AutoCloner

Multiple sequence alignment - TraesCS5B01G455800

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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	TraesCS5B01G455800	chr5B	100.000	8856	0	0	1001	9856	630295235	630286380	0.000000e+00	16355.0
1	TraesCS5B01G455800	chr5B	99.588	7280	25	3	1001	8276	625534672	625527394	0.000000e+00	13272.0
2	TraesCS5B01G455800	chr5B	92.347	967	16	19	8272	9190	625526209	625525253	0.000000e+00	1323.0
3	TraesCS5B01G455800	chr5B	100.000	529	0	0	1	529	630296235	630295707	0.000000e+00	977.0
4	TraesCS5B01G455800	chr5B	98.299	529	8	1	1	529	625535646	625535119	0.000000e+00	926.0
5	TraesCS5B01G455800	chr5B	91.812	574	29	10	9291	9856	625523672	625523109	0.000000e+00	784.0
6	TraesCS5B01G455800	chr5B	93.269	208	11	1	9184	9391	629276311	629276515	4.470000e-78	303.0
7	TraesCS5B01G455800	chr5B	93.269	208	11	1	9184	9391	629358881	629359085	4.470000e-78	303.0
8	TraesCS5B01G455800	chr5B	79.355	465	47	24	9381	9820	629276758	629277198	2.100000e-71	281.0
9	TraesCS5B01G455800	chr5B	79.355	465	47	24	9381	9820	629359328	629359768	2.100000e-71	281.0
10	TraesCS5B01G455800	chr5B	87.129	202	16	10	9328	9526	628587630	628587436	4.630000e-53	220.0
11	TraesCS5B01G455800	chr5B	86.634	202	17	10	9328	9526	625014794	625014600	2.160000e-51	215.0
12	TraesCS5B01G455800	chr5B	79.070	301	37	7	9524	9820	625014553	625014275	6.080000e-42	183.0
13	TraesCS5B01G455800	chr5B	79.070	301	37	7	9524	9820	628587389	628587111	6.080000e-42	183.0
14	TraesCS5B01G455800	chr5B	92.683	41	3	0	8265	8305	665204793	665204833	1.070000e-04	60.2
15	TraesCS5B01G455800	chr5A	94.760	4695	175	34	1004	5681	629700069	629704709	0.000000e+00	7241.0
16	TraesCS5B01G455800	chr5A	91.756	3360	164	51	5663	8979	629704740	629708029	0.000000e+00	4566.0
17	TraesCS5B01G455800	chr5A	92.805	681	30	11	9186	9856	629710116	629710787	0.000000e+00	968.0
18	TraesCS5B01G455800	chr5A	84.211	228	28	5	1	227	629699311	629699531	2.160000e-51	215.0
19	TraesCS5B01G455800	chr5D	94.107	3445	128	35	5679	9086	501779002	501775596	0.000000e+00	5168.0
20	TraesCS5B01G455800	chr5D	94.909	3084	118	15	1029	4108	501783557	501780509	0.000000e+00	4789.0
21	TraesCS5B01G455800	chr5D	95.406	1132	48	4	4551	5681	501780182	501779054	0.000000e+00	1799.0
22	TraesCS5B01G455800	chr5D	91.986	574	29	9	9291	9856	501774005	501773441	0.000000e+00	789.0
23	TraesCS5B01G455800	chr5D	91.369	336	21	4	4148	4482	501780508	501780180	4.200000e-123	453.0
24	TraesCS5B01G455800	chrUn	100.000	428	0	0	5650	6077	476416490	476416063	0.000000e+00	791.0
25	TraesCS5B01G455800	chrUn	93.333	45	2	1	8265	8309	11264202	11264245	2.300000e-06	65.8
26	TraesCS5B01G455800	chr3A	88.278	418	29	12	9184	9592	580561312	580561718	5.350000e-132	483.0
27	TraesCS5B01G455800	chr7A	88.038	418	30	12	9184	9592	676591509	676591103	2.490000e-130	477.0
