AutoCloner

Multiple sequence alignment - TraesCS1D01G135100

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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	TraesCS1D01G135100	chr1D	100.000	2370	0	0	1	2370	176208284	176210653	0.000000e+00	4377
1	TraesCS1D01G135100	chr1D	97.214	1364	34	4	1	1360	254383476	254382113	0.000000e+00	2305
2	TraesCS1D01G135100	chr1D	98.980	98	1	0	2273	2370	254481944	254482041	2.420000e-40	176
3	TraesCS1D01G135100	chr1D	98.980	98	1	0	2273	2370	446749073	446748976	2.420000e-40	176
4	TraesCS1D01G135100	chr5D	98.083	1356	21	4	1	1351	503243817	503245172	0.000000e+00	2355
5	TraesCS1D01G135100	chr5D	97.799	1363	27	3	1	1360	503266758	503265396	0.000000e+00	2348
6	TraesCS1D01G135100	chr5D	100.000	98	0	0	2273	2370	6219234	6219137	5.200000e-42	182
7	TraesCS1D01G135100	chr5D	100.000	98	0	0	2273	2370	483802809	483802712	5.200000e-42	182
8	TraesCS1D01G135100	chr7B	97.802	1365	25	4	1	1360	663100880	663099516	0.000000e+00	2350
9	TraesCS1D01G135100	chr7B	97.419	1356	30	4	1	1351	662724949	662726304	0.000000e+00	2305
10	TraesCS1D01G135100	chr7B	97.939	922	18	1	1353	2273	662726435	662727356	0.000000e+00	1596
11	TraesCS1D01G135100	chr6D	97.802	1365	25	4	1	1360	389247277	389245913	0.000000e+00	2350
12	TraesCS1D01G135100	chr6D	97.939	922	18	1	1353	2273	389245791	389244870	0.000000e+00	1596
13	TraesCS1D01G135100	chr3A	97.727	1364	27	4	1	1360	66006587	66005224	0.000000e+00	2344
14	TraesCS1D01G135100	chr2A	97.582	1365	28	4	1	1360	726907910	726906546	0.000000e+00	2333
15	TraesCS1D01G135100	chr2A	97.828	921	20	0	1353	2273	335847345	335848265	0.000000e+00	1591
16	TraesCS1D01G135100	chr3D	97.784	1354	26	4	1	1351	589264978	589263626	0.000000e+00	2331
17	TraesCS1D01G135100	chr3D	97.939	922	18	1	1353	2273	589263495	589262574	0.000000e+00	1596
18	TraesCS1D01G135100	chr3D	100.000	98	0	0	2273	2370	396621274	396621177	5.200000e-42	182
19	TraesCS1D01G135100	chr7D	97.939	922	18	1	1353	2273	231554395	231553474	0.000000e+00	1596
20	TraesCS1D01G135100	chr7D	100.000	97	0	0	2273	2369	231563029	231563125	1.870000e-41	180
21	TraesCS1D01G135100	chr2D	97.939	922	18	1	1353	2273	591984640	591985561	0.000000e+00	1596
22	TraesCS1D01G135100	chr2D	100.000	98	0	0	2273	2370	359629932	359629835	5.200000e-42	182
23	TraesCS1D01G135100	chr2D	100.000	98	0	0	2273	2370	643858308	643858405	5.200000e-42	182
