00	0.00	0.00	0.98
934	953	5.047164	AGGATTTGTTTGCTGCAATATCACA	60.047	36.000	16.77	14.17	0.00	3.58
1029	1048	9.527157	TTCCAGAAATTAGGAACAATGAATGTA	57.473	29.630	3.54	0.00	42.99	2.29
1141	1160	4.014569	TGTTCCATGAGATGACGGAAAA	57.985	40.909	0.00	0.00	39.18	2.29
1167	1186	0.884704	GGAGAACTGTTGCCGCAAGA	60.885	55.000	5.91	4.11	43.02	3.02
1212	1231	6.179756	ACCTGACACTGTTTCATATTGCATA	58.820	36.000	0.00	0.00	0.00	3.14
1223	1242	7.881775	AAGAGAATTAAACCTGACACTGTTT	57.118	32.000	4.33	4.33	38.22	2.83
1257	1276	6.918626	TGATAGTTTGACTCTGTTCAGAGAG	58.081	40.000	29.07	14.42	44.50	3.20
1277	1296	7.539034	TGTAGAAATGGAAGGATCGATGATA	57.461	36.000	0.54	0.00	0.00	2.15
1297	1316	9.935682	CAATACACTTGTTAATGGCTATTGTAG	57.064	33.333	5.42	0.46	0.00	2.74
1377	1396	6.237901	AGTCGGCAATATGGATAAAGCATTA	58.762	36.000	0.00	0.00	0.00	1.90
1482	1501	3.825328	AGGAAGGATTATGGATGCACAC	58.175	45.455	0.00	0.00	0.00	3.82
1496	1515	2.439507	AGTCTGTGCAAAGAAGGAAGGA	59.560	45.455	8.55	0.00	0.00	3.36
1579	1598	1.043022	AAAGCCAAGGAGCTGGTTTG	58.957	50.000	0.00	0.00	44.11	2.93
1661	1680	3.028850	CAGATGATTGCCATGGGAGTTT	58.971	45.455	15.13	0.00	35.17	2.66
2089	2111	4.042062	ACCAGATGGAGAAATGACAAGTCA	59.958	41.667	5.72	5.24	40.43	3.41
2091	2113	4.042062	TGACCAGATGGAGAAATGACAAGT	59.958	41.667	5.72	0.00	38.94	3.16
2095	2117	4.774124	TGATGACCAGATGGAGAAATGAC	58.226	43.478	5.72	0.00	38.94	3.06
2105	2127	2.104281	TGCTCCAGATGATGACCAGATG	59.896	50.000	0.00	0.00	0.00	2.90
2107	2129	1.761198	CTGCTCCAGATGATGACCAGA	59.239	52.381	0.00	0.00	32.44	3.86
2108	2130	1.202663	CCTGCTCCAGATGATGACCAG	60.203	57.143	0.00	0.00	32.44	4.00
2109	2131	0.835276	CCTGCTCCAGATGATGACCA	59.165	55.000	0.00	0.00	32.44	4.02
2110	2132	0.835941	ACCTGCTCCAGATGATGACC	59.164	55.000	0.00	0.00	32.44	4.02
2111	2133	1.537776	CGACCTGCTCCAGATGATGAC	60.538	57.143	0.00	0.00	32.44	3.06
2245	2572	1.863491	CGCAAAACGGACGGATGAA	59.137	52.632	0.00	0.00	38.44	2.57
2266	2593	2.039084	CACCTTCCTTAAGTGCCTCTGT	59.961	50.000	0.97	0.00	0.00	3.41
2321	2648	2.202676	CTTCGCTCGCCTCCTCAC	60.203	66.667	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.