AutoCloner

Multiple sequence alignment - TraesCS7B01G270700

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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	TraesCS7B01G270700	chr7B	100.000	2522	0	0	1	2522	496279471	496281992	0.000000e+00	4658.0
1	TraesCS7B01G270700	chr7B	91.520	2559	160	18	1	2522	593507801	593510339	0.000000e+00	3470.0
2	TraesCS7B01G270700	chr7B	89.185	1766	134	31	772	2522	702449611	702447888	0.000000e+00	2150.0
3	TraesCS7B01G270700	chr7B	79.717	991	171	16	518	1494	497963293	497962319	0.000000e+00	689.0
4	TraesCS7B01G270700	chr7B	88.363	507	49	7	273	773	702450329	702449827	3.590000e-168	601.0
5	TraesCS7B01G270700	chr7B	80.139	433	45	26	55	476	525836398	525836800	4.110000e-73	285.0
6	TraesCS7B01G270700	chr7B	85.859	198	15	5	1	197	702450511	702450326	5.500000e-47	198.0
7	TraesCS7B01G270700	chr2A	91.124	2535	172	35	3	2519	407350913	407353412	0.000000e+00	3386.0
8	TraesCS7B01G270700	chr1D	90.762	2284	177	22	250	2522	341359893	341357633	0.000000e+00	3018.0
9	TraesCS7B01G270700	chr1D	87.317	205	12	6	1	203	341360081	341359889	3.270000e-54	222.0
10	TraesCS7B01G270700	chr2B	89.381	1761	132	24	772	2519	506339976	506341694	0.000000e+00	2165.0
11	TraesCS7B01G270700	chr2B	88.868	530	50	6	250	773	506339235	506339761	0.000000e+00	643.0
12	TraesCS7B01G270700	chr2B	85.854	205	15	6	1	203	506339047	506339239	3.290000e-49	206.0
13	TraesCS7B01G270700	chr1A	88.372	1763	151	27	772	2522	19544309	19542589	0.000000e+00	2071.0
14	TraesCS7B01G270700	chr1A	87.736	530	56	6	250	773	19545577	19545051	5.960000e-171	610.0
15	TraesCS7B01G270700	chr1A	85.854	205	15	6	1	203	19545765	19545573	3.290000e-49	206.0
16	TraesCS7B01G270700	chr3B	89.752	1493	116	26	772	2246	749667998	749666525	0.000000e+00	1875.0
17	TraesCS7B01G270700	chr3B	88.136	531	52	6	250	773	749668740	749668214	2.760000e-174	621.0
18	TraesCS7B01G270700	chr3B	83.824	204	21	4	1	203	749668928	749668736	1.540000e-42	183.0
19	TraesCS7B01G270700	chrUn	80.412	970	163	21	540	1495	132706227	132707183	0.000000e+00	713.0
20	TraesCS7B01G270700	chrUn	81.290	155	28	1	1614	1768	132707261	132707414	9.470000e-25	124.0
21	TraesCS7B01G270700	chr5D	86.414	633	83	3	864	1495	158237044	158236414	0.000000e+00	689.0
22	TraesCS7B01G270700	chr7D	84.211	152	24	0	1617	1768	545349492	545349341	5.620000e-32	148.0
23	TraesCS7B01G270700	chr6A	97.917	48	0	1	429	475	261513183	261513136	5.780000e-12	82.4

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	TraesCS7B01G270700	chr7B	496279471	496281992	2521	False	4658.000000	4658	100.000000	1	2522	1	chr7B.!!$F1	2521
