AutoCloner

Multiple sequence alignment - TraesCS6A01G032400

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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	TraesCS6A01G032400	chr6A	100.000	3527	0	0	1	3527	15954413	15950887	0.000000e+00	6514
1	TraesCS6A01G032400	chr6A	91.763	2246	123	20	798	3042	16100366	16098182	0.000000e+00	3066
2	TraesCS6A01G032400	chr6A	85.303	1735	243	8	799	2526	16400901	16399172	0.000000e+00	1781
3	TraesCS6A01G032400	chr6A	85.385	520	43	17	3033	3527	16088875	16088364	3.140000e-140	508
4	TraesCS6A01G032400	chr6A	85.756	344	29	9	478	802	16100740	16100398	2.610000e-91	346
5	TraesCS6A01G032400	chr6D	92.787	3577	183	34	1	3527	15386175	15382624	0.000000e+00	5107
6	TraesCS6A01G032400	chr6D	94.821	1931	77	12	806	2733	15419808	15417898	0.000000e+00	2990
7	TraesCS6A01G032400	chr6D	85.418	1735	241	8	799	2526	15799469	15797740	0.000000e+00	1792
8	TraesCS6A01G032400	chr6D	85.672	1689	228	11	820	2500	15809028	15807346	0.000000e+00	1766
9	TraesCS6A01G032400	chr6D	81.726	197	18	9	2837	3033	15417887	15417709	7.890000e-32	148
10	TraesCS6A01G032400	chr6B	93.472	2160	128	12	653	2809	27124735	27122586	0.000000e+00	3195
11	TraesCS6A01G032400	chr6B	93.022	1863	113	8	797	2657	27171441	27169594	0.000000e+00	2704
12	TraesCS6A01G032400	chr6B	89.549	1598	147	17	1071	2655	27181753	27180163	0.000000e+00	2008
13	TraesCS6A01G032400	chr6B	88.156	667	57	11	1	652	27125494	27124835	0.000000e+00	774
14	TraesCS6A01G032400	chr6B	87.380	523	43	14	3026	3527	27122461	27121941	2.360000e-161	579
15	TraesCS6A01G032400	chr6B	80.595	706	62	39	2848	3527	27169480	27168824	3.190000e-130	475
16	TraesCS6A01G032400	chr6B	85.714	105	7	3	2841	2945	27122580	27122484	1.730000e-18	104
17	TraesCS6A01G032400	chr5B	77.215	237	36	12	63	287	471384474	471384704	4.780000e-24	122

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	TraesCS6A01G032400	chr6A	15950887	15954413	3526	True	6514.0	6514	100.0000	1	3527	1	chr6A.!!$R1	3526
1	TraesCS6A01G032400	chr6A	16399172	16400901	1729	True	1781.0	1781	85.3030	799	2526	1	chr6A.!!$R3	1727
2	TraesCS6A01G032400	chr6A	16098182	16100740	2558	True	1706.0	3066	88.7595	478	3042	2	chr6A.!!$R4	2564
3	TraesCS6A01G032400	chr6A	16088364	16088875	511	True	508.0	508	85.3850	3033	3527	1	chr6A.!!$R2	494
4	TraesCS6A01G032400	chr6D	15382624	15386175	3551	True	5107.0	5107	92.7870	1	3527	1	chr6D.!!$R1	3526
5	TraesCS6A01G032400	chr6D	15797740	15799469	1729	True	1792.0	1792	85.4180	799	2526	1	chr6D.!!$R2	1727
6	TraesCS6A01G032400	chr6D	15807346	15809028	1682	True	1766.0	1766	85.6720	820	2500	1	chr6D.!!$R3	1680
7	TraesCS6A01G032400	chr6D	15417709	15419808	2099	True	1569.0	2990	88.2735	806	3033	2	chr6D.!!$R4	2227
