AutoCloner

Multiple sequence alignment - TraesCS3D01G227200

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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	TraesCS3D01G227200	chr3D	100.000	3140	0	0	1	3140	308986850	308983711	0.000000e+00	5799.0
1	TraesCS3D01G227200	chr3D	82.791	1261	108	49	997	2220	501413264	501414452	0.000000e+00	1026.0
2	TraesCS3D01G227200	chr3D	86.873	777	99	3	2366	3140	589424305	589423530	0.000000e+00	867.0
3	TraesCS3D01G227200	chr3D	82.589	873	87	32	1349	2201	501331853	501332680	0.000000e+00	710.0
4	TraesCS3D01G227200	chr3D	89.753	283	16	3	975	1256	501331572	501331842	1.790000e-92	350.0
5	TraesCS3D01G227200	chr3A	95.304	1746	47	12	556	2266	428570744	428568999	0.000000e+00	2737.0
6	TraesCS3D01G227200	chr3A	83.255	1272	110	52	982	2224	640951828	640953025	0.000000e+00	1074.0
7	TraesCS3D01G227200	chr3A	83.176	1272	111	52	982	2224	641012122	641013319	0.000000e+00	1068.0
8	TraesCS3D01G227200	chr3A	82.236	805	86	24	1416	2201	640879934	640880700	2.640000e-180	641.0
9	TraesCS3D01G227200	chr3A	91.529	425	24	7	82	502	428571171	428570755	2.720000e-160	575.0
10	TraesCS3D01G227200	chr3A	91.698	265	9	6	997	1261	640879608	640879859	3.850000e-94	355.0
11	TraesCS3D01G227200	chr3A	87.129	101	8	3	847	947	640879433	640879528	3.310000e-20	110.0
12	TraesCS3D01G227200	chr3A	97.959	49	1	0	2279	2327	428568936	428568888	5.580000e-13	86.1
13	TraesCS3D01G227200	chr3A	100.000	31	0	0	517	547	428570769	428570739	1.220000e-04	58.4
14	TraesCS3D01G227200	chr3B	93.310	1689	52	18	628	2266	412595506	412597183	0.000000e+00	2436.0
15	TraesCS3D01G227200	chr3B	82.997	1188	115	48	1070	2220	663062316	663061179	0.000000e+00	994.0
16	TraesCS3D01G227200	chr3B	94.127	647	15	5	1	629	412594543	412595184	0.000000e+00	963.0
17	TraesCS3D01G227200	chr3B	81.050	876	87	31	1349	2201	663071974	663071155	2.660000e-175	625.0
18	TraesCS3D01G227200	chr3B	83.521	443	31	19	847	1266	663072400	663071977	2.960000e-100	375.0
19	TraesCS3D01G227200	chr7B	89.356	761	80	1	2381	3140	336645156	336644396	0.000000e+00	955.0
20	TraesCS3D01G227200	chr7B	86.918	795	95	9	2349	3139	44266771	44265982	0.000000e+00	883.0
21	TraesCS3D01G227200	chr7B	82.812	192	31	2	1065	1255	500169668	500169858	1.500000e-38	171.0
22	TraesCS3D01G227200	chr6D	89.096	752	80	2	2390	3140	413266182	413266932	0.000000e+00	933.0
23	TraesCS3D01G227200	chr4D	89.008	746	80	2	2385	3128	387753117	387752372	0.000000e+00	922.0
24	TraesCS3D01G227200	chr5D	88.579	753	75	4	2371	3122	549798015	549798757	0.000000e+00	904.0
25	TraesCS3D01G227200	chr5D	87.664	762	91	3	2380	3140	116627171	116627930	0.000000e+00	883.0
26	TraesCS3D01G227200	chr5D	76.684	193	42	3	1068	1259	461440808	461440618	1.540000e-18	104.0
27	TraesCS3D01G227200	chr2B	88.503	748	83	3	2395	3140	77246912	77247658	0.000000e+00	902.0
