AutoCloner

Multiple sequence alignment - TraesCS2D01G289900

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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	TraesCS2D01G289900	chr2D	100.000	3251	0	0	1	3251	372016867	372013617	0.000000e+00	6004.0
1	TraesCS2D01G289900	chr2D	87.962	1163	113	18	1062	2209	372224105	372225255	0.000000e+00	1347.0
2	TraesCS2D01G289900	chr2D	86.441	59	6	2	3189	3245	618179671	618179613	2.710000e-06	63.9
3	TraesCS2D01G289900	chr2B	93.729	2982	135	22	1	2949	441481384	441478422	0.000000e+00	4423.0
4	TraesCS2D01G289900	chr2B	88.306	1163	109	18	1062	2209	441792712	441793862	0.000000e+00	1369.0
5	TraesCS2D01G289900	chr2B	92.683	41	3	0	3211	3251	754740982	754740942	3.500000e-05	60.2
6	TraesCS2D01G289900	chr2A	94.733	2525	97	19	1	2495	502827131	502824613	0.000000e+00	3893.0
7	TraesCS2D01G289900	chr2A	87.468	1165	115	21	1062	2209	502933923	502935073	0.000000e+00	1314.0
8	TraesCS2D01G289900	chr2A	85.619	751	69	22	2502	3249	502824518	502823804	0.000000e+00	752.0
9	TraesCS2D01G289900	chr5B	83.691	932	127	16	1279	2193	550488914	550489837	0.000000e+00	856.0
10	TraesCS2D01G289900	chr5A	83.298	940	131	17	1279	2201	569793581	569794511	0.000000e+00	843.0
11	TraesCS2D01G289900	chr5D	83.262	932	131	16	1279	2193	450577904	450578827	0.000000e+00	833.0
12	TraesCS2D01G289900	chr5D	80.386	311	54	5	1476	1783	447508361	447508667	2.520000e-56	230.0
13	TraesCS2D01G289900	chr7D	92.857	42	3	0	3204	3245	97301437	97301478	9.740000e-06	62.1
14	TraesCS2D01G289900	chr3B	86.441	59	5	2	3190	3245	643850386	643850328	9.740000e-06	62.1
15	TraesCS2D01G289900	chr3A	90.909	44	4	0	3201	3244	86124755	86124798	3.500000e-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	TraesCS2D01G289900	chr2D	372013617	372016867	3250	True	6004.0	6004	100.000	1	3251	1	chr2D.!!$R1	3250
1	TraesCS2D01G289900	chr2D	372224105	372225255	1150	False	1347.0	1347	87.962	1062	2209	1	chr2D.!!$F1	1147
2	TraesCS2D01G289900	chr2B	441478422	441481384	2962	True	4423.0	4423	93.729	1	2949	1	chr2B.!!$R1	2948
3	TraesCS2D01G289900	chr2B	441792712	441793862	1150	False	1369.0	1369	88.306	1062	2209	1	chr2B.!!$F1	1147
4	TraesCS2D01G289900	chr2A	502823804	502827131	3327	True	2322.5	3893	90.176	1	3249	2	chr2A.!!$R1	3248
5	TraesCS2D01G289900	chr2A	502933923	502935073	1150	False	1314.0	1314	87.468	1062	2209	1	chr2A.!!$F1	1147
6	TraesCS2D01G289900	chr5B	550488914	550489837	923	False	856.0	856	83.691	1279	2193	1	chr5B.!!$F1	914
7	TraesCS2D01G289900	chr5A	569793581	569794511	930	False	843.0	843	83.298	1279	2201	1	chr5A.!!$F1	922
8	TraesCS2D01G289900	chr5D	450577904	450578827	923	False	833.0	833	83.262	1279	2193	1	chr5D.!!$F2	914

