AutoCloner

Multiple sequence alignment - TraesCS4D01G296100

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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	TraesCS4D01G296100	chr4D	100.000	2366	0	0	1	2366	465758588	465756223	0.000000e+00	4370
1	TraesCS4D01G296100	chr4D	91.541	331	24	3	93	420	472923970	472924299	9.970000e-124	453
2	TraesCS4D01G296100	chr4D	82.178	505	71	14	877	1369	504561986	504562483	1.310000e-112	416
3	TraesCS4D01G296100	chr4D	81.980	505	72	14	877	1369	504511513	504512010	6.090000e-111	411
4	TraesCS4D01G296100	chr4B	92.525	1418	78	12	453	1851	582752188	582750780	0.000000e+00	2006
5	TraesCS4D01G296100	chr4B	90.031	321	23	5	102	414	595270119	595270438	7.870000e-110	407
6	TraesCS4D01G296100	chr4B	81.600	500	73	11	877	1369	651147547	651148034	1.700000e-106	396
7	TraesCS4D01G296100	chr4A	88.952	1231	94	21	645	1856	4822620	4823827	0.000000e+00	1482
8	TraesCS4D01G296100	chr4A	94.907	432	16	3	1	430	4821914	4822341	0.000000e+00	671
9	TraesCS4D01G296100	chr4A	90.769	325	24	5	99	419	679973317	679973639	1.680000e-116	429
10	TraesCS4D01G296100	chr3D	99.023	512	5	0	1855	2366	141589526	141590037	0.000000e+00	918
11	TraesCS4D01G296100	chr3D	98.444	514	8	0	1853	2366	141358536	141359049	0.000000e+00	905
12	TraesCS4D01G296100	chr3D	99.200	500	4	0	1867	2366	141401619	141402118	0.000000e+00	902
13	TraesCS4D01G296100	chr3D	96.450	507	16	1	1862	2366	301338781	301338275	0.000000e+00	835
14	TraesCS4D01G296100	chr7D	97.656	512	8	2	1855	2366	39180742	39181249	0.000000e+00	876
15	TraesCS4D01G296100	chr7D	97.698	391	8	1	1977	2366	87186016	87186406	0.000000e+00	671
16	TraesCS4D01G296100	chr2A	94.358	514	26	2	1853	2366	766851828	766852338	0.000000e+00	785
17	TraesCS4D01G296100	chr2D	97.168	459	13	0	1908	2366	645888501	645888043	0.000000e+00	776
18	TraesCS4D01G296100	chr2D	93.200	250	12	4	1848	2095	466691672	466691426	1.730000e-96	363
19	TraesCS4D01G296100	chr7A	87.992	533	47	13	1846	2366	619557016	619557543	4.320000e-172	614
20	TraesCS4D01G296100	chr3A	86.500	400	33	10	1985	2366	192709526	192709922	1.010000e-113	420
21	TraesCS4D01G296100	chrUn	81.925	509	75	14	876	1368	394590822	394590315	4.700000e-112	414
22	TraesCS4D01G296100	chr5A	81.925	509	75	14	876	1368	689185635	689186142	4.700000e-112	414
23	TraesCS4D01G296100	chr5A	82.151	465	73	7	877	1335	689177284	689177744	7.930000e-105	390

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	TraesCS4D01G296100	chr4D	465756223	465758588	2365	True	4370.0	4370	100.0000	1	2366	1	chr4D.!!$R1	2365
1	TraesCS4D01G296100	chr4B	582750780	582752188	1408	True	2006.0	2006	92.5250	453	1851	1	chr4B.!!$R1	1398
