AutoCloner

Multiple sequence alignment - TraesCS6D01G302300

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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	TraesCS6D01G302300	chr6D	100.000	4475	0	0	1	4475	411618915	411614441	0.000000e+00	8264.0
1	TraesCS6D01G302300	chr6D	85.294	136	17	3	1111	1245	295143179	295143046	2.170000e-28	137.0
2	TraesCS6D01G302300	chr6D	78.212	179	27	10	2536	2710	438802637	438802467	2.200000e-18	104.0
3	TraesCS6D01G302300	chr6A	90.842	2457	133	31	1381	3801	556533562	556531162	0.000000e+00	3206.0
4	TraesCS6D01G302300	chr6A	90.244	697	49	15	3793	4475	556531108	556530417	0.000000e+00	893.0
5	TraesCS6D01G302300	chr6A	83.150	546	61	23	565	1086	556534407	556533869	1.880000e-128	470.0
6	TraesCS6D01G302300	chr6A	88.489	139	16	0	1230	1368	556533837	556533699	7.700000e-38	169.0
7	TraesCS6D01G302300	chr6A	85.950	121	15	2	1111	1231	60987464	60987346	1.310000e-25	128.0
8	TraesCS6D01G302300	chr6A	87.179	117	9	2	392	508	556534646	556534536	1.310000e-25	128.0
9	TraesCS6D01G302300	chr6A	91.892	74	6	0	1921	1994	64260717	64260790	2.200000e-18	104.0
10	TraesCS6D01G302300	chr6A	91.026	78	5	2	246	321	556536475	556536398	2.200000e-18	104.0
11	TraesCS6D01G302300	chr6B	89.909	1209	50	19	1396	2599	618944586	618943445	0.000000e+00	1491.0
12	TraesCS6D01G302300	chr6B	92.998	1014	61	7	2610	3617	618943385	618942376	0.000000e+00	1471.0
13	TraesCS6D01G302300	chr6B	89.396	613	38	13	515	1113	618945302	618944703	0.000000e+00	747.0
14	TraesCS6D01G302300	chr6B	93.095	420	24	4	4057	4475	618940464	618940049	1.060000e-170	610.0
15	TraesCS6D01G302300	chr6B	83.503	394	46	12	4	388	618946210	618945827	2.560000e-92	350.0
16	TraesCS6D01G302300	chr6B	90.625	256	8	7	3793	4037	618942019	618941769	4.320000e-85	326.0
17	TraesCS6D01G302300	chr6B	93.296	179	11	1	3615	3792	618942263	618942085	3.430000e-66	263.0
18	TraesCS6D01G302300	chr6B	92.233	103	6	1	1230	1330	618944689	618944587	1.300000e-30	145.0
19	TraesCS6D01G302300	chr6B	86.029	136	12	3	390	524	618945503	618945374	6.040000e-29	139.0
20	TraesCS6D01G302300	chr6B	91.892	74	6	0	1921	1994	512188517	512188590	2.200000e-18	104.0
21	TraesCS6D01G302300	chr2D	86.300	781	96	8	2802	3580	396670381	396669610	0.000000e+00	839.0
22	TraesCS6D01G302300	chr2D	81.157	605	78	17	3829	4410	396669282	396668691	1.900000e-123	453.0
23	TraesCS6D01G302300	chr2D	79.898	393	65	11	1991	2377	396670946	396670562	4.410000e-70	276.0
24	TraesCS6D01G302300	chr2D	85.714	224	22	5	1489	1711	396671477	396671263	1.250000e-55	228.0
25	TraesCS6D01G302300	chr2D	90.683	161	15	0	1709	1869	396671141	396670981	9.750000e-52	215.0
26	TraesCS6D01G302300	chr2D	83.007	153	23	3	2552	2702	326206914	326206763	7.810000e-28	135.0
27	TraesCS6D01G302300	chr2D	90.566	53	5	0	3744	3796	396669541	396669489	2.230000e-08	71.3
28	TraesCS6D01G302300	chr2D	88.889	54	6	0	2500	2553	140348645	140348698	2.890000e-07	67.6