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
160	163	0.323908	CTCAACCTCCTCGACTCCCT	60.324	60.0	0.00	0.0	0.00	4.20	F
1968	2003	0.037326	CCGTGCTCTTCAAGGTGCTA	60.037	55.0	5.22	0.0	39.17	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2139	2189	2.086054	AGAATGACGTGAACTCCTGC	57.914	50.0	0.0	0.0	0.00	4.85	R
2795	2934	5.070313	TCCCTCAAAAGGAAAAAGTTCATGG	59.930	40.0	0.0	0.0	46.67	3.66	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
36	37	2.106566	TGCTCACCTCAATCTCTCTCC	58.893	52.381	0.00	0.00	0.00	3.71
50	51	3.948473	TCTCTCTCCACCTTTGTATCTCG	59.052	47.826	0.00	0.00	0.00	4.04
82	83	0.900647	CGGACTCTGTTCCTCCCACT	60.901	60.000	0.00	0.00	32.88	4.00
124	127	0.462759	CCTGGCGTTTCCCATCTCTC	60.463	60.000	0.00	0.00	33.64	3.20
129	132	0.530744	CGTTTCCCATCTCTCCGACA	59.469	55.000	0.00	0.00	0.00	4.35
160	163	0.323908	CTCAACCTCCTCGACTCCCT	60.324	60.000	0.00	0.00	0.00	4.20
206	209	0.962855	CTCGACCTCCTCACTGCAGA	60.963	60.000	23.35	0.00	0.00	4.26
221	224	1.202687	TGCAGACTCACACCTCCTTTG	60.203	52.381	0.00	0.00	0.00	2.77
230	233	1.841556	ACCTCCTTTGCAGGTCGGA	60.842	57.895	9.08	3.56	40.54	4.55
241	244	0.824109	CAGGTCGGACATGGCTCTAA	59.176	55.000	14.60	0.00	0.00	2.10
296	299	1.731720	GCTGGACCTGCTCTAACAAG	58.268	55.000	15.65	0.00	0.00	3.16
298	301	2.233922	GCTGGACCTGCTCTAACAAGTA	59.766	50.000	15.65	0.00	0.00	2.24
356	359	1.010462	GGTGCCACGTCGTTTTCAC	60.010	57.895	0.00	4.07	0.00	3.18
359	362	1.019805	TGCCACGTCGTTTTCACACA	61.020	50.000	0.00	0.00	0.00	3.72
379	382	9.474920	TCACACAATTTTGACTAAATCAATTCC	57.525	29.630	0.00	0.00	46.80	3.01
415	418	4.060205	AGTTTGAATCAGGTTGCAATTGC	58.940	39.130	23.69	23.69	42.50	3.56
430	433	4.158394	TGCAATTGCTGAATTAAGAGGTCC	59.842	41.667	29.37	0.00	42.66	4.46
487	490	8.821817	ACTTTGGCCCATAACAAAAAGTATTAT	58.178	29.630	10.83	0.00	36.40	1.28
564	569	5.418310	AACACACAACGTCTCCTAAATTG	57.582	39.130	0.00	0.00	0.00	2.32
682	689	1.880186	GTATGCACAAACGTGGGGG	59.120	57.895	0.00	0.00	34.79	5.40
707	726	2.026169	TGGATAAAACGTGGGGTATGCA	60.026	45.455	0.00	0.00	0.00	3.96
860	888	3.513515	CCAAACAAAGGGCTGCCTATAAA	59.486	43.478	19.68	0.00	0.00	1.40
871	899	4.568592	GGCTGCCTATAAATATGCCCTTCT	60.569	45.833	12.43	0.00	33.45	2.85
883	911	2.492025	TGCCCTTCTACATCCCATTCT	58.508	47.619	0.00	0.00	0.00	2.40
943	978	5.522824	ACCAGTTTCAGTTTTCTCGTTAGTC	59.477	40.000	0.00	0.00	0.00	2.59
979	1014	1.827969	GCAACAGAGGAGGAAGAGCTA	59.172	52.381	0.00	0.00	0.00	3.32
987	1022	2.092699	AGGAGGAAGAGCTAATTGGTGC	60.093	50.000	0.00	0.00	0.00	5.01
1194	1229	3.246112	CCCCACTCCACCAACGGA	61.246	66.667	0.00	0.00	0.00	4.69
1440	1475	3.060866	GACCAGTTCGAGGTGGCT	58.939	61.111	13.62	3.33	40.09	4.75
1462	1497	3.322466	AGGCCGTGGAGAACTGGG	61.322	66.667	0.00	0.00	0.00	4.45
