AutoCloner

Multiple sequence alignment - TraesCS3D01G209700

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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	TraesCS3D01G209700	chr3D	100.000	5353	0	0	1	5353	277134936	277140288	0.000000e+00	9886
1	TraesCS3D01G209700	chr3D	88.291	316	34	2	4984	5296	457242271	457241956	5.060000e-100	375
2	TraesCS3D01G209700	chr3D	95.833	144	6	0	4	147	22928833	22928690	3.220000e-57	233
3	TraesCS3D01G209700	chr3D	79.876	323	39	10	149	456	543868340	543868029	4.200000e-51	213
4	TraesCS3D01G209700	chr3B	95.417	5411	138	31	1	5353	373135449	373130091	0.000000e+00	8517
5	TraesCS3D01G209700	chr3B	87.228	368	38	8	4941	5302	526193211	526193575	1.390000e-110	411
6	TraesCS3D01G209700	chr3B	77.542	472	61	19	160	589	458016019	458016487	5.360000e-60	243
7	TraesCS3D01G209700	chr3B	89.362	141	14	1	319	458	742146222	742146082	5.510000e-40	176
8	TraesCS3D01G209700	chr3A	93.891	2701	74	22	644	3300	362341799	362339146	0.000000e+00	3989
9	TraesCS3D01G209700	chr3A	96.287	1562	49	2	3298	4859	362339096	362337544	0.000000e+00	2555
10	TraesCS3D01G209700	chr3A	91.608	429	22	3	4858	5272	362337439	362337011	9.990000e-162	580
11	TraesCS3D01G209700	chr5B	87.316	339	37	6	4963	5296	711818252	711818589	3.020000e-102	383
12	TraesCS3D01G209700	chr5B	87.021	339	38	6	4963	5296	711820316	711820653	1.410000e-100	377
13	TraesCS3D01G209700	chr5B	86.391	338	41	5	4963	5296	711814127	711814463	1.100000e-96	364
14	TraesCS3D01G209700	chr5B	86.391	338	41	5	4963	5296	711816189	711816525	1.100000e-96	364
15	TraesCS3D01G209700	chr5B	78.059	474	61	10	158	590	667771426	667770955	5.320000e-65	259
16	TraesCS3D01G209700	chr5B	95.833	144	6	0	4	147	599794928	599795071	3.220000e-57	233
17	TraesCS3D01G209700	chr5B	76.744	473	67	14	158	589	703175847	703175377	1.940000e-54	224
18	TraesCS3D01G209700	chr5B	78.451	297	37	11	319	590	561873184	561872890	9.220000e-38	169
19	TraesCS3D01G209700	chr5B	77.592	299	37	14	319	589	84891048	84891344	2.580000e-33	154
20	TraesCS3D01G209700	chr1D	88.438	320	32	4	4985	5302	309632859	309632543	1.090000e-101	381
21	TraesCS3D01G209700	chr2B	78.378	481	62	18	148	589	535019204	535018727	1.900000e-69	274
22	TraesCS3D01G209700	chr2B	91.489	141	11	1	319	458	225847618	225847478	5.470000e-45	193
23	TraesCS3D01G209700	chr2B	77.178	241	35	8	208	432	150198902	150199138	7.280000e-24	122
24	TraesCS3D01G209700	chr7B	78.288	479	62	18	150	589	203281021	203281496	2.460000e-68	270
25	TraesCS3D01G209700	chr7B	96.528	144	5	0	4	147	652145145	652145288	6.930000e-59	239
26	TraesCS3D01G209700	chr7B	95.862	145	5	1	4	147	750048317	750048461	3.220000e-57	233
27	TraesCS3D01G209700	chr5D	81.503	346	42	10	129	458	122517814	122518153	1.140000e-66	265
