AutoCloner

Multiple sequence alignment - TraesCS5D01G322000

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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	TraesCS5D01G322000	chr5D	100.000	3375	0	0	1	3375	413763213	413759839	0.000000e+00	6233.0
1	TraesCS5D01G322000	chr5D	93.724	239	14	1	1	238	413771512	413771274	1.150000e-94	357.0
2	TraesCS5D01G322000	chr5D	89.130	46	4	1	776	820	209315019	209315064	4.700000e-04	56.5
3	TraesCS5D01G322000	chr5A	95.092	2710	85	16	684	3375	526402441	526399762	0.000000e+00	4224.0
4	TraesCS5D01G322000	chr5A	89.634	164	14	3	79	240	437086071	437085909	4.410000e-49	206.0
5	TraesCS5D01G322000	chr5B	95.253	2570	84	13	823	3375	498888925	498886377	0.000000e+00	4036.0
6	TraesCS5D01G322000	chr5B	93.317	808	41	5	1	802	498889787	498888987	0.000000e+00	1181.0
7	TraesCS5D01G322000	chr5B	89.130	46	4	1	776	820	580683510	580683555	4.700000e-04	56.5
8	TraesCS5D01G322000	chr5B	89.130	46	4	1	776	820	687073695	687073650	4.700000e-04	56.5
9	TraesCS5D01G322000	chrUn	100.000	396	0	0	2484	2879	479193544	479193149	0.000000e+00	732.0
10	TraesCS5D01G322000	chr7A	87.931	174	19	2	67	238	420110022	420110195	1.590000e-48	204.0
11	TraesCS5D01G322000	chr7A	87.931	174	19	2	67	238	420130196	420130369	1.590000e-48	204.0
12	TraesCS5D01G322000	chr7A	80.769	234	42	3	9	239	369464656	369464889	2.680000e-41	180.0
13	TraesCS5D01G322000	chr3A	87.931	174	19	2	67	238	182914261	182914434	1.590000e-48	204.0
14	TraesCS5D01G322000	chr1A	80.913	241	41	5	1	239	17538755	17538518	5.750000e-43	185.0
15	TraesCS5D01G322000	chr4A	80.165	242	42	6	1	238	189941559	189941798	3.460000e-40	176.0
16	TraesCS5D01G322000	chr7D	74.174	484	88	21	246	715	15067123	15067583	2.080000e-37	167.0
17	TraesCS5D01G322000	chr6A	83.942	137	18	3	548	681	112758542	112758677	9.830000e-26	128.0
18	TraesCS5D01G322000	chr6A	89.130	46	4	1	776	820	564097389	564097344	4.700000e-04	56.5
19	TraesCS5D01G322000	chr7B	80.220	91	18	0	1	91	509381933	509382023	6.040000e-08	69.4
20	TraesCS5D01G322000	chr7B	89.130	46	3	2	781	824	253649900	253649945	4.700000e-04	56.5
21	TraesCS5D01G322000	chr2B	100.000	32	0	0	776	807	5552912	5552943	3.640000e-05	60.2
22	TraesCS5D01G322000	chr2A	90.698	43	3	1	781	822	566588210	566588252	4.700000e-04	56.5
23	TraesCS5D01G322000	chr1B	96.970	33	1	0	776	808	169243764	169243796	4.700000e-04	56.5

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	TraesCS5D01G322000	chr5D	413759839	413763213	3374	True	6233.0	6233	100.000	1	3375	1	chr5D.!!$R1	3374
1	TraesCS5D01G322000	chr5A	526399762	526402441	2679	True	4224.0	4224	95.092	684	3375	1	chr5A.!!$R2	2691
