AutoCloner

Multiple sequence alignment - TraesCS5D01G166700

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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	TraesCS5D01G166700	chr5D	100.000	3013	0	0	1	3013	260108638	260105626	0.000000	5565.0
1	TraesCS5D01G166700	chr5A	94.191	2014	99	7	1006	3008	346131481	346133487	0.000000	3055.0
2	TraesCS5D01G166700	chr5A	87.300	1000	89	17	44	1015	346130338	346131327	0.000000	1109.0
3	TraesCS5D01G166700	chr5B	94.299	1982	90	10	572	2542	294122990	294124959	0.000000	3013.0
4	TraesCS5D01G166700	chr5B	94.347	513	22	6	3	512	294121732	294122240	0.000000	780.0
5	TraesCS5D01G166700	chr5B	85.331	709	91	9	2309	3007	412283534	412284239	0.000000	721.0
6	TraesCS5D01G166700	chr5B	100.000	34	0	0	510	543	294122252	294122285	0.000003	63.9
7	TraesCS5D01G166700	chr3D	86.441	708	89	3	2307	3007	380179895	380180602	0.000000	769.0
8	TraesCS5D01G166700	chr3D	83.853	706	105	5	2309	3007	414778355	414777652	0.000000	664.0
9	TraesCS5D01G166700	chr7B	85.169	708	95	6	2309	3006	640720358	640721065	0.000000	717.0
10	TraesCS5D01G166700	chr1B	84.151	713	100	5	2303	3007	639061675	639060968	0.000000	678.0
11	TraesCS5D01G166700	chr2D	84.062	709	102	8	2304	3007	23303667	23302965	0.000000	673.0
12	TraesCS5D01G166700	chr6B	83.921	709	107	3	2305	3007	560789917	560790624	0.000000	671.0
13	TraesCS5D01G166700	chr7A	83.544	711	107	6	2306	3007	572876956	572877665	0.000000	656.0

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	TraesCS5D01G166700	chr5D	260105626	260108638	3012	True	5565.000000	5565	100.000000	1	3013	1	chr5D.!!$R1	3012
1	TraesCS5D01G166700	chr5A	346130338	346133487	3149	False	2082.000000	3055	90.745500	44	3008	2	chr5A.!!$F1	2964
2	TraesCS5D01G166700	chr5B	294121732	294124959	3227	False	1285.633333	3013	96.215333	3	2542	3	chr5B.!!$F2	2539
3	TraesCS5D01G166700	chr5B	412283534	412284239	705	False	721.000000	721	85.331000	2309	3007	1	chr5B.!!$F1	698
4	TraesCS5D01G166700	chr3D	380179895	380180602	707	False	769.000000	769	86.441000	2307	3007	1	chr3D.!!$F1	700
5	TraesCS5D01G166700	chr3D	414777652	414778355	703	True	664.000000	664	83.853000	2309	3007	1	chr3D.!!$R1	698
6	TraesCS5D01G166700	chr7B	640720358	640721065	707	False	717.000000	717	85.169000	2309	3006	1	chr7B.!!$F1	697
7	TraesCS5D01G166700	chr1B	639060968	639061675	707	True	678.000000	678	84.151000	2303	3007	1	chr1B.!!$R1	704
8	TraesCS5D01G166700	chr2D	23302965	23303667	702	True	673.000000	673	84.062000	2304	3007	1	chr2D.!!$R1	703
9	TraesCS5D01G166700	chr6B	560789917	560790624	707	False	671.000000	671	83.921000	2305	3007	1	chr6B.!!$F1	702
10	TraesCS5D01G166700	chr7A	572876956	572877665	709	False	656.000000	656	83.544000	2306	3007	1	chr7A.!!$F1	701

