AutoCloner

Multiple sequence alignment - TraesCS5A01G556300

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	TraesCS5A01G556300	chr5A	100.000	2393	0	0	1	2393	707721226	707723618	0.000000e+00	4420.0
1	TraesCS5A01G556300	chr5A	87.691	1503	179	5	1	1501	622529042	622527544	0.000000e+00	1746.0
2	TraesCS5A01G556300	chr5A	95.364	604	23	1	1790	2393	551484544	551483946	0.000000e+00	955.0
3	TraesCS5A01G556300	chr3A	92.800	1500	108	0	1	1500	110312759	110311260	0.000000e+00	2172.0
4	TraesCS5A01G556300	chr3A	95.907	904	24	6	1497	2393	77932404	77931507	0.000000e+00	1452.0
5	TraesCS5A01G556300	chr2A	92.234	1455	113	0	1	1455	679988196	679986742	0.000000e+00	2061.0
6	TraesCS5A01G556300	chr2A	91.267	1500	131	0	1	1500	447899692	447898193	0.000000e+00	2045.0
7	TraesCS5A01G556300	chr2A	97.222	36	0	1	2007	2042	372375793	372375827	2.570000e-05	60.2
8	TraesCS5A01G556300	chr7A	91.712	1472	119	1	1	1469	7844591	7843120	0.000000e+00	2039.0
9	TraesCS5A01G556300	chr7A	87.209	1501	187	3	1	1499	20254408	20252911	0.000000e+00	1703.0
10	TraesCS5A01G556300	chr7A	86.285	1502	198	7	1	1498	270771073	270772570	0.000000e+00	1626.0
11	TraesCS5A01G556300	chr4A	91.563	1446	122	0	1	1446	546006792	546005347	0.000000e+00	1995.0
12	TraesCS5A01G556300	chr6B	84.431	1503	228	5	1	1500	68900866	68902365	0.000000e+00	1474.0
13	TraesCS5A01G556300	chr2D	96.816	534	11	2	1860	2393	428577475	428576948	0.000000e+00	887.0
14	TraesCS5A01G556300	chr2D	98.256	344	4	1	1497	1838	428577812	428577469	3.400000e-168	601.0
15	TraesCS5A01G556300	chr1D	88.636	132	8	4	1577	1701	468040460	468040591	1.150000e-33	154.0
16	TraesCS5A01G556300	chr1A	88.636	132	8	4	1577	1701	561124997	561124866	1.150000e-33	154.0
17	TraesCS5A01G556300	chr1B	84.000	125	7	3	1577	1697	646479809	646479694	9.050000e-20	108.0

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	TraesCS5A01G556300	chr5A	707721226	707723618	2392	False	4420	4420	100.000	1	2393	1	chr5A.!!$F1	2392
1	TraesCS5A01G556300	chr5A	622527544	622529042	1498	True	1746	1746	87.691	1	1501	1	chr5A.!!$R2	1500
2	TraesCS5A01G556300	chr5A	551483946	551484544	598	True	955	955	95.364	1790	2393	1	chr5A.!!$R1	603
3	TraesCS5A01G556300	chr3A	110311260	110312759	1499	True	2172	2172	92.800	1	1500	1	chr3A.!!$R2	1499
4	TraesCS5A01G556300	chr3A	77931507	77932404	897	True	1452	1452	95.907	1497	2393	1	chr3A.!!$R1	896
5	TraesCS5A01G556300	chr2A	679986742	679988196	1454	True	2061	2061	92.234	1	1455	1	chr2A.!!$R2	1454
6	TraesCS5A01G556300	chr2A	447898193	447899692	1499	True	2045	2045	91.267	1	1500	1	chr2A.!!$R1	1499