1	TraesCS7B01G270700	chr7B	593507801	593510339	2538	False	3470.000000	3470	91.520000	1	2522	1	chr7B.!!$F3	2521
2	TraesCS7B01G270700	chr7B	702447888	702450511	2623	True	983.000000	2150	87.802333	1	2522	3	chr7B.!!$R2	2521
3	TraesCS7B01G270700	chr7B	497962319	497963293	974	True	689.000000	689	79.717000	518	1494	1	chr7B.!!$R1	976
4	TraesCS7B01G270700	chr2A	407350913	407353412	2499	False	3386.000000	3386	91.124000	3	2519	1	chr2A.!!$F1	2516
5	TraesCS7B01G270700	chr1D	341357633	341360081	2448	True	1620.000000	3018	89.039500	1	2522	2	chr1D.!!$R1	2521
6	TraesCS7B01G270700	chr2B	506339047	506341694	2647	False	1004.666667	2165	88.034333	1	2519	3	chr2B.!!$F1	2518
7	TraesCS7B01G270700	chr1A	19542589	19545765	3176	True	962.333333	2071	87.320667	1	2522	3	chr1A.!!$R1	2521
8	TraesCS7B01G270700	chr3B	749666525	749668928	2403	True	893.000000	1875	87.237333	1	2246	3	chr3B.!!$R1	2245
9	TraesCS7B01G270700	chrUn	132706227	132707414	1187	False	418.500000	713	80.851000	540	1768	2	chrUn.!!$F1	1228
10	TraesCS7B01G270700	chr5D	158236414	158237044	630	True	689.000000	689	86.414000	864	1495	1	chr5D.!!$R1	631

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
763	863	0.595825	GTGTTGCCTCACTTTGCAGC	60.596	55.0	0.0	0.0	38.95	5.25	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2501	3431	1.269778	TGCCTGTCTCAGTTTCGTCAG	60.27	52.381	0.0	0.0	0.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	72	1.355381	TCACGGGAGGGTAGTAACTGA	59.645	52.381	0.00	0.00	0.00	3.41
97	99	7.998753	GCTTGCTTAGCTCATTCATTTAAAT	57.001	32.000	5.60	0.00	46.77	1.40
98	100	8.416485	GCTTGCTTAGCTCATTCATTTAAATT	57.584	30.769	5.60	0.00	46.77	1.82
99	101	8.876790	GCTTGCTTAGCTCATTCATTTAAATTT	58.123	29.630	5.60	0.00	46.77	1.82
147	149	1.138568	AGCTAGCCAGATGCCTGATT	58.861	50.000	12.13	0.00	43.02	2.57
151	153	3.243334	GCTAGCCAGATGCCTGATTTTTC	60.243	47.826	2.29	0.00	43.02	2.29
152	154	2.811410	AGCCAGATGCCTGATTTTTCA	58.189	42.857	0.00	0.00	43.02	2.69
197	199	1.225376	TGAACTTGCCTACGCGGTTG	61.225	55.000	12.47	0.00	38.08	3.77
202	204	2.356553	GCCTACGCGGTTGTCACA	60.357	61.111	12.47	0.00	34.25	3.58
203	205	2.380410	GCCTACGCGGTTGTCACAG	61.380	63.158	12.47	0.00	34.25	3.66
254	256	6.854496	TTAATTTTCTAACTGCACTCACGT	57.146	33.333	0.00	0.00	0.00	4.49
255	257	7.949903	TTAATTTTCTAACTGCACTCACGTA	57.050	32.000	0.00	0.00	0.00	3.57
256	258	6.854496	AATTTTCTAACTGCACTCACGTAA	57.146	33.333	0.00	0.00	0.00	3.18
257	259	5.646467	TTTTCTAACTGCACTCACGTAAC	57.354	39.130	0.00	0.00	0.00	2.50
258	260	3.994204	TCTAACTGCACTCACGTAACA	57.006	42.857	0.00	0.00	0.00	2.41
259	261	3.635331	TCTAACTGCACTCACGTAACAC	58.365	45.455	0.00	0.00	0.00	3.32
