AutoCloner

Multiple sequence alignment - TraesCS2D01G466900

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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	TraesCS2D01G466900	chr2D	100.000	4209	0	0	1	4209	572258158	572253950	0.000000e+00	7773.0
1	TraesCS2D01G466900	chr2D	84.758	2972	397	29	373	3317	482382831	482379889	0.000000e+00	2928.0
2	TraesCS2D01G466900	chr2D	87.000	1600	191	8	1670	3263	482350031	482348443	0.000000e+00	1786.0
3	TraesCS2D01G466900	chr2D	87.832	1241	147	3	1982	3219	626593929	626592690	0.000000e+00	1452.0
4	TraesCS2D01G466900	chr2D	81.854	1014	180	4	655	1666	482351081	482350070	0.000000e+00	850.0
5	TraesCS2D01G466900	chr2A	95.174	3916	158	13	304	4209	711468501	711464607	0.000000e+00	6156.0
6	TraesCS2D01G466900	chr2A	82.917	3366	475	62	2	3317	624968611	624965296	0.000000e+00	2939.0
7	TraesCS2D01G466900	chr2A	87.130	1655	194	10	1670	3317	624943006	624941364	0.000000e+00	1858.0
8	TraesCS2D01G466900	chr2A	82.708	1093	175	10	577	1667	624944124	624943044	0.000000e+00	959.0
9	TraesCS2D01G466900	chr2A	78.795	1311	248	26	628	1912	757555805	757554499	0.000000e+00	854.0
10	TraesCS2D01G466900	chr2A	96.528	288	9	1	1	287	711469266	711468979	3.810000e-130	475.0
11	TraesCS2D01G466900	chr2A	87.770	139	14	3	1	139	711472332	711472197	4.360000e-35	159.0
12	TraesCS2D01G466900	chr2B	94.907	3868	171	9	348	4208	687208062	687204214	0.000000e+00	6028.0
13	TraesCS2D01G466900	chr2B	83.675	3265	433	59	1	3222	566404093	566400886	0.000000e+00	2985.0
14	TraesCS2D01G466900	chr2B	81.777	2656	416	43	624	3219	768060375	768057728	0.000000e+00	2161.0
15	TraesCS2D01G466900	chr2B	87.083	1649	196	8	1675	3317	566391466	566389829	0.000000e+00	1849.0
16	TraesCS2D01G466900	chr2B	73.926	349	75	9	3870	4207	757969668	757970011	4.420000e-25	126.0
17	TraesCS2D01G466900	chr6D	86.510	341	43	3	3870	4209	344151910	344152248	5.140000e-99	372.0
18	TraesCS2D01G466900	chr6D	85.185	108	14	2	3687	3792	157669457	157669350	4.450000e-20	110.0
19	TraesCS2D01G466900	chr1B	77.101	345	70	7	3870	4209	314583006	314583346	1.540000e-44	191.0
20	TraesCS2D01G466900	chr1B	74.295	319	66	12	3873	4180	29836450	29836137	2.060000e-23	121.0
21	TraesCS2D01G466900	chr6B	75.568	352	64	15	3870	4207	30982495	30982838	2.030000e-33	154.0
22	TraesCS2D01G466900	chr6B	73.438	320	71	10	3871	4182	384448536	384448223	1.600000e-19	108.0
23	TraesCS2D01G466900	chr6A	84.076	157	25	0	3870	4026	238453157	238453313	7.290000e-33	152.0
24	TraesCS2D01G466900	chr4D	82.781	151	24	2	3873	4022	445668420	445668569	2.640000e-27	134.0
