AutoCloner

Multiple sequence alignment - TraesCS6A01G032500

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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	TraesCS6A01G032500	chr6A	100.000	3717	0	0	1	3717	16101283	16097567	0.000000e+00	6865.0
1	TraesCS6A01G032500	chr6A	91.763	2246	123	19	918	3102	15953616	15951372	0.000000e+00	3066.0
2	TraesCS6A01G032500	chr6A	84.837	1774	251	13	907	2669	16400916	16399150	0.000000e+00	1770.0
3	TraesCS6A01G032500	chr6A	85.349	1720	234	16	960	2669	16410188	16408477	0.000000e+00	1764.0
4	TraesCS6A01G032500	chr6A	85.756	344	29	9	544	886	15953936	15953612	2.750000e-91	346.0
5	TraesCS6A01G032500	chr6B	94.566	2521	83	16	544	3061	27171814	27169345	0.000000e+00	3847.0
6	TraesCS6A01G032500	chr6B	92.034	2134	149	11	918	3034	27124590	27122461	0.000000e+00	2979.0
7	TraesCS6A01G032500	chr6B	90.329	1489	138	5	1191	2678	27181753	27180270	0.000000e+00	1947.0
8	TraesCS6A01G032500	chr6B	96.875	192	6	0	3	194	27175059	27174868	4.630000e-84	322.0
9	TraesCS6A01G032500	chr6B	96.316	190	6	1	189	378	27174023	27173835	1.000000e-80	311.0
10	TraesCS6A01G032500	chr6B	95.364	151	6	1	404	553	27172343	27172193	4.800000e-59	239.0
11	TraesCS6A01G032500	chr6B	92.000	150	11	1	738	886	27124735	27124586	3.760000e-50	209.0
12	TraesCS6A01G032500	chr6B	80.928	194	19	8	544	737	27125010	27124835	1.800000e-28	137.0
13	TraesCS6A01G032500	chr6D	95.435	2300	89	10	544	2838	15420186	15417898	0.000000e+00	3651.0
14	TraesCS6A01G032500	chr6D	90.653	2236	156	16	918	3102	15385361	15383128	0.000000e+00	2922.0
15	TraesCS6A01G032500	chr6D	85.014	1775	250	11	905	2669	15809066	15807298	0.000000e+00	1790.0
16	TraesCS6A01G032500	chr6D	95.316	427	18	2	4	430	15423094	15422670	0.000000e+00	676.0
17	TraesCS6A01G032500	chr6D	99.465	187	1	0	2907	3093	15417895	15417709	1.280000e-89	340.0
18	TraesCS6A01G032500	chr6D	83.807	352	30	11	544	886	15385690	15385357	3.610000e-80	309.0
19	TraesCS6A01G032500	chr6D	87.365	277	21	3	1	268	15397679	15397408	4.660000e-79	305.0
20	TraesCS6A01G032500	chr6D	96.992	133	4	0	421	553	15420990	15420858	1.340000e-54	224.0
21	TraesCS6A01G032500	chr6D	95.000	40	1	1	269	307	134588772	134588733	1.110000e-05	62.1
22	TraesCS6A01G032500	chr3B	93.002	543	33	4	3103	3642	754207127	754206587	0.000000e+00	787.0
23	TraesCS6A01G032500	chr3B	94.286	70	4	0	3646	3715	754206243	754206174	1.410000e-19	108.0
24	TraesCS6A01G032500	chr3B	83.607	61	4	5	270	325	782338812	782338753	7.000000e-03	52.8
25	TraesCS6A01G032500	chr1A	89.666	629	49	10	3103	3717	513704947	513704321	0.000000e+00	787.0
26	TraesCS6A01G032500	chr2A	90.365	384	26	6	3297	3673	47593557	47593178	9.270000e-136	494.0
27	TraesCS6A01G032500	chr2A	97.959	49	1	0	3669	3717	47591594	47591546	6.610000e-13	86.1
