AutoCloner

Multiple sequence alignment - TraesCS1B01G075400

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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	TraesCS1B01G075400	chr1B	100.000	2320	0	0	1	2320	58325648	58327967	0.000000e+00	4285
1	TraesCS1B01G075400	chr1B	87.578	1755	215	3	567	2320	57789178	57790930	0.000000e+00	2030
2	TraesCS1B01G075400	chr1D	94.650	1869	100	0	452	2320	38557723	38559591	0.000000e+00	2898
3	TraesCS1B01G075400	chr1D	93.955	1737	102	1	583	2319	38581567	38583300	0.000000e+00	2623
4	TraesCS1B01G075400	chr1D	90.909	1793	163	0	528	2320	38365525	38367317	0.000000e+00	2409
5	TraesCS1B01G075400	chr1D	88.724	1756	195	3	567	2320	38257220	38258974	0.000000e+00	2143
6	TraesCS1B01G075400	chr1D	86.728	1733	227	3	589	2320	36622166	36623896	0.000000e+00	1923
7	TraesCS1B01G075400	chr1D	85.813	1734	240	6	589	2319	36615754	36617484	0.000000e+00	1834
8	TraesCS1B01G075400	chr1D	87.879	429	40	6	20	447	38556580	38556997	5.760000e-136	494
9	TraesCS1B01G075400	chr1A	94.168	1869	109	0	452	2320	37502756	37504624	0.000000e+00	2848
10	TraesCS1B01G075400	chr1A	86.024	1753	237	8	570	2319	36615645	36613898	0.000000e+00	1873
11	TraesCS1B01G075400	chr1A	90.183	438	39	4	11	447	37501563	37501997	3.350000e-158	568

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	TraesCS1B01G075400	chr1B	58325648	58327967	2319	False	4285	4285	100.0000	1	2320	1	chr1B.!!$F2	2319
1	TraesCS1B01G075400	chr1B	57789178	57790930	1752	False	2030	2030	87.5780	567	2320	1	chr1B.!!$F1	1753
2	TraesCS1B01G075400	chr1D	38581567	38583300	1733	False	2623	2623	93.9550	583	2319	1	chr1D.!!$F5	1736
3	TraesCS1B01G075400	chr1D	38365525	38367317	1792	False	2409	2409	90.9090	528	2320	1	chr1D.!!$F4	1792
4	TraesCS1B01G075400	chr1D	38257220	38258974	1754	False	2143	2143	88.7240	567	2320	1	chr1D.!!$F3	1753
5	TraesCS1B01G075400	chr1D	36622166	36623896	1730	False	1923	1923	86.7280	589	2320	1	chr1D.!!$F2	1731
6	TraesCS1B01G075400	chr1D	36615754	36617484	1730	False	1834	1834	85.8130	589	2319	1	chr1D.!!$F1	1730
7	TraesCS1B01G075400	chr1D	38556580	38559591	3011	False	1696	2898	91.2645	20	2320	2	chr1D.!!$F6	2300
8	TraesCS1B01G075400	chr1A	36613898	36615645	1747	True	1873	1873	86.0240	570	2319	1	chr1A.!!$R1	1749
9	TraesCS1B01G075400	chr1A	37501563	37504624	3061	False	1708	2848	92.1755	11	2320	2	chr1A.!!$F1	2309

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
