AutoCloner

Multiple sequence alignment - TraesCS6B01G335000

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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	TraesCS6B01G335000	chr6B	100.000	3496	0	0	1	3496	589452760	589456255	0.000000e+00	6457
1	TraesCS6B01G335000	chr4B	94.996	3497	168	6	1	3493	470135725	470139218	0.000000e+00	5481
2	TraesCS6B01G335000	chr4B	93.772	3484	202	14	1	3477	425954109	425950634	0.000000e+00	5217
3	TraesCS6B01G335000	chr7B	94.462	3431	172	14	57	3477	33969144	33972566	0.000000e+00	5267
4	TraesCS6B01G335000	chr1B	93.626	3483	207	13	1	3477	274297956	274301429	0.000000e+00	5188
5	TraesCS6B01G335000	chr1B	93.499	3492	205	17	1	3477	256486714	256483230	0.000000e+00	5171
6	TraesCS6B01G335000	chr1B	93.406	3488	206	20	1	3477	555898188	555894714	0.000000e+00	5145
7	TraesCS6B01G335000	chr3B	93.517	3486	208	17	1	3477	247151039	247154515	0.000000e+00	5169
8	TraesCS6B01G335000	chr3B	93.535	3434	203	16	56	3477	107250192	107253618	0.000000e+00	5094
9	TraesCS6B01G335000	chr3B	81.900	221	17	14	1	218	247150890	247151090	7.760000e-37	165
10	TraesCS6B01G335000	chr5B	93.679	3433	190	21	56	3477	221162636	221159220	0.000000e+00	5112
11	TraesCS6B01G335000	chr5B	81.448	221	19	13	1	218	400197154	400197355	1.000000e-35	161

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	TraesCS6B01G335000	chr6B	589452760	589456255	3495	False	6457	6457	100.0000	1	3496	1	chr6B.!!$F1	3495
1	TraesCS6B01G335000	chr4B	470135725	470139218	3493	False	5481	5481	94.9960	1	3493	1	chr4B.!!$F1	3492
2	TraesCS6B01G335000	chr4B	425950634	425954109	3475	True	5217	5217	93.7720	1	3477	1	chr4B.!!$R1	3476
3	TraesCS6B01G335000	chr7B	33969144	33972566	3422	False	5267	5267	94.4620	57	3477	1	chr7B.!!$F1	3420
4	TraesCS6B01G335000	chr1B	274297956	274301429	3473	False	5188	5188	93.6260	1	3477	1	chr1B.!!$F1	3476
5	TraesCS6B01G335000	chr1B	256483230	256486714	3484	True	5171	5171	93.4990	1	3477	1	chr1B.!!$R1	3476
6	TraesCS6B01G335000	chr1B	555894714	555898188	3474	True	5145	5145	93.4060	1	3477	1	chr1B.!!$R2	3476
7	TraesCS6B01G335000	chr3B	107250192	107253618	3426	False	5094	5094	93.5350	56	3477	1	chr3B.!!$F1	3421
8	TraesCS6B01G335000	chr3B	247150890	247154515	3625	False	2667	5169	87.7085	1	3477	2	chr3B.!!$F2	3476
9	TraesCS6B01G335000	chr5B	221159220	221162636	3416	True	5112	5112	93.6790	56	3477	1	chr5B.!!$R1	3421

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
768	935	0.474854	TTCTTCTAGGCCACCACCCA	60.475	55.0	5.01	0.0	0.00	4.51	F
1123	1290	0.035056	AATGCTCGAAGGGGTTGAGG	60.035	55.0	0.00	0.0	38.13	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2444	2632	1.001760	GTAGGGGTCAGCCTCCTGA	59.998	63.158	0.0	0.0	45.54	3.86	R
