AutoCloner

Multiple sequence alignment - TraesCS7B01G336300

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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	TraesCS7B01G336300	chr7B	100.000	3431	0	0	1	3431	591460949	591464379	0.000000e+00	6336.0
1	TraesCS7B01G336300	chr7B	85.308	211	18	7	485	684	216661041	216661249	4.490000e-49	206.0
2	TraesCS7B01G336300	chr7D	94.886	3324	103	26	3	3294	548230402	548233690	0.000000e+00	5134.0
3	TraesCS7B01G336300	chr7D	92.056	856	42	10	2452	3296	548235049	548235889	0.000000e+00	1181.0
4	TraesCS7B01G336300	chr7D	90.411	146	10	3	3287	3431	548233763	548233905	4.520000e-44	189.0
5	TraesCS7B01G336300	chr7D	89.655	145	12	2	3287	3431	548235959	548236100	7.560000e-42	182.0
6	TraesCS7B01G336300	chr7A	95.083	2766	90	17	1	2750	631983754	631986489	0.000000e+00	4313.0
7	TraesCS7B01G336300	chr7A	94.369	515	14	5	2781	3294	631986685	631987185	0.000000e+00	776.0
8	TraesCS7B01G336300	chr7A	89.510	143	15	0	3289	3431	631987259	631987401	7.560000e-42	182.0
9	TraesCS7B01G336300	chr5D	86.314	2740	242	78	601	3266	535497134	535494454	0.000000e+00	2859.0
10	TraesCS7B01G336300	chr5D	88.340	2307	179	43	331	2568	57819174	57821459	0.000000e+00	2687.0
11	TraesCS7B01G336300	chr5D	85.714	63	7	2	3314	3374	474810882	474810944	7.950000e-07	65.8
12	TraesCS7B01G336300	chr6D	86.345	2651	211	71	10	2588	51342280	51344851	0.000000e+00	2750.0
13	TraesCS7B01G336300	chr6D	85.958	2642	204	72	10	2588	51067590	51070127	0.000000e+00	2669.0
14	TraesCS7B01G336300	chr6D	85.748	2533	218	55	108	2587	50955828	50958270	0.000000e+00	2545.0
15	TraesCS7B01G336300	chr6D	86.117	2377	218	54	621	2920	51348748	51351089	0.000000e+00	2459.0
16	TraesCS7B01G336300	chr6D	85.955	2378	223	55	621	2920	51073966	51076310	0.000000e+00	2438.0
17	TraesCS7B01G336300	chr6D	84.903	722	65	16	2585	3294	53174059	53173370	0.000000e+00	689.0
18	TraesCS7B01G336300	chr6D	90.761	368	21	8	2804	3170	50958572	50958927	2.400000e-131	479.0
19	TraesCS7B01G336300	chr6D	86.880	343	23	12	2932	3270	51345352	51345676	7.000000e-97	364.0
20	TraesCS7B01G336300	chr6D	84.167	360	32	14	2582	2924	51344884	51345235	3.300000e-85	326.0
21	TraesCS7B01G336300	chr6D	83.611	360	34	14	2582	2924	51070160	51070511	7.150000e-82	315.0
22	TraesCS7B01G336300	chr6D	78.368	527	54	26	44	549	51073451	51073938	1.560000e-73	287.0
23	TraesCS7B01G336300	chr6D	78.368	527	53	27	44	549	51348234	51348720	5.600000e-73	285.0
24	TraesCS7B01G336300	chr6B	86.239	2616	212	64	100	2647	120595968	120593433	0.000000e+00	2700.0
25	TraesCS7B01G336300	chr6B	88.011	2252	175	33	363	2580	120355373	120353183	0.000000e+00	2575.0
26	TraesCS7B01G336300	chr6B	88.561	1967	147	31	657	2588	120317474	120315551	0.000000e+00	2314.0
27	TraesCS7B01G336300	chr6B	82.345	725	79	27	2585	3294	120315514	120314824	4.930000e-163	584.0
28	TraesCS7B01G336300	chr6B	86.707	331	24	10	2941	3270	120352696	120352385	1.960000e-92	350.0
29	TraesCS7B01G336300	chr6B	81.046	306	35	15	44	330	120355803	120355502	4.460000e-54	222.0
30	TraesCS7B01G336300	chr6B	76.821	302	30	24	60	355	120318146	120317879	2.150000e-27	134.0
31	TraesCS7B01G336300	chr6B	78.307	189	23	14	10	187	120133864	120133683	4.680000e-19	106.0
32	TraesCS7B01G336300	chr5B	88.046	2334	181	47	331	2588	60826357	60824046	0.000000e+00	2675.0
33	TraesCS7B01G336300	chr5B	87.179	78	9	1	3289	3366	507729534	507729458	1.700000e-13	87.9
34	TraesCS7B01G336300	chr3D	86.773	2374	215	45	266	2588	560025269	560022944	0.000000e+00	2553.0
35	TraesCS7B01G336300	chr3D	89.855	69	4	3	3307	3373	553220	553153	6.100000e-13	86.1
36	TraesCS7B01G336300	chr1B	86.249	2378	219	59	266	2588	4519380	4517056	0.000000e+00	2481.0
37	TraesCS7B01G336300	chr1B	88.861	1957	147	36	694	2588	70232797	70234744	0.000000e+00	2340.0
38	TraesCS7B01G336300	chr1B	81.651	109	9	5	221	318	46691155	46691263	2.840000e-11	80.5
39	TraesCS7B01G336300	chr1B	100.000	39	0	0	221	259	3935790	3935828	4.750000e-09	73.1
40	TraesCS7B01G336300	chr1B	100.000	38	0	0	221	258	4543455	4543418	1.710000e-08	71.3
41	TraesCS7B01G336300	chr6A	85.387	698	59	24	2585	3267	64165904	64165235	0.000000e+00	684.0
42	TraesCS7B01G336300	chr6A	76.791	698	71	43	100	776	64175652	64175025	1.200000e-79	307.0
43	TraesCS7B01G336300	chr6A	80.451	266	36	13	8	262	64168664	64168404	4.520000e-44	189.0
44	TraesCS7B01G336300	chr6A	90.741	54	3	2	3315	3366	604953901	604953954	1.710000e-08	71.3
45	TraesCS7B01G336300	chr1A	81.651	109	6	8	161	256	32545122	32545229	1.020000e-10	78.7
46	TraesCS7B01G336300	chr1A	93.750	48	3	0	3384	3431	392047927	392047880	4.750000e-09	73.1
47	TraesCS7B01G336300	chr1D	81.928	83	11	3	3287	3366	420833140	420833221	2.210000e-07	67.6
48	TraesCS7B01G336300	chr4A	94.737	38	2	0	3394	3431	492946065	492946102	3.700000e-05	60.2
49	TraesCS7B01G336300	chr3B	80.488	82	12	4	3287	3365	651378651	651378731	3.700000e-05	60.2