28	TraesCS5B01G455800	chr1B	93.750	64	4	0	8242	8305	237010343	237010406	8.150000e-16	97.1
29	TraesCS5B01G455800	chr1A	88.710	62	5	2	8244	8305	550888529	550888588	3.820000e-09	75.0
30	TraesCS5B01G455800	chr2B	89.286	56	4	2	5208	5262	74004641	74004695	1.780000e-07	69.4
31	TraesCS5B01G455800	chr7D	95.122	41	2	0	8265	8305	167528678	167528718	2.300000e-06	65.8
32	TraesCS5B01G455800	chr6B	100.000	34	0	0	8271	8304	67464126	67464159	8.260000e-06	63.9

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	TraesCS5B01G455800	chr5B	630286380	630296235	9855	True	8666.00	16355	100.0000	1	9856	2	chr5B.!!$R4	9855
1	TraesCS5B01G455800	chr5B	625523109	625535646	12537	True	4076.25	13272	95.5115	1	9856	4	chr5B.!!$R2	9855
2	TraesCS5B01G455800	chr5B	629276311	629277198	887	False	292.00	303	86.3120	9184	9820	2	chr5B.!!$F2	636
3	TraesCS5B01G455800	chr5B	629358881	629359768	887	False	292.00	303	86.3120	9184	9820	2	chr5B.!!$F3	636
4	TraesCS5B01G455800	chr5B	628587111	628587630	519	True	201.50	220	83.0995	9328	9820	2	chr5B.!!$R3	492
5	TraesCS5B01G455800	chr5A	629699311	629710787	11476	False	3247.50	7241	90.8830	1	9856	4	chr5A.!!$F1	9855
6	TraesCS5B01G455800	chr5D	501773441	501783557	10116	True	2599.60	5168	93.5554	1029	9856	5	chr5D.!!$R1	8827

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
125	126	1.083489	TCCGTCACCGATTCATTTGC	58.917	50.000	0.00	0.00	35.63	3.68	F
157	158	4.377431	GGAGTATGTGTCAGCGAAACTTTG	60.377	45.833	0.00	0.00	0.00	2.77	F
1612	1670	2.948979	TGTGATTGGCTCGAAACAGTTT	59.051	40.909	0.00	0.00	0.00	2.66	F
1873	1938	5.521010	TGAACAAAAATGAGAAAAGCTGCTG	59.479	36.000	1.35	0.00	0.00	4.41	F
2440	2505	2.771089	CTACAGTGGTGCACAACAGAT	58.229	47.619	25.99	12.91	36.74	2.90	F
5508	5577	2.073252	ATCATGTCTCGAGGTGCCTA	57.927	50.000	13.56	0.00	0.00	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1612	1670	1.668751	GACCAAAAGACGCACAACAGA	59.331	47.619	0.00	0.00	0.00	3.41	R
1873	1938	6.101332	TCAGAATTTCATAAGCAATTGCCAC	58.899	36.000	26.45	0.00	43.38	5.01	R
2440	2505	3.372897	TGGCCATTTATTTCAGGATGCA	58.627	40.909	0.00	0.00	34.76	3.96	R
4379	4445	4.035102	GAGGGAAAGGGCCACGCT	62.035	66.667	6.18	10.47	0.00	5.07	R
6169	6296	3.075148	GGAGCTAACCTCAAACAGAACC	58.925	50.000	0.00	0.00	42.62	3.62	R
8985	10369	0.106868	CCCTCCGTTTATTCCACCCC	60.107	60.000	0.00	0.00	0.00	4.95	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
73	74	3.910568	TGGATCCAAAATGGCAAATCC	57.089	42.857	13.46	8.09	38.34	3.01
125	126	1.083489	TCCGTCACCGATTCATTTGC	58.917	50.000	0.00	0.00	35.63	3.68
157	158	4.377431	GGAGTATGTGTCAGCGAAACTTTG	60.377	45.833	0.00	0.00	0.00	2.77
248	301	7.202038	CCCTCATGTAAAGAGAATCATGGAGTA	60.202	40.741	0.00	0.00	38.39	2.59
261	314	7.557719	AGAATCATGGAGTAGTAAATTTGTGGG	59.442	37.037	0.00	0.00	0.00	4.61
1612	1670	2.948979	TGTGATTGGCTCGAAACAGTTT	59.051	40.909	0.00	0.00	0.00	2.66
1873	1938	5.521010	TGAACAAAAATGAGAAAAGCTGCTG	59.479	36.000	1.35	0.00	0.00	4.41
