AutoCloner

Multiple sequence alignment - TraesCS2B01G025900

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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	TraesCS2B01G025900	chr2B	100.000	3000	0	0	1	3000	11907628	11910627	0.000000e+00	5541.0
1	TraesCS2B01G025900	chr2B	74.027	1490	289	77	208	1650	259687514	259688952	4.430000e-143	518.0
2	TraesCS2B01G025900	chr2B	76.316	722	118	35	2286	2996	259763330	259764009	1.330000e-88	337.0
3	TraesCS2B01G025900	chr3B	95.963	1734	51	4	568	2288	232566742	232568469	0.000000e+00	2796.0
4	TraesCS2B01G025900	chr3B	97.767	627	11	1	2374	3000	232605160	232605783	0.000000e+00	1077.0
5	TraesCS2B01G025900	chr3B	96.407	334	12	0	206	539	232564986	232565319	4.370000e-153	551.0
6	TraesCS2B01G025900	chr3B	94.000	200	11	1	1	200	232562571	232562769	4.860000e-78	302.0
7	TraesCS2B01G025900	chr3B	97.753	89	2	0	2286	2374	232605100	232605188	1.440000e-33	154.0
8	TraesCS2B01G025900	chr3B	93.333	45	3	0	537	581	232565332	232565376	1.930000e-07	67.6
9	TraesCS2B01G025900	chr1B	93.716	732	25	9	2286	3000	662069816	662070543	0.000000e+00	1077.0
10	TraesCS2B01G025900	chr5A	94.436	629	28	3	2374	3000	570186838	570186215	0.000000e+00	961.0
11	TraesCS2B01G025900	chr5A	89.590	634	47	8	1671	2288	570215965	570215335	0.000000e+00	787.0
12	TraesCS2B01G025900	chr5A	94.340	371	21	0	1302	1672	570216366	570215996	1.210000e-158	569.0
13	TraesCS2B01G025900	chr5A	92.605	311	22	1	202	511	570226837	570226527	2.120000e-121	446.0
14	TraesCS2B01G025900	chr5A	92.500	200	12	3	1	199	570229273	570229076	1.760000e-72	283.0
15	TraesCS2B01G025900	chr5A	97.802	91	2	0	2286	2376	570186898	570186808	1.110000e-34	158.0
16	TraesCS2B01G025900	chr7A	75.498	1457	265	65	234	1647	102056952	102058359	1.960000e-176	628.0
17	TraesCS2B01G025900	chr7A	77.540	748	124	32	914	1650	675496922	675497636	7.740000e-111	411.0
18	TraesCS2B01G025900	chr7A	74.716	617	125	23	224	815	675495925	675496535	2.310000e-61	246.0
19	TraesCS2B01G025900	chr5B	79.039	458	72	19	1198	1650	126446505	126446943	2.930000e-75	292.0
20	TraesCS2B01G025900	chr5B	75.667	637	120	24	208	819	126445230	126445856	4.890000e-73	285.0
21	TraesCS2B01G025900	chr5B	74.257	303	64	9	1704	2005	126447032	126447321	6.800000e-22	115.0

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	TraesCS2B01G025900	chr2B	11907628	11910627	2999	False	5541.000000	5541	100.00000	1	3000	1	chr2B.!!$F1	2999
1	TraesCS2B01G025900	chr2B	259687514	259688952	1438	False	518.000000	518	74.02700	208	1650	1	chr2B.!!$F2	1442
2	TraesCS2B01G025900	chr2B	259763330	259764009	679	False	337.000000	337	76.31600	2286	2996	1	chr2B.!!$F3	710
3	TraesCS2B01G025900	chr3B	232562571	232568469	5898	False	929.150000	2796	94.92575	1	2288	4	chr3B.!!$F1	2287