28	TraesCS6A01G032500	chr7A	90.312	320	26	4	3401	3717	75674314	75674631	7.430000e-112	414.0
29	TraesCS6A01G032500	chr7A	100.000	37	0	0	271	307	262474337	262474301	6.660000e-08	69.4
30	TraesCS6A01G032500	chr3D	88.131	337	39	1	3102	3437	23090887	23091223	2.080000e-107	399.0
31	TraesCS6A01G032500	chr5B	86.944	337	42	1	3103	3437	339286047	339285711	9.740000e-101	377.0
32	TraesCS6A01G032500	chr4D	84.911	338	45	6	3104	3437	503412056	503412391	1.650000e-88	337.0
33	TraesCS6A01G032500	chr2B	87.200	250	32	0	3103	3352	170855862	170856111	6.080000e-73	285.0
34	TraesCS6A01G032500	chr7B	95.122	41	2	0	270	310	265360420	265360380	8.620000e-07	65.8
35	TraesCS6A01G032500	chr2D	97.436	39	0	1	269	306	38220621	38220583	8.620000e-07	65.8
36	TraesCS6A01G032500	chr5D	97.297	37	1	0	271	307	223296259	223296295	3.100000e-06	63.9
37	TraesCS6A01G032500	chr1D	90.000	50	1	4	257	306	72629632	72629677	1.110000e-05	62.1

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	TraesCS6A01G032500	chr6A	16097567	16101283	3716	True	6865.000000	6865	100.000000	1	3717	1	chr6A.!!$R1	3716
1	TraesCS6A01G032500	chr6A	16399150	16400916	1766	True	1770.000000	1770	84.837000	907	2669	1	chr6A.!!$R2	1762
2	TraesCS6A01G032500	chr6A	16408477	16410188	1711	True	1764.000000	1764	85.349000	960	2669	1	chr6A.!!$R3	1709
3	TraesCS6A01G032500	chr6A	15951372	15953936	2564	True	1706.000000	3066	88.759500	544	3102	2	chr6A.!!$R4	2558
4	TraesCS6A01G032500	chr6B	27180270	27181753	1483	True	1947.000000	1947	90.329000	1191	2678	1	chr6B.!!$R1	1487
5	TraesCS6A01G032500	chr6B	27169345	27175059	5714	True	1179.750000	3847	95.780250	3	3061	4	chr6B.!!$R3	3058
6	TraesCS6A01G032500	chr6B	27122461	27125010	2549	True	1108.333333	2979	88.320667	544	3034	3	chr6B.!!$R2	2490
7	TraesCS6A01G032500	chr6D	15807298	15809066	1768	True	1790.000000	1790	85.014000	905	2669	1	chr6D.!!$R2	1764
8	TraesCS6A01G032500	chr6D	15383128	15385690	2562	True	1615.500000	2922	87.230000	544	3102	2	chr6D.!!$R4	2558
9	TraesCS6A01G032500	chr6D	15417709	15423094	5385	True	1222.750000	3651	96.802000	4	3093	4	chr6D.!!$R5	3089
10	TraesCS6A01G032500	chr3B	754206174	754207127	953	True	447.500000	787	93.644000	3103	3715	2	chr3B.!!$R2	612
11	TraesCS6A01G032500	chr1A	513704321	513704947	626	True	787.000000	787	89.666000	3103	3717	1	chr1A.!!$R1	614
12	TraesCS6A01G032500	chr2A	47591546	47593557	2011	True	290.050000	494	94.162000	3297	3717	2	chr2A.!!$R1	420

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
916	5718	1.826340	ATGGGGGCAAAAGGAAACGC	61.826	55.0	0.0	0.0	0.00	4.84	F
1503	6311	1.756375	GCATGTCCGTCATCGACAGC	61.756	60.0	0.0	0.0	39.71	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1935	6743	0.868406	CGTTGTTTGAGGTGAGCTCC	59.132	55.0	12.15	2.19	0.00	4.7	R