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	End Stability	Orientation
346	348	0.030504	TGCACATGAAAACACGCCAG	59.969	50.0	4.85	F
348	350	0.030504	CACATGAAAACACGCCAGCA	59.969	50.0	4.41	F
619	1312	0.036388	TGGCAGCTAGGGTTTCTTCG	60.036	55.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1240	2108	0.032403	GCACACATCAGCAAGGCAAA	59.968	50.0	0.0	0.00	0.00	3.68	R
1247	2115	0.867746	GAAAGACGCACACATCAGCA	59.132	50.0	0.0	0.00	0.00	4.41	R
2476	3358	1.122227	TGATCAGTGATGGATCCGCA	58.878	50.0	11.2	5.05	40.32	5.69	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
32	33	3.660970	TGCAAGGTAATTGAGCCCATA	57.339	42.857	0.00	0.00	41.83	2.74
65	67	7.230510	ACATGACCTTAAACAAAGATGCAACTA	59.769	33.333	0.00	0.00	37.38	2.24
139	141	3.123804	CCGTTACACCATCATAGCTCAC	58.876	50.000	0.00	0.00	0.00	3.51
231	233	6.558771	ACAAATCTCGTCAAATCATCACAA	57.441	33.333	0.00	0.00	0.00	3.33
252	254	5.145059	CAATAGTAGATCGTCGCGTACATT	58.855	41.667	5.77	0.90	0.00	2.71
292	294	1.134401	CAAGCATACTGACGATGGGGT	60.134	52.381	0.00	0.00	0.00	4.95
294	296	0.464036	GCATACTGACGATGGGGTCA	59.536	55.000	0.00	0.00	44.25	4.02
346	348	0.030504	TGCACATGAAAACACGCCAG	59.969	50.000	0.00	0.00	0.00	4.85
348	350	0.030504	CACATGAAAACACGCCAGCA	59.969	50.000	0.00	0.00	0.00	4.41
447	451	3.491792	GGCACCAAGAAAAACGATTGGAA	60.492	43.478	10.01	0.00	45.19	3.53
544	562	2.545969	GAGAATCCCCTTCCCTCCC	58.454	63.158	0.00	0.00	34.11	4.30
546	564	1.006227	GAATCCCCTTCCCTCCCCT	59.994	63.158	0.00	0.00	0.00	4.79
547	565	1.006227	AATCCCCTTCCCTCCCCTC	59.994	63.158	0.00	0.00	0.00	4.30
619	1312	0.036388	TGGCAGCTAGGGTTTCTTCG	60.036	55.000	0.00	0.00	0.00	3.79
682	1383	6.504398	TCACAGTACGATCTTATGAACATCC	58.496	40.000	0.00	0.00	0.00	3.51
684	1385	7.501225	TCACAGTACGATCTTATGAACATCCTA	59.499	37.037	0.00	0.00	0.00	2.94
723	1424	8.431593	GCAGAAATCTATGAATCTATCGTTCAC	58.568	37.037	0.00	0.00	38.31	3.18
727	1428	7.859613	ATCTATGAATCTATCGTTCACGTTG	57.140	36.000	0.00	0.00	38.31	4.10
767	1469	7.301054	GGTCACAAGTTCTGATCAGTAAAATG	58.699	38.462	21.92	16.57	0.00	2.32
794	1496	3.989104	AACACCAGTTCTCACCTCG	57.011	52.632	0.00	0.00	30.46	4.63
813	1515	2.037902	TCGGTTAATCTGTGGCTGTTGA	59.962	45.455	0.00	0.00	0.00	3.18
1118	1986	0.321122	AAGAGCGCCAAGAAGGACAG	60.321	55.000	2.29	0.00	41.22	3.51
1184	2052	2.304470	GCTTCTCCTCCCTTTCTTGTCT	59.696	50.000	0.00	0.00	0.00	3.41
1260	2128	2.132517	TTGCCTTGCTGATGTGTGCG	62.133	55.000	0.00	0.00	0.00	5.34
1281	2149	3.242608	CGTCTTTCTTGTTTCTTGCCGAA	60.243	43.478	0.00	0.00	0.00	4.30
1572	2440	3.234630	TTCCCGTCCCTGCGAACAG	62.235	63.158	0.00	0.00	44.05	3.16
1613	2481	3.382832	CTCCCCTCCAACGAGCGT	61.383	66.667	0.00	0.00	34.49	5.07
2032	2900	4.554036	GGACCTCGCCATGGCCTC	62.554	72.222	30.79	18.47	37.98	4.70
