AutoCloner

Multiple sequence alignment - TraesCS2A01G313300

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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	TraesCS2A01G313300	chr2A	100.000	3251	0	0	1	3251	537684957	537681707	0.000000e+00	6004.0
1	TraesCS2A01G313300	chr2B	95.178	3152	113	20	1	3124	475128954	475125814	0.000000e+00	4942.0
2	TraesCS2A01G313300	chr2B	93.966	116	4	2	3138	3251	475124791	475124677	4.310000e-39	172.0
3	TraesCS2A01G313300	chr2D	94.393	3157	129	23	1	3144	401115418	401112297	0.000000e+00	4806.0
4	TraesCS2A01G313300	chr2D	93.805	113	7	0	3139	3251	401112242	401112130	1.550000e-38	171.0
5	TraesCS2A01G313300	chr2D	78.571	168	29	6	326	490	264660749	264660586	1.600000e-18	104.0
6	TraesCS2A01G313300	chr6B	79.268	164	27	6	326	485	424018792	424018952	1.230000e-19	108.0
7	TraesCS2A01G313300	chr7D	78.528	163	29	5	326	485	204656084	204655925	5.740000e-18	102.0
8	TraesCS2A01G313300	chr1B	78.528	163	29	5	326	485	170924495	170924336	5.740000e-18	102.0
9	TraesCS2A01G313300	chr1A	78.788	165	25	9	326	485	274506203	274506362	5.740000e-18	102.0
10	TraesCS2A01G313300	chr3D	78.528	163	28	6	326	485	341148904	341149062	2.060000e-17	100.0
11	TraesCS2A01G313300	chr3D	77.914	163	30	5	326	485	251621919	251622078	2.670000e-16	97.1

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	TraesCS2A01G313300	chr2A	537681707	537684957	3250	True	6004.0	6004	100.000	1	3251	1	chr2A.!!$R1	3250
1	TraesCS2A01G313300	chr2B	475124677	475128954	4277	True	2557.0	4942	94.572	1	3251	2	chr2B.!!$R1	3250
2	TraesCS2A01G313300	chr2D	401112130	401115418	3288	True	2488.5	4806	94.099	1	3251	2	chr2D.!!$R2	3250

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
330	334	0.178068	ACAAAGTGTGTGGAGCTCGT	59.822	50.0	7.83	0.0	39.72	4.18	F
600	617	0.242825	AGAATTCGTCGTCGCCTCAA	59.757	50.0	0.00	0.0	36.96	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2208	2227	1.285078	TCATCGTCCTCTTCCTCCTCA	59.715	52.381	0.0	0.0	0.0	3.86	R
2273	2295	3.499338	ACTCTTTGAATCACCAATGCCA	58.501	40.909	0.0	0.0	0.0	4.92	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
19	20	0.962356	AACATTTGAGGAGCTGGCCG	60.962	55.000	0.00	0.00	0.00	6.13
47	48	2.975536	CCCGCGGACAACTAGGAA	59.024	61.111	30.73	0.00	0.00	3.36
126	127	7.012989	AGTGTCGTATACTACTATCATGCACAA	59.987	37.037	8.79	0.00	0.00	3.33
141	142	5.236263	TCATGCACAAAATACTAGCGTATGG	59.764	40.000	0.00	0.00	36.48	2.74
147	148	7.117812	GCACAAAATACTAGCGTATGGTATCAT	59.882	37.037	0.00	0.00	34.72	2.45
148	149	8.988934	CACAAAATACTAGCGTATGGTATCATT	58.011	33.333	0.00	0.00	34.72	2.57
194	195	8.913487	AGTGATCTCATTTATTGTCATGCATA	57.087	30.769	0.00	0.00	0.00	3.14
195	196	9.346005	AGTGATCTCATTTATTGTCATGCATAA	57.654	29.630	0.00	0.00	0.00	1.90
209	210	8.702163	TGTCATGCATAACCATATTACGATAG	57.298	34.615	0.00	0.00	46.19	2.08
279	283	5.898174	ACATGCATGATACTTTCATTGTGG	58.102	37.500	32.75	0.18	42.62	4.17
282	286	3.491447	GCATGATACTTTCATTGTGGCCC	60.491	47.826	0.00	0.00	42.62	5.80
