AutoCloner

Multiple sequence alignment - TraesCS3D01G098900

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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	TraesCS3D01G098900	chr3D	100.000	2786	0	0	1	2786	50548940	50551725	0.000000e+00	5145.0
1	TraesCS3D01G098900	chr3D	87.363	641	45	14	1163	1788	50536232	50536851	0.000000e+00	702.0
2	TraesCS3D01G098900	chr3D	86.296	270	30	4	895	1161	50515457	50515722	1.260000e-73	287.0
3	TraesCS3D01G098900	chr3D	77.619	210	22	11	555	763	50514389	50514574	1.360000e-18	104.0
4	TraesCS3D01G098900	chr3B	92.285	2035	89	24	790	2786	80162957	80164961	0.000000e+00	2826.0
5	TraesCS3D01G098900	chr3B	83.662	912	72	23	895	1788	80102810	80103662	0.000000e+00	787.0
6	TraesCS3D01G098900	chr3B	88.320	488	24	15	1	470	80159262	80159734	3.140000e-154	555.0
7	TraesCS3D01G098900	chr3B	97.987	149	3	0	464	612	80162447	80162595	2.750000e-65	259.0
8	TraesCS3D01G098900	chr3B	94.545	55	3	0	659	713	80162887	80162941	4.940000e-13	86.1
9	TraesCS3D01G098900	chr3A	88.139	1644	85	45	267	1887	63557544	63559100	0.000000e+00	1855.0
10	TraesCS3D01G098900	chr3A	90.888	878	56	12	1910	2786	63559646	63560500	0.000000e+00	1157.0
11	TraesCS3D01G098900	chr3A	89.071	183	8	2	99	269	63552481	63552663	1.680000e-52	217.0
12	TraesCS3D01G098900	chr3A	87.500	120	3	8	1	110	63552342	63552459	8.100000e-26	128.0
13	TraesCS3D01G098900	chr1B	80.880	591	78	17	1180	1757	44849438	44850006	1.530000e-117	433.0
14	TraesCS3D01G098900	chr1B	83.489	321	41	4	1468	1776	62197048	62196728	3.510000e-74	289.0
15	TraesCS3D01G098900	chr2D	80.392	612	82	23	1173	1767	467147671	467148261	5.510000e-117	431.0
16	TraesCS3D01G098900	chr5B	80.230	521	94	8	2269	2786	542931507	542930993	1.570000e-102	383.0

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	TraesCS3D01G098900	chr3D	50548940	50551725	2785	False	5145.000	5145	100.00000	1	2786	1	chr3D.!!$F2	2785
1	TraesCS3D01G098900	chr3D	50536232	50536851	619	False	702.000	702	87.36300	1163	1788	1	chr3D.!!$F1	625
2	TraesCS3D01G098900	chr3B	80159262	80164961	5699	False	931.525	2826	93.28425	1	2786	4	chr3B.!!$F2	2785
3	TraesCS3D01G098900	chr3B	80102810	80103662	852	False	787.000	787	83.66200	895	1788	1	chr3B.!!$F1	893
4	TraesCS3D01G098900	chr3A	63557544	63560500	2956	False	1506.000	1855	89.51350	267	2786	2	chr3A.!!$F2	2519
5	TraesCS3D01G098900	chr1B	44849438	44850006	568	False	433.000	433	80.88000	1180	1757	1	chr1B.!!$F1	577
