AutoCloner

Multiple sequence alignment - TraesCS4A01G209100

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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	TraesCS4A01G209100	chr4A	100.000	3320	0	0	1	3320	502358930	502355611	0.000000e+00	6131
1	TraesCS4A01G209100	chr4B	92.260	3230	136	40	1	3177	126731200	126728032	0.000000e+00	4475
2	TraesCS4A01G209100	chr4B	94.898	98	2	2	3225	3320	126728030	126727934	2.060000e-32	150
3	TraesCS4A01G209100	chr4D	96.749	2645	57	10	695	3320	89931292	89928658	0.000000e+00	4381
4	TraesCS4A01G209100	chr4D	92.878	337	23	1	329	665	89931627	89931292	3.850000e-134	488
5	TraesCS4A01G209100	chr4D	89.251	307	16	5	1	307	89932125	89931836	5.230000e-98	368
6	TraesCS4A01G209100	chr1A	85.508	1594	190	20	832	2397	586954261	586952681	0.000000e+00	1626
7	TraesCS4A01G209100	chr1A	85.283	265	22	7	1040	1296	586988851	586988596	1.180000e-64	257
8	TraesCS4A01G209100	chr1B	85.383	1594	193	23	832	2397	679749437	679747856	0.000000e+00	1616
9	TraesCS4A01G209100	chr1D	85.174	1612	186	23	832	2397	487953461	487951857	0.000000e+00	1604

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	TraesCS4A01G209100	chr4A	502355611	502358930	3319	True	6131.000000	6131	100.000000	1	3320	1	chr4A.!!$R1	3319
1	TraesCS4A01G209100	chr4B	126727934	126731200	3266	True	2312.500000	4475	93.579000	1	3320	2	chr4B.!!$R1	3319
2	TraesCS4A01G209100	chr4D	89928658	89932125	3467	True	1745.666667	4381	92.959333	1	3320	3	chr4D.!!$R1	3319
3	TraesCS4A01G209100	chr1A	586952681	586954261	1580	True	1626.000000	1626	85.508000	832	2397	1	chr1A.!!$R1	1565
4	TraesCS4A01G209100	chr1B	679747856	679749437	1581	True	1616.000000	1616	85.383000	832	2397	1	chr1B.!!$R1	1565
5	TraesCS4A01G209100	chr1D	487951857	487953461	1604	True	1604.000000	1604	85.174000	832	2397	1	chr1D.!!$R1	1565

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
326	348	0.030092	CCACCTCCCCCTAGATGGAA	60.030	60.0	38.35	3.53	F
422	632	0.827368	AACTCCCGCAAAAGCCAAAA	59.173	45.0	0.00	2.44	F
423	633	0.827368	ACTCCCGCAAAAGCCAAAAA	59.173	45.0	0.00	1.94	F
595	805	0.981183	ACCGCAGTGACAAATCCCTA	59.019	50.0	0.00	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1803	2076	1.062658	TCCCTCCTCAGATCATGCTCA	60.063	52.381	0.00	4.26	R
2001	2274	1.153168	ATGCGGATTGAACCTCCCG	60.153	57.895	44.34	5.14	R
2247	2520	2.024414	AGCTGAAGTTCCAAACGCTTT	58.976	42.857	36.23	3.51	R
2538	2822	6.566079	AATGATCCTCAAAGATACCTCACA	57.434	37.500	0.00	3.58	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
87	88	1.553690	GGAGGTTGGCAGGTGAGCTA	61.554	60.000	0.00	0.00	34.17	3.32
117	118	3.074836	AGTTCCCGTAAAAATCTTCCCCA	59.925	43.478	0.00	0.00	0.00	4.96
224	246	4.748679	GACGGTCGGTGTCGTCGG	62.749	72.222	0.00	0.00	44.55	4.79
266	288	2.622011	GCGAATTCCGGTTGTGGCA	61.622	57.895	0.00	0.00	39.04	4.92
289	311	3.064207	GCTGACGTGACAGTTTTATGGA	58.936	45.455	0.00	0.00	39.73	3.41
310	332	0.335019	ATGTTTAGGGGAAGGGCCAC	59.665	55.000	6.18	0.00	41.99	5.01
