AutoCloner

Multiple sequence alignment - TraesCS3A01G213700

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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	TraesCS3A01G213700	chr3A	100.000	3538	0	0	1	3538	386216138	386219675	0.000000e+00	6534
1	TraesCS3A01G213700	chr3D	96.890	2765	58	8	770	3528	293189945	293192687	0.000000e+00	4604
2	TraesCS3A01G213700	chr3B	96.403	2697	68	11	857	3538	386521590	386524272	0.000000e+00	4416
3	TraesCS3A01G213700	chr3B	88.288	111	13	0	1100	1210	745203196	745203086	2.220000e-27	134
4	TraesCS3A01G213700	chr3B	90.000	90	2	6	770	858	386521269	386521352	3.730000e-20	110
5	TraesCS3A01G213700	chr5D	94.048	756	39	5	1	755	343309865	343309115	0.000000e+00	1142
6	TraesCS3A01G213700	chr6B	92.308	754	54	3	1	754	20365485	20364736	0.000000e+00	1068
7	TraesCS3A01G213700	chr6B	89.426	766	64	7	1	756	117637962	117637204	0.000000e+00	950
8	TraesCS3A01G213700	chr6B	81.429	140	26	0	1100	1239	140366970	140366831	8.030000e-22	115
9	TraesCS3A01G213700	chr6B	82.258	124	22	0	1114	1237	139884075	139884198	1.340000e-19	108
10	TraesCS3A01G213700	chr1B	90.514	759	65	7	1	759	11988681	11989432	0.000000e+00	996
11	TraesCS3A01G213700	chr7A	90.571	753	66	5	1	753	608240420	608239673	0.000000e+00	992
12	TraesCS3A01G213700	chr1D	90.162	742	65	8	1	739	432303451	432304187	0.000000e+00	959
13	TraesCS3A01G213700	chr1D	79.054	592	114	9	13	602	365237592	365237009	7.120000e-107	398
14	TraesCS3A01G213700	chr2D	77.754	472	96	9	25	492	483636923	483636457	7.480000e-72	281
15	TraesCS3A01G213700	chr2A	72.910	598	141	17	13	603	694785551	694784968	1.680000e-43	187
16	TraesCS3A01G213700	chr6D	81.429	140	26	0	1100	1239	65360772	65360633	8.030000e-22	115
17	TraesCS3A01G213700	chr6D	82.258	124	22	0	1114	1237	65051962	65052085	1.340000e-19	108
18	TraesCS3A01G213700	chr6A	81.429	140	26	0	1100	1239	83435354	83435493	8.030000e-22	115

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	TraesCS3A01G213700	chr3A	386216138	386219675	3537	False	6534	6534	100.0000	1	3538	1	chr3A.!!$F1	3537
1	TraesCS3A01G213700	chr3D	293189945	293192687	2742	False	4604	4604	96.8900	770	3528	1	chr3D.!!$F1	2758
2	TraesCS3A01G213700	chr3B	386521269	386524272	3003	False	2263	4416	93.2015	770	3538	2	chr3B.!!$F1	2768
3	TraesCS3A01G213700	chr5D	343309115	343309865	750	True	1142	1142	94.0480	1	755	1	chr5D.!!$R1	754