4	TraesCS2B01G025900	chr3B	232605100	232605783	683	False	615.500000	1077	97.76000	2286	3000	2	chr3B.!!$F2	714
5	TraesCS2B01G025900	chr1B	662069816	662070543	727	False	1077.000000	1077	93.71600	2286	3000	1	chr1B.!!$F1	714
6	TraesCS2B01G025900	chr5A	570215335	570216366	1031	True	678.000000	787	91.96500	1302	2288	2	chr5A.!!$R2	986
7	TraesCS2B01G025900	chr5A	570186215	570186898	683	True	559.500000	961	96.11900	2286	3000	2	chr5A.!!$R1	714
8	TraesCS2B01G025900	chr5A	570226527	570229273	2746	True	364.500000	446	92.55250	1	511	2	chr5A.!!$R3	510
9	TraesCS2B01G025900	chr7A	102056952	102058359	1407	False	628.000000	628	75.49800	234	1647	1	chr7A.!!$F1	1413
10	TraesCS2B01G025900	chr7A	675495925	675497636	1711	False	328.500000	411	76.12800	224	1650	2	chr7A.!!$F2	1426
11	TraesCS2B01G025900	chr5B	126445230	126447321	2091	False	230.666667	292	76.32100	208	2005	3	chr5B.!!$F1	1797

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
485	2750	0.517316	GAAAACCTGCTCACGCGATT	59.483	50.0	15.93	0.0	39.65	3.34	F
1166	5114	0.609662	AGTGTCCCATTTTGCATGCC	59.390	50.0	16.68	0.0	0.00	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1824	6173	0.111639	AACTATGCGGTGTTTGGGGT	59.888	50.0	0.00	0.0	0.00	4.95	R
2380	6756	0.616891	AGCAGTCTGACATGGATGCA	59.383	50.0	17.61	0.0	36.15	3.96	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
85	86	1.669999	GCCCAGCATTGACCATGGAC	61.670	60.000	21.47	13.94	34.60	4.02
103	104	4.827692	TGGACGAACTAACTGCACATATT	58.172	39.130	0.00	0.00	0.00	1.28
132	133	7.419204	TCAGTTTACCGTTTAATTGAGGTTTG	58.581	34.615	0.00	0.00	38.12	2.93
172	173	6.992063	ATCAAGAGGTTAACTGCAATACTG	57.008	37.500	5.42	0.00	0.00	2.74
176	177	5.238583	AGAGGTTAACTGCAATACTGTCAC	58.761	41.667	5.42	0.00	0.00	3.67
195	196	4.068599	TCACGCACAATCTGTTCCAAATA	58.931	39.130	0.00	0.00	0.00	1.40
200	201	5.121611	CGCACAATCTGTTCCAAATACTGTA	59.878	40.000	0.00	0.00	0.00	2.74
201	202	6.348132	CGCACAATCTGTTCCAAATACTGTAA	60.348	38.462	0.00	0.00	0.00	2.41
202	203	6.801862	GCACAATCTGTTCCAAATACTGTAAC	59.198	38.462	0.00	0.00	0.00	2.50
203	204	7.308589	GCACAATCTGTTCCAAATACTGTAACT	60.309	37.037	0.00	0.00	0.00	2.24
204	205	8.017373	CACAATCTGTTCCAAATACTGTAACTG	58.983	37.037	0.00	0.00	0.00	3.16
485	2750	0.517316	GAAAACCTGCTCACGCGATT	59.483	50.000	15.93	0.00	39.65	3.34
571	2851	7.066284	ACCATAATGGAAATCGCTAGCAATATC	59.934	37.037	16.45	7.24	40.96	1.63
575	2855	3.987868	GGAAATCGCTAGCAATATCGTCA	59.012	43.478	16.45	0.00	0.00	4.35
599	4258	6.901887	CACATTTTACGATGATCTTACAGCAC	59.098	38.462	0.00	0.00	0.00	4.40
664	4324	3.063725	TCGTTTTGTTTGGGTCAACTACG	59.936	43.478	0.00	0.00	35.93	3.51
682	4342	4.529377	ACTACGGATGGAGTACCTTTGAAA	59.471	41.667	0.00	0.00	37.04	2.69
718	4378	1.248486	GCAACTTTGGAAGAGACCCC	58.752	55.000	0.00	0.00	0.00	4.95
843	4503	2.223572	CCATTACCGAGCCAGCAAATTC	60.224	50.000	0.00	0.00	0.00	2.17