326	348	0.030092	CCACCTCCCCCTAGATGGAA	60.030	60.000	0.00	0.00	38.35	3.53
362	571	5.932455	TGATTATACGGGGTCCCTTAAAAG	58.068	41.667	8.15	0.00	0.00	2.27
410	620	3.863606	TTTTTGGCCCAACTCCCG	58.136	55.556	0.00	0.00	0.00	5.14
418	628	2.650778	CCAACTCCCGCAAAAGCC	59.349	61.111	0.00	0.00	0.00	4.35
419	629	2.199652	CCAACTCCCGCAAAAGCCA	61.200	57.895	0.00	0.00	0.00	4.75
422	632	0.827368	AACTCCCGCAAAAGCCAAAA	59.173	45.000	0.00	0.00	0.00	2.44
423	633	0.827368	ACTCCCGCAAAAGCCAAAAA	59.173	45.000	0.00	0.00	0.00	1.94
460	670	2.350522	GAACTGTTGGTGATGCTCGAT	58.649	47.619	0.00	0.00	0.00	3.59
468	678	2.700371	TGGTGATGCTCGATGATTACCT	59.300	45.455	14.93	0.00	31.13	3.08
595	805	0.981183	ACCGCAGTGACAAATCCCTA	59.019	50.000	0.00	0.00	0.00	3.53
634	844	2.480073	CCTGATTGCCTAATTTGGTGCG	60.480	50.000	7.77	0.00	0.00	5.34
645	855	2.163818	TTTGGTGCGGTTCAGAGTAG	57.836	50.000	0.00	0.00	0.00	2.57
659	869	7.411588	CGGTTCAGAGTAGTGTATTTTAAGTGC	60.412	40.741	0.00	0.00	0.00	4.40
667	877	5.491982	AGTGTATTTTAAGTGCTCCAGAGG	58.508	41.667	0.00	0.00	0.00	3.69
670	880	2.743636	TTTAAGTGCTCCAGAGGTCG	57.256	50.000	0.00	0.00	0.00	4.79
677	887	3.008049	AGTGCTCCAGAGGTCGTTTTAAT	59.992	43.478	0.00	0.00	0.00	1.40
703	913	1.454201	TGCGATTATTGCCGTTCCAA	58.546	45.000	1.53	0.00	0.00	3.53
912	1146	6.064060	TCTCCAAATTTACTATGCAGGATGG	58.936	40.000	0.00	0.00	35.86	3.51
1073	1307	2.607635	GTGGTATGAATGTGCACGGTAG	59.392	50.000	13.13	0.00	0.00	3.18
1608	1881	1.005037	TCGTGGTACTGCTTGCAGG	60.005	57.895	23.98	7.58	0.00	4.85
1803	2076	6.951971	ACAGGTTGCTCTTAGATGTAAAGAT	58.048	36.000	0.00	0.00	32.72	2.40
1851	2124	1.767681	GCAGATCCTGAAGAGGGTGAT	59.232	52.381	0.00	0.00	40.25	3.06
2001	2274	1.871039	TCAAGCTCAAACGGTGTTAGC	59.129	47.619	0.00	0.00	0.00	3.09
2280	2553	5.470098	GGAACTTCAGCTAAGACACAATGAA	59.530	40.000	9.14	0.00	38.67	2.57
2514	2798	5.806366	TTACATGCACTGATCTCATGTTG	57.194	39.130	20.05	9.86	45.86	3.33
2538	2822	7.264947	TGTAGTTCATGTGATATTCGTGATGT	58.735	34.615	0.00	0.79	32.07	3.06
2546	2830	5.126384	TGTGATATTCGTGATGTGTGAGGTA	59.874	40.000	0.00	0.00	0.00	3.08
2658	2953	1.073603	TCATGCACATGGTGTTCCTGA	59.926	47.619	10.58	0.00	39.24	3.86
2676	2971	5.023452	TCCTGAGTGATACATAGTTGGTGT	58.977	41.667	0.00	0.00	0.00	4.16
2741	3036	2.283298	CATCAAAGACGCATGTAGCCT	58.717	47.619	0.00	0.00	41.38	4.58
2937	3232	6.715347	AGGGTTTCACTATCCAAATATTGC	57.285	37.500	0.00	0.00	0.00	3.56
2945	3240	1.832883	TCCAAATATTGCGGTGCAGT	58.167	45.000	0.00	0.00	40.61	4.40
3006	3301	1.944709	GTGGTTAGCTTCACACGGTTT	59.055	47.619	0.00	0.00	34.32	3.27
3158	3462	6.011981	ACTCCCAAGTCCCAATAAGTGAATTA	60.012	38.462	0.00	0.00	0.00	1.40
3215	3519	0.749818	TGGTTGACATGTGCGTTGGT	60.750	50.000	1.15	0.00	0.00	3.67
3283	3589	5.408356	TCTCGCATAACCAGTCTACTTTTC	58.592	41.667	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	88	4.722361	TTTTTACGGGAACTGCAAAAGT	57.278	36.364	0.00	0.00	40.53	2.66