4	TraesCS3A01G213700	chr6B	20364736	20365485	749	True	1068	1068	92.3080	1	754	1	chr6B.!!$R1	753
5	TraesCS3A01G213700	chr6B	117637204	117637962	758	True	950	950	89.4260	1	756	1	chr6B.!!$R2	755
6	TraesCS3A01G213700	chr1B	11988681	11989432	751	False	996	996	90.5140	1	759	1	chr1B.!!$F1	758
7	TraesCS3A01G213700	chr7A	608239673	608240420	747	True	992	992	90.5710	1	753	1	chr7A.!!$R1	752
8	TraesCS3A01G213700	chr1D	432303451	432304187	736	False	959	959	90.1620	1	739	1	chr1D.!!$F1	738
9	TraesCS3A01G213700	chr1D	365237009	365237592	583	True	398	398	79.0540	13	602	1	chr1D.!!$R1	589

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
225	226	0.035056	CCGCATCTCCCCTGAAGTTT	60.035	55.0	0.0	0.0	0.0	2.66	F
814	830	0.183731	GGAATGGGAGTTGGGCTAGG	59.816	60.0	0.0	0.0	0.0	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1083	1353	0.461548	GGTCATCGTCATCAGAGGCA	59.538	55.0	0.0	0.0	0.0	4.75	R
2707	2978	0.106918	TTCTTGACCACCACCACCAC	60.107	55.0	0.0	0.0	0.0	4.16	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
34	35	1.135083	AGACACGATAGAAGTTGCCCG	60.135	52.381	0.00	0.00	41.38	6.13
164	165	7.429340	CCATATGTCGATTGTTTCAAGCTTAAC	59.571	37.037	0.00	1.34	0.00	2.01
216	217	0.107703	TGATCAACACCGCATCTCCC	60.108	55.000	0.00	0.00	0.00	4.30
225	226	0.035056	CCGCATCTCCCCTGAAGTTT	60.035	55.000	0.00	0.00	0.00	2.66
394	403	9.726438	CTATAGGATTTGGGAGTATTAACCTTG	57.274	37.037	0.00	0.00	0.00	3.61
453	462	2.744202	GCACTTCATCGAAGACCACATT	59.256	45.455	10.58	0.00	41.71	2.71
471	480	0.537188	TTGTCCAGATCTTCCTCCGC	59.463	55.000	0.00	0.00	0.00	5.54
481	491	1.915078	CTTCCTCCGCCAGTCCCAAT	61.915	60.000	0.00	0.00	0.00	3.16
540	550	0.457851	CTCGAAGATCCGCCAGAAGT	59.542	55.000	0.00	0.00	33.89	3.01
580	590	1.153489	CAGACAGTGCAGATCGGGG	60.153	63.158	0.00	0.00	0.00	5.73
582	592	0.324368	AGACAGTGCAGATCGGGGTA	60.324	55.000	0.00	0.00	0.00	3.69
584	594	1.139058	GACAGTGCAGATCGGGGTATT	59.861	52.381	0.00	0.00	0.00	1.89
585	595	1.139058	ACAGTGCAGATCGGGGTATTC	59.861	52.381	0.00	0.00	0.00	1.75
586	596	1.414181	CAGTGCAGATCGGGGTATTCT	59.586	52.381	0.00	0.00	0.00	2.40
587	597	1.689273	AGTGCAGATCGGGGTATTCTC	59.311	52.381	0.00	0.00	0.00	2.87
592	603	0.977395	GATCGGGGTATTCTCCTGGG	59.023	60.000	0.00	0.00	0.00	4.45
745	760	4.558715	GGGAGGAGAGAAACCCTAACTAT	58.441	47.826	0.00	0.00	39.28	2.12
748	763	6.411789	GGGAGGAGAGAAACCCTAACTATAGA	60.412	46.154	6.78	0.00	39.28	1.98
