AutoCloner

Multiple sequence alignment - TraesCS2B01G252700

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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	TraesCS2B01G252700	chr2B	100.000	2471	0	0	1	2471	272614552	272617022	0.000000e+00	4564.0
1	TraesCS2B01G252700	chr2B	96.467	2434	79	7	1	2432	474916662	474914234	0.000000e+00	4012.0
2	TraesCS2B01G252700	chr5D	97.290	2435	62	4	1	2432	503226442	503224009	0.000000e+00	4128.0
3	TraesCS2B01G252700	chr5D	97.003	2436	68	5	1	2432	503270102	503272536	0.000000e+00	4089.0
4	TraesCS2B01G252700	chr5D	96.799	2437	72	6	1	2432	503236759	503234324	0.000000e+00	4063.0
5	TraesCS2B01G252700	chr5D	91.071	56	5	0	2416	2471	492207674	492207729	2.640000e-10	76.8
6	TraesCS2B01G252700	chr3A	97.125	2435	65	5	1	2432	66009399	66011831	0.000000e+00	4104.0
7	TraesCS2B01G252700	chrUn	96.713	2434	76	4	1	2432	216510384	216512815	0.000000e+00	4048.0
8	TraesCS2B01G252700	chrUn	96.713	2434	76	4	1	2432	286272999	286270568	0.000000e+00	4048.0
9	TraesCS2B01G252700	chr3B	96.675	2436	77	4	1	2432	201535253	201532818	0.000000e+00	4047.0
10	TraesCS2B01G252700	chr1B	96.550	2435	76	8	1	2432	633745675	633748104	0.000000e+00	4024.0
11	TraesCS2B01G252700	chr1B	92.727	55	4	0	2417	2471	159870654	159870708	2.040000e-11	80.5
12	TraesCS2B01G252700	chr7A	96.078	51	2	0	2421	2471	468893978	468893928	1.570000e-12	84.2
13	TraesCS2B01G252700	chr7A	96.078	51	1	1	2422	2471	643390299	643390249	5.660000e-12	82.4
14	TraesCS2B01G252700	chr1A	97.917	48	1	0	2424	2471	529765914	529765867	1.570000e-12	84.2
15	TraesCS2B01G252700	chr5A	92.982	57	1	3	2418	2471	647949327	647949271	2.040000e-11	80.5
16	TraesCS2B01G252700	chr3D	92.857	56	1	3	2419	2471	556586769	556586824	7.330000e-11	78.7
17	TraesCS2B01G252700	chr5B	91.071	56	5	0	2416	2471	210384838	210384893	2.640000e-10	76.8
18	TraesCS2B01G252700	chr2A	90.164	61	3	3	2412	2471	258014943	258014885	2.640000e-10	76.8

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	TraesCS2B01G252700	chr2B	272614552	272617022	2470	False	4564	4564	100.000	1	2471	1	chr2B.!!$F1	2470
1	TraesCS2B01G252700	chr2B	474914234	474916662	2428	True	4012	4012	96.467	1	2432	1	chr2B.!!$R1	2431
2	TraesCS2B01G252700	chr5D	503224009	503226442	2433	True	4128	4128	97.290	1	2432	1	chr5D.!!$R1	2431
3	TraesCS2B01G252700	chr5D	503270102	503272536	2434	False	4089	4089	97.003	1	2432	1	chr5D.!!$F2	2431
4	TraesCS2B01G252700	chr5D	503234324	503236759	2435	True	4063	4063	96.799	1	2432	1	chr5D.!!$R2	2431
