AutoCloner

Multiple sequence alignment - TraesCS5D01G527500

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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	TraesCS5D01G527500	chr5D	100.000	3894	0	0	1	3894	544698911	544695018	0.000000e+00	7191
1	TraesCS5D01G527500	chr1A	94.625	3628	125	19	302	3894	569449857	569453449	0.000000e+00	5555
2	TraesCS5D01G527500	chr1A	92.254	284	19	1	1	284	569448486	569448766	2.180000e-107	399
3	TraesCS5D01G527500	chr1A	88.291	316	32	3	3	317	569449499	569449810	1.320000e-99	374
4	TraesCS5D01G527500	chr1A	93.035	201	11	1	84	284	569449291	569449488	1.370000e-74	291
5	TraesCS5D01G527500	chr1A	80.890	382	57	12	5	384	569447493	569447860	1.770000e-73	287
6	TraesCS5D01G527500	chr5B	93.081	3064	132	20	1	3027	687163594	687166614	0.000000e+00	4410
7	TraesCS5D01G527500	chr5B	93.864	880	36	6	3026	3894	687166776	687167648	0.000000e+00	1310
8	TraesCS5D01G527500	chr2B	82.656	1107	178	8	1736	2841	752829809	752828716	0.000000e+00	968
9	TraesCS5D01G527500	chr2D	82.023	1107	185	8	1736	2841	617072793	617071700	0.000000e+00	929
10	TraesCS5D01G527500	chr3A	81.991	1105	187	9	1739	2840	10952690	10951595	0.000000e+00	928
11	TraesCS5D01G527500	chr3A	81.222	1113	201	6	1729	2840	11410066	11408961	0.000000e+00	891
12	TraesCS5D01G527500	chr2A	81.991	1105	184	9	1736	2839	747143676	747142586	0.000000e+00	924
13	TraesCS5D01G527500	chrUn	82.459	1049	181	3	1734	2782	296501505	296500460	0.000000e+00	915
14	TraesCS5D01G527500	chr3B	81.391	1107	198	7	1736	2841	28363683	28364782	0.000000e+00	896
15	TraesCS5D01G527500	chr4D	82.011	189	18	10	95	273	26252829	26252647	3.140000e-31	147

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	TraesCS5D01G527500	chr5D	544695018	544698911	3893	True	7191.0	7191	100.0000	1	3894	1	chr5D.!!$R1	3893
1	TraesCS5D01G527500	chr1A	569447493	569453449	5956	False	1381.2	5555	89.8190	1	3894	5	chr1A.!!$F1	3893
2	TraesCS5D01G527500	chr5B	687163594	687167648	4054	False	2860.0	4410	93.4725	1	3894	2	chr5B.!!$F1	3893
3	TraesCS5D01G527500	chr2B	752828716	752829809	1093	True	968.0	968	82.6560	1736	2841	1	chr2B.!!$R1	1105
4	TraesCS5D01G527500	chr2D	617071700	617072793	1093	True	929.0	929	82.0230	1736	2841	1	chr2D.!!$R1	1105
5	TraesCS5D01G527500	chr3A	10951595	10952690	1095	True	928.0	928	81.9910	1739	2840	1	chr3A.!!$R1	1101
6	TraesCS5D01G527500	chr3A	11408961	11410066	1105	True	891.0	891	81.2220	1729	2840	1	chr3A.!!$R2	1111
7	TraesCS5D01G527500	chr2A	747142586	747143676	1090	True	924.0	924	81.9910	1736	2839	1	chr2A.!!$R1	1103