7	TraesCS5A01G556300	chr7A	7843120	7844591	1471	True	2039	2039	91.712	1	1469	1	chr7A.!!$R1	1468
8	TraesCS5A01G556300	chr7A	20252911	20254408	1497	True	1703	1703	87.209	1	1499	1	chr7A.!!$R2	1498
9	TraesCS5A01G556300	chr7A	270771073	270772570	1497	False	1626	1626	86.285	1	1498	1	chr7A.!!$F1	1497
10	TraesCS5A01G556300	chr4A	546005347	546006792	1445	True	1995	1995	91.563	1	1446	1	chr4A.!!$R1	1445
11	TraesCS5A01G556300	chr6B	68900866	68902365	1499	False	1474	1474	84.431	1	1500	1	chr6B.!!$F1	1499
12	TraesCS5A01G556300	chr2D	428576948	428577812	864	True	744	887	97.536	1497	2393	2	chr2D.!!$R1	896

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
907	911	0.11714	TGATGAGGACACAGACCCCT	59.883	55.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2177	2188	0.884514	GAGAAAAAGGAGCACAGGGC	59.115	55.0	0.0	0.0	45.3	5.19	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
33	34	1.665599	GCAAAACAGCATTGCCGCT	60.666	52.632	4.70	0.00	45.73	5.52
105	106	3.886550	CTCCCCCACCAAACTGCCC	62.887	68.421	0.00	0.00	0.00	5.36
165	166	1.701031	TTCTCTTCGGTTGGGTGGCA	61.701	55.000	0.00	0.00	0.00	4.92
180	181	4.121669	GCACGCCTGCTCTCTCGA	62.122	66.667	0.00	0.00	40.63	4.04
276	277	5.163622	ACCAAAATCGATCATAGCCAAACTG	60.164	40.000	0.00	0.00	0.00	3.16
313	314	4.080863	GGGCTTTCTTCTGGTCTAATGAGA	60.081	45.833	0.00	0.00	0.00	3.27
327	328	0.607489	ATGAGACAACCTGCACTGGC	60.607	55.000	0.00	0.00	41.68	4.85
371	372	5.349270	GGAAAAACGTTTGCAAACCTAAAGT	59.651	36.000	31.14	21.46	35.30	2.66
498	499	1.286248	ACCACCACCAATACCCTCTC	58.714	55.000	0.00	0.00	0.00	3.20
507	508	0.179018	AATACCCTCTCGGCATTGCC	60.179	55.000	18.10	18.10	46.75	4.52
603	604	4.019792	TGTGCTCACATACAATGGTCTT	57.980	40.909	0.00	0.00	36.21	3.01
640	641	7.624360	TGGCTTGATAAATGGTTACTACAAG	57.376	36.000	0.00	0.00	34.68	3.16
645	646	6.953101	TGATAAATGGTTACTACAAGCTCCA	58.047	36.000	0.00	0.00	0.00	3.86
648	649	6.368779	AAATGGTTACTACAAGCTCCACTA	57.631	37.500	0.00	0.00	0.00	2.74
690	691	5.396548	CCTCTTCTCACACTCCATTGATGAT	60.397	44.000	0.00	0.00	0.00	2.45
691	692	5.425630	TCTTCTCACACTCCATTGATGATG	58.574	41.667	0.00	0.00	35.42	3.07
709	710	6.382859	TGATGATGAGGTTTTAGTGGCTACTA	59.617	38.462	5.74	5.74	38.36	1.82
719	720	6.902771	TTTAGTGGCTACTATTTGGCAAAA	57.097	33.333	17.70	5.78	39.08	2.44
758	759	2.649331	CGGAACCGTCTGTCTAATGT	57.351	50.000	4.99	0.00	34.35	2.71
873	877	0.532573	TCTCTGCCAAGAACGCCTAG	59.467	55.000	0.00	0.00	30.03	3.02
883	887	1.757699	AGAACGCCTAGTCCTCCATTC	59.242	52.381	0.00	0.00	0.00	2.67
891	895	3.390639	CCTAGTCCTCCATTCTTGCTGAT	59.609	47.826	0.00	0.00	0.00	2.90
894	898	3.118334	AGTCCTCCATTCTTGCTGATGAG	60.118	47.826	0.00	0.00	0.00	2.90
