AutoCloner

Multiple sequence alignment - TraesCS1B01G145900

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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	bitscore
0	TraesCS1B01G145900	chr1B	100.000	2450	0	0	1	2450	200995205	200997654	4525
1	TraesCS1B01G145900	chr1B	91.334	2458	185	20	1	2448	307385464	307383025	3334
2	TraesCS1B01G145900	chr1B	90.832	2465	197	16	1	2450	387430126	387427676	3273
3	TraesCS1B01G145900	chr1B	90.350	2456	198	26	1	2445	287516457	287518884	3186
4	TraesCS1B01G145900	chr3B	91.670	2461	174	19	1	2449	81050296	81052737	3380
5	TraesCS1B01G145900	chr3B	91.508	2461	177	14	1	2450	128995705	128993266	3358
6	TraesCS1B01G145900	chr3B	90.424	2454	202	21	1	2445	195665364	195667793	3199
7	TraesCS1B01G145900	chr3B	89.666	2458	233	16	1	2450	331024947	331027391	3112
8	TraesCS1B01G145900	chr2B	90.880	2478	191	21	1	2450	762706221	762708691	3291
9	TraesCS1B01G145900	chr2A	88.790	2462	244	24	1	2449	267980586	267983028	2988

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	TraesCS1B01G145900	chr1B	200995205	200997654	2449	False	4525	4525	100.000	1	2450	1	chr1B.!!$F1	2449
1	TraesCS1B01G145900	chr1B	307383025	307385464	2439	True	3334	3334	91.334	1	2448	1	chr1B.!!$R1	2447
2	TraesCS1B01G145900	chr1B	387427676	387430126	2450	True	3273	3273	90.832	1	2450	1	chr1B.!!$R2	2449
3	TraesCS1B01G145900	chr1B	287516457	287518884	2427	False	3186	3186	90.350	1	2445	1	chr1B.!!$F2	2444
4	TraesCS1B01G145900	chr3B	81050296	81052737	2441	False	3380	3380	91.670	1	2449	1	chr3B.!!$F1	2448
5	TraesCS1B01G145900	chr3B	128993266	128995705	2439	True	3358	3358	91.508	1	2450	1	chr3B.!!$R1	2449
6	TraesCS1B01G145900	chr3B	195665364	195667793	2429	False	3199	3199	90.424	1	2445	1	chr3B.!!$F2	2444
7	TraesCS1B01G145900	chr3B	331024947	331027391	2444	False	3112	3112	89.666	1	2450	1	chr3B.!!$F3	2449
8	TraesCS1B01G145900	chr2B	762706221	762708691	2470	False	3291	3291	90.880	1	2450	1	chr2B.!!$F1	2449
9	TraesCS1B01G145900	chr2A	267980586	267983028	2442	False	2988	2988	88.790	1	2449	1	chr2A.!!$F1	2448

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
296	297	0.107654	GGGTGGACTGAAATCCGGAG	60.108	60.000	11.34	0.0	42.24	4.63	F
742	749	1.133792	CCCTTGAGGTGTGTGAGGTTT	60.134	52.381	0.00	0.0	0.00	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1382	1392	0.956633	AACTCGGTCAACTCGCAGTA	59.043	50.000	0.00	0.00	0.00	2.74	R
1566	1581	1.001706	GAAACAGCTCACCGGGTTTTC	60.002	52.381	6.32	0.07	33.92	2.29	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
113	114	3.938289	GGATAGGCCTAGTTCTTACGG	57.062	52.381	19.33	0.00	0.00	4.02
283	284	4.927267	AAGAATTACTCACATGGGTGGA	57.073	40.909	1.53	0.00	45.32	4.02
293	294	1.340017	ACATGGGTGGACTGAAATCCG	60.340	52.381	0.00	0.00	42.24	4.18
296	297	0.107654	GGGTGGACTGAAATCCGGAG	60.108	60.000	11.34	0.00	42.24	4.63
319	320	7.124573	AGTATGTCATATAGGAGCAACAACA	57.875	36.000	0.00	0.00	0.00	3.33
332	333	5.411831	AGCAACAACACTGAGATCTCATA	57.588	39.130	25.30	4.16	39.13	2.15
338	339	6.169094	ACAACACTGAGATCTCATAGTTTGG	58.831	40.000	27.28	21.94	39.13	3.28
412	413	4.713553	TGCTCCACAACAGTCTTATTCAA	58.286	39.130	0.00	0.00	0.00	2.69
501	508	3.958018	ACCAACACCTTCAACACAAGTA	58.042	40.909	0.00	0.00	0.00	2.24
628	635	3.340814	TGAAGAAGATCAAGAGTGGGC	57.659	47.619	0.00	0.00	0.00	5.36
742	749	1.133792	CCCTTGAGGTGTGTGAGGTTT	60.134	52.381	0.00	0.00	0.00	3.27
750	757	2.088423	GTGTGTGAGGTTTCAACACCA	58.912	47.619	2.99	0.00	39.62	4.17
908	918	9.742144	ATCTACTACTGAAGAAGTACAAGAAGA	57.258	33.333	0.00	0.00	40.56	2.87
965	975	2.771372	TGCCTATTGTCATACCAGAGCA	59.229	45.455	0.00	0.00	0.00	4.26
1154	1164	6.519679	TCATAGTTACTTTCCTCGTGCTAA	57.480	37.500	0.00	0.00	0.00	3.09
1192	1202	6.326323	TGAAACATATCACTCCCATGCTAGTA	59.674	38.462	0.00	0.00	0.00	1.82
1318	1328	3.735237	TCGATGACTTAGAGGGCATTC	57.265	47.619	0.00	0.00	0.00	2.67
1321	1331	3.320541	CGATGACTTAGAGGGCATTCTCT	59.679	47.826	8.23	8.23	45.22	3.10
1324	1334	3.703556	TGACTTAGAGGGCATTCTCTCTG	59.296	47.826	4.86	0.00	42.57	3.35
1340	1350	4.284490	TCTCTCTGTCACTTGTATTGGCTT	59.716	41.667	0.00	0.00	0.00	4.35
1341	1351	4.318332	TCTCTGTCACTTGTATTGGCTTG	58.682	43.478	0.00	0.00	0.00	4.01
1342	1352	3.411446	TCTGTCACTTGTATTGGCTTGG	58.589	45.455	0.00	0.00	0.00	3.61
1344	1354	3.561143	TGTCACTTGTATTGGCTTGGTT	58.439	40.909	0.00	0.00	0.00	3.67
1366	1376	4.584874	TGTTGAGTGTTCTTTCAGGTTGA	58.415	39.130	0.00	0.00	0.00	3.18
1375	1385	3.554934	TCTTTCAGGTTGATGCTTGTGT	58.445	40.909	0.00	0.00	0.00	3.72