80	81	0.114954	TACCGGGACAACCACCTACT	59.885	55.0	6.32	0.0	40.22	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1385	2141	0.179073	CTTAGTCGGCCAGATGGGTG	60.179	60.0	2.24	0.0	39.65	4.61	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
56	57	5.574443	GCAACATACAGAATGAAGCCTTTTC	59.426	40.000	0.00	0.00	39.69	2.29
63	64	5.241728	ACAGAATGAAGCCTTTTCCAGTTAC	59.758	40.000	0.00	0.00	39.69	2.50
80	81	0.114954	TACCGGGACAACCACCTACT	59.885	55.000	6.32	0.00	40.22	2.57
149	150	4.635765	CGCTTTCTAATCCACCTCAATTCA	59.364	41.667	0.00	0.00	0.00	2.57
152	153	7.012327	CGCTTTCTAATCCACCTCAATTCATTA	59.988	37.037	0.00	0.00	0.00	1.90
177	178	2.035066	ACACAGTTTACGTCTAAGCGGT	59.965	45.455	0.00	0.00	35.98	5.68
205	206	3.887110	CCATCCATGATTAAGCAAGAGCA	59.113	43.478	0.00	0.00	45.49	4.26
217	218	1.093159	CAAGAGCATGAGAAGGGCAC	58.907	55.000	0.00	0.00	0.00	5.01
264	266	8.594550	AGATTACACTAGGTAAAAAGAAGCTGA	58.405	33.333	7.58	0.00	44.70	4.26
266	268	6.420913	ACACTAGGTAAAAAGAAGCTGAGA	57.579	37.500	0.00	0.00	0.00	3.27
268	270	7.454225	ACACTAGGTAAAAAGAAGCTGAGATT	58.546	34.615	0.00	0.00	0.00	2.40
276	278	5.956068	AAAGAAGCTGAGATTTGAGGAAC	57.044	39.130	0.00	0.00	0.00	3.62
278	280	4.577875	AGAAGCTGAGATTTGAGGAACAG	58.422	43.478	0.00	0.00	0.00	3.16
279	281	3.347077	AGCTGAGATTTGAGGAACAGG	57.653	47.619	0.00	0.00	0.00	4.00
314	316	1.562672	GGGTATGGTGGAGGCACACT	61.563	60.000	11.29	0.00	41.09	3.55
344	346	8.417106	CACTGTATATATGTGAGTTCCTGAAGT	58.583	37.037	11.22	0.00	33.95	3.01
347	349	2.867109	ATGTGAGTTCCTGAAGTGGG	57.133	50.000	0.00	0.00	0.00	4.61
367	369	0.163146	GAGGCGTAAACACAGCGAAC	59.837	55.000	0.00	0.00	0.00	3.95
382	384	2.514592	AACCGATGCGATGCTGGG	60.515	61.111	0.00	0.00	0.00	4.45
422	424	6.882610	ACTCAGTGTGATTTAATCAGCAAA	57.117	33.333	8.00	0.00	40.53	3.68
423	425	6.906659	ACTCAGTGTGATTTAATCAGCAAAG	58.093	36.000	8.00	9.67	40.53	2.77
430	432	6.855914	TGTGATTTAATCAGCAAAGAAACGTC	59.144	34.615	8.00	0.00	40.53	4.34
437	439	0.384353	GCAAAGAAACGTCGAGCACC	60.384	55.000	0.00	0.00	0.00	5.01
447	449	2.058001	TCGAGCACCGGATGACCAT	61.058	57.895	9.46	0.00	39.14	3.55
449	451	1.154205	CGAGCACCGGATGACCATTC	61.154	60.000	9.46	0.00	35.59	2.67
450	452	0.179000	GAGCACCGGATGACCATTCT	59.821	55.000	9.46	0.00	35.59	2.40
468	1224	4.794278	TTCTACACCGCAGAATGAACTA	57.206	40.909	0.00	0.00	39.69	2.24
483	1239	9.694520	CAGAATGAACTAAATGAAATAGTGACG	57.305	33.333	0.00	0.00	39.69	4.35
508	1264	0.386838	ACTTTCTGCAAGCAGGCAAC	59.613	50.000	20.78	0.00	44.40	4.17
