AutoCloner

Multiple sequence alignment - TraesCS2D01G395700

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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	TraesCS2D01G395700	chr2D	100.000	3921	0	0	1	3921	506793960	506790040	0.000000e+00	7241
1	TraesCS2D01G395700	chr2D	84.055	878	117	13	3065	3921	605371402	605370527	0.000000e+00	824
2	TraesCS2D01G395700	chr2B	95.207	3964	113	35	1	3921	594848176	594844247	0.000000e+00	6196
3	TraesCS2D01G395700	chr2B	83.827	878	118	17	3065	3921	735521449	735520575	0.000000e+00	813
4	TraesCS2D01G395700	chr2A	93.910	3957	144	56	1	3921	651611201	651607306	0.000000e+00	5882
5	TraesCS2D01G395700	chr2A	84.510	878	112	15	3065	3921	736549563	736548689	0.000000e+00	846
6	TraesCS2D01G395700	chr3D	74.454	779	162	34	1663	2425	310683051	310683808	6.370000e-78	302
7	TraesCS2D01G395700	chr3A	74.041	782	160	39	1663	2425	421720831	421720074	2.980000e-71	279
8	TraesCS2D01G395700	chr3B	74.013	785	155	39	1663	2425	410774953	410774196	1.390000e-69	274

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	TraesCS2D01G395700	chr2D	506790040	506793960	3920	True	7241	7241	100.000	1	3921	1	chr2D.!!$R1	3920
1	TraesCS2D01G395700	chr2D	605370527	605371402	875	True	824	824	84.055	3065	3921	1	chr2D.!!$R2	856
2	TraesCS2D01G395700	chr2B	594844247	594848176	3929	True	6196	6196	95.207	1	3921	1	chr2B.!!$R1	3920
3	TraesCS2D01G395700	chr2B	735520575	735521449	874	True	813	813	83.827	3065	3921	1	chr2B.!!$R2	856
4	TraesCS2D01G395700	chr2A	651607306	651611201	3895	True	5882	5882	93.910	1	3921	1	chr2A.!!$R1	3920
5	TraesCS2D01G395700	chr2A	736548689	736549563	874	True	846	846	84.510	3065	3921	1	chr2A.!!$R2	856
6	TraesCS2D01G395700	chr3D	310683051	310683808	757	False	302	302	74.454	1663	2425	1	chr3D.!!$F1	762
7	TraesCS2D01G395700	chr3A	421720074	421720831	757	True	279	279	74.041	1663	2425	1	chr3A.!!$R1	762
8	TraesCS2D01G395700	chr3B	410774196	410774953	757	True	274	274	74.013	1663	2425	1	chr3B.!!$R1	762

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	Hairpin	End Stability	Orientation
131	135	0.034380	ATCAGGAGGAACGAGACCGA	60.034	55.000	39.5	4.69	F
980	1007	0.535780	CACCTGAGTTCTTGCTGCCA	60.536	55.000	0.0	4.92	F
1602	1632	0.036388	TCTTGTCCTTGCCGATCACC	60.036	55.000	0.0	4.02	F
1609	1639	0.379669	CTTGCCGATCACCATGAAGC	59.620	55.000	0.0	3.86	F
1615	1645	1.063616	CGATCACCATGAAGCTGCAAG	59.936	52.381	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1219	1246	3.211963	GTCCATGCCCATCACCGC	61.212	66.667	0.00	0.00	5.68	R