2	TraesCS5D01G322000	chr5B	498886377	498889787	3410	True	2608.5	4036	94.285	1	3375	2	chr5B.!!$R2	3374

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
560	562	0.108945	GTACGTCGGCTAGCTTGGTT	60.109	55.0	15.72	0.0	0.0	3.67	F
852	903	0.166814	GCAGCAACAACGATCAGGTC	59.833	55.0	0.00	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2062	2124	1.003003	TCACCAATCTCCATTGACGCA	59.997	47.619	0.0	0.0	41.97	5.24	R
2380	2457	5.304101	TGGTGTTTGGCTCATACAAATTTCT	59.696	36.000	0.0	0.0	39.68	2.52	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
60	61	8.352942	TGTTGGTTTTGTTTTTACAATTGCTTT	58.647	25.926	5.05	0.00	0.00	3.51
64	65	7.362142	GGTTTTGTTTTTACAATTGCTTTGGGA	60.362	33.333	5.05	0.00	39.80	4.37
183	184	5.869888	AGTGAGGTTTAGAGAAGTAATTGCG	59.130	40.000	0.00	0.00	0.00	4.85
277	278	4.195334	CGATGCAGGGGAAGGGGG	62.195	72.222	0.00	0.00	0.00	5.40
323	324	6.618287	TGTTGTGACTCAATTAAAGTGGAG	57.382	37.500	0.00	0.00	38.38	3.86
339	340	1.045911	GGAGGTGAGAGGGGTAGCAG	61.046	65.000	0.00	0.00	0.00	4.24
340	341	1.002274	AGGTGAGAGGGGTAGCAGG	59.998	63.158	0.00	0.00	0.00	4.85
350	351	1.497161	GGGTAGCAGGCTTAGAAGGA	58.503	55.000	0.00	0.00	0.00	3.36
459	460	2.279810	TTCAGGACGTCCATGGCGA	61.280	57.895	35.00	19.54	38.89	5.54
539	541	2.846532	CCAGAGCTTGGTTGGGGT	59.153	61.111	6.74	0.00	42.41	4.95
560	562	0.108945	GTACGTCGGCTAGCTTGGTT	60.109	55.000	15.72	0.00	0.00	3.67
596	598	3.132289	GTCCGAGAACACATGGGAGAATA	59.868	47.826	0.00	0.00	0.00	1.75
634	636	2.775149	GACGAAACTAACTACTAGCGCG	59.225	50.000	0.00	0.00	0.00	6.86
644	646	1.059264	CTACTAGCGCGCAACTTGTTC	59.941	52.381	35.10	0.00	0.00	3.18
658	660	1.165907	TTGTTCGAGGCCACTTGCAG	61.166	55.000	5.01	0.00	43.89	4.41
703	705	2.151202	GGACTCATTCGCAGGTCAAAA	58.849	47.619	0.00	0.00	0.00	2.44
730	732	4.156556	GCTTTGACTATGTCCATTTCAGCA	59.843	41.667	0.00	0.00	0.00	4.41
733	735	5.627499	TGACTATGTCCATTTCAGCAAAC	57.373	39.130	0.00	0.00	0.00	2.93
735	737	4.666512	ACTATGTCCATTTCAGCAAACCT	58.333	39.130	0.00	0.00	0.00	3.50
751	753	2.683211	ACCTCTTGAGCAAACCCATT	57.317	45.000	0.00	0.00	0.00	3.16
852	903	0.166814	GCAGCAACAACGATCAGGTC	59.833	55.000	0.00	0.00	0.00	3.85
904	955	2.162408	GCTGTTGGACATTTGCTCTACC	59.838	50.000	0.00	0.00	0.00	3.18
919	970	2.952978	CTCTACCTAGATCGCACCAAGT	59.047	50.000	0.00	0.00	0.00	3.16
1019	1081	3.633094	CTCGCTCACTCCACCCACG	62.633	68.421	0.00	0.00	0.00	4.94
1564	1626	4.493747	CTTCCCGCCGTCGAGTCC	62.494	72.222	0.00	0.00	38.10	3.85
2062	2124	2.359900	GATGTCAAGCGGTTCAAGGAT	58.640	47.619	0.00	0.00	0.00	3.24
2376	2453	7.775053	TCCATTTTATTTGTGGAAAGCTACT	57.225	32.000	0.00	0.00	38.99	2.57
2377	2454	7.826690	TCCATTTTATTTGTGGAAAGCTACTC	58.173	34.615	0.00	0.00	38.99	2.59
