AutoCloner

Multiple sequence alignment - TraesCS5D01G566400

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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	TraesCS5D01G566400	chr5D	100.000	4397	0	0	2339	6735	564750911	564746515	0.000000e+00	8120.0
1	TraesCS5D01G566400	chr5D	100.000	1883	0	0	1	1883	564753249	564751367	0.000000e+00	3478.0
2	TraesCS5D01G566400	chr5D	91.879	1687	95	17	5088	6735	557355305	557353622	0.000000e+00	2318.0
3	TraesCS5D01G566400	chr5D	91.879	1687	95	17	5088	6735	557375743	557374060	0.000000e+00	2318.0
4	TraesCS5D01G566400	chr5D	91.879	1687	95	17	5088	6735	564727652	564725969	0.000000e+00	2318.0
5	TraesCS5D01G566400	chr5D	92.349	1490	90	14	5088	6554	557324455	557322967	0.000000e+00	2098.0
6	TraesCS5D01G566400	chr5D	89.888	1345	107	13	4592	5914	557284088	557282751	0.000000e+00	1703.0
7	TraesCS5D01G566400	chr5D	78.152	1158	123	57	791	1883	564788155	564789247	9.600000e-173	617.0
8	TraesCS5D01G566400	chr5D	82.692	728	89	23	4120	4832	564788379	564789084	4.460000e-171	612.0
9	TraesCS5D01G566400	chr5D	75.549	1321	236	52	4277	5577	483810134	483811387	2.730000e-158	569.0
10	TraesCS5D01G566400	chr5D	78.190	917	121	37	1030	1883	564749126	564748226	4.660000e-141	512.0
11	TraesCS5D01G566400	chr5D	78.190	917	121	37	4124	5024	564752220	564751367	4.660000e-141	512.0
12	TraesCS5D01G566400	chr5D	79.487	507	77	17	2373	2863	564758530	564758035	1.080000e-87	335.0
13	TraesCS5D01G566400	chr5D	94.836	213	9	1	6523	6735	557322968	557322758	1.400000e-86	331.0
14	TraesCS5D01G566400	chr5D	75.570	745	132	20	1178	1883	483810134	483810867	8.430000e-84	322.0
15	TraesCS5D01G566400	chr5D	93.836	146	9	0	6590	6735	557282234	557282089	3.160000e-53	220.0
16	TraesCS5D01G566400	chr5D	90.062	161	16	0	4241	4401	528279922	528279762	6.840000e-50	209.0
17	TraesCS5D01G566400	chr5D	78.656	253	38	7	540	776	564778316	564778568	3.250000e-33	154.0
18	TraesCS5D01G566400	chrUn	92.779	1371	78	11	5205	6554	404506401	404505031	0.000000e+00	1964.0
19	TraesCS5D01G566400	chrUn	90.216	971	74	11	5103	6052	376646545	376645575	0.000000e+00	1247.0
20	TraesCS5D01G566400	chr5B	88.928	1147	81	16	5164	6295	708408667	708407552	0.000000e+00	1373.0
21	TraesCS5D01G566400	chr5B	86.537	1233	106	19	2668	3849	708657461	708656238	0.000000e+00	1303.0
22	TraesCS5D01G566400	chr5B	86.698	857	65	22	492	1326	708658343	708657514	0.000000e+00	905.0
23	TraesCS5D01G566400	chr5B	87.195	656	73	8	4124	4770	708409336	708408683	0.000000e+00	736.0
24	TraesCS5D01G566400	chr5B	83.862	378	54	5	2389	2759	709245255	709245632	2.990000e-93	353.0
