AutoCloner

Multiple sequence alignment - TraesCS1A01G154800

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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	TraesCS1A01G154800	chr1A	100.000	4092	0	0	1	4092	270720747	270716656	0.000000e+00	7557.0
1	TraesCS1A01G154800	chr1A	96.113	4091	128	17	3	4092	177379866	177383926	0.000000e+00	6645.0
2	TraesCS1A01G154800	chr5A	96.554	4092	141	0	1	4092	685305974	685310065	0.000000e+00	6776.0
3	TraesCS1A01G154800	chr5A	95.626	4092	122	4	1	4092	155926921	155930955	0.000000e+00	6512.0
4	TraesCS1A01G154800	chr5A	96.581	2486	74	1	1607	4092	518788644	518786170	0.000000e+00	4109.0
5	TraesCS1A01G154800	chr3A	95.672	4090	149	2	3	4092	665688896	665684835	0.000000e+00	6547.0
6	TraesCS1A01G154800	chr3A	97.646	3229	75	1	861	4088	642857615	642860843	0.000000e+00	5541.0
7	TraesCS1A01G154800	chr3A	96.528	2304	63	2	1789	4092	92259237	92256951	0.000000e+00	3795.0
8	TraesCS1A01G154800	chr3A	97.943	2188	45	0	1905	4092	149210420	149212607	0.000000e+00	3792.0
9	TraesCS1A01G154800	chr3A	97.068	1569	46	0	1	1569	92260797	92259229	0.000000e+00	2643.0
10	TraesCS1A01G154800	chr3A	96.705	1548	50	1	1	1548	149208878	149210424	0.000000e+00	2575.0
11	TraesCS1A01G154800	chr3A	93.386	1633	77	5	1	1632	219227328	219225726	0.000000e+00	2388.0
12	TraesCS1A01G154800	chr3A	96.145	882	32	2	1	881	642856783	642857663	0.000000e+00	1439.0
13	TraesCS1A01G154800	chr3A	85.714	301	18	1	1702	1977	447659906	447659606	1.110000e-75	294.0
14	TraesCS1A01G154800	chr3A	85.382	301	19	4	1702	1977	18662461	18662161	5.180000e-74	289.0
15	TraesCS1A01G154800	chr3A	96.429	56	2	0	1630	1685	219225135	219225080	4.360000e-15	93.5
16	TraesCS1A01G154800	chr6A	97.614	2305	52	3	1789	4092	450322065	450324367	0.000000e+00	3949.0
17	TraesCS1A01G154800	chr6A	96.303	1569	57	1	1	1569	450320506	450322073	0.000000e+00	2575.0
18	TraesCS1A01G154800	chr7A	97.833	1661	35	1	2433	4092	271152929	271151269	0.000000e+00	2867.0

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	TraesCS1A01G154800	chr1A	270716656	270720747	4091	True	7557.00	7557	100.0000	1	4092	1	chr1A.!!$R1	4091
1	TraesCS1A01G154800	chr1A	177379866	177383926	4060	False	6645.00	6645	96.1130	3	4092	1	chr1A.!!$F1	4089
2	TraesCS1A01G154800	chr5A	685305974	685310065	4091	False	6776.00	6776	96.5540	1	4092	1	chr5A.!!$F2	4091
3	TraesCS1A01G154800	chr5A	155926921	155930955	4034	False	6512.00	6512	95.6260	1	4092	1	chr5A.!!$F1	4091