5	TraesCS2B01G252700	chr3A	66009399	66011831	2432	False	4104	4104	97.125	1	2432	1	chr3A.!!$F1	2431
6	TraesCS2B01G252700	chrUn	216510384	216512815	2431	False	4048	4048	96.713	1	2432	1	chrUn.!!$F1	2431
7	TraesCS2B01G252700	chrUn	286270568	286272999	2431	True	4048	4048	96.713	1	2432	1	chrUn.!!$R1	2431
8	TraesCS2B01G252700	chr3B	201532818	201535253	2435	True	4047	4047	96.675	1	2432	1	chr3B.!!$R1	2431
9	TraesCS2B01G252700	chr1B	633745675	633748104	2429	False	4024	4024	96.550	1	2432	1	chr1B.!!$F2	2431

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
22	23	1.584724	GGGATGGAGTGGAAGAAGGA	58.415	55.000	0.00	0.00	0.0	3.36	F
1268	1275	1.127225	CGACGCGGAAAGTTTCGAC	59.873	57.895	12.47	3.32	0.0	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1331	1338	1.299620	ATATTTCGACCCGGACGCG	60.300	57.895	0.73	3.53	0.0	6.01	R
2383	2392	1.306141	AAGCTCGATCTCCACCCCA	60.306	57.895	0.00	0.00	0.0	4.96	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
22	23	1.584724	GGGATGGAGTGGAAGAAGGA	58.415	55.000	0.00	0.00	0.00	3.36
34	35	2.438411	GAAGAAGGACGGAGACTCTCA	58.562	52.381	8.35	0.00	31.08	3.27
46	47	4.570930	GGAGACTCTCAAACGAGGAAAAT	58.429	43.478	8.35	0.00	35.33	1.82
48	49	4.962155	AGACTCTCAAACGAGGAAAATGT	58.038	39.130	0.00	0.00	35.33	2.71
133	134	4.436079	AGGGACAGTAAGGGTGACTTATT	58.564	43.478	0.00	0.00	43.20	1.40
223	224	7.557719	ACGATTAACCTCTGGATTTGAAATCAT	59.442	33.333	18.55	1.40	0.00	2.45
264	265	9.463443	GTATTGGCCATAATTTACAAGAACATC	57.537	33.333	6.09	0.00	0.00	3.06
306	307	4.188733	AGGAAGGGTTAAGGATTTACCCA	58.811	43.478	16.65	0.00	42.87	4.51
363	364	7.755591	AGATGTTGTCGTAGTAAAGAATCGTA	58.244	34.615	0.00	0.00	0.00	3.43
445	446	6.052360	TGCCATGTAAATCGCTAGAAACATA	58.948	36.000	0.00	0.00	31.47	2.29
520	521	3.879892	GCTACCATGAGACAAAAGATCCC	59.120	47.826	0.00	0.00	0.00	3.85
537	538	7.516450	AAGATCCCCTTTCTAAAGAGATTCA	57.484	36.000	4.01	0.00	38.28	2.57
583	584	8.480501	CCAAGGTCAATATGGAAATTCTTTCAT	58.519	33.333	2.39	0.00	41.43	2.57
658	661	1.699730	TCAGAACAGGTCCGAGTCAA	58.300	50.000	0.00	0.00	0.00	3.18
722	725	2.688958	CGGAAACCTAAGGACTCGATCT	59.311	50.000	0.00	0.00	0.00	2.75
776	779	1.856920	AGTGGGAAAAGGAGGGAAACA	59.143	47.619	0.00	0.00	0.00	2.83
845	848	9.253832	CTCATAGATCCCTATAGAATTCTGTGT	57.746	37.037	18.47	6.64	33.98	3.72
850	853	9.440761	AGATCCCTATAGAATTCTGTGTAAAGT	57.559	33.333	18.47	0.00	0.00	2.66
937	941	3.182887	ACAATATGGGGTCAAAAGGCA	57.817	42.857	0.00	0.00	0.00	4.75
1018	1024	2.934553	CTCATGTCACGTCGAGGTACTA	59.065	50.000	10.91	0.40	41.55	1.82