260	262	2.596904	AACTGCACTCACGTAACACT	57.403	45.000	0.00	0.00	0.00	3.55
261	263	1.852942	ACTGCACTCACGTAACACTG	58.147	50.000	0.00	0.00	0.00	3.66
262	264	1.136305	ACTGCACTCACGTAACACTGT	59.864	47.619	0.00	0.00	0.00	3.55
263	265	2.201732	CTGCACTCACGTAACACTGTT	58.798	47.619	0.00	0.00	0.00	3.16
264	266	2.607635	CTGCACTCACGTAACACTGTTT	59.392	45.455	0.00	0.00	0.00	2.83
265	267	3.004171	TGCACTCACGTAACACTGTTTT	58.996	40.909	0.00	0.00	0.00	2.43
266	268	4.182339	TGCACTCACGTAACACTGTTTTA	58.818	39.130	0.00	0.00	0.00	1.52
267	269	4.812091	TGCACTCACGTAACACTGTTTTAT	59.188	37.500	0.00	0.00	0.00	1.40
268	270	5.984323	TGCACTCACGTAACACTGTTTTATA	59.016	36.000	0.00	0.00	0.00	0.98
269	271	6.074195	TGCACTCACGTAACACTGTTTTATAC	60.074	38.462	0.00	0.00	0.00	1.47
270	272	6.145048	GCACTCACGTAACACTGTTTTATACT	59.855	38.462	0.00	0.00	0.00	2.12
271	273	7.306983	GCACTCACGTAACACTGTTTTATACTT	60.307	37.037	0.00	0.00	0.00	2.24
272	274	8.002107	CACTCACGTAACACTGTTTTATACTTG	58.998	37.037	0.00	0.00	0.00	3.16
273	275	7.707893	ACTCACGTAACACTGTTTTATACTTGT	59.292	33.333	0.00	0.00	0.00	3.16
274	276	8.422973	TCACGTAACACTGTTTTATACTTGTT	57.577	30.769	0.00	0.00	37.41	2.83
275	277	8.542132	TCACGTAACACTGTTTTATACTTGTTC	58.458	33.333	0.00	0.00	36.08	3.18
308	390	2.483714	GCAGCGAATAATGTCTGGGAGA	60.484	50.000	0.00	0.00	0.00	3.71
484	574	5.248248	TCTCCATGTGTTCTTTCATGTCCTA	59.752	40.000	0.00	0.00	39.53	2.94
622	713	7.823665	GCCATCAGATATTGATAGCAATGAAA	58.176	34.615	16.31	0.00	46.27	2.69
645	736	5.745312	AGATATCCACCGATGCTGATAAA	57.255	39.130	0.00	0.00	0.00	1.40
694	791	4.991687	GTCTCGACAAAGACCTTGAAGATT	59.008	41.667	0.00	0.00	39.85	2.40
742	840	4.018960	AGACTGCTGGAAATGAGGTAATGT	60.019	41.667	0.00	0.00	0.00	2.71
763	863	0.595825	GTGTTGCCTCACTTTGCAGC	60.596	55.000	0.00	0.00	38.95	5.25
898	1766	4.725304	AGGGTTTTAAGAATAGGGGATCGT	59.275	41.667	0.00	0.00	0.00	3.73
988	1857	7.246027	AGAGTTTAGGGGTTTGTTGGATATTT	58.754	34.615	0.00	0.00	0.00	1.40
1121	1990	4.210331	AGTGTGCATAGAATTTGGGGATC	58.790	43.478	0.00	0.00	0.00	3.36
1190	2083	4.925054	CACAAAGGCCATTTACAACATCTG	59.075	41.667	5.01	0.00	0.00	2.90
1245	2138	2.954318	AGCATGGTGTAAGATGATTGGC	59.046	45.455	0.00	0.00	0.00	4.52
1340	2233	5.413833	CACCATCAACAAGTCTAAGCATCTT	59.586	40.000	0.00	0.00	0.00	2.40
1370	2263	0.394762	TTCCCTGCTGTCATGGATGC	60.395	55.000	0.00	0.00	36.96	3.91
1500	2393	8.856153	TCCATCTTGTAGTAAGTGCATTTAAA	57.144	30.769	2.90	0.00	0.00	1.52
1502	2395	8.730680	CCATCTTGTAGTAAGTGCATTTAAACT	58.269	33.333	2.90	3.12	0.00	2.66
1503	2396	9.546909	CATCTTGTAGTAAGTGCATTTAAACTG	57.453	33.333	2.90	4.01	0.00	3.16
1504	2397	8.671384	TCTTGTAGTAAGTGCATTTAAACTGT	57.329	30.769	2.90	0.00	0.00	3.55
