AutoCloner

Multiple sequence alignment - TraesCS5B01G293200

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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	TraesCS5B01G293200	chr5B	100.000	2465	0	0	1	2465	478335154	478337618	0.000000e+00	4553.0
1	TraesCS5B01G293200	chr5B	94.906	1060	51	1	1406	2465	129968808	129969864	0.000000e+00	1655.0
2	TraesCS5B01G293200	chr5B	94.717	1060	56	0	1406	2465	67611568	67612627	0.000000e+00	1648.0
3	TraesCS5B01G293200	chr5B	74.854	1197	195	60	256	1406	478425277	478426413	1.740000e-121	446.0
4	TraesCS5B01G293200	chr5A	90.776	1431	102	22	1	1406	503398025	503399450	0.000000e+00	1884.0
5	TraesCS5B01G293200	chr5A	84.067	659	54	17	195	827	503268052	503268685	2.730000e-164	588.0
6	TraesCS5B01G293200	chr5A	76.137	1253	208	51	194	1406	503438889	503440090	7.650000e-160	573.0
7	TraesCS5B01G293200	chr5A	77.128	975	147	45	463	1406	503485460	503486389	1.700000e-136	496.0
8	TraesCS5B01G293200	chr1B	95.180	1058	50	1	1408	2465	141222360	141223416	0.000000e+00	1670.0
9	TraesCS5B01G293200	chr4B	95.000	1060	53	0	1406	2465	434431093	434432152	0.000000e+00	1664.0
10	TraesCS5B01G293200	chr4B	94.906	1060	53	1	1406	2465	419744341	419745399	0.000000e+00	1657.0
11	TraesCS5B01G293200	chr7B	94.906	1060	54	0	1406	2465	205347747	205346688	0.000000e+00	1659.0
12	TraesCS5B01G293200	chr2B	94.906	1060	53	1	1406	2465	428022267	428023325	0.000000e+00	1657.0
13	TraesCS5B01G293200	chr3B	94.816	1061	55	0	1405	2465	329570161	329571221	0.000000e+00	1655.0
14	TraesCS5B01G293200	chr6B	94.811	1060	54	1	1406	2465	637648473	637647415	0.000000e+00	1652.0
15	TraesCS5B01G293200	chr5D	91.458	878	49	9	539	1406	398331039	398331900	0.000000e+00	1182.0
16	TraesCS5B01G293200	chr5D	83.447	1317	145	27	128	1406	398245076	398246357	0.000000e+00	1157.0
17	TraesCS5B01G293200	chr5D	87.006	531	43	11	1	519	398324342	398324858	2.130000e-160	575.0
18	TraesCS5B01G293200	chr5D	76.395	860	147	34	573	1406	398482775	398483604	1.760000e-111	412.0
19	TraesCS5B01G293200	chr5D	100.000	34	0	0	930	963	398547942	398547975	2.050000e-06	63.9
20	TraesCS5B01G293200	chr5D	94.737	38	2	0	570	607	398455876	398455913	2.650000e-05	60.2

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	TraesCS5B01G293200	chr5B	478335154	478337618	2464	False	4553	4553	100.000	1	2465	1	chr5B.!!$F3	2464
1	TraesCS5B01G293200	chr5B	129968808	129969864	1056	False	1655	1655	94.906	1406	2465	1	chr5B.!!$F2	1059
2	TraesCS5B01G293200	chr5B	67611568	67612627	1059	False	1648	1648	94.717	1406	2465	1	chr5B.!!$F1	1059
3	TraesCS5B01G293200	chr5B	478425277	478426413	1136	False	446	446	74.854	256	1406	1	chr5B.!!$F4	1150