4	TraesCS1A01G154800	chr5A	518786170	518788644	2474	True	4109.00	4109	96.5810	1607	4092	1	chr5A.!!$R1	2485
5	TraesCS1A01G154800	chr3A	665684835	665688896	4061	True	6547.00	6547	95.6720	3	4092	1	chr3A.!!$R3	4089
6	TraesCS1A01G154800	chr3A	642856783	642860843	4060	False	3490.00	5541	96.8955	1	4088	2	chr3A.!!$F2	4087
7	TraesCS1A01G154800	chr3A	92256951	92260797	3846	True	3219.00	3795	96.7980	1	4092	2	chr3A.!!$R4	4091
8	TraesCS1A01G154800	chr3A	149208878	149212607	3729	False	3183.50	3792	97.3240	1	4092	2	chr3A.!!$F1	4091
9	TraesCS1A01G154800	chr3A	219225080	219227328	2248	True	1240.75	2388	94.9075	1	1685	2	chr3A.!!$R5	1684
10	TraesCS1A01G154800	chr6A	450320506	450324367	3861	False	3262.00	3949	96.9585	1	4092	2	chr6A.!!$F1	4091
11	TraesCS1A01G154800	chr7A	271151269	271152929	1660	True	2867.00	2867	97.8330	2433	4092	1	chr7A.!!$R1	1659

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
517	518	0.036671	TGCCACTGAGCTCATGACAG	60.037	55.000	18.63	7.67	37.62	3.51	F
834	836	0.107165	GGGGAAGCTGATACCCACAC	60.107	60.000	16.60	1.15	44.87	3.82	F
1011	1067	0.250510	TTGCTACAATGTCGGGTGCA	60.251	50.000	0.00	0.00	0.00	4.57	F
2934	3162	1.740905	GCTTCTACTCCGCCTACCC	59.259	63.158	0.00	0.00	0.00	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1587	1644	0.906775	TTTAAGACTGTAGCCCGGGG	59.093	55.000	25.28	9.31	0.00	5.73	R
2712	2940	3.603365	GCCTGGCGTAAAATGGCT	58.397	55.556	1.35	0.00	40.36	4.75	R
2979	3207	1.533469	GGACTCCCACACGTACTGCT	61.533	60.000	0.00	0.00	0.00	4.24	R
3943	4354	4.879598	AGTAACAGTACTTCTTTCCCACG	58.120	43.478	0.00	0.00	37.25	4.94	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
202	203	0.191064	TTCCTAGATCCATCCGCCCT	59.809	55.000	0.00	0.00	0.00	5.19
511	512	2.616256	CCAATACTTGCCACTGAGCTCA	60.616	50.000	17.19	17.19	0.00	4.26
517	518	0.036671	TGCCACTGAGCTCATGACAG	60.037	55.000	18.63	7.67	37.62	3.51
526	527	1.556451	AGCTCATGACAGTGCCATGTA	59.444	47.619	17.62	5.58	41.45	2.29
549	550	0.324091	CTTGGGCCCTCTGATGCTTT	60.324	55.000	25.70	0.00	0.00	3.51
557	558	2.036992	CCCTCTGATGCTTTCTCGCTAT	59.963	50.000	0.00	0.00	0.00	2.97
595	596	8.409358	AACACAATTGCTTACTCCTAAAATCT	57.591	30.769	5.05	0.00	0.00	2.40
667	668	4.778213	ATCATACTCCAGGCTTGCTTAA	57.222	40.909	0.00	0.00	0.00	1.85
834	836	0.107165	GGGGAAGCTGATACCCACAC	60.107	60.000	16.60	1.15	44.87	3.82
844	846	2.244117	ATACCCACACAGCCAGCTCG	62.244	60.000	0.00	0.00	0.00	5.03
867	869	0.393132	TCACTGTGTTTGACCGCCAA	60.393	50.000	7.79	0.00	0.00	4.52
871	900	0.393132	TGTGTTTGACCGCCAACTCA	60.393	50.000	0.00	0.00	33.85	3.41