289	293	3.385111	ACTTTCATTGTGGCCCGTTTAAA	59.615	39.130	0.00	0.00	0.00	1.52
296	300	1.406180	GTGGCCCGTTTAAACAACACT	59.594	47.619	18.07	0.00	0.00	3.55
330	334	0.178068	ACAAAGTGTGTGGAGCTCGT	59.822	50.000	7.83	0.00	39.72	4.18
375	379	7.817641	TGTTTACCGATGCATTAATTACAACA	58.182	30.769	0.00	2.45	0.00	3.33
433	437	9.146984	CTGTTACATGCATTGATGAATTTTCTT	57.853	29.630	0.00	0.00	0.00	2.52
469	473	3.727723	GCAGCGATTTAATGCATCTCAAC	59.272	43.478	0.00	0.00	39.75	3.18
600	617	0.242825	AGAATTCGTCGTCGCCTCAA	59.757	50.000	0.00	0.00	36.96	3.02
607	624	2.507992	CGTCGCCTCAAGCTCCTG	60.508	66.667	0.00	0.00	40.39	3.86
609	626	1.890894	GTCGCCTCAAGCTCCTGTA	59.109	57.895	0.00	0.00	40.39	2.74
610	627	0.458716	GTCGCCTCAAGCTCCTGTAC	60.459	60.000	0.00	0.00	40.39	2.90
702	720	1.177401	GAGGAACAATGGGTGGAAGC	58.823	55.000	0.00	0.00	0.00	3.86
1458	1477	1.132643	GTCTCGTCGTGGCAGTTCTAT	59.867	52.381	0.00	0.00	0.00	1.98
1842	1861	4.537433	GAGCAGGCCGCCGAGATT	62.537	66.667	14.64	0.00	44.04	2.40
2208	2227	2.581354	GGTGAGCAGAGCGGTGAT	59.419	61.111	0.00	0.00	0.00	3.06
2459	2481	2.822399	CTCCCGCCCTGTACCATC	59.178	66.667	0.00	0.00	0.00	3.51
2480	2502	6.349115	CCATCTGCTAGCCACATAATTTCATC	60.349	42.308	13.29	0.00	0.00	2.92
2597	2620	0.106769	TTCTTTGCCAGACTGTGCCA	60.107	50.000	11.80	0.81	0.00	4.92
2625	2648	4.558095	GCACCAGCAGCCTGAATTATTATG	60.558	45.833	0.00	0.00	41.77	1.90
2629	2652	5.068198	CCAGCAGCCTGAATTATTATGTGTT	59.932	40.000	0.00	0.00	41.77	3.32
2630	2653	6.262944	CCAGCAGCCTGAATTATTATGTGTTA	59.737	38.462	0.00	0.00	41.77	2.41
2699	2724	2.927014	GCAGAACTAACTGACTGACCCG	60.927	54.545	0.00	0.00	39.94	5.28
2714	2739	5.124645	ACTGACCCGTGTTTTACAATGTTA	58.875	37.500	0.00	0.00	0.00	2.41
2715	2740	5.766174	ACTGACCCGTGTTTTACAATGTTAT	59.234	36.000	0.00	0.00	0.00	1.89
2730	2755	7.281040	ACAATGTTATATGAAGATTGCCTGG	57.719	36.000	10.27	0.00	35.18	4.45
2780	2809	2.521126	TGTCATGAACCTGTAGTCCGA	58.479	47.619	0.00	0.00	0.00	4.55
2921	2950	5.048224	AGCTGATTGTTGATGTTTCCTTCTG	60.048	40.000	0.00	0.00	0.00	3.02
3006	3037	4.024893	TGCACAGAGTCGAATGTTTCTTTC	60.025	41.667	0.00	0.00	0.00	2.62
3240	4285	8.916628	AAGGAAAATAGAGATCTAGCCAATTC	57.083	34.615	0.00	0.00	0.00	2.17
3241	4286	7.457561	AGGAAAATAGAGATCTAGCCAATTCC	58.542	38.462	13.68	13.68	33.36	3.01
3245	4290	2.371510	AGAGATCTAGCCAATTCCTGCC	59.628	50.000	0.00	0.00	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
167	168	8.146479	TGCATGACAATAAATGAGATCACTAC	57.854	34.615	0.00	0.00	0.00	2.73
194	195	9.915629	GAGAAGATTGACTATCGTAATATGGTT	57.084	33.333	0.00	0.00	38.36	3.67
195	196	9.303116	AGAGAAGATTGACTATCGTAATATGGT	57.697	33.333	0.00	0.00	38.36	3.55
204	205	7.834068	TGGAAAAAGAGAAGATTGACTATCG	57.166	36.000	0.00	0.00	38.36	2.92
279	283	3.117794	GGAAAGTGTTGTTTAAACGGGC	58.882	45.455	13.45	6.73	0.00	6.13
282	286	8.953990	CAGAAATAGGAAAGTGTTGTTTAAACG	58.046	33.333	13.45	0.00	0.00	3.60
