AutoCloner

Multiple sequence alignment - TraesCS3A01G493200

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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	TraesCS3A01G493200	chr3A	100.000	3637	0	0	1	3637	719823504	719819868	0.000000e+00	6717.0
1	TraesCS3A01G493200	chr3D	94.941	2866	92	23	794	3637	590069685	590066851	0.000000e+00	4440.0
2	TraesCS3A01G493200	chr3D	86.825	1890	204	29	801	2672	590123353	590125215	0.000000e+00	2069.0
3	TraesCS3A01G493200	chr3D	90.909	110	10	0	2124	2233	590089283	590089174	8.140000e-32	148.0
4	TraesCS3A01G493200	chr3D	100.000	29	0	0	2778	2806	590067754	590067726	2.000000e-03	54.7
5	TraesCS3A01G493200	chr3B	88.309	1762	171	17	926	2675	788949406	788951144	0.000000e+00	2080.0
6	TraesCS3A01G493200	chr3B	93.098	681	16	3	1	652	736932178	736931500	0.000000e+00	968.0
7	TraesCS3A01G493200	chr3B	79.310	377	69	6	3266	3637	789180833	789180461	4.660000e-64	255.0
8	TraesCS3A01G493200	chr6A	98.489	794	10	1	1	794	185243294	185244085	0.000000e+00	1399.0
9	TraesCS3A01G493200	chr6A	91.373	823	16	10	1	794	530589972	530589176	0.000000e+00	1075.0
10	TraesCS3A01G493200	chr7A	97.607	794	14	3	1	794	581698575	581699363	0.000000e+00	1356.0
11	TraesCS3A01G493200	chr5A	94.303	825	13	5	1	794	310187044	310187865	0.000000e+00	1232.0
12	TraesCS3A01G493200	chr2B	92.710	823	26	6	1	794	35415555	35416372	0.000000e+00	1157.0
13	TraesCS3A01G493200	chr6B	89.576	825	20	15	1	796	181124341	181123554	0.000000e+00	987.0
14	TraesCS3A01G493200	chr6B	95.276	508	17	4	292	794	546661576	546662081	0.000000e+00	798.0
15	TraesCS3A01G493200	chr6B	98.305	295	5	0	1	295	546661256	546661550	5.380000e-143	518.0
16	TraesCS3A01G493200	chr1B	87.321	836	47	15	2	794	8693673	8694492	0.000000e+00	902.0
17	TraesCS3A01G493200	chr1B	86.380	837	54	20	2	794	8960215	8959395	0.000000e+00	859.0
18	TraesCS3A01G493200	chr5B	85.986	842	52	18	2	794	693103466	693104290	0.000000e+00	841.0

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	TraesCS3A01G493200	chr3A	719819868	719823504	3636	True	6717.00	6717	100.0000	1	3637	1	chr3A.!!$R1	3636
1	TraesCS3A01G493200	chr3D	590066851	590069685	2834	True	2247.35	4440	97.4705	794	3637	2	chr3D.!!$R2	2843
2	TraesCS3A01G493200	chr3D	590123353	590125215	1862	False	2069.00	2069	86.8250	801	2672	1	chr3D.!!$F1	1871
3	TraesCS3A01G493200	chr3B	788949406	788951144	1738	False	2080.00	2080	88.3090	926	2675	1	chr3B.!!$F1	1749
4	TraesCS3A01G493200	chr3B	736931500	736932178	678	True	968.00	968	93.0980	1	652	1	chr3B.!!$R1	651
