AutoCloner

Multiple sequence alignment - TraesCS1B01G171000

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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	TraesCS1B01G171000	chr1B	100.000	3514	0	0	1	3514	303223205	303226718	0.000000e+00	6490.0
1	TraesCS1B01G171000	chr1B	95.023	3315	96	29	1	3283	304381457	304384734	0.000000e+00	5144.0
2	TraesCS1B01G171000	chr1B	95.631	206	9	0	3308	3513	304386863	304387068	7.270000e-87	331.0
3	TraesCS1B01G171000	chr1A	94.731	3321	114	29	1	3283	268124750	268121453	0.000000e+00	5107.0
4	TraesCS1B01G171000	chr1D	95.459	2885	98	11	405	3283	212080279	212077422	0.000000e+00	4571.0
5	TraesCS1B01G171000	chr3A	92.523	107	7	1	3308	3414	725145698	725145803	6.080000e-33	152.0
6	TraesCS1B01G171000	chr3A	89.720	107	8	1	3308	3414	725229635	725229738	2.200000e-27	134.0
7	TraesCS1B01G171000	chr3A	88.679	53	5	1	3449	3501	608745777	608745726	2.930000e-06	63.9
8	TraesCS1B01G171000	chr3B	90.566	106	10	0	3308	3413	798146705	798146810	1.320000e-29	141.0
9	TraesCS1B01G171000	chr2A	89.720	107	11	0	3308	3414	699806027	699805921	1.700000e-28	137.0
10	TraesCS1B01G171000	chr6D	87.963	108	11	2	3308	3414	380997461	380997355	3.680000e-25	126.0
11	TraesCS1B01G171000	chr6D	89.362	47	2	2	3456	3502	336512242	336512199	4.900000e-04	56.5
12	TraesCS1B01G171000	chr4B	83.459	133	17	5	3308	3438	118893340	118893469	6.160000e-23	119.0
13	TraesCS1B01G171000	chr5D	87.500	96	10	2	3308	3402	564891665	564891759	3.710000e-20	110.0
14	TraesCS1B01G171000	chr7D	85.185	108	13	3	3308	3414	631680828	631680723	1.330000e-19	108.0

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	TraesCS1B01G171000	chr1B	303223205	303226718	3513	False	6490.0	6490	100.000	1	3514	1	chr1B.!!$F1	3513
1	TraesCS1B01G171000	chr1B	304381457	304387068	5611	False	2737.5	5144	95.327	1	3513	2	chr1B.!!$F2	3512
2	TraesCS1B01G171000	chr1A	268121453	268124750	3297	True	5107.0	5107	94.731	1	3283	1	chr1A.!!$R1	3282
3	TraesCS1B01G171000	chr1D	212077422	212080279	2857	True	4571.0	4571	95.459	405	3283	1	chr1D.!!$R1	2878

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
981	1019	0.738389	CGCAGGGGCAAATCGTATTT	59.262	50.0	0.0	0.0	41.24	1.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2797	2835	1.066587	CACGCTCTAGTGGCTAGCC	59.933	63.158	27.71	27.71	38.4	3.93	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
40	41	2.125952	GCCGACCATTTTGCAGCC	60.126	61.111	0.00	0.00	0.00	4.85
46	47	2.769893	GACCATTTTGCAGCCATTGTT	58.230	42.857	0.00	0.00	0.00	2.83
47	48	3.140623	GACCATTTTGCAGCCATTGTTT	58.859	40.909	0.00	0.00	0.00	2.83