2440	2505	2.771089	CTACAGTGGTGCACAACAGAT	58.229	47.619	25.99	12.91	36.74	2.90
4379	4445	2.224281	CCCGCTATCTTAACTGGATGCA	60.224	50.000	0.00	0.00	0.00	3.96
5508	5577	2.073252	ATCATGTCTCGAGGTGCCTA	57.927	50.000	13.56	0.00	0.00	3.93
5648	5717	5.103000	CCAGAGTACGGAGAACTTATGTTG	58.897	45.833	0.00	0.00	36.39	3.33
7120	7271	8.868522	AATATTCATGTCCTCTCTTTGTTTGA	57.131	30.769	0.00	0.00	0.00	2.69
7594	7749	1.082679	CACATCAGTGCCAGAGCTCG	61.083	60.000	8.37	3.24	39.21	5.03
7616	7771	0.381089	CCGCTTAGAGTCAGGTACCG	59.619	60.000	6.18	1.56	0.00	4.02
8248	8407	5.104900	ACATGAATAGTGTCACTTACTCCCC	60.105	44.000	11.54	0.00	0.00	4.81
8637	9992	1.604378	CAGCCGGGTTTCTGATCCT	59.396	57.895	1.64	0.00	32.26	3.24
8665	10025	2.046892	GTGCCCGATGAGCAGTGT	60.047	61.111	0.00	0.00	41.87	3.55
8977	10361	3.077907	GCCTGTGCCAGTAGGGAA	58.922	61.111	0.00	0.00	36.80	3.97
8978	10362	1.078143	GCCTGTGCCAGTAGGGAAG	60.078	63.158	0.00	0.00	36.80	3.46
8982	10366	0.474854	TGTGCCAGTAGGGAAGGGAA	60.475	55.000	0.00	0.00	36.80	3.97
8983	10367	0.253327	GTGCCAGTAGGGAAGGGAAG	59.747	60.000	0.00	0.00	36.80	3.46
8985	10369	0.833949	GCCAGTAGGGAAGGGAAGAG	59.166	60.000	0.00	0.00	40.01	2.85
9092	10756	2.186160	CATGTGTGTGTGTGGCGGT	61.186	57.895	0.00	0.00	0.00	5.68
9122	10809	2.887783	AGAAGATACACGGCATCGATCT	59.112	45.455	0.00	0.00	40.11	2.75
9123	10810	3.319405	AGAAGATACACGGCATCGATCTT	59.681	43.478	0.00	0.00	38.96	2.40
9147	10834	1.284715	GCGGCCAAAAAGTAGCGTT	59.715	52.632	2.24	0.00	0.00	4.84
9148	10835	0.318360	GCGGCCAAAAAGTAGCGTTT	60.318	50.000	2.24	0.00	0.00	3.60
9194	12659	3.902318	GCTCTGGCTTCCTCTTGC	58.098	61.111	0.00	0.00	35.22	4.01
9195	12660	1.299321	GCTCTGGCTTCCTCTTGCT	59.701	57.895	0.00	0.00	35.22	3.91
9196	12661	0.744057	GCTCTGGCTTCCTCTTGCTC	60.744	60.000	0.00	0.00	35.22	4.26
9299	12773	1.304464	GGGGGAAGGCTCTGGTTTG	60.304	63.158	0.00	0.00	0.00	2.93
9304	12783	0.875059	GAAGGCTCTGGTTTGGTTCG	59.125	55.000	0.00	0.00	0.00	3.95
9305	12784	0.182775	AAGGCTCTGGTTTGGTTCGT	59.817	50.000	0.00	0.00	0.00	3.85
9379	12858	1.485066	AGTTTCGCCCAATCGTCCTAT	59.515	47.619	0.00	0.00	0.00	2.57
9498	13231	5.874810	TGTCTGATTGTAGTATTGAACCTGC	59.125	40.000	0.00	0.00	0.00	4.85
9541	13329	4.009002	TCAGATGCATTGAACCGAAATCA	58.991	39.130	0.00	0.00	0.00	2.57
9682	13480	3.845775	CGATTTAAAGCACACATTCCACG	59.154	43.478	4.10	0.00	0.00	4.94
9827	13625	1.026182	CAGAGCCACCTATTTGCGCA	61.026	55.000	5.66	5.66	0.00	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	2.167693	TGGTGACGAGAACTTTGACACT	59.832	45.455	0.00	0.00	36.48	3.55
125	126	3.092301	TGACACATACTCCCTCTGTGAG	58.908	50.000	8.74	0.00	42.20	3.51
248	301	5.304357	CCAAAGAGTTCCCCACAAATTTACT	59.696	40.000	0.00	0.00	0.00	2.24
261	314	3.132111	TGCCAAAGAAACCAAAGAGTTCC	59.868	43.478	0.00	0.00	0.00	3.62
1612	1670	1.668751	GACCAAAAGACGCACAACAGA	59.331	47.619	0.00	0.00	0.00	3.41