8	TraesCS6A01G032400	chr6B	27180163	27181753	1590	True	2008.0	2008	89.5490	1071	2655	1	chr6B.!!$R1	1584
9	TraesCS6A01G032400	chr6B	27168824	27171441	2617	True	1589.5	2704	86.8085	797	3527	2	chr6B.!!$R3	2730
10	TraesCS6A01G032400	chr6B	27121941	27125494	3553	True	1163.0	3195	88.6805	1	3527	4	chr6B.!!$R2	3526

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
713	859	0.389025	GTTCAACCAAACAGCCCTGG	59.611	55.0	0.00	0.0	38.77	4.45	F
1149	1345	2.291800	CCACCTTGGATGGATGTCCTTT	60.292	50.0	0.09	0.0	40.96	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1686	1882	1.376037	GAGGTTCCTCAGGTTGCCG	60.376	63.158	13.31	0.0	33.58	5.69	R
3126	3337	0.385473	CACCGCCATCGTTGTTGTTC	60.385	55.000	0.00	0.0	0.00	3.18	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
60	63	7.944729	ATGCTCTGGTATGAACAGTAAAATT	57.055	32.000	0.00	0.00	37.25	1.82
147	150	4.978580	GGAGTTCTTGCAAAGTTTCATCAC	59.021	41.667	0.00	0.00	46.34	3.06
164	175	4.394610	TCATCACGTAATCACATTTGTGGG	59.605	41.667	10.60	0.00	45.65	4.61
168	179	4.215399	CACGTAATCACATTTGTGGGAGTT	59.785	41.667	10.60	4.46	45.65	3.01
169	180	4.825085	ACGTAATCACATTTGTGGGAGTTT	59.175	37.500	10.60	1.45	45.65	2.66
207	222	9.744468	GAACTCCTAAATGCTTTTGAAAGTAAA	57.256	29.630	7.78	0.00	38.28	2.01
217	232	8.130307	TGCTTTTGAAAGTAAAATTTCAGAGC	57.870	30.769	22.47	22.47	46.70	4.09
218	233	8.130307	GCTTTTGAAAGTAAAATTTCAGAGCA	57.870	30.769	23.37	5.29	46.70	4.26
219	234	8.768019	GCTTTTGAAAGTAAAATTTCAGAGCAT	58.232	29.630	23.37	0.00	46.70	3.79
253	270	4.746535	TGCCACTAATTCCACGAATCTA	57.253	40.909	0.00	0.00	30.29	1.98
262	279	9.193133	ACTAATTCCACGAATCTAATTACATCG	57.807	33.333	0.00	7.77	39.30	3.84
279	296	2.473530	TCGTGAAACTTTGCAAGCAG	57.526	45.000	0.00	0.00	31.75	4.24
320	337	9.807649	ACTGCTTATCACCATTTTATTGAATTC	57.192	29.630	0.00	0.00	0.00	2.17
321	338	9.806203	CTGCTTATCACCATTTTATTGAATTCA	57.194	29.630	3.38	3.38	0.00	2.57
336	353	6.582677	TTGAATTCAATTTACCATCCGTGT	57.417	33.333	16.91	0.00	0.00	4.49
337	354	6.582677	TGAATTCAATTTACCATCCGTGTT	57.417	33.333	5.45	0.00	0.00	3.32
340	357	4.022413	TCAATTTACCATCCGTGTTCCA	57.978	40.909	0.00	0.00	0.00	3.53
359	376	5.614923	TCCAATTAAATGCGTTCGAAAGA	57.385	34.783	15.53	0.78	39.20	2.52
421	448	5.221783	ACTCCACGTTTCCTTTACTTGGTAT	60.222	40.000	0.00	0.00	36.57	2.73
422	449	4.998672	TCCACGTTTCCTTTACTTGGTATG	59.001	41.667	0.00	0.00	36.57	2.39
432	459	5.627780	CCTTTACTTGGTATGTTTGAAACGC	59.372	40.000	3.37	0.00	0.00	4.84
710	856	3.572255	TGATAAGTTCAACCAAACAGCCC	59.428	43.478	0.00	0.00	0.00	5.19
711	857	2.159179	AAGTTCAACCAAACAGCCCT	57.841	45.000	0.00	0.00	0.00	5.19
712	858	1.402787	AGTTCAACCAAACAGCCCTG	58.597	50.000	0.00	0.00	0.00	4.45
713	859	0.389025	GTTCAACCAAACAGCCCTGG	59.611	55.000	0.00	0.00	38.77	4.45