25	TraesCS5D01G566400	chr5B	75.294	765	141	33	4273	5026	595018391	595019118	8.430000e-84	322.0
26	TraesCS5D01G566400	chr5B	88.889	216	21	2	138	352	708658734	708658521	5.180000e-66	263.0
27	TraesCS5D01G566400	chr5B	83.784	296	26	10	4127	4414	708657806	708657525	1.860000e-65	261.0
28	TraesCS5D01G566400	chr5B	75.965	570	94	25	2432	2977	708453287	708452737	3.120000e-63	254.0
29	TraesCS5D01G566400	chr5B	76.483	472	85	17	5127	5581	709245276	709245738	4.060000e-57	233.0
30	TraesCS5D01G566400	chr5B	94.521	146	8	0	6590	6735	709246703	709246848	6.800000e-55	226.0
31	TraesCS5D01G566400	chr5B	94.400	125	6	1	1	125	708659474	708659351	2.480000e-44	191.0
32	TraesCS5D01G566400	chr5B	95.918	49	2	0	432	480	708658385	708658337	5.600000e-11	80.5
33	TraesCS5D01G566400	chr4A	85.559	921	85	28	2948	3849	605767869	605766978	0.000000e+00	920.0
34	TraesCS5D01G566400	chr4A	86.470	643	63	17	3200	3827	605867701	605867068	0.000000e+00	684.0
35	TraesCS5D01G566400	chr4A	88.654	520	44	7	3343	3849	606006116	606005599	2.670000e-173	619.0
36	TraesCS5D01G566400	chr4A	88.654	520	44	7	3343	3849	606106794	606106277	2.670000e-173	619.0
37	TraesCS5D01G566400	chr4A	88.654	520	44	7	3343	3849	606251035	606250518	2.670000e-173	619.0
38	TraesCS5D01G566400	chr4A	88.654	520	44	7	3343	3849	606252755	606252238	2.670000e-173	619.0
39	TraesCS5D01G566400	chr4A	88.654	520	44	7	3343	3849	606323596	606323079	2.670000e-173	619.0
40	TraesCS5D01G566400	chr4A	88.145	523	47	7	3340	3849	606187708	606187188	5.780000e-170	608.0
41	TraesCS5D01G566400	chr4A	84.139	662	54	22	3940	4596	605765679	605765064	1.620000e-165	593.0
42	TraesCS5D01G566400	chr4A	81.349	697	85	23	2352	3028	606339858	606340529	5.980000e-145	525.0
43	TraesCS5D01G566400	chr4A	80.505	554	85	19	5127	5671	606339910	606340449	2.930000e-108	403.0
44	TraesCS5D01G566400	chr4A	87.372	293	28	6	4106	4395	606339426	606339712	1.810000e-85	327.0
45	TraesCS5D01G566400	chr4A	81.654	387	52	7	2392	2759	605750776	605750390	3.050000e-78	303.0
46	TraesCS5D01G566400	chr4A	83.281	317	28	8	992	1296	606339409	606339712	1.110000e-67	268.0
47	TraesCS5D01G566400	chr4A	79.607	407	48	23	1085	1472	605765452	605765062	6.700000e-65	259.0
48	TraesCS5D01G566400	chr4A	95.890	146	6	0	6590	6735	605749303	605749158	3.140000e-58	237.0
49	TraesCS5D01G566400	chr4A	87.879	198	19	4	6540	6735	605766637	605766443	1.890000e-55	228.0
50	TraesCS5D01G566400	chr4A	74.750	400	61	19	1496	1872	605751243	605750861	7.040000e-30	143.0
51	TraesCS5D01G566400	chr4A	88.679	106	11	1	1770	1874	606339727	606339832	1.970000e-25	128.0
