AutoCloner

Multiple sequence alignment - TraesCS3A01G068800

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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	TraesCS3A01G068800	chr3A	100.000	5054	0	0	1	5054	41148964	41154017	0.000000e+00	9334
1	TraesCS3A01G068800	chr3A	88.539	3272	340	22	825	4077	41047933	41051188	0.000000e+00	3932
2	TraesCS3A01G068800	chr3A	86.417	2746	349	17	880	3620	41616605	41619331	0.000000e+00	2983
3	TraesCS3A01G068800	chr3A	96.673	571	14	2	1	570	80390548	80389982	0.000000e+00	944
4	TraesCS3A01G068800	chr3A	95.752	565	18	3	1	564	582960061	582960620	0.000000e+00	905
5	TraesCS3A01G068800	chr3A	84.021	970	113	12	3338	4298	41362908	41363844	0.000000e+00	894
6	TraesCS3A01G068800	chr3A	100.000	190	0	0	4493	4682	49479023	49479212	8.050000e-93	351
7	TraesCS3A01G068800	chr3A	100.000	185	0	0	4499	4683	83748868	83748684	4.850000e-90	342
8	TraesCS3A01G068800	chr3A	91.071	168	10	3	4723	4890	41613072	41613234	6.590000e-54	222
9	TraesCS3A01G068800	chr3A	83.505	194	18	9	4704	4889	41364244	41364431	8.700000e-38	169
10	TraesCS3A01G068800	chr3A	85.714	112	11	3	4749	4860	41220247	41220353	4.140000e-21	113
11	TraesCS3A01G068800	chr3A	85.185	108	9	4	4762	4863	41080553	41080659	2.490000e-18	104
12	TraesCS3A01G068800	chr3B	90.094	3190	291	15	978	4156	52426307	52429482	0.000000e+00	4117
13	TraesCS3A01G068800	chr3B	85.487	3211	431	31	875	4070	51243213	51246403	0.000000e+00	3315
14	TraesCS3A01G068800	chr3B	84.728	3156	443	31	910	4050	52777839	52774708	0.000000e+00	3121
15	TraesCS3A01G068800	chr3B	84.019	3185	469	34	884	4054	51915870	51919028	0.000000e+00	3025
16	TraesCS3A01G068800	chr3B	85.066	2866	395	18	1325	4171	52551643	52554494	0.000000e+00	2891
17	TraesCS3A01G068800	chr3B	82.312	3149	519	26	910	4048	52742732	52739612	0.000000e+00	2695
18	TraesCS3A01G068800	chr3B	97.980	198	4	0	4499	4696	642821353	642821156	1.350000e-90	344
19	TraesCS3A01G068800	chr3B	88.716	257	17	7	3925	4171	52407464	52407718	2.290000e-78	303
20	TraesCS3A01G068800	chr3B	94.709	189	9	1	4316	4503	52554583	52554771	4.950000e-75	292
21	TraesCS3A01G068800	chr3B	90.521	211	10	7	4680	4890	52555034	52555234	2.320000e-68	270
22	TraesCS3A01G068800	chr3B	96.815	157	5	0	4345	4501	52429536	52429692	3.880000e-66	263
23	TraesCS3A01G068800	chr3B	95.161	124	4	1	4767	4890	52417695	52417816	1.440000e-45	195
24	TraesCS3A01G068800	chr3B	86.705	173	16	3	4315	4486	51246651	51246817	8.640000e-43	185
25	TraesCS3A01G068800	chr3B	90.654	107	5	2	4197	4298	52554492	52554598	2.450000e-28	137
26	TraesCS3A01G068800	chr3D	82.592	3194	507	36	874	4051	30278206	30281366	0.000000e+00	2772
27	TraesCS3A01G068800	chr7A	96.466	566	18	2	1	564	677891143	677890578	0.000000e+00	933
