AutoCloner

Multiple sequence alignment - TraesCS6D01G167600

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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	TraesCS6D01G167600	chr6D	100.000	2930	0	0	1	2930	151506033	151508962	0.000000e+00	5411.0
1	TraesCS6D01G167600	chr6B	96.124	1961	46	14	370	2330	275924932	275926862	0.000000e+00	3173.0
2	TraesCS6D01G167600	chr6B	94.595	518	24	3	2291	2806	275926880	275927395	0.000000e+00	798.0
3	TraesCS6D01G167600	chr6B	85.774	239	10	11	115	349	275923896	275924114	6.310000e-57	231.0
4	TraesCS6D01G167600	chr6A	97.512	1728	33	6	614	2340	192831228	192829510	0.000000e+00	2944.0
5	TraesCS6D01G167600	chr6A	94.531	640	33	2	2292	2930	192829501	192828863	0.000000e+00	987.0
6	TraesCS6D01G167600	chr6A	94.080	473	19	4	3	474	192831689	192831225	0.000000e+00	710.0
7	TraesCS6D01G167600	chr6A	76.389	216	41	10	2294	2507	355290773	355290566	1.110000e-19	108.0
8	TraesCS6D01G167600	chr7A	93.919	148	9	0	2783	2930	316635057	316634910	1.060000e-54	224.0
9	TraesCS6D01G167600	chr7A	93.333	150	9	1	2781	2930	252012862	252012714	1.370000e-53	220.0
10	TraesCS6D01G167600	chr5D	93.333	150	10	0	2781	2930	148225584	148225435	3.800000e-54	222.0
11	TraesCS6D01G167600	chr5A	93.333	150	10	0	2781	2930	10677183	10677034	3.800000e-54	222.0
12	TraesCS6D01G167600	chr5A	93.333	150	10	0	2781	2930	168597880	168598029	3.800000e-54	222.0
13	TraesCS6D01G167600	chr5B	90.798	163	14	1	2768	2930	589675357	589675196	1.770000e-52	217.0
14	TraesCS6D01G167600	chr5B	76.950	282	43	16	2312	2578	645044444	645044170	1.090000e-29	141.0
15	TraesCS6D01G167600	chr4D	92.667	150	11	0	2781	2930	75141116	75140967	1.770000e-52	217.0
16	TraesCS6D01G167600	chr1D	92.667	150	11	0	2781	2930	235886258	235886407	1.770000e-52	217.0
17	TraesCS6D01G167600	chr7D	75.000	288	61	9	2294	2575	373998330	373998048	3.970000e-24	122.0
18	TraesCS6D01G167600	chr7D	100.000	30	0	0	816	845	431269779	431269750	4.080000e-04	56.5
19	TraesCS6D01G167600	chr4B	73.737	297	70	5	2294	2585	116689089	116688796	3.090000e-20	110.0

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	TraesCS6D01G167600	chr6D	151506033	151508962	2929	False	5411.000000	5411	100.000000	1	2930	1	chr6D.!!$F1	2929
1	TraesCS6D01G167600	chr6B	275923896	275927395	3499	False	1400.666667	3173	92.164333	115	2806	3	chr6B.!!$F1	2691
2	TraesCS6D01G167600	chr6A	192828863	192831689	2826	True	1547.000000	2944	95.374333	3	2930	3	chr6A.!!$R2	2927

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
354	359	0.693049	CGCCCCTTATTGGATAGGCT	59.307	55.0	0.0	0.0	38.17	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1954	2756	1.431496	TAACCTTTCTAACGTGCCGC	58.569	50.0	0.0	0.0	0.0	6.53	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
79	80	2.418368	TAATCCATGCCAGTGACACC	57.582	50.000	0.84	0.00	0.00	4.16
98	99	9.828852	GTGACACCGACATATTTTTGTTTATAA	57.171	29.630	0.00	0.00	0.00	0.98
136	137	5.632347	CCAAGTTTTGATCATTGAGAACAGC	59.368	40.000	8.10	0.00	30.16	4.40
323	328	4.457257	AGGTGAAAATTAGAGAGCAAGCAC	59.543	41.667	0.00	0.00	0.00	4.40