3360	8245	0.601311	AAGAACGTCTCTGGCAGCAC	60.601	55.0	10.34	7.97	33.37	4.4	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
38	39	6.961359	TGTTCCGAGAACACATAAACTATG	57.039	37.500	13.34	0.00	41.88	2.23
175	176	5.755409	TGGAGCTGTCATAAACCTCTAAA	57.245	39.130	0.00	0.00	0.00	1.85
187	188	9.667107	TCATAAACCTCTAAAGAAATACACCAG	57.333	33.333	0.00	0.00	0.00	4.00
246	1097	3.440173	AGCCGTTCCTCAACAATTATGTG	59.560	43.478	0.00	0.00	40.46	3.21
468	4474	3.965379	TGGAGCCAACGAGTTAACATA	57.035	42.857	8.61	0.00	0.00	2.29
799	5598	2.549754	AGTTCAACGAAACAGCCTGATG	59.450	45.455	0.00	0.00	0.00	3.07
903	5702	2.091994	AGCAGATCAAGAGAAATGGGGG	60.092	50.000	0.00	0.00	0.00	5.40
916	5718	1.826340	ATGGGGGCAAAAGGAAACGC	61.826	55.000	0.00	0.00	0.00	4.84
1166	5974	3.434319	CACCGCAGCATCCACCAC	61.434	66.667	0.00	0.00	0.00	4.16
1503	6311	1.756375	GCATGTCCGTCATCGACAGC	61.756	60.000	0.00	0.00	39.71	4.40
1935	6743	1.457823	ATGGCTATTGCATGGGCGTG	61.458	55.000	0.66	0.00	45.35	5.34
1971	6779	1.117150	ACGTGATTGCCGGGTACTAT	58.883	50.000	2.18	0.00	0.00	2.12
2049	6857	1.832883	TGGCCAATATCTTTGCACGT	58.167	45.000	0.61	0.00	0.00	4.49
2457	7265	1.826921	GCAGTGGGGATCCATGCTG	60.827	63.158	15.23	17.35	46.09	4.41
2649	7458	1.144969	CGCCACAACACGTGTAAGAT	58.855	50.000	23.69	2.56	44.78	2.40
2684	7495	3.838244	ACCTCAATGTATACCATGCGT	57.162	42.857	0.00	0.00	32.82	5.24
2727	7551	0.395036	CACCATCCCATTTGCCGGTA	60.395	55.000	1.90	0.00	0.00	4.02
2778	7602	4.551388	CGCTTATCTAGGCCTTAGTCAAG	58.449	47.826	12.58	9.89	0.00	3.02
2849	7678	2.724839	GCATCGTTTCTTACACCTTGCG	60.725	50.000	0.00	0.00	0.00	4.85
2869	7698	7.095439	CCTTGCGTATCTCTCCTTAATTTCATC	60.095	40.741	0.00	0.00	0.00	2.92
3128	8002	1.681780	GGATTTTCTCCCATGCACGGA	60.682	52.381	0.00	1.59	38.19	4.69
3155	8029	3.869272	GCATGCTCCAGCCGTTCG	61.869	66.667	11.37	0.00	41.18	3.95
3266	8143	4.955811	AGTCAGATACGCATTAATGGGA	57.044	40.909	32.16	18.95	42.66	4.37
3291	8168	5.615289	ACAGATAAAACACTGTTCTGAGCT	58.385	37.500	13.32	0.00	43.52	4.09
3299	8176	2.036992	CACTGTTCTGAGCTCAGGAACT	59.963	50.000	36.92	22.18	43.91	3.01
3306	8183	5.745312	TCTGAGCTCAGGAACTTAAATGA	57.255	39.130	36.92	15.53	43.91	2.57
3395	8284	0.417437	TCTTCCTCCTCCCATCACCA	59.583	55.000	0.00	0.00	0.00	4.17
3447	8336	7.890127	TCTCATCCATTTGTTTAGGAATCACTT	59.110	33.333	0.00	0.00	34.62	3.16
3489	8380	2.555199	CCGAGGACATCAACAAGATCC	58.445	52.381	0.00	0.00	33.72	3.36
3537	8428	5.955488	TCTTCGAGTTCTTTGTAGATCCAG	58.045	41.667	0.00	0.00	0.00	3.86
3555	8446	2.369860	CCAGACCCTGCTGCAATCTATA	59.630	50.000	3.02	0.00	34.56	1.31
3614	8506	5.223449	TCTGTCCTTCCTTTCGTATGTTT	57.777	39.130	0.00	0.00	0.00	2.83
3615	8507	4.994852	TCTGTCCTTCCTTTCGTATGTTTG	59.005	41.667	0.00	0.00	0.00	2.93