2557	2609	0.244450	TCGTCATGGGGAACGTGTAC	59.756	55.000	4.80	37.38	2.90	R
2704	2756	1.446099	CGAGCGCCAGTAGAAAGCA	60.446	57.895	2.29	0.00	3.91	R
2707	2759	1.446099	CAGCGAGCGCCAGTAGAAA	60.446	57.895	11.66	43.17	2.52	R
3507	3618	2.517166	GAAGGGGAGAATGCGGCC	60.517	66.667	0.00	0.00	6.13	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
66	68	3.440173	TCTTAGGCTTAGCACATGTTTGC	59.560	43.478	6.53	0.00	43.34	3.68
95	99	7.663043	TCCACACCACACACATACTTATATA	57.337	36.000	0.00	0.00	0.00	0.86
96	100	7.494211	TCCACACCACACACATACTTATATAC	58.506	38.462	0.00	0.00	0.00	1.47
98	102	7.418597	CCACACCACACACATACTTATATACCT	60.419	40.741	0.00	0.00	0.00	3.08
99	103	7.985184	CACACCACACACATACTTATATACCTT	59.015	37.037	0.00	0.00	0.00	3.50
100	104	8.545472	ACACCACACACATACTTATATACCTTT	58.455	33.333	0.00	0.00	0.00	3.11
101	105	8.826710	CACCACACACATACTTATATACCTTTG	58.173	37.037	0.00	0.00	0.00	2.77
131	135	0.034380	ATCAGGAGGAACGAGACCGA	60.034	55.000	0.00	0.00	39.50	4.69
140	144	4.554163	CGAGACCGAAAACTCGCT	57.446	55.556	0.00	0.00	46.54	4.93
210	226	1.000396	GCAGTTCAATCAGGGCCCT	60.000	57.895	22.28	22.28	0.00	5.19
213	229	0.909610	AGTTCAATCAGGGCCCTCGA	60.910	55.000	25.77	23.11	0.00	4.04
215	231	1.910580	TTCAATCAGGGCCCTCGACC	61.911	60.000	25.77	0.00	0.00	4.79
243	259	1.146041	AGCTCCACGCAGACAACAA	59.854	52.632	0.00	0.00	42.61	2.83
379	395	2.328819	ATGCTGGAAGATGACTGAGC	57.671	50.000	0.00	0.00	34.07	4.26
473	489	2.224354	CCCATCTGCCAGTTTTTGCTTT	60.224	45.455	0.00	0.00	0.00	3.51
495	511	6.811253	TTATGTTTTTACGCCATCTGAACT	57.189	33.333	0.00	0.00	0.00	3.01
496	512	4.742438	TGTTTTTACGCCATCTGAACTC	57.258	40.909	0.00	0.00	0.00	3.01
502	518	1.135373	ACGCCATCTGAACTCGTAGTG	60.135	52.381	0.79	0.00	0.00	2.74
503	519	1.799181	CGCCATCTGAACTCGTAGTGG	60.799	57.143	0.00	0.00	0.00	4.00
505	521	2.353803	GCCATCTGAACTCGTAGTGGTT	60.354	50.000	0.00	0.00	0.00	3.67
507	523	4.315803	CCATCTGAACTCGTAGTGGTTTT	58.684	43.478	0.00	0.00	0.00	2.43
508	524	4.389077	CCATCTGAACTCGTAGTGGTTTTC	59.611	45.833	0.00	0.00	0.00	2.29
510	526	4.617959	TCTGAACTCGTAGTGGTTTTCTG	58.382	43.478	0.00	0.00	0.00	3.02
519	539	4.500887	CGTAGTGGTTTTCTGGTTCTGAGA	60.501	45.833	0.00	0.00	0.00	3.27
723	749	1.676635	CACACCCAGTGGATGCCAG	60.677	63.158	11.95	0.00	44.69	4.85
980	1007	0.535780	CACCTGAGTTCTTGCTGCCA	60.536	55.000	0.00	0.00	0.00	4.92
983	1010	1.093159	CTGAGTTCTTGCTGCCATCC	58.907	55.000	0.00	0.00	0.00	3.51