8	TraesCS5D01G527500	chrUn	296500460	296501505	1045	True	915.0	915	82.4590	1734	2782	1	chrUn.!!$R1	1048
9	TraesCS5D01G527500	chr3B	28363683	28364782	1099	False	896.0	896	81.3910	1736	2841	1	chr3B.!!$F1	1105

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
801	2871	0.370273	GCGAGTGCGGAGTTACATTG	59.630	55.0	0.0	0.0	38.16	2.82	F
1181	3266	0.181350	CCTTCCTGTGGATACCTGGC	59.819	60.0	0.0	0.0	0.00	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2602	4705	2.586914	TGCATCTCATCTGCCGCG	60.587	61.111	0.0	0.0	38.89	6.46	R
3159	5425	1.485066	CGCCCTACTCTGTAAATGGGT	59.515	52.381	0.0	0.0	37.09	4.51	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
78	1072	1.561542	CTTATCTGCCAGAGGGGTTGT	59.438	52.381	0.00	0.00	39.65	3.32
157	1151	1.177895	AATGTTCATGTGGCCGCACA	61.178	50.000	23.94	15.73	39.62	4.57
202	1196	8.940397	TTCAAAAGATAAATCTATCATCCCCC	57.060	34.615	0.00	0.00	37.05	5.40
203	1197	7.168219	TCAAAAGATAAATCTATCATCCCCCG	58.832	38.462	0.00	0.00	37.05	5.73
224	1218	4.148000	CCGAAAAACACAAATCCATGTTCG	59.852	41.667	0.00	0.00	38.08	3.95
381	2445	5.181811	CACCTTATGAGATGACAGCACAAAA	59.818	40.000	0.00	0.00	0.00	2.44
382	2446	5.769662	ACCTTATGAGATGACAGCACAAAAA	59.230	36.000	0.00	0.00	0.00	1.94
459	2523	4.092091	GCTTGGAGAAAGAATACACGTCTG	59.908	45.833	0.00	0.00	38.24	3.51
463	2527	4.562963	GGAGAAAGAATACACGTCTGGGTT	60.563	45.833	0.00	0.00	0.00	4.11
469	2533	2.443887	TACACGTCTGGGTTAGCAAC	57.556	50.000	0.00	0.00	0.00	4.17
480	2544	4.258543	TGGGTTAGCAACAGCATACTAAC	58.741	43.478	0.00	0.00	42.31	2.34
524	2590	2.770164	AGTGACTGCCACCTGTTATC	57.230	50.000	0.00	0.00	46.87	1.75
612	2679	1.537202	GGCAGAACAAGAGCGAACATT	59.463	47.619	0.00	0.00	0.00	2.71
718	2788	2.325082	GGGCGTCGTCATGCTTGTT	61.325	57.895	0.00	0.00	34.60	2.83
800	2870	0.739813	GGCGAGTGCGGAGTTACATT	60.740	55.000	0.00	0.00	44.10	2.71
801	2871	0.370273	GCGAGTGCGGAGTTACATTG	59.630	55.000	0.00	0.00	38.16	2.82
978	3048	2.817839	GCCTTACCTCTTTGGCCTTGAA	60.818	50.000	3.32	0.00	39.49	2.69
1041	3126	4.201724	CGCTCAGTTATGTTTGCTACCTTC	60.202	45.833	0.00	0.00	0.00	3.46
1181	3266	0.181350	CCTTCCTGTGGATACCTGGC	59.819	60.000	0.00	0.00	0.00	4.85
1183	3274	2.398588	CTTCCTGTGGATACCTGGCTA	58.601	52.381	0.00	0.00	0.00	3.93
1187	3278	2.037772	CCTGTGGATACCTGGCTATGAC	59.962	54.545	0.00	0.00	0.00	3.06
1237	3328	9.712359	CATATTATGCAAATTATGGAGATGTCG	57.288	33.333	0.00	0.00	30.55	4.35
1286	3377	4.455877	AGTTAGTTTTCCGCAAGATCTTGG	59.544	41.667	31.41	22.06	40.74	3.61
1453	3556	1.529152	CTTGGCATGGTCTTGCAGCA	61.529	55.000	10.29	0.00	44.59	4.41
1466	3569	4.325472	GTCTTGCAGCAAATTAATCAGTGC	59.675	41.667	9.65	9.57	37.26	4.40
