AutoCloner

Multiple sequence alignment - TraesCS7A01G280500

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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	TraesCS7A01G280500	chr7A	100.000	3517	0	0	1	3517	299568503	299572019	0.000000e+00	6495
1	TraesCS7A01G280500	chr7A	99.413	341	2	0	1	341	296604347	296604007	1.390000e-173	619
2	TraesCS7A01G280500	chr7A	97.668	343	6	1	1	341	305708823	305709165	3.910000e-164	588
3	TraesCS7A01G280500	chr2A	99.089	3185	29	0	333	3517	678124295	678121111	0.000000e+00	5722
4	TraesCS7A01G280500	chr2A	98.992	3176	31	1	342	3517	57916518	57913344	0.000000e+00	5686
5	TraesCS7A01G280500	chr2A	96.411	3176	90	12	342	3517	672845011	672848162	0.000000e+00	5212
6	TraesCS7A01G280500	chr2A	84.722	216	13	10	30	245	715964253	715964448	7.700000e-47	198
7	TraesCS7A01G280500	chr1D	98.553	3179	44	2	339	3517	283557061	283560237	0.000000e+00	5614
8	TraesCS7A01G280500	chr3B	98.395	3177	47	2	342	3517	245008829	245012002	0.000000e+00	5581
9	TraesCS7A01G280500	chr3B	98.093	2675	51	0	843	3517	259399586	259396912	0.000000e+00	4658
10	TraesCS7A01G280500	chr3B	95.289	467	21	1	351	817	259400045	259399580	0.000000e+00	739
11	TraesCS7A01G280500	chr4D	97.764	3176	50	3	342	3517	281202809	281199655	0.000000e+00	5452
12	TraesCS7A01G280500	chr4D	93.519	108	6	1	1	108	441486814	441486708	3.630000e-35	159
13	TraesCS7A01G280500	chr1B	96.883	3176	68	12	342	3517	682092121	682088977	0.000000e+00	5288
14	TraesCS7A01G280500	chr1B	98.815	2785	33	0	342	3126	611146109	611148893	0.000000e+00	4961
15	TraesCS7A01G280500	chr4B	95.751	3177	117	11	341	3517	637596055	637599213	0.000000e+00	5103
16	TraesCS7A01G280500	chr6A	98.827	341	4	0	1	341	58306625	58306285	3.000000e-170	608
17	TraesCS7A01G280500	chr7B	92.614	352	13	3	1	341	511462094	511462443	8.770000e-136	494
18	TraesCS7A01G280500	chr7B	93.519	108	6	1	1	108	420072796	420072690	3.630000e-35	159
19	TraesCS7A01G280500	chr2B	91.705	217	7	2	1	206	296067367	296067583	1.240000e-74	291
20	TraesCS7A01G280500	chr2B	95.745	141	6	0	105	245	695410265	695410405	9.820000e-56	228
21	TraesCS7A01G280500	chr2B	95.745	141	6	0	105	245	695436952	695437092	9.820000e-56	228
22	TraesCS7A01G280500	chr2B	98.182	110	2	0	232	341	296069228	296069337	3.580000e-45	193
23	TraesCS7A01G280500	chr2D	92.857	112	7	1	1	111	631794975	631795086	1.010000e-35	161
24	TraesCS7A01G280500	chr2D	87.395	119	15	0	107	225	577800580	577800698	1.700000e-28	137
25	TraesCS7A01G280500	chr4A	91.304	115	8	2	1	114	692657453	692657340	4.700000e-34	156

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	TraesCS7A01G280500	chr7A	299568503	299572019	3516	False	6495.0	6495	100.0000	1	3517	1	chr7A.!!$F1	3516