1055	1061	5.870978	CAGCAAAATCCGATCCAATTTTTCT	59.129	36.000	9.04	7.74	33.86	2.52
1191	1198	9.034800	ACAAATCCACTATTGGTTTTACATCAT	57.965	29.630	7.60	0.00	41.16	2.45
1234	1241	9.681062	CTCCCAATATAGGAGTAAAAACAAGAA	57.319	33.333	11.89	0.00	45.05	2.52
1268	1275	1.127225	CGACGCGGAAAGTTTCGAC	59.873	57.895	12.47	3.32	0.00	4.20
1331	1338	6.330278	GTTGGTTATTAGAAGCATCCCAAAC	58.670	40.000	0.00	0.00	32.94	2.93
1369	1376	9.651913	GAAATATGGCTTTCAAATTAAGTTCCA	57.348	29.630	0.00	0.00	35.61	3.53
1440	1447	2.131183	GCGACTCATAGAATGGCAGAC	58.869	52.381	0.00	0.00	0.00	3.51
1442	1449	2.033424	CGACTCATAGAATGGCAGACGA	59.967	50.000	0.00	0.00	29.06	4.20
1509	1516	7.010160	TCTATGTATGTAGACACATGGATCCA	58.990	38.462	18.88	18.88	45.17	3.41
1551	1558	7.552050	AGAATCAATAGAAGGAGAATCGGAT	57.448	36.000	0.00	0.00	34.37	4.18
1623	1630	4.033009	TCATGATCAACTAAGCCCTCTCA	58.967	43.478	0.00	0.00	0.00	3.27
1710	1717	6.598064	CCTATTCATGGGGATTCCGTAAATAC	59.402	42.308	0.00	0.00	38.76	1.89
1787	1794	7.056006	ACTAATTCATGATCTGGCATGTACAA	58.944	34.615	0.00	0.00	44.59	2.41
2058	2067	8.341903	GGAAATTTCCAAACGAACAATTTCAAT	58.658	29.630	28.76	0.00	46.76	2.57
2132	2141	9.516546	TCTATCCGTAGAGTACATTGAATGTAT	57.483	33.333	19.70	9.88	38.64	2.29
2208	2217	6.099341	GGGAATGTTTTTATGTGGTGCTAAG	58.901	40.000	0.00	0.00	0.00	2.18
2383	2392	6.753913	TCTCTTGGCTATATGGTTCATCTT	57.246	37.500	0.00	0.00	0.00	2.40
2388	2397	3.074538	GGCTATATGGTTCATCTTGGGGT	59.925	47.826	0.00	0.00	0.00	4.95
2432	2442	8.506168	AATTGTGAACGGTCTTATCAATACAT	57.494	30.769	0.33	0.00	0.00	2.29
2433	2443	6.902224	TGTGAACGGTCTTATCAATACATG	57.098	37.500	0.33	0.00	0.00	3.21
2434	2444	6.635755	TGTGAACGGTCTTATCAATACATGA	58.364	36.000	0.33	0.00	43.67	3.07
2441	2451	6.533730	GGTCTTATCAATACATGATGACCCA	58.466	40.000	13.17	0.00	46.36	4.51
2442	2452	6.428159	GGTCTTATCAATACATGATGACCCAC	59.572	42.308	13.17	0.00	46.36	4.61
2443	2453	7.905329	GGTCTTATCAATACATGATGACCCACA	60.905	40.741	13.17	0.00	46.36	4.17
2446	2456	5.178096	TCAATACATGATGACCCACAAGT	57.822	39.130	0.00	0.00	31.50	3.16
2447	2457	6.306643	TCAATACATGATGACCCACAAGTA	57.693	37.500	0.00	0.00	31.50	2.24
2448	2458	6.899089	TCAATACATGATGACCCACAAGTAT	58.101	36.000	0.00	0.00	31.50	2.12
2449	2459	8.028652	TCAATACATGATGACCCACAAGTATA	57.971	34.615	0.00	0.00	31.50	1.47
2450	2460	8.150296	TCAATACATGATGACCCACAAGTATAG	58.850	37.037	0.00	0.00	31.50	1.31
2451	2461	5.296151	ACATGATGACCCACAAGTATAGG	57.704	43.478	0.00	0.00	0.00	2.57
2460	2470	5.941555	CCCACAAGTATAGGGGATCTATC	57.058	47.826	0.00	0.00	43.57	2.08