4	TraesCS5B01G293200	chr5A	503398025	503399450	1425	False	1884	1884	90.776	1	1406	1	chr5A.!!$F2	1405
5	TraesCS5B01G293200	chr5A	503268052	503268685	633	False	588	588	84.067	195	827	1	chr5A.!!$F1	632
6	TraesCS5B01G293200	chr5A	503438889	503440090	1201	False	573	573	76.137	194	1406	1	chr5A.!!$F3	1212
7	TraesCS5B01G293200	chr5A	503485460	503486389	929	False	496	496	77.128	463	1406	1	chr5A.!!$F4	943
8	TraesCS5B01G293200	chr1B	141222360	141223416	1056	False	1670	1670	95.180	1408	2465	1	chr1B.!!$F1	1057
9	TraesCS5B01G293200	chr4B	434431093	434432152	1059	False	1664	1664	95.000	1406	2465	1	chr4B.!!$F2	1059
10	TraesCS5B01G293200	chr4B	419744341	419745399	1058	False	1657	1657	94.906	1406	2465	1	chr4B.!!$F1	1059
11	TraesCS5B01G293200	chr7B	205346688	205347747	1059	True	1659	1659	94.906	1406	2465	1	chr7B.!!$R1	1059
12	TraesCS5B01G293200	chr2B	428022267	428023325	1058	False	1657	1657	94.906	1406	2465	1	chr2B.!!$F1	1059
13	TraesCS5B01G293200	chr3B	329570161	329571221	1060	False	1655	1655	94.816	1405	2465	1	chr3B.!!$F1	1060
14	TraesCS5B01G293200	chr6B	637647415	637648473	1058	True	1652	1652	94.811	1406	2465	1	chr6B.!!$R1	1059
15	TraesCS5B01G293200	chr5D	398331039	398331900	861	False	1182	1182	91.458	539	1406	1	chr5D.!!$F3	867
16	TraesCS5B01G293200	chr5D	398245076	398246357	1281	False	1157	1157	83.447	128	1406	1	chr5D.!!$F1	1278
17	TraesCS5B01G293200	chr5D	398324342	398324858	516	False	575	575	87.006	1	519	1	chr5D.!!$F2	518
18	TraesCS5B01G293200	chr5D	398482775	398483604	829	False	412	412	76.395	573	1406	1	chr5D.!!$F5	833

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
890	1006	0.179078	CCTGATCAGCCAGCTCTCAC	60.179	60.0	17.76	0.0	32.97	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2346	2476	0.482446	AAGGCATGGGTGAAAGTGGA	59.518	50.0	0.0	0.0	0.0	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
30	31	1.597663	GCACCAACTCCGTATATGCAC	59.402	52.381	0.00	0.00	0.00	4.57
155	158	0.319211	TCCGTGATGACGTTGTGACC	60.319	55.000	3.53	0.00	44.54	4.02
156	159	0.598942	CCGTGATGACGTTGTGACCA	60.599	55.000	3.53	0.00	44.54	4.02
176	182	5.366460	ACCATTGAGTTCTATCTGCATGAG	58.634	41.667	0.00	0.00	0.00	2.90
268	286	0.750911	GCATGGAGGAGAGGCAAAGG	60.751	60.000	0.00	0.00	0.00	3.11
320	339	2.739379	CAGCGGAGGAAAGAAGAAGAAC	59.261	50.000	0.00	0.00	0.00	3.01
340	365	1.867919	AACAGAGACGCGCTAGCTGT	61.868	55.000	13.93	12.36	41.19	4.40
395	434	2.272146	GCCGAGGAAATCTGCCCA	59.728	61.111	0.00	0.00	32.37	5.36
396	435	2.115291	GCCGAGGAAATCTGCCCAC	61.115	63.158	0.00	0.00	32.37	4.61
