AutoCloner

Multiple sequence alignment - TraesCS5D01G257200

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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	TraesCS5D01G257200	chr5D	100.000	2288	0	0	1	2288	363341338	363339051	0.000000e+00	4226
1	TraesCS5D01G257200	chr5D	96.407	1781	23	16	530	2288	363976844	363975083	0.000000e+00	2896
2	TraesCS5D01G257200	chr5D	92.723	1333	43	21	323	1624	363178777	363177468	0.000000e+00	1875
3	TraesCS5D01G257200	chr5D	96.369	661	23	1	1628	2288	363177357	363176698	0.000000e+00	1086
4	TraesCS5D01G257200	chr5D	85.012	407	34	12	1	394	363179127	363178735	2.760000e-104	388
5	TraesCS5D01G257200	chr5A	94.675	1108	28	12	530	1624	464635393	464634304	0.000000e+00	1690
6	TraesCS5D01G257200	chr5A	97.143	665	14	2	1628	2288	464634232	464633569	0.000000e+00	1118
7	TraesCS5D01G257200	chr5B	93.543	1115	32	17	530	1624	429821227	429820133	0.000000e+00	1624
8	TraesCS5D01G257200	chr5B	94.083	845	18	13	798	1625	429727948	429727119	0.000000e+00	1254
9	TraesCS5D01G257200	chr5B	96.369	661	23	1	1628	2288	429727042	429726383	0.000000e+00	1086
10	TraesCS5D01G257200	chr5B	96.218	661	23	2	1628	2288	429820061	429819403	0.000000e+00	1081
11	TraesCS5D01G257200	chr5B	97.239	507	14	0	864	1370	429883657	429883151	0.000000e+00	859
12	TraesCS5D01G257200	chr5B	88.608	632	56	11	1628	2256	429882823	429882205	0.000000e+00	754
13	TraesCS5D01G257200	chr5B	80.747	348	42	13	9	334	429728683	429728339	4.880000e-62	248
14	TraesCS5D01G257200	chr5B	92.073	164	8	1	1401	1559	429883154	429882991	2.290000e-55	226
15	TraesCS5D01G257200	chr6B	82.700	474	80	2	881	1353	179464594	179464122	9.770000e-114	420
16	TraesCS5D01G257200	chrUn	77.632	304	57	11	1058	1355	22056440	22056738	8.400000e-40	174
17	TraesCS5D01G257200	chr2D	77.181	298	60	8	1058	1351	474749987	474750280	1.410000e-37	167

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	TraesCS5D01G257200	chr5D	363339051	363341338	2287	True	4226.000000	4226	100.000000	1	2288	1	chr5D.!!$R1	2287
1	TraesCS5D01G257200	chr5D	363975083	363976844	1761	True	2896.000000	2896	96.407000	530	2288	1	chr5D.!!$R2	1758
2	TraesCS5D01G257200	chr5D	363176698	363179127	2429	True	1116.333333	1875	91.368000	1	2288	3	chr5D.!!$R3	2287
3	TraesCS5D01G257200	chr5A	464633569	464635393	1824	True	1404.000000	1690	95.909000	530	2288	2	chr5A.!!$R1	1758
4	TraesCS5D01G257200	chr5B	429819403	429821227	1824	True	1352.500000	1624	94.880500	530	2288	2	chr5B.!!$R2	1758
5	TraesCS5D01G257200	chr5B	429726383	429728683	2300	True	862.666667	1254	90.399667	9	2288	3	chr5B.!!$R1	2279
6	TraesCS5D01G257200	chr5B	429882205	429883657	1452	True	613.000000	859	92.640000	864	2256	3	chr5B.!!$R3	1392

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
514	571	0.593128	CCCAACCAAAGCTGACGAAG	59.407	55.0	0.0	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1486	1637	3.274393	CCGGAGGCAGAAGTTATCG	57.726	57.895	0.0	0.0	46.14	2.92	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	61	2.981859	ATATGAAGTCGGGTCACACC	57.018	50.000	0.00	0.00	37.60	4.16