862	4522	7.331440	GCAAATTCCATATGTGTCATCAAAACA	59.669	33.333	1.24	0.00	0.00	2.83
878	4538	7.870445	TCATCAAAACAACTTTATAGTTTGCCC	59.130	33.333	0.00	0.00	41.85	5.36
893	4553	2.300956	TGCCCCACTCTAAAATGCAA	57.699	45.000	0.00	0.00	0.00	4.08
895	4555	2.496871	TGCCCCACTCTAAAATGCAATG	59.503	45.455	0.00	0.00	0.00	2.82
896	4556	2.739609	GCCCCACTCTAAAATGCAATGC	60.740	50.000	0.00	0.00	0.00	3.56
897	4557	2.496871	CCCCACTCTAAAATGCAATGCA	59.503	45.455	11.44	11.44	44.86	3.96
996	4944	1.267235	CGACAGCTTGCGCTAAATGAG	60.267	52.381	9.73	0.00	46.99	2.90
1147	5095	8.833231	TGTTTCACAAAGTTTTCATTTTGGTA	57.167	26.923	2.54	0.00	38.33	3.25
1158	5106	6.739331	TTTCATTTTGGTAGTGTCCCATTT	57.261	33.333	0.00	0.00	0.00	2.32
1163	5111	3.168035	TGGTAGTGTCCCATTTTGCAT	57.832	42.857	0.00	0.00	0.00	3.96
1166	5114	0.609662	AGTGTCCCATTTTGCATGCC	59.390	50.000	16.68	0.00	0.00	4.40
1376	5648	3.188460	ACAGACCATTAACATGTGCGTTC	59.812	43.478	0.00	0.00	0.00	3.95
1824	6173	1.864263	TTGTCACACCCCACCCAACA	61.864	55.000	0.00	0.00	0.00	3.33
1827	6176	3.828023	ACACCCCACCCAACACCC	61.828	66.667	0.00	0.00	0.00	4.61
1954	6321	1.692411	GGAACCAAACTTCAGTGGCT	58.308	50.000	0.00	0.00	38.58	4.75
2013	6380	5.120830	CAGCCCTATAAAATAGCACATCGTC	59.879	44.000	0.00	0.00	0.00	4.20
2032	6399	2.030717	GTCGATCGGTCTGCTCATGTAT	60.031	50.000	16.41	0.00	0.00	2.29
2036	6403	4.271049	CGATCGGTCTGCTCATGTATTTTT	59.729	41.667	7.38	0.00	0.00	1.94
2124	6497	6.484643	GTGATCCTAGCATGCAAATTCTTAGA	59.515	38.462	21.98	3.49	0.00	2.10
2148	6521	8.754080	AGACATTAACTAGTACATCAGAGCTTT	58.246	33.333	0.00	0.00	0.00	3.51
2150	6523	9.726438	ACATTAACTAGTACATCAGAGCTTTTT	57.274	29.630	0.00	0.00	0.00	1.94
2194	6567	2.417933	CTCACATGCCAGCTACAAGTTC	59.582	50.000	0.00	0.00	0.00	3.01
2251	6627	1.300971	GATCAGTGCAAGCGCCTTCA	61.301	55.000	2.29	0.00	37.32	3.02
2267	6643	2.437281	CCTTCACATAGCTGATCCCTGT	59.563	50.000	0.00	0.00	0.00	4.00
2369	6745	2.007608	CACTGCATCCATGTCAGACTG	58.992	52.381	14.21	0.00	36.29	3.51
2376	6752	2.533916	TCCATGTCAGACTGCTCTCTT	58.466	47.619	1.31	0.00	0.00	2.85
2377	6753	2.495270	TCCATGTCAGACTGCTCTCTTC	59.505	50.000	1.31	0.00	0.00	2.87
2378	6754	2.233186	CCATGTCAGACTGCTCTCTTCA	59.767	50.000	1.31	0.00	0.00	3.02
2379	6755	3.252400	CATGTCAGACTGCTCTCTTCAC	58.748	50.000	1.31	0.00	0.00	3.18
2380	6756	2.591923	TGTCAGACTGCTCTCTTCACT	58.408	47.619	1.31	0.00	0.00	3.41
2381	6757	2.295629	TGTCAGACTGCTCTCTTCACTG	59.704	50.000	1.31	0.00	0.00	3.66
2382	6758	1.271934	TCAGACTGCTCTCTTCACTGC	59.728	52.381	0.00	0.00	0.00	4.40
2384	6760	1.901159	AGACTGCTCTCTTCACTGCAT	59.099	47.619	0.00	0.00	34.79	3.96
2386	6762	1.066286	ACTGCTCTCTTCACTGCATCC	60.066	52.381	0.00	0.00	34.79	3.51
2388	6764	1.558294	TGCTCTCTTCACTGCATCCAT	59.442	47.619	0.00	0.00	0.00	3.41
2389	6765	1.941294	GCTCTCTTCACTGCATCCATG	59.059	52.381	0.00	0.00	0.00	3.66
