AutoCloner

Multiple sequence alignment - TraesCS3B01G128300

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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	TraesCS3B01G128300	chr3B	100.000	3496	0	0	1	3496	107250140	107253635	0	6457
1	TraesCS3B01G128300	chr3B	93.600	3453	198	22	53	3496	247151094	247154532	0	5131
2	TraesCS3B01G128300	chr5B	94.613	3471	161	18	34	3496	221162655	221159203	0	5350
3	TraesCS3B01G128300	chr7B	94.262	3503	183	16	1	3496	33969092	33972583	0	5339
4	TraesCS3B01G128300	chr4B	93.685	3452	196	18	53	3496	425954054	425950617	0	5147
5	TraesCS3B01G128300	chr4B	93.621	3433	203	13	53	3479	470135780	470139202	0	5112
6	TraesCS3B01G128300	chr1B	93.592	3449	203	16	53	3496	274298011	274301446	0	5129
7	TraesCS3B01G128300	chr1B	93.376	3457	206	18	53	3496	256486659	256483213	0	5094
8	TraesCS3B01G128300	chr1B	93.370	3454	202	23	53	3496	555898133	555894697	0	5084
9	TraesCS3B01G128300	chr6B	93.535	3434	203	16	53	3479	589452815	589456236	0	5094

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	TraesCS3B01G128300	chr3B	107250140	107253635	3495	False	6457	6457	100.000	1	3496	1	chr3B.!!$F1	3495
1	TraesCS3B01G128300	chr3B	247151094	247154532	3438	False	5131	5131	93.600	53	3496	1	chr3B.!!$F2	3443
2	TraesCS3B01G128300	chr5B	221159203	221162655	3452	True	5350	5350	94.613	34	3496	1	chr5B.!!$R1	3462
3	TraesCS3B01G128300	chr7B	33969092	33972583	3491	False	5339	5339	94.262	1	3496	1	chr7B.!!$F1	3495
4	TraesCS3B01G128300	chr4B	425950617	425954054	3437	True	5147	5147	93.685	53	3496	1	chr4B.!!$R1	3443
5	TraesCS3B01G128300	chr4B	470135780	470139202	3422	False	5112	5112	93.621	53	3479	1	chr4B.!!$F1	3426
6	TraesCS3B01G128300	chr1B	274298011	274301446	3435	False	5129	5129	93.592	53	3496	1	chr1B.!!$F1	3443
7	TraesCS3B01G128300	chr1B	256483213	256486659	3446	True	5094	5094	93.376	53	3496	1	chr1B.!!$R1	3443
8	TraesCS3B01G128300	chr1B	555894697	555898133	3436	True	5084	5084	93.370	53	3496	1	chr1B.!!$R2	3443
9	TraesCS3B01G128300	chr6B	589452815	589456236	3421	False	5094	5094	93.535	53	3479	1	chr6B.!!$F1	3426

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
835	846	0.690192	CCATGACCACTACACCCACA	59.31	55.0	0.0	0.0	0.0	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2500	2529	1.082169	GCGAGCAACACGAATGCAA	60.082	52.632	12.72	0.0	46.22	4.08	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
229	230	9.693739	TTATATAAAATCTGTCCACACCACAAT	57.306	29.630	0.00	0.00	0.00	2.71
242	243	2.813754	CACCACAATGAACGATCTGGTT	59.186	45.455	2.13	0.00	29.23	3.67
339	343	5.349817	CAGTACTAAAACAGCAGGATCAGTG	59.650	44.000	0.00	0.00	0.00	3.66
357	361	2.603473	AGGCCACTCGCACCACTA	60.603	61.111	5.01	0.00	40.31	2.74
437	441	9.563748	AGTACTAAACCATAAGTGCACTAAAAA	57.436	29.630	22.01	6.69	31.54	1.94
440	444	9.073475	ACTAAACCATAAGTGCACTAAAAATGA	57.927	29.630	22.01	1.75	0.00	2.57
441	445	9.559958	CTAAACCATAAGTGCACTAAAAATGAG	57.440	33.333	22.01	15.61	0.00	2.90
442	446	7.759489	AACCATAAGTGCACTAAAAATGAGA	57.241	32.000	22.01	0.00	0.00	3.27