5	TraesCS3A01G493200	chr6A	185243294	185244085	791	False	1399.00	1399	98.4890	1	794	1	chr6A.!!$F1	793
6	TraesCS3A01G493200	chr6A	530589176	530589972	796	True	1075.00	1075	91.3730	1	794	1	chr6A.!!$R1	793
7	TraesCS3A01G493200	chr7A	581698575	581699363	788	False	1356.00	1356	97.6070	1	794	1	chr7A.!!$F1	793
8	TraesCS3A01G493200	chr5A	310187044	310187865	821	False	1232.00	1232	94.3030	1	794	1	chr5A.!!$F1	793
9	TraesCS3A01G493200	chr2B	35415555	35416372	817	False	1157.00	1157	92.7100	1	794	1	chr2B.!!$F1	793
10	TraesCS3A01G493200	chr6B	181123554	181124341	787	True	987.00	987	89.5760	1	796	1	chr6B.!!$R1	795
11	TraesCS3A01G493200	chr6B	546661256	546662081	825	False	658.00	798	96.7905	1	794	2	chr6B.!!$F1	793
12	TraesCS3A01G493200	chr1B	8693673	8694492	819	False	902.00	902	87.3210	2	794	1	chr1B.!!$F1	792
13	TraesCS3A01G493200	chr1B	8959395	8960215	820	True	859.00	859	86.3800	2	794	1	chr1B.!!$R1	792
14	TraesCS3A01G493200	chr5B	693103466	693104290	824	False	841.00	841	85.9860	2	794	1	chr5B.!!$F1	792

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
880	940	0.175073	GGACCTACATGTGTCGGGTC	59.825	60.0	22.45	22.45	43.69	4.46	F
1206	1277	0.036164	TGGCTCACCGTTAGCACAAT	59.964	50.0	7.01	0.00	41.93	2.71	F
1254	1325	0.183971	ACGACGATGAGGAGGAGGAT	59.816	55.0	0.00	0.00	0.00	3.24	F
1953	2024	0.475906	ACTTGGAGCTGTCAGGCTTT	59.524	50.0	1.14	0.00	43.20	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1953	2024	1.408969	TAGTGCGCACCATATCTCCA	58.591	50.000	35.51	7.97	0.00	3.86	R
2297	2375	1.909986	GAGAGTAAGCTTCCCAAGGGT	59.090	52.381	0.00	0.00	36.47	4.34	R
2571	2650	2.305927	AGTCCCTTTGTACCATGGACAG	59.694	50.000	21.47	7.54	46.29	3.51	R
3574	3658	1.336332	TGTGAGCGCTTCTGAACTCTC	60.336	52.381	13.26	0.00	0.00	3.20	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
480	535	2.441164	GGAGAGAGCGAGGGAGCA	60.441	66.667	0.00	0.00	40.15	4.26
536	595	7.429633	CACACATTGGTAGGAAAAACATGTTA	58.570	34.615	12.39	0.00	0.00	2.41
538	597	9.303116	ACACATTGGTAGGAAAAACATGTTATA	57.697	29.630	12.39	0.00	0.00	0.98
592	651	6.068010	TCATTGTGTTTGTTCCCTATCTGTT	58.932	36.000	0.00	0.00	0.00	3.16
849	909	1.019673	CGGCCCACTTTGATGATCTG	58.980	55.000	0.00	0.00	0.00	2.90
853	913	2.096496	GCCCACTTTGATGATCTGTTCG	59.904	50.000	0.00	0.00	0.00	3.95
873	933	3.436001	GTCCACGGACCTACATGTG	57.564	57.895	9.11	0.00	39.08	3.21
874	934	0.606604	GTCCACGGACCTACATGTGT	59.393	55.000	9.11	0.00	39.08	3.72
877	937	0.457853	CACGGACCTACATGTGTCGG	60.458	60.000	9.11	14.36	36.97	4.79