2390	6766	2.680221	GCTCTCTTCACTGCATCCATGT	60.680	50.000	0.00	0.00	0.00	3.21
2392	6768	2.568509	TCTCTTCACTGCATCCATGTCA	59.431	45.455	0.00	0.00	0.00	3.58
2395	6771	2.391616	TCACTGCATCCATGTCAGAC	57.608	50.000	14.21	0.00	36.29	3.51
2396	6772	1.904537	TCACTGCATCCATGTCAGACT	59.095	47.619	14.21	0.00	36.29	3.24
2530	6923	7.390440	CCCACATTATTGTCTCTCAACTGTTTA	59.610	37.037	0.00	0.00	38.97	2.01
2827	7234	4.670221	GCTCTAGCATAATAAATGTGCGGC	60.670	45.833	0.00	0.00	43.37	6.53
2832	7239	3.243367	GCATAATAAATGTGCGGCTTCCA	60.243	43.478	0.00	0.00	0.00	3.53
2885	7294	2.117051	TGCATGCATCTCTTCCTCTCT	58.883	47.619	18.46	0.00	0.00	3.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	1.267732	GCACGCTACAGCACATGATTC	60.268	52.381	0.00	0.00	42.21	2.52
85	86	8.604035	ACTGAATAAATATGTGCAGTTAGTTCG	58.396	33.333	0.00	0.00	33.19	3.95
103	104	9.287373	ACCTCAATTAAACGGTAAACTGAATAA	57.713	29.630	0.00	0.00	0.00	1.40
149	150	6.476378	ACAGTATTGCAGTTAACCTCTTGAT	58.524	36.000	0.88	0.00	0.00	2.57
172	173	1.225855	TGGAACAGATTGTGCGTGAC	58.774	50.000	0.00	0.00	0.00	3.67
176	177	4.083324	ACAGTATTTGGAACAGATTGTGCG	60.083	41.667	0.00	0.00	42.39	5.34
195	196	3.307480	GGGAGGTACATTGCAGTTACAGT	60.307	47.826	0.00	0.00	0.00	3.55
200	201	2.621407	CCATGGGAGGTACATTGCAGTT	60.621	50.000	2.85	0.00	0.00	3.16
201	202	1.064463	CCATGGGAGGTACATTGCAGT	60.064	52.381	2.85	0.00	0.00	4.40
202	203	1.683943	CCATGGGAGGTACATTGCAG	58.316	55.000	2.85	0.00	0.00	4.41
203	204	0.395586	GCCATGGGAGGTACATTGCA	60.396	55.000	15.13	0.00	37.07	4.08
204	205	0.395586	TGCCATGGGAGGTACATTGC	60.396	55.000	15.13	0.00	37.46	3.56
485	2750	0.179020	AGTGCAACAACAGCCTGCTA	60.179	50.000	0.00	0.00	41.43	3.49
571	2851	7.216920	TGTAAGATCATCGTAAAATGTGACG	57.783	36.000	0.00	0.00	40.43	4.35
575	2855	6.818644	AGTGCTGTAAGATCATCGTAAAATGT	59.181	34.615	0.00	0.00	34.07	2.71
599	4258	9.632807	GATCTCAGCATAATAAGTAACCAGTAG	57.367	37.037	0.00	0.00	0.00	2.57
664	4324	6.834168	TCAATTTTCAAAGGTACTCCATCC	57.166	37.500	0.00	0.00	38.49	3.51
682	4342	7.318141	CAAAGTTGCATTGAGGTAGATCAATT	58.682	34.615	0.00	0.00	45.44	2.32
718	4378	0.393537	GGACTGATCCAGCAACCCAG	60.394	60.000	0.00	0.00	45.47	4.45
843	4503	9.859427	ATAAAGTTGTTTTGATGACACATATGG	57.141	29.630	7.80	0.00	0.00	2.74
893	4553	3.799366	CAATTATGGTGTGGCAATGCAT	58.201	40.909	7.79	0.00	0.00	3.96
895	4555	1.935199	GCAATTATGGTGTGGCAATGC	59.065	47.619	0.00	0.00	0.00	3.56
896	4556	3.191669	CTGCAATTATGGTGTGGCAATG	58.808	45.455	0.00	0.00	0.00	2.82
897	4557	2.168936	CCTGCAATTATGGTGTGGCAAT	59.831	45.455	0.00	0.00	0.00	3.56
898	4558	1.549620	CCTGCAATTATGGTGTGGCAA	59.450	47.619	0.00	0.00	0.00	4.52
899	4559	1.184431	CCTGCAATTATGGTGTGGCA	58.816	50.000	0.00	0.00	0.00	4.92
900	4560	1.473258	TCCTGCAATTATGGTGTGGC	58.527	50.000	0.00	0.00	0.00	5.01