614	622	2.680841	CACACGGAAAAACCTCACAGAA	59.319	45.455	0.00	0.00	36.31	3.02
620	629	4.513692	CGGAAAAACCTCACAGAACATACA	59.486	41.667	0.00	0.00	36.31	2.29
835	846	0.690192	CCATGACCACTACACCCACA	59.310	55.000	0.00	0.00	0.00	4.17
887	899	2.161410	GTCGATGCACTGCAAAATACCA	59.839	45.455	8.03	0.00	43.62	3.25
986	998	1.152030	TCTCCCAAGCCCACAGTCT	60.152	57.895	0.00	0.00	0.00	3.24
1056	1068	3.290308	GAGACTTCGAACAAGAGCAGA	57.710	47.619	0.00	0.00	0.00	4.26
1122	1134	1.770294	AAACGCTCAAAGGGGTTGAA	58.230	45.000	0.00	0.00	45.67	2.69
1125	1137	1.418637	ACGCTCAAAGGGGTTGAACTA	59.581	47.619	0.00	0.00	45.67	2.24
1160	1172	0.247460	CTGGAGATCGTCTGCACCAA	59.753	55.000	5.39	0.00	39.98	3.67
1373	1385	4.968719	ACCCATACTACTGGTCATTCATCA	59.031	41.667	0.00	0.00	34.23	3.07
1497	1509	8.389779	TCAAGTTACATGCATTTCTGAAACTA	57.610	30.769	4.73	0.00	0.00	2.24
1616	1629	5.106634	GCATAGATTCTGATCTTGATGCACC	60.107	44.000	14.62	0.00	45.40	5.01
1755	1768	6.886459	ACAAAGATGTATCAAGCACTGGTATT	59.114	34.615	0.00	0.00	38.24	1.89
1806	1819	1.135489	ACTTGAATCAAGCAGCGCATG	60.135	47.619	21.69	6.31	44.43	4.06
1908	1924	9.887406	AAAATAACACGGTGTAGTTGAATTTAG	57.113	29.630	15.11	0.00	0.00	1.85
1945	1961	9.826574	TTGTGTACTAGTTTCTGAACTACATTT	57.173	29.630	0.00	0.00	44.13	2.32
2115	2142	3.437049	GCAGGAGGAGAAATTGTACACAC	59.563	47.826	0.00	0.00	0.00	3.82
2141	2168	2.450476	GGTTTCAGCATTGGAGGTGAT	58.550	47.619	0.00	0.00	44.50	3.06
2241	2268	3.881937	AGACCACCAAATACTACGACC	57.118	47.619	0.00	0.00	0.00	4.79
2286	2313	3.677700	CGTCATCCACCCATTCTACGAAA	60.678	47.826	0.00	0.00	0.00	3.46
2354	2381	2.281761	CCGCTGCCAGACAACCTT	60.282	61.111	0.00	0.00	0.00	3.50
2355	2382	2.620112	CCGCTGCCAGACAACCTTG	61.620	63.158	0.00	0.00	0.00	3.61
2373	2400	3.444916	CTTGTCACGTACGCAGGAATAT	58.555	45.455	16.72	0.00	0.00	1.28
2500	2529	3.181493	GCGGATGAAGATGCATGAAAGTT	60.181	43.478	2.46	0.00	0.00	2.66
2536	2565	2.496070	TCGCGCTTATGCCTATCCTTAT	59.504	45.455	5.56	0.00	35.36	1.73
2543	2572	7.097192	CGCTTATGCCTATCCTTATTCTTGTA	58.903	38.462	0.00	0.00	35.36	2.41
2690	2720	8.458843	GTTTGCTAGCTTCCTATTTTGTTGATA	58.541	33.333	17.23	0.00	0.00	2.15
2827	2861	7.814587	GCAGATAACTAAGGACAAAAGCAAATT	59.185	33.333	0.00	0.00	0.00	1.82
2857	2891	5.638596	TCGATGCTCAGTACAACTTAGAA	57.361	39.130	0.00	0.00	0.00	2.10
2861	2895	5.862924	TGCTCAGTACAACTTAGAAATGC	57.137	39.130	0.00	0.00	0.00	3.56
3008	3047	6.296026	TCACTAAGTACTGCAACAGGAAAAT	58.704	36.000	0.00	0.00	35.51	1.82
3094	3134	9.066892	ACACTTGAACACATAGTACATTCATTT	57.933	29.630	0.00	0.00	0.00	2.32
3143	3183	4.142381	GCTTCAGTTCGCATTCCCTAAAAT	60.142	41.667	0.00	0.00	0.00	1.82
3153	3193	5.123186	CGCATTCCCTAAAATAGTGACACAA	59.877	40.000	8.59	0.00	0.00	3.33
3154	3194	6.348950	CGCATTCCCTAAAATAGTGACACAAA	60.349	38.462	8.59	0.00	0.00	2.83
3347	3390	3.805422	CACAACAGAAAACGTACTAGCCA	59.195	43.478	0.00	0.00	0.00	4.75
3460	3504	8.537728	TGATACCAATTAATGCCTTGAGAAAT	57.462	30.769	0.00	0.00	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