880	940	0.175073	GGACCTACATGTGTCGGGTC	59.825	60.000	22.45	22.45	43.69	4.46
881	941	0.175073	GACCTACATGTGTCGGGTCC	59.825	60.000	21.10	10.57	41.20	4.46
882	942	0.543410	ACCTACATGTGTCGGGTCCA	60.543	55.000	9.11	0.00	35.40	4.02
884	944	0.457853	CTACATGTGTCGGGTCCACG	60.458	60.000	9.11	0.00	35.56	4.94
896	956	2.911509	TCCACGGACCGACGGAAA	60.912	61.111	23.38	2.67	38.39	3.13
918	984	2.489528	ATTAGGGTCCGGGAGAATCA	57.510	50.000	0.00	0.00	36.25	2.57
952	1018	2.861006	GGCGTCAAGAAAGCGGAC	59.139	61.111	0.00	0.00	0.00	4.79
971	1037	2.045926	GGCCCTGCAACGTGAGAT	60.046	61.111	0.00	0.00	0.00	2.75
976	1042	1.134580	CCCTGCAACGTGAGATCAGAT	60.135	52.381	0.00	0.00	0.00	2.90
1012	1078	2.342650	GCTTCCATGGCCAAGCGAA	61.343	57.895	19.20	10.94	35.97	4.70
1013	1079	1.876497	GCTTCCATGGCCAAGCGAAA	61.876	55.000	19.20	0.00	35.97	3.46
1083	1149	3.009140	GACATCATGTCGCGCCTG	58.991	61.111	0.93	0.00	37.67	4.85
1198	1269	2.047274	CATCCGTGGCTCACCGTT	60.047	61.111	0.50	0.00	39.70	4.44
1206	1277	0.036164	TGGCTCACCGTTAGCACAAT	59.964	50.000	7.01	0.00	41.93	2.71
1227	1298	0.536460	TGAGCTTCAAACCCCGGTTC	60.536	55.000	0.00	0.00	37.35	3.62
1254	1325	0.183971	ACGACGATGAGGAGGAGGAT	59.816	55.000	0.00	0.00	0.00	3.24
1272	1343	3.054802	AGGATGAGGAGCTCGACAAATTT	60.055	43.478	7.83	0.00	32.35	1.82
1491	1562	2.681778	CCTCCTCTGGCGTCTGGT	60.682	66.667	0.00	0.00	0.00	4.00
1567	1638	1.229428	TTTTGAGAAGCACCTCAGCG	58.771	50.000	7.88	0.00	43.28	5.18
1678	1749	1.803334	TGTTGATAACTCGCCCACAC	58.197	50.000	0.00	0.00	0.00	3.82
1683	1754	0.623723	ATAACTCGCCCACACCCAAT	59.376	50.000	0.00	0.00	0.00	3.16
1693	1764	2.315176	CCACACCCAATGAAGGAACAA	58.685	47.619	0.00	0.00	31.28	2.83
1699	1770	4.022329	CACCCAATGAAGGAACAAGGTTAC	60.022	45.833	0.00	0.00	0.00	2.50
1700	1771	4.148838	CCCAATGAAGGAACAAGGTTACA	58.851	43.478	0.00	0.00	0.00	2.41
1755	1826	0.938168	ACCTCGTCGTTCAGTTTCGC	60.938	55.000	0.00	0.00	0.00	4.70
1953	2024	0.475906	ACTTGGAGCTGTCAGGCTTT	59.524	50.000	1.14	0.00	43.20	3.51
1972	2043	1.408969	TGGAGATATGGTGCGCACTA	58.591	50.000	36.84	33.23	0.00	2.74
1973	2044	1.760029	TGGAGATATGGTGCGCACTAA	59.240	47.619	36.84	26.38	0.00	2.24
2130	2208	2.417243	CGGGGTTTTATCGAACTACGGT	60.417	50.000	0.00	0.00	42.82	4.83
2297	2375	4.502604	GGTCCTTCTTGCATAATACGCCTA	60.503	45.833	0.00	0.00	0.00	3.93
2304	2382	2.224426	TGCATAATACGCCTACCCTTGG	60.224	50.000	0.00	0.00	0.00	3.61
2349	2428	8.343168	TGTGGGGTACATACTTTTAATTTCAG	57.657	34.615	0.00	0.00	33.42	3.02