28	TraesCS3A01G068800	chr6A	96.466	566	14	3	1	564	566898315	566898876	0.000000e+00	929
29	TraesCS3A01G068800	chr6A	96.113	566	14	4	1	564	596390934	596390375	0.000000e+00	917
30	TraesCS3A01G068800	chr6A	95.767	567	22	2	1	565	21166477	21167043	0.000000e+00	913
31	TraesCS3A01G068800	chr2A	96.460	565	15	2	1	564	686738459	686739019	0.000000e+00	928
32	TraesCS3A01G068800	chr2A	98.469	196	3	0	4493	4688	377320213	377320018	3.750000e-91	346
33	TraesCS3A01G068800	chr4A	96.134	569	16	3	1	567	506147659	506147095	0.000000e+00	924
34	TraesCS3A01G068800	chr5A	95.606	569	22	2	1	567	6177623	6177056	0.000000e+00	909
35	TraesCS3A01G068800	chr7B	99.487	195	0	1	4499	4693	395552189	395552382	2.240000e-93	353
36	TraesCS3A01G068800	chr7B	97.573	206	2	3	4498	4701	413255440	413255236	2.900000e-92	350
37	TraesCS3A01G068800	chr6B	98.974	195	1	1	4499	4692	308522627	308522821	1.040000e-91	348
38	TraesCS3A01G068800	chr1B	97.990	199	2	2	4485	4683	187703013	187703209	1.350000e-90	344
39	TraesCS3A01G068800	chr4B	96.602	206	5	2	4499	4702	146013653	146013448	1.740000e-89	340

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	TraesCS3A01G068800	chr3A	41148964	41154017	5053	False	9334.0	9334	100.0000	1	5054	1	chr3A.!!$F3	5053
1	TraesCS3A01G068800	chr3A	41047933	41051188	3255	False	3932.0	3932	88.5390	825	4077	1	chr3A.!!$F1	3252
2	TraesCS3A01G068800	chr3A	41613072	41619331	6259	False	1602.5	2983	88.7440	880	4890	2	chr3A.!!$F8	4010
3	TraesCS3A01G068800	chr3A	80389982	80390548	566	True	944.0	944	96.6730	1	570	1	chr3A.!!$R1	569
4	TraesCS3A01G068800	chr3A	582960061	582960620	559	False	905.0	905	95.7520	1	564	1	chr3A.!!$F6	563
5	TraesCS3A01G068800	chr3A	41362908	41364431	1523	False	531.5	894	83.7630	3338	4889	2	chr3A.!!$F7	1551
6	TraesCS3A01G068800	chr3B	52774708	52777839	3131	True	3121.0	3121	84.7280	910	4050	1	chr3B.!!$R2	3140
7	TraesCS3A01G068800	chr3B	51915870	51919028	3158	False	3025.0	3025	84.0190	884	4054	1	chr3B.!!$F1	3170
8	TraesCS3A01G068800	chr3B	52739612	52742732	3120	True	2695.0	2695	82.3120	910	4048	1	chr3B.!!$R1	3138
9	TraesCS3A01G068800	chr3B	52426307	52429692	3385	False	2190.0	4117	93.4545	978	4501	2	chr3B.!!$F5	3523
10	TraesCS3A01G068800	chr3B	51243213	51246817	3604	False	1750.0	3315	86.0960	875	4486	2	chr3B.!!$F4	3611
11	TraesCS3A01G068800	chr3B	52551643	52555234	3591	False	897.5	2891	90.2375	1325	4890	4	chr3B.!!$F6	3565
12	TraesCS3A01G068800	chr3D	30278206	30281366	3160	False	2772.0	2772	82.5920	874	4051	1	chr3D.!!$F1	3177
13	TraesCS3A01G068800	chr7A	677890578	677891143	565	True	933.0	933	96.4660	1	564	1	chr7A.!!$R1	563
14	TraesCS3A01G068800	chr6A	566898315	566898876	561	False	929.0	929	96.4660	1	564	1	chr6A.!!$F2	563
