AutoCloner

Multiple sequence alignment - TraesCS5D01G465800

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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	TraesCS5D01G465800	chr5D	100.000	3053	0	0	1	3053	508518611	508521663	0.000000e+00	5638.0
1	TraesCS5D01G465800	chr5D	97.051	2509	63	5	556	3053	77002193	77004701	0.000000e+00	4213.0
2	TraesCS5D01G465800	chr5D	100.000	38	0	0	397	434	508518975	508519012	1.520000e-08	71.3
3	TraesCS5D01G465800	chr5D	100.000	38	0	0	365	402	508519007	508519044	1.520000e-08	71.3
4	TraesCS5D01G465800	chr3A	92.383	3072	179	32	2	3053	32183215	32180179	0.000000e+00	4325.0
5	TraesCS5D01G465800	chr6D	97.402	2502	55	4	562	3053	266791541	266789040	0.000000e+00	4252.0
6	TraesCS5D01G465800	chr6D	97.083	2503	65	3	559	3053	459053595	459056097	0.000000e+00	4211.0
7	TraesCS5D01G465800	chr2D	97.321	2501	59	4	560	3053	345860609	345863108	0.000000e+00	4241.0
8	TraesCS5D01G465800	chr2D	97.204	2504	55	6	560	3053	579180357	579182855	0.000000e+00	4222.0
9	TraesCS5D01G465800	chr3D	97.279	2499	62	2	561	3053	374976725	374974227	0.000000e+00	4233.0
10	TraesCS5D01G465800	chr3D	97.239	2499	62	3	562	3053	239610075	239607577	0.000000e+00	4226.0
11	TraesCS5D01G465800	chr3D	97.163	2503	61	4	561	3053	540242996	540245498	0.000000e+00	4220.0
12	TraesCS5D01G465800	chr4D	97.160	2500	61	4	564	3053	365416567	365419066	0.000000e+00	4215.0
13	TraesCS5D01G465800	chr6B	92.419	2625	172	11	454	3053	307117941	307115319	0.000000e+00	3720.0
14	TraesCS5D01G465800	chr6B	93.622	392	15	4	3	388	307118323	307117936	7.340000e-161	577.0
15	TraesCS5D01G465800	chr6B	93.151	219	12	3	3	219	123870398	123870181	4.910000e-83	318.0
16	TraesCS5D01G465800	chr6B	95.122	41	2	0	270	310	123869943	123869903	7.070000e-07	65.8
17	TraesCS5D01G465800	chr7A	94.045	403	18	5	3	401	365462514	365462114	9.360000e-170	606.0
18	TraesCS5D01G465800	chr5B	94.545	220	8	3	3	219	184778516	184778298	1.360000e-88	337.0
19	TraesCS5D01G465800	chr4A	94.495	218	10	2	3	219	521816536	521816752	4.880000e-88	335.0
20	TraesCS5D01G465800	chr4A	93.182	220	8	4	3	219	362070463	362070678	1.770000e-82	316.0
21	TraesCS5D01G465800	chr6A	93.151	219	12	3	3	219	66382549	66382766	4.910000e-83	318.0
22	TraesCS5D01G465800	chr6A	92.793	222	11	5	3	224	495139464	495139248	1.770000e-82	316.0