1149	1345	2.291800	CCACCTTGGATGGATGTCCTTT	60.292	50.000	0.09	0.00	40.96	3.11
1686	1882	2.657066	GGGACAGGACCTTCCCGAC	61.657	68.421	19.83	4.67	42.35	4.79
2465	2662	0.178767	AGCATATCTGAGCGTGGCAA	59.821	50.000	0.00	0.00	35.48	4.52
2481	2678	1.079875	GCAAACGCAATGCCATCCTG	61.080	55.000	0.00	0.00	37.85	3.86
2526	2723	4.021650	ACGCCACAACACGTGTAG	57.978	55.556	23.69	14.64	44.78	2.74
2671	2881	6.628398	GCGCTTATCTAGGCCTTAGTCAATAT	60.628	42.308	12.58	0.00	0.00	1.28
2672	2882	7.416438	GCGCTTATCTAGGCCTTAGTCAATATA	60.416	40.741	12.58	0.00	0.00	0.86
2673	2883	8.634444	CGCTTATCTAGGCCTTAGTCAATATAT	58.366	37.037	12.58	0.00	0.00	0.86
2857	3067	7.599054	CATATATGCCATGCGATTAATTTCG	57.401	36.000	0.00	0.00	41.99	3.46
2890	3100	6.757947	TGTAAGGGCTTGTAATATGTTACGAC	59.242	38.462	7.72	0.00	42.50	4.34
2891	3101	5.609533	AGGGCTTGTAATATGTTACGACT	57.390	39.130	7.72	0.00	42.50	4.18
2892	3102	5.985911	AGGGCTTGTAATATGTTACGACTT	58.014	37.500	7.72	0.00	42.50	3.01
2893	3103	7.116075	AGGGCTTGTAATATGTTACGACTTA	57.884	36.000	7.72	0.00	42.50	2.24
2894	3104	6.982724	AGGGCTTGTAATATGTTACGACTTAC	59.017	38.462	7.72	0.00	42.50	2.34
2895	3105	6.074676	GGGCTTGTAATATGTTACGACTTACG	60.075	42.308	7.72	0.00	42.50	3.18
2896	3106	6.692681	GGCTTGTAATATGTTACGACTTACGA	59.307	38.462	7.72	0.00	42.50	3.43
2987	3197	0.028242	CACGCCAAAGTACAAACGCA	59.972	50.000	0.00	0.00	0.00	5.24
2989	3199	1.326576	CGCCAAAGTACAAACGCATG	58.673	50.000	0.00	0.00	0.00	4.06
3080	3291	1.204062	CGTGATGCGAACTTGCGTT	59.796	52.632	0.00	0.00	44.77	4.84
3114	3325	6.153680	ACACCAAAGTACAGAACCATTCAAAA	59.846	34.615	0.00	0.00	0.00	2.44
3115	3326	6.697019	CACCAAAGTACAGAACCATTCAAAAG	59.303	38.462	0.00	0.00	0.00	2.27
3126	3337	3.941483	ACCATTCAAAAGGCGACTCTATG	59.059	43.478	0.00	0.00	42.68	2.23
3256	3477	9.616156	TCTAACCAAGTCAATAAAGTTGTTGTA	57.384	29.630	1.20	0.00	32.07	2.41
3299	3520	3.633986	AGTTTGCCAAAAGAACAGGAGAG	59.366	43.478	0.00	0.00	0.00	3.20
3303	3525	4.277476	TGCCAAAAGAACAGGAGAGAAAA	58.723	39.130	0.00	0.00	0.00	2.29
3304	3526	4.895297	TGCCAAAAGAACAGGAGAGAAAAT	59.105	37.500	0.00	0.00	0.00	1.82
3343	3565	4.874396	GTGGTCCGAATTTCTACCTTTAGG	59.126	45.833	15.01	0.00	42.17	2.69
3403	3625	1.154357	TCGATCGACACGTGGTTCG	60.154	57.895	21.57	20.23	46.00	3.95
3439	3661	7.149973	ACTGTTTACTAGCTATTTTGACGACA	58.850	34.615	0.00	0.00	0.00	4.35
3442	3664	8.995220	TGTTTACTAGCTATTTTGACGACAAAT	58.005	29.630	13.54	7.09	43.99	2.32
3446	3668	8.997621	ACTAGCTATTTTGACGACAAATAAGA	57.002	30.769	13.54	0.00	43.99	2.10
3447	3669	8.870879	ACTAGCTATTTTGACGACAAATAAGAC	58.129	33.333	13.54	9.86	43.99	3.01
3448	3670	6.762108	AGCTATTTTGACGACAAATAAGACG	58.238	36.000	13.54	0.00	43.99	4.18
3449	3671	6.367969	AGCTATTTTGACGACAAATAAGACGT	59.632	34.615	13.54	0.00	43.99	4.34