889	918	3.136763	CTCATGCTCACTGTGTTTGACT	58.863	45.455	7.79	0.00	0.00	3.41
1011	1067	0.250510	TTGCTACAATGTCGGGTGCA	60.251	50.000	0.00	0.00	0.00	4.57
1249	1306	6.864360	GCTAGCTAGCTAACTAGTACAAGA	57.136	41.667	33.71	0.40	46.56	3.02
1475	1532	5.768980	TCTTGTCTGAATCATCCCTCTTT	57.231	39.130	0.00	0.00	0.00	2.52
1477	1534	6.546484	TCTTGTCTGAATCATCCCTCTTTTT	58.454	36.000	0.00	0.00	0.00	1.94
1506	1563	6.428159	GTCTTTATGAAGCTTTGGAACTGAGA	59.572	38.462	0.00	0.00	32.75	3.27
1510	1567	2.849294	AGCTTTGGAACTGAGAGACC	57.151	50.000	0.00	0.00	0.00	3.85
1613	1670	5.293569	CCGGGCTACAGTCTTAAAGTAATTG	59.706	44.000	0.00	0.00	0.00	2.32
1640	1697	5.043737	ACCTAGTTAGTGTTTGGAAGCAA	57.956	39.130	0.00	0.00	0.00	3.91
1961	2151	3.362399	CTGCAGGACTCGACGGCAT	62.362	63.158	5.57	0.00	33.50	4.40
2093	2283	4.060205	GCTTTCCTGTTCATGCATGTTTT	58.940	39.130	25.43	0.00	0.00	2.43
2257	2447	8.709308	AGTGATTATCTTTATGTCCTTGCTACT	58.291	33.333	0.00	0.00	0.00	2.57
2412	2627	6.270815	AGACATTTCATGCATGTTTATGAGC	58.729	36.000	28.30	22.14	34.89	4.26
2712	2940	5.221224	GCAGCATTGGCCATTAATTACACTA	60.221	40.000	6.09	0.00	42.56	2.74
2934	3162	1.740905	GCTTCTACTCCGCCTACCC	59.259	63.158	0.00	0.00	0.00	3.69
2979	3207	1.260297	CATGAAGCACAACAACGACGA	59.740	47.619	0.00	0.00	0.00	4.20
3033	3261	2.099263	CCTTCACCGTCACTCGTGATAT	59.901	50.000	2.75	0.00	42.18	1.63
3167	3395	4.158025	GTGGTTCTCTGCTTAGTGTAGCTA	59.842	45.833	0.00	0.00	41.76	3.32
3208	3569	7.502226	TGAGATGTCCACTCTTGTTTTGTTAAT	59.498	33.333	0.00	0.00	35.66	1.40
3303	3665	3.806625	TGCGTAGGTGGTTATAGGTTC	57.193	47.619	0.00	0.00	0.00	3.62
3435	3797	2.582636	ACCCAGCCCAATGAATCTAACT	59.417	45.455	0.00	0.00	0.00	2.24
3574	3937	3.855950	GCATCAAAACTGCTTCATGCTAC	59.144	43.478	0.00	0.00	43.37	3.58
3615	3978	8.634444	AGATGCTAGTTTGGTTACTATCTGTAG	58.366	37.037	0.00	0.00	30.65	2.74
4007	4418	4.705023	TGGCTGTAAATAAAAGAGGGCTTC	59.295	41.667	0.00	0.00	31.82	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
202	203	1.860240	AGATAGGGTGAGCAGAGGGTA	59.140	52.381	0.00	0.00	0.00	3.69
511	512	3.920231	AGTGATACATGGCACTGTCAT	57.080	42.857	14.71	0.00	43.26	3.06
517	518	0.740737	GCCCAAGTGATACATGGCAC	59.259	55.000	0.00	2.50	35.74	5.01
526	527	0.549950	CATCAGAGGGCCCAAGTGAT	59.450	55.000	27.56	24.10	0.00	3.06
549	550	2.147150	CATCGAGAGACCATAGCGAGA	58.853	52.381	0.00	0.00	46.97	4.04
557	558	3.961480	ATTGTGTTCATCGAGAGACCA	57.039	42.857	0.00	0.00	46.97	4.02
595	596	6.672657	AGCAAGAGTAAACCCTAGGAATTAGA	59.327	38.462	11.48	0.00	0.00	2.10