2	TraesCS4D01G296100	chr4A	4821914	4823827	1913	False	1076.5	1482	91.9295	1	1856	2	chr4A.!!$F2	1855
3	TraesCS4D01G296100	chr3D	141589526	141590037	511	False	918.0	918	99.0230	1855	2366	1	chr3D.!!$F3	511
4	TraesCS4D01G296100	chr3D	141358536	141359049	513	False	905.0	905	98.4440	1853	2366	1	chr3D.!!$F1	513
5	TraesCS4D01G296100	chr3D	301338275	301338781	506	True	835.0	835	96.4500	1862	2366	1	chr3D.!!$R1	504
6	TraesCS4D01G296100	chr7D	39180742	39181249	507	False	876.0	876	97.6560	1855	2366	1	chr7D.!!$F1	511
7	TraesCS4D01G296100	chr2A	766851828	766852338	510	False	785.0	785	94.3580	1853	2366	1	chr2A.!!$F1	513
8	TraesCS4D01G296100	chr7A	619557016	619557543	527	False	614.0	614	87.9920	1846	2366	1	chr7A.!!$F1	520
9	TraesCS4D01G296100	chrUn	394590315	394590822	507	True	414.0	414	81.9250	876	1368	1	chrUn.!!$R1	492
10	TraesCS4D01G296100	chr5A	689185635	689186142	507	False	414.0	414	81.9250	876	1368	1	chr5A.!!$F2	492

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
828	1028	1.44714	CGCCGTTTCCTCCGATTGA	60.447	57.895	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1752	1974	1.669604	TTTGTGACTGGTTTGCGCTA	58.33	45.0	9.73	0.0	0.0	4.26	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
39	40	9.758651	ATTTATACTACTATGCATGTTCGTTGA	57.241	29.630	10.16	0.00	0.00	3.18
229	230	5.592282	TGGTTAGCAACTCAAACTTGATGAA	59.408	36.000	0.00	0.00	36.46	2.57
378	381	7.223971	TCAGAAATTGTGTGCTATATTCGTACC	59.776	37.037	0.00	0.00	0.00	3.34
388	391	8.080417	TGTGCTATATTCGTACCTATTTCTCAC	58.920	37.037	0.00	0.00	0.00	3.51
684	835	7.440198	CAAGAGTAATATCAGCCTTCAGATCA	58.560	38.462	0.00	0.00	0.00	2.92
685	836	7.230849	AGAGTAATATCAGCCTTCAGATCAG	57.769	40.000	0.00	0.00	0.00	2.90
686	837	6.211184	AGAGTAATATCAGCCTTCAGATCAGG	59.789	42.308	0.00	0.00	34.08	3.86
687	838	6.080682	AGTAATATCAGCCTTCAGATCAGGA	58.919	40.000	1.77	0.00	32.41	3.86
688	839	5.486735	AATATCAGCCTTCAGATCAGGAG	57.513	43.478	1.77	0.00	32.41	3.69
689	840	2.539432	TCAGCCTTCAGATCAGGAGA	57.461	50.000	1.77	0.00	32.41	3.71
690	841	2.825223	TCAGCCTTCAGATCAGGAGAA	58.175	47.619	1.77	0.00	32.41	2.87
691	842	3.176411	TCAGCCTTCAGATCAGGAGAAA	58.824	45.455	1.77	0.00	32.41	2.52
692	843	3.584406	TCAGCCTTCAGATCAGGAGAAAA	59.416	43.478	1.77	0.00	32.41	2.29
693	844	4.226846	TCAGCCTTCAGATCAGGAGAAAAT	59.773	41.667	1.77	0.00	32.41	1.82
694	845	5.426509	TCAGCCTTCAGATCAGGAGAAAATA	59.573	40.000	1.77	0.00	32.41	1.40
695	846	6.070021	TCAGCCTTCAGATCAGGAGAAAATAA	60.070	38.462	1.77	0.00	32.41	1.40
696	847	6.038050	CAGCCTTCAGATCAGGAGAAAATAAC	59.962	42.308	1.77	0.00	32.41	1.89
697	848	6.069731	AGCCTTCAGATCAGGAGAAAATAACT	60.070	38.462	1.77	0.00	32.41	2.24
698	849	6.601217	GCCTTCAGATCAGGAGAAAATAACTT	59.399	38.462	1.77	0.00	32.41	2.66