24	TraesCS1D01G135100	chr2D	98.980	98	1	0	2273	2370	628291549	628291452	2.420000e-40	176
25	TraesCS1D01G135100	chr3B	97.831	922	19	1	1353	2273	201539553	201540474	0.000000e+00	1591
26	TraesCS1D01G135100	chr3B	97.831	922	19	1	1353	2273	201614987	201615908	0.000000e+00	1591
27	TraesCS1D01G135100	chr5B	97.725	923	19	1	1353	2273	44988931	44989853	0.000000e+00	1587

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	TraesCS1D01G135100	chr1D	176208284	176210653	2369	False	4377.0	4377	100.0000	1	2370	1	chr1D.!!$F1	2369
1	TraesCS1D01G135100	chr1D	254382113	254383476	1363	True	2305.0	2305	97.2140	1	1360	1	chr1D.!!$R1	1359
2	TraesCS1D01G135100	chr5D	503243817	503245172	1355	False	2355.0	2355	98.0830	1	1351	1	chr5D.!!$F1	1350
3	TraesCS1D01G135100	chr5D	503265396	503266758	1362	True	2348.0	2348	97.7990	1	1360	1	chr5D.!!$R3	1359
4	TraesCS1D01G135100	chr7B	663099516	663100880	1364	True	2350.0	2350	97.8020	1	1360	1	chr7B.!!$R1	1359
5	TraesCS1D01G135100	chr7B	662724949	662727356	2407	False	1950.5	2305	97.6790	1	2273	2	chr7B.!!$F1	2272
6	TraesCS1D01G135100	chr6D	389244870	389247277	2407	True	1973.0	2350	97.8705	1	2273	2	chr6D.!!$R1	2272
7	TraesCS1D01G135100	chr3A	66005224	66006587	1363	True	2344.0	2344	97.7270	1	1360	1	chr3A.!!$R1	1359
8	TraesCS1D01G135100	chr2A	726906546	726907910	1364	True	2333.0	2333	97.5820	1	1360	1	chr2A.!!$R1	1359
9	TraesCS1D01G135100	chr2A	335847345	335848265	920	False	1591.0	1591	97.8280	1353	2273	1	chr2A.!!$F1	920
10	TraesCS1D01G135100	chr3D	589262574	589264978	2404	True	1963.5	2331	97.8615	1	2273	2	chr3D.!!$R2	2272
11	TraesCS1D01G135100	chr7D	231553474	231554395	921	True	1596.0	1596	97.9390	1353	2273	1	chr7D.!!$R1	920
12	TraesCS1D01G135100	chr2D	591984640	591985561	921	False	1596.0	1596	97.9390	1353	2273	1	chr2D.!!$F1	920
13	TraesCS1D01G135100	chr3B	201539553	201540474	921	False	1591.0	1591	97.8310	1353	2273	1	chr3B.!!$F1	920
14	TraesCS1D01G135100	chr3B	201614987	201615908	921	False	1591.0	1591	97.8310	1353	2273	1	chr3B.!!$F2	920
15	TraesCS1D01G135100	chr5B	44988931	44989853	922	False	1587.0	1587	97.7250	1353	2273	1	chr5B.!!$F1	920

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
317	318	1.187087	ACCTGTCCTCAGTTCGGATC	58.813	55.0	0.0	0.0	39.82	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1479	1618	1.218047	CATCCTTCCCGAACGCAGA	59.782	57.895	0.0	0.0	0.0	4.26	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