29	TraesCS6D01G302300	chr2A	86.189	782	97	8	2801	3580	534632541	534631769	0.000000e+00	835.0
30	TraesCS6D01G302300	chr2A	81.157	605	78	17	3829	4410	534631438	534630847	1.900000e-123	453.0
31	TraesCS6D01G302300	chr2A	81.269	331	57	5	2054	2381	534633045	534632717	3.430000e-66	263.0
32	TraesCS6D01G302300	chr2A	89.840	187	16	2	1526	1711	534633606	534633422	2.080000e-58	237.0
33	TraesCS6D01G302300	chr2A	90.683	161	15	0	1709	1869	534633300	534633140	9.750000e-52	215.0
34	TraesCS6D01G302300	chr2A	84.314	153	21	3	2552	2702	391901710	391901861	3.610000e-31	147.0
35	TraesCS6D01G302300	chr2A	92.453	53	4	0	3744	3796	534631700	534631648	4.800000e-10	76.8
36	TraesCS6D01G302300	chr2B	87.064	688	86	2	2805	3492	470066562	470065878	0.000000e+00	774.0
37	TraesCS6D01G302300	chr2B	81.952	543	62	20	3829	4346	470065485	470064954	1.150000e-115	427.0
38	TraesCS6D01G302300	chr2B	79.747	395	69	10	1991	2381	470067131	470066744	4.410000e-70	276.0
39	TraesCS6D01G302300	chr2B	89.305	187	17	2	1526	1711	470067633	470067449	9.680000e-57	231.0
40	TraesCS6D01G302300	chr2B	89.441	161	17	0	1709	1869	470067326	470067166	2.110000e-48	204.0
41	TraesCS6D01G302300	chr2B	84.028	144	20	3	2561	2702	395532872	395532730	7.810000e-28	135.0
42	TraesCS6D01G302300	chr2B	91.667	72	6	0	1921	1992	754008463	754008534	2.850000e-17	100.0
43	TraesCS6D01G302300	chr2B	87.500	72	6	2	3725	3796	470065765	470065697	3.710000e-11	80.5
44	TraesCS6D01G302300	chr7B	87.023	131	13	4	1117	1245	627977368	627977240	1.300000e-30	145.0
45	TraesCS6D01G302300	chr1D	86.029	136	17	2	1111	1245	95876311	95876445	1.300000e-30	145.0
46	TraesCS6D01G302300	chr1D	87.603	121	14	1	1111	1231	437905814	437905695	6.040000e-29	139.0
47	TraesCS6D01G302300	chr1D	85.401	137	17	3	1110	1245	470591752	470591618	6.040000e-29	139.0
48	TraesCS6D01G302300	chr1D	92.958	71	5	0	1921	1991	320590018	320589948	2.200000e-18	104.0
49	TraesCS6D01G302300	chr1D	87.805	82	9	1	1923	2003	319515818	319515737	1.330000e-15	95.3
50	TraesCS6D01G302300	chr7D	86.400	125	15	2	1107	1231	591456899	591456777	7.810000e-28	135.0
51	TraesCS6D01G302300	chr7D	83.942	137	17	4	1111	1245	562201650	562201783	4.700000e-25	126.0
52	TraesCS6D01G302300	chr7D	79.769	173	26	7	2552	2719	550977022	550977190	2.830000e-22	117.0
53	TraesCS6D01G302300	chr1B	83.824	136	19	3	1111	1245	634251274	634251407	4.700000e-25	126.0
54	TraesCS6D01G302300	chr5A	80.795	151	26	3	2553	2701	110379744	110379595	1.020000e-21	115.0
55	TraesCS6D01G302300	chr5B	81.119	143	26	1	2563	2704	648746401	648746543	3.660000e-21	113.0
56	TraesCS6D01G302300	chr4D	90.278	72	7	0	1921	1992	230473093	230473164	1.330000e-15	95.3
57	TraesCS6D01G302300	chr4A	90.278	72	7	0	1923	1994	567678325	567678254	1.330000e-15	95.3

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	TraesCS6D01G302300	chr6D	411614441	411618915	4474	True	8264.000000	8264	100.000000	1	4475	1	chr6D.!!$R2	4474