1	TraesCS7A01G280500	chr2A	678121111	678124295	3184	True	5722.0	5722	99.0890	333	3517	1	chr2A.!!$R2	3184
2	TraesCS7A01G280500	chr2A	57913344	57916518	3174	True	5686.0	5686	98.9920	342	3517	1	chr2A.!!$R1	3175
3	TraesCS7A01G280500	chr2A	672845011	672848162	3151	False	5212.0	5212	96.4110	342	3517	1	chr2A.!!$F1	3175
4	TraesCS7A01G280500	chr1D	283557061	283560237	3176	False	5614.0	5614	98.5530	339	3517	1	chr1D.!!$F1	3178
5	TraesCS7A01G280500	chr3B	245008829	245012002	3173	False	5581.0	5581	98.3950	342	3517	1	chr3B.!!$F1	3175
6	TraesCS7A01G280500	chr3B	259396912	259400045	3133	True	2698.5	4658	96.6910	351	3517	2	chr3B.!!$R1	3166
7	TraesCS7A01G280500	chr4D	281199655	281202809	3154	True	5452.0	5452	97.7640	342	3517	1	chr4D.!!$R1	3175
8	TraesCS7A01G280500	chr1B	682088977	682092121	3144	True	5288.0	5288	96.8830	342	3517	1	chr1B.!!$R1	3175
9	TraesCS7A01G280500	chr1B	611146109	611148893	2784	False	4961.0	4961	98.8150	342	3126	1	chr1B.!!$F1	2784
10	TraesCS7A01G280500	chr4B	637596055	637599213	3158	False	5103.0	5103	95.7510	341	3517	1	chr4B.!!$F1	3176
11	TraesCS7A01G280500	chr2B	296067367	296069337	1970	False	242.0	291	94.9435	1	341	2	chr2B.!!$F3	340

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
321	438	0.035317	TGGTCGTTGCAGCATTCTCT	59.965	50.0	0.0	0.0	0.0	3.10	F
322	439	1.160137	GGTCGTTGCAGCATTCTCTT	58.840	50.0	0.0	0.0	0.0	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2080	2913	2.325583	TGCTGTTCGTTCCTCTTGTT	57.674	45.000	0.0	0.0	0.0	2.83	R
2767	3601	3.947910	ATGAACAAGCACAAATGGGAG	57.052	42.857	0.0	0.0	0.0	4.30	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
45	56	7.851228	ACTTGTCACAGAAATGGATGTATCTA	58.149	34.615	0.00	0.00	0.00	1.98
86	97	8.909923	TCTAGATACATCCATTTCTACGACAAA	58.090	33.333	0.00	0.00	0.00	2.83
88	99	8.594881	AGATACATCCATTTCTACGACAAATC	57.405	34.615	0.00	0.00	0.00	2.17
99	110	2.346803	ACGACAAATCATTCCGGACAG	58.653	47.619	1.83	0.00	0.00	3.51
135	146	7.605691	GTGCAAGGCAATAGATTCTAGTGATAT	59.394	37.037	21.83	6.40	41.47	1.63
216	333	4.761739	CCACTGCCATCTAGAACTTTTGAA	59.238	41.667	0.00	0.00	0.00	2.69
251	368	6.709018	TTATAATAAGAAAGCAACAGGGCC	57.291	37.500	0.00	0.00	0.00	5.80
252	369	2.603075	ATAAGAAAGCAACAGGGCCA	57.397	45.000	6.18	0.00	0.00	5.36
253	370	1.616159	TAAGAAAGCAACAGGGCCAC	58.384	50.000	6.18	0.00	0.00	5.01
254	371	0.396974	AAGAAAGCAACAGGGCCACA	60.397	50.000	6.18	0.00	0.00	4.17
255	372	1.109323	AGAAAGCAACAGGGCCACAC	61.109	55.000	6.18	0.00	0.00	3.82
257	374	2.870035	AAAGCAACAGGGCCACACCA	62.870	55.000	6.18	0.00	42.05	4.17
266	383	2.741092	GCCACACCAGTCGAAGGA	59.259	61.111	11.80	0.00	0.00	3.36
267	384	1.070786	GCCACACCAGTCGAAGGAA	59.929	57.895	11.80	0.00	0.00	3.36
269	386	0.393077	CCACACCAGTCGAAGGAAGT	59.607	55.000	11.80	7.07	0.00	3.01