2523	2602	4.024048	AGTTGGTAGAAATCAAGCACAACG	60.024	41.667	0.00	0.00	41.13	4.10
2571	2650	3.350833	ACTGCACAAATGGAGAAGATCC	58.649	45.455	2.60	0.00	46.84	3.36
2606	2685	1.140375	GGACTTACCGGTGGCTACG	59.860	63.158	19.93	0.00	0.00	3.51
2624	2703	4.508124	GCTACGAAGATCCATGTTACCAAG	59.492	45.833	0.00	0.00	0.00	3.61
2744	2825	2.351157	GCAACAATGGACTGCTGAGTTC	60.351	50.000	0.00	0.00	33.20	3.01
2875	2956	3.910989	TGGACAGGCTGATTACTAGCTA	58.089	45.455	23.66	0.00	40.92	3.32
2955	3036	3.625764	TGTCCTTGTTTCTTTGTTCCTCG	59.374	43.478	0.00	0.00	0.00	4.63
2956	3037	3.626217	GTCCTTGTTTCTTTGTTCCTCGT	59.374	43.478	0.00	0.00	0.00	4.18
2957	3038	4.095932	GTCCTTGTTTCTTTGTTCCTCGTT	59.904	41.667	0.00	0.00	0.00	3.85
2958	3039	4.703093	TCCTTGTTTCTTTGTTCCTCGTTT	59.297	37.500	0.00	0.00	0.00	3.60
2959	3040	5.184287	TCCTTGTTTCTTTGTTCCTCGTTTT	59.816	36.000	0.00	0.00	0.00	2.43
3026	3107	6.543100	GTGTAAGCTATCACTACCTGTACTCT	59.457	42.308	12.15	0.00	0.00	3.24
3039	3120	9.696572	ACTACCTGTACTCTAAGATATGTTCAA	57.303	33.333	0.00	0.00	0.00	2.69
3141	3225	4.842139	GTTCCTACGAACACATGATCAC	57.158	45.455	0.00	0.00	46.49	3.06
3451	3535	3.563223	CCTCTGCTGGATGAATTTCCAT	58.437	45.455	0.00	0.00	44.66	3.41
3452	3536	3.958798	CCTCTGCTGGATGAATTTCCATT	59.041	43.478	0.00	0.00	44.66	3.16
3453	3537	5.135383	CCTCTGCTGGATGAATTTCCATTA	58.865	41.667	0.00	0.00	44.66	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
480	535	0.481607	TCCCAATTCCCCCTTCCCTT	60.482	55.000	0.00	0.00	0.00	3.95
592	651	8.528643	CATCCGACATTAAGGTTATGGTATCTA	58.471	37.037	0.00	0.00	0.00	1.98
669	729	8.465999	GTGGATGGACAAATTTACAATCATACA	58.534	33.333	11.50	6.95	0.00	2.29
744	804	1.336240	GCTGCATTGGCGACTTCTTTT	60.336	47.619	0.00	0.00	45.35	2.27
745	805	0.242017	GCTGCATTGGCGACTTCTTT	59.758	50.000	0.00	0.00	45.35	2.52
798	858	1.735700	CGCATGAAGAGCTCCGTTACA	60.736	52.381	10.93	4.32	0.00	2.41
810	870	2.028523	CGTTTACAGCTCTCGCATGAAG	59.971	50.000	0.00	0.00	39.10	3.02
830	890	1.019673	CAGATCATCAAAGTGGGCCG	58.980	55.000	0.00	0.00	0.00	6.13
866	926	1.587568	CGTGGACCCGACACATGTA	59.412	57.895	0.00	0.00	38.74	2.29
867	927	2.342279	CGTGGACCCGACACATGT	59.658	61.111	0.00	0.00	38.74	3.21
880	940	0.108709	TAATTTCCGTCGGTCCGTGG	60.109	55.000	11.88	14.48	0.00	4.94
881	941	1.930567	ATAATTTCCGTCGGTCCGTG	58.069	50.000	11.88	5.23	0.00	4.94
882	942	2.678471	AATAATTTCCGTCGGTCCGT	57.322	45.000	11.88	0.00	0.00	4.69
884	944	3.181462	ACCCTAATAATTTCCGTCGGTCC	60.181	47.826	11.88	0.00	0.00	4.46
896	956	4.499472	TGATTCTCCCGGACCCTAATAAT	58.501	43.478	0.73	0.00	0.00	1.28