15	TraesCS3A01G068800	chr6A	596390375	596390934	559	True	917.0	917	96.1130	1	564	1	chr6A.!!$R1	563
16	TraesCS3A01G068800	chr6A	21166477	21167043	566	False	913.0	913	95.7670	1	565	1	chr6A.!!$F1	564
17	TraesCS3A01G068800	chr2A	686738459	686739019	560	False	928.0	928	96.4600	1	564	1	chr2A.!!$F1	563
18	TraesCS3A01G068800	chr4A	506147095	506147659	564	True	924.0	924	96.1340	1	567	1	chr4A.!!$R1	566
19	TraesCS3A01G068800	chr5A	6177056	6177623	567	True	909.0	909	95.6060	1	567	1	chr5A.!!$R1	566

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
748	754	0.837272	GCTTCTATGCACCAGGGGTA	59.163	55.000	0.00	0.0	32.11	3.69	F
1128	3793	0.666274	TGTTGCGGCGAGTAGAACTG	60.666	55.000	12.98	0.0	0.00	3.16	F
2036	4702	2.885135	TGGAGGAGCATGAACATTGT	57.115	45.000	0.00	0.0	0.00	2.71	F
3855	6528	1.005450	GGGTATTGTGAAGGCCTGGAA	59.995	52.381	5.69	0.0	0.00	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1970	4636	5.169992	TGACATGAGATCAACTTGATGGT	57.830	39.13	9.08	0.00	37.20	3.55	R
2818	5485	1.025041	GAGCCAATGGATTCCGGAAC	58.975	55.00	21.56	13.35	0.00	3.62	R
3927	6600	0.102844	GCTGCTGCAAACTGTCCAAA	59.897	50.00	11.11	0.00	39.41	3.28	R
5000	7881	0.036164	AGGCTTGGCGACACATGTTA	59.964	50.00	0.00	0.00	42.67	2.41	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
394	399	4.344359	AAATGTATTTTGCCGGGTTTGT	57.656	36.364	2.18	0.00	0.00	2.83
493	498	3.497879	CCGCGGGGATGAAAAGAC	58.502	61.111	20.10	0.00	34.06	3.01
571	577	3.817084	CCGTTGCCATCATGAATCATACT	59.183	43.478	0.00	0.00	0.00	2.12
572	578	4.276678	CCGTTGCCATCATGAATCATACTT	59.723	41.667	0.00	0.00	0.00	2.24
574	580	6.365839	CGTTGCCATCATGAATCATACTTAC	58.634	40.000	0.00	0.00	0.00	2.34
577	583	7.443259	TGCCATCATGAATCATACTTACATG	57.557	36.000	0.00	0.00	39.40	3.21
584	590	9.875691	TCATGAATCATACTTACATGTATAGCC	57.124	33.333	6.36	0.00	39.18	3.93
585	591	9.657419	CATGAATCATACTTACATGTATAGCCA	57.343	33.333	6.36	0.59	35.22	4.75
587	593	9.710900	TGAATCATACTTACATGTATAGCCAAG	57.289	33.333	6.36	4.33	32.48	3.61
592	598	9.710900	CATACTTACATGTATAGCCAAGATGAA	57.289	33.333	6.36	0.00	32.48	2.57
625	631	8.642432	AGTAACATTTCTAGTCTAGCATATGCA	58.358	33.333	28.62	13.96	45.16	3.96
627	633	7.060383	ACATTTCTAGTCTAGCATATGCACT	57.940	36.000	28.62	23.51	45.16	4.40
628	634	6.927936	ACATTTCTAGTCTAGCATATGCACTG	59.072	38.462	28.62	17.28	45.16	3.66
630	636	6.715347	TTCTAGTCTAGCATATGCACTGAA	57.285	37.500	28.62	21.55	45.16	3.02
631	637	6.324561	TCTAGTCTAGCATATGCACTGAAG	57.675	41.667	28.62	17.14	45.16	3.02
632	638	4.333913	AGTCTAGCATATGCACTGAAGG	57.666	45.455	28.62	10.44	45.16	3.46
633	639	3.708631	AGTCTAGCATATGCACTGAAGGT	59.291	43.478	28.62	8.65	45.16	3.50