52	TraesCS5D01G566400	chr4A	83.212	137	20	3	4776	4912	612532409	612532542	9.170000e-24	122.0
53	TraesCS5D01G566400	chr4A	88.889	72	8	0	4594	4665	605751271	605751200	9.300000e-14	89.8
54	TraesCS5D01G566400	chr5A	75.441	1759	305	68	4076	5793	656216738	656215066	0.000000e+00	737.0
55	TraesCS5D01G566400	chr5A	76.107	1310	224	53	4277	5565	605249108	605250349	2.690000e-168	603.0
56	TraesCS5D01G566400	chr5A	78.367	943	141	42	5803	6727	656214988	656214091	2.740000e-153	553.0
57	TraesCS5D01G566400	chr5A	75.908	743	131	26	1178	1882	605249108	605249840	3.010000e-88	337.0
58	TraesCS5D01G566400	chr5A	75.444	676	120	26	4625	5296	605350353	605350986	3.070000e-73	287.0
59	TraesCS5D01G566400	chr5A	74.255	470	100	14	4444	4905	605349821	605350277	1.930000e-40	178.0
60	TraesCS5D01G566400	chr3A	81.178	696	87	26	2352	3028	744098081	744097411	2.780000e-143	520.0
61	TraesCS5D01G566400	chr3A	84.615	455	57	6	1430	1874	744098558	744098107	2.230000e-119	440.0
62	TraesCS5D01G566400	chr3A	80.108	553	88	18	5127	5671	744098029	744097491	6.330000e-105	392.0
63	TraesCS5D01G566400	chr3A	78.769	471	67	19	4556	5014	744098558	744098109	1.110000e-72	285.0
64	TraesCS5D01G566400	chr3A	87.075	147	17	2	1178	1323	742784870	742785015	1.500000e-36	165.0
65	TraesCS5D01G566400	chr3A	90.000	80	8	0	2767	2846	742786047	742786126	3.320000e-18	104.0
66	TraesCS5D01G566400	chr7A	73.952	668	130	24	4273	4912	91496645	91497296	5.250000e-56	230.0
67	TraesCS5D01G566400	chr3D	87.582	153	17	2	1178	1329	609232362	609232513	6.940000e-40	176.0
68	TraesCS5D01G566400	chr3D	91.250	80	7	0	2767	2846	609233539	609233618	7.140000e-20	110.0
69	TraesCS5D01G566400	chr2A	83.453	139	17	6	1174	1309	62488663	62488798	2.550000e-24	124.0
70	TraesCS5D01G566400	chr6B	91.667	48	1	2	3856	3902	661925969	661926014	5.640000e-06	63.9

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	TraesCS5D01G566400	chr5D	564746515	564753249	6734	True	3155.500000	8120	89.095000	1	6735	4	chr5D.!!$R8	6734
1	TraesCS5D01G566400	chr5D	557353622	557355305	1683	True	2318.000000	2318	91.879000	5088	6735	1	chr5D.!!$R2	1647
2	TraesCS5D01G566400	chr5D	557374060	557375743	1683	True	2318.000000	2318	91.879000	5088	6735	1	chr5D.!!$R3	1647
3	TraesCS5D01G566400	chr5D	564725969	564727652	1683	True	2318.000000	2318	91.879000	5088	6735	1	chr5D.!!$R4	1647
4	TraesCS5D01G566400	chr5D	557322758	557324455	1697	True	1214.500000	2098	93.592500	5088	6735	2	chr5D.!!$R7	1647
5	TraesCS5D01G566400	chr5D	557282089	557284088	1999	True	961.500000	1703	91.862000	4592	6735	2	chr5D.!!$R6	2143