25	TraesCS2D01G466900	chr7B	86.111	72	9	1	3680	3751	437328382	437328452	4.510000e-10	76.8
26	TraesCS2D01G466900	chrUn	81.333	75	11	3	3678	3750	361364271	361364198	1.630000e-04	58.4
27	TraesCS2D01G466900	chr5B	81.333	75	11	3	3678	3750	614352544	614352617	1.630000e-04	58.4

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	TraesCS2D01G466900	chr2D	572253950	572258158	4208	True	7773.000000	7773	100.000000	1	4209	1	chr2D.!!$R2	4208
1	TraesCS2D01G466900	chr2D	482379889	482382831	2942	True	2928.000000	2928	84.758000	373	3317	1	chr2D.!!$R1	2944
2	TraesCS2D01G466900	chr2D	626592690	626593929	1239	True	1452.000000	1452	87.832000	1982	3219	1	chr2D.!!$R3	1237
3	TraesCS2D01G466900	chr2D	482348443	482351081	2638	True	1318.000000	1786	84.427000	655	3263	2	chr2D.!!$R4	2608
4	TraesCS2D01G466900	chr2A	624965296	624968611	3315	True	2939.000000	2939	82.917000	2	3317	1	chr2A.!!$R1	3315
5	TraesCS2D01G466900	chr2A	711464607	711472332	7725	True	2263.333333	6156	93.157333	1	4209	3	chr2A.!!$R4	4208
6	TraesCS2D01G466900	chr2A	624941364	624944124	2760	True	1408.500000	1858	84.919000	577	3317	2	chr2A.!!$R3	2740
7	TraesCS2D01G466900	chr2A	757554499	757555805	1306	True	854.000000	854	78.795000	628	1912	1	chr2A.!!$R2	1284
8	TraesCS2D01G466900	chr2B	687204214	687208062	3848	True	6028.000000	6028	94.907000	348	4208	1	chr2B.!!$R3	3860
9	TraesCS2D01G466900	chr2B	566400886	566404093	3207	True	2985.000000	2985	83.675000	1	3222	1	chr2B.!!$R2	3221
10	TraesCS2D01G466900	chr2B	768057728	768060375	2647	True	2161.000000	2161	81.777000	624	3219	1	chr2B.!!$R4	2595
11	TraesCS2D01G466900	chr2B	566389829	566391466	1637	True	1849.000000	1849	87.083000	1675	3317	1	chr2B.!!$R1	1642

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	Hairpin	End Stability	Orientation
226	3302	0.449388	CCAAGACTCTGAATTGCCGC	59.551	55.000	0.00	0.00	6.53	F
846	4428	1.035385	TCGATCCTGGTTGCTCGCTA	61.035	55.000	0.00	0.00	4.26	F
1263	4848	0.104304	ACGACACAACTTTCTCGGCT	59.896	50.000	0.00	0.00	5.52	F
1490	5075	2.044650	ATGCCTCAGCGCCAACAT	60.045	55.556	2.29	44.31	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1063	4648	1.308998	GTGAACCTGTTCTGGGTGTG	58.691	55.000	11.03	0.00	40.14	3.82	R
2630	6305	1.267806	GTCTGACACTTTGGCCATGTG	59.732	52.381	27.53	27.53	37.67	3.21	R
3049	6724	0.179000	GTACCCAGGGATGCAGTGAG	59.821	60.000	14.54	0.00	0.00	3.51	R
3356	7036	1.876322	TGAACACACATCGCACATCA	58.124	45.000	0.00	0.00	0.00	3.07	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
113	3182	9.559958	GTTTCAGGTGAATTTTACATCAGTATG	57.440	33.333	0.00	0.00	35.10	2.39