2378	2455	6.747280	CCATTTTATTTGTGGAAAGCTACTCG	59.253	38.462	0.00	0.00	34.94	4.18
2379	2456	6.870971	TTTTATTTGTGGAAAGCTACTCGT	57.129	33.333	0.00	0.00	0.00	4.18
2380	2457	7.966246	TTTTATTTGTGGAAAGCTACTCGTA	57.034	32.000	0.00	0.00	0.00	3.43
2450	2527	5.669164	AAGCAGTGGTAAGTTTTTCCAAA	57.331	34.783	0.00	0.00	32.82	3.28
2879	2957	0.603707	GTGCTGCCACTAAGACTGCA	60.604	55.000	0.00	0.00	38.93	4.41
3151	3231	8.861086	AGAGGGTTAGAGTAACATATGTATGTG	58.139	37.037	9.21	0.00	45.55	3.21
3152	3232	8.548880	AGGGTTAGAGTAACATATGTATGTGT	57.451	34.615	9.21	0.00	45.55	3.72
3153	3233	9.650714	AGGGTTAGAGTAACATATGTATGTGTA	57.349	33.333	9.21	0.00	45.55	2.90
3154	3234	9.909644	GGGTTAGAGTAACATATGTATGTGTAG	57.090	37.037	9.21	0.00	45.55	2.74
3155	3235	9.408069	GGTTAGAGTAACATATGTATGTGTAGC	57.592	37.037	9.21	1.98	45.55	3.58
3192	3272	5.780958	AGATTATAGGTGAAATAGGGCCC	57.219	43.478	16.46	16.46	0.00	5.80
3298	3378	2.487934	CATTCTATGCTTAGCAGCCGT	58.512	47.619	13.74	0.00	46.74	5.68
3322	3402	6.876257	GTCATTTACATCAGAGGTGTTTCTCT	59.124	38.462	0.00	0.00	44.25	3.10
3365	3445	3.759581	AGTGTTGATGTGAAGGAAGCAT	58.240	40.909	0.00	0.00	0.00	3.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	7.440523	AGCAATTGTAAAAACAAAACCAACA	57.559	28.000	7.40	0.00	32.94	3.33
137	138	6.257630	CACTTTGTTCCAAACCGAATTCAAAT	59.742	34.615	6.22	0.00	0.00	2.32
146	147	2.021457	ACCTCACTTTGTTCCAAACCG	58.979	47.619	0.00	0.00	0.00	4.44
183	184	3.544684	TCACTAATGGTGCCATGTCATC	58.455	45.455	4.26	0.00	44.98	2.92
226	227	1.007336	GCGGTCACTGTAACACTCGG	61.007	60.000	0.00	0.00	0.00	4.63
229	230	1.006571	CCGCGGTCACTGTAACACT	60.007	57.895	19.50	0.00	0.00	3.55
256	257	1.301244	CCTTCCCCTGCATCGATCG	60.301	63.158	9.36	9.36	0.00	3.69
257	258	1.072159	CCCTTCCCCTGCATCGATC	59.928	63.158	0.00	0.00	0.00	3.69
258	259	2.455565	CCCCTTCCCCTGCATCGAT	61.456	63.158	0.00	0.00	0.00	3.59
259	260	3.089874	CCCCTTCCCCTGCATCGA	61.090	66.667	0.00	0.00	0.00	3.59
260	261	4.195334	CCCCCTTCCCCTGCATCG	62.195	72.222	0.00	0.00	0.00	3.84
261	262	4.529731	GCCCCCTTCCCCTGCATC	62.530	72.222	0.00	0.00	0.00	3.91
323	324	2.736826	GCCTGCTACCCCTCTCACC	61.737	68.421	0.00	0.00	0.00	4.02
339	340	1.410224	CCACCCCATTCCTTCTAAGCC	60.410	57.143	0.00	0.00	0.00	4.35
340	341	2.024306	GCCACCCCATTCCTTCTAAGC	61.024	57.143	0.00	0.00	0.00	3.09
350	351	3.229697	GCTATAAGAAGCCACCCCATT	57.770	47.619	0.00	0.00	36.45	3.16
433	434	1.737008	GACGTCCTGAACTTCGCCC	60.737	63.158	3.51	0.00	0.00	6.13
459	460	1.497286	CTAGACCTCCCCTAGACTGCT	59.503	57.143	0.00	0.00	36.58	4.24
523	525	1.604593	CCACCCCAACCAAGCTCTG	60.605	63.158	0.00	0.00	0.00	3.35
538	540	0.801067	CAAGCTAGCCGACGTACCAC	60.801	60.000	12.13	0.00	0.00	4.16
