AutoCloner

Multiple sequence alignment - TraesCS4A01G310300

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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	TraesCS4A01G310300	chr4A	100.000	2702	0	0	1	2702	603126053	603123352	0.000000e+00	4990.0
1	TraesCS4A01G310300	chr3B	95.673	1918	60	13	799	2702	787399495	787401403	0.000000e+00	3061.0
2	TraesCS4A01G310300	chr3B	81.545	466	78	5	2241	2702	792751397	792751858	7.060000e-101	377.0
3	TraesCS4A01G310300	chr1D	95.266	1204	33	5	1517	2702	441041263	441042460	0.000000e+00	1886.0
4	TraesCS4A01G310300	chr1D	86.047	774	67	19	3	760	24216404	24217152	0.000000e+00	793.0
5	TraesCS4A01G310300	chr1D	82.361	720	71	25	4	701	468342461	468341776	2.330000e-160	575.0
6	TraesCS4A01G310300	chr1D	75.426	1115	248	21	821	1919	337209858	337208754	3.990000e-143	518.0
7	TraesCS4A01G310300	chr1D	87.209	430	46	6	1	427	38593872	38593449	5.230000e-132	481.0
8	TraesCS4A01G310300	chr1D	97.872	94	2	0	1517	1610	441039215	441039308	2.150000e-36	163.0
9	TraesCS4A01G310300	chr1D	96.809	94	3	0	1517	1610	441038732	441038825	1.000000e-34	158.0
10	TraesCS4A01G310300	chr1D	89.394	66	7	0	719	784	468341487	468341422	1.720000e-12	84.2
11	TraesCS4A01G310300	chr7A	82.175	1554	251	18	1164	2702	714060450	714061992	0.000000e+00	1312.0
12	TraesCS4A01G310300	chr7A	79.944	354	66	5	819	1168	714052959	714053311	3.450000e-64	255.0
13	TraesCS4A01G310300	chr6D	86.028	773	68	18	3	760	101719584	101720331	0.000000e+00	793.0
14	TraesCS4A01G310300	chr4B	84.852	779	67	25	1	760	534953612	534954358	0.000000e+00	737.0
15	TraesCS4A01G310300	chr4B	96.750	400	12	1	390	788	27872265	27872664	0.000000e+00	665.0
16	TraesCS4A01G310300	chr4B	94.659	337	15	2	1	337	27871931	27872264	1.110000e-143	520.0
17	TraesCS4A01G310300	chr4B	74.101	973	228	20	996	1955	665456048	665457009	1.960000e-101	379.0
18	TraesCS4A01G310300	chr2D	96.675	421	12	2	2283	2702	597829154	597829573	0.000000e+00	699.0
19	TraesCS4A01G310300	chr2D	96.437	421	13	2	2283	2702	641883078	641883497	0.000000e+00	693.0
20	TraesCS4A01G310300	chr2D	76.671	733	151	13	1040	1762	155159952	155159230	3.260000e-104	388.0
21	TraesCS4A01G310300	chr2A	76.628	1121	226	27	821	1920	551242774	551241669	1.080000e-163	586.0
22	TraesCS4A01G310300	chr2A	81.488	551	94	6	2158	2702	551241420	551240872	1.910000e-121	446.0
23	TraesCS4A01G310300	chr2A	79.570	465	88	6	2242	2702	773298436	773298897	2.590000e-85	326.0
24	TraesCS4A01G310300	chr2A	78.829	222	36	7	271	486	31848437	31848221	3.630000e-29	139.0
25	TraesCS4A01G310300	chr3D	75.238	1155	256	23	819	1955	326711410	326712552	3.080000e-144	521.0
26	TraesCS4A01G310300	chr3D	87.209	430	44	7	1	427	24622209	24621788	1.880000e-131	479.0
27	TraesCS4A01G310300	chr5D	87.907	430	43	6	1	427	548796330	548795907	5.200000e-137	497.0
28	TraesCS4A01G310300	chr5D	87.442	430	45	6	1	427	317674691	317674268	1.120000e-133	486.0
29	TraesCS4A01G310300	chr7B	87.354	427	45	6	1	424	48345476	48345056	5.230000e-132	481.0