251	273	2.914908	GCGTGCCACAACCGGAATT	61.915	57.895	9.46	0.00	0.00	2.17
277	299	7.013834	TCCCCTAAACATTTCCATAAAACTGT	58.986	34.615	0.00	0.00	0.00	3.55
289	311	1.435168	TGGCCCTTCCCCTAAACATTT	59.565	47.619	0.00	0.00	0.00	2.32
310	332	3.172208	CCTTCCATCTAGGGGGAGG	57.828	63.158	12.69	12.69	38.24	4.30
326	348	1.912862	ATAATCAGCCCAACTCCCCT	58.087	50.000	0.00	0.00	0.00	4.79
422	632	3.167485	GTTCCCCTTTCCCCGTAATTTT	58.833	45.455	0.00	0.00	0.00	1.82
423	633	2.380932	AGTTCCCCTTTCCCCGTAATTT	59.619	45.455	0.00	0.00	0.00	1.82
424	634	1.997791	AGTTCCCCTTTCCCCGTAATT	59.002	47.619	0.00	0.00	0.00	1.40
425	635	1.283905	CAGTTCCCCTTTCCCCGTAAT	59.716	52.381	0.00	0.00	0.00	1.89
430	640	0.541998	CCAACAGTTCCCCTTTCCCC	60.542	60.000	0.00	0.00	0.00	4.81
634	844	7.603024	AGCACTTAAAATACACTACTCTGAACC	59.397	37.037	0.00	0.00	0.00	3.62
645	855	5.246307	ACCTCTGGAGCACTTAAAATACAC	58.754	41.667	0.00	0.00	0.00	2.90
659	869	4.003648	AGCAATTAAAACGACCTCTGGAG	58.996	43.478	0.00	0.00	0.00	3.86
667	877	4.939948	TCGCAAAAGCAATTAAAACGAC	57.060	36.364	0.00	0.00	0.00	4.34
670	880	7.216130	GGCAATAATCGCAAAAGCAATTAAAAC	59.784	33.333	0.00	0.00	0.00	2.43
677	887	2.257894	CGGCAATAATCGCAAAAGCAA	58.742	42.857	0.00	0.00	0.00	3.91
703	913	2.526888	TGTAACTCCGATCTCCAGGT	57.473	50.000	0.00	0.00	0.00	4.00
912	1146	4.388773	TGTCACATGTCTTCGCTTCAATAC	59.611	41.667	0.00	0.00	0.00	1.89
1057	1291	1.656652	GAGCTACCGTGCACATTCAT	58.343	50.000	18.64	0.00	34.99	2.57
1093	1327	5.827797	TGAATAGCTGTTTTCCTGAGTTTGT	59.172	36.000	0.00	0.00	0.00	2.83
1097	1331	4.762251	GGTTGAATAGCTGTTTTCCTGAGT	59.238	41.667	0.00	0.00	0.00	3.41
1608	1881	1.963515	AGTGCTGGATTTTCCACAACC	59.036	47.619	0.00	0.00	42.67	3.77
1671	1944	6.292596	GCTTAGAGTTCAATATCTTCCTTGCG	60.293	42.308	0.00	0.00	0.00	4.85
1803	2076	1.062658	TCCCTCCTCAGATCATGCTCA	60.063	52.381	0.00	0.00	0.00	4.26
2001	2274	1.153168	ATGCGGATTGAACCTCCCG	60.153	57.895	0.00	0.00	44.34	5.14
2247	2520	2.024414	AGCTGAAGTTCCAAACGCTTT	58.976	42.857	0.00	0.00	36.23	3.51
2514	2798	7.222805	ACACATCACGAATATCACATGAACTAC	59.777	37.037	0.00	0.00	0.00	2.73
2538	2822	6.566079	AATGATCCTCAAAGATACCTCACA	57.434	37.500	0.00	0.00	0.00	3.58
2546	2830	8.534496	CAAAAACCCTTAATGATCCTCAAAGAT	58.466	33.333	0.00	0.00	0.00	2.40
2582	2869	7.897575	AGTTGATGATCTAACTGACACTTTC	57.102	36.000	8.69	0.00	35.91	2.62
2685	2980	9.314133	AGGGTAATGAAAGCTTCTATTTTCTTT	57.686	29.630	0.00	0.00	35.85	2.52
2848	3143	3.331591	TCCGGGCACTATCACTATAGGTA	59.668	47.826	0.00	0.00	39.63	3.08
2909	3204	9.574516	AATATTTGGATAGTGAAACCCTATGTC	57.425	33.333	0.00	0.00	37.80	3.06
3006	3301	1.681793	GCCCAGAGAGATACGCTTACA	59.318	52.381	0.00	0.00	0.00	2.41
3158	3462	8.290325	GCAAAACTAAGCAATAAGTAACAGACT	58.710	33.333	0.00	0.00	41.56	3.24
3215	3519	5.512060	GCATCTCTTCATAGCCTACCAATCA	60.512	44.000	0.00	0.00	0.00	2.57
3283	3589	4.687948	CAGCCGGTCTATCATTTGATACAG	59.312	45.833	1.90	0.00	36.05	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.