3121	3319	3.627395	TTAGGGAATGCGAACTGATGT	57.373	42.857	0.0	0.0	0.00	3.06	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
158	311	8.958119	TCTGACAAGTTCAACTACTAAAATGT	57.042	30.769	0.00	0.00	32.21	2.71
159	312	8.826710	TCTGACAAGTTCAACTACTAAAATGTG	58.173	33.333	0.00	0.00	32.21	3.21
266	420	3.946558	TCGTAAAATAATCCCAAACCCCG	59.053	43.478	0.00	0.00	0.00	5.73
404	563	5.682862	GCGCTGTATGAAATTACAATTCAGG	59.317	40.000	0.00	0.00	39.92	3.86
533	694	2.287977	AGTCCCAGGGCACTAAAAAC	57.712	50.000	0.00	0.00	0.00	2.43
650	816	2.829720	AGTGCAAAATGCCATCATCACT	59.170	40.909	0.00	0.00	44.23	3.41
665	831	0.604511	TCACTACCGCAGAGACGTGA	60.605	55.000	0.00	0.00	0.00	4.35
722	888	2.969990	AGACTAATCAGTGCAGCAGTG	58.030	47.619	22.56	22.56	34.21	3.66
755	922	3.640029	TGTCTTGGACGGTTAGTTCTTCT	59.360	43.478	0.00	0.00	34.95	2.85
768	935	0.474854	TTCTTCTAGGCCACCACCCA	60.475	55.000	5.01	0.00	0.00	4.51
806	973	2.872557	CCACGATGCACTGCAAGG	59.127	61.111	8.03	5.50	43.62	3.61
838	1005	3.632080	CCACTACACCCACGCCCA	61.632	66.667	0.00	0.00	0.00	5.36
921	1088	3.996921	ATCTGCCTCATTCACAGAACT	57.003	42.857	0.00	0.00	43.23	3.01
922	1089	3.049708	TCTGCCTCATTCACAGAACTG	57.950	47.619	0.00	0.00	37.49	3.16
987	1154	2.847234	TCCCAAGCCCACAGTCGT	60.847	61.111	0.00	0.00	0.00	4.34
998	1165	1.228490	ACAGTCGTCGGAGGAAGGT	60.228	57.895	1.41	1.26	0.00	3.50
1123	1290	0.035056	AATGCTCGAAGGGGTTGAGG	60.035	55.000	0.00	0.00	38.13	3.86
1162	1329	1.515020	GAGATCGTCTGCACCAGCT	59.485	57.895	0.00	0.00	42.74	4.24
1290	1457	1.685765	ACAGATGGCGGCAGTCCTA	60.686	57.895	19.29	0.00	0.00	2.94
1372	1539	8.211629	GGTAACCCATACTACTCTTCATTCATT	58.788	37.037	0.00	0.00	34.74	2.57
1460	1629	0.390340	TCTGAAGTGGATGCACGAGC	60.390	55.000	12.02	6.01	42.57	5.03
1494	1663	6.142139	TCAAGTTACATGCATTTCTGAAACG	58.858	36.000	4.73	0.00	0.00	3.60
1522	1691	5.880901	AGTGGATTGTTTCACCAGATTAGT	58.119	37.500	0.00	0.00	34.67	2.24
1561	1731	7.812690	TTATAGCATTCTGAACTTGATGCAT	57.187	32.000	13.52	0.00	37.48	3.96
1582	1752	8.020861	TGCATCAAATTAATTTCTGAACTTGC	57.979	30.769	17.99	16.16	0.00	4.01
1585	1755	9.414295	CATCAAATTAATTTCTGAACTTGCTGA	57.586	29.630	10.53	2.34	0.00	4.26
1815	1985	2.669924	AGCAGCGCATATATCATTGACG	59.330	45.455	11.47	0.00	0.00	4.35
1876	2046	6.089954	GGTGAAGCAATGAAGATAGCAAAAAC	59.910	38.462	0.00	0.00	0.00	2.43
1902	2075	5.352643	AAAATAACACGGTGTAGTTGAGC	57.647	39.130	15.11	0.00	0.00	4.26
2136	2324	1.974265	TGTCGGTTTCAGCATTGGAA	58.026	45.000	0.00	0.00	0.00	3.53
2186	2374	4.445592	GGTTTGGAAATCAACCCCAACAAT	60.446	41.667	0.00	0.00	39.43	2.71
2306	2494	4.792513	AGGCATGAAGAAGAAGATGGAT	57.207	40.909	0.00	0.00	0.00	3.41
2376	2564	4.037565	TCATCACGTACGCAGGAATAGATT	59.962	41.667	16.72	0.00	0.00	2.40