2461	2471	4.402793	CCCACAAGTATAGGGGATCTATCG	59.597	50.000	0.00	0.00	43.57	2.92
2462	2472	5.017490	CCACAAGTATAGGGGATCTATCGT	58.983	45.833	0.00	0.00	39.30	3.73
2463	2473	6.185511	CCACAAGTATAGGGGATCTATCGTA	58.814	44.000	0.00	0.00	39.30	3.43
2464	2474	6.319152	CCACAAGTATAGGGGATCTATCGTAG	59.681	46.154	0.00	0.00	39.30	3.51
2465	2475	6.885376	CACAAGTATAGGGGATCTATCGTAGT	59.115	42.308	0.00	0.00	39.30	2.73
2466	2476	7.066043	CACAAGTATAGGGGATCTATCGTAGTC	59.934	44.444	0.00	0.00	39.30	2.59
2467	2477	6.251255	AGTATAGGGGATCTATCGTAGTCC	57.749	45.833	0.00	0.00	39.30	3.85
2468	2478	5.971881	AGTATAGGGGATCTATCGTAGTCCT	59.028	44.000	0.00	0.00	39.30	3.85
2469	2479	5.799978	ATAGGGGATCTATCGTAGTCCTT	57.200	43.478	0.00	0.00	33.60	3.36
2470	2480	4.472690	AGGGGATCTATCGTAGTCCTTT	57.527	45.455	0.00	0.00	0.00	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.178944	TCCGTCCTTCTTCCACTCCA	60.179	55.000	0.00	0.00	0.00	3.86
22	23	0.882474	CCTCGTTTGAGAGTCTCCGT	59.118	55.000	17.57	0.00	45.57	4.69
46	47	3.818773	GGTCAATTCTTTCGAAGGGAACA	59.181	43.478	14.73	3.68	33.42	3.18
48	49	3.071479	CGGTCAATTCTTTCGAAGGGAA	58.929	45.455	7.49	11.86	31.60	3.97
133	134	4.753107	GGTTGATAGTGGAAAAGTCGACAA	59.247	41.667	19.50	0.00	35.08	3.18
223	224	5.073827	TGGCCAATACCAGGTATATAAGCAA	59.926	40.000	12.88	4.56	33.75	3.91
264	265	7.449086	CCTTCCTCCTCTTACTAATACTACAGG	59.551	44.444	0.00	0.00	0.00	4.00
306	307	6.013842	TCGAATAATGCGATATCTCACACT	57.986	37.500	0.00	0.00	32.09	3.55
363	364	1.235724	GCACTAGAACGCCCTTGTTT	58.764	50.000	0.00	0.00	30.75	2.83
429	430	7.849804	ACACTTCATATGTTTCTAGCGATTT	57.150	32.000	1.90	0.00	0.00	2.17
445	446	4.584638	TTGGGTTAGCCATACACTTCAT	57.415	40.909	3.24	0.00	36.17	2.57
520	521	7.849804	TCCGAATTGAATCTCTTTAGAAAGG	57.150	36.000	2.29	0.00	36.67	3.11
537	538	6.992715	CCTTGGACATATAAGAGTTCCGAATT	59.007	38.462	0.00	0.00	0.00	2.17
583	584	5.935789	CACGGACAAAGTAAGGGAAAATCTA	59.064	40.000	0.00	0.00	0.00	1.98
586	587	4.466827	ACACGGACAAAGTAAGGGAAAAT	58.533	39.130	0.00	0.00	0.00	1.82
658	661	5.587844	AGAAGTGCTTCGAATCATTGCTATT	59.412	36.000	4.82	1.40	43.97	1.73
1032	1038	6.041423	AGAAAAATTGGATCGGATTTTGCT	57.959	33.333	15.06	15.06	36.66	3.91
1055	1061	8.795842	AACCACCATGTTAACTAATCGATTAA	57.204	30.769	18.08	3.28	0.00	1.40
1187	1194	6.448006	GGAGTTACTCTACGTATTGCATGAT	58.552	40.000	12.41	0.00	0.00	2.45
1191	1198	4.018490	TGGGAGTTACTCTACGTATTGCA	58.982	43.478	12.41	0.00	0.00	4.08
1268	1275	9.323985	CTCTTCCTTGTTTAGATCCTATTTCAG	57.676	37.037	0.00	0.00	0.00	3.02