270	387	1.202651	CCACACCAGTCGAAGGAAGTT	60.203	52.381	11.80	0.00	0.00	2.66
271	388	2.561569	CACACCAGTCGAAGGAAGTTT	58.438	47.619	11.80	0.00	0.00	2.66
275	392	2.169769	ACCAGTCGAAGGAAGTTTGTGA	59.830	45.455	11.80	0.00	0.00	3.58
277	394	2.221981	CAGTCGAAGGAAGTTTGTGAGC	59.778	50.000	0.00	0.00	0.00	4.26
278	395	2.158957	AGTCGAAGGAAGTTTGTGAGCA	60.159	45.455	0.00	0.00	0.00	4.26
283	400	2.576615	AGGAAGTTTGTGAGCACCTTC	58.423	47.619	8.62	8.62	34.55	3.46
284	401	1.264288	GGAAGTTTGTGAGCACCTTCG	59.736	52.381	10.08	0.00	35.40	3.79
285	402	2.210116	GAAGTTTGTGAGCACCTTCGA	58.790	47.619	0.00	0.00	0.00	3.71
286	403	2.550830	AGTTTGTGAGCACCTTCGAT	57.449	45.000	0.00	0.00	0.00	3.59
288	405	4.207891	AGTTTGTGAGCACCTTCGATAT	57.792	40.909	0.00	0.00	0.00	1.63
289	406	5.339008	AGTTTGTGAGCACCTTCGATATA	57.661	39.130	0.00	0.00	0.00	0.86
290	407	5.918608	AGTTTGTGAGCACCTTCGATATAT	58.081	37.500	0.00	0.00	0.00	0.86
291	408	7.050970	AGTTTGTGAGCACCTTCGATATATA	57.949	36.000	0.00	0.00	0.00	0.86
293	410	8.803235	AGTTTGTGAGCACCTTCGATATATATA	58.197	33.333	0.00	0.00	0.00	0.86
294	411	9.587772	GTTTGTGAGCACCTTCGATATATATAT	57.412	33.333	4.86	4.86	0.00	0.86
295	412	9.586435	TTTGTGAGCACCTTCGATATATATATG	57.414	33.333	10.03	3.49	0.00	1.78
296	413	7.716612	TGTGAGCACCTTCGATATATATATGG	58.283	38.462	10.03	8.98	0.00	2.74
297	414	6.642950	GTGAGCACCTTCGATATATATATGGC	59.357	42.308	10.03	3.07	0.00	4.40
298	415	6.323739	TGAGCACCTTCGATATATATATGGCA	59.676	38.462	10.03	0.00	0.00	4.92
301	418	6.463049	GCACCTTCGATATATATATGGCACCT	60.463	42.308	10.03	0.00	0.00	4.00
302	419	7.500992	CACCTTCGATATATATATGGCACCTT	58.499	38.462	10.03	0.00	0.00	3.50
303	420	7.439356	CACCTTCGATATATATATGGCACCTTG	59.561	40.741	10.03	0.96	0.00	3.61
304	421	6.931281	CCTTCGATATATATATGGCACCTTGG	59.069	42.308	10.03	2.83	0.00	3.61
306	423	7.050970	TCGATATATATATGGCACCTTGGTC	57.949	40.000	10.03	0.00	0.00	4.02
307	424	5.920840	CGATATATATATGGCACCTTGGTCG	59.079	44.000	10.03	0.50	0.00	4.79
309	426	3.857157	ATATATGGCACCTTGGTCGTT	57.143	42.857	0.00	0.00	0.00	3.85
310	427	1.750193	ATATGGCACCTTGGTCGTTG	58.250	50.000	0.00	0.00	0.00	4.10
311	428	0.958382	TATGGCACCTTGGTCGTTGC	60.958	55.000	0.00	0.00	0.00	4.17
312	429	2.904866	GGCACCTTGGTCGTTGCA	60.905	61.111	0.00	0.00	0.00	4.08
313	430	2.639286	GCACCTTGGTCGTTGCAG	59.361	61.111	0.00	0.00	0.00	4.41
314	431	2.639286	CACCTTGGTCGTTGCAGC	59.361	61.111	0.00	0.00	0.00	5.25
315	432	2.186160	CACCTTGGTCGTTGCAGCA	61.186	57.895	0.24	0.00	0.00	4.41
316	433	1.228245	ACCTTGGTCGTTGCAGCAT	60.228	52.632	0.00	0.00	0.00	3.79
319	436	0.877071	CTTGGTCGTTGCAGCATTCT	59.123	50.000	0.00	0.00	0.00	2.40
320	437	0.874390	TTGGTCGTTGCAGCATTCTC	59.126	50.000	0.00	0.00	0.00	2.87
321	438	0.035317	TGGTCGTTGCAGCATTCTCT	59.965	50.000	0.00	0.00	0.00	3.10