6	TraesCS5D01G566400	chr5D	564788155	564789247	1092	False	614.500000	617	80.422000	791	4832	2	chr5D.!!$F3	4041
7	TraesCS5D01G566400	chr5D	483810134	483811387	1253	False	445.500000	569	75.559500	1178	5577	2	chr5D.!!$F2	4399
8	TraesCS5D01G566400	chrUn	404505031	404506401	1370	True	1964.000000	1964	92.779000	5205	6554	1	chrUn.!!$R2	1349
9	TraesCS5D01G566400	chrUn	376645575	376646545	970	True	1247.000000	1247	90.216000	5103	6052	1	chrUn.!!$R1	949
10	TraesCS5D01G566400	chr5B	708407552	708409336	1784	True	1054.500000	1373	88.061500	4124	6295	2	chr5B.!!$R2	2171
11	TraesCS5D01G566400	chr5B	708656238	708659474	3236	True	500.583333	1303	89.371000	1	4414	6	chr5B.!!$R3	4413
12	TraesCS5D01G566400	chr5B	595018391	595019118	727	False	322.000000	322	75.294000	4273	5026	1	chr5B.!!$F1	753
13	TraesCS5D01G566400	chr5B	709245255	709246848	1593	False	270.666667	353	84.955333	2389	6735	3	chr5B.!!$F2	4346
14	TraesCS5D01G566400	chr5B	708452737	708453287	550	True	254.000000	254	75.965000	2432	2977	1	chr5B.!!$R1	545
15	TraesCS5D01G566400	chr4A	605867068	605867701	633	True	684.000000	684	86.470000	3200	3827	1	chr4A.!!$R1	627
16	TraesCS5D01G566400	chr4A	606005599	606006116	517	True	619.000000	619	88.654000	3343	3849	1	chr4A.!!$R2	506
17	TraesCS5D01G566400	chr4A	606106277	606106794	517	True	619.000000	619	88.654000	3343	3849	1	chr4A.!!$R3	506
18	TraesCS5D01G566400	chr4A	606250518	606252755	2237	True	619.000000	619	88.654000	3343	3849	2	chr4A.!!$R8	506
19	TraesCS5D01G566400	chr4A	606323079	606323596	517	True	619.000000	619	88.654000	3343	3849	1	chr4A.!!$R5	506
20	TraesCS5D01G566400	chr4A	606187188	606187708	520	True	608.000000	608	88.145000	3340	3849	1	chr4A.!!$R4	509
21	TraesCS5D01G566400	chr4A	605765062	605767869	2807	True	500.000000	920	84.296000	1085	6735	4	chr4A.!!$R7	5650
22	TraesCS5D01G566400	chr4A	606339409	606340529	1120	False	330.200000	525	84.237200	992	5671	5	chr4A.!!$F2	4679
23	TraesCS5D01G566400	chr5A	656214091	656216738	2647	True	645.000000	737	76.904000	4076	6727	2	chr5A.!!$R1	2651
24	TraesCS5D01G566400	chr5A	605249108	605250349	1241	False	470.000000	603	76.007500	1178	5565	2	chr5A.!!$F1	4387
25	TraesCS5D01G566400	chr5A	605349821	605350986	1165	False	232.500000	287	74.849500	4444	5296	2	chr5A.!!$F2	852
26	TraesCS5D01G566400	chr3A	744097411	744098558	1147	True	409.250000	520	81.167500	1430	5671	4	chr3A.!!$R1	4241
27	TraesCS5D01G566400	chr7A	91496645	91497296	651	False	230.000000	230	73.952000	4273	4912	1	chr7A.!!$F1	639

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