1	TraesCS6D01G302300	chr6A	556530417	556536475	6058	True	828.333333	3206	88.488333	246	4475	6	chr6A.!!$R2	4229
2	TraesCS6D01G302300	chr6B	618940049	618946210	6161	True	615.777778	1491	90.120444	4	4475	9	chr6B.!!$R1	4471
3	TraesCS6D01G302300	chr2D	396668691	396671477	2786	True	347.050000	839	85.719667	1489	4410	6	chr2D.!!$R2	2921
4	TraesCS6D01G302300	chr2A	534630847	534633606	2759	True	346.633333	835	86.931833	1526	4410	6	chr2A.!!$R1	2884
5	TraesCS6D01G302300	chr2B	470064954	470067633	2679	True	332.083333	774	85.834833	1526	4346	6	chr2B.!!$R2	2820

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
511	2198	0.028242	CGAGGAATCCACTCTCGTCG	59.972	60.0	0.61	0.0	43.51	5.12	F
585	2384	0.096976	CGCCCAACATAAGTCGCAAG	59.903	55.0	0.00	0.0	0.00	4.01	F
586	2385	0.179163	GCCCAACATAAGTCGCAAGC	60.179	55.0	0.00	0.0	37.18	4.01	F
596	2395	0.251354	AGTCGCAAGCCATCACTCAT	59.749	50.0	0.00	0.0	37.18	2.90	F
622	2421	0.533032	GACTCAGACCTACAGCACCC	59.467	60.0	0.00	0.0	0.00	4.61	F
1346	3207	0.586319	TTTTGCTGCTTTCCTCGTCG	59.414	50.0	0.00	0.0	0.00	5.12	F
3105	5321	0.036010	AGGCATCAGACTCAAACCCG	60.036	55.0	0.00	0.0	0.00	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1332	3193	0.241213	TGAGTCGACGAGGAAAGCAG	59.759	55.000	10.46	0.0	0.00	4.24	R
1706	3709	0.613777	CAGGAGTGTCCTTGTACCCC	59.386	60.000	0.00	0.0	46.91	4.95	R
2183	4319	0.879765	CTGAAAAGCTGCACAGGGAG	59.120	55.000	1.02	0.0	35.23	4.30	R
2398	4534	0.881118	GCGCAAAATGTCAGAAGGGA	59.119	50.000	0.30	0.0	0.00	4.20	R
2402	4538	1.603456	TGGAGCGCAAAATGTCAGAA	58.397	45.000	11.47	0.0	0.00	3.02	R
3195	5411	0.319555	GCGGGGTTTCAAGCTTTTCC	60.320	55.000	0.00	0.0	0.00	3.13	R
4086	7920	2.095110	TCATTCCAAAGCGTGATTGCAG	60.095	45.455	0.00	0.0	37.31	4.41	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	7.703058	GGAGATGGAAAACAATTAGGAGAAA	57.297	36.000	0.00	0.00	0.00	2.52
32	33	5.443230	AACAATTAGGAGAAAGAGAGGGG	57.557	43.478	0.00	0.00	0.00	4.79
34	35	2.642171	TTAGGAGAAAGAGAGGGGCA	57.358	50.000	0.00	0.00	0.00	5.36
40	41	0.951040	GAAAGAGAGGGGCACGTGTG	60.951	60.000	18.38	0.00	0.00	3.82
81	83	5.478679	CGATGATAAGGAGGAGAGGTACAAT	59.521	44.000	0.00	0.00	0.00	2.71
97	99	2.996631	ACAATCTCCTCTTGGATGTGC	58.003	47.619	0.00	0.00	42.29	4.57
107	109	4.515361	CTCTTGGATGTGCAAAGAGAGAT	58.485	43.478	16.74	0.00	46.46	2.75
117	119	7.750229	TGTGCAAAGAGAGATGATAAAGTTT	57.250	32.000	0.00	0.00	0.00	2.66
121	123	9.017509	TGCAAAGAGAGATGATAAAGTTTGATT	57.982	29.630	0.00	0.00	0.00	2.57
149	152	6.540438	AAAAGTACGGAGAGGTTCATGATA	57.460	37.500	0.00	0.00	0.00	2.15
150	153	5.776173	AAGTACGGAGAGGTTCATGATAG	57.224	43.478	0.00	0.00	0.00	2.08
160	163	6.537355	AGAGGTTCATGATAGAGAGAGAGAG	58.463	44.000	0.00	0.00	0.00	3.20
162	165	6.537355	AGGTTCATGATAGAGAGAGAGAGAG	58.463	44.000	0.00	0.00	0.00	3.20
163	166	6.329986	AGGTTCATGATAGAGAGAGAGAGAGA	59.670	42.308	0.00	0.00	0.00	3.10