907	911	0.117140	TGATGAGGACACAGACCCCT	59.883	55.000	0.00	0.00	0.00	4.79
927	931	0.251341	ACCATGACTTTGTCTGGGCC	60.251	55.000	0.00	0.00	36.17	5.80
934	938	1.063266	ACTTTGTCTGGGCCTCCAAAA	60.063	47.619	4.53	0.00	43.51	2.44
960	964	3.000724	CGATCAAAGTCAAGATCTTCGCC	59.999	47.826	4.57	0.00	38.75	5.54
970	974	1.382420	ATCTTCGCCTGGCTCCTCT	60.382	57.895	17.92	0.00	0.00	3.69
973	977	1.610673	TTCGCCTGGCTCCTCTTCT	60.611	57.895	17.92	0.00	0.00	2.85
975	979	2.588989	GCCTGGCTCCTCTTCTGG	59.411	66.667	12.43	0.00	0.00	3.86
981	985	2.896443	CTCCTCTTCTGGGACCGC	59.104	66.667	0.00	0.00	0.00	5.68
1062	1066	3.594134	CTGTCAAGACCCTCATGAAGAC	58.406	50.000	0.00	0.00	0.00	3.01
1065	1069	0.108615	AAGACCCTCATGAAGACGCG	60.109	55.000	3.53	3.53	0.00	6.01
1096	1100	3.026630	TCTCCAACTGTTCTTACGCTG	57.973	47.619	0.00	0.00	0.00	5.18
1098	1102	1.070134	TCCAACTGTTCTTACGCTGCT	59.930	47.619	0.00	0.00	0.00	4.24
1125	1129	2.206900	TCCTCCTTGGGACTGCCA	59.793	61.111	0.00	0.00	36.20	4.92
1162	1166	2.680913	GCGCTGCTACAACACCCAG	61.681	63.158	0.00	0.00	0.00	4.45
1163	1167	1.005037	CGCTGCTACAACACCCAGA	60.005	57.895	0.00	0.00	0.00	3.86
1177	1181	1.523258	CCAGAGCTTCATGGCCTCG	60.523	63.158	3.32	0.00	0.00	4.63
1195	1199	2.038952	CTCGATCCCAATATCTGGCCAA	59.961	50.000	7.01	0.00	44.90	4.52
1224	1228	4.737352	GCTCTGACTATCTCTTGGAAGCTG	60.737	50.000	0.00	0.00	0.00	4.24
1245	1249	2.383527	GGACTCCAGAAACGCGCTG	61.384	63.158	5.73	5.50	0.00	5.18
1269	1273	4.082463	GTCTTCAGAAACGAGGATCACTCT	60.082	45.833	0.00	0.00	44.33	3.24
1284	1288	4.897509	TCACTCTCACAGAACCATGATT	57.102	40.909	0.00	0.00	0.00	2.57
1359	1363	5.240623	AGAAGACAATATCTCCGCTAGACAG	59.759	44.000	0.00	0.00	36.27	3.51
1386	1390	5.178438	GCTTTACTTCCTCTCTTCAGTTGTG	59.822	44.000	0.00	0.00	0.00	3.33
1391	1395	1.610102	CCTCTCTTCAGTTGTGCCCTG	60.610	57.143	0.00	0.00	0.00	4.45
1394	1399	3.173151	TCTCTTCAGTTGTGCCCTGATA	58.827	45.455	0.00	0.00	38.66	2.15
1396	1401	4.041567	TCTCTTCAGTTGTGCCCTGATAAA	59.958	41.667	0.00	0.00	38.66	1.40
1407	1412	5.714333	TGTGCCCTGATAAACATGTTGTAAT	59.286	36.000	12.82	6.45	0.00	1.89
1408	1413	6.210385	TGTGCCCTGATAAACATGTTGTAATT	59.790	34.615	12.82	0.00	0.00	1.40
1422	1427	8.946085	ACATGTTGTAATTGAACTACTATGGTG	58.054	33.333	0.00	0.00	0.00	4.17
1423	1428	8.946085	CATGTTGTAATTGAACTACTATGGTGT	58.054	33.333	0.00	0.00	0.00	4.16
1430	1436	5.717078	TGAACTACTATGGTGTTTCTCGT	57.283	39.130	0.00	0.00	0.00	4.18
1431	1437	6.092955	TGAACTACTATGGTGTTTCTCGTT	57.907	37.500	0.00	0.00	0.00	3.85
1432	1438	6.154445	TGAACTACTATGGTGTTTCTCGTTC	58.846	40.000	0.00	0.00	0.00	3.95