28	TraesCS3D01G209700	chr5D	90.071	141	13	1	319	458	129648337	129648197	1.180000e-41	182
29	TraesCS3D01G209700	chr6D	81.931	321	41	5	150	456	224055341	224055658	6.880000e-64	255
30	TraesCS3D01G209700	chr6D	90.845	142	11	2	319	458	448696949	448697090	7.080000e-44	189
31	TraesCS3D01G209700	chr2A	96.552	145	4	1	4	147	7915766	7915622	6.930000e-59	239
32	TraesCS3D01G209700	chr2A	74.099	444	65	26	189	589	762473544	762473980	2.600000e-28	137
33	TraesCS3D01G209700	chr1B	96.552	145	4	1	4	147	683992173	683992029	6.930000e-59	239
34	TraesCS3D01G209700	chr1B	80.251	319	41	9	158	458	352900124	352899810	2.510000e-53	220
35	TraesCS3D01G209700	chr1B	79.530	298	33	16	319	589	529162871	529163167	2.550000e-43	187
36	TraesCS3D01G209700	chr6B	95.833	144	6	0	4	147	508172196	508172339	3.220000e-57	233
37	TraesCS3D01G209700	chr6B	80.471	297	32	11	319	589	410875789	410876085	2.530000e-48	204
38	TraesCS3D01G209700	chr6B	79.048	315	42	9	158	455	195123168	195123475	1.520000e-45	195
39	TraesCS3D01G209700	chr6B	83.088	136	22	1	454	589	637865299	637865433	7.280000e-24	122
40	TraesCS3D01G209700	chr1A	95.833	144	6	0	4	147	246130727	246130870	3.220000e-57	233
41	TraesCS3D01G209700	chr2D	78.683	319	46	9	158	458	14839186	14838872	5.470000e-45	193
42	TraesCS3D01G209700	chr2D	90.071	141	13	1	319	458	601807906	601808046	1.180000e-41	182
43	TraesCS3D01G209700	chr4B	89.362	141	14	1	319	458	273393923	273393783	5.510000e-40	176

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	TraesCS3D01G209700	chr3D	277134936	277140288	5352	False	9886.000000	9886	100.000000	1	5353	1	chr3D.!!$F1	5352
1	TraesCS3D01G209700	chr3B	373130091	373135449	5358	True	8517.000000	8517	95.417000	1	5353	1	chr3B.!!$R1	5352
2	TraesCS3D01G209700	chr3A	362337011	362341799	4788	True	2374.666667	3989	93.928667	644	5272	3	chr3A.!!$R1	4628
3	TraesCS3D01G209700	chr5B	711814127	711820653	6526	False	372.000000	383	86.779750	4963	5296	4	chr5B.!!$F3	333

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
180	181	0.750911	CCCATCTTGCTCTCTTGGGC	60.751	60.000	0.00	0.00	40.55	5.36	F
181	182	1.094073	CCATCTTGCTCTCTTGGGCG	61.094	60.000	0.00	0.00	0.00	6.13	F
298	299	1.719246	CACACTGTCAACCACGTATCG	59.281	52.381	0.00	0.00	0.00	2.92	F
571	597	1.803519	GCGGCTCACAAGTCTCGAG	60.804	63.158	5.93	5.93	0.00	4.04	F
1934	1968	0.752658	TCATCTGGCCAGGACATACG	59.247	55.000	32.23	12.76	0.00	3.06	F
2630	2689	2.107950	TAGCGGATGGTGTGAAAAGG	57.892	50.000	0.00	0.00	0.00	3.11	F
3252	3323	0.586319	ATTCAGTTGTTCCACGTGCG	59.414	50.000	10.91	3.66	0.00	5.34	F
4236	4359	2.038952	TCACATCCAAGTTCAGACCCAG	59.961	50.000	0.00	0.00	0.00	4.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1455	1489	1.339097	ACTCCTCCAGTAACGCAACT	58.661	50.000	0.00	0.00	31.37	3.16	R