48	49	3.553904	ACCATTTTGCAGCCATTGTTTT	58.446	36.364	0.00	0.00	0.00	2.43
232	244	7.890717	CGTGATGAACTTTTTGTTAAACACAAC	59.109	33.333	0.00	0.00	45.54	3.32
279	295	6.805713	AGCGTATTTTAAAGGCTGCATATTT	58.194	32.000	0.50	2.05	36.75	1.40
327	343	6.477053	TCACAAGGTGGATGAAAAATTTGA	57.523	33.333	0.00	0.00	33.87	2.69
328	344	7.065120	TCACAAGGTGGATGAAAAATTTGAT	57.935	32.000	0.00	0.00	33.87	2.57
329	345	7.507829	TCACAAGGTGGATGAAAAATTTGATT	58.492	30.769	0.00	0.00	33.87	2.57
396	417	8.486383	TGAACATATTTTCTGAATGTTTTTGCG	58.514	29.630	8.12	0.00	42.35	4.85
397	418	8.586570	AACATATTTTCTGAATGTTTTTGCGA	57.413	26.923	2.19	0.00	40.07	5.10
479	512	1.607612	CCCTGGCCCGTCAAATAGT	59.392	57.895	0.00	0.00	0.00	2.12
646	682	2.995872	GCTCAGCTCTTCCGGTCGT	61.996	63.158	0.00	0.00	0.00	4.34
820	856	4.685924	CAGCTTGTTCTTGTGAAATGGTT	58.314	39.130	0.00	0.00	33.52	3.67
884	920	1.002792	GCCCGGTCATTTCGCTAATTC	60.003	52.381	0.00	0.00	0.00	2.17
896	932	0.924090	GCTAATTCTCGCTGTCACGG	59.076	55.000	0.00	0.00	0.00	4.94
901	937	1.170442	TTCTCGCTGTCACGGATACA	58.830	50.000	0.00	0.00	0.00	2.29
928	964	5.469479	TCCCTTTTCGCTGATTCAAAATTC	58.531	37.500	0.00	0.00	0.00	2.17
930	966	5.473039	CCTTTTCGCTGATTCAAAATTCCT	58.527	37.500	0.00	0.00	0.00	3.36
935	971	5.496556	TCGCTGATTCAAAATTCCTCCTTA	58.503	37.500	0.00	0.00	0.00	2.69
941	977	8.434589	TGATTCAAAATTCCTCCTTACCAATT	57.565	30.769	0.00	0.00	0.00	2.32
946	982	6.994421	AAATTCCTCCTTACCAATTTGTGT	57.006	33.333	0.00	0.00	29.31	3.72
981	1019	0.738389	CGCAGGGGCAAATCGTATTT	59.262	50.000	0.00	0.00	41.24	1.40
1304	1342	1.607467	GTGCAGCCCCTGGAAATGT	60.607	57.895	0.00	0.00	32.80	2.71
1886	1924	2.360801	GCAAAAACTGTGGTCCTAAGCA	59.639	45.455	0.00	0.00	0.00	3.91
2135	2173	5.489249	TGCACATATGAACCATGCAAATTT	58.511	33.333	13.74	0.00	43.00	1.82
2260	2298	6.604735	AATGTTTTCCTGATATAGTGACGC	57.395	37.500	0.00	0.00	0.00	5.19
2548	2586	3.181526	GCTCTTGAATCGTACACTTGCTG	60.182	47.826	0.00	0.00	0.00	4.41
2783	2821	6.118852	GCAAGATAGTGAAAGAAGATTCCCT	58.881	40.000	0.00	0.00	0.00	4.20
2797	2835	1.021202	TTCCCTTGTTGTGTTGAGCG	58.979	50.000	0.00	0.00	0.00	5.03
2849	2887	9.347934	GATACTTCGTAGTCATGAAATATGGAG	57.652	37.037	12.32	12.32	35.78	3.86
2882	2920	4.038642	CCTAGCAGATAACTCCTGGAAGTC	59.961	50.000	0.00	0.00	32.51	3.01
3180	3221	7.665559	TCAACTGCCTCATGTTTACTTATTTCT	59.334	33.333	0.00	0.00	0.00	2.52
3273	3314	5.378292	TTTTATATTTGCAACAGTCGCCA	57.622	34.783	0.00	0.00	0.00	5.69
3288	3329	3.309582	CCACGGTCAGGGCACTAT	58.690	61.111	0.00	0.00	0.00	2.12
3289	3330	1.602237	CCACGGTCAGGGCACTATT	59.398	57.895	0.00	0.00	0.00	1.73