2378	2566	3.379057	TCACGTACGCAGGAATAGATTCA	59.621	43.478	16.72	0.00	38.53	2.57
2444	2632	6.953520	TGACAGGTTGGGATATTTCAAAAGAT	59.046	34.615	0.00	0.00	0.00	2.40
2527	2716	1.523484	TGTTGCTCGCACTTCTGCA	60.523	52.632	0.00	0.00	44.50	4.41
2613	2802	4.133820	TGTTATGTGTGTCAGGGTTTGAG	58.866	43.478	0.00	0.00	36.21	3.02
2698	2887	7.014038	AGCTTCCTATTTTGTTGATCCATCATC	59.986	37.037	0.00	0.00	36.56	2.92
2768	2957	7.965107	CAGCACTAGTCATGGAGAAATAAAAAC	59.035	37.037	0.00	0.00	0.00	2.43
2845	3037	3.740141	GCAAATAGTAGCCTTGGACGCTA	60.740	47.826	0.00	0.00	37.79	4.26
2878	3070	5.670149	AGACATGAACGGTAGTACTATCG	57.330	43.478	29.36	29.36	44.60	2.92
2887	3080	5.814783	ACGGTAGTACTATCGCACTAAAAG	58.185	41.667	30.56	6.44	42.98	2.27
2893	3087	9.512435	GTAGTACTATCGCACTAAAAGAATCAA	57.488	33.333	5.75	0.00	0.00	2.57
3057	3255	9.276688	TTCCTAGTCACTAGCATGCTAGGACTA	62.277	44.444	40.73	40.73	45.24	2.59
3123	3321	8.422566	ACAAAATATAAAAAGGAACGGGAAACA	58.577	29.630	0.00	0.00	0.00	2.83
3208	3406	9.610705	AATCTCAGTACAACTAAGTCTATACGA	57.389	33.333	0.00	0.00	0.00	3.43
3239	3437	7.287466	TGCTATGATTATACCAAACATTGCCTT	59.713	33.333	0.00	0.00	38.29	4.35
3328	3531	7.785033	AGGAGAAAAATCACAAGAAACACAAT	58.215	30.769	0.00	0.00	0.00	2.71
3336	3539	9.868277	AAATCACAAGAAACACAATAGAAAACA	57.132	25.926	0.00	0.00	0.00	2.83
3359	3562	6.320164	ACATACTAGCCTCAAACAACACAAAA	59.680	34.615	0.00	0.00	0.00	2.44
3427	3630	9.987272	AGTACAACTTAGTTTATTCGGTAAGTT	57.013	29.630	0.00	0.00	43.33	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
200	353	9.113876	GTGTGCACCGATTTTATATAAATAAGC	57.886	33.333	15.69	8.16	0.00	3.09
257	411	3.655350	GATGGGGGTCGGGGTTTGG	62.655	68.421	0.00	0.00	0.00	3.28
404	563	6.128634	GCACTTATGGTTTAGTACTGTGTGAC	60.129	42.308	5.39	0.00	0.00	3.67
512	673	3.138653	TGTTTTTAGTGCCCTGGGACTTA	59.861	43.478	19.27	8.31	44.30	2.24
515	676	1.989706	TGTTTTTAGTGCCCTGGGAC	58.010	50.000	19.27	11.90	36.69	4.46
650	816	0.956633	ACTTTCACGTCTCTGCGGTA	59.043	50.000	0.00	0.00	35.98	4.02
665	831	4.222124	ACGATCTGCTAAATCCCACTTT	57.778	40.909	0.00	0.00	0.00	2.66
782	949	2.108514	AGTGCATCGTGGCAATCGG	61.109	57.895	5.39	0.00	46.93	4.18
785	952	1.525718	TTGCAGTGCATCGTGGCAAT	61.526	50.000	20.50	2.00	46.93	3.56
884	1051	4.646492	GGCAGATATGGAAGACAATGGTTT	59.354	41.667	0.00	0.00	0.00	3.27
885	1052	4.079558	AGGCAGATATGGAAGACAATGGTT	60.080	41.667	0.00	0.00	0.00	3.67
886	1053	3.461085	AGGCAGATATGGAAGACAATGGT	59.539	43.478	0.00	0.00	0.00	3.55
901	1068	3.607741	CAGTTCTGTGAATGAGGCAGAT	58.392	45.455	0.00	0.00	38.79	2.90
921	1088	0.323999	AGATGGAAGCAGCAATGGCA	60.324	50.000	0.00	0.00	44.61	4.92
922	1089	0.384669	GAGATGGAAGCAGCAATGGC	59.615	55.000	0.00	0.00	41.61	4.40