3682	10502	2.084101	CGTCGCGTCCGTTCAATCA	61.084	57.895	5.77	0.00	35.54	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.069016	TCGGAACAACAGAGCTAAAGTGA	59.931	43.478	0.00	0.00	0.00	3.41
1	2	3.390135	TCGGAACAACAGAGCTAAAGTG	58.610	45.455	0.00	0.00	0.00	3.16
38	39	3.319405	TGGAATCTAGCTAGCTAGTGTGC	59.681	47.826	38.27	31.83	44.59	4.57
175	176	7.496346	TTCTAAGATGGACTGGTGTATTTCT	57.504	36.000	0.00	0.00	0.00	2.52
468	4474	0.672342	AGTAGTGTTCGTGCCGTTCT	59.328	50.000	0.00	0.00	0.00	3.01
529	4536	2.265367	TGCATGAAAGGTGGGAGTAGA	58.735	47.619	0.00	0.00	0.00	2.59
799	5598	3.246619	GTCCATCTGTCTCGTTGAACTC	58.753	50.000	0.00	0.00	0.00	3.01
903	5702	0.603065	ATCCTGGCGTTTCCTTTTGC	59.397	50.000	0.00	0.00	35.26	3.68
916	5718	1.743958	ACGTTCTCTGTCGTATCCTGG	59.256	52.381	0.00	0.00	38.52	4.45
1503	6311	2.030562	GTGATGTATCCGGCGGGG	59.969	66.667	27.98	0.32	37.02	5.73
1629	6437	2.286425	CCCATGTCTCCCCACCCT	60.286	66.667	0.00	0.00	0.00	4.34
1935	6743	0.868406	CGTTGTTTGAGGTGAGCTCC	59.132	55.000	12.15	2.19	0.00	4.70
1971	6779	7.255035	CGAAGGTCGAGGTAGAAACTATCATAA	60.255	40.741	0.00	0.00	43.74	1.90
2684	7495	7.956943	GTGCGTACGTATGTATGTATGTATACA	59.043	37.037	17.90	8.27	46.21	2.29
2778	7602	6.062095	ACATGATACAAGCCCCAGTTATTAC	58.938	40.000	0.00	0.00	0.00	1.89
2882	7712	8.918202	AGCCATCTCGGAAAATACAAATATTA	57.082	30.769	0.00	0.00	36.56	0.98
3128	8002	2.437359	GAGCATGCACCGGAGCTT	60.437	61.111	24.52	15.80	37.48	3.74
3155	8029	4.166011	GCATCTCCGCGCCACAAC	62.166	66.667	0.00	0.00	0.00	3.32
3165	8039	2.631012	AAATCCAGGCGGGCATCTCC	62.631	60.000	3.78	0.00	36.21	3.71
3215	8090	5.221185	GGTGAGGTATTATACAGAACAGCGA	60.221	44.000	4.67	0.00	0.00	4.93
3291	8168	4.540099	AGGGGATGTCATTTAAGTTCCTGA	59.460	41.667	0.00	0.00	0.00	3.86
3299	8176	4.141574	CGGGTAGAAGGGGATGTCATTTAA	60.142	45.833	0.00	0.00	0.00	1.52
3306	8183	0.690077	GGACGGGTAGAAGGGGATGT	60.690	60.000	0.00	0.00	0.00	3.06
3360	8245	0.601311	AAGAACGTCTCTGGCAGCAC	60.601	55.000	10.34	7.97	33.37	4.40
3395	8284	5.158141	TCCTCATAGAGCTATTCCATGGTT	58.842	41.667	12.58	3.29	0.00	3.67
3415	8304	7.413446	TCCTAAACAAATGGATGAGATTTCCT	58.587	34.615	0.00	0.00	34.17	3.36
3425	8314	8.193953	ACAAAGTGATTCCTAAACAAATGGAT	57.806	30.769	0.00	0.00	0.00	3.41
3447	8336	5.235186	CGGGCATCAAACAATACAAAAACAA	59.765	36.000	0.00	0.00	0.00	2.83
3489	8380	0.603569	AGCAGTAGACACGAACCTGG	59.396	55.000	0.00	0.00	0.00	4.45
3537	8428	3.760580	ACTATAGATTGCAGCAGGGTC	57.239	47.619	6.78	0.00	0.00	4.46
3614	8506	2.504367	GCTTCTGCTTAGTTTCCCACA	58.496	47.619	0.00	0.00	36.03	4.17
3615	8507	1.464997	CGCTTCTGCTTAGTTTCCCAC	59.535	52.381	0.00	0.00	36.97	4.61
3682	10502	6.699575	AAGAAAAACATGCAGTTCACTAGT	57.300	33.333	0.00	0.00	40.26	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.