AutoCloner

Multiple sequence alignment - TraesCS7D01G163600

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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	TraesCS7D01G163600	chr7D	100.000	4960	0	0	1	4960	113224701	113219742	0.000000e+00	9160.0
1	TraesCS7D01G163600	chr7D	100.000	38	0	0	355	392	113224311	113224274	2.480000e-08	71.3
2	TraesCS7D01G163600	chr7D	100.000	38	0	0	391	428	113224347	113224310	2.480000e-08	71.3
3	TraesCS7D01G163600	chr7B	92.124	4571	181	56	1	4520	72615939	72611497	0.000000e+00	6281.0
4	TraesCS7D01G163600	chr7B	100.000	38	0	0	391	428	72615566	72615529	2.480000e-08	71.3
5	TraesCS7D01G163600	chr7B	94.737	38	0	2	355	392	72615530	72615495	1.930000e-04	58.4
6	TraesCS7D01G163600	chr7A	93.688	2741	118	17	391	3117	118330451	118327752	0.000000e+00	4052.0
7	TraesCS7D01G163600	chr7A	94.844	1377	48	12	3155	4520	118327759	118326395	0.000000e+00	2128.0
8	TraesCS7D01G163600	chr7A	86.095	338	22	8	67	392	118330738	118330414	1.710000e-89	340.0
9	TraesCS7D01G163600	chr7A	96.089	179	4	3	4540	4716	118326336	118326159	6.280000e-74	289.0

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	TraesCS7D01G163600	chr7D	113219742	113224701	4959	True	3100.866667	9160	100.000000	1	4960	3	chr7D.!!$R1	4959
1	TraesCS7D01G163600	chr7B	72611497	72615939	4442	True	2136.900000	6281	95.620333	1	4520	3	chr7B.!!$R1	4519
2	TraesCS7D01G163600	chr7A	118326159	118330738	4579	True	1702.250000	4052	92.679000	67	4716	4	chr7A.!!$R1	4649

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	Hairpin	End Stability	Orientation
50	51	0.343726	AGCCCTAAGCCTACCTTCCT	59.656	55.000	45.47	3.36	F
196	232	0.956410	TACCCGGTGAATTTGGCGTG	60.956	55.000	0.00	5.34	F
1581	1624	1.134788	CCTACCACGGGCTTTACTGAG	60.135	57.143	0.00	3.35	F
2403	2447	0.940126	CATGGCTTGATACTGGCGAC	59.060	55.000	0.00	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1032	1075	1.167851	ACATTGACCTTGCATCACCG	58.832	50.000	0.00	0.00	4.94	R
1591	1634	1.270041	TGATGCTGCAACGTACTCACA	60.270	47.619	6.36	0.00	3.58	R
2672	2720	1.025812	CTGTTGGGCCACGTACAAAA	58.974	50.000	5.23	0.00	2.44	R
4256	4324	0.036010	AATGCCGACTGGAACTGAGG	60.036	55.000	0.00	37.49	3.86	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
21	22	4.679373	AGCTGTGTATGATTCCGATTCT	57.321	40.909	0.00	0.00	0.00	2.40
48	49	1.340568	CGTAGCCCTAAGCCTACCTTC	59.659	57.143	0.00	0.00	45.47	3.46
50	51	0.343726	AGCCCTAAGCCTACCTTCCT	59.656	55.000	0.00	0.00	45.47	3.36
52	53	2.022330	AGCCCTAAGCCTACCTTCCTTA	60.022	50.000	0.00	0.00	45.47	2.69
63	64	5.354513	GCCTACCTTCCTTATTCTGTTGTTC	59.645	44.000	0.00	0.00	0.00	3.18
65	66	7.168905	CCTACCTTCCTTATTCTGTTGTTCTT	58.831	38.462	0.00	0.00	0.00	2.52
71	72	6.610830	TCCTTATTCTGTTGTTCTTTCCCTT	58.389	36.000	0.00	0.00	0.00	3.95
81	82	6.603997	TGTTGTTCTTTCCCTTTTTACTGCTA	59.396	34.615	0.00	0.00	0.00	3.49
91	92	5.633182	CCCTTTTTACTGCTACGTTACGTTA	59.367	40.000	17.42	0.00	41.54	3.18
123	147	3.630312	GGGAATTTACTGATTTAGCGGCA	59.370	43.478	1.45	0.00	0.00	5.69
150	185	2.021457	AGTTATTGGCCAATGCGTACC	58.979	47.619	36.21	18.41	38.85	3.34
179	215	7.447243	AAGCGTTAGATATTTCAACGTCTAC	57.553	36.000	14.74	3.59	45.08	2.59
196	232	0.956410	TACCCGGTGAATTTGGCGTG	60.956	55.000	0.00	0.00	0.00	5.34
209	245	1.438651	TGGCGTGTAGAAACTGCATC	58.561	50.000	0.00	0.00	31.74	3.91
214	251	2.738643	CGTGTAGAAACTGCATCGGGAT	60.739	50.000	0.00	0.00	0.00	3.85
225	262	2.007360	CATCGGGATATGCAGCTCTC	57.993	55.000	0.00	0.00	0.00	3.20
332	369	3.268330	CCCTACTCTAACGCCCTTTTTC	58.732	50.000	0.00	0.00	0.00	2.29
397	434	7.110810	GGAAACTTCTATTACAAGTAGGCCTT	58.889	38.462	12.58	0.00	32.71	4.35
455	492	7.016563	TGGTGATAATACTATTGCCATCTCTGT	59.983	37.037	0.00	0.00	0.00	3.41
510	548	5.107133	CCGAACTGTACGATTTAATGGACT	58.893	41.667	0.00	0.00	0.00	3.85
533	571	6.876257	ACTGACTAGTTTGGCAATTCTAAGAG	59.124	38.462	0.00	6.05	31.66	2.85
551	590	9.646427	TTCTAAGAGAACTTTTCTAGCTGAATC	57.354	33.333	0.00	0.00	40.87	2.52
552	591	8.807118	TCTAAGAGAACTTTTCTAGCTGAATCA	58.193	33.333	0.00	0.00	40.87	2.57
555	594	8.266392	AGAGAACTTTTCTAGCTGAATCAATG	57.734	34.615	0.00	0.00	40.87	2.82
659	699	8.773033	AGAATTACTCAAATAATTGGAGCCAT	57.227	30.769	0.00	0.00	35.38	4.40