750	765	6.616577	AGGAGAGAAACCCTAACTATAGAGG	58.383	44.000	6.78	3.54	0.00	3.69
761	776	7.457024	CCTAACTATAGAGGGAAAGACTAGC	57.543	44.000	6.78	0.00	0.00	3.42
762	777	7.005296	CCTAACTATAGAGGGAAAGACTAGCA	58.995	42.308	6.78	0.00	0.00	3.49
763	778	6.969993	AACTATAGAGGGAAAGACTAGCAG	57.030	41.667	6.78	0.00	0.00	4.24
764	779	4.830600	ACTATAGAGGGAAAGACTAGCAGC	59.169	45.833	6.78	0.00	0.00	5.25
765	780	1.199615	AGAGGGAAAGACTAGCAGCC	58.800	55.000	0.00	0.00	0.00	4.85
766	781	1.199615	GAGGGAAAGACTAGCAGCCT	58.800	55.000	0.00	0.00	0.00	4.58
767	782	0.908198	AGGGAAAGACTAGCAGCCTG	59.092	55.000	0.00	0.00	0.00	4.85
768	783	0.615850	GGGAAAGACTAGCAGCCTGT	59.384	55.000	0.00	0.00	0.00	4.00
814	830	0.183731	GGAATGGGAGTTGGGCTAGG	59.816	60.000	0.00	0.00	0.00	3.02
838	854	3.195825	CAGGAAGTTGGAGTAGAACCGAT	59.804	47.826	0.00	0.00	0.00	4.18
840	856	3.933332	GGAAGTTGGAGTAGAACCGATTG	59.067	47.826	0.00	0.00	0.00	2.67
841	857	4.562963	GGAAGTTGGAGTAGAACCGATTGT	60.563	45.833	0.00	0.00	0.00	2.71
842	858	4.618920	AGTTGGAGTAGAACCGATTGTT	57.381	40.909	0.00	0.00	40.81	2.83
860	1115	5.751243	TTGTTCCTTTTTCACTGCTAGAC	57.249	39.130	0.00	0.00	0.00	2.59
883	1138	4.141390	CCTGAACTGGGCTAACCTTCATAT	60.141	45.833	0.00	0.00	41.11	1.78
892	1147	3.688414	GCTAACCTTCATATGGCCCAACT	60.688	47.826	0.00	0.00	0.00	3.16
893	1148	2.736670	ACCTTCATATGGCCCAACTC	57.263	50.000	0.00	0.00	0.00	3.01
901	1158	4.721776	TCATATGGCCCAACTCTTTACTCT	59.278	41.667	0.00	0.00	0.00	3.24
925	1182	1.198713	GGGCTTCACCTGATCTCTCA	58.801	55.000	0.00	0.00	39.10	3.27
1014	1284	1.518774	GGCGATGGACGAAACCCTA	59.481	57.895	0.00	0.00	45.77	3.53
1083	1353	2.361357	CCGTCCTCCTCGTCCACT	60.361	66.667	0.00	0.00	0.00	4.00
1089	1359	1.680651	CTCCTCGTCCACTGCCTCT	60.681	63.158	0.00	0.00	0.00	3.69
1257	1527	1.592400	CTGGACTCGTTCCTACCGCA	61.592	60.000	7.25	0.00	46.10	5.69
1670	1940	2.766263	GGTACATCCACATCTGGTCAGA	59.234	50.000	2.93	2.93	38.90	3.27
1830	2100	6.156519	GCTGAAAATTTTCGGGTACTTTGAT	58.843	36.000	31.32	0.00	42.46	2.57
1839	2109	3.000727	CGGGTACTTTGATGTTGGACTC	58.999	50.000	0.00	0.00	0.00	3.36
1887	2157	3.903090	TGATCAAGGTGGCCTGAATTTTT	59.097	39.130	3.32	0.00	32.13	1.94
1926	2196	8.746052	TTATTTCCCACAATTAGATGGTACTG	57.254	34.615	0.00	0.00	33.80	2.74
1927	2197	5.772393	TTCCCACAATTAGATGGTACTGT	57.228	39.130	0.00	0.00	33.80	3.55
