AutoCloner

Multiple sequence alignment - TraesCS2D01G320500

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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	TraesCS2D01G320500	chr2D	100.000	3993	0	0	1	3993	411706307	411702315	0.000000e+00	7374
1	TraesCS2D01G320500	chr2D	96.933	4010	74	19	1	3993	411420205	411416228	0.000000e+00	6678
2	TraesCS2D01G320500	chr2A	94.724	2521	120	8	649	3167	579212704	579210195	0.000000e+00	3906
3	TraesCS2D01G320500	chr2A	94.320	845	40	5	3157	3993	579143474	579142630	0.000000e+00	1288
4	TraesCS2D01G320500	chr2A	88.244	672	53	8	1	653	579213409	579212745	0.000000e+00	780
5	TraesCS2D01G320500	chr4B	87.261	471	60	0	996	1466	423777152	423776682	4.540000e-149	538
6	TraesCS2D01G320500	chr4B	85.976	492	68	1	993	1484	424060246	424060736	3.540000e-145	525
7	TraesCS2D01G320500	chr4A	87.049	471	61	0	996	1466	125027942	125028412	2.110000e-147	532
8	TraesCS2D01G320500	chr4A	86.837	471	62	0	996	1466	124405884	124405414	9.830000e-146	527
9	TraesCS2D01G320500	chr4D	86.837	471	62	0	996	1466	341697082	341696612	9.830000e-146	527
10	TraesCS2D01G320500	chr4D	85.569	492	70	1	993	1484	341922805	341923295	7.650000e-142	514
11	TraesCS2D01G320500	chr5A	86.412	471	64	0	996	1466	604312714	604312244	2.130000e-142	516

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	TraesCS2D01G320500	chr2D	411702315	411706307	3992	True	7374	7374	100.000	1	3993	1	chr2D.!!$R2	3992
1	TraesCS2D01G320500	chr2D	411416228	411420205	3977	True	6678	6678	96.933	1	3993	1	chr2D.!!$R1	3992
2	TraesCS2D01G320500	chr2A	579210195	579213409	3214	True	2343	3906	91.484	1	3167	2	chr2A.!!$R2	3166
3	TraesCS2D01G320500	chr2A	579142630	579143474	844	True	1288	1288	94.320	3157	3993	1	chr2A.!!$R1	836

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	Hairpin	End Stability	Orientation
493	520	0.691078	TCCCCATCTTTCCCTCCTCG	60.691	60.000	0.0	4.63	F
500	527	1.066143	TCTTTCCCTCCTCGTGCATTC	60.066	52.381	0.0	2.67	F
1019	1091	1.661463	ATGGTGAAGGAGAAGAGCCA	58.339	50.000	0.0	4.75	F
2378	2452	1.757699	CTCCCAGGTACTCTAAGGCAC	59.242	57.143	34.6	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2364	2438	1.064654	CGTACCGTGCCTTAGAGTACC	59.935	57.143	0.00	31.65	3.34	R
2383	2457	3.310774	CCACCTGCTTCACTATTTCATCG	59.689	47.826	0.00	0.00	3.84	R
2990	3065	1.280133	CTCAACCTCCTTGCCAGATCA	59.720	52.381	0.00	0.00	2.92	R
3477	3553	1.134098	CACTCTCCATAAACGGGCCAT	60.134	52.381	4.39	0.00	4.40	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
165	173	1.293498	CCTCCAACTGGTGAGACCG	59.707	63.158	0.00	0.00	42.58	4.79
169	177	1.961277	CAACTGGTGAGACCGTGGC	60.961	63.158	0.00	0.00	42.58	5.01
366	383	1.672356	CCAAGCCACAACCTCCTCG	60.672	63.158	0.00	0.00	0.00	4.63