1505	2398	8.770828	TCTTGTAGTAAGTGCATTTAAACTGTC	58.229	33.333	2.90	0.56	0.00	3.51
1506	2399	7.429636	TGTAGTAAGTGCATTTAAACTGTCC	57.570	36.000	2.90	0.00	0.00	4.02
1507	2400	7.221450	TGTAGTAAGTGCATTTAAACTGTCCT	58.779	34.615	2.90	0.00	0.00	3.85
1508	2401	7.717875	TGTAGTAAGTGCATTTAAACTGTCCTT	59.282	33.333	2.90	0.00	0.00	3.36
1509	2402	7.582667	AGTAAGTGCATTTAAACTGTCCTTT	57.417	32.000	2.90	0.00	0.00	3.11
1510	2403	8.685838	AGTAAGTGCATTTAAACTGTCCTTTA	57.314	30.769	2.90	0.00	0.00	1.85
1551	2444	5.635278	TCATTCTCAATGCTATCCTCCAA	57.365	39.130	0.00	0.00	38.77	3.53
1552	2445	6.196918	TCATTCTCAATGCTATCCTCCAAT	57.803	37.500	0.00	0.00	38.77	3.16
1571	2466	8.997323	CCTCCAATTTTGTTTGTTATATTTGCA	58.003	29.630	0.00	0.00	0.00	4.08
1654	2554	1.386533	GCTGGATGTGGATGAACCTG	58.613	55.000	0.00	0.00	39.86	4.00
1670	2570	4.652421	TGAACCTGTACCAAGTTCTACACT	59.348	41.667	16.19	0.00	40.42	3.55
1691	2591	6.320418	ACACTAAGAGTTTCGGTTTGGAATTT	59.680	34.615	0.00	0.00	0.00	1.82
1768	2668	6.096282	TGGAAAACTGAGGGTAAGTCTTTTTG	59.904	38.462	0.00	0.00	0.00	2.44
1770	2670	6.694877	AAACTGAGGGTAAGTCTTTTTGAC	57.305	37.500	0.00	0.00	45.67	3.18
2101	3025	2.107041	TTTCCCGGTGTGCTGACGAT	62.107	55.000	0.00	0.00	0.00	3.73
2112	3036	3.066203	TGTGCTGACGATAGCTTATTCGA	59.934	43.478	17.02	0.00	44.01	3.71
2155	3079	5.473066	AATTTGTTGCAGCAAGATTACCT	57.527	34.783	15.79	0.00	0.00	3.08
2211	3137	6.680148	ACCTTGGCAATTTATAAACCTGTT	57.320	33.333	0.00	0.00	0.00	3.16
2257	3183	2.800881	GGCAACTCCACTTTTCAAGG	57.199	50.000	0.00	0.00	34.01	3.61
2264	3190	6.761242	GCAACTCCACTTTTCAAGGTTTATTT	59.239	34.615	0.00	0.00	0.00	1.40
2302	3229	5.234972	GCAAAAGGTTTGAAGTCCAAGATTG	59.765	40.000	4.93	0.00	35.94	2.67
2501	3431	1.578583	GCATTTGGCAGGATTGATGC	58.421	50.000	0.00	0.00	43.97	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	4.517453	CCTCCCGTGATAAAGTTTGACAAA	59.483	41.667	0.00	0.00	0.00	2.83
97	99	6.118170	TGCCAATGTCAAAATGGAAAAGAAA	58.882	32.000	6.81	0.00	36.27	2.52
98	100	5.678583	TGCCAATGTCAAAATGGAAAAGAA	58.321	33.333	6.81	0.00	36.27	2.52
99	101	5.287674	TGCCAATGTCAAAATGGAAAAGA	57.712	34.783	6.81	0.00	36.27	2.52
113	115	3.217626	GCTAGCTAAAGGATGCCAATGT	58.782	45.455	7.70	0.00	0.00	2.71
114	116	2.555757	GGCTAGCTAAAGGATGCCAATG	59.444	50.000	15.72	0.00	40.04	2.82
147	149	6.344500	TCTGCTAAGCAAAAACCATTGAAAA	58.656	32.000	0.00	0.00	38.41	2.29
151	153	4.240096	CCTCTGCTAAGCAAAAACCATTG	58.760	43.478	0.00	0.00	38.41	2.82
152	154	3.306294	GCCTCTGCTAAGCAAAAACCATT	60.306	43.478	0.00	0.00	38.41	3.16
189	191	2.879813	AAACCCTGTGACAACCGCGT	62.880	55.000	4.92	0.00	0.00	6.01