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	TraesCS5D01G465800	chr5D	508518611	508521663	3052	False	1926.866667	5638	100.0000	1	3053	3	chr5D.!!$F2	3052
1	TraesCS5D01G465800	chr5D	77002193	77004701	2508	False	4213.000000	4213	97.0510	556	3053	1	chr5D.!!$F1	2497
2	TraesCS5D01G465800	chr3A	32180179	32183215	3036	True	4325.000000	4325	92.3830	2	3053	1	chr3A.!!$R1	3051
3	TraesCS5D01G465800	chr6D	266789040	266791541	2501	True	4252.000000	4252	97.4020	562	3053	1	chr6D.!!$R1	2491
4	TraesCS5D01G465800	chr6D	459053595	459056097	2502	False	4211.000000	4211	97.0830	559	3053	1	chr6D.!!$F1	2494
5	TraesCS5D01G465800	chr2D	345860609	345863108	2499	False	4241.000000	4241	97.3210	560	3053	1	chr2D.!!$F1	2493
6	TraesCS5D01G465800	chr2D	579180357	579182855	2498	False	4222.000000	4222	97.2040	560	3053	1	chr2D.!!$F2	2493
7	TraesCS5D01G465800	chr3D	374974227	374976725	2498	True	4233.000000	4233	97.2790	561	3053	1	chr3D.!!$R2	2492
8	TraesCS5D01G465800	chr3D	239607577	239610075	2498	True	4226.000000	4226	97.2390	562	3053	1	chr3D.!!$R1	2491
9	TraesCS5D01G465800	chr3D	540242996	540245498	2502	False	4220.000000	4220	97.1630	561	3053	1	chr3D.!!$F1	2492
10	TraesCS5D01G465800	chr4D	365416567	365419066	2499	False	4215.000000	4215	97.1600	564	3053	1	chr4D.!!$F1	2489
11	TraesCS5D01G465800	chr6B	307115319	307118323	3004	True	2148.500000	3720	93.0205	3	3053	2	chr6B.!!$R2	3050

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
381	390	0.035317	TGTGCTAGCTGTGTTCCTGG	59.965	55.0	17.23	0.0	0.0	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2345	2386	0.834687	GGAGCCGGACCCCATACATA	60.835	60.0	5.05	0.0	0.0	2.29	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
99	108	3.624777	CCTCATGGGAATACAAGTTGCT	58.375	45.455	1.81	0.00	37.23	3.91
119	128	9.914834	AGTTGCTTATTCCTAACATGGTATTAA	57.085	29.630	0.00	0.00	0.00	1.40
130	139	5.727243	ACATGGTATTAAAGCCTTAGGGT	57.273	39.130	0.00	0.00	33.45	4.34
169	178	1.478510	ACTCGTGCTCTCGATCCAATT	59.521	47.619	0.00	0.00	39.12	2.32
272	281	4.079850	CGTCAGCAGCTCCAGCCT	62.080	66.667	0.00	0.00	43.38	4.58
349	358	3.506096	CGTAGACTCCGCCTCGCA	61.506	66.667	0.00	0.00	0.00	5.10
381	390	0.035317	TGTGCTAGCTGTGTTCCTGG	59.965	55.000	17.23	0.00	0.00	4.45
382	391	0.035458	GTGCTAGCTGTGTTCCTGGT	59.965	55.000	17.23	0.00	0.00	4.00
383	392	0.035317	TGCTAGCTGTGTTCCTGGTG	59.965	55.000	17.23	0.00	0.00	4.17
384	393	1.301677	GCTAGCTGTGTTCCTGGTGC	61.302	60.000	7.70	0.00	0.00	5.01