1331	1338	1.299620	ATATTTCGACCCGGACGCG	60.300	57.895	0.73	3.53	0.00	6.01
1369	1376	4.646492	CCCTTTGGCAGCATCTACTAATTT	59.354	41.667	0.00	0.00	0.00	1.82
1440	1447	4.871993	ATGTGCAAGAGCTCTATTTTCG	57.128	40.909	18.59	2.89	42.74	3.46
1442	1449	6.088824	CGAAAATGTGCAAGAGCTCTATTTT	58.911	36.000	24.32	24.32	42.74	1.82
1480	1487	7.896811	TCCATGTGTCTACATACATAGATTCC	58.103	38.462	0.00	0.00	45.53	3.01
1509	1516	6.749139	TGATTCTTTTCCGATCGAGATGTAT	58.251	36.000	18.66	1.92	0.00	2.29
1595	1602	7.071698	AGAGGGCTTAGTTGATCATGATTTCTA	59.928	37.037	10.14	9.86	0.00	2.10
1623	1630	6.948309	TCTTTCTTATTCTTAAGCAAGCCCTT	59.052	34.615	0.00	0.00	38.09	3.95
1660	1667	9.077885	GGATCAAACCTTATTCCATGCTATTTA	57.922	33.333	0.00	0.00	0.00	1.40
1710	1717	6.799926	ATTGTTTCGATTTTTGAAATGGGG	57.200	33.333	0.00	0.00	37.62	4.96
2284	2293	6.124316	AGTAGCCTCATTAGACCGTAGATA	57.876	41.667	0.00	0.00	0.00	1.98
2383	2392	1.306141	AAGCTCGATCTCCACCCCA	60.306	57.895	0.00	0.00	0.00	4.96
2388	2397	3.961480	TTTCTTGAAGCTCGATCTCCA	57.039	42.857	0.00	0.00	0.00	3.86
2432	2442	3.045634	CCCCTATACTTGTGGGTCATCA	58.954	50.000	0.00	0.00	39.31	3.07
2433	2443	3.314693	TCCCCTATACTTGTGGGTCATC	58.685	50.000	0.00	0.00	39.31	2.92
2434	2444	3.431411	TCCCCTATACTTGTGGGTCAT	57.569	47.619	0.00	0.00	39.31	3.06
2435	2445	2.953093	TCCCCTATACTTGTGGGTCA	57.047	50.000	0.00	0.00	39.31	4.02
2436	2446	3.588569	AGATCCCCTATACTTGTGGGTC	58.411	50.000	0.00	0.00	39.31	4.46
2437	2447	3.726837	AGATCCCCTATACTTGTGGGT	57.273	47.619	0.00	0.00	39.31	4.51
2438	2448	4.402793	CGATAGATCCCCTATACTTGTGGG	59.597	50.000	0.00	0.00	38.17	4.61
2439	2449	5.017490	ACGATAGATCCCCTATACTTGTGG	58.983	45.833	0.00	0.00	38.17	4.17
2440	2450	6.885376	ACTACGATAGATCCCCTATACTTGTG	59.115	42.308	0.00	0.00	38.17	3.33
2441	2451	7.030234	ACTACGATAGATCCCCTATACTTGT	57.970	40.000	0.00	0.00	38.17	3.16
2442	2452	6.543100	GGACTACGATAGATCCCCTATACTTG	59.457	46.154	0.00	0.00	38.17	3.16
2443	2453	6.447735	AGGACTACGATAGATCCCCTATACTT	59.552	42.308	0.00	0.00	38.17	2.24
2444	2454	5.971881	AGGACTACGATAGATCCCCTATACT	59.028	44.000	0.00	0.00	38.17	2.12
2445	2455	6.251255	AGGACTACGATAGATCCCCTATAC	57.749	45.833	0.00	0.00	38.17	1.47
2446	2456	6.905067	AAGGACTACGATAGATCCCCTATA	57.095	41.667	0.00	0.00	38.17	1.31
2447	2457	5.799978	AAGGACTACGATAGATCCCCTAT	57.200	43.478	0.00	0.00	40.66	2.57
2448	2458	5.595814	AAAGGACTACGATAGATCCCCTA	57.404	43.478	0.00	0.00	41.38	3.53
2449	2459	4.472690	AAAGGACTACGATAGATCCCCT	57.527	45.455	0.00	0.00	41.38	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.