28	TraesCS3D01G227200	chr1D	87.130	777	86	9	2366	3140	452206640	452205876	0.000000e+00	869.0
29	TraesCS3D01G227200	chr1D	90.141	71	7	0	1186	1256	457851932	457851862	3.330000e-15	93.5
30	TraesCS3D01G227200	chr7A	82.812	192	31	2	1065	1255	520060578	520060388	1.500000e-38	171.0
31	TraesCS3D01G227200	chr7D	82.292	192	32	2	1065	1255	475873812	475874002	6.970000e-37	165.0
32	TraesCS3D01G227200	chr5A	88.506	87	7	3	1174	1259	581488002	581487918	5.540000e-18	102.0
33	TraesCS3D01G227200	chr5A	75.648	193	41	6	1068	1257	619689761	619689950	1.200000e-14	91.6
34	TraesCS3D01G227200	chr4A	92.424	66	5	0	1190	1255	19622373	19622308	9.270000e-16	95.3
35	TraesCS3D01G227200	chr1A	90.000	70	7	0	1186	1255	550314081	550314012	1.200000e-14	91.6

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	TraesCS3D01G227200	chr3D	308983711	308986850	3139	True	5799.000000	5799	100.0000	1	3140	1	chr3D.!!$R1	3139
1	TraesCS3D01G227200	chr3D	501413264	501414452	1188	False	1026.000000	1026	82.7910	997	2220	1	chr3D.!!$F1	1223
2	TraesCS3D01G227200	chr3D	589423530	589424305	775	True	867.000000	867	86.8730	2366	3140	1	chr3D.!!$R2	774
3	TraesCS3D01G227200	chr3D	501331572	501332680	1108	False	530.000000	710	86.1710	975	2201	2	chr3D.!!$F2	1226
4	TraesCS3D01G227200	chr3A	640951828	640953025	1197	False	1074.000000	1074	83.2550	982	2224	1	chr3A.!!$F1	1242
5	TraesCS3D01G227200	chr3A	641012122	641013319	1197	False	1068.000000	1068	83.1760	982	2224	1	chr3A.!!$F2	1242
6	TraesCS3D01G227200	chr3A	428568888	428571171	2283	True	864.125000	2737	96.1980	82	2327	4	chr3A.!!$R1	2245
7	TraesCS3D01G227200	chr3A	640879433	640880700	1267	False	368.666667	641	87.0210	847	2201	3	chr3A.!!$F3	1354
8	TraesCS3D01G227200	chr3B	412594543	412597183	2640	False	1699.500000	2436	93.7185	1	2266	2	chr3B.!!$F1	2265
9	TraesCS3D01G227200	chr3B	663061179	663062316	1137	True	994.000000	994	82.9970	1070	2220	1	chr3B.!!$R1	1150
10	TraesCS3D01G227200	chr3B	663071155	663072400	1245	True	500.000000	625	82.2855	847	2201	2	chr3B.!!$R2	1354
11	TraesCS3D01G227200	chr7B	336644396	336645156	760	True	955.000000	955	89.3560	2381	3140	1	chr7B.!!$R2	759
12	TraesCS3D01G227200	chr7B	44265982	44266771	789	True	883.000000	883	86.9180	2349	3139	1	chr7B.!!$R1	790
13	TraesCS3D01G227200	chr6D	413266182	413266932	750	False	933.000000	933	89.0960	2390	3140	1	chr6D.!!$F1	750
14	TraesCS3D01G227200	chr4D	387752372	387753117	745	True	922.000000	922	89.0080	2385	3128	1	chr4D.!!$R1	743
15	TraesCS3D01G227200	chr5D	549798015	549798757	742	False	904.000000	904	88.5790	2371	3122	1	chr5D.!!$F2	751
16	TraesCS3D01G227200	chr5D	116627171	116627930	759	False	883.000000	883	87.6640	2380	3140	1	chr5D.!!$F1	760
17	TraesCS3D01G227200	chr2B	77246912	77247658	746	False	902.000000	902	88.5030	2395	3140	1	chr2B.!!$F1	745