699	850	7.121907	GCCTTCAGATCAGGAGAAAATAACTTT	59.878	37.037	1.77	0.00	32.41	2.66
700	851	9.018582	CCTTCAGATCAGGAGAAAATAACTTTT	57.981	33.333	0.00	0.00	33.73	2.27
730	881	8.378565	TGAGACAAAGATCAGGAGAAAATAACT	58.621	33.333	0.00	0.00	0.00	2.24
828	1028	1.447140	CGCCGTTTCCTCCGATTGA	60.447	57.895	0.00	0.00	0.00	2.57
1029	1244	1.323271	CCTCGTCCTCAAGGCTGCTA	61.323	60.000	0.00	0.00	34.44	3.49
1100	1315	0.389166	GTGAGCTTCACGGTGGAGAG	60.389	60.000	20.60	10.92	37.67	3.20
1212	1427	2.431683	GAGTGGCAGCCCTTGACA	59.568	61.111	9.64	0.00	44.55	3.58
1381	1596	1.548081	TTGATCCTTCCGTCGGTGTA	58.452	50.000	11.88	0.00	0.00	2.90
1440	1657	4.749598	TCATTATCGTTGCATGTATTCGCT	59.250	37.500	0.00	0.00	0.00	4.93
1462	1679	5.518128	GCTCTCATGCGTGGATAATACATAG	59.482	44.000	5.98	0.00	0.00	2.23
1469	1686	6.327154	TGCGTGGATAATACATAGTTATCGG	58.673	40.000	0.00	0.00	38.72	4.18
1482	1699	0.601558	TTATCGGCGCCTATGAGGTC	59.398	55.000	26.68	0.00	37.80	3.85
1510	1727	1.825090	TACGGTAGGAGAAGCAACGA	58.175	50.000	0.00	0.00	0.00	3.85
1514	1731	0.458025	GTAGGAGAAGCAACGACGGG	60.458	60.000	0.00	0.00	0.00	5.28
1529	1746	1.966451	CGGGTGTGTTTGCTCTCCC	60.966	63.158	0.00	0.00	38.10	4.30
1537	1758	1.741401	TTTGCTCTCCCGTGCATCG	60.741	57.895	0.00	0.00	39.16	3.84
1549	1770	1.534805	CGTGCATCGACTGTCTATGCT	60.535	52.381	33.22	1.19	43.45	3.79
1589	1810	6.363577	TGTATCCGAATTTTGCTCAAGATC	57.636	37.500	0.00	0.00	0.00	2.75
1649	1870	9.294030	GATTTTGGCTATGTTTGATTCTACTTG	57.706	33.333	0.00	0.00	0.00	3.16
1784	2006	4.210537	CCAGTCACAAAACTAACTACCACG	59.789	45.833	0.00	0.00	0.00	4.94
1788	2010	6.594937	AGTCACAAAACTAACTACCACGAAAA	59.405	34.615	0.00	0.00	0.00	2.29
1815	2037	5.989777	AGGATATAAACATTCGGGAAAGTCG	59.010	40.000	0.00	0.00	0.00	4.18
1836	2058	5.179368	GTCGAGAACCATGTTCAATTTCTCA	59.821	40.000	9.42	0.00	41.47	3.27
2285	2522	3.386237	GAGTGCTGGGCCGAGACT	61.386	66.667	20.35	17.70	0.00	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	9.758651	AACGAACATGCATAGTAGTATAAATGA	57.241	29.630	0.00	0.00	0.00	2.57
18	19	7.892778	TTTTCAACGAACATGCATAGTAGTA	57.107	32.000	0.00	0.00	0.00	1.82
19	20	6.795098	TTTTCAACGAACATGCATAGTAGT	57.205	33.333	0.00	2.21	0.00	2.73
72	73	9.433153	TGTACTCTATTATACACCTGTATCTCG	57.567	37.037	1.09	0.00	41.18	4.04
155	156	7.832187	TGGCATTGACATGATGATATATCACAT	59.168	33.333	17.60	17.70	40.03	3.21
355	356	7.478520	AGGTACGAATATAGCACACAATTTC	57.521	36.000	0.00	0.00	0.00	2.17
388	391	7.688478	ATTTATGCAAATGATGTGACATTCG	57.312	32.000	0.00	0.00	39.19	3.34
538	689	3.199880	ACATGAAGGCCGATAAGGAAG	57.800	47.619	0.00	0.00	45.00	3.46
700	851	7.880160	TTTCTCCTGATCTTTGTCTCAAAAA	57.120	32.000	0.00	0.00	0.00	1.94
701	852	7.880160	TTTTCTCCTGATCTTTGTCTCAAAA	57.120	32.000	0.00	0.00	0.00	2.44