1482	3585	3.583806	CAGTGCACTGAAGTCTAGAAGG	58.416	50.000	38.12	9.27	46.59	3.46
1596	3699	1.136891	GCCCAGTGGATTGCAATAACC	59.863	52.381	12.97	11.05	0.00	2.85
1699	3802	6.347888	GGGAAATTTGCAGTTTGTTGATCATG	60.348	38.462	12.05	0.00	0.00	3.07
1882	3985	2.501723	CCCAATCAGGTACAGCTACACT	59.498	50.000	0.00	0.00	34.66	3.55
2071	4174	1.098050	GCAGGATCCACCATGTCAAC	58.902	55.000	15.82	0.00	42.04	3.18
2602	4705	4.762289	ACAAGAAGTGGGTGAGATATCC	57.238	45.455	0.00	0.00	0.00	2.59
2833	4936	0.323816	TGACTGCTCTGTCGGAGGAT	60.324	55.000	10.75	0.00	41.47	3.24
2847	4950	3.706086	TCGGAGGATGATGAGTTTGATGA	59.294	43.478	0.00	0.00	0.00	2.92
2888	4991	1.063174	GCGCTGGTCTTAGAAATGCAG	59.937	52.381	0.00	0.00	0.00	4.41
2889	4992	2.621338	CGCTGGTCTTAGAAATGCAGA	58.379	47.619	0.00	0.00	0.00	4.26
2890	4993	2.606725	CGCTGGTCTTAGAAATGCAGAG	59.393	50.000	0.00	0.00	0.00	3.35
2891	4994	3.604582	GCTGGTCTTAGAAATGCAGAGT	58.395	45.455	0.00	0.00	0.00	3.24
2892	4995	4.678044	CGCTGGTCTTAGAAATGCAGAGTA	60.678	45.833	0.00	0.00	0.00	2.59
2893	4996	4.808364	GCTGGTCTTAGAAATGCAGAGTAG	59.192	45.833	0.00	0.00	0.00	2.57
2894	4997	5.625656	GCTGGTCTTAGAAATGCAGAGTAGT	60.626	44.000	0.00	0.00	0.00	2.73
2895	4998	5.967088	TGGTCTTAGAAATGCAGAGTAGTC	58.033	41.667	0.00	0.00	0.00	2.59
2896	4999	5.480422	TGGTCTTAGAAATGCAGAGTAGTCA	59.520	40.000	0.00	0.00	0.00	3.41
2897	5000	6.014584	TGGTCTTAGAAATGCAGAGTAGTCAA	60.015	38.462	0.00	0.00	0.00	3.18
3014	5117	1.298157	TTGCTGCTGTACGTGGATGC	61.298	55.000	0.00	0.00	0.00	3.91
3159	5425	3.330701	ACTCTGAATGCAACCCTTCCTTA	59.669	43.478	0.00	0.00	0.00	2.69
3366	5649	4.069304	TGAAAACAACGGTGAATCTAGGG	58.931	43.478	7.88	0.00	0.00	3.53
3386	5669	4.790790	AGGGTAGATCAAATGGAGGAAGTT	59.209	41.667	0.00	0.00	0.00	2.66
3396	5679	0.253327	GGAGGAAGTTGGGCTACTGG	59.747	60.000	0.00	0.00	0.00	4.00
3454	5737	7.582319	CGGTTCTGCATTTTGTTTTGTTTTATC	59.418	33.333	0.00	0.00	0.00	1.75
3480	5763	5.687285	AGCAAAACAAAATCATTCACGAGAC	59.313	36.000	0.00	0.00	0.00	3.36
3553	5836	0.981943	GTGGGTAGTACAAGGCCTGT	59.018	55.000	5.69	9.73	42.47	4.00
3554	5837	1.350019	GTGGGTAGTACAAGGCCTGTT	59.650	52.381	5.69	0.00	39.64	3.16
3555	5838	2.059490	TGGGTAGTACAAGGCCTGTTT	58.941	47.619	5.69	0.00	39.64	2.83
3622	5905	2.496070	CCGAACCATTCTCTACTGACCA	59.504	50.000	0.00	0.00	0.00	4.02
3632	5927	5.906113	TCTCTACTGACCAACTTCATCTC	57.094	43.478	0.00	0.00	0.00	2.75
3640	5935	1.197721	CCAACTTCATCTCCGCACAAC	59.802	52.381	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	1013	3.838120	TCGAGCAAGTCTACAATCACAG	58.162	45.455	0.00	0.00	0.00	3.66