453	499	5.125900	CCATGGATCAATGAGCTTTACAACA	59.874	40.000	11.98	0.00	0.00	3.33
536	594	5.869344	GCCCTTTGTGACCTCATTTAAATTC	59.131	40.000	0.00	0.00	0.00	2.17
578	636	4.009370	AGTTCCTTGCTTAGTTCCACTC	57.991	45.455	0.00	0.00	0.00	3.51
672	742	3.530265	TTATCACGCGAGGTACCAAAT	57.470	42.857	15.93	0.00	0.00	2.32
704	778	8.121305	TGGTGACATGAGCAAAGTTTAATTAT	57.879	30.769	0.00	0.00	33.40	1.28
831	940	7.147976	CCTACACCATTTCTTTCTTTTCAAGG	58.852	38.462	0.00	0.00	0.00	3.61
890	1006	0.179078	CCTGATCAGCCAGCTCTCAC	60.179	60.000	17.76	0.00	32.97	3.51
991	1120	2.055042	ATCCTCGCCTCGCTTCAGT	61.055	57.895	0.00	0.00	0.00	3.41
1156	1285	2.419713	GCAGCCAATCTGTCTCATCAGA	60.420	50.000	0.00	0.00	46.39	3.27
1170	1299	1.561076	CATCAGATGGAGGTGTTGGGA	59.439	52.381	1.95	0.00	0.00	4.37
1194	1323	0.106369	ATGATGGTCATGGTGGCTGG	60.106	55.000	0.00	0.00	35.43	4.85
1282	1411	2.159327	TGATGATGCGGATGTGCTAG	57.841	50.000	0.00	0.00	35.36	3.42
1344	1473	2.995283	CTGGATGTGATCAGGAGCAAA	58.005	47.619	0.00	0.00	0.00	3.68
1459	1588	1.080093	TCCCGATCTGTGCGTCAAC	60.080	57.895	0.00	0.00	0.00	3.18
1606	1735	3.829601	CCACGAGATCCTAGAGGCTAAAT	59.170	47.826	0.00	0.00	34.44	1.40
1778	1907	0.756294	TTCCACGCAAAGGAGAGTCA	59.244	50.000	0.00	0.00	36.33	3.41
2015	2144	3.054434	ACTCAAATCATGTCCGGATCCAA	60.054	43.478	7.81	0.00	0.00	3.53
2072	2201	6.419710	ATGATATTTCACAAATGCAATCTGCG	59.580	34.615	0.00	0.00	39.68	5.18
2104	2233	6.647212	TTTCTGATGACGTGACATGTTATC	57.353	37.500	20.32	20.32	32.59	1.75
2160	2289	7.391554	CCACAACCAGCTATAATGCATATTACT	59.608	37.037	0.00	0.00	31.90	2.24
2179	2308	1.000955	CTAGGCGGTTTCTGTGACACT	59.999	52.381	7.20	0.00	0.00	3.55
2277	2406	0.965363	AATCGTGGCGCTTGGGAAAT	60.965	50.000	7.64	0.00	0.00	2.17
2346	2476	7.616313	CGCCTCTATAAAGGGATAAGATTTCT	58.384	38.462	0.00	0.00	36.88	2.52
2350	2480	9.936759	CTCTATAAAGGGATAAGATTTCTCCAC	57.063	37.037	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	95	8.252624	ACTTTTATTAAGTTTGGGGTGCTTTA	57.747	30.769	0.00	0.00	0.00	1.85
155	158	7.549615	TTTCTCATGCAGATAGAACTCAATG	57.450	36.000	7.47	0.00	0.00	2.82
156	159	8.571461	TTTTTCTCATGCAGATAGAACTCAAT	57.429	30.769	7.47	0.00	0.00	2.57
188	194	2.677914	TCTCCCTGATAAATCGGAGCA	58.322	47.619	8.33	0.00	35.13	4.26
211	225	9.692749	CGCTCATCAACCTATAAAAGTAGAATA	57.307	33.333	0.00	0.00	0.00	1.75
212	226	8.421784	TCGCTCATCAACCTATAAAAGTAGAAT	58.578	33.333	0.00	0.00	0.00	2.40
222	239	1.269723	CCGCTCGCTCATCAACCTATA	59.730	52.381	0.00	0.00	0.00	1.31
223	240	0.032678	CCGCTCGCTCATCAACCTAT	59.967	55.000	0.00	0.00	0.00	2.57
224	241	1.437573	CCGCTCGCTCATCAACCTA	59.562	57.895	0.00	0.00	0.00	3.08