6	TraesCS3D01G098900	chr2D	467147671	467148261	590	False	431.000	431	80.39200	1173	1767	1	chr2D.!!$F1	594
7	TraesCS3D01G098900	chr5B	542930993	542931507	514	True	383.000	383	80.23000	2269	2786	1	chr5B.!!$R1	517

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
444	471	0.03582	TGCACCGGTAGATGGGAAAC	60.036	55.0	6.87	0.0	0.0	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2360	6015	0.455295	CGAGCGGGATCTTATCGAGC	60.455	60.0	0.0	0.0	35.47	5.03	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
85	86	1.673329	GGCCTCGTCTTCTTTGGTCTC	60.673	57.143	0.00	0.00	0.00	3.36
86	87	1.673329	GCCTCGTCTTCTTTGGTCTCC	60.673	57.143	0.00	0.00	0.00	3.71
87	88	1.896465	CCTCGTCTTCTTTGGTCTCCT	59.104	52.381	0.00	0.00	0.00	3.69
88	89	2.094442	CCTCGTCTTCTTTGGTCTCCTC	60.094	54.545	0.00	0.00	0.00	3.71
90	91	1.066787	CGTCTTCTTTGGTCTCCTCCC	60.067	57.143	0.00	0.00	0.00	4.30
91	92	1.978580	GTCTTCTTTGGTCTCCTCCCA	59.021	52.381	0.00	0.00	0.00	4.37
246	256	3.081409	GGAGGCCGCTCTGGGTTA	61.081	66.667	6.40	0.00	38.63	2.85
247	257	2.187163	GAGGCCGCTCTGGGTTAC	59.813	66.667	0.00	0.00	38.63	2.50
248	258	3.387225	GAGGCCGCTCTGGGTTACC	62.387	68.421	0.00	0.00	38.63	2.85
407	434	2.621407	GGGGGTGTGAATGTGATGTGAT	60.621	50.000	0.00	0.00	0.00	3.06
425	452	0.873054	ATGTGAACTCGACTCGACGT	59.127	50.000	0.00	0.00	34.70	4.34
434	461	2.969806	GACTCGACGTGCACCGGTA	61.970	63.158	6.87	0.00	42.24	4.02
444	471	0.035820	TGCACCGGTAGATGGGAAAC	60.036	55.000	6.87	0.00	0.00	2.78
480	3233	4.686091	GCCTTGTTAAGCCTTTTGATTGAC	59.314	41.667	0.00	0.00	0.00	3.18
529	3340	2.507769	TGATGAGTCTGCGCTGCG	60.508	61.111	19.17	19.17	0.00	5.18
580	3391	1.277273	CTCATCCTGCTCAACACTGGA	59.723	52.381	0.00	0.00	39.18	3.86
646	3461	5.803237	AGTAGTACTCCTAGAGAGAGAGC	57.197	47.826	13.28	1.84	46.50	4.09
699	3755	0.675083	TCACGGCAAGTTAACTCGGA	59.325	50.000	8.95	5.61	0.00	4.55
700	3756	1.274167	TCACGGCAAGTTAACTCGGAT	59.726	47.619	8.95	0.00	0.00	4.18
701	3757	1.659098	CACGGCAAGTTAACTCGGATC	59.341	52.381	8.95	0.81	0.00	3.36
732	3788	1.968017	CTTGGTCCAGTGCACGCAT	60.968	57.895	12.01	0.00	0.00	4.73
757	3813	0.676184	TGGACACACTGCTCACTCTC	59.324	55.000	0.00	0.00	0.00	3.20
758	3814	0.965439	GGACACACTGCTCACTCTCT	59.035	55.000	0.00	0.00	0.00	3.10
759	3815	2.163509	GGACACACTGCTCACTCTCTA	58.836	52.381	0.00	0.00	0.00	2.43
760	3816	2.163412	GGACACACTGCTCACTCTCTAG	59.837	54.545	0.00	0.00	0.00	2.43