301	302	3.487372	GGTGAGCTAACTCCAAAAACCT	58.513	45.455	0.00	0.00	42.74	3.50
317	318	1.187087	ACCTGTCCTCAGTTCGGATC	58.813	55.000	0.00	0.00	39.82	3.36
653	654	5.059833	GTCTGAGCTAAACTTGGATATGGG	58.940	45.833	0.00	0.00	0.00	4.00
814	816	5.304357	TCAAAAGGAAAGGGATGGAGTTTTC	59.696	40.000	0.00	0.00	0.00	2.29
1054	1057	4.095782	TGAAACCAAACAAACTTCTCCTCG	59.904	41.667	0.00	0.00	0.00	4.63
1070	1073	0.115349	CTCGGGAGGATAGATGGGGT	59.885	60.000	0.00	0.00	0.00	4.95
1126	1129	3.075005	CACTCGTGGGATCCGGGT	61.075	66.667	5.45	0.00	40.23	5.28
1351	1361	3.834489	TTTTTCATGCTTTTCCTGGCA	57.166	38.095	0.00	0.00	42.80	4.92
2063	2204	6.916360	ATGTAGCAAAAGGAAGGAAAATCA	57.084	33.333	0.00	0.00	0.00	2.57
2070	2211	6.742363	GCAAAAGGAAGGAAAATCAATGGACT	60.742	38.462	0.00	0.00	0.00	3.85
2090	2231	1.151587	ACCCCATTGTCTCCACCCT	60.152	57.895	0.00	0.00	0.00	4.34
2221	2362	1.848652	CAGTAAGGGTCGGAGAAGGA	58.151	55.000	0.00	0.00	39.69	3.36
2273	2414	0.806492	GATCAAAGAGTCGGGCGGAC	60.806	60.000	16.56	16.56	46.45	4.79
2280	2421	2.183555	GTCGGGCGGACGAGATTT	59.816	61.111	9.54	0.00	44.42	2.17
2281	2422	1.447314	GTCGGGCGGACGAGATTTT	60.447	57.895	9.54	0.00	44.42	1.82
2282	2423	1.017701	GTCGGGCGGACGAGATTTTT	61.018	55.000	9.54	0.00	44.42	1.94
2313	2454	9.783256	AAGTTTCATTTACGCCTAATTAACATC	57.217	29.630	0.00	0.00	0.00	3.06
2314	2455	8.120465	AGTTTCATTTACGCCTAATTAACATCG	58.880	33.333	0.00	0.00	0.00	3.84
2315	2456	7.773864	TTCATTTACGCCTAATTAACATCGA	57.226	32.000	0.00	0.00	0.00	3.59
2316	2457	7.402811	TCATTTACGCCTAATTAACATCGAG	57.597	36.000	0.00	0.00	0.00	4.04
2317	2458	6.982141	TCATTTACGCCTAATTAACATCGAGT	59.018	34.615	0.00	0.00	0.00	4.18
2318	2459	8.136800	TCATTTACGCCTAATTAACATCGAGTA	58.863	33.333	0.00	0.00	0.00	2.59
2319	2460	7.919313	TTTACGCCTAATTAACATCGAGTAG	57.081	36.000	0.00	0.00	0.00	2.57
2320	2461	5.762825	ACGCCTAATTAACATCGAGTAGA	57.237	39.130	0.00	0.00	0.00	2.59
2321	2462	5.517904	ACGCCTAATTAACATCGAGTAGAC	58.482	41.667	0.00	0.00	0.00	2.59
2322	2463	4.916249	CGCCTAATTAACATCGAGTAGACC	59.084	45.833	0.00	0.00	0.00	3.85
2323	2464	5.228665	GCCTAATTAACATCGAGTAGACCC	58.771	45.833	0.00	0.00	0.00	4.46
2324	2465	5.010820	GCCTAATTAACATCGAGTAGACCCT	59.989	44.000	0.00	0.00	0.00	4.34
2325	2466	6.448006	CCTAATTAACATCGAGTAGACCCTG	58.552	44.000	0.00	0.00	0.00	4.45
