AutoCloner

Multiple sequence alignment - TraesCS3D01G214700

Loading Multiple Alignment...

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	TraesCS3D01G214700	chr3D	100.000	5361	0	0	1	5361	290021138	290015778	0.000000e+00	9901
1	TraesCS3D01G214700	chr3D	85.327	443	61	4	2	441	588129406	588128965	6.330000e-124	455
2	TraesCS3D01G214700	chr3B	98.719	4373	38	4	996	5361	382323090	382318729	0.000000e+00	7749
3	TraesCS3D01G214700	chr3B	90.457	1006	68	6	1	978	382324377	382323372	0.000000e+00	1301
4	TraesCS3D01G214700	chr3A	97.671	4422	93	4	943	5361	381297908	381293494	0.000000e+00	7587
5	TraesCS3D01G214700	chr6B	78.673	844	148	20	1	823	512574992	512574160	2.840000e-147	532
6	TraesCS3D01G214700	chr5A	86.036	444	59	3	1	441	552640980	552641423	1.750000e-129	473
7	TraesCS3D01G214700	chr5D	85.618	445	59	4	2	441	437614226	437614670	3.780000e-126	462
8	TraesCS3D01G214700	chr7A	85.135	444	62	4	1	441	57694207	57693765	8.190000e-123	451
9	TraesCS3D01G214700	chr6A	84.494	445	65	4	1	441	590210675	590210231	2.290000e-118	436
10	TraesCS3D01G214700	chr6D	83.108	444	69	4	1	441	441674562	441674122	3.010000e-107	399
11	TraesCS3D01G214700	chr2D	82.774	447	68	8	1	441	420980790	420981233	1.810000e-104	390
12	TraesCS3D01G214700	chr2B	79.897	194	33	5	587	779	197144004	197143816	2.600000e-28	137
13	TraesCS3D01G214700	chr1D	79.605	152	27	4	674	823	332453468	332453319	7.340000e-19	106

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	TraesCS3D01G214700	chr3D	290015778	290021138	5360	True	9901	9901	100.000	1	5361	1	chr3D.!!$R1	5360
1	TraesCS3D01G214700	chr3B	382318729	382324377	5648	True	4525	7749	94.588	1	5361	2	chr3B.!!$R1	5360
2	TraesCS3D01G214700	chr3A	381293494	381297908	4414	True	7587	7587	97.671	943	5361	1	chr3A.!!$R1	4418
3	TraesCS3D01G214700	chr6B	512574160	512574992	832	True	532	532	78.673	1	823	1	chr6B.!!$R1	822

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
992	1070	0.034896	ATTCTGCCGGAAACAGACGT	59.965	50.000	5.05	43.64	4.34	F
1049	1360	0.172352	CTCACACTCCGCTTCTCCTC	59.828	60.000	0.00	0.00	3.71	F
2737	3048	2.649312	TCCAAAATGATGAGGAGTGGGT	59.351	45.455	0.00	0.00	4.51	F
3374	3685	5.185454	TCCAGACCATGTCACATTTATCAC	58.815	41.667	0.00	34.60	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2910	3221	0.040958	CCGAAAACAGCTGCTCACAC	60.041	55.0	15.27	0.0	0.00	3.82	R
2988	3299	1.779221	CCTCCTGCAAATGGCCATTA	58.221	50.0	30.84	15.0	43.89	1.90	R
4344	4656	1.438469	CATCTTGGGATAGGGAGGCA	58.562	55.0	0.00	0.0	0.00	4.75	R