1968	2003	0.037326	CCGTGCTCTTCAAGGTGCTA	60.037	55.000	5.22	0.00	39.17	3.49
2139	2189	0.390866	AGAATGCACTCGCTGAGGTG	60.391	55.000	9.75	6.98	39.64	4.00
2223	2273	4.301505	GGCGTTGCCTCATCTGAA	57.698	55.556	0.00	0.00	46.69	3.02
2251	2301	3.924686	GTCGGCTTATTCGTCTTCTTGAA	59.075	43.478	0.00	0.00	0.00	2.69
2305	2356	7.222031	CCATCGAGTAATTAATCGTGTTCTTCA	59.778	37.037	28.21	12.01	43.38	3.02
2377	2428	7.549488	ACCTCAGTAAATATACTTGTGACTTGC	59.451	37.037	0.00	0.00	40.44	4.01
2391	2442	3.799420	GTGACTTGCGAGATAGATGAACC	59.201	47.826	8.31	0.00	0.00	3.62
2508	2647	7.502561	GGGACTGTCCTAATGCTTATACAAAAT	59.497	37.037	25.01	0.00	36.57	1.82
2534	2673	4.265073	ACAATAAACTGAGAGGTGGATGC	58.735	43.478	0.00	0.00	0.00	3.91
2554	2693	6.476706	GGATGCCAAATTAATTAACAGCACTC	59.523	38.462	13.35	11.94	0.00	3.51
2574	2713	5.470098	CACTCCACACTATAAAACAGCACTT	59.530	40.000	0.00	0.00	0.00	3.16
2594	2733	5.925397	CACTTGTATGGATCTCATCTACTGC	59.075	44.000	0.00	0.00	37.30	4.40
2597	2736	2.364972	TGGATCTCATCTACTGCCGA	57.635	50.000	0.00	0.00	0.00	5.54
2641	2780	7.125755	CGCATTTTGATTCACGACATAAGTAT	58.874	34.615	0.00	0.00	0.00	2.12
2723	2862	3.588842	ACCTCCAAAACCATCTGATCTGA	59.411	43.478	4.63	4.63	0.00	3.27
2809	2948	5.175127	ACAAACACACCATGAACTTTTTCC	58.825	37.500	0.00	0.00	0.00	3.13
2858	2997	2.269241	GGGAGGCCACTTTCTCGG	59.731	66.667	5.01	0.00	0.00	4.63
2859	2998	2.269241	GGAGGCCACTTTCTCGGG	59.731	66.667	5.01	0.00	0.00	5.14
2914	3053	9.748100	TTTCGTTTTCACTTTTGCTTTATTTTC	57.252	25.926	0.00	0.00	0.00	2.29
2915	3054	8.696410	TCGTTTTCACTTTTGCTTTATTTTCT	57.304	26.923	0.00	0.00	0.00	2.52
3007	3147	8.599055	TTTGCAAAGTGTTATTCATGCATTTA	57.401	26.923	8.05	0.00	42.64	1.40
3009	3149	8.599055	TGCAAAGTGTTATTCATGCATTTAAA	57.401	26.923	0.00	0.00	38.73	1.52
3010	3150	9.049523	TGCAAAGTGTTATTCATGCATTTAAAA	57.950	25.926	0.00	0.00	38.73	1.52
3192	3333	8.934023	ATGTATGAAAAAGTAGACCTCCAAAA	57.066	30.769	0.00	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	2.430332	GGTGGAGAGAGATTGAGGTGAG	59.570	54.545	0.00	0.00	0.00	3.51
36	37	4.950050	AGGAATAGCGAGATACAAAGGTG	58.050	43.478	0.00	0.00	0.00	4.00
50	51	2.552315	CAGAGTCCGAGAGAGGAATAGC	59.448	54.545	0.00	0.00	42.77	2.97
82	83	7.287927	CAGGGAGGAAGATTATAACACTAGTCA	59.712	40.741	0.00	0.00	0.00	3.41
96	97	0.253327	GAAACGCCAGGGAGGAAGAT	59.747	55.000	0.00	0.00	41.22	2.40
99	102	2.754375	GGAAACGCCAGGGAGGAA	59.246	61.111	0.00	0.00	41.22	3.36
124	127	0.108138	GAGGAAGATGGTGGTGTCGG	60.108	60.000	0.00	0.00	0.00	4.79
129	132	1.630878	GAGGTTGAGGAAGATGGTGGT	59.369	52.381	0.00	0.00	0.00	4.16
160	163	2.680352	GGCACCCGAGAGACAGGA	60.680	66.667	0.00	0.00	0.00	3.86
206	209	0.109342	CCTGCAAAGGAGGTGTGAGT	59.891	55.000	0.00	0.00	0.00	3.41