78	1072	5.888724	TCGCCCAATCAGTTATTTATTTCCA	59.111	36.000	0.00	0.00	0.00	3.53
157	1151	0.330604	AATGTCCACATCTGCCTGCT	59.669	50.000	0.00	0.00	35.10	4.24
202	1196	4.148000	CCGAACATGGATTTGTGTTTTTCG	59.852	41.667	0.00	0.00	38.57	3.46
203	1197	4.084589	GCCGAACATGGATTTGTGTTTTTC	60.085	41.667	0.00	0.00	38.57	2.29
243	1237	4.144555	CGACAAATTCTGCTTCGAAGAAC	58.855	43.478	28.95	12.35	45.90	3.01
389	2453	0.464735	CAGTTTCCGTTGACACCCCA	60.465	55.000	0.00	0.00	0.00	4.96
393	2457	4.495184	CCAGTAAACAGTTTCCGTTGACAC	60.495	45.833	0.48	0.00	31.09	3.67
394	2458	3.623960	CCAGTAAACAGTTTCCGTTGACA	59.376	43.478	0.48	0.00	31.09	3.58
395	2459	3.547413	GCCAGTAAACAGTTTCCGTTGAC	60.547	47.826	0.48	0.00	0.00	3.18
397	2461	2.616842	AGCCAGTAAACAGTTTCCGTTG	59.383	45.455	0.48	0.00	0.00	4.10
398	2462	2.927028	AGCCAGTAAACAGTTTCCGTT	58.073	42.857	0.48	0.00	0.00	4.44
459	2523	4.332819	CAGTTAGTATGCTGTTGCTAACCC	59.667	45.833	14.35	0.00	42.28	4.11
463	2527	3.932710	GCACAGTTAGTATGCTGTTGCTA	59.067	43.478	5.46	0.00	43.27	3.49
469	2533	2.679837	CAAGGGCACAGTTAGTATGCTG	59.320	50.000	0.00	0.00	39.38	4.41
480	2544	3.379372	CCAAAGACATATCAAGGGCACAG	59.621	47.826	0.00	0.00	0.00	3.66
524	2590	9.034544	CCTTATGAAAGAAAAAGAAACAAGTGG	57.965	33.333	0.00	0.00	34.37	4.00
612	2679	2.116983	GAGCCTCACCAGGAGTTGCA	62.117	60.000	0.00	0.00	43.65	4.08
718	2788	0.179004	TGGCCGCAAGAAAAAGGAGA	60.179	50.000	0.00	0.00	43.02	3.71
754	2824	3.665675	CTCTCCGGCGGAAAGGGTG	62.666	68.421	30.59	17.01	0.00	4.61
800	2870	1.667830	GTGCAAGCCAGCTCGTACA	60.668	57.895	0.00	0.00	34.99	2.90
801	2871	2.391389	GGTGCAAGCCAGCTCGTAC	61.391	63.158	0.00	0.00	38.87	3.67
978	3048	4.660168	TGTACTCCGAGACTTCTAACCTT	58.340	43.478	1.33	0.00	0.00	3.50
989	3071	4.338400	CCAGTTCATACATGTACTCCGAGA	59.662	45.833	7.96	0.00	36.46	4.04
1041	3126	1.699656	CCTCCTGCGAGCAATTCACG	61.700	60.000	0.00	0.00	34.49	4.35
1181	3266	5.601662	TCTCGCCTTCCAAAATAGTCATAG	58.398	41.667	0.00	0.00	0.00	2.23
1183	3274	4.162320	TCTCTCGCCTTCCAAAATAGTCAT	59.838	41.667	0.00	0.00	0.00	3.06
1187	3278	3.738282	CGATCTCTCGCCTTCCAAAATAG	59.262	47.826	0.00	0.00	38.20	1.73
1237	3328	2.985896	TCCGTTTCTCATGGATTCCAC	58.014	47.619	7.76	0.00	35.38	4.02
1286	3377	1.269778	GCAAGGGTCCAAAGCTTGTTC	60.270	52.381	0.00	0.00	0.00	3.18
1466	3569	6.458478	CCACGTATACCTTCTAGACTTCAGTG	60.458	46.154	0.00	0.00	0.00	3.66
1482	3585	6.746745	TCCAAAATCTTTTCCCACGTATAC	57.253	37.500	0.00	0.00	0.00	1.47
1596	3699	0.391661	ATGGCTGTGAAGTACCAGCG	60.392	55.000	13.47	0.00	41.21	5.18
2602	4705	2.586914	TGCATCTCATCTGCCGCG	60.587	61.111	0.00	0.00	38.89	6.46