322	439	1.160137	GGTCGTTGCAGCATTCTCTT	58.840	50.000	0.00	0.00	0.00	2.85
324	441	1.532868	GTCGTTGCAGCATTCTCTTGT	59.467	47.619	0.00	0.00	0.00	3.16
325	442	2.736721	GTCGTTGCAGCATTCTCTTGTA	59.263	45.455	0.00	0.00	0.00	2.41
329	446	5.048782	TCGTTGCAGCATTCTCTTGTATTTT	60.049	36.000	0.00	0.00	0.00	1.82
330	447	5.060077	CGTTGCAGCATTCTCTTGTATTTTG	59.940	40.000	0.00	0.00	0.00	2.44
335	452	8.347771	TGCAGCATTCTCTTGTATTTTGATATC	58.652	33.333	0.00	0.00	0.00	1.63
2767	3601	3.827876	GAGTAAGGGGCTCAGGAGTATAC	59.172	52.174	0.00	0.00	33.45	1.47

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	97	1.343478	ACTCCCTCTGTCCGGAATGAT	60.343	52.381	5.23	0.00	0.00	2.45
88	99	1.776662	TACTCCCTCTGTCCGGAATG	58.223	55.000	5.23	1.33	0.00	2.67
99	110	0.253044	TGCCTTGCACATACTCCCTC	59.747	55.000	0.00	0.00	31.71	4.30
157	168	8.948631	TCTTATTTCACTTTCATCGCTTCTAT	57.051	30.769	0.00	0.00	0.00	1.98
158	169	8.948631	ATCTTATTTCACTTTCATCGCTTCTA	57.051	30.769	0.00	0.00	0.00	2.10
228	345	6.096282	GTGGCCCTGTTGCTTTCTTATTATAA	59.904	38.462	0.00	0.00	0.00	0.98
229	346	5.592688	GTGGCCCTGTTGCTTTCTTATTATA	59.407	40.000	0.00	0.00	0.00	0.98
230	347	4.402474	GTGGCCCTGTTGCTTTCTTATTAT	59.598	41.667	0.00	0.00	0.00	1.28
231	348	3.761752	GTGGCCCTGTTGCTTTCTTATTA	59.238	43.478	0.00	0.00	0.00	0.98
232	349	2.562738	GTGGCCCTGTTGCTTTCTTATT	59.437	45.455	0.00	0.00	0.00	1.40
233	350	2.171003	GTGGCCCTGTTGCTTTCTTAT	58.829	47.619	0.00	0.00	0.00	1.73
235	352	0.396974	TGTGGCCCTGTTGCTTTCTT	60.397	50.000	0.00	0.00	0.00	2.52
238	355	2.133641	GGTGTGGCCCTGTTGCTTT	61.134	57.895	0.00	0.00	0.00	3.51
239	356	2.521708	GGTGTGGCCCTGTTGCTT	60.522	61.111	0.00	0.00	0.00	3.91
240	357	3.797507	CTGGTGTGGCCCTGTTGCT	62.798	63.158	0.00	0.00	36.04	3.91
241	358	3.297620	CTGGTGTGGCCCTGTTGC	61.298	66.667	0.00	0.00	36.04	4.17
242	359	1.898574	GACTGGTGTGGCCCTGTTG	60.899	63.158	0.00	0.00	36.86	3.33
243	360	2.515901	GACTGGTGTGGCCCTGTT	59.484	61.111	0.00	0.00	36.86	3.16
245	362	3.177194	TTCGACTGGTGTGGCCCTG	62.177	63.158	0.00	0.00	36.04	4.45
251	368	2.240493	AACTTCCTTCGACTGGTGTG	57.760	50.000	3.88	0.00	0.00	3.82
252	369	2.093128	ACAAACTTCCTTCGACTGGTGT	60.093	45.455	3.88	2.60	0.00	4.16
253	370	2.287915	CACAAACTTCCTTCGACTGGTG	59.712	50.000	3.88	0.00	0.00	4.17
254	371	2.169769	TCACAAACTTCCTTCGACTGGT	59.830	45.455	3.88	0.00	0.00	4.00
255	372	2.802816	CTCACAAACTTCCTTCGACTGG	59.197	50.000	0.00	0.00	0.00	4.00
257	374	2.158957	TGCTCACAAACTTCCTTCGACT	60.159	45.455	0.00	0.00	0.00	4.18
266	383	2.325583	TCGAAGGTGCTCACAAACTT	57.674	45.000	2.21	0.00	0.00	2.66
267	384	2.550830	ATCGAAGGTGCTCACAAACT	57.449	45.000	2.21	0.00	0.00	2.66
269	386	9.586435	CATATATATATCGAAGGTGCTCACAAA	57.414	33.333	2.03	0.00	0.00	2.83