779	3835	1.036707	GCTAGCTCACTCTACTGGGG	58.963	60.000	7.70	0.00	0.00	4.96
796	3852	2.167693	TGGGGTAGCTTTATCTGACACG	59.832	50.000	0.00	0.00	0.00	4.49
832	3888	3.305516	GCAGCCAACCCAACCCAG	61.306	66.667	0.00	0.00	0.00	4.45
881	3940	4.385405	GCCACTCTCTGCCGCTGT	62.385	66.667	0.00	0.00	0.00	4.40
904	3970	1.198759	TGCTACCACCTCCAACTCCC	61.199	60.000	0.00	0.00	0.00	4.30
1400	4472	0.539051	ATCTTCCTGAAGGTGCTCCG	59.461	55.000	7.03	0.00	38.88	4.63
1788	4902	1.836802	AGGATCTCCTTGGAGTGAAGC	59.163	52.381	15.44	0.68	46.09	3.86
1830	4944	2.797156	AGTATGCGATTTCTCGTGCATC	59.203	45.455	1.34	0.00	44.21	3.91
1850	4968	2.235650	TCTTGCTGCTAGAACTGCTGAT	59.764	45.455	11.30	0.00	35.70	2.90
1904	5544	3.502595	CCTAACAGAGTCGTTCAGTCAGA	59.497	47.826	4.07	0.00	0.00	3.27
1935	5582	3.024547	AGCTGCTCGAGATTAAGTACCA	58.975	45.455	18.75	0.00	0.00	3.25
1936	5583	3.117046	GCTGCTCGAGATTAAGTACCAC	58.883	50.000	18.75	0.00	0.00	4.16
1943	5590	6.563753	GCTCGAGATTAAGTACCACTACGTAG	60.564	46.154	20.97	20.97	0.00	3.51
1960	5607	9.059485	CACTACGTAGTACTAGTTCAACATTTC	57.941	37.037	26.95	0.00	45.11	2.17
1972	5619	9.778993	CTAGTTCAACATTTCTAACATGAATGG	57.221	33.333	0.00	0.00	0.00	3.16
1973	5620	8.408043	AGTTCAACATTTCTAACATGAATGGA	57.592	30.769	0.00	0.00	0.00	3.41
1974	5621	9.028284	AGTTCAACATTTCTAACATGAATGGAT	57.972	29.630	0.00	0.00	0.00	3.41
1975	5622	9.079833	GTTCAACATTTCTAACATGAATGGATG	57.920	33.333	0.00	3.21	0.00	3.51
1976	5623	8.578448	TCAACATTTCTAACATGAATGGATGA	57.422	30.769	0.00	5.41	0.00	2.92
1977	5624	9.192642	TCAACATTTCTAACATGAATGGATGAT	57.807	29.630	0.00	0.00	0.00	2.45
1978	5625	9.244799	CAACATTTCTAACATGAATGGATGATG	57.755	33.333	0.00	5.99	0.00	3.07
2056	5707	8.641541	ACATTTTACTCAACTTGACCATGAATT	58.358	29.630	0.00	0.00	0.00	2.17
2061	5712	5.107109	TCAACTTGACCATGAATTTGACG	57.893	39.130	0.00	0.00	0.00	4.35
2130	5785	7.789273	ACATCTGAAATCATCTGCTTCTAAG	57.211	36.000	0.00	0.00	0.00	2.18
2131	5786	7.337167	ACATCTGAAATCATCTGCTTCTAAGT	58.663	34.615	0.00	0.00	0.00	2.24
2132	5787	7.828223	ACATCTGAAATCATCTGCTTCTAAGTT	59.172	33.333	0.00	0.00	0.00	2.66
2133	5788	7.840342	TCTGAAATCATCTGCTTCTAAGTTC	57.160	36.000	0.00	0.00	0.00	3.01
2134	5789	7.619050	TCTGAAATCATCTGCTTCTAAGTTCT	58.381	34.615	0.00	0.00	0.00	3.01
2135	5790	8.753133	TCTGAAATCATCTGCTTCTAAGTTCTA	58.247	33.333	0.00	0.00	0.00	2.10
2136	5791	9.545105	CTGAAATCATCTGCTTCTAAGTTCTAT	57.455	33.333	0.00	0.00	0.00	1.98