226	3302	0.449388	CCAAGACTCTGAATTGCCGC	59.551	55.000	0.00	0.00	0.00	6.53
289	3365	1.707106	TCCTCACCCTTGTGTTACGA	58.293	50.000	0.00	0.00	43.26	3.43
291	3367	1.607251	CCTCACCCTTGTGTTACGACC	60.607	57.143	0.00	0.00	43.26	4.79
294	3370	1.125633	ACCCTTGTGTTACGACCTGT	58.874	50.000	0.00	0.00	0.00	4.00
297	3373	2.132762	CCTTGTGTTACGACCTGTGAC	58.867	52.381	0.00	0.00	37.58	3.67
301	3377	2.124903	GTGTTACGACCTGTGACTGTG	58.875	52.381	0.00	0.00	37.91	3.66
302	3378	2.025898	TGTTACGACCTGTGACTGTGA	58.974	47.619	0.00	0.00	37.91	3.58
308	3845	2.095668	CGACCTGTGACTGTGAGTAGAC	60.096	54.545	0.00	0.00	0.00	2.59
331	3868	5.767168	ACTTTCTTAAAGCAGAGTCAAGCAT	59.233	36.000	9.80	0.00	42.27	3.79
416	3985	7.833682	TCCCTGCTTCATTCATTAACATAGAAA	59.166	33.333	0.00	0.00	0.00	2.52
419	3988	9.844790	CTGCTTCATTCATTAACATAGAAACAA	57.155	29.630	0.00	0.00	0.00	2.83
575	4145	5.833082	ACTCGTGCCTGTATATTTAGAGTG	58.167	41.667	0.00	0.00	35.44	3.51
593	4163	5.264395	AGAGTGATCCCCAAATTTAACTGG	58.736	41.667	0.00	0.00	0.00	4.00
669	4248	4.806330	TGTCGATTTAGTTGACAGTCTCC	58.194	43.478	1.31	0.00	44.52	3.71
711	4290	4.736793	CCGAACAATATGCAAATGCTCTTC	59.263	41.667	6.97	0.00	42.66	2.87
730	4309	1.667722	CAGCTTGGCCTTGGTTTCC	59.332	57.895	3.32	0.00	0.00	3.13
825	4407	4.039973	GTCGAGATACCATACCCATTTGGA	59.960	45.833	0.00	0.00	36.79	3.53
846	4428	1.035385	TCGATCCTGGTTGCTCGCTA	61.035	55.000	0.00	0.00	0.00	4.26
1015	4597	2.659428	GGAGCATGGAGTATTTTGGCT	58.341	47.619	0.00	0.00	0.00	4.75
1063	4648	2.522193	CTCCCTACCGGCTCTCCC	60.522	72.222	0.00	0.00	0.00	4.30
1230	4815	3.761897	CTCCCAGACCACAATACCAAAA	58.238	45.455	0.00	0.00	0.00	2.44
1263	4848	0.104304	ACGACACAACTTTCTCGGCT	59.896	50.000	0.00	0.00	0.00	5.52
1349	4934	3.128242	GCAGCATTTGAGTTCAGCACTAT	59.872	43.478	0.00	0.00	35.01	2.12
1490	5075	2.044650	ATGCCTCAGCGCCAACAT	60.045	55.556	2.29	0.00	44.31	2.71
1977	5648	9.817809	TTTACACTATTCATCACCTCAATCTAC	57.182	33.333	0.00	0.00	0.00	2.59
2096	5768	9.933723	AAATGATAATTCAAAAGAGAAACCTGG	57.066	29.630	0.00	0.00	34.96	4.45
2630	6305	4.037208	CCAACATCCTGCTTGATGATAACC	59.963	45.833	18.81	0.00	43.94	2.85
3241	6917	8.553696	CATGTATTGTAATCGGTTAAACCTACC	58.446	37.037	0.00	0.00	35.66	3.18
3386	7069	4.618912	CGATGTGTGTTCAACAACAAAACA	59.381	37.500	8.86	6.95	44.32	2.83
3403	7086	9.566530	CAACAAAACATATTGGATATTCGTTCA	57.433	29.630	0.00	0.00	34.56	3.18
3651	7334	1.474478	ACACCGAAAATGCACACAACA	59.526	42.857	0.00	0.00	0.00	3.33
3665	7348	1.464608	CACAACACGCAAAGATCCGAT	59.535	47.619	0.00	0.00	0.00	4.18
3673	7356	4.092821	CACGCAAAGATCCGATTACAAGAA	59.907	41.667	0.00	0.00	0.00	2.52