1928	2198	5.097742	TCCCACAATTAGATGGTACTGTG	57.902	43.478	0.00	0.00	33.80	3.66
1929	2199	4.534500	TCCCACAATTAGATGGTACTGTGT	59.466	41.667	6.80	0.00	33.86	3.72
1947	2217	6.378582	ACTGTGTTACATAATTGCTTTTCGG	58.621	36.000	0.00	0.00	0.00	4.30
1981	2251	3.469859	TGGGATAGGGATGAAGGTGAAA	58.530	45.455	0.00	0.00	0.00	2.69
2005	2275	2.267961	GCGATGGTTCGGACCCTT	59.732	61.111	11.33	0.00	45.92	3.95
2038	2308	1.967319	TGAAGGTGCAGTTTGGAGAC	58.033	50.000	0.00	0.00	0.00	3.36
2120	2390	7.547697	TTGTATATCAAGGTATCGATTCCCA	57.452	36.000	16.66	3.30	0.00	4.37
2354	2625	4.314522	TGTCATGGAAAGAGCCCAAATA	57.685	40.909	0.00	0.00	37.22	1.40
2411	2682	4.142071	TGCTCTAGAGATGTTGTGCTAAGG	60.142	45.833	24.24	0.00	0.00	2.69
2428	2699	5.109903	GCTAAGGCGTTTATCTTCAGAAGA	58.890	41.667	15.44	15.44	42.69	2.87
2707	2978	3.032017	TGTTGTTGTTGTTGTTGGTGG	57.968	42.857	0.00	0.00	0.00	4.61
2709	2980	2.732412	TGTTGTTGTTGTTGGTGGTG	57.268	45.000	0.00	0.00	0.00	4.17
2712	2983	0.891373	TGTTGTTGTTGGTGGTGGTG	59.109	50.000	0.00	0.00	0.00	4.17
2715	2986	0.967887	TGTTGTTGGTGGTGGTGGTG	60.968	55.000	0.00	0.00	0.00	4.17
2716	2987	1.380515	TTGTTGGTGGTGGTGGTGG	60.381	57.895	0.00	0.00	0.00	4.61
2717	2988	2.156496	TTGTTGGTGGTGGTGGTGGT	62.156	55.000	0.00	0.00	0.00	4.16
2718	2989	2.124693	GTTGGTGGTGGTGGTGGTG	61.125	63.158	0.00	0.00	0.00	4.17
2719	2990	3.366406	TTGGTGGTGGTGGTGGTGG	62.366	63.158	0.00	0.00	0.00	4.61
2974	3245	5.996513	AGATTACCATCATTGACTCATGAGC	59.003	40.000	22.83	15.26	0.00	4.26
3003	3274	5.371526	TGATAATTGAATCAGAGGTGCTCC	58.628	41.667	0.00	0.00	32.18	4.70
3017	3288	6.017605	CAGAGGTGCTCCATTTTGATATGTAC	60.018	42.308	7.70	0.00	35.89	2.90
3043	3314	5.651139	AGTCATTAATGCAATCAAGTGAGCT	59.349	36.000	10.76	0.00	0.00	4.09
3254	3527	3.644265	TGGTGTGTGTACTATTCTGGTGT	59.356	43.478	0.00	0.00	0.00	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.799420	GCAACTTCTATCGTGTCTGGATC	59.201	47.826	0.00	0.00	0.00	3.36
11	12	2.094182	GGCAACTTCTATCGTGTCTGGA	60.094	50.000	0.00	0.00	0.00	3.86
34	35	3.665745	ACCACCATCAAATGACTTTGC	57.334	42.857	0.00	0.00	41.29	3.68
164	165	1.156736	GATCACACAACCCTCAACCG	58.843	55.000	0.00	0.00	0.00	4.44
193	194	1.019673	GATGCGGTGTTGATCATGCT	58.980	50.000	0.00	0.00	33.48	3.79
203	204	1.903877	CTTCAGGGGAGATGCGGTGT	61.904	60.000	0.00	0.00	0.00	4.16
225	226	3.308832	GGGTAATGAACAATGGTCCCTGA	60.309	47.826	0.00	0.00	0.00	3.86