225	242	2.185350	CCGCTCGCTCATCAACCT	59.815	61.111	0.00	0.00	0.00	3.50
268	286	5.836821	TCCTGTATGTGAGATCTGTGTAC	57.163	43.478	0.00	0.00	0.00	2.90
320	339	1.153939	AGCTAGCGCGTCTCTGTTG	60.154	57.895	9.55	0.00	42.32	3.33
340	365	2.874014	TGTGATTCATGCCCAAAGTCA	58.126	42.857	0.00	0.00	0.00	3.41
433	473	6.441093	TCATGTTGTAAAGCTCATTGATCC	57.559	37.500	0.00	0.00	0.00	3.36
453	499	4.164030	GGGTCCCAAATTGCCTTTAATCAT	59.836	41.667	1.78	0.00	0.00	2.45
578	636	6.478344	GGAGTGAGCACTATAAGAATGTTGAG	59.522	42.308	2.65	0.00	42.66	3.02
641	711	2.935849	TCGCGTGATAAAGCATGTGAAT	59.064	40.909	5.77	0.00	40.28	2.57
672	742	2.861274	TGCTCATGTCACCATCAAACA	58.139	42.857	0.00	0.00	0.00	2.83
704	778	0.978667	TGGGGATGCAACTAGCCGTA	60.979	55.000	0.00	0.00	44.83	4.02
831	940	1.661341	CAAGTAGTGGATGCCTCAGC	58.339	55.000	0.00	0.00	40.48	4.26
890	1006	5.412594	TCTTTCCGATCTTCATCTTTGTTGG	59.587	40.000	0.00	0.00	0.00	3.77
1058	1187	2.480416	GCCTTGTGATAGTCCAGTCTCG	60.480	54.545	0.00	0.00	0.00	4.04
1063	1192	3.119708	GCAAAAGCCTTGTGATAGTCCAG	60.120	47.826	0.00	0.00	0.00	3.86
1156	1285	1.444933	TCTTGTCCCAACACCTCCAT	58.555	50.000	0.00	0.00	34.35	3.41
1170	1299	2.947243	GCCACCATGACCATCATCTTGT	60.947	50.000	0.00	0.00	34.28	3.16
1194	1323	1.270305	TGTAGTGACCAGTCAGCTTGC	60.270	52.381	0.00	0.00	40.75	4.01
1261	1390	1.235724	AGCACATCCGCATCATCATG	58.764	50.000	0.00	0.00	0.00	3.07
1282	1411	1.083806	TCTTGATCGCACGCATCCAC	61.084	55.000	0.00	0.00	0.00	4.02
1344	1473	1.068121	CCAACCCCTCAACCTCTCTT	58.932	55.000	0.00	0.00	0.00	2.85
1422	1551	2.197875	CCCCTACCCGAGATCCGT	59.802	66.667	0.00	0.00	36.31	4.69
1459	1588	1.009829	GCTTCCTGTTACCATCAGCG	58.990	55.000	0.00	0.00	0.00	5.18
1594	1723	6.127730	GCTAGCTCTTAGGATTTAGCCTCTAG	60.128	46.154	7.70	0.00	39.50	2.43
1606	1735	4.202727	ACCATCATAGGCTAGCTCTTAGGA	60.203	45.833	15.72	12.06	0.00	2.94
1682	1811	1.229359	CCTAGCCCTCTCCGGTGTA	59.771	63.158	0.00	0.00	0.00	2.90
1740	1869	2.819595	GCAAGCTTGGCGATCCGA	60.820	61.111	27.10	0.00	34.14	4.55
2015	2144	5.009610	ACAGCGGTGTGTAAAGATCATTTTT	59.990	36.000	21.19	0.00	34.75	1.94
2072	2201	4.272504	TCACGTCATCAGAAAAAGTTGTCC	59.727	41.667	0.00	0.00	0.00	4.02
2104	2233	4.152402	GGTTCGAATAATGATCCGACCATG	59.848	45.833	0.00	0.00	0.00	3.66
2160	2289	1.045407	AGTGTCACAGAAACCGCCTA	58.955	50.000	5.62	0.00	0.00	3.93
2179	2308	3.742882	CACGATCTCTGCTTTGACAAGAA	59.257	43.478	0.00	0.00	30.57	2.52
2346	2476	0.482446	AAGGCATGGGTGAAAGTGGA	59.518	50.000	0.00	0.00	0.00	4.02
2350	2480	1.821136	GGAAGAAGGCATGGGTGAAAG	59.179	52.381	0.00	0.00	0.00	2.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.