30	TraesCS4A01G310300	chr7B	75.171	1023	213	27	812	1818	14162806	14163803	6.860000e-121	444.0
31	TraesCS4A01G310300	chr7B	73.852	1067	253	20	821	1872	635887534	635888589	4.190000e-108	401.0
32	TraesCS4A01G310300	chr7D	79.140	465	90	5	2242	2702	184212640	184212179	5.620000e-82	315.0

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	TraesCS4A01G310300	chr4A	603123352	603126053	2701	True	4990.000000	4990	100.0000	1	2702	1	chr4A.!!$R1	2701
1	TraesCS4A01G310300	chr3B	787399495	787401403	1908	False	3061.000000	3061	95.6730	799	2702	1	chr3B.!!$F1	1903
2	TraesCS4A01G310300	chr1D	24216404	24217152	748	False	793.000000	793	86.0470	3	760	1	chr1D.!!$F1	757
3	TraesCS4A01G310300	chr1D	441038732	441042460	3728	False	735.666667	1886	96.6490	1517	2702	3	chr1D.!!$F2	1185
4	TraesCS4A01G310300	chr1D	337208754	337209858	1104	True	518.000000	518	75.4260	821	1919	1	chr1D.!!$R2	1098
5	TraesCS4A01G310300	chr1D	468341422	468342461	1039	True	329.600000	575	85.8775	4	784	2	chr1D.!!$R3	780
6	TraesCS4A01G310300	chr7A	714060450	714061992	1542	False	1312.000000	1312	82.1750	1164	2702	1	chr7A.!!$F2	1538
7	TraesCS4A01G310300	chr6D	101719584	101720331	747	False	793.000000	793	86.0280	3	760	1	chr6D.!!$F1	757
8	TraesCS4A01G310300	chr4B	534953612	534954358	746	False	737.000000	737	84.8520	1	760	1	chr4B.!!$F1	759
9	TraesCS4A01G310300	chr4B	27871931	27872664	733	False	592.500000	665	95.7045	1	788	2	chr4B.!!$F3	787
10	TraesCS4A01G310300	chr4B	665456048	665457009	961	False	379.000000	379	74.1010	996	1955	1	chr4B.!!$F2	959
11	TraesCS4A01G310300	chr2D	155159230	155159952	722	True	388.000000	388	76.6710	1040	1762	1	chr2D.!!$R1	722
12	TraesCS4A01G310300	chr2A	551240872	551242774	1902	True	516.000000	586	79.0580	821	2702	2	chr2A.!!$R2	1881
13	TraesCS4A01G310300	chr3D	326711410	326712552	1142	False	521.000000	521	75.2380	819	1955	1	chr3D.!!$F1	1136
14	TraesCS4A01G310300	chr7B	14162806	14163803	997	False	444.000000	444	75.1710	812	1818	1	chr7B.!!$F1	1006
15	TraesCS4A01G310300	chr7B	635887534	635888589	1055	False	401.000000	401	73.8520	821	1872	1	chr7B.!!$F2	1051

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
793	1107	1.005924	ACAATGGGCCAAGAAGGTAGG	59.994	52.381	11.89	0.0	40.61	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2385	5304	0.17576	GCTATCAAGGTGCGTCTCCA	59.824	55.0	1.81	0.0	0.0	3.86	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
53	59	6.416415	AGACTTATCTAGTTCAGACGAAGGA	58.584	40.000	0.00	0.00	37.17	3.36
117	136	6.568040	AGGAATAGATGGAAGGGGATTACAAT	59.432	38.462	0.00	0.00	34.61	2.71
186	208	1.968704	TCTCGATCGAGCCATACAGT	58.031	50.000	34.92	0.00	41.71	3.55
258	284	8.968242	CCTAAAAAGTGCAAATCTAAAACAGAC	58.032	33.333	0.00	0.00	35.62	3.51
268	294	4.789095	TCTAAAACAGACGAACAACAGC	57.211	40.909	0.00	0.00	0.00	4.40
269	295	4.439057	TCTAAAACAGACGAACAACAGCT	58.561	39.130	0.00	0.00	0.00	4.24