2326	2467	5.934402	AATTAACATCGAGTAGACCCTGT	57.066	39.130	0.00	0.00	0.00	4.00
2327	2468	5.934402	ATTAACATCGAGTAGACCCTGTT	57.066	39.130	2.71	2.71	34.86	3.16
2328	2469	7.414222	AATTAACATCGAGTAGACCCTGTTA	57.586	36.000	0.00	0.00	33.26	2.41
2329	2470	7.598759	ATTAACATCGAGTAGACCCTGTTAT	57.401	36.000	5.18	0.00	34.04	1.89
2330	2471	5.934402	AACATCGAGTAGACCCTGTTATT	57.066	39.130	0.00	0.00	30.36	1.40
2331	2472	5.263968	ACATCGAGTAGACCCTGTTATTG	57.736	43.478	0.00	0.00	0.00	1.90
2332	2473	4.710375	ACATCGAGTAGACCCTGTTATTGT	59.290	41.667	0.00	0.00	0.00	2.71
2333	2474	4.713824	TCGAGTAGACCCTGTTATTGTG	57.286	45.455	0.00	0.00	0.00	3.33
2334	2475	4.338012	TCGAGTAGACCCTGTTATTGTGA	58.662	43.478	0.00	0.00	0.00	3.58
2335	2476	4.398358	TCGAGTAGACCCTGTTATTGTGAG	59.602	45.833	0.00	0.00	0.00	3.51
2336	2477	4.398358	CGAGTAGACCCTGTTATTGTGAGA	59.602	45.833	0.00	0.00	0.00	3.27
2337	2478	5.105877	CGAGTAGACCCTGTTATTGTGAGAA	60.106	44.000	0.00	0.00	0.00	2.87
2338	2479	6.405953	CGAGTAGACCCTGTTATTGTGAGAAT	60.406	42.308	0.00	0.00	0.00	2.40
2339	2480	7.259088	AGTAGACCCTGTTATTGTGAGAATT	57.741	36.000	0.00	0.00	0.00	2.17
2340	2481	7.331791	AGTAGACCCTGTTATTGTGAGAATTC	58.668	38.462	0.00	0.00	0.00	2.17
2341	2482	6.380079	AGACCCTGTTATTGTGAGAATTCT	57.620	37.500	7.95	7.95	0.00	2.40
2342	2483	6.784031	AGACCCTGTTATTGTGAGAATTCTT	58.216	36.000	9.87	0.00	0.00	2.52
2343	2484	7.918076	AGACCCTGTTATTGTGAGAATTCTTA	58.082	34.615	9.87	1.94	0.00	2.10
2344	2485	8.383175	AGACCCTGTTATTGTGAGAATTCTTAA	58.617	33.333	9.87	6.34	0.00	1.85
2345	2486	9.178758	GACCCTGTTATTGTGAGAATTCTTAAT	57.821	33.333	9.87	12.66	0.00	1.40
2346	2487	9.533831	ACCCTGTTATTGTGAGAATTCTTAATT	57.466	29.630	9.87	0.00	0.00	1.40
2364	2505	8.263854	TCTTAATTCAAGAGTTATAGGGAGGG	57.736	38.462	0.00	0.00	38.39	4.30
2365	2506	8.071854	TCTTAATTCAAGAGTTATAGGGAGGGA	58.928	37.037	0.00	0.00	38.39	4.20
2366	2507	6.502074	AATTCAAGAGTTATAGGGAGGGAC	57.498	41.667	0.00	0.00	0.00	4.46
2368	2509	5.222278	TCAAGAGTTATAGGGAGGGACTT	57.778	43.478	0.00	0.00	41.55	3.01
2369	2510	6.351317	TCAAGAGTTATAGGGAGGGACTTA	57.649	41.667	0.00	0.00	41.55	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	4.308458	CCTGTGTCCGCGTTCCCA	62.308	66.667	4.92	0.00	0.00	4.37
301	302	1.248101	TGCGATCCGAACTGAGGACA	61.248	55.000	0.00	0.00	41.10	4.02
396	397	2.032071	GGCGGTGTGTACAAGGCT	59.968	61.111	0.00	0.00	0.00	4.58