4574	4886	2.094762	ACAAGCTATTCACACCGACC	57.905	50.0	0.00	0.0	0.00	4.79	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
75	77	0.661020	CCCAGAACGGTTGAACACAC	59.339	55.000	0.00	0.00	0.00	3.82
77	79	0.315869	CAGAACGGTTGAACACACGC	60.316	55.000	0.00	0.00	0.00	5.34
99	101	3.124921	CCATCCGAAAACGGCGCT	61.125	61.111	6.90	0.00	0.00	5.92
173	177	0.470341	GTAGGCAATGACCCTCCCTC	59.530	60.000	0.00	0.00	33.88	4.30
244	249	2.743636	GCCGCTGCCTACTAATATGA	57.256	50.000	0.00	0.00	0.00	2.15
266	271	1.597854	TGGACGACCAAAGCAGCAG	60.598	57.895	3.49	0.00	43.91	4.24
301	312	5.591099	TCATCATCGAACGAAGAATCATCA	58.409	37.500	6.26	0.00	0.00	3.07
403	415	1.696832	GCATCGTGGAAGAAGCCGAC	61.697	60.000	0.00	0.00	31.43	4.79
443	467	0.526662	CTCCGAGAACAGGTAGCGTT	59.473	55.000	0.00	2.58	0.00	4.84
462	486	2.835705	CGACGAGCGAGGTAGCCAT	61.836	63.158	0.00	0.00	44.57	4.40
526	550	2.589442	GTCCGGGTGTTGCGACAA	60.589	61.111	8.77	0.00	37.57	3.18
539	563	1.413008	GCGACAATGGCGAAAATGGC	61.413	55.000	14.82	0.00	0.00	4.40
567	591	3.925090	CCGGAGTATGGGGCCGTC	61.925	72.222	0.00	0.00	43.35	4.79
606	631	1.327690	GGGAGGTATGTGAGTGCGGA	61.328	60.000	0.00	0.00	0.00	5.54
610	635	1.076533	GGTATGTGAGTGCGGACGTG	61.077	60.000	0.00	0.00	0.00	4.49
611	636	0.388134	GTATGTGAGTGCGGACGTGT	60.388	55.000	0.00	0.00	0.00	4.49
674	702	0.528684	GACCAGATGTGCTAGCCGTC	60.529	60.000	13.29	13.88	0.00	4.79
730	758	3.242291	GGCGGACTAGGGGGATGG	61.242	72.222	0.00	0.00	0.00	3.51
794	822	1.895051	CAAACGCGCCTAAATTCAGG	58.105	50.000	5.73	0.00	38.86	3.86
808	836	6.151648	CCTAAATTCAGGCTTGAAATGAGTCA	59.848	38.462	15.81	0.00	45.82	3.41
814	842	2.677836	GGCTTGAAATGAGTCACGCATA	59.322	45.455	0.00	0.00	42.83	3.14
850	884	6.765512	TGAATACAATTAGATCGGCATGTTGA	59.234	34.615	0.00	0.00	0.00	3.18
871	918	6.189677	TGAATCGACTTTTGTGTCTGTTTT	57.810	33.333	0.00	0.00	35.00	2.43
874	921	8.402472	TGAATCGACTTTTGTGTCTGTTTTAAT	58.598	29.630	0.00	0.00	35.00	1.40
894	941	2.546778	TCCAAACGAATATCGGACAGC	58.453	47.619	4.66	0.00	45.59	4.40
907	954	0.390998	GGACAGCTGGAGTTGCTCTC	60.391	60.000	19.93	2.47	38.92	3.20
908	955	0.735632	GACAGCTGGAGTTGCTCTCG	60.736	60.000	19.93	0.00	43.60	4.04
935	982	2.435410	GGCCCCGGTGTTTCTACG	60.435	66.667	0.00	0.00	0.00	3.51
941	988	1.278238	CCGGTGTTTCTACGATCAGC	58.722	55.000	0.00	0.00	0.00	4.26
963	1010	1.134788	AGAGCGGGAGTCATTTTACCG	60.135	52.381	0.00	0.00	46.78	4.02
992	1070	0.034896	ATTCTGCCGGAAACAGACGT	59.965	50.000	5.05	0.00	43.64	4.34
1044	1355	1.374758	CCACCTCACACTCCGCTTC	60.375	63.158	0.00	0.00	0.00	3.86
1045	1356	1.668294	CACCTCACACTCCGCTTCT	59.332	57.895	0.00	0.00	0.00	2.85