1873	1938	6.101332	TCAGAATTTCATAAGCAATTGCCAC	58.899	36.000	26.45	0.00	43.38	5.01
2440	2505	3.372897	TGGCCATTTATTTCAGGATGCA	58.627	40.909	0.00	0.00	34.76	3.96
4379	4445	4.035102	GAGGGAAAGGGCCACGCT	62.035	66.667	6.18	10.47	0.00	5.07
6161	6288	4.816392	ACCTCAAACAGAACCAACAAAAC	58.184	39.130	0.00	0.00	0.00	2.43
6162	6289	5.476091	AACCTCAAACAGAACCAACAAAA	57.524	34.783	0.00	0.00	0.00	2.44
6166	6293	3.883489	AGCTAACCTCAAACAGAACCAAC	59.117	43.478	0.00	0.00	0.00	3.77
6167	6294	4.134563	GAGCTAACCTCAAACAGAACCAA	58.865	43.478	0.00	0.00	40.45	3.67
6169	6296	3.075148	GGAGCTAACCTCAAACAGAACC	58.925	50.000	0.00	0.00	42.62	3.62
7594	7749	2.357323	GGTACCTGACTCTAAGCGGTAC	59.643	54.545	4.06	8.08	45.79	3.34
7616	7771	7.349412	AGTGACCTATTAGATCAAGTACACC	57.651	40.000	0.00	0.00	0.00	4.16
7824	7981	6.053005	CCAACACTTGGTTAGAGAGTAAACA	58.947	40.000	0.00	0.00	45.93	2.83
7881	8040	3.244215	TGACACAACCCACTCTCATCTTC	60.244	47.826	0.00	0.00	0.00	2.87
8634	9989	2.598394	GCACCTTGGCAAGCAGGA	60.598	61.111	21.77	0.00	33.90	3.86
8975	10359	1.299939	ATTCCACCCCTCTTCCCTTC	58.700	55.000	0.00	0.00	0.00	3.46
8977	10361	2.581246	GTTTATTCCACCCCTCTTCCCT	59.419	50.000	0.00	0.00	0.00	4.20
8978	10362	2.682858	CGTTTATTCCACCCCTCTTCCC	60.683	54.545	0.00	0.00	0.00	3.97
8982	10366	1.838077	CTCCGTTTATTCCACCCCTCT	59.162	52.381	0.00	0.00	0.00	3.69
8983	10367	1.134189	CCTCCGTTTATTCCACCCCTC	60.134	57.143	0.00	0.00	0.00	4.30
8985	10369	0.106868	CCCTCCGTTTATTCCACCCC	60.107	60.000	0.00	0.00	0.00	4.95
9092	10756	4.100344	TGCCGTGTATCTTCTGCCTATAAA	59.900	41.667	0.00	0.00	0.00	1.40
9122	10809	2.611225	ACTTTTTGGCCGCATGAAAA	57.389	40.000	0.00	0.00	0.00	2.29
9123	10810	2.609244	GCTACTTTTTGGCCGCATGAAA	60.609	45.455	0.00	0.00	0.00	2.69
9194	12659	0.255318	ATCCAAGCAAGCAGGAGGAG	59.745	55.000	11.07	0.00	34.40	3.69
9195	12660	0.700564	AATCCAAGCAAGCAGGAGGA	59.299	50.000	11.07	5.20	34.40	3.71
9196	12661	1.101331	GAATCCAAGCAAGCAGGAGG	58.899	55.000	11.07	0.39	34.40	4.30
9299	12773	3.003378	CCTGTTTTCTCCAAGAACGAACC	59.997	47.826	0.00	0.00	33.26	3.62
9304	12783	4.390264	AGCTACCTGTTTTCTCCAAGAAC	58.610	43.478	0.00	0.00	33.26	3.01
9305	12784	4.102524	TGAGCTACCTGTTTTCTCCAAGAA	59.897	41.667	0.00	0.00	31.28	2.52
9541	13329	1.482593	CAATCTAGTCCTGCCTCCGTT	59.517	52.381	0.00	0.00	0.00	4.44
9549	13337	4.040829	TCCCATATGCACAATCTAGTCCTG	59.959	45.833	0.00	0.00	0.00	3.86
9615	13409	8.543774	AGTATTCACTGTTTGATTGATCCTACT	58.456	33.333	0.00	0.00	32.84	2.57
9616	13410	8.723942	AGTATTCACTGTTTGATTGATCCTAC	57.276	34.615	0.00	0.00	32.84	3.18
9617	13411	9.166173	CAAGTATTCACTGTTTGATTGATCCTA	57.834	33.333	0.00	0.00	34.36	2.94
9618	13412	7.667219	ACAAGTATTCACTGTTTGATTGATCCT	59.333	33.333	0.00	0.00	34.36	3.24
9619	13413	7.820648	ACAAGTATTCACTGTTTGATTGATCC	58.179	34.615	0.00	0.00	34.36	3.36
9682	13480	7.100409	ACAGCTTCACTAGAGAGGAAAAATAC	58.900	38.462	3.45	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.