1437	1443	1.124780	TGGTGTTTCTCGTTCCCTCA	58.875	50.000	0.00	0.00	0.00	3.86
1554	1560	8.940397	TTCTAAGGTGGAGATGAGAAAATTTT	57.060	30.769	2.28	2.28	0.00	1.82
1767	1775	6.863126	CGAAGCAATCCTGTTACTGAATTTTT	59.137	34.615	0.00	0.00	0.00	1.94
2002	2013	0.322277	AGAGCCTGGACATGTGCAAG	60.322	55.000	21.10	16.14	0.00	4.01
2192	2203	2.985847	GCGCCCTGTGCTCCTTTT	60.986	61.111	0.00	0.00	38.05	2.27
2212	2223	2.734673	CTCGGAGCAAGCAAGCGAC	61.735	63.158	0.00	0.00	40.15	5.19
2298	2309	1.306997	TCCTCCACCACCATCTCCC	60.307	63.158	0.00	0.00	0.00	4.30
2299	2310	2.735772	CCTCCACCACCATCTCCCG	61.736	68.421	0.00	0.00	0.00	5.14
2300	2311	2.687200	TCCACCACCATCTCCCGG	60.687	66.667	0.00	0.00	0.00	5.73
2301	2312	4.489771	CCACCACCATCTCCCGGC	62.490	72.222	0.00	0.00	0.00	6.13
2302	2313	4.489771	CACCACCATCTCCCGGCC	62.490	72.222	0.00	0.00	0.00	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	3.013921	GGATAAGGAACAACCAATCGCA	58.986	45.455	0.00	0.00	42.04	5.10
105	106	1.738099	CGGGTCGAAAGCTGTGAGG	60.738	63.158	0.00	0.00	0.00	3.86
180	181	4.640690	AGGGTGAGACGTGCCCCT	62.641	66.667	0.00	0.00	43.32	4.79
371	372	5.765576	TTTAATGCCTAGACCACCAGTAA	57.234	39.130	0.00	0.00	0.00	2.24
447	448	0.856982	AGGGGATGTTTGGGTGTTGA	59.143	50.000	0.00	0.00	0.00	3.18
507	508	3.450817	AGGAGGGTTTTGAGGTTTTTGTG	59.549	43.478	0.00	0.00	0.00	3.33
508	509	3.719871	AGGAGGGTTTTGAGGTTTTTGT	58.280	40.909	0.00	0.00	0.00	2.83
579	580	4.456911	AGACCATTGTATGTGAGCACAAAG	59.543	41.667	7.46	0.00	45.41	2.77
603	604	3.025322	TCAAGCCAAAAGAAGGTGGAA	57.975	42.857	0.00	0.00	37.03	3.53
640	641	4.098807	TGGGAAAACTTTTTGTAGTGGAGC	59.901	41.667	0.00	0.00	0.00	4.70
645	646	6.439375	AGAGGTTTGGGAAAACTTTTTGTAGT	59.561	34.615	1.76	0.00	38.87	2.73
648	649	5.755409	AGAGGTTTGGGAAAACTTTTTGT	57.245	34.783	1.76	0.00	38.87	2.83
690	691	6.177610	CCAAATAGTAGCCACTAAAACCTCA	58.822	40.000	0.00	0.00	40.61	3.86
691	692	5.066117	GCCAAATAGTAGCCACTAAAACCTC	59.934	44.000	0.00	0.00	40.61	3.85
709	710	2.944349	CCAACAAGCTGTTTTGCCAAAT	59.056	40.909	0.00	0.00	38.77	2.32
719	720	0.107831	TAGGTTCGCCAACAAGCTGT	59.892	50.000	0.00	0.00	40.60	4.40
834	838	4.468689	GGTAGGCCGTGGGTGAGC	62.469	72.222	0.00	0.00	0.00	4.26
846	850	0.895530	TCTTGGCAGAGAACGGTAGG	59.104	55.000	0.00	0.00	0.00	3.18
873	877	3.204526	CTCATCAGCAAGAATGGAGGAC	58.795	50.000	0.00	0.00	0.00	3.85
883	887	2.344950	GTCTGTGTCCTCATCAGCAAG	58.655	52.381	0.00	0.00	0.00	4.01
891	895	0.252103	GGTAGGGGTCTGTGTCCTCA	60.252	60.000	0.00	0.00	32.46	3.86
894	898	0.541863	CATGGTAGGGGTCTGTGTCC	59.458	60.000	0.00	0.00	0.00	4.02
907	911	1.004277	GGCCCAGACAAAGTCATGGTA	59.996	52.381	0.00	0.00	34.60	3.25