219	824	0.032416	TACTCACCTAGCCCACCTCC	60.032	60.0	0.00	0.00	0.00	4.30	F
274	879	0.035317	GTGATCCGCATATGCAGGGA	59.965	55.0	26.52	24.01	42.21	4.20	F
1636	2421	0.102300	CGTCCATGGCGAGTACATCA	59.898	55.0	19.72	0.00	0.00	3.07	F
2561	3359	0.107945	CTAACCTGCAGAGGCTCACC	60.108	60.0	17.39	7.37	44.33	4.02	F
4099	6770	0.109226	CGTCGGTCTTTCTCCTCACC	60.109	60.0	0.00	0.00	0.00	4.02	F
4208	6884	0.035317	AGAACAGCCGACATGCTTGA	59.965	50.0	6.60	0.00	40.32	3.02	F
4325	7007	0.249447	CTCCACGCCATTCTATCGCA	60.249	55.0	0.00	0.00	0.00	5.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1786	2580	0.174389	CTGGTCATCACGTCCTCCTG	59.826	60.000	0.00	0.0	0.00	3.86	R
1849	2644	0.452122	CGTGACCGCAAAATTCGACC	60.452	55.000	0.00	0.0	0.00	4.79	R
2652	3457	0.040958	CAAGACCTGTTGAACAGCGC	60.041	55.000	19.45	12.7	44.63	5.92	R
4195	6871	0.099436	GTGGATTCAAGCATGTCGGC	59.901	55.000	0.00	0.0	0.00	5.54	R
5257	8333	0.615331	TGAGCTTCTGCAGGTTAGGG	59.385	55.000	15.13	0.0	42.74	3.53	R
5602	8698	1.349688	TCGGCCATAGTGAGTTTGGTT	59.650	47.619	2.24	0.0	32.90	3.67	R
5747	8860	2.426522	ACAATGTCAACCATCCGACAG	58.573	47.619	0.00	0.0	44.83	3.51	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)

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	2.025416	TCCGGATTGATGTGTGGGATTT	60.025	45.455	0.00	0.00	0.00	2.17
33	34	3.193267	CGGATTGATGTGTGGGATTTTGT	59.807	43.478	0.00	0.00	0.00	2.83
106	107	2.874457	GCGGTGGTTGGTGTCTAGAAAT	60.874	50.000	0.00	0.00	0.00	2.17
107	108	3.408634	CGGTGGTTGGTGTCTAGAAATT	58.591	45.455	0.00	0.00	0.00	1.82
142	143	6.957631	TCTATCCTTTAAGAGCAATCCAACA	58.042	36.000	0.00	0.00	0.00	3.33
144	145	4.724399	TCCTTTAAGAGCAATCCAACACA	58.276	39.130	0.00	0.00	0.00	3.72
145	146	4.761739	TCCTTTAAGAGCAATCCAACACAG	59.238	41.667	0.00	0.00	0.00	3.66
146	147	4.082571	CCTTTAAGAGCAATCCAACACAGG	60.083	45.833	0.00	0.00	0.00	4.00
147	148	2.664402	AAGAGCAATCCAACACAGGT	57.336	45.000	0.00	0.00	0.00	4.00
148	149	2.191128	AGAGCAATCCAACACAGGTC	57.809	50.000	0.00	0.00	0.00	3.85
149	150	1.168714	GAGCAATCCAACACAGGTCC	58.831	55.000	0.00	0.00	0.00	4.46
150	151	0.251341	AGCAATCCAACACAGGTCCC	60.251	55.000	0.00	0.00	0.00	4.46
172	777	3.323243	CGTCCTCGTTACATCCTTTTGT	58.677	45.455	0.00	0.00	0.00	2.83
173	778	3.122948	CGTCCTCGTTACATCCTTTTGTG	59.877	47.826	0.00	0.00	0.00	3.33
189	794	5.006165	CCTTTTGTGAGTTTTGCGCATAAAA	59.994	36.000	12.75	7.12	42.21	1.52
190	795	5.382573	TTTGTGAGTTTTGCGCATAAAAC	57.617	34.783	23.74	23.74	46.02	2.43
219	824	0.032416	TACTCACCTAGCCCACCTCC	60.032	60.000	0.00	0.00	0.00	4.30
223	828	2.041265	CCTAGCCCACCTCCCTGT	59.959	66.667	0.00	0.00	0.00	4.00