2833	4936	5.521372	CGTAGAAGCATCATCAAACTCATCA	59.479	40.000	0.00	0.00	0.00	3.07
2888	4991	7.277098	CACTCTACTGACTACTCTTGACTACTC	59.723	44.444	0.00	0.00	0.00	2.59
2889	4992	7.101054	CACTCTACTGACTACTCTTGACTACT	58.899	42.308	0.00	0.00	0.00	2.57
2890	4993	6.314400	CCACTCTACTGACTACTCTTGACTAC	59.686	46.154	0.00	0.00	0.00	2.73
2891	4994	6.408035	CCACTCTACTGACTACTCTTGACTA	58.592	44.000	0.00	0.00	0.00	2.59
2892	4995	5.250200	CCACTCTACTGACTACTCTTGACT	58.750	45.833	0.00	0.00	0.00	3.41
2893	4996	4.396790	CCCACTCTACTGACTACTCTTGAC	59.603	50.000	0.00	0.00	0.00	3.18
2894	4997	4.043059	ACCCACTCTACTGACTACTCTTGA	59.957	45.833	0.00	0.00	0.00	3.02
2895	4998	4.337145	ACCCACTCTACTGACTACTCTTG	58.663	47.826	0.00	0.00	0.00	3.02
2896	4999	4.661247	ACCCACTCTACTGACTACTCTT	57.339	45.455	0.00	0.00	0.00	2.85
2897	5000	4.043059	TGAACCCACTCTACTGACTACTCT	59.957	45.833	0.00	0.00	0.00	3.24
2976	5079	6.909357	GCAGCAAGATTTCAATCATAGTACAC	59.091	38.462	0.00	0.00	37.89	2.90
3159	5425	1.485066	CGCCCTACTCTGTAAATGGGT	59.515	52.381	0.00	0.00	37.09	4.51
3269	5538	0.396435	ATTCTGCACCCGACTCAACA	59.604	50.000	0.00	0.00	0.00	3.33
3270	5539	0.798776	CATTCTGCACCCGACTCAAC	59.201	55.000	0.00	0.00	0.00	3.18
3355	5638	7.067496	TCCATTTGATCTACCCTAGATTCAC	57.933	40.000	0.00	0.00	45.16	3.18
3366	5649	4.884164	CCCAACTTCCTCCATTTGATCTAC	59.116	45.833	0.00	0.00	0.00	2.59
3386	5669	2.225293	ACTACTCTGTTCCAGTAGCCCA	60.225	50.000	6.76	0.00	45.07	5.36
3396	5679	5.774630	AGAAACACTGCTACTACTCTGTTC	58.225	41.667	0.00	0.00	0.00	3.18
3454	5737	7.059945	GTCTCGTGAATGATTTTGTTTTGCTAG	59.940	37.037	0.00	0.00	0.00	3.42
3480	5763	5.234116	GGTTCTGCACCTTTAACATTTTGTG	59.766	40.000	0.00	0.00	43.29	3.33
3536	5819	2.039348	TGAAACAGGCCTTGTACTACCC	59.961	50.000	0.00	0.00	39.73	3.69
3537	5820	3.007614	TCTGAAACAGGCCTTGTACTACC	59.992	47.826	0.00	0.00	39.73	3.18
3553	5836	4.594920	AGATCACAAGAGGAGGTTCTGAAA	59.405	41.667	0.00	0.00	0.00	2.69
3554	5837	4.163427	AGATCACAAGAGGAGGTTCTGAA	58.837	43.478	0.00	0.00	0.00	3.02
3555	5838	3.766591	GAGATCACAAGAGGAGGTTCTGA	59.233	47.826	0.00	0.00	0.00	3.27
3622	5905	1.148310	CGTTGTGCGGAGATGAAGTT	58.852	50.000	0.00	0.00	36.85	2.66
3632	5927	0.516877	ATGATCAACACGTTGTGCGG	59.483	50.000	9.60	0.00	46.52	5.69
3640	5935	3.808174	AGATGCATCTGATGATCAACACG	59.192	43.478	28.21	0.00	35.42	4.49
3673	5968	5.768980	TCTTGAATCCTGGATCTCAACTT	57.231	39.130	20.56	3.88	0.00	2.66
3741	6036	6.418226	CGAAATGTAATGCACTAGACTAGACC	59.582	42.308	16.55	6.82	0.00	3.85
3861	6160	0.835971	TTGCTCTAGGTGTGGCTGGA	60.836	55.000	0.00	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.