927	931	4.009675	TGACTTTGATCGGGATTTTGGAG	58.990	43.478	0.00	0.00	0.00	3.86
934	938	5.363939	GAAGATCTTGACTTTGATCGGGAT	58.636	41.667	14.00	0.00	42.62	3.85
960	964	1.621672	GGTCCCAGAAGAGGAGCCAG	61.622	65.000	0.00	0.00	44.49	4.85
970	974	0.035739	GTGTTTAGGCGGTCCCAGAA	59.964	55.000	0.00	0.00	35.39	3.02
973	977	1.756408	TTCGTGTTTAGGCGGTCCCA	61.756	55.000	0.00	0.00	35.39	4.37
975	979	1.017701	CCTTCGTGTTTAGGCGGTCC	61.018	60.000	0.00	0.00	0.00	4.46
981	985	2.380084	TGCTAGCCTTCGTGTTTAGG	57.620	50.000	13.29	0.00	34.54	2.69
1020	1024	1.651240	GCGGACATGCAGCAGATTGT	61.651	55.000	0.00	0.00	37.65	2.71
1062	1066	1.006805	GGAGATGAGGTGGATCGCG	60.007	63.158	0.00	0.00	0.00	5.87
1065	1069	2.503356	ACAGTTGGAGATGAGGTGGATC	59.497	50.000	0.00	0.00	0.00	3.36
1096	1100	0.907230	AAGGAGGACCAGACCTGAGC	60.907	60.000	5.81	0.00	40.73	4.26
1098	1102	0.545309	CCAAGGAGGACCAGACCTGA	60.545	60.000	5.81	0.00	40.73	3.86
1146	1150	1.301677	GCTCTGGGTGTTGTAGCAGC	61.302	60.000	0.00	0.00	36.26	5.25
1162	1166	0.602372	GGATCGAGGCCATGAAGCTC	60.602	60.000	5.01	0.00	0.00	4.09
1163	1167	1.449353	GGATCGAGGCCATGAAGCT	59.551	57.895	5.01	0.00	0.00	3.74
1195	1199	1.064314	AGAGATAGTCAGAGCCACCGT	60.064	52.381	0.00	0.00	0.00	4.83
1224	1228	2.027625	CGCGTTTCTGGAGTCCCAC	61.028	63.158	6.74	0.00	37.58	4.61
1245	1249	3.056465	AGTGATCCTCGTTTCTGAAGACC	60.056	47.826	0.00	0.00	0.00	3.85
1269	1273	4.384940	TGTTTCGAATCATGGTTCTGTGA	58.615	39.130	16.47	4.08	0.00	3.58
1284	1288	5.239306	AGAGAAATCAGCAACAATGTTTCGA	59.761	36.000	0.00	0.00	32.46	3.71
1359	1363	4.249661	CTGAAGAGAGGAAGTAAAGCCAC	58.750	47.826	0.00	0.00	0.00	5.01
1366	1370	3.006967	GGCACAACTGAAGAGAGGAAGTA	59.993	47.826	0.00	0.00	0.00	2.24
1386	1390	6.862209	TCAATTACAACATGTTTATCAGGGC	58.138	36.000	8.77	0.00	31.56	5.19
1396	1401	8.946085	CACCATAGTAGTTCAATTACAACATGT	58.054	33.333	0.00	0.00	0.00	3.21
1407	1412	6.092955	ACGAGAAACACCATAGTAGTTCAA	57.907	37.500	0.00	0.00	0.00	2.69
1408	1413	5.717078	ACGAGAAACACCATAGTAGTTCA	57.283	39.130	0.00	0.00	0.00	3.18
1419	1424	2.474410	ATGAGGGAACGAGAAACACC	57.526	50.000	0.00	0.00	0.00	4.16
1422	1427	5.035784	CTCAAAATGAGGGAACGAGAAAC	57.964	43.478	0.00	0.00	40.71	2.78
1437	1443	9.354673	CCACCTGAATATATTACCACTCAAAAT	57.645	33.333	0.00	0.00	0.00	1.82
1554	1560	7.819415	CCATACTGAGTGTTCTATCTTGTTCAA	59.181	37.037	0.00	0.00	0.00	2.69
1767	1775	4.945543	AGGGATGACGCACGTATATATACA	59.054	41.667	20.24	2.26	32.87	2.29
2177	2188	0.884514	GAGAAAAAGGAGCACAGGGC	59.115	55.000	0.00	0.00	45.30	5.19
2192	2203	2.029288	CGCTTGCTTGCTCCGAGAA	61.029	57.895	0.00	0.00	0.00	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.