385	394	0.322975	CTAGCTGTGTTCCTGGTGCT	59.677	55.000	0.00	0.00	34.92	4.40
386	395	0.035317	TAGCTGTGTTCCTGGTGCTG	59.965	55.000	0.00	0.00	32.72	4.41
387	396	2.263741	GCTGTGTTCCTGGTGCTGG	61.264	63.158	0.00	0.00	0.00	4.85
388	397	1.451504	CTGTGTTCCTGGTGCTGGA	59.548	57.895	0.00	0.00	0.00	3.86
389	398	0.037303	CTGTGTTCCTGGTGCTGGAT	59.963	55.000	0.00	0.00	31.78	3.41
390	399	0.478072	TGTGTTCCTGGTGCTGGATT	59.522	50.000	0.00	0.00	31.78	3.01
391	400	1.168714	GTGTTCCTGGTGCTGGATTC	58.831	55.000	0.00	0.00	31.78	2.52
392	401	0.038166	TGTTCCTGGTGCTGGATTCC	59.962	55.000	0.00	0.00	31.78	3.01
393	402	0.329596	GTTCCTGGTGCTGGATTCCT	59.670	55.000	3.95	0.00	31.78	3.36
394	403	1.075601	TTCCTGGTGCTGGATTCCTT	58.924	50.000	3.95	0.00	31.78	3.36
395	404	1.075601	TCCTGGTGCTGGATTCCTTT	58.924	50.000	3.95	0.00	0.00	3.11
396	405	1.428912	TCCTGGTGCTGGATTCCTTTT	59.571	47.619	3.95	0.00	0.00	2.27
397	406	1.547372	CCTGGTGCTGGATTCCTTTTG	59.453	52.381	3.95	0.00	0.00	2.44
398	407	0.968405	TGGTGCTGGATTCCTTTTGC	59.032	50.000	3.95	4.26	0.00	3.68
399	408	1.260544	GGTGCTGGATTCCTTTTGCT	58.739	50.000	3.95	0.00	0.00	3.91
400	409	2.224992	TGGTGCTGGATTCCTTTTGCTA	60.225	45.455	3.95	0.00	0.00	3.49
401	410	2.424956	GGTGCTGGATTCCTTTTGCTAG	59.575	50.000	3.95	0.00	0.00	3.42
402	411	2.094675	TGCTGGATTCCTTTTGCTAGC	58.905	47.619	8.10	8.10	0.00	3.42
403	412	2.291153	TGCTGGATTCCTTTTGCTAGCT	60.291	45.455	17.23	0.00	0.00	3.32
404	413	2.098770	GCTGGATTCCTTTTGCTAGCTG	59.901	50.000	17.23	3.61	0.00	4.24
405	414	3.350833	CTGGATTCCTTTTGCTAGCTGT	58.649	45.455	17.23	0.00	0.00	4.40
406	415	3.084039	TGGATTCCTTTTGCTAGCTGTG	58.916	45.455	17.23	3.61	0.00	3.66
407	416	3.084786	GGATTCCTTTTGCTAGCTGTGT	58.915	45.455	17.23	0.00	0.00	3.72
418	427	0.035317	TAGCTGTGTTCCTGGTGCTG	59.965	55.000	0.00	0.00	32.72	4.41
517	527	2.508751	GGCCGGATCCCACCTCTAC	61.509	68.421	5.05	0.00	0.00	2.59
558	584	0.105593	GATTGCCTGCTCGGATCTCA	59.894	55.000	0.00	0.00	33.16	3.27
609	636	0.179234	TTGTTGTTCCTCGCTGTCCA	59.821	50.000	0.00	0.00	0.00	4.02
839	866	3.129109	CTGCTGATCGTGCTTATGATGT	58.871	45.455	11.02	0.00	0.00	3.06
943	970	1.079819	GCCGCAGCTGTTCTCACTA	60.080	57.895	16.64	0.00	35.50	2.74
995	1022	4.669866	TTCTGGGTCTTCCTACTGTCTA	57.330	45.455	0.00	0.00	36.20	2.59
1186	1213	1.599518	CGTACTTGCCCCTGTTGCA	60.600	57.895	0.00	0.00	36.84	4.08
1283	1310	0.657312	CGTGCTCAGTTGTTTGCTCA	59.343	50.000	0.00	0.00	0.00	4.26