1744	1778	2.508716	AGTGCTGATCTGAATCACCCAT	59.491	45.455	3.42	0.00	36.98	4.00	R
1934	1968	3.730715	CGTTGAAAGCAAATTCAGACACC	59.269	43.478	0.00	0.00	40.21	4.16	R
2382	2441	2.294233	GAGCCTGCAAAGTTTGTCATGA	59.706	45.455	16.70	0.00	0.00	3.07	R
3238	3309	0.593773	AAATGCGCACGTGGAACAAC	60.594	50.000	14.90	0.00	44.16	3.32	R
3950	4073	0.901827	TTACTGAGATGCCGGCAAGA	59.098	50.000	36.33	16.27	0.00	3.02	R
4332	4455	1.331756	CTAACTGCCAGCGCCAAATAG	59.668	52.381	2.29	0.00	0.00	1.73	R
5267	6512	1.151668	GCTGCGAGATCAACAAGTGT	58.848	50.000	0.00	0.00	0.00	3.55	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
139	140	7.731729	CGACATATCATCTTGAAATTTACGACG	59.268	37.037	0.00	0.00	0.00	5.12
154	155	2.657296	ACGTCACCGTCGTGCTTG	60.657	61.111	0.00	0.00	46.28	4.01
162	163	2.435059	GTCGTGCTTGGGAGAGCC	60.435	66.667	0.00	0.00	42.01	4.70
180	181	0.750911	CCCATCTTGCTCTCTTGGGC	60.751	60.000	0.00	0.00	40.55	5.36
181	182	1.094073	CCATCTTGCTCTCTTGGGCG	61.094	60.000	0.00	0.00	0.00	6.13
200	201	2.802816	GCGAACTAGCAATAGATGGTGG	59.197	50.000	0.00	0.00	43.01	4.61
221	222	3.103007	GTTTTCGTGGACGGAAAACAAG	58.897	45.455	19.52	0.00	46.92	3.16
253	254	3.855950	GTGCATATGCTGAGAACTTTTGC	59.144	43.478	27.13	0.00	42.66	3.68
257	258	5.406175	GCATATGCTGAGAACTTTTGCAAAA	59.594	36.000	22.61	22.61	37.20	2.44
287	288	7.151999	ACAACAGAATTTTAACACACTGTCA	57.848	32.000	0.00	0.00	37.57	3.58
298	299	1.719246	CACACTGTCAACCACGTATCG	59.281	52.381	0.00	0.00	0.00	2.92
346	347	9.083080	GCTTCCATGTTTGTTGGTAAATATAAC	57.917	33.333	0.00	0.00	35.64	1.89
528	554	8.949953	GTTTCTTTTCGAGTCGATCTCTAATAG	58.050	37.037	17.34	5.03	40.75	1.73
530	556	8.078959	TCTTTTCGAGTCGATCTCTAATAGAG	57.921	38.462	17.34	10.93	43.64	2.43
531	557	7.711772	TCTTTTCGAGTCGATCTCTAATAGAGT	59.288	37.037	17.34	4.89	42.83	3.24
571	597	1.803519	GCGGCTCACAAGTCTCGAG	60.804	63.158	5.93	5.93	0.00	4.04
606	632	4.884164	GCCCTACAAGCAATTGACTAAGAT	59.116	41.667	10.34	0.00	0.00	2.40
1128	1162	2.204136	TCCCACTGCCTCCACCAT	60.204	61.111	0.00	0.00	0.00	3.55
1744	1778	4.480115	TGGAACTGAAGAAGACAGACCTA	58.520	43.478	0.00	0.00	38.55	3.08
1934	1968	0.752658	TCATCTGGCCAGGACATACG	59.247	55.000	32.23	12.76	0.00	3.06
1977	2011	4.082408	ACGCCTAAAATTAAAGGAACCAGC	60.082	41.667	9.64	0.00	34.58	4.85
2106	2140	4.207955	CACTGCCTGATACTGAGGTACTA	58.792	47.826	0.00	0.00	41.55	1.82
2382	2441	6.125029	AGAAGCACTGACATTAAATATGCCT	58.875	36.000	0.00	0.00	31.94	4.75
2630	2689	2.107950	TAGCGGATGGTGTGAAAAGG	57.892	50.000	0.00	0.00	0.00	3.11
2747	2806	6.239289	CCACCAACTTATTGTTCACTTGGAAT	60.239	38.462	0.00	0.00	37.93	3.01
2752	2811	9.994432	CAACTTATTGTTCACTTGGAATAGATC	57.006	33.333	0.00	0.00	37.93	2.75