3452	3688	5.721876	TTTGACGACAAATAAGACGTGTT	57.278	34.783	8.97	2.58	40.47	3.32
3457	3693	3.428870	CGACAAATAAGACGTGTTGCTCT	59.571	43.478	8.42	0.00	0.00	4.09
3476	3712	5.481824	TGCTCTGAGATTCTTAACCTTGAGA	59.518	40.000	9.28	0.00	0.00	3.27
3485	3721	6.867662	TTCTTAACCTTGAGAAGCTCTTTG	57.132	37.500	0.00	0.00	30.50	2.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	0.176680	AGCATTTGAGCTCGATCCGT	59.823	50.000	9.64	0.00	42.18	4.69
114	117	4.998671	TGCAAGAACTCCAAACATTTCA	57.001	36.364	0.00	0.00	0.00	2.69
129	132	5.743026	TTACGTGATGAAACTTTGCAAGA	57.257	34.783	0.00	0.00	0.00	3.02
179	190	8.011844	ACTTTCAAAAGCATTTAGGAGTTCTT	57.988	30.769	2.43	0.00	37.28	2.52
240	257	7.207383	TCACGATGTAATTAGATTCGTGGAAT	58.793	34.615	27.17	0.00	46.08	3.01
253	270	6.991485	CTTGCAAAGTTTCACGATGTAATT	57.009	33.333	0.00	0.00	39.70	1.40
290	307	9.461312	TCAATAAAATGGTGATAAGCAGTAAGT	57.539	29.630	0.00	0.00	0.00	2.24
295	312	9.806203	TGAATTCAATAAAATGGTGATAAGCAG	57.194	29.630	5.45	0.00	0.00	4.24
320	337	4.775058	TTGGAACACGGATGGTAAATTG	57.225	40.909	0.00	0.00	39.29	2.32
321	338	5.993748	AATTGGAACACGGATGGTAAATT	57.006	34.783	0.00	0.00	39.29	1.82
322	339	7.469537	TTTAATTGGAACACGGATGGTAAAT	57.530	32.000	0.00	0.00	39.29	1.40
323	340	6.896021	TTTAATTGGAACACGGATGGTAAA	57.104	33.333	0.00	0.00	39.29	2.01
324	341	6.626181	GCATTTAATTGGAACACGGATGGTAA	60.626	38.462	0.00	0.00	39.29	2.85
336	353	6.003234	TCTTTCGAACGCATTTAATTGGAA	57.997	33.333	0.00	0.00	0.00	3.53
337	354	5.614923	TCTTTCGAACGCATTTAATTGGA	57.385	34.783	0.00	0.00	0.00	3.53
421	448	1.946768	CCCTCTCAAGCGTTTCAAACA	59.053	47.619	0.22	0.00	0.00	2.83
422	449	1.266989	CCCCTCTCAAGCGTTTCAAAC	59.733	52.381	0.00	0.00	0.00	2.93
432	459	1.065126	CAACCTTAGGCCCCTCTCAAG	60.065	57.143	0.00	0.00	0.00	3.02
533	561	6.375377	TGTACGCTACAATTTGTTTTCCATC	58.625	36.000	7.45	0.00	35.38	3.51
550	578	1.185618	TCCTGGAGCTGTTGTACGCT	61.186	55.000	0.00	0.00	39.61	5.07
710	856	4.238761	TCTGTCTCGTTGAACTTACCAG	57.761	45.455	0.00	0.00	0.00	4.00
711	857	4.556233	CATCTGTCTCGTTGAACTTACCA	58.444	43.478	0.00	0.00	0.00	3.25
712	858	3.927142	CCATCTGTCTCGTTGAACTTACC	59.073	47.826	0.00	0.00	0.00	2.85
713	859	4.621886	GTCCATCTGTCTCGTTGAACTTAC	59.378	45.833	0.00	0.00	0.00	2.34
1149	1345	0.179234	TGGAGACAACGCAGGTGAAA	59.821	50.000	0.61	0.00	37.44	2.69
1686	1882	1.376037	GAGGTTCCTCAGGTTGCCG	60.376	63.158	13.31	0.00	33.58	5.69
2526	2723	9.448294	CATTGAGGTAAGAAGATACTAACGTAC	57.552	37.037	0.00	0.00	0.00	3.67
2671	2881	5.082633	TGATACAAGCCCCAGGTACTATA	57.917	43.478	0.00	0.00	36.02	1.31
2672	2882	3.936461	TGATACAAGCCCCAGGTACTAT	58.064	45.455	0.00	0.00	36.02	2.12
2673	2883	3.408157	TGATACAAGCCCCAGGTACTA	57.592	47.619	0.00	0.00	36.02	1.82
2674	2884	2.263895	TGATACAAGCCCCAGGTACT	57.736	50.000	0.00	0.00	43.88	2.73