74	79	7.358848	GGTCACACCAAGTAATTTTTATTTGCG	60.359	37.037	0.00	0.00	38.42	4.85
101	117	9.036671	GGAAGAATCCGTTTAAATTTTGTTGAA	57.963	29.630	0.00	0.00	35.59	2.69
104	120	8.822855	AGAATCCGTTTAAATTTTGTTGAAACC	58.177	29.630	0.00	0.00	0.00	3.27
121	137	1.880941	ACCTAGTTGCTCTTAGGGGG	58.119	55.000	11.09	0.00	34.13	5.40
163	179	1.723003	CGGACTTAAAAAGGACGGTCG	59.277	52.381	1.43	0.00	0.00	4.79
165	181	2.733552	GGACTTAAAAAGGACGGTCGAC	59.266	50.000	7.13	7.13	0.00	4.20
170	186	3.457610	AAAAAGGACGGTCGACACTTA	57.542	42.857	18.91	0.00	0.00	2.24
171	187	3.672767	AAAAGGACGGTCGACACTTAT	57.327	42.857	18.91	0.00	0.00	1.73
296	320	7.910441	ATGATTTGTGGGATCAATGTTTTTC	57.090	32.000	0.00	0.00	37.11	2.29
413	470	5.373981	AAACTGTAACAAACGAACCACAA	57.626	34.783	0.00	0.00	0.00	3.33
422	479	4.747605	ACAAACGAACCACAATAAATTGCC	59.252	37.500	2.60	0.00	41.38	4.52
428	485	2.560542	ACCACAATAAATTGCCGCTTCA	59.439	40.909	2.60	0.00	41.38	3.02
446	503	3.313012	TCACATTCGACCCACACTTAG	57.687	47.619	0.00	0.00	0.00	2.18
447	504	2.894765	TCACATTCGACCCACACTTAGA	59.105	45.455	0.00	0.00	0.00	2.10
505	562	2.375014	ACCCAAGTACCCAACCAAAG	57.625	50.000	0.00	0.00	0.00	2.77
510	567	2.271944	AGTACCCAACCAAAGCTGAC	57.728	50.000	0.00	0.00	0.00	3.51
514	571	0.593128	CCCAACCAAAGCTGACGAAG	59.407	55.000	0.00	0.00	0.00	3.79
626	694	4.475016	GGACTTGCAGATATACCCCCATAT	59.525	45.833	0.00	0.00	0.00	1.78
627	695	5.044846	GGACTTGCAGATATACCCCCATATT	60.045	44.000	0.00	0.00	0.00	1.28
709	795	7.486407	AAGATCCAAGCCTAAACATCAAATT	57.514	32.000	0.00	0.00	0.00	1.82
746	839	3.728845	AGTGTGAAACTGTGAATACGCT	58.271	40.909	0.00	0.00	37.88	5.07
747	840	4.127171	AGTGTGAAACTGTGAATACGCTT	58.873	39.130	0.00	0.00	37.88	4.68
748	841	5.294356	AGTGTGAAACTGTGAATACGCTTA	58.706	37.500	0.00	0.00	37.88	3.09
750	843	5.176958	GTGTGAAACTGTGAATACGCTTACT	59.823	40.000	0.00	0.00	38.04	2.24
751	844	6.364165	GTGTGAAACTGTGAATACGCTTACTA	59.636	38.462	0.00	0.00	38.04	1.82
752	845	6.584942	TGTGAAACTGTGAATACGCTTACTAG	59.415	38.462	0.00	0.00	38.04	2.57
753	846	6.585322	GTGAAACTGTGAATACGCTTACTAGT	59.415	38.462	0.00	0.00	0.00	2.57
1486	1637	1.203287	AGGCTTACCGAAGTTCCGTAC	59.797	52.381	3.88	0.00	42.76	3.67
2270	2595	1.229820	AGCTGGGTGGTGGTATGGA	60.230	57.895	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
44	49	2.467566	ATTACTTGGTGTGACCCGAC	57.532	50.000	0.00	0.00	37.50	4.79
56	61	8.527567	TTCTTCCCGCAAATAAAAATTACTTG	57.472	30.769	0.00	0.00	0.00	3.16
74	79	7.654116	TCAACAAAATTTAAACGGATTCTTCCC	59.346	33.333	0.00	0.00	39.01	3.97
91	96	6.715347	AGAGCAACTAGGTTTCAACAAAAT	57.285	33.333	0.00	0.00	0.00	1.82
92	97	6.524101	AAGAGCAACTAGGTTTCAACAAAA	57.476	33.333	0.00	0.00	0.00	2.44
93	98	6.262273	CCTAAGAGCAACTAGGTTTCAACAAA	59.738	38.462	0.00	0.00	0.00	2.83
94	99	5.763204	CCTAAGAGCAACTAGGTTTCAACAA	59.237	40.000	0.00	0.00	0.00	2.83