1515	1542	0.605589	CTCTCAACAAGAGCGTCCCT	59.394	55.000	0.00	0.00	44.95	4.20
1602	1632	0.036388	TCTTGTCCTTGCCGATCACC	60.036	55.000	0.00	0.00	0.00	4.02
1607	1637	0.617935	TCCTTGCCGATCACCATGAA	59.382	50.000	0.00	0.00	0.00	2.57
1608	1638	1.019673	CCTTGCCGATCACCATGAAG	58.980	55.000	0.00	0.00	0.00	3.02
1609	1639	0.379669	CTTGCCGATCACCATGAAGC	59.620	55.000	0.00	0.00	0.00	3.86
1615	1645	1.063616	CGATCACCATGAAGCTGCAAG	59.936	52.381	0.00	0.00	0.00	4.01
2296	2331	3.736224	CCCATGGAGCTGCACCCT	61.736	66.667	15.22	0.46	0.00	4.34
2638	2690	1.447489	CTTCACGAGCAGAGCCCTG	60.447	63.158	0.00	0.00	43.22	4.45
2704	2756	2.125912	GTGTCGACGCTCCTGCAT	60.126	61.111	21.55	0.00	39.64	3.96
2707	2759	3.763356	TCGACGCTCCTGCATGCT	61.763	61.111	20.33	0.00	39.64	3.79
2926	2978	7.784470	AGAGGAGAAAACAGACTAGTTGTAT	57.216	36.000	0.00	0.00	0.00	2.29
2927	2979	8.880991	AGAGGAGAAAACAGACTAGTTGTATA	57.119	34.615	0.00	0.00	0.00	1.47
2928	2980	9.482175	AGAGGAGAAAACAGACTAGTTGTATAT	57.518	33.333	0.00	0.00	0.00	0.86
2962	3014	6.072728	TGTGTGATTAAACAGCATTACAGGAC	60.073	38.462	0.00	0.00	0.00	3.85
2964	3016	6.714810	TGTGATTAAACAGCATTACAGGACTT	59.285	34.615	0.00	0.00	0.00	3.01
3084	3169	7.214467	AGAGCTGTACATCTCTTAGCTTATC	57.786	40.000	20.87	2.81	44.11	1.75
3507	3618	4.376146	GAGGCAGTAGCTTCTCATTTAGG	58.624	47.826	0.00	0.00	43.00	2.69
3654	3765	7.993183	CCACTCCATATTGTTATACCTTTGTCT	59.007	37.037	0.00	0.00	0.00	3.41
3669	3780	3.819564	TTGTCTGTGTAGCACTTCACT	57.180	42.857	8.58	0.00	35.11	3.41
3761	3876	1.362932	AGGTATGTCCTGACCAGTCCT	59.637	52.381	0.00	0.00	46.19	3.85
3762	3877	1.482593	GGTATGTCCTGACCAGTCCTG	59.517	57.143	0.00	0.00	35.65	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	5.366482	TGCCTTTAGAACATACCTGCATA	57.634	39.130	0.00	0.00	0.00	3.14
66	68	5.245531	AGTATGTGTGTGGTGTGGAAATAG	58.754	41.667	0.00	0.00	0.00	1.73
95	99	6.715264	CCTCCTGATTAACAGTAAACAAAGGT	59.285	38.462	0.00	0.00	44.40	3.50
96	100	6.940298	TCCTCCTGATTAACAGTAAACAAAGG	59.060	38.462	0.00	0.00	44.40	3.11
98	102	7.041644	CGTTCCTCCTGATTAACAGTAAACAAA	60.042	37.037	0.00	0.00	44.40	2.83
99	103	6.425721	CGTTCCTCCTGATTAACAGTAAACAA	59.574	38.462	0.00	0.00	44.40	2.83
100	104	5.929992	CGTTCCTCCTGATTAACAGTAAACA	59.070	40.000	0.00	0.00	44.40	2.83
101	105	6.161381	TCGTTCCTCCTGATTAACAGTAAAC	58.839	40.000	0.00	0.00	44.40	2.01
140	144	4.302455	CTGCTCTTTTCTCTCTTTCGTCA	58.698	43.478	0.00	0.00	0.00	4.35
379	395	4.728534	TGTTTCTCCACGACAACAAAAAG	58.271	39.130	0.00	0.00	0.00	2.27