408	435	2.286418	CGGTGTTCTGCAAACTTGAGTC	60.286	50.000	11.34	0.00	0.00	3.36
624	664	1.609210	TCTGGTGGACATCTCGCCA	60.609	57.895	0.00	0.00	41.87	5.69
686	727	1.276421	GGCAGAGAGGCAAGTCTGTTA	59.724	52.381	11.07	0.00	41.99	2.41
788	1102	3.443681	ACGAATAACAATGGGCCAAGAAG	59.556	43.478	11.89	3.02	0.00	2.85
789	1103	3.181487	CGAATAACAATGGGCCAAGAAGG	60.181	47.826	11.89	0.52	41.84	3.46
790	1104	2.990740	TAACAATGGGCCAAGAAGGT	57.009	45.000	11.89	1.46	40.61	3.50
791	1105	2.990740	AACAATGGGCCAAGAAGGTA	57.009	45.000	11.89	0.00	40.61	3.08
792	1106	2.514458	ACAATGGGCCAAGAAGGTAG	57.486	50.000	11.89	0.00	40.61	3.18
793	1107	1.005924	ACAATGGGCCAAGAAGGTAGG	59.994	52.381	11.89	0.00	40.61	3.18
804	1118	5.684704	CCAAGAAGGTAGGCAAATCAGATA	58.315	41.667	0.00	0.00	0.00	1.98
806	1120	6.206243	CCAAGAAGGTAGGCAAATCAGATATG	59.794	42.308	0.00	0.00	0.00	1.78
807	1121	5.312079	AGAAGGTAGGCAAATCAGATATGC	58.688	41.667	0.00	0.00	39.33	3.14
810	1124	5.068636	AGGTAGGCAAATCAGATATGCTTG	58.931	41.667	0.00	0.00	39.94	4.01
813	1127	2.658285	GCAAATCAGATATGCTTGCCG	58.342	47.619	13.11	0.00	37.10	5.69
890	1204	2.516930	CCGCCGCAATCAATCCCT	60.517	61.111	0.00	0.00	0.00	4.20
982	1312	1.636769	CCCTCTCCAAGGTTAGGGCC	61.637	65.000	13.20	0.00	44.56	5.80
1134	1464	6.217280	AGGAGGAATTCAAAGAGGAGAAGATT	59.783	38.462	7.93	0.00	0.00	2.40
1158	1489	2.046892	AAGTGGCTTGCGATCGCT	60.047	55.556	37.01	15.56	42.51	4.93
1241	1581	2.203422	CCCAGCAAAACCGGTCCA	60.203	61.111	8.04	0.00	0.00	4.02
1407	1747	9.529325	AAATCGATCGTTCTGAATAAGATAACA	57.471	29.630	15.94	0.00	33.93	2.41
1485	1825	2.092429	GGGCATGTGTAGAAAGATGGGA	60.092	50.000	0.00	0.00	0.00	4.37
1699	4570	2.703536	TGGTATCAGGAATGCGGTACAT	59.296	45.455	0.00	0.00	42.30	2.29
1984	4855	5.039920	TGTGCAGAATGGTATGAATAGCT	57.960	39.130	0.00	0.00	35.86	3.32
2037	4908	3.081409	ACGGCGGCTGATACCCTT	61.081	61.111	17.15	0.00	0.00	3.95
2069	4950	4.398358	GCCAGAACCAGTTAATTAGTTCCC	59.602	45.833	5.82	0.00	39.52	3.97
2261	5180	2.989824	ATATCGGCGTCCTCCCGG	60.990	66.667	6.85	0.00	45.60	5.73
2385	5304	1.960689	CCCCGAGGTGATGTTTTTGTT	59.039	47.619	0.00	0.00	0.00	2.83
2409	5328	3.226777	AGACGCACCTTGATAGCTATCT	58.773	45.455	29.20	10.77	33.88	1.98
2435	5354	3.748568	AGAGTGTCTTCGGAAAAGATTGC	59.251	43.478	0.00	0.00	0.00	3.56
2472	5391	6.786967	ACTAGTTTGTCCGAGTAATGGTAT	57.213	37.500	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	59	8.755018	CGATTTTCTTTTGTTTGCTTGTAATCT	58.245	29.630	0.00	0.00	0.00	2.40
136	158	6.929625	TCACTTCTGTTGTTGAATCCAAAAA	58.070	32.000	0.00	0.00	33.49	1.94
186	208	3.443052	TCCTTTGGTACGGGTGATCTAA	58.557	45.455	0.00	0.00	0.00	2.10
230	252	9.528018	CTGTTTTAGATTTGCACTTTTTAGGAA	57.472	29.630	0.00	0.00	0.00	3.36
231	253	8.908903	TCTGTTTTAGATTTGCACTTTTTAGGA	58.091	29.630	0.00	0.00	0.00	2.94
234	256	8.399425	TCGTCTGTTTTAGATTTGCACTTTTTA	58.601	29.630	0.00	0.00	37.83	1.52
250	276	3.270877	AGAGCTGTTGTTCGTCTGTTTT	58.729	40.909	0.00	0.00	0.00	2.43