3291	3332	1.613255	CCACGGTCAGGGCACTATTTT	60.613	52.381	0.00	0.00	0.00	1.82
3292	3333	1.468520	CACGGTCAGGGCACTATTTTG	59.531	52.381	0.00	0.00	0.00	2.44
3293	3334	1.349688	ACGGTCAGGGCACTATTTTGA	59.650	47.619	0.00	0.00	0.00	2.69
3294	3335	2.224670	ACGGTCAGGGCACTATTTTGAA	60.225	45.455	0.00	0.00	0.00	2.69
3295	3336	3.016736	CGGTCAGGGCACTATTTTGAAT	58.983	45.455	0.00	0.00	0.00	2.57
3296	3337	4.196193	CGGTCAGGGCACTATTTTGAATA	58.804	43.478	0.00	0.00	0.00	1.75
3297	3338	4.638421	CGGTCAGGGCACTATTTTGAATAA	59.362	41.667	0.00	0.00	0.00	1.40
3299	3340	6.183360	CGGTCAGGGCACTATTTTGAATAATT	60.183	38.462	0.00	0.00	0.00	1.40
3301	3342	7.147915	GGTCAGGGCACTATTTTGAATAATTCA	60.148	37.037	0.00	0.00	38.04	2.57
3302	3343	7.917505	GTCAGGGCACTATTTTGAATAATTCAG	59.082	37.037	0.00	0.00	41.38	3.02
3304	3345	7.917505	CAGGGCACTATTTTGAATAATTCAGTC	59.082	37.037	0.00	0.00	41.38	3.51
3306	3347	7.917505	GGGCACTATTTTGAATAATTCAGTCTG	59.082	37.037	0.00	0.00	41.38	3.51
3357	5502	2.723530	TAGGGAAATTTTTGGGGCCA	57.276	45.000	4.39	0.00	0.00	5.36
3359	5504	0.327924	GGGAAATTTTTGGGGCCAGG	59.672	55.000	4.39	0.00	0.00	4.45
3380	5525	7.942894	GCCAGGGTAAAAATATACTCCACTAAT	59.057	37.037	0.00	0.00	0.00	1.73
3384	5529	7.148689	GGGTAAAAATATACTCCACTAATCGCG	60.149	40.741	0.00	0.00	0.00	5.87
3405	5550	0.905337	ATAGGGGATCGGCTAGGTGC	60.905	60.000	0.00	0.00	41.94	5.01
3460	5605	3.063045	GGTGCCGGAGTAAATTTTACTCG	59.937	47.826	29.51	25.11	43.53	4.18
3481	5626	4.646492	TCGACTAACCAGTTATAGGGGTTC	59.354	45.833	7.74	0.00	43.53	3.62
3507	5652	6.210784	GGTTAGAAATGCCCTAAGAGGTTTTT	59.789	38.462	0.00	0.00	31.93	1.94
3513	5658	0.454452	CCTAAGAGGTTTTTGCGCGC	60.454	55.000	27.26	27.26	0.00	6.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
394	415	8.451748	AGAAACCTTACATCTTATTTTTCTCGC	58.548	33.333	0.00	0.00	28.23	5.03
479	512	2.203938	AAGGAAGGAGGCGTCCCA	60.204	61.111	21.60	0.00	45.26	4.37
598	631	3.808771	CTCGGCCGGATTCGTCTCG	62.809	68.421	27.83	0.00	33.95	4.04
642	678	3.664223	GACGAGGCGAGGTCACGAC	62.664	68.421	0.00	0.00	42.10	4.34
820	856	0.331954	AGAGGTCTCCGCCACTAGAA	59.668	55.000	0.00	0.00	0.00	2.10
884	920	1.335182	AGATGTATCCGTGACAGCGAG	59.665	52.381	0.00	0.00	38.25	5.03
896	932	4.442706	TCAGCGAAAAGGGAAGATGTATC	58.557	43.478	0.00	0.00	0.00	2.24
901	937	3.955471	TGAATCAGCGAAAAGGGAAGAT	58.045	40.909	0.00	0.00	0.00	2.40
928	964	4.018779	TCCCTACACAAATTGGTAAGGAGG	60.019	45.833	13.05	5.15	29.15	4.30
930	966	4.563993	CGTCCCTACACAAATTGGTAAGGA	60.564	45.833	13.05	8.72	29.75	3.36
935	971	1.422402	ACCGTCCCTACACAAATTGGT	59.578	47.619	0.00	0.00	0.00	3.67
941	977	2.745037	GCCACCGTCCCTACACAA	59.255	61.111	0.00	0.00	0.00	3.33