236	237	3.849574	TGATTGGGAGAGGGTAATGAACA	59.150	43.478	0.00	0.00	0.00	3.18
394	403	1.959282	CCTAGATGGATTGCTTTGGCC	59.041	52.381	0.00	0.00	38.35	5.36
453	462	1.330655	GGCGGAGGAAGATCTGGACA	61.331	60.000	0.00	0.00	0.00	4.02
471	480	3.129988	GCTGATGAAAGAATTGGGACTGG	59.870	47.826	0.00	0.00	0.00	4.00
481	491	6.088173	CGATGTTGAATTGCTGATGAAAGAA	58.912	36.000	0.00	0.00	0.00	2.52
540	550	4.832823	TGCTTCGGGTGAGAGATATAATGA	59.167	41.667	0.00	0.00	0.00	2.57
592	603	1.600638	CCGACTGGTTAGGGTTCCC	59.399	63.158	0.00	0.00	0.00	3.97
611	622	2.365105	CCCTAGCAGGAACGGGGA	60.365	66.667	4.00	0.00	37.67	4.81
745	760	2.023888	AGGCTGCTAGTCTTTCCCTCTA	60.024	50.000	0.00	0.00	0.00	2.43
748	763	0.908198	CAGGCTGCTAGTCTTTCCCT	59.092	55.000	0.00	0.00	0.00	4.20
750	765	2.079925	CAACAGGCTGCTAGTCTTTCC	58.920	52.381	15.89	0.00	0.00	3.13
751	766	1.466558	GCAACAGGCTGCTAGTCTTTC	59.533	52.381	15.89	0.00	39.34	2.62
755	770	2.103042	CGGCAACAGGCTGCTAGTC	61.103	63.158	15.89	5.14	43.10	2.59
756	771	2.046892	CGGCAACAGGCTGCTAGT	60.047	61.111	15.89	0.00	43.10	2.57
762	777	3.866379	TTGGCATCGGCAACAGGCT	62.866	57.895	0.00	0.00	42.98	4.58
763	778	3.372730	TTGGCATCGGCAACAGGC	61.373	61.111	0.00	0.00	42.98	4.85
814	830	2.615747	GGTTCTACTCCAACTTCCTGGC	60.616	54.545	0.00	0.00	36.32	4.85
838	854	4.578928	GGTCTAGCAGTGAAAAAGGAACAA	59.421	41.667	0.00	0.00	0.00	2.83
840	856	4.214332	CAGGTCTAGCAGTGAAAAAGGAAC	59.786	45.833	0.00	0.00	0.00	3.62
841	857	4.102524	TCAGGTCTAGCAGTGAAAAAGGAA	59.897	41.667	0.00	0.00	0.00	3.36
842	858	3.646162	TCAGGTCTAGCAGTGAAAAAGGA	59.354	43.478	0.00	0.00	0.00	3.36
843	859	4.008074	TCAGGTCTAGCAGTGAAAAAGG	57.992	45.455	0.00	0.00	0.00	3.11
860	1115	1.351017	TGAAGGTTAGCCCAGTTCAGG	59.649	52.381	0.00	0.00	34.66	3.86
883	1138	2.441750	ACAAGAGTAAAGAGTTGGGCCA	59.558	45.455	0.00	0.00	0.00	5.36
892	1147	2.631062	TGAAGCCCGACAAGAGTAAAGA	59.369	45.455	0.00	0.00	0.00	2.52
893	1148	2.737252	GTGAAGCCCGACAAGAGTAAAG	59.263	50.000	0.00	0.00	0.00	1.85
901	1158	0.036388	GATCAGGTGAAGCCCGACAA	60.036	55.000	0.00	0.00	38.26	3.18
955	1225	2.436824	GAGGAAGCGGAACAGGGC	60.437	66.667	0.00	0.00	0.00	5.19
1014	1284	1.380112	GTAGGAGAGGACGGTGGCT	60.380	63.158	0.00	0.00	0.00	4.75
1083	1353	0.461548	GGTCATCGTCATCAGAGGCA	59.538	55.000	0.00	0.00	0.00	4.75
1089	1359	3.272766	GATGCGGTCATCGTCATCA	57.727	52.632	9.11	0.00	44.18	3.07