539	541	1.509463	CAAGCTAGCCGACGTACCA	59.491	57.895	12.13	0.00	0.00	3.25
596	598	1.196012	GTCATCTCGTCCTTTCCCCT	58.804	55.000	0.00	0.00	0.00	4.79
634	636	1.166531	AGTGGCCTCGAACAAGTTGC	61.167	55.000	3.32	0.00	0.00	4.17
673	675	2.595009	GAATGAGTCCCACGCTCCCC	62.595	65.000	0.00	0.00	32.31	4.81
687	689	1.265635	CGGTTTTTGACCTGCGAATGA	59.734	47.619	0.00	0.00	46.92	2.57
703	705	2.851263	TGGACATAGTCAAAGCGGTT	57.149	45.000	0.00	0.00	33.68	4.44
730	732	2.452600	TGGGTTTGCTCAAGAGGTTT	57.547	45.000	0.00	0.00	0.00	3.27
733	735	3.445096	CCTTAATGGGTTTGCTCAAGAGG	59.555	47.826	0.00	0.00	0.00	3.69
809	829	7.072454	TGCTTCATCTATTCAATACCCCTTAGT	59.928	37.037	0.00	0.00	0.00	2.24
811	831	7.387265	TGCTTCATCTATTCAATACCCCTTA	57.613	36.000	0.00	0.00	0.00	2.69
874	925	1.298014	GTCCAACAGCTCCCCTGAG	59.702	63.158	0.00	0.00	44.64	3.35
904	955	1.864435	GCGGTACTTGGTGCGATCTAG	60.864	57.143	0.00	0.00	0.00	2.43
919	970	1.448189	CCGTCGGATTTTGGCGGTA	60.448	57.895	4.91	0.00	37.87	4.02
1142	1204	2.706071	GGGGAGGAGGTGGGAGAT	59.294	66.667	0.00	0.00	0.00	2.75
1321	1383	1.002274	GGAGAGGAGGAAGAGGCCA	59.998	63.158	5.01	0.00	0.00	5.36
1831	1893	1.831652	CTCGCACCTTCCTGTTCCCT	61.832	60.000	0.00	0.00	0.00	4.20
2062	2124	1.003003	TCACCAATCTCCATTGACGCA	59.997	47.619	0.00	0.00	41.97	5.24
2375	2452	6.662414	TTGGCTCATACAAATTTCTACGAG	57.338	37.500	0.00	0.00	0.00	4.18
2376	2453	6.428465	TGTTTGGCTCATACAAATTTCTACGA	59.572	34.615	0.00	0.00	39.68	3.43
2377	2454	6.523201	GTGTTTGGCTCATACAAATTTCTACG	59.477	38.462	0.00	0.00	39.68	3.51
2378	2455	6.806739	GGTGTTTGGCTCATACAAATTTCTAC	59.193	38.462	0.00	0.00	39.68	2.59
2379	2456	6.491745	TGGTGTTTGGCTCATACAAATTTCTA	59.508	34.615	0.00	0.00	39.68	2.10
2380	2457	5.304101	TGGTGTTTGGCTCATACAAATTTCT	59.696	36.000	0.00	0.00	39.68	2.52
2879	2957	6.543831	GCATATTCACAGTACCTGGAGATTTT	59.456	38.462	0.00	0.00	35.51	1.82
3178	3258	1.203758	CAAAACGGGCCCTATTTCACC	59.796	52.381	22.43	0.00	0.00	4.02
3189	3269	3.442273	TCCTCATAAATGTCAAAACGGGC	59.558	43.478	0.00	0.00	0.00	6.13
3190	3270	4.700213	AGTCCTCATAAATGTCAAAACGGG	59.300	41.667	0.00	0.00	0.00	5.28
3192	3272	8.883731	AGATAAGTCCTCATAAATGTCAAAACG	58.116	33.333	0.00	0.00	0.00	3.60
3248	3328	8.948853	TCTTCAGTCAACAATTAAATTAAGCG	57.051	30.769	0.00	0.00	0.00	4.68
3259	3339	5.944599	AGAATGCTCATCTTCAGTCAACAAT	59.055	36.000	0.00	0.00	30.57	2.71
3260	3340	5.311265	AGAATGCTCATCTTCAGTCAACAA	58.689	37.500	0.00	0.00	30.57	2.83
3298	3378	7.009179	AGAGAAACACCTCTGATGTAAATGA	57.991	36.000	0.00	0.00	41.63	2.57
3322	3402	4.175787	ACGTACCTGCAAAAACAAACAA	57.824	36.364	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.