667	668	4.782019	TCTAAGCGTGGAATTGCAATTT	57.218	36.364	24.81	10.40	0.00	1.82
844	846	0.304705	CGGTCAAACACAGTGAGCAC	59.695	55.000	7.81	0.00	42.35	4.40
848	850	0.393132	TTGGCGGTCAAACACAGTGA	60.393	50.000	7.81	0.00	31.46	3.41
850	852	0.393808	AGTTGGCGGTCAAACACAGT	60.394	50.000	0.00	0.00	37.08	3.55
867	869	2.874701	GTCAAACACAGTGAGCATGAGT	59.125	45.455	7.81	0.00	0.00	3.41
871	900	1.605710	GCAGTCAAACACAGTGAGCAT	59.394	47.619	7.81	0.00	0.00	3.79
1011	1067	0.457035	CAAGTTTGCAGCACACCACT	59.543	50.000	8.12	0.00	0.00	4.00
1249	1306	3.456380	ACTGTTCCTATTGGGTTGCAT	57.544	42.857	0.00	0.00	36.25	3.96
1451	1508	7.443302	AAAGAGGGATGATTCAGACAAGATA	57.557	36.000	0.00	0.00	0.00	1.98
1475	1532	8.357402	GTTCCAAAGCTTCATAAAGACCTAAAA	58.643	33.333	0.00	0.00	34.14	1.52
1477	1534	7.174946	CAGTTCCAAAGCTTCATAAAGACCTAA	59.825	37.037	0.00	0.00	34.14	2.69
1506	1563	2.755655	CAAGTAGTCAGATCCACGGTCT	59.244	50.000	0.00	0.00	0.00	3.85
1510	1567	2.100197	TCCCAAGTAGTCAGATCCACG	58.900	52.381	0.00	0.00	0.00	4.94
1587	1644	0.906775	TTTAAGACTGTAGCCCGGGG	59.093	55.000	25.28	9.31	0.00	5.73
1613	1670	6.073385	GCTTCCAAACACTAACTAGGTAACAC	60.073	42.308	0.00	0.00	41.41	3.32
1640	1697	5.041191	ACTTTTCTCACATTCACTCCAGT	57.959	39.130	0.00	0.00	0.00	4.00
1920	2110	3.744719	AACTCGCACCGCTCGCTA	61.745	61.111	0.00	0.00	0.00	4.26
1930	2120	4.560743	TGCAGCCACCAACTCGCA	62.561	61.111	0.00	0.00	0.00	5.10
2257	2447	9.391006	CAAAACAAGCTATTAACCATCCTACTA	57.609	33.333	0.00	0.00	0.00	1.82
2412	2627	7.812309	TTTGTGACATCTGTAGAATTCGTAG	57.188	36.000	0.00	0.37	0.00	3.51
2712	2940	3.603365	GCCTGGCGTAAAATGGCT	58.397	55.556	1.35	0.00	40.36	4.75
2934	3162	2.125912	CGACCCTCTCGGCAACAG	60.126	66.667	0.00	0.00	38.87	3.16
2979	3207	1.533469	GGACTCCCACACGTACTGCT	61.533	60.000	0.00	0.00	0.00	4.24
3033	3261	2.032528	CGAGCTGCTCCCCAAACA	59.967	61.111	22.97	0.00	0.00	2.83
3167	3395	9.019656	GTGGACATCTCATAGTGAGTCTAATAT	57.980	37.037	6.83	0.00	44.58	1.28
3435	3797	1.269883	TGGCGAGAACTAAACGAGCAA	60.270	47.619	0.00	0.00	0.00	3.91
3615	3978	4.953667	TGCATCAAGTAGACCTGATGATC	58.046	43.478	20.49	8.11	40.19	2.92
3784	4165	5.316167	TGTATCTTGCAGGTTCAAATCACT	58.684	37.500	0.00	0.00	0.00	3.41
3925	4336	7.364149	TCCCACGGTAATAACACAAGTATAT	57.636	36.000	0.00	0.00	0.00	0.86
3943	4354	4.879598	AGTAACAGTACTTCTTTCCCACG	58.120	43.478	0.00	0.00	37.25	4.94
4007	4418	4.974368	TTTTACAATCCAATAGTGGGCG	57.026	40.909	9.77	0.67	46.01	6.13

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.