2033	2901	3.474570	GACCTCGCCATGGCCTCT	61.475	66.667	30.79	10.83	37.98	3.69
2034	2902	3.453070	GACCTCGCCATGGCCTCTC	62.453	68.421	30.79	15.74	37.98	3.20
2162	3030	7.653311	GCTTCAGATGGTTTTACTTTCAACAAT	59.347	33.333	0.00	0.00	0.00	2.71
2377	3249	1.808411	AGCCACACAAACACCGATAG	58.192	50.000	0.00	0.00	0.00	2.08
2382	3254	4.250464	CCACACAAACACCGATAGTACAT	58.750	43.478	0.00	0.00	0.00	2.29
2428	3310	2.769893	GCAAAAACCAATGCATGTCCT	58.230	42.857	0.00	0.00	42.12	3.85
2476	3358	1.202330	CCTCTTCACCTGAGCTGGAT	58.798	55.000	0.00	0.00	0.00	3.41
2520	3402	3.325716	AGCTTTACGGACCTCCAAAGTAA	59.674	43.478	9.66	0.00	33.78	2.24
2528	3410	4.595986	GGACCTCCAAAGTAATTTGCCTA	58.404	43.478	10.10	0.00	35.64	3.93
2589	3471	2.275418	GTCCCCGGACATGCCATT	59.725	61.111	0.73	0.00	44.02	3.16
2696	3585	1.840635	ACCTTCTTCCAGCTATCACCC	59.159	52.381	0.00	0.00	0.00	4.61
2707	3596	1.470285	GCTATCACCCGCGTAGACAAA	60.470	52.381	4.92	0.00	0.00	2.83
2711	3600	1.153353	CACCCGCGTAGACAAATGTT	58.847	50.000	4.92	0.00	0.00	2.71
2784	3673	0.460284	AACGCCGCAGTAAGATGGAG	60.460	55.000	0.00	0.00	0.00	3.86
2958	3847	3.950395	GTGGAGCTGAGGCAGATTTATTT	59.050	43.478	0.00	0.00	41.70	1.40
3008	3900	2.215196	GCTCACCACGACCTACAAAAA	58.785	47.619	0.00	0.00	0.00	1.94
3009	3901	2.223377	GCTCACCACGACCTACAAAAAG	59.777	50.000	0.00	0.00	0.00	2.27
3010	3902	3.724374	CTCACCACGACCTACAAAAAGA	58.276	45.455	0.00	0.00	0.00	2.52
3011	3903	4.124238	CTCACCACGACCTACAAAAAGAA	58.876	43.478	0.00	0.00	0.00	2.52
3012	3904	4.515361	TCACCACGACCTACAAAAAGAAA	58.485	39.130	0.00	0.00	0.00	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.371548	TCAATTACCTTGCATCTAGTTGTGTC	59.628	38.462	2.85	0.00	34.66	3.67
1	2	6.237901	TCAATTACCTTGCATCTAGTTGTGT	58.762	36.000	2.85	0.00	34.66	3.72
13	14	4.159506	TGTTTATGGGCTCAATTACCTTGC	59.840	41.667	0.00	0.00	34.66	4.01
32	33	5.821516	TTGTTTAAGGTCATGTCGTGTTT	57.178	34.783	0.00	0.00	0.00	2.83
65	67	9.236006	AGAATTTTGAGACATATAGCTGTTTGT	57.764	29.630	6.27	6.27	0.00	2.83
139	141	4.576053	TCTTGGTGTTGTCAATTGTGAGAG	59.424	41.667	5.13	0.00	33.27	3.20
209	211	8.393366	ACTATTGTGATGATTTGACGAGATTTG	58.607	33.333	0.00	0.00	0.00	2.32
231	233	4.378149	CCAATGTACGCGACGATCTACTAT	60.378	45.833	15.93	0.00	0.00	2.12
252	254	2.331893	CGCGATTTGCCAACCTCCA	61.332	57.895	0.00	0.00	42.08	3.86
292	294	8.747471	TGCAACATTATCTTTTTGGTATGATGA	58.253	29.630	0.00	0.00	0.00	2.92
294	296	8.752187	ACTGCAACATTATCTTTTTGGTATGAT	58.248	29.630	0.00	0.00	0.00	2.45
346	348	5.971763	TGGTTGGTTATTTGTATTCCATGC	58.028	37.500	0.00	0.00	0.00	4.06
382	385	5.013391	AGAGTTTTTGGAGTCCCCGTTATTA	59.987	40.000	6.74	0.00	37.93	0.98
544	562	4.087892	CTCACTGTGGGGCGGAGG	62.088	72.222	8.11	0.00	0.00	4.30