Showing 1 to 25 of 40 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	8.088981	TCTTACCTATCAGTTCTTGAACACTTC	58.911	37.037	14.80	0.00	39.77	3.01
113	114	2.224646	GGATGGCCTCTGGAATAAGGAC	60.225	54.545	3.32	0.00	41.48	3.85
264	265	3.941483	CAGTCCACCCATGTGAGTAATTC	59.059	47.826	0.00	0.00	45.76	2.17
283	284	6.672266	ATATGACATACTCCGGATTTCAGT	57.328	37.500	3.57	0.56	0.00	3.41
293	294	6.346477	TGTTGCTCCTATATGACATACTCC	57.654	41.667	0.00	0.00	0.00	3.85
296	297	6.986817	AGTGTTGTTGCTCCTATATGACATAC	59.013	38.462	0.00	0.00	0.00	2.39
319	320	6.865834	AGAACCAAACTATGAGATCTCAGT	57.134	37.500	28.26	19.43	43.61	3.41
332	333	7.716998	CCTGCATATGATTACTAGAACCAAACT	59.283	37.037	6.97	0.00	0.00	2.66
338	339	8.854614	AAATCCCTGCATATGATTACTAGAAC	57.145	34.615	6.97	0.00	0.00	3.01
412	413	5.482175	GGTGCTGAGGTATATGAATAGGAGT	59.518	44.000	0.00	0.00	0.00	3.85
490	497	6.266786	TCATCTTGAGTAGGTACTTGTGTTGA	59.733	38.462	0.00	0.00	41.75	3.18
628	635	5.127845	TCCTTACTTCTTCCACTAGCTCATG	59.872	44.000	0.00	0.00	0.00	3.07
729	736	1.404035	GGTGTTGAAACCTCACACACC	59.596	52.381	16.54	16.54	45.60	4.16
730	737	2.088423	TGGTGTTGAAACCTCACACAC	58.912	47.619	4.22	6.74	41.16	3.82
731	738	2.498644	TGGTGTTGAAACCTCACACA	57.501	45.000	4.22	0.00	41.16	3.72
732	739	2.948979	TGATGGTGTTGAAACCTCACAC	59.051	45.455	0.00	0.00	41.16	3.82
742	749	2.815503	CAGCTGAATGTGATGGTGTTGA	59.184	45.455	8.42	0.00	0.00	3.18
750	757	3.345508	TCTTGCTCAGCTGAATGTGAT	57.654	42.857	18.85	0.00	0.00	3.06
908	918	6.647229	TGTTCTTCATCTTCATCTACAGCAT	58.353	36.000	0.00	0.00	0.00	3.79
965	975	5.882557	GGATTGAGTAAACCTGACACATCAT	59.117	40.000	0.00	0.00	33.22	2.45
1179	1189	4.348863	AAGCTCAATACTAGCATGGGAG	57.651	45.455	0.00	0.00	42.62	4.30
1299	1309	3.320541	AGAGAATGCCCTCTAAGTCATCG	59.679	47.826	0.00	0.00	41.41	3.84
1318	1328	4.199432	AGCCAATACAAGTGACAGAGAG	57.801	45.455	0.00	0.00	0.00	3.20
1321	1331	3.181445	ACCAAGCCAATACAAGTGACAGA	60.181	43.478	0.00	0.00	0.00	3.41
1324	1334	3.317993	ACAACCAAGCCAATACAAGTGAC	59.682	43.478	0.00	0.00	0.00	3.67

Showing 1 to 25 of 46 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.