2288	5943	1.168714	CAGGGAAAACTACTGGCTGC	58.831	55.000	0.00	0.00	0.00	5.25
2348	6003	0.478507	CCCACAAACTGTTCTCCCCT	59.521	55.000	0.00	0.00	0.00	4.79
2433	6088	0.250727	TGTGGCAGCCTCTTGTAACC	60.251	55.000	14.15	0.00	0.00	2.85
2528	6183	2.949177	TACTGAACCCAATGTGTGCT	57.051	45.000	0.00	0.00	0.00	4.40
2551	6206	5.250982	TGAAAGATCATTGAGTGACTGCAT	58.749	37.500	0.00	0.00	40.28	3.96
2567	6222	6.318648	GTGACTGCATGGATAGTTTGGATAAA	59.681	38.462	0.00	0.00	0.00	1.40
2593	6248	1.078918	CAGCATGCAAGAGGGACGA	60.079	57.895	21.98	0.00	0.00	4.20
2657	6312	4.366586	TCTCTAGCAATTCATCGAGCAAG	58.633	43.478	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	6.492254	GTCCTTTTCGTTTTTAAGCAAGAGA	58.508	36.000	0.00	0.00	0.00	3.10
12	13	5.395486	CGTCCTTTTCGTTTTTAAGCAAGAG	59.605	40.000	0.00	0.00	0.00	2.85
85	86	1.748591	GCAGGTAGCAGAAATGGGAGG	60.749	57.143	0.00	0.00	44.79	4.30
86	87	1.673168	GCAGGTAGCAGAAATGGGAG	58.327	55.000	0.00	0.00	44.79	4.30
87	88	3.882131	GCAGGTAGCAGAAATGGGA	57.118	52.632	0.00	0.00	44.79	4.37
110	120	2.030363	TGTTGAAACATGATGGGCGAAC	60.030	45.455	0.00	0.00	33.17	3.95
117	127	3.813800	CACCGTCTGTTGAAACATGATG	58.186	45.455	0.00	0.00	38.41	3.07
162	172	4.828296	CCCCACATGCTCCTGCCC	62.828	72.222	0.00	0.00	38.71	5.36
258	268	2.760385	AGCTGGTCCGGAGCTACC	60.760	66.667	31.97	18.45	45.17	3.18
303	325	3.029735	CGTGCCAAAAGTTGCCGC	61.030	61.111	0.00	0.00	0.00	6.53
407	434	0.041576	CACGTCGAGTCGAGTTCACA	60.042	55.000	17.12	0.00	36.23	3.58
425	452	0.035820	GTTTCCCATCTACCGGTGCA	60.036	55.000	19.93	2.98	0.00	4.57
434	461	5.749462	CAAGGTGAGATAAGTTTCCCATCT	58.251	41.667	0.00	0.00	0.00	2.90
444	471	5.163713	GCTTAACAAGGCAAGGTGAGATAAG	60.164	44.000	0.00	0.00	0.00	1.73
480	3233	0.595053	ACACTCGTGCTGTCTTGTCG	60.595	55.000	0.00	0.00	0.00	4.35
529	3340	0.234884	GCAAGTGTACACCGAGCAAC	59.765	55.000	22.28	2.04	0.00	4.17
580	3391	1.463674	GGATCGAAGGGCAACAACAT	58.536	50.000	0.00	0.00	39.74	2.71
615	3426	6.822676	TCTCTAGGAGTACTACTAGTTTGTGC	59.177	42.308	32.31	4.74	43.18	4.57
699	3755	5.147032	TGGACCAAGACCAAAAGATTTGAT	58.853	37.500	4.47	0.00	34.25	2.57
700	3756	4.541705	TGGACCAAGACCAAAAGATTTGA	58.458	39.130	4.47	0.00	34.25	2.69
701	3757	4.342092	ACTGGACCAAGACCAAAAGATTTG	59.658	41.667	0.00	0.00	36.95	2.32
737	3793	0.390860	AGAGTGAGCAGTGTGTCCAC	59.609	55.000	0.00	0.00	42.17	4.02
757	3813	3.146066	CCCAGTAGAGTGAGCTAGCTAG	58.854	54.545	19.38	16.84	0.00	3.42