354	359	0.693049	CGCCCCTTATTGGATAGGCT	59.307	55.000	0.00	0.00	38.17	4.58
434	1234	9.494271	TGAACAGGATTATACATAAAGAGATGC	57.506	33.333	0.00	0.00	0.00	3.91
563	1363	8.553459	TCTATTTCTTTTGTTTTTGTTTGGCA	57.447	26.923	0.00	0.00	0.00	4.92
564	1364	9.003658	TCTATTTCTTTTGTTTTTGTTTGGCAA	57.996	25.926	0.00	0.00	34.87	4.52
565	1365	9.617975	CTATTTCTTTTGTTTTTGTTTGGCAAA	57.382	25.926	8.93	8.93	44.52	3.68
566	1366	7.685532	TTTCTTTTGTTTTTGTTTGGCAAAC	57.314	28.000	30.99	30.99	45.70	2.93
567	1367	6.625873	TCTTTTGTTTTTGTTTGGCAAACT	57.374	29.167	35.03	0.00	45.70	2.66
568	1368	6.433766	TCTTTTGTTTTTGTTTGGCAAACTG	58.566	32.000	35.03	16.29	45.70	3.16
569	1369	4.756084	TTGTTTTTGTTTGGCAAACTGG	57.244	36.364	35.03	0.00	45.70	4.00
570	1370	2.485814	TGTTTTTGTTTGGCAAACTGGC	59.514	40.909	35.03	22.77	45.70	4.85
611	1411	1.687297	GGCTGGTGAGGGGTAGTAGC	61.687	65.000	0.00	0.00	0.00	3.58
659	1459	6.777091	TCTTCTCTTCCTCTCTCCTTCATATG	59.223	42.308	0.00	0.00	0.00	1.78
799	1599	7.063780	CACAGCTTTCCTTGCTTAATAATTTGG	59.936	37.037	0.00	0.00	38.92	3.28
935	1735	8.423906	AGATAAGATAGAGGCGGAATAAAGAA	57.576	34.615	0.00	0.00	0.00	2.52
936	1736	8.871125	AGATAAGATAGAGGCGGAATAAAGAAA	58.129	33.333	0.00	0.00	0.00	2.52
1672	2474	1.226262	GGGCCGGTGGTGATAATGT	59.774	57.895	1.90	0.00	0.00	2.71
2029	2831	2.738643	GCATCTCGAAGGATTTCCGTGA	60.739	50.000	0.00	0.00	42.08	4.35
2061	2863	6.061441	TGCATACCATTTCGGATCTTGTTAT	58.939	36.000	0.00	0.00	38.63	1.89
2195	2998	7.041030	GGCTAGCACCTTATATTCTTCCTTTTC	60.041	40.741	18.24	0.00	0.00	2.29
2231	3034	2.370281	ACTAGTCATCAACCTGTGCG	57.630	50.000	0.00	0.00	0.00	5.34
2336	3196	3.303938	TGGGTTGTTTGGTTCACATGAT	58.696	40.909	0.00	0.00	0.00	2.45
2512	3372	5.821516	TTCCTGCGTTTTCTTTGAAACTA	57.178	34.783	0.00	0.00	37.37	2.24
2530	3390	8.924511	TGAAACTAAGATCAAAGGAAATGTCT	57.075	30.769	0.00	0.00	0.00	3.41
2629	3489	3.258622	ACTTTTGTCCCTCTACTTCTCCG	59.741	47.826	0.00	0.00	0.00	4.63
2700	3560	8.644619	CAGCATTCAGTTGTTTGAATTAAGATG	58.355	33.333	0.00	0.00	43.41	2.90
2774	3634	8.496872	TGTAAGCGCAAGTTCTTTAATTTTAC	57.503	30.769	11.47	4.83	41.68	2.01
2776	3636	6.986424	AGCGCAAGTTCTTTAATTTTACAC	57.014	33.333	11.47	0.00	41.68	2.90
2841	3702	3.251484	TCTCTTCAACCAAGGGAGATGT	58.749	45.455	0.00	0.00	36.60	3.06
2847	3708	4.335416	TCAACCAAGGGAGATGTTGAATC	58.665	43.478	0.00	0.00	42.81	2.52
2875	3736	8.300495	GGAATTAATTCCGTAGTTTGCAAAAA	57.700	30.769	27.25	3.67	46.01	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	110	6.096705	TGTTCTCAATGATCAAAACTTGGTGT	59.903	34.615	0.00	0.00	0.00	4.16
113	114	5.341462	CGCTGTTCTCAATGATCAAAACTTG	59.659	40.000	0.00	0.00	0.00	3.16
208	209	8.743085	ATTTTATGCTACATCATCAGTTGTCT	57.257	30.769	0.00	0.00	0.00	3.41
235	240	8.049721	CAGTCTTTAGTCTCTCCCCATTTATTT	58.950	37.037	0.00	0.00	0.00	1.40
236	241	7.403231	TCAGTCTTTAGTCTCTCCCCATTTATT	59.597	37.037	0.00	0.00	0.00	1.40
237	242	6.903534	TCAGTCTTTAGTCTCTCCCCATTTAT	59.096	38.462	0.00	0.00	0.00	1.40
238	243	6.261435	TCAGTCTTTAGTCTCTCCCCATTTA	58.739	40.000	0.00	0.00	0.00	1.40