1830	2100	1.351076	TGAGCTGATGGAGTCCAACA	58.649	50.000	19.94	19.94	36.95	3.33
1839	2109	0.883814	GGCCGATCTTGAGCTGATGG	60.884	60.000	0.00	0.00	0.00	3.51
1887	2157	7.174413	TGTGGGAAATAAGATGATGTGAAAGA	58.826	34.615	0.00	0.00	0.00	2.52
1907	2177	4.843728	ACACAGTACCATCTAATTGTGGG	58.156	43.478	11.02	0.00	40.01	4.61
1926	2196	6.858993	TGAACCGAAAAGCAATTATGTAACAC	59.141	34.615	0.00	0.00	0.00	3.32
1927	2197	6.971602	TGAACCGAAAAGCAATTATGTAACA	58.028	32.000	0.00	0.00	0.00	2.41
1928	2198	8.460831	AATGAACCGAAAAGCAATTATGTAAC	57.539	30.769	0.00	0.00	0.00	2.50
1947	2217	7.348274	TCATCCCTATCCCATCCTATAATGAAC	59.652	40.741	0.00	0.00	0.00	3.18
1981	2251	3.794270	CGAACCATCGCATTCGGT	58.206	55.556	0.00	0.00	43.08	4.69
2005	2275	3.355378	CACCTTCAATGCCAATGTCCTA	58.645	45.455	0.00	0.00	0.00	2.94
2038	2308	0.795085	CCAGCTTGACTTGCTTCTCG	59.205	55.000	0.00	0.00	38.92	4.04
2120	2390	7.176165	ACAAACAATGATGATGATGAAGTGACT	59.824	33.333	0.00	0.00	0.00	3.41
2228	2499	2.026262	GTGGCCTACTTGATCCCAGAAA	60.026	50.000	3.32	0.00	0.00	2.52
2354	2625	2.496899	AAACACGCATCTCCTCCAAT	57.503	45.000	0.00	0.00	0.00	3.16
2411	2682	6.017933	CACACATTCTTCTGAAGATAAACGC	58.982	40.000	19.93	0.00	37.38	4.84
2428	2699	2.195741	AGCATCTGCAGACACACATT	57.804	45.000	20.97	0.00	45.16	2.71
2553	2824	8.508883	TGTTTACAAACAAAGAGTAAGCCTTA	57.491	30.769	5.08	0.00	45.17	2.69
2707	2978	0.106918	TTCTTGACCACCACCACCAC	60.107	55.000	0.00	0.00	0.00	4.16
2709	2980	1.133915	TCTTTCTTGACCACCACCACC	60.134	52.381	0.00	0.00	0.00	4.61
2712	2983	2.640316	ACTCTTTCTTGACCACCACC	57.360	50.000	0.00	0.00	0.00	4.61
2715	2986	5.998363	AGTTTCATACTCTTTCTTGACCACC	59.002	40.000	0.00	0.00	28.23	4.61
2716	2987	7.497925	AAGTTTCATACTCTTTCTTGACCAC	57.502	36.000	0.00	0.00	35.54	4.16
2717	2988	9.052759	GTAAAGTTTCATACTCTTTCTTGACCA	57.947	33.333	0.00	0.00	35.54	4.02
2718	2989	8.504815	GGTAAAGTTTCATACTCTTTCTTGACC	58.495	37.037	0.00	0.00	35.54	4.02
2719	2990	9.052759	TGGTAAAGTTTCATACTCTTTCTTGAC	57.947	33.333	0.00	0.00	35.54	3.18
2974	3245	7.423199	CACCTCTGATTCAATTATCAATGGTG	58.577	38.462	18.13	18.13	43.42	4.17
3017	3288	6.252869	GCTCACTTGATTGCATTAATGACTTG	59.747	38.462	19.73	4.54	0.00	3.16
3026	3297	5.474532	TCAACTAAGCTCACTTGATTGCATT	59.525	36.000	0.00	0.00	36.57	3.56
3254	3527	1.522668	CGAGTTGATCTGCCACCAAA	58.477	50.000	0.00	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.