758	3814	2.158593	CCCCAGTAGAGTGAGCTAGCTA	60.159	54.545	19.38	3.38	0.00	3.32
759	3815	1.410932	CCCCAGTAGAGTGAGCTAGCT	60.411	57.143	19.45	19.45	0.00	3.32
760	3816	1.036707	CCCCAGTAGAGTGAGCTAGC	58.963	60.000	6.62	6.62	0.00	3.42
779	3835	2.530700	GCGTCGTGTCAGATAAAGCTAC	59.469	50.000	0.00	0.00	0.00	3.58
796	3852	2.504244	CCTCGGAGAACGTGCGTC	60.504	66.667	6.58	0.00	44.69	5.19
804	3860	1.913262	TTGGCTGCTCCTCGGAGAA	60.913	57.895	16.92	5.24	44.53	2.87
850	3906	4.402528	TGGCATTGGACGACGGGG	62.403	66.667	0.00	0.00	0.00	5.73
851	3907	3.124921	GTGGCATTGGACGACGGG	61.125	66.667	0.00	0.00	0.00	5.28
881	3940	0.250727	GTTGGAGGTGGTAGCAGCAA	60.251	55.000	24.51	8.84	0.00	3.91
920	3986	2.236959	GAGGGCTGAGGGAGAGGAGT	62.237	65.000	0.00	0.00	0.00	3.85
950	4016	2.893682	GAACCCCGGGCAAGATCAGG	62.894	65.000	17.73	0.00	0.00	3.86
1788	4902	0.919981	GCTGCTCGATCTTCACTTCG	59.080	55.000	0.00	0.00	36.72	3.79
1830	4944	2.090400	TCAGCAGTTCTAGCAGCAAG	57.910	50.000	0.00	0.00	0.00	4.01
1850	4968	4.703575	ACGAACTAGTAGTGGTAATCTGCA	59.296	41.667	2.90	0.00	0.00	4.41
1904	5544	5.782893	ATCTCGAGCAGCTAACTAGAAAT	57.217	39.130	7.81	0.00	0.00	2.17
1970	5617	9.357161	TGATACATCAATTTCATTCATCATCCA	57.643	29.630	0.00	0.00	33.08	3.41
1971	5618	9.841880	CTGATACATCAATTTCATTCATCATCC	57.158	33.333	0.00	0.00	36.18	3.51
2003	5653	1.000938	GCACTTGCAAACCAGAAGGAG	60.001	52.381	0.00	0.00	41.59	3.69
2056	5707	8.786826	AATAACTTGGATTTCATACTCGTCAA	57.213	30.769	0.00	0.00	0.00	3.18
2098	5751	8.356657	AGCAGATGATTTCAGATGTACTACTAC	58.643	37.037	0.00	0.00	0.00	2.73
2179	5834	5.640147	TGGTCCCAGTTTAGATGAACAAAT	58.360	37.500	0.00	0.00	31.94	2.32
2360	6015	0.455295	CGAGCGGGATCTTATCGAGC	60.455	60.000	0.00	0.00	35.47	5.03
2516	6171	2.821378	TGATCTTTCAGCACACATTGGG	59.179	45.455	0.00	0.00	0.00	4.12
2519	6174	5.475909	ACTCAATGATCTTTCAGCACACATT	59.524	36.000	0.00	0.00	34.73	2.71
2520	6175	5.008331	ACTCAATGATCTTTCAGCACACAT	58.992	37.500	0.00	0.00	34.73	3.21
2528	6183	4.644498	TGCAGTCACTCAATGATCTTTCA	58.356	39.130	0.00	0.00	40.28	2.69
2567	6222	3.256631	CCCTCTTGCATGCTGTAAAACTT	59.743	43.478	20.33	0.00	0.00	2.66
2593	6248	5.244626	CCAAAGGATTTCAGAAACATGGAGT	59.755	40.000	0.00	0.00	35.03	3.85
2657	6312	4.327854	GTCATTCGACATTGTCTTCCAC	57.672	45.455	14.54	2.02	42.13	4.02
2688	6343	3.325135	GGGATATCAGTTCCATCTTCGGT	59.675	47.826	4.83	0.00	34.77	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.