229	230	8.786826	AGATTATTTTACAACCAGATCGTTCA	57.213	30.769	0.00	0.00	0.00	3.18
242	243	5.717654	GGTGGGGGTTTGAGATTATTTTACA	59.282	40.000	0.00	0.00	0.00	2.41
339	343	1.961180	ATAGTGGTGCGAGTGGCCTC	61.961	60.000	3.32	0.00	42.61	4.70
357	361	5.644636	GCATGGGTTTGAAATTTGATGTCAT	59.355	36.000	0.00	0.00	0.00	3.06
399	403	9.701098	TTATGGTTTAGTACTGTGTGAACTAAG	57.299	33.333	5.39	0.00	37.11	2.18
401	405	8.863086	ACTTATGGTTTAGTACTGTGTGAACTA	58.137	33.333	5.39	1.66	0.00	2.24
438	442	9.528489	AGGCCTTTATAGTTTTTGTATTTCTCA	57.472	29.630	0.00	0.00	0.00	3.27
606	614	6.873605	TGTTTAGGTGATGTATGTTCTGTGAG	59.126	38.462	0.00	0.00	0.00	3.51
614	622	4.905429	TGCACTGTTTAGGTGATGTATGT	58.095	39.130	0.00	0.00	36.89	2.29
620	629	4.559153	GCATTTTGCACTGTTTAGGTGAT	58.441	39.130	0.00	0.00	44.26	3.06
887	899	2.575279	AGGCAGAGATGGAAGACAATGT	59.425	45.455	0.00	0.00	0.00	2.71
986	998	3.154473	CCATCGCCTTCCTCCGGA	61.154	66.667	2.93	2.93	0.00	5.14
1056	1068	1.269413	ACGTGAATGTCGACGAGGTTT	60.269	47.619	11.62	0.00	38.94	3.27
1122	1134	0.317479	GTGTCTCCTTGCCGTGTAGT	59.683	55.000	0.00	0.00	0.00	2.73
1125	1137	1.069765	CAGTGTCTCCTTGCCGTGT	59.930	57.895	0.00	0.00	0.00	4.49
1160	1172	0.249398	GTCGGCCTTGTCTGGTATGT	59.751	55.000	0.00	0.00	0.00	2.29
1212	1224	0.178068	TGAAGCTCGGATACAAGCCC	59.822	55.000	0.00	0.00	0.00	5.19
1363	1375	6.398918	AGTACTGGTACAACTGATGAATGAC	58.601	40.000	12.54	0.00	38.70	3.06
1373	1385	8.469309	TTTTAGTGAGTAGTACTGGTACAACT	57.531	34.615	7.76	6.73	38.70	3.16
1408	1420	8.336801	AGTTCATATAGTTGGGAAACAAGTTC	57.663	34.615	0.00	0.00	42.58	3.01
1497	1509	4.728772	TCTGGTGAAACAATCCACTTCAT	58.271	39.130	0.00	0.00	39.98	2.57
1908	1924	7.494952	AGAAACTAGTACACAAAGTCCTGAAAC	59.505	37.037	0.00	0.00	0.00	2.78
2028	2048	9.831737	CACACATTTAAAGATTAGTCTTCCTTG	57.168	33.333	0.40	0.97	43.80	3.61
2031	2051	9.220767	AGACACACATTTAAAGATTAGTCTTCC	57.779	33.333	0.40	0.00	43.80	3.46
2115	2142	1.879380	TCCAATGCTGAAACCGACAAG	59.121	47.619	0.00	0.00	0.00	3.16
2241	2268	2.676121	TGCAACATCGGCCAAGGG	60.676	61.111	2.24	0.00	0.00	3.95
2286	2313	4.515361	CTGTCCATCTTCTTCTTCATGCT	58.485	43.478	0.00	0.00	0.00	3.79
2354	2381	4.542735	CATATATTCCTGCGTACGTGACA	58.457	43.478	17.90	5.50	0.00	3.58
2355	2382	3.364023	GCATATATTCCTGCGTACGTGAC	59.636	47.826	17.90	0.27	0.00	3.67
2500	2529	1.082169	GCGAGCAACACGAATGCAA	60.082	52.632	12.72	0.00	46.22	4.08
2557	2587	6.183360	GCTGGTTCAACATAACAAAAGCAAAA	60.183	34.615	0.00	0.00	34.54	2.44
2566	2596	4.634012	AGGTAGCTGGTTCAACATAACA	57.366	40.909	0.00	0.00	0.00	2.41
2690	2720	7.502226	TCAACCTACTTCAACTTCAAATGATGT	59.498	33.333	0.00	0.00	37.59	3.06
2827	2861	1.186200	ACTGAGCATCGAAGGCTACA	58.814	50.000	14.08	12.37	42.78	2.74
2857	2891	4.401519	AGTGTGATAGTACTACCGTGCATT	59.598	41.667	4.31	0.00	0.00	3.56
3008	3047	7.446013	AGGAAATACGTATTGGTGTTTCTTTGA	59.554	33.333	21.00	0.00	43.41	2.69
3188	3228	7.201145	CACTTGCCGTATAGACTTAGTTGTAT	58.799	38.462	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.