323	328	5.278463	CCAATAAGGGGCGACAGAATAATTG	60.278	44.000	0.00	0.00	0.00	2.32
422	1222	5.300034	TGTTTAGGGCATGCATCTCTTTATG	59.700	40.000	21.36	0.00	0.00	1.90
431	1231	1.545582	GTGTGTGTTTAGGGCATGCAT	59.454	47.619	21.36	10.08	0.00	3.96
432	1232	0.958091	GTGTGTGTTTAGGGCATGCA	59.042	50.000	21.36	0.00	0.00	3.96
433	1233	1.200020	GAGTGTGTGTTTAGGGCATGC	59.800	52.381	9.90	9.90	0.00	4.06
434	1234	1.464608	CGAGTGTGTGTTTAGGGCATG	59.535	52.381	0.00	0.00	0.00	4.06
475	1275	0.462225	GGGCTAGCTTCTCGGGAAAC	60.462	60.000	15.72	0.00	0.00	2.78
537	1337	9.003658	TGCCAAACAAAAACAAAAGAAATAGAA	57.996	25.926	0.00	0.00	0.00	2.10
561	1361	0.612744	AGAGAGAGAGGCCAGTTTGC	59.387	55.000	5.01	0.00	0.00	3.68
562	1362	2.354604	GGAAGAGAGAGAGGCCAGTTTG	60.355	54.545	5.01	0.00	0.00	2.93
563	1363	1.905894	GGAAGAGAGAGAGGCCAGTTT	59.094	52.381	5.01	0.00	0.00	2.66
564	1364	1.203237	TGGAAGAGAGAGAGGCCAGTT	60.203	52.381	5.01	0.00	0.00	3.16
565	1365	0.411452	TGGAAGAGAGAGAGGCCAGT	59.589	55.000	5.01	0.00	0.00	4.00
566	1366	1.792115	ATGGAAGAGAGAGAGGCCAG	58.208	55.000	5.01	0.00	0.00	4.85
567	1367	2.260639	AATGGAAGAGAGAGAGGCCA	57.739	50.000	5.01	0.00	0.00	5.36
568	1368	3.643199	AAAATGGAAGAGAGAGAGGCC	57.357	47.619	0.00	0.00	0.00	5.19
593	1393	1.823976	GCTACTACCCCTCACCAGC	59.176	63.158	0.00	0.00	0.00	4.85
634	1434	4.666412	TGAAGGAGAGAGGAAGAGAAGA	57.334	45.455	0.00	0.00	0.00	2.87
728	1528	3.756434	CGGCAAGGAAAAGATGTAAAGGA	59.244	43.478	0.00	0.00	0.00	3.36
799	1599	1.567357	AGAGGGAGGAGAAGAACTGC	58.433	55.000	0.00	0.00	37.22	4.40
935	1735	5.360591	TCTCTCTCGTTTCTCTTGCTTTTT	58.639	37.500	0.00	0.00	0.00	1.94
936	1736	4.950050	TCTCTCTCGTTTCTCTTGCTTTT	58.050	39.130	0.00	0.00	0.00	2.27
1672	2474	1.733041	CGTTCGCGAAGGAAGCTGA	60.733	57.895	31.78	0.94	44.71	4.26
1954	2756	1.431496	TAACCTTTCTAACGTGCCGC	58.569	50.000	0.00	0.00	0.00	6.53
2029	2831	7.667219	AGATCCGAAATGGTATGCAATAATTCT	59.333	33.333	0.00	0.00	39.52	2.40
2061	2863	2.247358	TCCTGATGCGGACATGCTATA	58.753	47.619	0.00	0.00	36.35	1.31
2195	2998	9.462174	GATGACTAGTATCTGAACATGAGAAAG	57.538	37.037	0.00	0.00	0.00	2.62
2351	3211	5.596836	TTTGGCCATGTTTATCAGGATTC	57.403	39.130	6.09	0.00	0.00	2.52
2512	3372	5.896963	AGGGAAGACATTTCCTTTGATCTT	58.103	37.500	5.96	0.00	42.33	2.40
2527	3387	2.037251	GGGCAAAGGAAAAAGGGAAGAC	59.963	50.000	0.00	0.00	0.00	3.01
2530	3390	1.344496	TGGGGCAAAGGAAAAAGGGAA	60.344	47.619	0.00	0.00	0.00	3.97
2613	3473	2.444421	TCAACGGAGAAGTAGAGGGAC	58.556	52.381	0.00	0.00	0.00	4.46
2614	3474	2.824341	GTTCAACGGAGAAGTAGAGGGA	59.176	50.000	0.00	0.00	0.00	4.20
2629	3489	1.704641	AAGGGCCTCTTTGGTTCAAC	58.295	50.000	6.46	0.00	38.35	3.18
2726	3586	6.545666	ACATATCAAAAGTCACTTGGTTGTCA	59.454	34.615	0.00	0.00	0.00	3.58
2774	3634	4.030913	TGGAAAGGAGGGAGTACATAGTG	58.969	47.826	0.00	0.00	0.00	2.74
2776	3636	4.290942	ACTGGAAAGGAGGGAGTACATAG	58.709	47.826	0.00	0.00	0.00	2.23
2827	3688	3.244911	ACGATTCAACATCTCCCTTGGTT	60.245	43.478	0.00	0.00	0.00	3.67
2899	3760	9.114952	TGCATCGGTATACATAAAATTTTGAGA	57.885	29.630	13.76	0.00	0.00	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.