258	284	3.577649	TTCTCCTAGAGCTGTTGTTCG	57.422	47.619	0.00	0.00	0.00	3.95
268	294	7.604164	TCAATTACTTGTGCTTTTCTCCTAGAG	59.396	37.037	0.00	0.00	33.87	2.43
269	295	7.450074	TCAATTACTTGTGCTTTTCTCCTAGA	58.550	34.615	0.00	0.00	33.87	2.43
350	377	1.102222	GCCCTCGTCTACGGATCTGT	61.102	60.000	12.79	12.79	40.29	3.41
588	617	0.672342	GACGCCGGGTATGTGTATCT	59.328	55.000	2.18	0.00	0.00	1.98
589	618	0.672342	AGACGCCGGGTATGTGTATC	59.328	55.000	2.18	0.00	0.00	2.24
686	727	1.000396	GAAGAAGCCCCAGCCACAT	60.000	57.895	0.00	0.00	41.25	3.21
788	1102	4.320788	GCAAGCATATCTGATTTGCCTACC	60.321	45.833	23.49	10.52	37.98	3.18
789	1103	4.791974	GCAAGCATATCTGATTTGCCTAC	58.208	43.478	23.49	12.80	37.98	3.18
793	1107	2.033801	ACGGCAAGCATATCTGATTTGC	59.966	45.455	20.83	20.83	40.69	3.68
794	1108	3.562973	AGACGGCAAGCATATCTGATTTG	59.437	43.478	0.00	0.00	0.00	2.32
795	1109	3.813443	AGACGGCAAGCATATCTGATTT	58.187	40.909	0.00	0.00	0.00	2.17
796	1110	3.482156	AGACGGCAAGCATATCTGATT	57.518	42.857	0.00	0.00	0.00	2.57
797	1111	3.576118	ACTAGACGGCAAGCATATCTGAT	59.424	43.478	0.00	0.00	0.00	2.90
804	1118	1.139058	CCCTAACTAGACGGCAAGCAT	59.861	52.381	0.00	0.00	0.00	3.79
806	1120	0.535797	ACCCTAACTAGACGGCAAGC	59.464	55.000	0.00	0.00	0.00	4.01
807	1121	3.259902	GAAACCCTAACTAGACGGCAAG	58.740	50.000	0.00	0.00	0.00	4.01
810	1124	1.474077	TCGAAACCCTAACTAGACGGC	59.526	52.381	0.00	0.00	0.00	5.68
813	1127	4.462132	AGGAGTTCGAAACCCTAACTAGAC	59.538	45.833	15.59	0.00	33.72	2.59
911	1228	3.774959	CTTCCGCCGGGTGAGATCG	62.775	68.421	9.67	0.00	33.83	3.69
982	1312	2.241722	CATAGCGAACGCCAACAAAAG	58.758	47.619	15.44	0.00	43.17	2.27
1020	1350	0.551396	TGCCCTGACGAGATCCTCTA	59.449	55.000	0.00	0.00	0.00	2.43
1134	1464	0.250684	TCGCAAGCCACTTGGATTCA	60.251	50.000	9.23	0.00	42.75	2.57
1158	1489	7.332557	TGAAACTCTTTTCAGTGTGTACCTTA	58.667	34.615	0.00	0.00	45.08	2.69
1241	1581	4.415150	CATCCACCCTGCGCCAGT	62.415	66.667	4.18	0.00	0.00	4.00
1407	1747	2.270434	TGAGGATCCTAGCCCAAACT	57.730	50.000	16.16	0.00	0.00	2.66
1699	4570	8.231692	TCAAGTTTGGTTAAATCATGTTCTCA	57.768	30.769	0.00	0.00	0.00	3.27
1779	4650	0.463833	GATTTCTACCAGCCCCACGG	60.464	60.000	0.00	0.00	0.00	4.94
1780	4651	0.463833	GGATTTCTACCAGCCCCACG	60.464	60.000	0.00	0.00	0.00	4.94
1781	4652	0.919710	AGGATTTCTACCAGCCCCAC	59.080	55.000	0.00	0.00	0.00	4.61
1984	4855	6.646267	ACACGTTATTATTTCTAGCCTCCAA	58.354	36.000	0.00	0.00	0.00	3.53
2037	4908	2.343758	GGTTCTGGCGCTGACTGA	59.656	61.111	7.64	0.00	0.00	3.41
2069	4950	3.307242	CCTTTGAAGATTTAGTCGCTCCG	59.693	47.826	0.00	0.00	0.00	4.63
2261	5180	3.162154	GTCCGGTCATCCCCCTCC	61.162	72.222	0.00	0.00	0.00	4.30
2385	5304	0.175760	GCTATCAAGGTGCGTCTCCA	59.824	55.000	1.81	0.00	0.00	3.86
2409	5328	0.756294	TTTCCGAAGACACTCTGCCA	59.244	50.000	0.00	0.00	0.00	4.92
2435	5354	6.391227	ACAAACTAGTTTTTGGTCCATCTG	57.609	37.500	18.25	6.09	40.25	2.90
2570	5489	3.300009	CAGTCAAACGCCAAACAGAATC	58.700	45.455	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.