1303	1330	3.387699	TCATGGCCGTATTTCTCTCATGA	59.612	43.478	0.00	0.00	37.68	3.07
1402	1429	0.685097	TCGGGTTTCTTCCACTCCAG	59.315	55.000	0.00	0.00	0.00	3.86
1406	1433	1.202818	GGTTTCTTCCACTCCAGCTGT	60.203	52.381	13.81	0.00	0.00	4.40
1517	1544	5.163488	ACTGCAACAATGATGGTCATATTGG	60.163	40.000	13.97	5.82	35.76	3.16
1642	1669	6.609212	TGAGCAGGATATTCTGAGACTTAAGT	59.391	38.462	15.70	8.13	36.93	2.24
1878	1905	4.220821	CCACTTTCTGTTGCTAGTAGAGGA	59.779	45.833	0.00	0.00	0.00	3.71
1913	1949	6.126863	TCCTTATTCTGTTCCTGATGTTGT	57.873	37.500	0.00	0.00	0.00	3.32
2014	2050	3.648067	TGACTCTTGTTCTGTCCAGGATT	59.352	43.478	0.00	0.00	0.00	3.01
2302	2343	7.112122	AGCAGATTCAGTTACCATATTCACAA	58.888	34.615	0.00	0.00	0.00	3.33
2345	2386	5.581085	CGTCCTTTCGATTTAGTCCATTCTT	59.419	40.000	0.00	0.00	0.00	2.52
2584	2625	1.891919	GCGTGGTGTCCTTGCTGAA	60.892	57.895	0.00	0.00	0.00	3.02
2615	2656	2.496899	TGCCCAATTCTCTTGTCCTC	57.503	50.000	0.00	0.00	0.00	3.71
3008	3050	4.038042	AGACGTGACTTTTGATGAGTCTCA	59.962	41.667	4.68	4.68	43.07	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	4.601406	TGCAGGAAACCCCTTATACAAT	57.399	40.909	0.00	0.00	44.85	2.71
99	108	9.930158	AAGGCTTTAATACCATGTTAGGAATAA	57.070	29.630	0.00	0.00	0.00	1.40
169	178	4.728102	CGGCTGCGTGGACGGTAA	62.728	66.667	0.71	0.00	40.23	2.85
349	358	4.722700	GCACACCCACGGCTCCAT	62.723	66.667	0.00	0.00	0.00	3.41
381	390	2.159324	GCTAGCAAAAGGAATCCAGCAC	60.159	50.000	10.63	0.00	0.00	4.40
382	391	2.094675	GCTAGCAAAAGGAATCCAGCA	58.905	47.619	10.63	0.00	0.00	4.41
383	392	2.098770	CAGCTAGCAAAAGGAATCCAGC	59.901	50.000	18.83	0.00	0.00	4.85
384	393	3.128242	CACAGCTAGCAAAAGGAATCCAG	59.872	47.826	18.83	0.00	0.00	3.86
385	394	3.084039	CACAGCTAGCAAAAGGAATCCA	58.916	45.455	18.83	0.00	0.00	3.41
386	395	3.084786	ACACAGCTAGCAAAAGGAATCC	58.915	45.455	18.83	0.00	0.00	3.01
387	396	4.379918	GGAACACAGCTAGCAAAAGGAATC	60.380	45.833	18.83	4.53	0.00	2.52
388	397	3.507622	GGAACACAGCTAGCAAAAGGAAT	59.492	43.478	18.83	0.00	0.00	3.01
389	398	2.884639	GGAACACAGCTAGCAAAAGGAA	59.115	45.455	18.83	0.00	0.00	3.36
390	399	2.106511	AGGAACACAGCTAGCAAAAGGA	59.893	45.455	18.83	0.00	0.00	3.36
391	400	2.227388	CAGGAACACAGCTAGCAAAAGG	59.773	50.000	18.83	3.95	0.00	3.11
392	401	2.227388	CCAGGAACACAGCTAGCAAAAG	59.773	50.000	18.83	6.22	0.00	2.27
393	402	2.229792	CCAGGAACACAGCTAGCAAAA	58.770	47.619	18.83	0.00	0.00	2.44