270	387	8.197439	CCATATATATATCGAAGGTGCTCACAA	58.803	37.037	2.03	0.00	0.00	3.33
271	388	7.684428	GCCATATATATATCGAAGGTGCTCACA	60.684	40.741	2.03	0.00	0.00	3.58
275	392	6.463049	GGTGCCATATATATATCGAAGGTGCT	60.463	42.308	2.03	0.00	0.00	4.40
277	394	7.055667	AGGTGCCATATATATATCGAAGGTG	57.944	40.000	2.03	0.00	0.00	4.00
278	395	7.419057	CCAAGGTGCCATATATATATCGAAGGT	60.419	40.741	2.03	0.00	0.00	3.50
283	400	5.920840	CGACCAAGGTGCCATATATATATCG	59.079	44.000	2.03	0.00	0.00	2.92
284	401	6.817184	ACGACCAAGGTGCCATATATATATC	58.183	40.000	2.03	0.00	0.00	1.63
285	402	6.808321	ACGACCAAGGTGCCATATATATAT	57.192	37.500	0.00	0.00	0.00	0.86
286	403	6.403049	CAACGACCAAGGTGCCATATATATA	58.597	40.000	0.00	0.00	0.00	0.86
288	405	4.637276	CAACGACCAAGGTGCCATATATA	58.363	43.478	0.00	0.00	0.00	0.86
289	406	3.476552	CAACGACCAAGGTGCCATATAT	58.523	45.455	0.00	0.00	0.00	0.86
290	407	2.912771	CAACGACCAAGGTGCCATATA	58.087	47.619	0.00	0.00	0.00	0.86
291	408	1.750193	CAACGACCAAGGTGCCATAT	58.250	50.000	0.00	0.00	0.00	1.78
293	410	4.079446	CAACGACCAAGGTGCCAT	57.921	55.556	0.00	0.00	0.00	4.40
297	414	1.518056	ATGCTGCAACGACCAAGGTG	61.518	55.000	6.36	0.00	0.00	4.00
298	415	0.823356	AATGCTGCAACGACCAAGGT	60.823	50.000	6.36	0.00	0.00	3.50
301	418	0.874390	GAGAATGCTGCAACGACCAA	59.126	50.000	6.36	0.00	0.00	3.67
302	419	0.035317	AGAGAATGCTGCAACGACCA	59.965	50.000	6.36	0.00	0.00	4.02
303	420	1.135859	CAAGAGAATGCTGCAACGACC	60.136	52.381	6.36	0.00	0.00	4.79
304	421	1.532868	ACAAGAGAATGCTGCAACGAC	59.467	47.619	6.36	4.69	0.00	4.34
306	423	4.346734	AATACAAGAGAATGCTGCAACG	57.653	40.909	6.36	0.00	0.00	4.10
307	424	6.151691	TCAAAATACAAGAGAATGCTGCAAC	58.848	36.000	6.36	4.14	0.00	4.17
309	426	5.963176	TCAAAATACAAGAGAATGCTGCA	57.037	34.783	4.13	4.13	0.00	4.41
310	427	7.806960	GGATATCAAAATACAAGAGAATGCTGC	59.193	37.037	4.83	0.00	0.00	5.25
311	428	9.064706	AGGATATCAAAATACAAGAGAATGCTG	57.935	33.333	4.83	0.00	0.00	4.41
312	429	9.638176	AAGGATATCAAAATACAAGAGAATGCT	57.362	29.630	4.83	0.00	0.00	3.79
324	441	9.104965	CGGTTCAACAGTAAGGATATCAAAATA	57.895	33.333	4.83	0.00	0.00	1.40
325	442	7.067008	CCGGTTCAACAGTAAGGATATCAAAAT	59.933	37.037	4.83	0.00	0.00	1.82
329	446	4.468510	ACCGGTTCAACAGTAAGGATATCA	59.531	41.667	0.00	0.00	0.00	2.15
330	447	5.019785	ACCGGTTCAACAGTAAGGATATC	57.980	43.478	0.00	0.00	0.00	1.63
335	452	3.267483	CCATACCGGTTCAACAGTAAGG	58.733	50.000	15.04	0.00	0.00	2.69
1567	2387	4.808414	TTCTAGCTATCACTGCACACTT	57.192	40.909	0.00	0.00	0.00	3.16
2080	2913	2.325583	TGCTGTTCGTTCCTCTTGTT	57.674	45.000	0.00	0.00	0.00	2.83
2767	3601	3.947910	ATGAACAAGCACAAATGGGAG	57.052	42.857	0.00	0.00	0.00	4.30
3003	3837	1.967779	GATAGGAACTCTCCCAGCCTC	59.032	57.143	0.00	0.00	43.64	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.