226	831	0.909610	CTAGCCCACCTCCCTGTTCA	60.910	60.000	0.00	0.00	0.00	3.18
242	847	0.459585	TTCAACGGACCTCTATGCGC	60.460	55.000	0.00	0.00	36.83	6.09
251	856	1.224592	CTCTATGCGCCCCCACTTT	59.775	57.895	4.18	0.00	0.00	2.66
262	867	1.453155	CCCCACTTTTCTGTGATCCG	58.547	55.000	0.00	0.00	40.12	4.18
264	869	1.522668	CCACTTTTCTGTGATCCGCA	58.477	50.000	0.00	0.00	40.12	5.69
268	873	4.260907	CCACTTTTCTGTGATCCGCATATG	60.261	45.833	0.00	0.00	40.12	1.78
271	876	2.159327	TCTGTGATCCGCATATGCAG	57.841	50.000	26.52	16.39	42.21	4.41

Showing 1 to 25 of 371 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	3.193267	ACAAAATCCCACACATCAATCCG	59.807	43.478	0.00	0.00	0.00	4.18
59	60	7.285172	CAGTCATGTCCCATGTTTATAATCCAA	59.715	37.037	4.30	0.00	0.00	3.53
72	73	1.078214	CACCGCAGTCATGTCCCAT	60.078	57.895	0.00	0.00	0.00	4.00
125	126	4.469657	ACCTGTGTTGGATTGCTCTTAAA	58.530	39.130	0.00	0.00	0.00	1.52
126	127	4.072131	GACCTGTGTTGGATTGCTCTTAA	58.928	43.478	0.00	0.00	0.00	1.85
127	128	3.559171	GGACCTGTGTTGGATTGCTCTTA	60.559	47.826	0.00	0.00	0.00	2.10
128	129	2.508526	GACCTGTGTTGGATTGCTCTT	58.491	47.619	0.00	0.00	0.00	2.85
129	130	1.271597	GGACCTGTGTTGGATTGCTCT	60.272	52.381	0.00	0.00	0.00	4.09
130	131	1.168714	GGACCTGTGTTGGATTGCTC	58.831	55.000	0.00	0.00	0.00	4.26
146	147	0.101939	GATGTAACGAGGACGGGGAC	59.898	60.000	0.00	0.00	44.46	4.46
147	148	1.039233	GGATGTAACGAGGACGGGGA	61.039	60.000	0.00	0.00	44.46	4.81
148	149	1.041447	AGGATGTAACGAGGACGGGG	61.041	60.000	0.00	0.00	44.46	5.73
149	150	0.822164	AAGGATGTAACGAGGACGGG	59.178	55.000	0.00	0.00	44.46	5.28
150	151	2.667473	AAAGGATGTAACGAGGACGG	57.333	50.000	0.00	0.00	44.46	4.79
172	777	3.794028	GTGTGTTTTATGCGCAAAACTCA	59.206	39.130	28.36	27.33	44.86	3.41
173	778	4.041723	AGTGTGTTTTATGCGCAAAACTC	58.958	39.130	28.36	25.68	44.86	3.01
189	794	3.195825	GCTAGGTGAGTATTGGAGTGTGT	59.804	47.826	0.00	0.00	0.00	3.72
190	795	3.430929	GGCTAGGTGAGTATTGGAGTGTG	60.431	52.174	0.00	0.00	0.00	3.82
219	824	2.893637	CATAGAGGTCCGTTGAACAGG	58.106	52.381	0.00	0.00	0.00	4.00
223	828	0.459585	GCGCATAGAGGTCCGTTGAA	60.460	55.000	0.30	0.00	0.00	2.69
226	831	2.499685	GGCGCATAGAGGTCCGTT	59.500	61.111	10.83	0.00	0.00	4.44
242	847	1.839424	GGATCACAGAAAAGTGGGGG	58.161	55.000	0.00	0.00	39.93	5.40
251	856	2.618442	TGCATATGCGGATCACAGAA	57.382	45.000	22.21	0.00	45.83	3.02
262	867	3.350833	CCTATTTCCTCCCTGCATATGC	58.649	50.000	21.09	21.09	42.50	3.14
264	869	2.922283	CCCCTATTTCCTCCCTGCATAT	59.078	50.000	0.00	0.00	0.00	1.78

Showing 1 to 25 of 335 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.