96	101	4.695928	CCCTAAGAGCAACTAGGTTTCAAC	59.304	45.833	0.00	0.00	0.00	3.18
101	117	2.197465	CCCCCTAAGAGCAACTAGGTT	58.803	52.381	0.00	0.00	0.00	3.50
102	118	1.365028	TCCCCCTAAGAGCAACTAGGT	59.635	52.381	0.00	0.00	0.00	3.08
104	120	4.779993	ATTTCCCCCTAAGAGCAACTAG	57.220	45.455	0.00	0.00	0.00	2.57
213	231	1.066071	TCGGGTTGGCGAAATCACATA	60.066	47.619	0.00	0.00	0.00	2.29
239	262	3.186047	CTACCGAAGTTGCCGCCG	61.186	66.667	0.00	0.00	0.00	6.46
242	265	0.460311	AGATCCTACCGAAGTTGCCG	59.540	55.000	0.00	0.00	0.00	5.69
243	266	1.757699	AGAGATCCTACCGAAGTTGCC	59.242	52.381	0.00	0.00	0.00	4.52
244	267	2.223852	GGAGAGATCCTACCGAAGTTGC	60.224	54.545	0.00	0.00	0.00	4.17
245	268	3.292460	AGGAGAGATCCTACCGAAGTTG	58.708	50.000	0.00	0.00	38.58	3.16
246	269	3.673543	AGGAGAGATCCTACCGAAGTT	57.326	47.619	0.00	0.00	38.58	2.66
247	270	3.673543	AAGGAGAGATCCTACCGAAGT	57.326	47.619	0.00	0.00	39.65	3.01
248	271	4.975631	TCTAAGGAGAGATCCTACCGAAG	58.024	47.826	0.00	0.00	39.65	3.79
249	272	5.586155	ATCTAAGGAGAGATCCTACCGAA	57.414	43.478	0.00	0.00	39.65	4.30
250	273	6.444171	TCATATCTAAGGAGAGATCCTACCGA	59.556	42.308	0.00	0.00	39.65	4.69
251	274	6.654959	TCATATCTAAGGAGAGATCCTACCG	58.345	44.000	0.00	0.00	39.65	4.02
403	460	2.669950	GCGGCAATTTATTGTGGTTCGT	60.670	45.455	0.00	0.00	39.88	3.85
404	461	1.917303	GCGGCAATTTATTGTGGTTCG	59.083	47.619	0.00	3.37	39.88	3.95
405	462	3.230743	AGCGGCAATTTATTGTGGTTC	57.769	42.857	1.45	0.00	39.88	3.62
413	470	3.376859	TCGAATGTGAAGCGGCAATTTAT	59.623	39.130	1.45	0.00	0.00	1.40
422	479	0.948623	TGTGGGTCGAATGTGAAGCG	60.949	55.000	0.00	0.00	0.00	4.68
428	485	3.162666	TCTCTAAGTGTGGGTCGAATGT	58.837	45.455	0.00	0.00	0.00	2.71
462	519	6.076981	ACACGATTCATTGCTCTTCTTTTT	57.923	33.333	0.00	0.00	0.00	1.94
466	523	4.184629	GGTACACGATTCATTGCTCTTCT	58.815	43.478	0.00	0.00	0.00	2.85
709	795	9.357161	AGTTTCACACTGGTGGTAATAAAAATA	57.643	29.630	5.70	0.00	45.32	1.40
743	836	4.357996	GCAACCCTAGTAACTAGTAAGCG	58.642	47.826	0.00	0.00	32.62	4.68
744	837	4.096984	TCGCAACCCTAGTAACTAGTAAGC	59.903	45.833	0.00	0.00	32.62	3.09
745	838	5.824904	TCGCAACCCTAGTAACTAGTAAG	57.175	43.478	0.00	0.00	32.62	2.34
746	839	5.887598	TGATCGCAACCCTAGTAACTAGTAA	59.112	40.000	0.00	0.00	32.62	2.24
747	840	5.439721	TGATCGCAACCCTAGTAACTAGTA	58.560	41.667	0.00	0.00	32.62	1.82
748	841	4.275810	TGATCGCAACCCTAGTAACTAGT	58.724	43.478	0.00	0.00	32.62	2.57
750	843	4.647853	ACATGATCGCAACCCTAGTAACTA	59.352	41.667	0.00	0.00	0.00	2.24
751	844	3.451178	ACATGATCGCAACCCTAGTAACT	59.549	43.478	0.00	0.00	0.00	2.24
752	845	3.793559	ACATGATCGCAACCCTAGTAAC	58.206	45.455	0.00	0.00	0.00	2.50
753	846	3.181469	GGACATGATCGCAACCCTAGTAA	60.181	47.826	0.00	0.00	0.00	2.24
810	934	2.624364	AGTGCTGTTGATTGTTGCATGA	59.376	40.909	0.00	0.00	36.04	3.07
1486	1637	3.274393	CCGGAGGCAGAAGTTATCG	57.726	57.895	0.00	0.00	46.14	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.