18	TraesCS3D01G227200	chr1D	452205876	452206640	764	True	869.000000	869	87.1300	2366	3140	1	chr1D.!!$R1	774

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
372	378	0.042013	GTACAGTCGATCGAGGCGAG	60.042	60.000	20.09	9.16	39.91	5.03	F
962	1333	1.301716	GGAGCGAACTCAAGTGCCA	60.302	57.895	0.00	0.00	45.42	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1599	2051	0.176680	CCTCCACTTCGTCTCCCATG	59.823	60.0	0.00	0.0	0.0	3.66	R
2413	2978	0.108992	GATACGCGGGTGTGAAGACA	60.109	55.0	16.34	0.0	0.0	3.41	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
48	49	3.583086	GCTTTCGCCCGCCCATAC	61.583	66.667	0.00	0.00	0.00	2.39
189	195	2.025418	GCACCGGTGACACGTAAGG	61.025	63.158	38.30	7.91	46.39	2.69
201	207	0.107654	ACGTAAGGGAGCATCTTGCC	60.108	55.000	0.00	0.00	44.29	4.52
328	334	9.974750	CTTTACATTTTTCTAGTACAAGCTAGC	57.025	33.333	6.62	6.62	38.58	3.42
372	378	0.042013	GTACAGTCGATCGAGGCGAG	60.042	60.000	20.09	9.16	39.91	5.03
455	461	3.214250	CTACTCCGCGGCCAGATCC	62.214	68.421	23.51	0.00	0.00	3.36
644	986	6.455647	TCACATATATCACCGGAAATCTCAC	58.544	40.000	9.46	0.00	0.00	3.51
731	1081	3.745803	GTCCCGTTCTCCGAGCGT	61.746	66.667	0.00	0.00	39.56	5.07
761	1111	9.228949	AGACGCCTATATATATAGATTAACCCG	57.771	37.037	25.30	17.48	38.30	5.28
830	1180	3.124921	ACGCACGCTGCCCATAAC	61.125	61.111	0.00	0.00	41.12	1.89
935	1305	2.050351	ACGTCCGCGAGTGAGTTG	60.050	61.111	8.23	0.00	42.00	3.16
955	1325	1.682394	GGAGTAGAGGGAGCGAACTCA	60.682	57.143	7.21	0.00	45.42	3.41
962	1333	1.301716	GGAGCGAACTCAAGTGCCA	60.302	57.895	0.00	0.00	45.42	4.92
1297	1707	3.423154	CCAGTGCCGCCGTCTTTC	61.423	66.667	0.00	0.00	0.00	2.62
1560	2012	2.659610	GCCTCCTGCTCGTCTGTT	59.340	61.111	0.00	0.00	36.87	3.16
1569	2021	3.553437	CTCGTCTGTTGTCGGCGGT	62.553	63.158	7.21	0.00	0.00	5.68
1572	2024	3.542676	TCTGTTGTCGGCGGTGGT	61.543	61.111	7.21	0.00	0.00	4.16
1599	2051	3.964875	CAGCACGTGGTGGCCAAC	61.965	66.667	34.27	15.99	39.67	3.77
1812	2264	0.042731	CCACCTCCCTCCACCTTCTA	59.957	60.000	0.00	0.00	0.00	2.10
1823	2275	2.972713	TCCACCTTCTAGAACAAGCAGT	59.027	45.455	0.00	0.00	0.00	4.40
1996	2466	4.457496	AGCCGATGCCACTGACGG	62.457	66.667	0.00	0.00	46.74	4.79
2000	2482	3.490759	GATGCCACTGACGGTGCG	61.491	66.667	9.05	3.94	44.08	5.34
2276	2806	3.445450	ACTCATTCAGTACGTGCTCTGAT	59.555	43.478	2.06	0.00	39.85	2.90
2292	2857	1.781429	CTGATTATTCGGTCAGTCGCG	59.219	52.381	0.00	0.00	37.62	5.87
2333	2898	3.509517	GCCCATGCTCTTGGATCTT	57.490	52.632	3.63	0.00	39.25	2.40
2334	2899	2.645838	GCCCATGCTCTTGGATCTTA	57.354	50.000	3.63	0.00	39.25	2.10
2335	2900	2.502295	GCCCATGCTCTTGGATCTTAG	58.498	52.381	3.63	0.00	39.25	2.18
2336	2901	2.105477	GCCCATGCTCTTGGATCTTAGA	59.895	50.000	3.63	0.00	39.25	2.10
2337	2902	3.806507	GCCCATGCTCTTGGATCTTAGAG	60.807	52.174	15.85	15.85	39.25	2.43