918	984	4.693566	TGACGCCGAAATTTGTTTAGATCT	59.306	37.500	0.00	0.00	0.00	2.75
971	1037	0.690744	TGCTGGGGAATCCGATCTGA	60.691	55.000	0.00	0.00	38.76	3.27
976	1042	1.832219	CAGATGCTGGGGAATCCGA	59.168	57.895	0.00	0.00	38.76	4.55
996	1062	1.876497	GCTTTCGCTTGGCCATGGAA	61.876	55.000	18.40	16.61	0.00	3.53
1023	1089	2.202797	CTCAGCCGGTCCACATCG	60.203	66.667	1.90	0.00	0.00	3.84
1065	1131	2.202932	AGGCGCGACATGATGTCC	60.203	61.111	17.71	11.13	44.20	4.02
1198	1269	3.253188	GGTTTGAAGCTCACATTGTGCTA	59.747	43.478	12.04	0.00	45.23	3.49
1206	1277	1.228124	CCGGGGTTTGAAGCTCACA	60.228	57.895	0.00	0.00	0.00	3.58
1227	1298	1.297967	CTCATCGTCGTCCTCGCTG	60.298	63.158	0.00	0.00	36.96	5.18
1254	1325	3.067106	GTCAAATTTGTCGAGCTCCTCA	58.933	45.455	17.47	4.72	0.00	3.86
1678	1749	4.022329	GTGTAACCTTGTTCCTTCATTGGG	60.022	45.833	0.00	0.00	0.00	4.12
1683	1754	4.165372	AGGAAGTGTAACCTTGTTCCTTCA	59.835	41.667	0.00	0.00	43.71	3.02
1693	1764	1.538950	GTCGACGAGGAAGTGTAACCT	59.461	52.381	0.00	0.00	37.80	3.50
1699	1770	2.504244	GGCGTCGACGAGGAAGTG	60.504	66.667	39.74	10.32	43.02	3.16
1700	1771	3.745803	GGGCGTCGACGAGGAAGT	61.746	66.667	39.74	0.00	43.02	3.01
1953	2024	1.408969	TAGTGCGCACCATATCTCCA	58.591	50.000	35.51	7.97	0.00	3.86
1972	2043	5.493133	TGTGTGTTCGCTAATTGAAACTT	57.507	34.783	0.00	0.00	0.00	2.66
1973	2044	5.689383	ATGTGTGTTCGCTAATTGAAACT	57.311	34.783	0.00	0.00	0.00	2.66
2130	2208	2.696989	ATCATCATCACTTGTCCGCA	57.303	45.000	0.00	0.00	0.00	5.69
2297	2375	1.909986	GAGAGTAAGCTTCCCAAGGGT	59.090	52.381	0.00	0.00	36.47	4.34
2304	2382	5.335191	CCACAATTGTTGAGAGTAAGCTTCC	60.335	44.000	8.77	0.00	0.00	3.46
2523	2602	2.941720	GGACTTCATGGTCATCTCTTGC	59.058	50.000	4.76	0.00	37.91	4.01
2571	2650	2.305927	AGTCCCTTTGTACCATGGACAG	59.694	50.000	21.47	7.54	46.29	3.51
2624	2703	8.983789	TGAAGGGGGTTATATTAATTTTTGACC	58.016	33.333	0.00	0.00	0.00	4.02
2744	2825	9.941664	CTTGTCCTTTATTAAACATCTGCATAG	57.058	33.333	0.00	0.00	0.00	2.23
2959	3040	4.025061	CCATTGTTGCATGCGAAAGAAAAA	60.025	37.500	9.83	0.61	0.00	1.94
2964	3045	2.350899	TCCATTGTTGCATGCGAAAG	57.649	45.000	9.83	0.77	0.00	2.62
3135	3219	7.679783	TCTCACCAAGAAAAGATTAGTGATCA	58.320	34.615	0.00	0.00	37.22	2.92
3327	3411	7.377397	TGCAATGTTAAACAACGAGAATGTTAC	59.623	33.333	0.00	0.00	39.98	2.50
3357	3441	3.374220	TCGACTAACCACGTCAAATGT	57.626	42.857	0.00	0.00	0.00	2.71
3574	3658	1.336332	TGTGAGCGCTTCTGAACTCTC	60.336	52.381	13.26	0.00	0.00	3.20

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.