981	1019	1.271856	TTCTACTGAACCGCCATGGA	58.728	50.000	18.40	0.00	42.00	3.41
1304	1342	1.614525	ACATCCCCAGCTGCTCTGA	60.615	57.895	8.66	1.52	45.72	3.27
1886	1924	3.972133	TCATTCAAGACTTCCATGGCAT	58.028	40.909	6.96	0.00	0.00	4.40
2135	2173	1.630369	AGGCAGTAACATCAGGCTCAA	59.370	47.619	0.00	0.00	30.35	3.02
2190	2228	2.289320	ACCAATAGCCTGATCGAGATGC	60.289	50.000	0.00	0.00	0.00	3.91
2260	2298	2.884012	TGGCATTTAGGAGTGTGTTGTG	59.116	45.455	0.00	0.00	0.00	3.33
2548	2586	8.896744	AGTAGTTACTTTAACCTGAAAACCAAC	58.103	33.333	0.00	0.00	39.47	3.77
2635	2673	8.902540	TTAATTTCTGATACCATTACTCGCAT	57.097	30.769	0.00	0.00	0.00	4.73
2783	2821	1.225855	CTAGCCGCTCAACACAACAA	58.774	50.000	0.00	0.00	0.00	2.83
2797	2835	1.066587	CACGCTCTAGTGGCTAGCC	59.933	63.158	27.71	27.71	38.40	3.93
2804	2842	1.134995	TCTTGGCATCACGCTCTAGTG	60.135	52.381	0.00	0.00	43.11	2.74
2882	2920	1.596260	CTTGCCGAGACACTATGCATG	59.404	52.381	10.16	1.82	0.00	4.06
3034	3074	5.065988	TCCTTTTGAAACAACACTAGAGCAC	59.934	40.000	0.00	0.00	0.00	4.40
3273	3314	1.349688	TCAAAATAGTGCCCTGACCGT	59.650	47.619	0.00	0.00	0.00	4.83
3291	3332	7.094377	GGCCAAGTAAACAGACTGAATTATTCA	60.094	37.037	10.08	7.46	38.17	2.57
3292	3333	7.251281	GGCCAAGTAAACAGACTGAATTATTC	58.749	38.462	10.08	0.00	0.00	1.75
3293	3334	6.128007	CGGCCAAGTAAACAGACTGAATTATT	60.128	38.462	10.08	2.64	0.00	1.40
3294	3335	5.354234	CGGCCAAGTAAACAGACTGAATTAT	59.646	40.000	10.08	0.00	0.00	1.28
3295	3336	4.693566	CGGCCAAGTAAACAGACTGAATTA	59.306	41.667	10.08	5.50	0.00	1.40
3296	3337	3.502211	CGGCCAAGTAAACAGACTGAATT	59.498	43.478	10.08	6.49	0.00	2.17
3297	3338	3.074412	CGGCCAAGTAAACAGACTGAAT	58.926	45.455	10.08	0.00	0.00	2.57
3299	3340	1.876416	GCGGCCAAGTAAACAGACTGA	60.876	52.381	10.08	0.00	0.00	3.41
3301	3342	0.605589	GGCGGCCAAGTAAACAGACT	60.606	55.000	15.62	0.00	0.00	3.24
3302	3343	0.887387	TGGCGGCCAAGTAAACAGAC	60.887	55.000	21.55	0.00	0.00	3.51
3304	3345	2.336341	TTGGCGGCCAAGTAAACAG	58.664	52.632	29.66	0.00	38.75	3.16
3341	5486	0.327924	CCCTGGCCCCAAAAATTTCC	59.672	55.000	0.00	0.00	0.00	3.13
3357	5502	7.876582	GCGATTAGTGGAGTATATTTTTACCCT	59.123	37.037	0.00	0.00	0.00	4.34
3359	5504	7.727017	CGCGATTAGTGGAGTATATTTTTACC	58.273	38.462	0.00	0.00	0.00	2.85
3380	5525	2.675423	CCGATCCCCTATCCGCGA	60.675	66.667	8.23	0.00	0.00	5.87
3384	5529	0.041386	ACCTAGCCGATCCCCTATCC	59.959	60.000	0.00	0.00	0.00	2.59
3460	5605	4.202192	CCGAACCCCTATAACTGGTTAGTC	60.202	50.000	0.00	0.00	42.27	2.59
3481	5626	3.118371	ACCTCTTAGGGCATTTCTAACCG	60.118	47.826	0.00	0.00	40.58	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.