941	1697	0.328258	ACCAACCCACTGGCTGATAC	59.672	55.000	0.00	0.00	40.45	2.24
1087	1843	4.083537	TCGCTTCGTCTGCACAATTATTTT	60.084	37.500	0.00	0.00	0.00	1.82
1316	2072	8.000709	TCCATTTCTACAATAGCCATCAAGAAT	58.999	33.333	0.00	0.00	0.00	2.40
1703	2460	6.182627	TCTCATTGAACTTGTCCATAGCATT	58.817	36.000	0.00	0.00	0.00	3.56
1863	2621	8.316946	TCAATTAATATGGTGAAAACATGGCAA	58.683	29.630	0.00	0.00	0.00	4.52
1972	2730	3.203442	GGTACGAGACGGCATCCA	58.797	61.111	0.00	0.00	0.00	3.41
2056	2814	4.261994	GCTTGCAAAGGGAAGTCATTAACA	60.262	41.667	0.00	0.00	46.35	2.41
2178	2936	7.040961	TGGATCATGCAATTATATGTCACTGTG	60.041	37.037	0.17	0.17	0.00	3.66
2220	2978	2.763448	GACCATCTGCTGAAGGACTAGT	59.237	50.000	20.11	0.00	34.87	2.57
2235	2993	3.526534	GACTAGTTCTGCCTTGTCCATC	58.473	50.000	0.00	0.00	33.05	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	9.480053	AAACTTTGGTTACATCAAAATGATGAG	57.520	29.630	23.16	12.35	44.36	2.90
5	6	9.258826	TGAAACTTTGGTTACATCAAAATGATG	57.741	29.630	16.60	16.60	45.55	3.07
6	7	9.480053	CTGAAACTTTGGTTACATCAAAATGAT	57.520	29.630	0.00	0.00	34.62	2.45
7	8	7.437862	GCTGAAACTTTGGTTACATCAAAATGA	59.562	33.333	0.00	0.00	34.21	2.57
8	9	7.224362	TGCTGAAACTTTGGTTACATCAAAATG	59.776	33.333	0.00	0.00	35.33	2.32
9	10	7.271511	TGCTGAAACTTTGGTTACATCAAAAT	58.728	30.769	0.00	0.00	34.26	1.82
10	11	6.634805	TGCTGAAACTTTGGTTACATCAAAA	58.365	32.000	0.00	0.00	34.26	2.44
11	12	6.214191	TGCTGAAACTTTGGTTACATCAAA	57.786	33.333	0.00	0.00	34.90	2.69
12	13	5.843673	TGCTGAAACTTTGGTTACATCAA	57.156	34.783	0.00	0.00	34.90	2.57
13	14	5.126222	TGTTGCTGAAACTTTGGTTACATCA	59.874	36.000	0.00	0.00	39.70	3.07
14	15	5.587289	TGTTGCTGAAACTTTGGTTACATC	58.413	37.500	0.00	0.00	39.70	3.06
56	57	0.604511	GTGGTTGTCCCGGTAACTGG	60.605	60.000	0.00	0.00	43.47	4.00
63	64	1.295423	CAGTAGGTGGTTGTCCCGG	59.705	63.158	0.00	0.00	35.15	5.73
80	81	7.344612	TGGAAATATGGAACTCTAGAAGTAGCA	59.655	37.037	0.00	0.00	37.17	3.49
149	150	7.795272	CGCTTAGACGTAAACTGTGTTTTTAAT	59.205	33.333	0.94	0.00	0.00	1.40
152	153	5.495502	CGCTTAGACGTAAACTGTGTTTTT	58.504	37.500	0.94	0.00	0.00	1.94
177	178	3.216800	GCTTAATCATGGATGGACAGCA	58.783	45.455	0.00	0.00	0.00	4.41
217	218	3.084039	TGAAAATAGCAGAAGGTGGCTG	58.916	45.455	0.00	0.00	41.25	4.85
221	222	7.335422	AGTGTAATCTGAAAATAGCAGAAGGTG	59.665	37.037	0.00	0.00	44.71	4.00
264	266	3.265479	CCCTCTTCCTGTTCCTCAAATCT	59.735	47.826	0.00	0.00	0.00	2.40
266	268	3.260205	TCCCTCTTCCTGTTCCTCAAAT	58.740	45.455	0.00	0.00	0.00	2.32