394	403	1.142870	ACCAGGAACACAGCTAGCAAA	59.857	47.619	18.83	0.00	0.00	3.68
395	404	0.764890	ACCAGGAACACAGCTAGCAA	59.235	50.000	18.83	0.00	0.00	3.91
396	405	0.035317	CACCAGGAACACAGCTAGCA	59.965	55.000	18.83	0.00	0.00	3.49
397	406	1.301677	GCACCAGGAACACAGCTAGC	61.302	60.000	6.62	6.62	0.00	3.42
398	407	0.322975	AGCACCAGGAACACAGCTAG	59.677	55.000	0.00	0.00	0.00	3.42
399	408	0.035317	CAGCACCAGGAACACAGCTA	59.965	55.000	0.00	0.00	0.00	3.32
400	409	1.228063	CAGCACCAGGAACACAGCT	60.228	57.895	0.00	0.00	0.00	4.24
401	410	2.263741	CCAGCACCAGGAACACAGC	61.264	63.158	0.00	0.00	0.00	4.40
402	411	0.037303	ATCCAGCACCAGGAACACAG	59.963	55.000	0.00	0.00	38.93	3.66
403	412	0.478072	AATCCAGCACCAGGAACACA	59.522	50.000	0.00	0.00	38.93	3.72
404	413	1.168714	GAATCCAGCACCAGGAACAC	58.831	55.000	0.00	0.00	38.93	3.32
405	414	0.038166	GGAATCCAGCACCAGGAACA	59.962	55.000	0.00	0.00	38.93	3.18
406	415	0.329596	AGGAATCCAGCACCAGGAAC	59.670	55.000	0.61	0.00	38.93	3.62
407	416	1.075601	AAGGAATCCAGCACCAGGAA	58.924	50.000	0.61	0.00	38.93	3.36
438	447	0.738762	CACACAGCTAGCGCACTCAT	60.739	55.000	11.47	0.00	39.10	2.90
609	636	8.251721	GTGTAGTTAGTACCATCAAAGATCACT	58.748	37.037	0.00	0.00	0.00	3.41
839	866	2.647299	TCCTCATAAGCCAAAACCCTCA	59.353	45.455	0.00	0.00	0.00	3.86
943	970	3.733337	CAAACTGAGGCAGAACACTAGT	58.267	45.455	0.82	0.00	35.18	2.57
995	1022	2.167281	CGAAGACAGGTCCACATCTGAT	59.833	50.000	0.00	0.00	35.20	2.90
1283	1310	4.384056	CTTCATGAGAGAAATACGGCCAT	58.616	43.478	2.24	0.00	0.00	4.40
1303	1330	1.338200	ACGAATCTCTGAAAGCGCCTT	60.338	47.619	2.29	0.00	0.00	4.35
1406	1433	2.361104	GAGAATGGGGCGGTGCAA	60.361	61.111	0.00	0.00	0.00	4.08
1517	1544	1.523758	CTTTGTGTAGCACTGGGACC	58.476	55.000	0.90	0.00	35.11	4.46
1878	1905	6.380079	ACAGAATAAGGAGTGGAAAGATGT	57.620	37.500	0.00	0.00	0.00	3.06
1913	1949	4.221924	TCATGGTAAGTCGAGGAACATGAA	59.778	41.667	15.83	4.31	39.90	2.57
2014	2050	3.268603	CCAAGTGTGCGTGCGACA	61.269	61.111	0.00	0.00	0.00	4.35
2302	2343	2.623889	ACGCTTAGACACTGACTCACTT	59.376	45.455	0.00	0.00	0.00	3.16
2345	2386	0.834687	GGAGCCGGACCCCATACATA	60.835	60.000	5.05	0.00	0.00	2.29
2615	2656	0.656259	CCATTCTGAGCATGAGCACG	59.344	55.000	0.00	0.00	45.49	5.34
2827	2868	1.816224	ACACAACCAAACAAGCGAAGT	59.184	42.857	0.00	0.00	0.00	3.01
3008	3050	0.912487	TGGGCGTGGGTAGAAAGGAT	60.912	55.000	0.00	0.00	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.