3708	7391	2.840753	GGAGGTTGAACCCCTGGCA	61.841	63.158	11.41	0.00	39.75	4.92
3849	7536	2.339769	GCCCCCACTATCTAGAACCAT	58.660	52.381	0.00	0.00	0.00	3.55
3859	7546	5.721960	ACTATCTAGAACCATGGTCAACACT	59.278	40.000	20.07	14.35	0.00	3.55
3863	7550	2.705658	AGAACCATGGTCAACACTGAGA	59.294	45.455	20.07	0.00	30.14	3.27
3907	7594	0.546747	ACGAGGGTTTGGATCCTCCA	60.547	55.000	14.23	0.00	46.61	3.86
3931	7618	1.813102	GAACTGGGGGAGAGGATGAT	58.187	55.000	0.00	0.00	0.00	2.45
3939	7626	2.158325	GGGGAGAGGATGATGAGAGACT	60.158	54.545	0.00	0.00	0.00	3.24
4050	7737	3.777106	ACCGATGCAAGGTATGATCAT	57.223	42.857	13.81	13.81	40.80	2.45
4061	7748	2.897969	GGTATGATCATCCCACCTACGT	59.102	50.000	12.53	0.00	0.00	3.57
4084	7771	1.842052	TACCACCATCTGTCGTGCTA	58.158	50.000	0.00	0.00	0.00	3.49
4124	7811	1.046204	AGAAGAGGGTCGAACCGTTT	58.954	50.000	15.29	12.68	39.83	3.60
4138	7825	0.652592	CCGTTTCGATGGCTGATCAC	59.347	55.000	0.00	0.00	0.00	3.06
4140	7827	0.026803	GTTTCGATGGCTGATCACGC	59.973	55.000	8.20	8.20	0.00	5.34
4157	7844	4.189580	CCGCCCCCGTGGATGAAT	62.190	66.667	0.00	0.00	42.83	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
121	3191	9.435688	AACTGAAAGCTTGTAAAAGACAATTTT	57.564	25.926	0.00	0.00	42.07	1.82
148	3219	6.868864	TCAAACTTCACGGAAATTGAAAAACA	59.131	30.769	9.81	0.00	32.61	2.83
226	3302	1.210155	GTTTGCTGTTAGCTGGCGG	59.790	57.895	0.00	0.00	42.97	6.13
289	3365	3.231207	AGTCTACTCACAGTCACAGGT	57.769	47.619	0.00	0.00	0.00	4.00
291	3367	5.446143	AGAAAGTCTACTCACAGTCACAG	57.554	43.478	0.00	0.00	0.00	3.66
294	3370	6.924060	GCTTTAAGAAAGTCTACTCACAGTCA	59.076	38.462	0.00	0.00	40.64	3.41
297	3373	7.148641	TCTGCTTTAAGAAAGTCTACTCACAG	58.851	38.462	0.00	0.00	40.64	3.66
301	3377	7.371936	TGACTCTGCTTTAAGAAAGTCTACTC	58.628	38.462	16.69	0.26	40.64	2.59
302	3378	7.291411	TGACTCTGCTTTAAGAAAGTCTACT	57.709	36.000	16.69	0.00	40.64	2.57
308	3845	5.679734	TGCTTGACTCTGCTTTAAGAAAG	57.320	39.130	0.00	0.00	41.46	2.62
416	3985	1.068127	AGTCCTAACGAACGCTGTTGT	59.932	47.619	0.00	0.00	0.00	3.32
419	3988	1.779569	CAAGTCCTAACGAACGCTGT	58.220	50.000	0.00	0.00	0.00	4.40
516	4086	8.647256	ATCCTGAGAGAACAGAAATGATTTTT	57.353	30.769	0.00	0.00	39.94	1.94
520	4090	7.673641	AGTATCCTGAGAGAACAGAAATGAT	57.326	36.000	0.00	0.00	39.94	2.45
555	4125	5.864474	GGATCACTCTAAATATACAGGCACG	59.136	44.000	0.00	0.00	0.00	5.34
575	4145	3.103742	TGGCCAGTTAAATTTGGGGATC	58.896	45.455	0.00	0.00	34.96	3.36
669	4248	2.349817	CGGCTGCAGAACAAGTAAACAG	60.350	50.000	20.43	0.00	0.00	3.16
711	4290	1.667722	GAAACCAAGGCCAAGCTGG	59.332	57.895	5.01	8.66	41.55	4.85
756	4338	1.894282	GCTAGGAGCCGCAATTCCC	60.894	63.158	0.00	0.00	34.48	3.97