221	224	1.676678	TAGAGCCATGTCCGACCTGC	61.677	60.000	0.00	0.00	0.00	4.85
230	233	1.279496	TCTGCCACTTAGAGCCATGT	58.721	50.000	0.00	0.00	0.00	3.21
241	244	2.511600	GCCGCGTATTCTGCCACT	60.512	61.111	4.92	0.00	0.00	4.00
296	299	8.268738	GCACACAAAATGAAAAACTGAAGATAC	58.731	33.333	0.00	0.00	0.00	2.24
298	301	6.817641	TGCACACAAAATGAAAAACTGAAGAT	59.182	30.769	0.00	0.00	0.00	2.40
318	321	2.358582	CCAATCTCACACACTTTGCACA	59.641	45.455	0.00	0.00	0.00	4.57
379	382	8.388103	CCTGATTCAAACTTTACATTAGGTACG	58.612	37.037	0.00	0.00	0.00	3.67
415	418	3.274288	GCCAGTGGACCTCTTAATTCAG	58.726	50.000	15.20	0.00	0.00	3.02
430	433	4.699735	TGACCACTTATGTTAATGCCAGTG	59.300	41.667	0.00	0.00	32.96	3.66
464	467	8.367660	TGATAATACTTTTTGTTATGGGCCAA	57.632	30.769	11.89	0.00	0.00	4.52
465	468	7.962995	TGATAATACTTTTTGTTATGGGCCA	57.037	32.000	9.61	9.61	0.00	5.36
509	514	0.625849	AATGAAGGATCCCAAGCCGT	59.374	50.000	8.55	0.00	35.54	5.68
682	689	2.786777	ACCCCACGTTTTATCCAAGAC	58.213	47.619	0.00	0.00	0.00	3.01
860	888	4.854436	AGAATGGGATGTAGAAGGGCATAT	59.146	41.667	0.00	0.00	0.00	1.78
871	899	2.968574	GCTGAGAGGAGAATGGGATGTA	59.031	50.000	0.00	0.00	0.00	2.29
916	944	4.258543	ACGAGAAAACTGAAACTGGTTGA	58.741	39.130	0.00	0.00	0.00	3.18
918	946	5.878669	ACTAACGAGAAAACTGAAACTGGTT	59.121	36.000	0.00	0.00	35.96	3.67
943	978	3.599343	TGTTGCTATTGCTGGTAGAGTG	58.401	45.455	0.00	0.00	40.48	3.51
979	1014	0.035739	ACTAACCGACCGCACCAATT	59.964	50.000	0.00	0.00	0.00	2.32
987	1022	0.806102	CAGCCATGACTAACCGACCG	60.806	60.000	0.00	0.00	0.00	4.79
2139	2189	2.086054	AGAATGACGTGAACTCCTGC	57.914	50.000	0.00	0.00	0.00	4.85
2223	2273	1.001597	GACGAATAAGCCGACGAGGAT	60.002	52.381	0.00	0.00	45.00	3.24
2274	2324	7.085116	ACACGATTAATTACTCGATGGAGATC	58.915	38.462	26.15	2.18	43.27	2.75
2377	2428	2.297597	GGACAGGGGTTCATCTATCTCG	59.702	54.545	0.00	0.00	0.00	4.04
2391	2442	0.895530	TTACTCAGCGAAGGACAGGG	59.104	55.000	0.00	0.00	0.00	4.45
2508	2647	7.094377	GCATCCACCTCTCAGTTTATTGTTTAA	60.094	37.037	0.00	0.00	0.00	1.52
2534	2673	6.586082	GTGTGGAGTGCTGTTAATTAATTTGG	59.414	38.462	5.91	0.00	0.00	3.28
2554	2693	5.689383	ACAAGTGCTGTTTTATAGTGTGG	57.311	39.130	0.00	0.00	32.99	4.17
2574	2713	3.507622	CGGCAGTAGATGAGATCCATACA	59.492	47.826	0.00	0.00	35.17	2.29
2594	2733	4.976731	CGTATAAGTTTGTCTCCTGATCGG	59.023	45.833	0.00	0.00	0.00	4.18
2597	2736	5.339008	TGCGTATAAGTTTGTCTCCTGAT	57.661	39.130	0.00	0.00	0.00	2.90
2795	2934	5.070313	TCCCTCAAAAGGAAAAAGTTCATGG	59.930	40.000	0.00	0.00	46.67	3.66
2809	2948	5.451937	GGACCTCTTGTTTTTCCCTCAAAAG	60.452	44.000	0.00	0.00	35.34	2.27
3167	3308	8.934023	TTTTGGAGGTCTACTTTTTCATACAT	57.066	30.769	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.