987	1154	2.721167	CGCCATCACCTTCCTCCGA	61.721	63.158	0.00	0.00	0.00	4.55
1092	1259	3.678056	TCGAGCATTTTGGTGTACTCT	57.322	42.857	0.00	0.00	0.00	3.24
1123	1290	1.668151	GTGTCTCCTTGCCGTGGAC	60.668	63.158	0.00	0.00	0.00	4.02
1162	1329	1.180456	TCGTCGGCCTTGTCTGGTAA	61.180	55.000	0.00	0.00	0.00	2.85
1290	1457	1.544691	AGTTCCTCGACGCACAACTAT	59.455	47.619	4.05	0.00	0.00	2.12
1442	1611	0.671472	TGCTCGTGCATCCACTTCAG	60.671	55.000	8.30	0.00	45.31	3.02
1460	1629	5.761003	TGCATGTAACTTGAGAAACATGTG	58.239	37.500	20.56	8.34	46.93	3.21
1561	1731	9.248291	GTTCAGCAAGTTCAGAAATTAATTTGA	57.752	29.630	17.98	8.20	0.00	2.69
1582	1752	6.088016	AGATCAGAAGCTATGCTAGTTCAG	57.912	41.667	0.00	0.00	38.25	3.02
1585	1755	6.477053	TCAAGATCAGAAGCTATGCTAGTT	57.523	37.500	0.00	0.00	38.25	2.24
1596	1766	8.575589	ACTATACTAGTGCATCAAGATCAGAAG	58.424	37.037	5.39	0.00	37.69	2.85
1815	1985	7.603784	ACCAAATTCAAGAATCATTTTACCAGC	59.396	33.333	0.00	0.00	0.00	4.85
1901	2074	7.203255	AGTACACAAAGTCCTGAAATTAAGC	57.797	36.000	0.00	0.00	0.00	3.09
1902	2075	9.490379	ACTAGTACACAAAGTCCTGAAATTAAG	57.510	33.333	0.00	0.00	0.00	1.85
1967	2140	6.617782	AGTGATAATCCATGAGGTAGATGG	57.382	41.667	0.00	0.00	41.70	3.51
2154	2342	5.069119	GGTTGATTTCCAAACCAGACTTCTT	59.931	40.000	0.00	0.00	36.47	2.52
2186	2374	1.297456	TGCGCTGCATGTCGATGAAA	61.297	50.000	9.73	0.00	31.71	2.69
2306	2494	1.136828	ACAGTTTGTGGTCTGCCCTA	58.863	50.000	0.00	0.00	35.37	3.53
2376	2564	6.355747	TCCATGACTTGTACATTGCATATGA	58.644	36.000	6.97	0.00	0.00	2.15
2378	2566	7.012704	GTCTTCCATGACTTGTACATTGCATAT	59.987	37.037	0.00	0.00	34.39	1.78
2444	2632	1.001760	GTAGGGGTCAGCCTCCTGA	59.998	63.158	0.00	0.00	45.54	3.86
2527	2716	6.591935	TCTGAAACAACAAGACTAAGGACAT	58.408	36.000	0.00	0.00	0.00	3.06
2698	2887	6.538742	TCAACTTCAACCTACTTCAACTTCAG	59.461	38.462	0.00	0.00	0.00	3.02
2768	2957	9.855361	TTTTTGTGCGAAAATATTTATGTGTTG	57.145	25.926	0.01	0.00	0.00	3.33
2805	2997	9.350951	ACTATTTGCTTTTGTCCTTAGTTAGTT	57.649	29.630	0.00	0.00	0.00	2.24
2845	3037	4.021368	ACCGTTCATGTCTAAGCTGTACTT	60.021	41.667	0.00	0.00	42.76	2.24
3057	3255	5.708230	TGTGTTCAAGTGTACCAGAACTTTT	59.292	36.000	14.26	0.00	40.62	2.27
3121	3319	3.627395	TTAGGGAATGCGAACTGATGT	57.373	42.857	0.00	0.00	0.00	3.06
3123	3321	4.331968	TGTTTTAGGGAATGCGAACTGAT	58.668	39.130	0.00	0.00	0.00	2.90
3208	3406	8.752005	ATGTTTGGTATAATCATAGCACTTGT	57.248	30.769	0.00	0.00	43.12	3.16
3239	3437	2.889512	TCTAGGCTGTGGTTCTTCTCA	58.110	47.619	0.00	0.00	0.00	3.27
3328	3531	7.934665	TGTTGTTTGAGGCTAGTATGTTTTCTA	59.065	33.333	0.00	0.00	0.00	2.10
3336	3539	6.952773	TTTTGTGTTGTTTGAGGCTAGTAT	57.047	33.333	0.00	0.00	0.00	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.