996	4944	1.325355	CCATCTCATGGGTCATTGGC	58.675	55.000	0.00	0.00	46.86	4.52
1158	5106	1.470996	GGGTGGTGAAAGGCATGCAA	61.471	55.000	21.36	0.00	0.00	4.08
1163	5111	2.203480	GCAGGGTGGTGAAAGGCA	60.203	61.111	0.00	0.00	0.00	4.75
1166	5114	2.281761	AGCGCAGGGTGGTGAAAG	60.282	61.111	11.47	0.00	0.00	2.62
1376	5648	1.865865	GGGATGTACCACTGCATACG	58.134	55.000	0.00	0.00	41.20	3.06
1824	6173	0.111639	AACTATGCGGTGTTTGGGGT	59.888	50.000	0.00	0.00	0.00	4.95
1827	6176	2.159572	GCAGTAACTATGCGGTGTTTGG	60.160	50.000	0.00	0.00	33.31	3.28
1893	6260	2.406596	TATCATCAAGCTGCTGTGCA	57.593	45.000	1.35	0.00	36.92	4.57
1984	6351	6.364701	TGTGCTATTTTATAGGGCTGTGAAT	58.635	36.000	0.00	0.00	0.00	2.57
2013	6380	2.713895	ATACATGAGCAGACCGATCG	57.286	50.000	8.51	8.51	30.45	3.69
2124	6497	9.726438	AAAAAGCTCTGATGTACTAGTTAATGT	57.274	29.630	0.00	0.00	0.00	2.71
2148	6521	5.825593	AGATCTCAAGGGTGTAACTGAAA	57.174	39.130	0.00	0.00	36.74	2.69
2150	6523	4.402793	GCTAGATCTCAAGGGTGTAACTGA	59.597	45.833	0.00	0.00	36.74	3.41
2194	6567	5.520288	CAGTGTCAATCTACGTAGGGAAATG	59.480	44.000	22.01	13.34	0.00	2.32
2251	6627	2.840038	TCAACACAGGGATCAGCTATGT	59.160	45.455	0.00	0.00	0.00	2.29
2267	6643	5.122239	GTGCAAGATAATGTAGCAGTCAACA	59.878	40.000	0.00	0.00	35.66	3.33
2369	6745	1.941294	CATGGATGCAGTGAAGAGAGC	59.059	52.381	0.00	0.00	0.00	4.09
2376	6752	1.904537	AGTCTGACATGGATGCAGTGA	59.095	47.619	10.88	0.00	35.18	3.41
2377	6753	2.007608	CAGTCTGACATGGATGCAGTG	58.992	52.381	10.88	0.00	35.18	3.66
2378	6754	1.678123	GCAGTCTGACATGGATGCAGT	60.678	52.381	10.88	0.00	35.18	4.40
2379	6755	1.015109	GCAGTCTGACATGGATGCAG	58.985	55.000	10.88	0.00	35.05	4.41
2380	6756	0.616891	AGCAGTCTGACATGGATGCA	59.383	50.000	17.61	0.00	36.15	3.96
2381	6757	1.134461	AGAGCAGTCTGACATGGATGC	60.134	52.381	10.88	10.41	0.00	3.91
2382	6758	2.431419	AGAGAGCAGTCTGACATGGATG	59.569	50.000	10.88	0.05	30.97	3.51
2384	6760	1.823610	CAGAGAGCAGTCTGACATGGA	59.176	52.381	10.88	0.00	46.02	3.41
2386	6762	3.316071	AACAGAGAGCAGTCTGACATG	57.684	47.619	19.20	6.72	46.02	3.21
2388	6764	3.891977	ACTAAACAGAGAGCAGTCTGACA	59.108	43.478	19.20	5.59	46.02	3.58
2389	6765	4.513198	ACTAAACAGAGAGCAGTCTGAC	57.487	45.455	19.20	0.00	46.02	3.51
2390	6766	5.509840	GGAAACTAAACAGAGAGCAGTCTGA	60.510	44.000	19.20	0.02	46.02	3.27
2392	6768	4.591072	AGGAAACTAAACAGAGAGCAGTCT	59.409	41.667	0.00	0.00	40.61	3.24
2395	6771	5.784177	TGTAGGAAACTAAACAGAGAGCAG	58.216	41.667	0.00	0.00	46.54	4.24
2396	6772	5.538813	TCTGTAGGAAACTAAACAGAGAGCA	59.461	40.000	0.10	0.00	46.21	4.26
2827	7234	4.955925	TGTGCGGTATGTAATTTGGAAG	57.044	40.909	0.00	0.00	0.00	3.46
2832	7239	3.504134	TGTGCTTGTGCGGTATGTAATTT	59.496	39.130	0.00	0.00	43.34	1.82
2885	7294	5.050644	TCGCGAAAAGTAGACTGAATGTA	57.949	39.130	6.20	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.