577	1270	6.418101	CACAAAATCAATCTCCTCTTCCCTA	58.582	40.000	0.00	0.00	0.00	3.53
582	1275	4.410099	TGCCACAAAATCAATCTCCTCTT	58.590	39.130	0.00	0.00	0.00	2.85
619	1312	9.632807	TTGTGTGTAATATAAAACCTTCATTGC	57.367	29.630	0.00	0.00	0.00	3.56
635	1328	6.714810	TGAAAGGCTAAGTGATTGTGTGTAAT	59.285	34.615	0.00	0.00	0.00	1.89
637	1330	5.468746	GTGAAAGGCTAAGTGATTGTGTGTA	59.531	40.000	0.00	0.00	0.00	2.90
682	1383	4.944962	TTTCTGCGGTTCATGAACATAG	57.055	40.909	33.42	26.40	42.85	2.23
684	1385	4.012374	AGATTTCTGCGGTTCATGAACAT	58.988	39.130	33.42	19.65	42.85	2.71
767	1469	0.586802	GAACTGGTGTTCCACTTCGC	59.413	55.000	0.00	0.00	44.93	4.70
780	1482	3.195825	AGATTAACCGAGGTGAGAACTGG	59.804	47.826	0.00	0.00	0.00	4.00
794	1496	4.702131	AGATTCAACAGCCACAGATTAACC	59.298	41.667	0.00	0.00	0.00	2.85
813	1515	3.130516	TCGCTGACCGTTAGATTGAGATT	59.869	43.478	0.00	0.00	38.35	2.40
1184	2052	2.092429	AGCCGCCATGAAATCCTTCTTA	60.092	45.455	0.00	0.00	32.33	2.10
1240	2108	0.032403	GCACACATCAGCAAGGCAAA	59.968	50.000	0.00	0.00	0.00	3.68
1245	2113	0.870393	AAGACGCACACATCAGCAAG	59.130	50.000	0.00	0.00	0.00	4.01
1247	2115	0.867746	GAAAGACGCACACATCAGCA	59.132	50.000	0.00	0.00	0.00	4.41
1254	2122	3.675467	AGAAACAAGAAAGACGCACAC	57.325	42.857	0.00	0.00	0.00	3.82
1260	2128	3.963383	TCGGCAAGAAACAAGAAAGAC	57.037	42.857	0.00	0.00	0.00	3.01
2032	2900	5.064962	GCTTCAGTCATCATCAAAGAAGGAG	59.935	44.000	0.00	0.00	33.49	3.69
2033	2901	4.940046	GCTTCAGTCATCATCAAAGAAGGA	59.060	41.667	0.00	0.00	33.49	3.36
2034	2902	4.096081	GGCTTCAGTCATCATCAAAGAAGG	59.904	45.833	0.00	0.00	33.49	3.46
2162	3030	5.101648	TCACAGATTCAGATACAATGCCA	57.898	39.130	0.00	0.00	0.00	4.92
2281	3149	9.762933	GAGAGAGAGATAGAAATACTGCAATTT	57.237	33.333	0.00	0.00	0.00	1.82
2350	3222	3.181480	GGTGTTTGTGTGGCTTGTAACAT	60.181	43.478	0.00	0.00	0.00	2.71
2377	3249	9.141400	GATTATCCTATCTTTTCGGTCATGTAC	57.859	37.037	0.00	0.00	0.00	2.90
2428	3310	4.788925	TCTCCTTTTTCTTGGTGGAGAA	57.211	40.909	7.48	0.00	46.91	2.87
2476	3358	1.122227	TGATCAGTGATGGATCCGCA	58.878	50.000	11.20	5.05	40.32	5.69
2481	3363	3.928005	AGCTGTTGATCAGTGATGGAT	57.072	42.857	11.20	0.00	45.23	3.41
2528	3410	3.818180	TCAATGGCAATGGTTTTGCTTT	58.182	36.364	2.15	2.69	44.36	3.51
2589	3471	2.370849	GGGGTGTCAGTTCTGGAGTTTA	59.629	50.000	0.00	0.00	0.00	2.01
2696	3585	1.238281	CGCAAACATTTGTCTACGCG	58.762	50.000	3.53	3.53	40.24	6.01
2707	3596	1.019278	CCTGGAGTACGCGCAAACAT	61.019	55.000	5.73	0.00	0.00	2.71
2711	3600	2.260434	GTCCTGGAGTACGCGCAA	59.740	61.111	5.73	0.00	0.00	4.85
2784	3673	0.534873	GTGTCTCCCCTTCTGCTCTC	59.465	60.000	0.00	0.00	0.00	3.20
2980	3869	4.308458	CGTGGTGAGCCGTTGGGA	62.308	66.667	0.00	0.00	37.67	4.37

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.