1046	1357	0.389166	CACCTCACACTCCGCTTCTC	60.389	60.000	0.00	0.00	0.00	2.87
1047	1358	1.216710	CCTCACACTCCGCTTCTCC	59.783	63.158	0.00	0.00	0.00	3.71
1048	1359	1.254284	CCTCACACTCCGCTTCTCCT	61.254	60.000	0.00	0.00	0.00	3.69
1049	1360	0.172352	CTCACACTCCGCTTCTCCTC	59.828	60.000	0.00	0.00	0.00	3.71
1786	2097	2.697431	TACTTTGTTCACGGCAATGC	57.303	45.000	0.00	0.00	0.00	3.56
2737	3048	2.649312	TCCAAAATGATGAGGAGTGGGT	59.351	45.455	0.00	0.00	0.00	4.51
2988	3299	9.872684	AATTCAATGATTTCAGGGTACATCTAT	57.127	29.630	0.00	0.00	0.00	1.98
3261	3572	6.965500	CCATGAATCAGAAAAATGAGTTCTCG	59.035	38.462	0.00	0.00	32.96	4.04
3374	3685	5.185454	TCCAGACCATGTCACATTTATCAC	58.815	41.667	0.00	0.00	34.60	3.06
4782	5096	9.520515	CACCCAGCTTAGTTAAATATTATGGAT	57.479	33.333	8.54	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	77	1.762222	CGTTTTCGGATGGCTAGGCG	61.762	60.000	12.19	0.00	39.94	5.52
99	101	4.518970	GCTCTTCAAACACCACCTATTTCA	59.481	41.667	0.00	0.00	0.00	2.69
244	249	1.742761	CTGCTTTGGTCGTCCATGAT	58.257	50.000	1.21	0.00	43.91	2.45
266	271	2.057316	CGATGATGAGGAGATTGCGAC	58.943	52.381	0.00	0.00	0.00	5.19
301	312	9.883142	TTTTTCCACAGTTTTATTTGTGATTCT	57.117	25.926	6.21	0.00	45.79	2.40
403	415	4.554363	CGCGAGGCTCTACACCGG	62.554	72.222	13.50	0.00	0.00	5.28
443	467	3.200593	GGCTACCTCGCTCGTCGA	61.201	66.667	0.00	0.00	46.29	4.20
462	486	3.279116	GTCGGCAGCACACAAGCA	61.279	61.111	0.00	0.00	36.85	3.91
512	536	2.560861	CCATTGTCGCAACACCCG	59.439	61.111	0.00	0.00	34.35	5.28
518	542	1.668337	CCATTTTCGCCATTGTCGCAA	60.668	47.619	0.00	0.00	0.00	4.85
522	546	3.049227	GGCCATTTTCGCCATTGTC	57.951	52.632	0.00	0.00	46.27	3.18
539	563	2.530958	ATACTCCGGCGTTTGGTGGG	62.531	60.000	0.59	0.00	0.00	4.61
567	591	3.242897	TAGAAACACGCCACCCCCG	62.243	63.158	0.00	0.00	0.00	5.73
580	605	4.030913	CACTCACATACCTCCCCTAGAAA	58.969	47.826	0.00	0.00	0.00	2.52
610	635	2.203480	TTTCAGTGCCCAGGCCAC	60.203	61.111	5.01	0.00	41.09	5.01
611	636	2.203480	GTTTCAGTGCCCAGGCCA	60.203	61.111	5.01	0.00	41.09	5.36
646	674	3.402681	CATCTGGTCGCCCCACCT	61.403	66.667	0.00	0.00	38.72	4.00
668	696	2.363795	TTCCTCCCATCGACGGCT	60.364	61.111	0.00	0.00	0.00	5.52
674	702	1.071385	CATTCCTCCTTCCTCCCATCG	59.929	57.143	0.00	0.00	0.00	3.84
718	746	1.697754	CCCTTGCCATCCCCCTAGT	60.698	63.158	0.00	0.00	0.00	2.57
791	819	1.135859	GCGTGACTCATTTCAAGCCTG	60.136	52.381	0.21	0.00	42.97	4.85
796	824	4.565022	TGTCTATGCGTGACTCATTTCAA	58.435	39.130	0.00	0.00	35.63	2.69
823	851	7.750229	ACATGCCGATCTAATTGTATTCATT	57.250	32.000	0.00	0.00	0.00	2.57