268	270	2.158158	TCTCCCTCTTCCTGTTCCTCAA	60.158	50.000	0.00	0.00	0.00	3.02
276	278	0.247736	CGTTGGTCTCCCTCTTCCTG	59.752	60.000	0.00	0.00	0.00	3.86
278	280	1.597461	CCGTTGGTCTCCCTCTTCC	59.403	63.158	0.00	0.00	0.00	3.46
279	281	1.192803	ACCCGTTGGTCTCCCTCTTC	61.193	60.000	0.00	0.00	43.06	2.87
291	293	1.451387	GCCTCCACCATACCCGTTG	60.451	63.158	0.00	0.00	0.00	4.10
294	296	2.189521	GTGCCTCCACCATACCCG	59.810	66.667	0.00	0.00	35.92	5.28
306	308	1.944177	ATACAGTGAGGAGTGTGCCT	58.056	50.000	0.00	0.00	42.17	4.75
320	322	7.869937	CCACTTCAGGAACTCACATATATACAG	59.130	40.741	0.00	0.00	34.60	2.74
335	337	2.592993	CGCCTCCCCACTTCAGGAA	61.593	63.158	0.00	0.00	0.00	3.36
344	346	1.373435	CTGTGTTTACGCCTCCCCA	59.627	57.895	0.00	0.00	0.00	4.96
347	349	0.947180	TTCGCTGTGTTTACGCCTCC	60.947	55.000	0.00	0.00	0.00	4.30
367	369	2.664185	CTCCCAGCATCGCATCGG	60.664	66.667	0.00	0.00	0.00	4.18
382	384	2.029844	GTGGGACGAAGCACTGCTC	61.030	63.158	3.40	0.00	38.25	4.26
422	424	1.874345	ATCCGGTGCTCGACGTTTCT	61.874	55.000	0.00	0.00	42.43	2.52
423	425	1.445582	ATCCGGTGCTCGACGTTTC	60.446	57.895	0.00	0.00	42.43	2.78
430	432	1.153369	AATGGTCATCCGGTGCTCG	60.153	57.895	0.00	0.00	36.30	5.03
437	439	1.852942	CGGTGTAGAATGGTCATCCG	58.147	55.000	0.00	0.00	36.30	4.18
447	449	3.678056	AGTTCATTCTGCGGTGTAGAA	57.322	42.857	0.00	0.00	38.49	2.10
449	451	5.580691	TCATTTAGTTCATTCTGCGGTGTAG	59.419	40.000	0.00	0.00	0.00	2.74
450	452	5.483811	TCATTTAGTTCATTCTGCGGTGTA	58.516	37.500	0.00	0.00	0.00	2.90
468	1224	9.099454	GAAAGTAGATCCGTCACTATTTCATTT	57.901	33.333	0.00	0.00	0.00	2.32
508	1264	6.351711	CCTCCTGCCAGTATAAGATATCCAAG	60.352	46.154	0.00	0.00	0.00	3.61
542	1298	5.523188	CAGCATTGTTGAACCTTTTGCTTTA	59.477	36.000	8.13	0.00	36.87	1.85
686	1442	5.424121	TGAAGCTTCAACTACTTCTTTGC	57.576	39.130	26.61	0.00	40.36	3.68
896	1652	5.864474	CCTAATGCTTCTACTTACGGCATAG	59.136	44.000	0.00	0.00	41.85	2.23
1316	2072	9.899661	AGCCTAATGTTGTTACATATAGTTCAA	57.100	29.630	0.00	0.00	44.14	2.69
1385	2141	0.179073	CTTAGTCGGCCAGATGGGTG	60.179	60.000	2.24	0.00	39.65	4.61
1703	2460	2.124736	GATTGCGTAGGCTGGCCA	60.125	61.111	14.39	4.71	40.82	5.36
1863	2621	2.446435	AGCAATGGTTTTGTAGCCGAT	58.554	42.857	0.00	0.00	0.00	4.18
2220	2978	0.391661	GAGCGATGGACAAGGCAGAA	60.392	55.000	0.00	0.00	0.00	3.02
2235	2993	2.338015	ATTGTGCAAGGCCAGAGCG	61.338	57.895	5.01	0.00	41.24	5.03
2266	3024	3.390135	CTGATGTGGTGACGTACAACTT	58.610	45.455	0.00	0.00	37.08	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.