3153	3224	7.377766	TGACAAAATCTAAGGTATGTGCTTC	57.622	36.000	0.00	0.00	0.00	3.86
3179	3250	3.923017	AGTTTTTATGTCTGCCTGCAC	57.077	42.857	0.00	0.00	0.00	4.57
3194	3265	5.315348	TGCCTGCACTATTCATTATGCATA	58.685	37.500	1.16	1.16	46.35	3.14
3235	3306	3.822735	GTCCATGTATGTATGGCTGCATT	59.177	43.478	0.50	0.00	45.83	3.56
3238	3309	4.082949	CCATGTATGTATGGCTGCATTCAG	60.083	45.833	0.50	0.00	41.02	3.02
3252	3323	0.586319	ATTCAGTTGTTCCACGTGCG	59.414	50.000	10.91	3.66	0.00	5.34
3689	3812	6.627395	TTTTCTCATGTGGTACGTGATTTT	57.373	33.333	0.00	0.00	42.61	1.82
3762	3885	3.593442	AGTTCCACCCTGTGAATTGAA	57.407	42.857	0.00	0.00	35.23	2.69
3950	4073	9.100197	ACCAAACATTACTCCATCCTTAAAAAT	57.900	29.630	0.00	0.00	0.00	1.82
4150	4273	3.306294	GCTGAAGAAGGGGACAAAAATGG	60.306	47.826	0.00	0.00	0.00	3.16
4236	4359	2.038952	TCACATCCAAGTTCAGACCCAG	59.961	50.000	0.00	0.00	0.00	4.45
4332	4455	5.121298	GCTTCAAGAATTTTGCAGGAATTCC	59.879	40.000	23.25	17.31	41.97	3.01
4477	4600	4.441495	GCTTGTTTTGGTACTTTTGGCTCT	60.441	41.667	0.00	0.00	0.00	4.09
4633	4756	2.936498	CACCGTGGGTACATGAAGATTC	59.064	50.000	0.00	0.00	35.58	2.52
4803	4926	0.947244	CACGCTTTGGAAGTTGCTCT	59.053	50.000	0.00	0.00	0.00	4.09
4844	4967	6.033091	GCGGATTTTTAAATGTTACCTTGTCG	59.967	38.462	0.00	0.00	0.00	4.35
5041	6282	1.178534	ATTTGCAACCACGGTCCCTG	61.179	55.000	0.00	0.00	0.00	4.45
5267	6512	5.894298	AGATCACCCAGAAGTTGCATATA	57.106	39.130	0.00	0.00	0.00	0.86
5322	6567	6.737254	TCATCATCATCATCATCATTTCGG	57.263	37.500	0.00	0.00	0.00	4.30
5342	6587	1.345741	GCATCCTCATCCTCCGAATCA	59.654	52.381	0.00	0.00	0.00	2.57
5348	6593	3.305950	CCTCATCCTCCGAATCAGATGAC	60.306	52.174	0.00	0.00	40.03	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
162	163	1.094073	CGCCCAAGAGAGCAAGATGG	61.094	60.000	0.00	0.00	0.00	3.51
180	181	4.060038	ACCACCATCTATTGCTAGTTCG	57.940	45.455	0.00	0.00	0.00	3.95
181	182	6.456988	CGAAAACCACCATCTATTGCTAGTTC	60.457	42.308	0.00	0.00	0.00	3.01
200	201	2.828874	TGTTTTCCGTCCACGAAAAC	57.171	45.000	20.71	20.71	42.48	2.43
221	222	5.124457	TCTCAGCATATGCACCTTTCTTTTC	59.876	40.000	28.62	0.00	45.16	2.29
257	258	9.267084	AGTGTGTTAAAATTCTGTTGTTGTTTT	57.733	25.926	0.00	0.00	0.00	2.43
261	262	7.540400	TGACAGTGTGTTAAAATTCTGTTGTTG	59.460	33.333	0.00	0.00	36.49	3.33
263	264	7.151999	TGACAGTGTGTTAAAATTCTGTTGT	57.848	32.000	0.00	0.00	36.49	3.32
264	265	7.009174	GGTTGACAGTGTGTTAAAATTCTGTTG	59.991	37.037	0.00	0.00	36.49	3.33
266	267	6.151985	TGGTTGACAGTGTGTTAAAATTCTGT	59.848	34.615	0.00	5.68	38.56	3.41
267	268	6.472163	GTGGTTGACAGTGTGTTAAAATTCTG	59.528	38.462	0.00	0.00	27.45	3.02
269	270	5.454232	CGTGGTTGACAGTGTGTTAAAATTC	59.546	40.000	0.00	0.00	27.45	2.17
270	271	5.106078	ACGTGGTTGACAGTGTGTTAAAATT	60.106	36.000	0.00	0.00	27.45	1.82