836	870	2.159043	AGTCGATTCAACATGCCGATCT	60.159	45.455	0.00	0.00	0.00	2.75
838	872	2.315925	AGTCGATTCAACATGCCGAT	57.684	45.000	0.00	0.00	0.00	4.18
840	874	2.900122	AAAGTCGATTCAACATGCCG	57.100	45.000	0.00	0.00	0.00	5.69
844	878	5.296780	ACAGACACAAAAGTCGATTCAACAT	59.703	36.000	0.00	0.00	43.24	2.71
850	884	7.860872	GGATTAAAACAGACACAAAAGTCGATT	59.139	33.333	0.00	0.00	43.24	3.34
871	918	4.748102	GCTGTCCGATATTCGTTTGGATTA	59.252	41.667	0.00	0.00	38.40	1.75
874	921	2.167693	AGCTGTCCGATATTCGTTTGGA	59.832	45.455	0.00	0.00	38.40	3.53
894	941	0.891373	TTCTCCGAGAGCAACTCCAG	59.109	55.000	0.00	3.01	42.18	3.86
926	973	2.478031	GCTCTCGCTGATCGTAGAAACA	60.478	50.000	0.00	0.00	43.58	2.83
928	975	1.268083	CGCTCTCGCTGATCGTAGAAA	60.268	52.381	0.00	0.00	43.58	2.52
935	982	2.334653	CTCCCGCTCTCGCTGATC	59.665	66.667	0.00	0.00	0.00	2.92
941	988	2.194271	GTAAAATGACTCCCGCTCTCG	58.806	52.381	0.00	0.00	0.00	4.04
963	1010	0.168128	CCGGCAGAATTTCACGTTCC	59.832	55.000	0.00	0.00	0.00	3.62
992	1070	4.083003	GGAGTTTGCGGTTCATGTATTTGA	60.083	41.667	0.00	0.00	0.00	2.69
1044	1355	1.292941	TGGAGGAGGAGGAGGAGGAG	61.293	65.000	0.00	0.00	0.00	3.69
1045	1356	1.230650	TGGAGGAGGAGGAGGAGGA	60.231	63.158	0.00	0.00	0.00	3.71
1046	1357	1.232792	CTGGAGGAGGAGGAGGAGG	59.767	68.421	0.00	0.00	0.00	4.30
1047	1358	1.457455	GCTGGAGGAGGAGGAGGAG	60.457	68.421	0.00	0.00	0.00	3.69
1048	1359	1.938596	AGCTGGAGGAGGAGGAGGA	60.939	63.158	0.00	0.00	0.00	3.71
1049	1360	1.457455	GAGCTGGAGGAGGAGGAGG	60.457	68.421	0.00	0.00	0.00	4.30
1194	1505	1.679305	GAGGAGGTCAGCGTGAGGA	60.679	63.158	0.00	0.00	0.00	3.71
2737	3048	3.544698	TGTAACCTTATTTGGGGCCAA	57.455	42.857	4.39	0.00	0.00	4.52
2751	3062	7.080353	AGCCAATAAGTTAACGAATGTAACC	57.920	36.000	0.00	0.00	0.00	2.85
2910	3221	0.040958	CCGAAAACAGCTGCTCACAC	60.041	55.000	15.27	0.00	0.00	3.82
2988	3299	1.779221	CCTCCTGCAAATGGCCATTA	58.221	50.000	30.84	15.00	43.89	1.90
3017	3328	3.192001	ACTGTGCATCATAAGCCAAACAG	59.808	43.478	0.00	0.00	38.64	3.16
3102	3413	3.805108	GCATCTCCATTCCACGCTCTAAT	60.805	47.826	0.00	0.00	0.00	1.73
3261	3572	7.254932	GCATAACCAGAAATCATAGAGTTCCAC	60.255	40.741	3.87	0.00	37.35	4.02
3374	3685	4.991153	TGACTACAGGCAGATAGAACAG	57.009	45.455	0.00	0.00	0.00	3.16
4344	4656	1.438469	CATCTTGGGATAGGGAGGCA	58.562	55.000	0.00	0.00	0.00	4.75
4574	4886	2.094762	ACAAGCTATTCACACCGACC	57.905	50.000	0.00	0.00	0.00	4.79
4782	5096	6.640518	AGTTTGAGTGAGTTGAGTTAGTTGA	58.359	36.000	0.00	0.00	0.00	3.18
4976	5290	3.070878	TCATTTGTGCTGTCCTGTCAGTA	59.929	43.478	0.00	0.00	37.70	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.