582	583	6.378564	TGAAGAAGTGTCAAACCAAAATACCA	59.621	34.615	0.00	0.00	0.00	3.25
653	654	4.879598	TCACCCTAAACGAAAGAAGACTC	58.120	43.478	0.00	0.00	0.00	3.36
980	983	2.368439	TGCTAATGTGCCTTGGATGAC	58.632	47.619	0.00	0.00	0.00	3.06
1054	1057	2.350863	ATCACCCCATCTATCCTCCC	57.649	55.000	0.00	0.00	0.00	4.30
1070	1073	3.117745	ACATGGGATCTCACCTGAATCA	58.882	45.455	0.00	0.00	0.00	2.57
1347	1357	2.042762	ATACCCTCCTGGCTGCCA	59.957	61.111	21.96	21.96	37.83	4.92
1351	1361	2.040178	CGTTAAGATACCCTCCTGGCT	58.960	52.381	0.00	0.00	37.83	4.75
1363	1502	4.082733	GCAGAAAAAGGAAGGCGTTAAGAT	60.083	41.667	0.00	0.00	0.00	2.40
1479	1618	1.218047	CATCCTTCCCGAACGCAGA	59.782	57.895	0.00	0.00	0.00	4.26
1547	1686	4.642429	GTGAAGTAAATCATCGCCCCTAT	58.358	43.478	0.00	0.00	0.00	2.57
1969	2110	2.041620	CCAACTTGATCCTCTTCCCCAA	59.958	50.000	0.00	0.00	0.00	4.12
2070	2211	1.497309	GGGTGGAGACAATGGGGTCA	61.497	60.000	0.00	0.00	46.06	4.02
2090	2231	4.210331	GGGGTAATCTCGTAGTTCCTACA	58.790	47.826	2.66	0.00	36.83	2.74
2107	2248	2.686106	GAGGGCGTCCTTGGGGTA	60.686	66.667	11.49	0.00	45.05	3.69
2143	2284	1.583054	GAACATGGTCTATGGTCGGC	58.417	55.000	2.64	0.00	43.17	5.54
2221	2362	5.277828	GCTGGTTTTAAGAACGAGTGATTGT	60.278	40.000	0.00	0.00	0.00	2.71
2287	2428	9.783256	GATGTTAATTAGGCGTAAATGAAACTT	57.217	29.630	2.52	4.36	0.00	2.66
2288	2429	8.120465	CGATGTTAATTAGGCGTAAATGAAACT	58.880	33.333	2.52	0.00	0.00	2.66
2289	2430	8.117988	TCGATGTTAATTAGGCGTAAATGAAAC	58.882	33.333	2.52	6.25	0.00	2.78
2290	2431	8.199176	TCGATGTTAATTAGGCGTAAATGAAA	57.801	30.769	2.52	0.00	0.00	2.69
2291	2432	7.493320	ACTCGATGTTAATTAGGCGTAAATGAA	59.507	33.333	2.52	0.00	0.00	2.57
2292	2433	6.982141	ACTCGATGTTAATTAGGCGTAAATGA	59.018	34.615	2.52	0.00	0.00	2.57
2293	2434	7.173863	ACTCGATGTTAATTAGGCGTAAATG	57.826	36.000	2.52	0.00	0.00	2.32
2294	2435	8.355169	TCTACTCGATGTTAATTAGGCGTAAAT	58.645	33.333	2.52	0.00	0.00	1.40
2295	2436	7.645340	GTCTACTCGATGTTAATTAGGCGTAAA	59.355	37.037	2.52	0.00	0.00	2.01
2296	2437	7.134815	GTCTACTCGATGTTAATTAGGCGTAA	58.865	38.462	0.64	0.64	0.00	3.18
2297	2438	6.293626	GGTCTACTCGATGTTAATTAGGCGTA	60.294	42.308	0.00	0.00	0.00	4.42
2298	2439	5.506982	GGTCTACTCGATGTTAATTAGGCGT	60.507	44.000	0.00	0.00	0.00	5.68
2299	2440	4.916249	GGTCTACTCGATGTTAATTAGGCG	59.084	45.833	0.00	0.00	0.00	5.52
2300	2441	5.010820	AGGGTCTACTCGATGTTAATTAGGC	59.989	44.000	0.00	0.00	0.00	3.93