635	641	2.048444	AGCATATGCACTGAAGGTGG	57.952	50.000	28.62	0.00	45.44	4.61
640	646	3.942351	TGCACTGAAGGTGGATCTG	57.058	52.632	0.00	0.00	45.44	2.90
642	648	1.002430	TGCACTGAAGGTGGATCTGAC	59.998	52.381	0.00	0.00	45.44	3.51
643	649	1.002430	GCACTGAAGGTGGATCTGACA	59.998	52.381	0.00	0.00	45.44	3.58
646	652	3.499918	CACTGAAGGTGGATCTGACAAAC	59.500	47.826	0.00	0.00	41.90	2.93
647	653	3.077359	CTGAAGGTGGATCTGACAAACC	58.923	50.000	0.00	0.00	0.00	3.27
648	654	2.441375	TGAAGGTGGATCTGACAAACCA	59.559	45.455	7.10	0.00	33.13	3.67
651	657	3.909732	AGGTGGATCTGACAAACCAAAA	58.090	40.909	7.10	0.00	34.11	2.44

Showing 1 to 25 of 425 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	55	5.917462	TGCTCTAGTTATGCTGCTGAAATA	58.083	37.500	0.00	0.00	0.00	1.40
394	399	4.006357	CCCGAACCCGAAACCCGA	62.006	66.667	0.00	0.00	41.76	5.14
599	605	8.642432	TGCATATGCTAGACTAGAAATGTTACT	58.358	33.333	27.13	0.00	42.66	2.24
600	606	8.704234	GTGCATATGCTAGACTAGAAATGTTAC	58.296	37.037	27.13	8.01	42.66	2.50
601	607	8.642432	AGTGCATATGCTAGACTAGAAATGTTA	58.358	33.333	27.13	0.00	42.66	2.41
602	608	7.440556	CAGTGCATATGCTAGACTAGAAATGTT	59.559	37.037	27.13	0.00	42.66	2.71
603	609	6.927936	CAGTGCATATGCTAGACTAGAAATGT	59.072	38.462	27.13	1.92	42.66	2.71
605	611	7.295322	TCAGTGCATATGCTAGACTAGAAAT	57.705	36.000	27.13	8.25	42.66	2.17
606	612	6.715347	TCAGTGCATATGCTAGACTAGAAA	57.285	37.500	27.13	7.45	42.66	2.52
607	613	6.239148	CCTTCAGTGCATATGCTAGACTAGAA	60.239	42.308	27.13	21.80	42.66	2.10
608	614	5.242615	CCTTCAGTGCATATGCTAGACTAGA	59.757	44.000	27.13	17.52	42.66	2.43
609	615	5.010516	ACCTTCAGTGCATATGCTAGACTAG	59.989	44.000	27.13	16.30	42.66	2.57
612	618	3.806521	CACCTTCAGTGCATATGCTAGAC	59.193	47.826	27.13	17.41	40.28	2.59
613	619	3.181462	CCACCTTCAGTGCATATGCTAGA	60.181	47.826	27.13	18.52	45.83	2.43
615	621	2.771372	TCCACCTTCAGTGCATATGCTA	59.229	45.455	27.13	11.93	45.83	3.49
616	622	1.561076	TCCACCTTCAGTGCATATGCT	59.439	47.619	27.13	6.44	45.83	3.79
618	624	3.813724	CAGATCCACCTTCAGTGCATATG	59.186	47.826	0.00	0.00	45.83	1.78
619	625	3.713248	TCAGATCCACCTTCAGTGCATAT	59.287	43.478	0.00	0.00	45.83	1.78
620	626	3.106827	TCAGATCCACCTTCAGTGCATA	58.893	45.455	0.00	0.00	45.83	3.14
621	627	1.911357	TCAGATCCACCTTCAGTGCAT	59.089	47.619	0.00	0.00	45.83	3.96
622	628	1.002430	GTCAGATCCACCTTCAGTGCA	59.998	52.381	0.00	0.00	45.83	4.57
623	629	1.002430	TGTCAGATCCACCTTCAGTGC	59.998	52.381	0.00	0.00	45.83	4.40
624	630	3.407424	TTGTCAGATCCACCTTCAGTG	57.593	47.619	0.00	0.00	46.83	3.66
625	631	3.496870	GGTTTGTCAGATCCACCTTCAGT	60.497	47.826	0.00	0.00	0.00	3.41
627	633	2.441375	TGGTTTGTCAGATCCACCTTCA	59.559	45.455	0.00	0.00	0.00	3.02

Showing 1 to 25 of 426 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.