Showing 1 to 25 of 219 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	8.622948	AAAGAACAACAGAATAAGGAAGGTAG	57.377	34.615	0.00	0.00	0.00	3.18
44	45	6.071896	GGGAAAGAACAACAGAATAAGGAAGG	60.072	42.308	0.00	0.00	0.00	3.46
45	46	6.717084	AGGGAAAGAACAACAGAATAAGGAAG	59.283	38.462	0.00	0.00	0.00	3.46
48	49	6.901081	AAGGGAAAGAACAACAGAATAAGG	57.099	37.500	0.00	0.00	0.00	2.69
52	53	8.197439	CAGTAAAAAGGGAAAGAACAACAGAAT	58.803	33.333	0.00	0.00	0.00	2.40
63	64	5.684550	AACGTAGCAGTAAAAAGGGAAAG	57.315	39.130	0.00	0.00	0.00	2.62
65	66	4.685628	CGTAACGTAGCAGTAAAAAGGGAA	59.314	41.667	0.00	0.00	0.00	3.97
71	72	4.621034	GGCTAACGTAACGTAGCAGTAAAA	59.379	41.667	16.53	0.00	39.99	1.52
91	92	3.016736	CAGTAAATTCCCATGAACGGCT	58.983	45.455	0.00	0.00	32.13	5.52
96	97	6.039270	CCGCTAAATCAGTAAATTCCCATGAA	59.961	38.462	0.00	0.00	34.33	2.57
123	147	1.917872	TTGGCCAATAACTTCGCCTT	58.082	45.000	16.05	0.00	39.21	4.35
150	185	5.191059	GTTGAAATATCTAACGCTTCGCTG	58.809	41.667	0.00	0.00	0.00	5.18
179	215	0.956410	TACACGCCAAATTCACCGGG	60.956	55.000	6.32	0.00	0.00	5.73
209	245	0.665670	CACGAGAGCTGCATATCCCG	60.666	60.000	1.02	0.00	0.00	5.14
214	251	1.226688	GCGTCACGAGAGCTGCATA	60.227	57.895	0.00	0.00	0.00	3.14
316	353	2.088950	TCCGAAAAAGGGCGTTAGAG	57.911	50.000	0.00	0.00	0.00	2.43
332	369	1.038280	AGCCGGTAGGTATCTTTCCG	58.962	55.000	1.90	10.96	40.50	4.30
442	479	6.098838	TGTTACTATCAGACAGAGATGGCAAT	59.901	38.462	0.00	0.00	0.00	3.56
482	520	0.892755	AATCGTACAGTTCGGCTCCA	59.107	50.000	0.00	0.00	0.00	3.86
484	522	4.025979	CCATTAAATCGTACAGTTCGGCTC	60.026	45.833	0.00	0.00	0.00	4.70
485	523	3.869246	CCATTAAATCGTACAGTTCGGCT	59.131	43.478	0.00	0.00	0.00	5.52
486	524	3.866910	TCCATTAAATCGTACAGTTCGGC	59.133	43.478	0.00	0.00	0.00	5.54
489	527	6.812160	AGTCAGTCCATTAAATCGTACAGTTC	59.188	38.462	0.00	0.00	0.00	3.01
510	548	7.004555	TCTCTTAGAATTGCCAAACTAGTCA	57.995	36.000	0.00	0.00	0.00	3.41
533	571	6.958193	CGACATTGATTCAGCTAGAAAAGTTC	59.042	38.462	0.00	0.00	40.22	3.01

Showing 1 to 25 of 209 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.