825	4407	3.179181	AGCGAGCAACCAGGATCGATT	62.179	52.381	0.00	0.00	43.20	3.34
834	4416	1.225855	CTTGTGTTAGCGAGCAACCA	58.774	50.000	0.00	0.00	0.00	3.67
837	4419	0.250295	AGGCTTGTGTTAGCGAGCAA	60.250	50.000	7.49	0.00	45.34	3.91
846	4428	0.468226	TGAGGTCGAAGGCTTGTGTT	59.532	50.000	3.46	0.00	0.00	3.32
1063	4648	1.308998	GTGAACCTGTTCTGGGTGTG	58.691	55.000	11.03	0.00	40.14	3.82
1230	4815	5.709164	AGTTGTGTCGTAGTAGTACATCCTT	59.291	40.000	8.43	0.00	0.00	3.36
1263	4848	6.037098	CCAAATTTGACTTGTGTTAACCGAA	58.963	36.000	19.86	0.00	0.00	4.30
1349	4934	8.815189	CATTGAATTTGTTTGTGTTCACATACA	58.185	29.630	19.42	19.42	30.96	2.29
1702	5339	4.191033	TGGATTGTGGTTGCATTCATTC	57.809	40.909	0.00	0.00	0.00	2.67
1977	5648	8.185003	TGTCGTTAGATGAGACAATTATGTTG	57.815	34.615	0.00	0.00	41.30	3.33
2092	5764	5.104259	ACTCCTGCTTAACTTTATCCAGG	57.896	43.478	0.00	0.00	40.84	4.45
2096	5768	7.518529	GCGGAAATACTCCTGCTTAACTTTATC	60.519	40.741	0.00	0.00	42.85	1.75
2630	6305	1.267806	GTCTGACACTTTGGCCATGTG	59.732	52.381	27.53	27.53	37.67	3.21
3049	6724	0.179000	GTACCCAGGGATGCAGTGAG	59.821	60.000	14.54	0.00	0.00	3.51
3085	6760	5.368523	TCCTCCAAGAAGGTTTTCTACTTCA	59.631	40.000	7.12	0.00	42.80	3.02
3241	6917	9.843334	GGTATAGAAGGAACATAAGTATCTTCG	57.157	37.037	0.00	0.00	39.64	3.79
3356	7036	1.876322	TGAACACACATCGCACATCA	58.124	45.000	0.00	0.00	0.00	3.07
3363	7043	4.618912	TGTTTTGTTGTTGAACACACATCG	59.381	37.500	0.00	0.00	41.92	3.84
3651	7334	3.857052	TCTTGTAATCGGATCTTTGCGT	58.143	40.909	0.00	0.00	37.97	5.24
3792	7475	2.371841	AGTCTGTAGGTGTTGAATGGCA	59.628	45.455	0.00	0.00	0.00	4.92
3849	7536	1.069090	GGCGTCTCAGTGTTGACCA	59.931	57.895	11.38	0.00	0.00	4.02
3859	7546	3.923864	ACACTTGCGGGCGTCTCA	61.924	61.111	0.00	0.00	0.00	3.27
3863	7550	2.515057	TTTCACACTTGCGGGCGT	60.515	55.556	0.00	0.00	0.00	5.68
3907	7594	0.324460	CCTCTCCCCCAGTTCGTAGT	60.324	60.000	0.00	0.00	0.00	2.73
3931	7618	2.419713	GCCAAGATGCATCAGTCTCTCA	60.420	50.000	27.81	0.00	0.00	3.27
3939	7626	0.462375	GCATTGGCCAAGATGCATCA	59.538	50.000	30.43	6.28	46.03	3.07
4012	7699	1.883926	GGTATTGCCGTTGGTGTTCTT	59.116	47.619	0.00	0.00	0.00	2.52
4050	7737	2.765699	GGTGGTAATTACGTAGGTGGGA	59.234	50.000	9.46	0.00	0.00	4.37
4061	7748	3.196901	AGCACGACAGATGGTGGTAATTA	59.803	43.478	0.00	0.00	42.61	1.40
4084	7771	2.203640	TGTGGTCCGCTCTCACCT	60.204	61.111	3.62	0.00	33.36	4.00
4140	7827	2.124507	ATATTCATCCACGGGGGCGG	62.125	60.000	2.42	0.00	36.21	6.13
4157	7844	5.664457	CCTCCTCCATGACATCATCCATATA	59.336	44.000	0.00	0.00	33.61	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.