197	199	1.620822	AAGGCATGAAACCCTGTGAC	58.379	50.000	0.00	0.00	0.00	3.67
266	268	9.289303	CGCTGCAAAAATAATAAGAACAAGTAT	57.711	29.630	0.00	0.00	0.00	2.12
267	269	8.508062	TCGCTGCAAAAATAATAAGAACAAGTA	58.492	29.630	0.00	0.00	0.00	2.24
268	270	7.367285	TCGCTGCAAAAATAATAAGAACAAGT	58.633	30.769	0.00	0.00	0.00	3.16
269	271	7.795431	TCGCTGCAAAAATAATAAGAACAAG	57.205	32.000	0.00	0.00	0.00	3.16
270	272	8.755696	ATTCGCTGCAAAAATAATAAGAACAA	57.244	26.923	0.00	0.00	0.00	2.83
271	273	9.847706	TTATTCGCTGCAAAAATAATAAGAACA	57.152	25.926	0.00	0.00	0.00	3.18
308	390	2.196595	TGCTGGATGCCCTTACTACTT	58.803	47.619	0.00	0.00	42.00	2.24
622	713	5.745312	TTATCAGCATCGGTGGATATCTT	57.255	39.130	0.00	0.00	0.00	2.40
645	736	1.555075	TCTTTATCAACTCCAGCGGCT	59.445	47.619	0.00	0.00	0.00	5.52
884	1752	2.088104	TGCAGACGATCCCCTATTCT	57.912	50.000	0.00	0.00	0.00	2.40
898	1766	2.638480	AGTTTGTACAGCCTTGCAGA	57.362	45.000	0.00	0.00	0.00	4.26
970	1838	5.738619	GTTGAAATATCCAACAAACCCCT	57.261	39.130	13.11	0.00	42.40	4.79
988	1857	5.675684	TCTGCATCCATACTAGTTGTTGA	57.324	39.130	0.00	0.00	0.00	3.18
1190	2083	4.009675	TGAGTTCTTGGTGGTGATATTGC	58.990	43.478	0.00	0.00	0.00	3.56
1245	2138	7.336931	TCATCATCATGAGCTCCATTCATATTG	59.663	37.037	12.15	0.31	33.80	1.90
1340	2233	0.760189	AGCAGGGAAGCTTTTTGGCA	60.760	50.000	0.00	0.00	43.70	4.92
1370	2263	6.049149	ACATTCGTCTCTGTTATACCATTGG	58.951	40.000	0.00	0.00	0.00	3.16
1654	2554	7.325579	CGAAACTCTTAGTGTAGAACTTGGTAC	59.674	40.741	0.00	0.00	40.56	3.34
1670	2570	5.010213	CCCAAATTCCAAACCGAAACTCTTA	59.990	40.000	0.00	0.00	0.00	2.10
1691	2591	4.646945	TCACAACTTTTGCAATTAGACCCA	59.353	37.500	14.08	0.00	0.00	4.51
1791	2691	6.826741	ACTTGCACTTTAGACAAAGAAACCTA	59.173	34.615	4.23	0.00	43.32	3.08
1793	2693	5.891451	ACTTGCACTTTAGACAAAGAAACC	58.109	37.500	4.23	0.00	43.32	3.27
1794	2694	6.469275	GTGACTTGCACTTTAGACAAAGAAAC	59.531	38.462	4.23	0.00	43.32	2.78
1851	2756	4.573900	CTGACAAGACTTGCCAGACTTAT	58.426	43.478	22.89	0.00	42.87	1.73
2112	3036	2.989909	TCGTGATGTGATCCATGCTTT	58.010	42.857	1.91	0.00	32.56	3.51
2155	3079	9.453572	TGACTTACTTCTTTATCGTAGGAGTTA	57.546	33.333	0.00	0.00	33.51	2.24
2211	3137	4.826733	TCTCAAGTAAGAAATTGCCTGCAA	59.173	37.500	7.06	7.06	40.47	4.08
2264	3190	8.950210	TCAAACCTTTTGCACATTAAAAATGAA	58.050	25.926	6.64	0.00	0.00	2.57
2302	3229	7.666804	TCCTGGTAAGTTTAAATCTTGGGTTAC	59.333	37.037	11.12	0.00	0.00	2.50
2323	3251	5.418840	AGTTGCCTATAAAAACACATCCTGG	59.581	40.000	0.00	0.00	0.00	4.45
2421	3351	5.393787	GCACATTTCATGGACAATGACTGAT	60.394	40.000	15.80	0.00	45.17	2.90
2501	3431	1.269778	TGCCTGTCTCAGTTTCGTCAG	60.270	52.381	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.