493	520	0.691078	TCCCCATCTTTCCCTCCTCG	60.691	60.000	0.00	0.00	0.00	4.63
500	527	1.066143	TCTTTCCCTCCTCGTGCATTC	60.066	52.381	0.00	0.00	0.00	2.67
531	558	3.311110	TTGCCTCGCTTCCCTCGT	61.311	61.111	0.00	0.00	0.00	4.18
584	611	2.126850	GCTTTCGCGGCTTGTTCC	60.127	61.111	6.13	0.00	0.00	3.62
637	664	3.351416	GTGTGGTTTCCGCGGGAC	61.351	66.667	27.83	23.16	36.72	4.46
1017	1089	1.742268	GCAATGGTGAAGGAGAAGAGC	59.258	52.381	0.00	0.00	0.00	4.09
1019	1091	1.661463	ATGGTGAAGGAGAAGAGCCA	58.339	50.000	0.00	0.00	0.00	4.75
1105	1177	3.723097	TTGCTTGGGGGCGTTGACA	62.723	57.895	0.00	0.00	34.52	3.58
1535	1607	2.294791	ACTATGATACGTCTCAGCTGCC	59.705	50.000	9.47	0.00	0.00	4.85
1567	1639	7.850982	CACTTCCATGTTTTACGTTATCTATGC	59.149	37.037	0.00	0.00	0.00	3.14
1701	1774	7.720442	TGATCTGTGTAGTCTTGGAATATCTG	58.280	38.462	0.00	0.00	0.00	2.90
1750	1823	3.371898	TCATTGTCATTCAACTGCTAGCG	59.628	43.478	10.77	7.61	38.97	4.26
1818	1892	4.387559	GTCCGTTGGCCATTAATTTTGTTC	59.612	41.667	6.09	0.00	0.00	3.18
1891	1965	2.899976	TCTGCTTCTTTGTTCGACACA	58.100	42.857	0.00	0.00	0.00	3.72
2305	2379	3.870419	TGTTGCCTTGAAGTTTGCAATTC	59.130	39.130	9.84	2.54	44.57	2.17
2364	2438	2.437281	AGATGGATTGCACTACTCCCAG	59.563	50.000	0.00	0.00	0.00	4.45
2378	2452	1.757699	CTCCCAGGTACTCTAAGGCAC	59.242	57.143	0.00	0.00	34.60	5.01
2383	2457	2.098770	CAGGTACTCTAAGGCACGGTAC	59.901	54.545	0.00	0.00	34.60	3.34
2885	2960	4.806247	GCTTCACTTCGCAGATTATAGTGT	59.194	41.667	0.00	0.00	41.06	3.55
2990	3065	1.774254	TGGTGACCAAGATTGACAGGT	59.226	47.619	0.00	0.00	37.00	4.00
3072	3147	3.003689	GTGAATATGATTCCCACCAAGCG	59.996	47.826	0.00	0.00	0.00	4.68
3160	3235	1.136695	ACGGTCGTTGTTGGAGTTGTA	59.863	47.619	0.00	0.00	0.00	2.41
3239	3314	0.679002	GCCTCTGCTGCCTCAATTGA	60.679	55.000	8.12	8.12	33.53	2.57
3393	3468	6.880484	TCAAGTTGACCTACTTTGTCAGTTA	58.120	36.000	0.08	0.00	43.14	2.24
3477	3553	1.891150	GAAGGGAACAGACACCTACGA	59.109	52.381	0.00	0.00	33.37	3.43
3520	3596	4.974888	GCAGAAAAGAAACTGAAGAGCAAG	59.025	41.667	0.00	0.00	36.38	4.01
3565	3641	1.227089	CAGGAATGAGACTCCGGCG	60.227	63.158	0.00	0.00	38.08	6.46
3604	3680	0.664761	GTGTGCACACTGAGTTGCAT	59.335	50.000	36.77	0.00	43.25	3.96
3967	4051	2.741517	TGTTCACATTAGTGTCCATGCG	59.258	45.455	0.00	0.00	46.01	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	4.379243	CGGAGCCAGAACTGCGGT	62.379	66.667	0.00	0.00	46.34	5.68
146	154	1.679898	GGTCTCACCAGTTGGAGGG	59.320	63.158	4.92	0.00	38.42	4.30
148	156	0.319900	CACGGTCTCACCAGTTGGAG	60.320	60.000	4.92	0.00	38.47	3.86
153	161	3.626924	GGCCACGGTCTCACCAGT	61.627	66.667	0.00	0.00	38.47	4.00
200	208	1.379176	CAGGCAGAGAGTCGGGAGA	60.379	63.158	0.00	0.00	0.00	3.71