2413	2978	1.073444	TCGGGCACTCTCTATATCCGT	59.927	52.381	0.00	0.00	37.54	4.69
2444	3009	4.750098	CACCCGCGTATCTCATATTTTCTT	59.250	41.667	4.92	0.00	0.00	2.52
2551	3116	3.109044	AGATCACATCCGAAGCATCAG	57.891	47.619	0.00	0.00	0.00	2.90
2651	3217	1.118965	TCTTCACCACTTCCTCGCCA	61.119	55.000	0.00	0.00	0.00	5.69
2978	3547	3.827898	GTCCTCCTCGTCGGGCAG	61.828	72.222	0.00	0.00	0.00	4.85
3012	3581	1.384989	CGGACTGCGTAGACCCATCT	61.385	60.000	15.44	0.00	35.65	2.90
3128	3697	3.003173	TAGAACCCAGCGCTGCCT	61.003	61.111	31.96	23.92	0.00	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	0.517316	GGACGCCTGTAGCAACAAAG	59.483	55.000	0.00	0.00	44.04	2.77
189	195	1.452833	GGACCTGGCAAGATGCTCC	60.453	63.158	2.00	0.00	44.28	4.70
328	334	5.117355	TGACTGAGAAGGTAGTACAAACG	57.883	43.478	2.06	0.00	0.00	3.60
372	378	1.328680	CTGTGCTGGTAATGTGATCGC	59.671	52.381	0.00	0.00	0.00	4.58
455	461	1.549620	TCTCTCAAGCTTGCTCCTCTG	59.450	52.381	21.99	7.22	0.00	3.35
761	1111	3.334583	TGTGATGAGCTTACCTGTTCC	57.665	47.619	0.00	0.00	0.00	3.62
935	1305	1.026584	GAGTTCGCTCCCTCTACTCC	58.973	60.000	0.00	0.00	38.28	3.85
962	1333	1.608717	CCTCCTGCGTACTTGCCTCT	61.609	60.000	0.00	0.00	0.00	3.69
1297	1707	3.128938	CCTTACTAGGACACCAGAAGACG	59.871	52.174	0.00	0.00	45.05	4.18
1569	2021	1.673337	GTGCTGATGCTGCTCACCA	60.673	57.895	0.00	0.00	40.48	4.17
1572	2024	2.030958	CACGTGCTGATGCTGCTCA	61.031	57.895	0.82	1.50	40.48	4.26
1581	2033	4.182433	TTGGCCACCACGTGCTGA	62.182	61.111	3.88	0.00	30.78	4.26
1599	2051	0.176680	CCTCCACTTCGTCTCCCATG	59.823	60.000	0.00	0.00	0.00	3.66
1812	2264	3.648009	CTTCTTCTCGACTGCTTGTTCT	58.352	45.455	0.00	0.00	0.00	3.01
1823	2275	2.125912	GCTGGCGCTTCTTCTCGA	60.126	61.111	7.64	0.00	0.00	4.04
2276	2806	1.517694	GCCGCGACTGACCGAATAA	60.518	57.895	8.23	0.00	0.00	1.40
2292	2857	2.279650	TAATCTAACGGCCGCGCC	60.280	61.111	28.58	4.82	46.75	6.53
2327	2892	5.400066	GGAACCTAGATGCTCTAAGATCC	57.600	47.826	0.00	0.00	0.00	3.36
2349	2914	0.442310	CGCGCCCACGAATATATTGG	59.558	55.000	1.78	4.17	43.93	3.16
2350	2915	0.179225	GCGCGCCCACGAATATATTG	60.179	55.000	23.24	0.00	43.93	1.90
2351	2916	1.296056	GGCGCGCCCACGAATATATT	61.296	55.000	39.89	0.00	43.93	1.28
2381	2946	4.451150	GCCCGATCAGTGTCCGCA	62.451	66.667	0.00	0.00	0.00	5.69
2413	2978	0.108992	GATACGCGGGTGTGAAGACA	60.109	55.000	16.34	0.00	0.00	3.41
2490	3055	4.779987	CATTTGTATGTCCGCTCATGATG	58.220	43.478	0.00	0.00	0.00	3.07
2551	3116	9.109393	TGTATTATGTGAACTTTGGCTATCTTC	57.891	33.333	0.00	0.00	0.00	2.87
3002	3571	1.760875	GGCGGGTCAGATGGGTCTA	60.761	63.158	0.00	0.00	32.09	2.59
3071	3640	2.121538	CGGATGCGGACTCCAGAGA	61.122	63.158	0.00	0.00	32.72	3.10
3100	3669	2.359967	GGGTTCTAGTGCCCGCTCT	61.360	63.158	8.25	0.00	34.90	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.