2851	3061	5.067954	AGCCCTTACAAGTACAACGAAATT	58.932	37.500	0.00	0.00	0.00	1.82
2857	3067	6.812879	ATTACAAGCCCTTACAAGTACAAC	57.187	37.500	0.00	0.00	0.00	3.32
2890	3100	7.864882	TGCTCTCATATTGATCTTTCTCGTAAG	59.135	37.037	0.00	0.00	0.00	2.34
2891	3101	7.716612	TGCTCTCATATTGATCTTTCTCGTAA	58.283	34.615	0.00	0.00	0.00	3.18
2892	3102	7.277174	TGCTCTCATATTGATCTTTCTCGTA	57.723	36.000	0.00	0.00	0.00	3.43
2893	3103	6.154203	TGCTCTCATATTGATCTTTCTCGT	57.846	37.500	0.00	0.00	0.00	4.18
2894	3104	7.360185	CCAATGCTCTCATATTGATCTTTCTCG	60.360	40.741	0.00	0.00	36.61	4.04
2895	3105	7.444792	ACCAATGCTCTCATATTGATCTTTCTC	59.555	37.037	0.00	0.00	36.61	2.87
2896	3106	7.288560	ACCAATGCTCTCATATTGATCTTTCT	58.711	34.615	0.00	0.00	36.61	2.52
2953	3163	1.137513	GCGTGCAAGAAGTTCGTACT	58.862	50.000	2.99	0.00	35.68	2.73
3077	3288	2.943033	ACTTTGGTGTGGAAGAAGAACG	59.057	45.455	0.00	0.00	0.00	3.95
3080	3291	4.407621	TCTGTACTTTGGTGTGGAAGAAGA	59.592	41.667	0.00	0.00	0.00	2.87
3114	3325	3.326747	GTTGTTGTTCATAGAGTCGCCT	58.673	45.455	0.00	0.00	0.00	5.52
3115	3326	2.092211	CGTTGTTGTTCATAGAGTCGCC	59.908	50.000	0.00	0.00	0.00	5.54
3126	3337	0.385473	CACCGCCATCGTTGTTGTTC	60.385	55.000	0.00	0.00	0.00	3.18
3149	3365	2.159282	AGTACTCCGTACGCTTTCATGG	60.159	50.000	10.49	0.00	43.05	3.66
3272	3493	3.506810	TGTTCTTTTGGCAAACTTGACG	58.493	40.909	13.10	0.00	39.74	4.35
3299	3520	5.793457	CCACCGACTCGTTTGATTTATTTTC	59.207	40.000	0.00	0.00	0.00	2.29
3303	3525	3.930848	GACCACCGACTCGTTTGATTTAT	59.069	43.478	0.00	0.00	0.00	1.40
3304	3526	3.319755	GACCACCGACTCGTTTGATTTA	58.680	45.455	0.00	0.00	0.00	1.40
3343	3565	2.480419	ACTCTTTGCGTGCTGAATGTAC	59.520	45.455	0.00	0.00	0.00	2.90
3403	3625	5.127356	AGCTAGTAAACAGTCCTGTCCATAC	59.873	44.000	0.00	5.42	44.13	2.39
3406	3628	3.507411	AGCTAGTAAACAGTCCTGTCCA	58.493	45.455	0.00	0.00	44.13	4.02
3439	3661	4.883083	TCTCAGAGCAACACGTCTTATTT	58.117	39.130	0.00	0.00	0.00	1.40
3442	3664	4.218635	AGAATCTCAGAGCAACACGTCTTA	59.781	41.667	0.00	0.00	0.00	2.10
3444	3666	2.560542	AGAATCTCAGAGCAACACGTCT	59.439	45.455	0.00	0.00	0.00	4.18
3445	3667	2.953020	AGAATCTCAGAGCAACACGTC	58.047	47.619	0.00	0.00	0.00	4.34
3446	3668	3.393089	AAGAATCTCAGAGCAACACGT	57.607	42.857	0.00	0.00	0.00	4.49
3447	3669	4.092091	GGTTAAGAATCTCAGAGCAACACG	59.908	45.833	0.00	0.00	0.00	4.49
3448	3670	5.241662	AGGTTAAGAATCTCAGAGCAACAC	58.758	41.667	0.00	0.00	0.00	3.32
3449	3671	5.489792	AGGTTAAGAATCTCAGAGCAACA	57.510	39.130	0.00	0.00	0.00	3.33
3452	3688	5.481824	TCTCAAGGTTAAGAATCTCAGAGCA	59.518	40.000	0.00	0.00	0.00	4.26
3457	3693	6.212388	AGAGCTTCTCAAGGTTAAGAATCTCA	59.788	38.462	14.69	0.00	42.81	3.27
3485	3721	9.218359	GCCGAAAAGCTAGTAAACATAAAATAC	57.782	33.333	0.00	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.