702	853	9.573166	TTATTTTCTCCTGATCTTTGTCTCAAA	57.427	29.630	0.00	0.00	0.00	2.69
703	854	9.003658	GTTATTTTCTCCTGATCTTTGTCTCAA	57.996	33.333	0.00	0.00	0.00	3.02
704	855	8.378565	AGTTATTTTCTCCTGATCTTTGTCTCA	58.621	33.333	0.00	0.00	0.00	3.27
705	856	8.663911	CAGTTATTTTCTCCTGATCTTTGTCTC	58.336	37.037	0.00	0.00	0.00	3.36
706	857	7.120432	GCAGTTATTTTCTCCTGATCTTTGTCT	59.880	37.037	0.00	0.00	0.00	3.41
707	858	7.120432	AGCAGTTATTTTCTCCTGATCTTTGTC	59.880	37.037	0.00	0.00	0.00	3.18
708	859	6.944862	AGCAGTTATTTTCTCCTGATCTTTGT	59.055	34.615	0.00	0.00	0.00	2.83
709	860	7.120285	TGAGCAGTTATTTTCTCCTGATCTTTG	59.880	37.037	0.00	0.00	40.16	2.77
710	861	7.170965	TGAGCAGTTATTTTCTCCTGATCTTT	58.829	34.615	0.00	0.00	40.16	2.52
711	862	6.715280	TGAGCAGTTATTTTCTCCTGATCTT	58.285	36.000	0.00	0.00	40.16	2.40
712	863	6.305272	TGAGCAGTTATTTTCTCCTGATCT	57.695	37.500	0.00	0.00	40.16	2.75
713	864	8.845413	ATATGAGCAGTTATTTTCTCCTGATC	57.155	34.615	0.00	0.00	39.97	2.92
714	865	8.435187	TGATATGAGCAGTTATTTTCTCCTGAT	58.565	33.333	0.00	0.00	0.00	2.90
715	866	7.795047	TGATATGAGCAGTTATTTTCTCCTGA	58.205	34.615	0.00	0.00	0.00	3.86
716	867	8.341173	GTTGATATGAGCAGTTATTTTCTCCTG	58.659	37.037	0.00	0.00	0.00	3.86
730	881	9.330063	CAATTAAGTCCTAAGTTGATATGAGCA	57.670	33.333	0.00	0.00	0.00	4.26
1085	1300	2.266055	CCCTCTCCACCGTGAAGC	59.734	66.667	0.00	0.00	0.00	3.86
1239	1454	1.673033	CCAACGAGGTCCTTGCTACAG	60.673	57.143	5.98	0.00	0.00	2.74
1381	1596	9.462606	AAGGGAAAACTTGAATCGACTAATAAT	57.537	29.630	0.00	0.00	0.00	1.28
1440	1657	6.590234	ACTATGTATTATCCACGCATGAGA	57.410	37.500	2.50	0.00	0.00	3.27
1462	1679	0.317479	ACCTCATAGGCGCCGATAAC	59.683	55.000	22.30	0.00	39.63	1.89
1469	1686	1.135460	GTATACGGACCTCATAGGCGC	60.135	57.143	0.00	0.00	39.63	6.53
1510	1727	1.227853	GGAGAGCAAACACACCCGT	60.228	57.895	0.00	0.00	0.00	5.28
1514	1731	1.941812	CACGGGAGAGCAAACACAC	59.058	57.895	0.00	0.00	0.00	3.82
1549	1770	4.753107	GGATACAAACGGAACAAGACTGAA	59.247	41.667	0.00	0.00	0.00	3.02
1615	1836	5.649782	AACATAGCCAAAATCAAGGTGAG	57.350	39.130	0.00	0.00	0.00	3.51
1649	1870	4.153475	TCTTGTATTGCGTTACCTCAAAGC	59.847	41.667	0.00	0.00	41.45	3.51
1743	1965	5.644206	TGACTGGTTTGCGCTAATATTAACA	59.356	36.000	9.73	2.90	0.00	2.41
1752	1974	1.669604	TTTGTGACTGGTTTGCGCTA	58.330	45.000	9.73	0.00	0.00	4.26
1784	2006	8.391075	TCCCGAATGTTTATATCCTCATTTTC	57.609	34.615	0.00	0.00	31.87	2.29
1788	2010	7.518188	ACTTTCCCGAATGTTTATATCCTCAT	58.482	34.615	0.00	0.00	0.00	2.90
1815	2037	7.149569	TCATGAGAAATTGAACATGGTTCTC	57.850	36.000	10.14	2.92	42.89	2.87
2112	2347	3.200825	AGAGTTCGAATCCCATTGTCCAT	59.799	43.478	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.