271	272	4.396790	ACGTGGTTGACAGTGTGTTAAAAT	59.603	37.500	0.00	0.00	27.45	1.82
272	273	3.752222	ACGTGGTTGACAGTGTGTTAAAA	59.248	39.130	0.00	0.00	27.45	1.52
287	288	3.385755	AGGCCTAATTACGATACGTGGTT	59.614	43.478	1.29	4.59	41.39	3.67
298	299	7.809546	AGCTTGAAGATTTAGGCCTAATTAC	57.190	36.000	25.70	18.17	0.00	1.89
346	347	9.603298	CATATATGTTGTCCATGATTTTCTTCG	57.397	33.333	4.43	0.00	34.86	3.79
550	576	1.803519	GAGACTTGTGAGCCGCTCG	60.804	63.158	15.58	3.83	32.35	5.03
606	632	3.047280	GATTGCACGACGCCACCA	61.047	61.111	0.00	0.00	41.33	4.17
1455	1489	1.339097	ACTCCTCCAGTAACGCAACT	58.661	50.000	0.00	0.00	31.37	3.16
1744	1778	2.508716	AGTGCTGATCTGAATCACCCAT	59.491	45.455	3.42	0.00	36.98	4.00
1934	1968	3.730715	CGTTGAAAGCAAATTCAGACACC	59.269	43.478	0.00	0.00	40.21	4.16
2195	2229	7.439356	TGATAACTTGCATCTCACAAGCTATAC	59.561	37.037	3.52	0.00	46.81	1.47
2246	2305	9.158233	CATGTGATGGAATTTAAGCAAGAAATT	57.842	29.630	3.67	3.67	38.81	1.82
2382	2441	2.294233	GAGCCTGCAAAGTTTGTCATGA	59.706	45.455	16.70	0.00	0.00	3.07
2630	2689	3.923017	ATAACTGGTGCAAGTTTCAGC	57.077	42.857	8.99	0.00	40.77	4.26
2747	2806	6.986250	AGAATCAGCAATACATGACGATCTA	58.014	36.000	0.00	0.00	0.00	1.98
3153	3224	6.127925	TGCAGGCAGACATAAAAACTTCTATG	60.128	38.462	0.00	0.00	0.00	2.23
3194	3265	5.744171	TGGACATGCACTAATATCACAGTT	58.256	37.500	0.00	0.00	0.00	3.16
3235	3306	2.530497	GCGCACGTGGAACAACTGA	61.530	57.895	18.88	0.00	44.16	3.41
3238	3309	0.593773	AAATGCGCACGTGGAACAAC	60.594	50.000	14.90	0.00	44.16	3.32
3739	3862	5.055265	TCAATTCACAGGGTGGAACTAAA	57.945	39.130	0.00	0.00	36.74	1.85
3950	4073	0.901827	TTACTGAGATGCCGGCAAGA	59.098	50.000	36.33	16.27	0.00	3.02
4150	4273	5.975939	GCTGATCTCTGTTTATTTGGAATGC	59.024	40.000	0.00	0.00	0.00	3.56
4236	4359	4.749976	CCAGTAGGCAAACTAGTTCTCTC	58.250	47.826	8.95	0.00	32.96	3.20
4332	4455	1.331756	CTAACTGCCAGCGCCAAATAG	59.668	52.381	2.29	0.00	0.00	1.73
4477	4600	8.449397	GCAATATGCAATTACAAAATGGAAACA	58.551	29.630	0.00	0.00	44.26	2.83
4633	4756	6.255887	GGAAGTGAGTTGACTGGATAATAACG	59.744	42.308	0.00	0.00	0.00	3.18
4803	4926	3.394674	TCCGCACACTCATTAAACTCA	57.605	42.857	0.00	0.00	0.00	3.41
5001	6241	1.537202	GCCAAGTTTTGATGCTCGTCT	59.463	47.619	0.00	0.00	0.00	4.18
5041	6282	5.065731	TGCATGGATTTGGTGTTTTGAAAAC	59.934	36.000	13.55	13.55	0.00	2.43
5267	6512	1.151668	GCTGCGAGATCAACAAGTGT	58.848	50.000	0.00	0.00	0.00	3.55
5308	6553	3.181452	TGAGGATGCCGAAATGATGATGA	60.181	43.478	0.00	0.00	0.00	2.92
5309	6554	3.143728	TGAGGATGCCGAAATGATGATG	58.856	45.455	0.00	0.00	0.00	3.07
5310	6555	3.497103	TGAGGATGCCGAAATGATGAT	57.503	42.857	0.00	0.00	0.00	2.45
5322	6567	1.345741	TGATTCGGAGGATGAGGATGC	59.654	52.381	0.00	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.