473	489	5.062934	CGAGTTCAGATGGCGTAAAAACATA	59.937	40.000	0.00	0.00	0.00	2.29
495	511	3.385433	TCAGAACCAGAAAACCACTACGA	59.615	43.478	0.00	0.00	0.00	3.43
496	512	3.724374	TCAGAACCAGAAAACCACTACG	58.276	45.455	0.00	0.00	0.00	3.51
502	518	4.389374	TGTGATCTCAGAACCAGAAAACC	58.611	43.478	0.00	0.00	0.00	3.27
503	519	5.618640	GCATGTGATCTCAGAACCAGAAAAC	60.619	44.000	3.58	0.00	0.00	2.43
505	521	4.005650	GCATGTGATCTCAGAACCAGAAA	58.994	43.478	3.58	0.00	0.00	2.52
507	523	2.093288	GGCATGTGATCTCAGAACCAGA	60.093	50.000	3.58	0.00	0.00	3.86
508	524	2.286872	GGCATGTGATCTCAGAACCAG	58.713	52.381	3.58	0.00	0.00	4.00
510	526	2.408271	TGGCATGTGATCTCAGAACC	57.592	50.000	3.58	5.33	0.00	3.62
519	539	0.324645	GAACCCCCTTGGCATGTGAT	60.325	55.000	0.00	0.00	37.83	3.06
703	729	2.034687	GCATCCACTGGGTGTGCT	59.965	61.111	10.18	0.00	44.92	4.40
769	796	0.467474	CATGGATCACTGCCAGCCAT	60.467	55.000	0.00	0.00	39.11	4.40
780	807	1.971505	GCCGAGGACACCATGGATCA	61.972	60.000	21.47	0.00	0.00	2.92
918	945	1.862201	CGTCCAGCGCCGATATAAAAA	59.138	47.619	2.29	0.00	0.00	1.94
980	1007	1.467678	CCCGCAGCTAGCTACTGGAT	61.468	60.000	18.86	0.00	42.61	3.41
983	1010	0.319383	CATCCCGCAGCTAGCTACTG	60.319	60.000	18.86	8.27	42.61	2.74
1219	1246	3.211963	GTCCATGCCCATCACCGC	61.212	66.667	0.00	0.00	0.00	5.68
1602	1632	5.296035	TCAGTATGATTCTTGCAGCTTCATG	59.704	40.000	5.29	0.00	42.56	3.07
2296	2331	2.159099	GGCGATGAACATGGAGTAGACA	60.159	50.000	0.00	0.00	0.00	3.41
2468	2503	4.312443	TGAATCGAAAGGTGGTACAAGAC	58.688	43.478	0.00	0.00	44.16	3.01
2557	2609	0.244450	TCGTCATGGGGAACGTGTAC	59.756	55.000	4.80	0.00	37.38	2.90
2704	2756	1.446099	CGAGCGCCAGTAGAAAGCA	60.446	57.895	2.29	0.00	0.00	3.91
2707	2759	1.446099	CAGCGAGCGCCAGTAGAAA	60.446	57.895	11.66	0.00	43.17	2.52
2785	2837	2.852075	TTCCTCCCCTTGCCGTGT	60.852	61.111	0.00	0.00	0.00	4.49
3177	3264	5.284079	ACATTTCATCAGTTGTTCAACAGC	58.716	37.500	16.31	0.00	0.00	4.40
3507	3618	2.517166	GAAGGGGAGAATGCGGCC	60.517	66.667	0.00	0.00	0.00	6.13
3654	3765	2.100087	TGAACGAGTGAAGTGCTACACA	59.900	45.455	0.00	0.00	39.18	3.72
3669	3780	3.738982	AGAATGTGTTGGACATGAACGA	58.261	40.909	0.00	0.00	45.12	3.85
3761	3876	5.187381	ACAATCATTTACAATGTGCCATCCA	59.813	36.000	0.00	0.00	0.00	3.41
3762	3877	5.663456	ACAATCATTTACAATGTGCCATCC	58.337	37.500	0.00	0.00	0.00	3.51
3763	3878	6.036300	CCAACAATCATTTACAATGTGCCATC	59.964	38.462	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.