166	169	7.237209	TCATGATAGAGAGAGAGAGAGAGAG	57.763	44.000	0.00	0.00	0.00	3.20
170	173	7.244558	TGATAGAGAGAGAGAGAGAGAGAGAT	58.755	42.308	0.00	0.00	0.00	2.75
171	174	5.804944	AGAGAGAGAGAGAGAGAGAGATG	57.195	47.826	0.00	0.00	0.00	2.90
181	184	4.493547	AGAGAGAGAGATGTGAAAAAGCG	58.506	43.478	0.00	0.00	0.00	4.68
198	201	9.180678	TGAAAAAGCGAGAGAAATATGAAAAAC	57.819	29.630	0.00	0.00	0.00	2.43
201	204	7.440523	AAGCGAGAGAAATATGAAAAACAGT	57.559	32.000	0.00	0.00	0.00	3.55
228	231	3.005684	TGAAAAGGCGAAGACAATGCAAT	59.994	39.130	0.00	0.00	39.87	3.56
229	232	4.217334	TGAAAAGGCGAAGACAATGCAATA	59.783	37.500	0.00	0.00	39.87	1.90
230	233	4.782019	AAAGGCGAAGACAATGCAATAA	57.218	36.364	0.00	0.00	39.87	1.40
231	234	4.782019	AAGGCGAAGACAATGCAATAAA	57.218	36.364	0.00	0.00	39.87	1.40
232	235	4.989279	AGGCGAAGACAATGCAATAAAT	57.011	36.364	0.00	0.00	39.87	1.40

Showing 1 to 25 of 171 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	8.567285	TCTTTCTCCTAATTGTTTTCCATCTC	57.433	34.615	0.00	0.00	0.00	2.75
2	3	8.386264	TCTCTTTCTCCTAATTGTTTTCCATCT	58.614	33.333	0.00	0.00	0.00	2.90
4	5	7.613411	CCTCTCTTTCTCCTAATTGTTTTCCAT	59.387	37.037	0.00	0.00	0.00	3.41
5	6	6.942576	CCTCTCTTTCTCCTAATTGTTTTCCA	59.057	38.462	0.00	0.00	0.00	3.53
6	7	6.375736	CCCTCTCTTTCTCCTAATTGTTTTCC	59.624	42.308	0.00	0.00	0.00	3.13
7	8	6.375736	CCCCTCTCTTTCTCCTAATTGTTTTC	59.624	42.308	0.00	0.00	0.00	2.29
9	10	5.808050	GCCCCTCTCTTTCTCCTAATTGTTT	60.808	44.000	0.00	0.00	0.00	2.83
13	14	3.201045	GTGCCCCTCTCTTTCTCCTAATT	59.799	47.826	0.00	0.00	0.00	1.40
14	15	2.774809	GTGCCCCTCTCTTTCTCCTAAT	59.225	50.000	0.00	0.00	0.00	1.73
15	16	2.188817	GTGCCCCTCTCTTTCTCCTAA	58.811	52.381	0.00	0.00	0.00	2.69
16	17	1.867363	GTGCCCCTCTCTTTCTCCTA	58.133	55.000	0.00	0.00	0.00	2.94
17	18	1.261238	CGTGCCCCTCTCTTTCTCCT	61.261	60.000	0.00	0.00	0.00	3.69
18	19	1.219393	CGTGCCCCTCTCTTTCTCC	59.781	63.158	0.00	0.00	0.00	3.71
24	25	2.203640	TCACACGTGCCCCTCTCT	60.204	61.111	17.22	0.00	0.00	3.10
32	33	0.306533	AAAATGTCCGTCACACGTGC	59.693	50.000	17.22	0.00	40.58	5.34
54	55	2.560542	CCTCTCCTCCTTATCATCGGTG	59.439	54.545	0.00	0.00	0.00	4.94
55	56	2.178106	ACCTCTCCTCCTTATCATCGGT	59.822	50.000	0.00	0.00	0.00	4.69
56	57	2.883026	ACCTCTCCTCCTTATCATCGG	58.117	52.381	0.00	0.00	0.00	4.18
58	59	6.723977	AGATTGTACCTCTCCTCCTTATCATC	59.276	42.308	0.00	0.00	0.00	2.92
60	61	6.031964	AGATTGTACCTCTCCTCCTTATCA	57.968	41.667	0.00	0.00	0.00	2.15
85	87	3.935315	TCTCTCTTTGCACATCCAAGAG	58.065	45.455	15.90	15.90	0.00	2.85
129	131	5.050126	TCTATCATGAACCTCTCCGTACT	57.950	43.478	0.00	0.00	0.00	2.73
149	152	5.070180	CACATCTCTCTCTCTCTCTCTCTCT	59.930	48.000	0.00	0.00	0.00	3.10
150	153	5.069648	TCACATCTCTCTCTCTCTCTCTCTC	59.930	48.000	0.00	0.00	0.00	3.20
160	163	4.489810	TCGCTTTTTCACATCTCTCTCTC	58.510	43.478	0.00	0.00	0.00	3.20

Showing 1 to 25 of 170 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.