2301	2442	6.040616	ACAGGGTCTACTCGATGTTAATTAGG	59.959	42.308	0.00	0.00	0.00	2.69
2302	2443	7.040473	ACAGGGTCTACTCGATGTTAATTAG	57.960	40.000	0.00	0.00	0.00	1.73
2303	2444	7.414222	AACAGGGTCTACTCGATGTTAATTA	57.586	36.000	0.00	0.00	0.00	1.40
2304	2445	5.934402	ACAGGGTCTACTCGATGTTAATT	57.066	39.130	0.00	0.00	0.00	1.40
2305	2446	5.934402	AACAGGGTCTACTCGATGTTAAT	57.066	39.130	0.00	0.00	0.00	1.40
2306	2447	7.093640	ACAATAACAGGGTCTACTCGATGTTAA	60.094	37.037	7.76	0.00	36.88	2.01
2307	2448	6.379133	ACAATAACAGGGTCTACTCGATGTTA	59.621	38.462	6.48	6.48	37.48	2.41
2308	2449	5.187186	ACAATAACAGGGTCTACTCGATGTT	59.813	40.000	2.71	2.71	35.28	2.71
2309	2450	4.710375	ACAATAACAGGGTCTACTCGATGT	59.290	41.667	0.00	0.00	0.00	3.06
2310	2451	5.043903	CACAATAACAGGGTCTACTCGATG	58.956	45.833	0.00	0.00	0.00	3.84
2311	2452	4.954202	TCACAATAACAGGGTCTACTCGAT	59.046	41.667	0.00	0.00	0.00	3.59
2312	2453	4.338012	TCACAATAACAGGGTCTACTCGA	58.662	43.478	0.00	0.00	0.00	4.04
2313	2454	4.398358	TCTCACAATAACAGGGTCTACTCG	59.602	45.833	0.00	0.00	0.00	4.18
2314	2455	5.916661	TCTCACAATAACAGGGTCTACTC	57.083	43.478	0.00	0.00	0.00	2.59
2315	2456	6.875972	ATTCTCACAATAACAGGGTCTACT	57.124	37.500	0.00	0.00	0.00	2.57
2316	2457	7.331791	AGAATTCTCACAATAACAGGGTCTAC	58.668	38.462	0.88	0.00	0.00	2.59
2317	2458	7.496346	AGAATTCTCACAATAACAGGGTCTA	57.504	36.000	0.88	0.00	0.00	2.59
2318	2459	6.380079	AGAATTCTCACAATAACAGGGTCT	57.620	37.500	0.88	0.00	0.00	3.85
2319	2460	8.561738	TTAAGAATTCTCACAATAACAGGGTC	57.438	34.615	8.78	0.00	0.00	4.46
2320	2461	9.533831	AATTAAGAATTCTCACAATAACAGGGT	57.466	29.630	8.78	0.00	0.00	4.34
2338	2479	8.714906	CCCTCCCTATAACTCTTGAATTAAGAA	58.285	37.037	0.00	0.00	44.47	2.52
2339	2480	8.071854	TCCCTCCCTATAACTCTTGAATTAAGA	58.928	37.037	0.00	0.00	43.01	2.10
2340	2481	8.151596	GTCCCTCCCTATAACTCTTGAATTAAG	58.848	40.741	0.00	0.00	37.76	1.85
2341	2482	7.849904	AGTCCCTCCCTATAACTCTTGAATTAA	59.150	37.037	0.00	0.00	0.00	1.40
2342	2483	7.371043	AGTCCCTCCCTATAACTCTTGAATTA	58.629	38.462	0.00	0.00	0.00	1.40
2343	2484	6.213525	AGTCCCTCCCTATAACTCTTGAATT	58.786	40.000	0.00	0.00	0.00	2.17
2344	2485	5.793967	AGTCCCTCCCTATAACTCTTGAAT	58.206	41.667	0.00	0.00	0.00	2.57
2345	2486	5.222278	AGTCCCTCCCTATAACTCTTGAA	57.778	43.478	0.00	0.00	0.00	2.69
2346	2487	4.901785	AGTCCCTCCCTATAACTCTTGA	57.098	45.455	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.