289	293	8.514330	TTGTTACAGAAATAGGAAAGTGTTGT	57.486	30.769	0.00	0.00	0.00	3.32
296	300	8.402472	CACACACTTTGTTACAGAAATAGGAAA	58.598	33.333	0.00	0.00	35.67	3.13
348	352	9.938670	GTTGTAATTAATGCATCGGTAAACATA	57.061	29.630	0.00	0.00	0.00	2.29
375	379	8.631480	ATCATTTAGTGATCATGTATGCATGT	57.369	30.769	21.21	10.38	44.23	3.21
401	405	5.711506	TCATCAATGCATGTAACAGTCCTTT	59.288	36.000	0.00	0.00	0.00	3.11
433	437	9.632807	ATTAAATCGCTGCATACAAAAACTAAA	57.367	25.926	0.00	0.00	0.00	1.85
437	441	6.177822	GCATTAAATCGCTGCATACAAAAAC	58.822	36.000	0.00	0.00	35.96	2.43
440	444	4.991472	TGCATTAAATCGCTGCATACAAA	58.009	34.783	0.00	0.00	40.75	2.83
450	454	5.755813	AGATGTTGAGATGCATTAAATCGC	58.244	37.500	0.00	0.00	0.00	4.58
526	543	9.123902	GGTTTAAAGGTCCTGTCTTACTTTTTA	57.876	33.333	0.00	0.00	33.79	1.52
529	546	5.761726	CGGTTTAAAGGTCCTGTCTTACTTT	59.238	40.000	0.00	0.00	35.71	2.66
530	547	5.303165	CGGTTTAAAGGTCCTGTCTTACTT	58.697	41.667	0.00	0.00	0.00	2.24
531	548	4.262765	CCGGTTTAAAGGTCCTGTCTTACT	60.263	45.833	0.00	0.00	0.00	2.24
532	549	3.999001	CCGGTTTAAAGGTCCTGTCTTAC	59.001	47.826	0.00	0.00	0.00	2.34
600	617	2.294078	GCAGGGTGGTACAGGAGCT	61.294	63.158	0.00	0.00	41.80	4.09
607	624	4.934989	GCACTAGCAGGGTGGTAC	57.065	61.111	0.00	0.00	41.58	3.34
748	766	1.899142	GGTATTTTGGGCTTCCTGCAA	59.101	47.619	0.00	0.00	45.15	4.08
1635	1654	2.088180	GTCGGACGACTCAGACGAT	58.912	57.895	16.81	0.00	41.57	3.73
1777	1796	1.352156	GCCTCACCAAAGCGTCGTAG	61.352	60.000	0.00	0.00	0.00	3.51
2018	2037	2.967599	TCTCGATGTGGAATCTGGTG	57.032	50.000	0.00	0.00	0.00	4.17
2131	2150	1.525619	GTACTGATAATGCGGGCGAAC	59.474	52.381	0.00	0.00	0.00	3.95
2204	2223	1.407258	CGTCCTCTTCCTCCTCATCAC	59.593	57.143	0.00	0.00	0.00	3.06
2208	2227	1.285078	TCATCGTCCTCTTCCTCCTCA	59.715	52.381	0.00	0.00	0.00	3.86
2273	2295	3.499338	ACTCTTTGAATCACCAATGCCA	58.501	40.909	0.00	0.00	0.00	4.92
2459	2481	5.996513	AGAGATGAAATTATGTGGCTAGCAG	59.003	40.000	18.24	0.00	0.00	4.24
2480	2502	9.575783	GGTGTTCTTGTAACTAGATAAAGAGAG	57.424	37.037	0.00	0.00	0.00	3.20
2625	2648	8.228464	GCTGGTGATAAGAGTACTTTTTAACAC	58.772	37.037	20.86	20.86	37.53	3.32
2629	2652	8.154856	ACAAGCTGGTGATAAGAGTACTTTTTA	58.845	33.333	3.70	3.88	37.53	1.52
2630	2653	6.998673	ACAAGCTGGTGATAAGAGTACTTTTT	59.001	34.615	3.70	1.69	37.53	1.94
2647	2671	2.238942	TCACACACAGTACAAGCTGG	57.761	50.000	0.00	0.00	40.59	4.85
2714	2739	4.816385	CGTAACACCAGGCAATCTTCATAT	59.184	41.667	0.00	0.00	0.00	1.78
2715	2740	4.188462	CGTAACACCAGGCAATCTTCATA	58.812	43.478	0.00	0.00	0.00	2.15
2730	2755	1.128513	GCAAAGGCAAAGCGTAACAC	58.871	50.000	0.00	0.00	40.72	3.32
2921	2950	3.690422	TGCAGAAAACGTCAACAATCAC	58.310	40.909	0.00	0.00	0.00	3.06
3022	3054	6.930731	ACAACTGTTGGCTTTTCTTCTTTTA	58.069	32.000	23.15	0.00	34.12	1.52
3023	3055	5.793817	ACAACTGTTGGCTTTTCTTCTTTT	58.206	33.333	23.15	0.00	34.12	2.27
3024	3056	5.405935	ACAACTGTTGGCTTTTCTTCTTT	57.594	34.783	23.15	0.00	34.12	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.