297	307	0.387239	GCGTGTTGGGCATTTCAGTC	60.387	55.000	0.00	0.00	0.00	3.51
298	308	1.659794	GCGTGTTGGGCATTTCAGT	59.340	52.632	0.00	0.00	0.00	3.41
299	309	1.080569	GGCGTGTTGGGCATTTCAG	60.081	57.895	0.00	0.00	0.00	3.02
300	310	2.913765	CGGCGTGTTGGGCATTTCA	61.914	57.895	0.00	0.00	0.00	2.69
301	311	2.126502	CGGCGTGTTGGGCATTTC	60.127	61.111	0.00	0.00	0.00	2.17
366	383	4.803426	CCTCGGTCTGTGCGCTCC	62.803	72.222	9.73	0.00	0.00	4.70
500	527	3.730761	GCAACTGAGGCAGCACGG	61.731	66.667	0.00	0.00	34.37	4.94
531	558	1.274358	TGGGGTTCAGATCCTGGATGA	60.274	52.381	15.25	4.75	31.51	2.92
584	611	2.095668	CGGATCGGAACTAGGAATCGAG	60.096	54.545	0.00	0.00	33.32	4.04
637	664	1.523032	GATAACAACCCGGGCCGAG	60.523	63.158	30.79	19.04	0.00	4.63
899	971	2.930826	ATTGGCTACGATAAGGTGGG	57.069	50.000	0.00	0.00	0.00	4.61
1017	1089	5.413833	GCCTATGACCACAATATTCAGATGG	59.586	44.000	3.94	3.94	36.46	3.51
1019	1091	5.073554	TGGCCTATGACCACAATATTCAGAT	59.926	40.000	3.32	0.00	30.29	2.90
1105	1177	0.039326	AGCCTCTCAATTGCAAGCCT	59.961	50.000	4.94	0.00	0.00	4.58
1535	1607	5.757886	ACGTAAAACATGGAAGTGTTGATG	58.242	37.500	0.00	0.00	41.22	3.07
1567	1639	7.773213	ACATTACATGTCTGGTGCTTTTGCG	62.773	44.000	0.00	0.00	44.43	4.85
1680	1753	5.053145	GGCAGATATTCCAAGACTACACAG	58.947	45.833	0.00	0.00	0.00	3.66
1684	1757	5.675538	ACAAGGCAGATATTCCAAGACTAC	58.324	41.667	0.00	0.00	0.00	2.73
1701	1774	7.320399	ACTTGTAATTTATAAGGCAACAAGGC	58.680	34.615	22.42	0.00	44.04	4.35
1750	1823	6.491403	ACCCACATATCAAGAAATTATCTGCC	59.509	38.462	0.00	0.00	38.79	4.85
1818	1892	6.899393	ATTGCAACCCTATACAACATATGG	57.101	37.500	0.00	0.00	0.00	2.74
2180	2254	8.946085	GGATGTATAGATCAGTCTAGAACAGAG	58.054	40.741	11.64	0.00	40.16	3.35
2305	2379	8.120465	ACACAACATTCTCTTTTAGTTAACACG	58.880	33.333	8.61	0.00	0.00	4.49
2364	2438	1.064654	CGTACCGTGCCTTAGAGTACC	59.935	57.143	0.00	0.00	31.65	3.34
2378	2452	4.109766	TGCTTCACTATTTCATCGTACCG	58.890	43.478	0.00	0.00	0.00	4.02
2383	2457	3.310774	CCACCTGCTTCACTATTTCATCG	59.689	47.826	0.00	0.00	0.00	3.84
2885	2960	2.296752	TGATAACTCCGGTGTCGTTCAA	59.703	45.455	10.05	0.00	33.95	2.69
2990	3065	1.280133	CTCAACCTCCTTGCCAGATCA	59.720	52.381	0.00	0.00	0.00	2.92
3072	3147	3.132467	GGTGAAGGTCTCCACTACCATAC	59.868	52.174	0.00	0.00	39.64	2.39
3160	3235	2.232452	CTCCATCTTCACGACACTCCTT	59.768	50.000	0.00	0.00	0.00	3.36
3239	3314	2.026822	CAGTGATGTCCCTAGCCTTTGT	60.027	50.000	0.00	0.00	0.00	2.83
3477	3553	1.134098	CACTCTCCATAAACGGGCCAT	60.134	52.381	4.39	0.00	0.00	4.40
3520	3596	2.143925	ACAAGGAAAACTAGCTCACGC	58.856	47.619	0.00	0.00	0.00	5.34
3565	3641	2.137523	CAAGCAATCAACAAACCTGCC	58.862	47.619	0.00	0.00	33.41	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.