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	TraesCS7B01G336300	chr7B	591460949	591464379	3430	False	6336.000000	6336	100.000000	1	3431	1	chr7B.!!$F2	3430
1	TraesCS7B01G336300	chr7D	548230402	548236100	5698	False	1671.500000	5134	91.752000	3	3431	4	chr7D.!!$F1	3428
2	TraesCS7B01G336300	chr7A	631983754	631987401	3647	False	1757.000000	4313	92.987333	1	3431	3	chr7A.!!$F1	3430
3	TraesCS7B01G336300	chr5D	535494454	535497134	2680	True	2859.000000	2859	86.314000	601	3266	1	chr5D.!!$R1	2665
4	TraesCS7B01G336300	chr5D	57819174	57821459	2285	False	2687.000000	2687	88.340000	331	2568	1	chr5D.!!$F1	2237
5	TraesCS7B01G336300	chr6D	50955828	50958927	3099	False	1512.000000	2545	88.254500	108	3170	2	chr6D.!!$F1	3062
6	TraesCS7B01G336300	chr6D	51067590	51076310	8720	False	1427.250000	2669	83.473000	10	2924	4	chr6D.!!$F2	2914
7	TraesCS7B01G336300	chr6D	51342280	51351089	8809	False	1236.800000	2750	84.375400	10	3270	5	chr6D.!!$F3	3260
8	TraesCS7B01G336300	chr6D	53173370	53174059	689	True	689.000000	689	84.903000	2585	3294	1	chr6D.!!$R1	709
9	TraesCS7B01G336300	chr6B	120593433	120595968	2535	True	2700.000000	2700	86.239000	100	2647	1	chr6B.!!$R2	2547
10	TraesCS7B01G336300	chr6B	120352385	120355803	3418	True	1049.000000	2575	85.254667	44	3270	3	chr6B.!!$R4	3226
11	TraesCS7B01G336300	chr6B	120314824	120318146	3322	True	1010.666667	2314	82.575667	60	3294	3	chr6B.!!$R3	3234
12	TraesCS7B01G336300	chr5B	60824046	60826357	2311	True	2675.000000	2675	88.046000	331	2588	1	chr5B.!!$R1	2257
13	TraesCS7B01G336300	chr3D	560022944	560025269	2325	True	2553.000000	2553	86.773000	266	2588	1	chr3D.!!$R2	2322
14	TraesCS7B01G336300	chr1B	4517056	4519380	2324	True	2481.000000	2481	86.249000	266	2588	1	chr1B.!!$R1	2322
15	TraesCS7B01G336300	chr1B	70232797	70234744	1947	False	2340.000000	2340	88.861000	694	2588	1	chr1B.!!$F3	1894
16	TraesCS7B01G336300	chr6A	64165235	64168664	3429	True	436.500000	684	82.919000	8	3267	2	chr6A.!!$R2	3259
17	TraesCS7B01G336300	chr6A	64175025	64175652	627	True	307.000000	307	76.791000	100	776	1	chr6A.!!$R1	676

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
881	1555	0.389296	CAATGAGTGTCGCCGGTGTA	60.389	55.0	16.01	2.5	0.0	2.90	F
2107	2813	0.804989	CTGCCCAATTCGTGTTCTCC	59.195	55.0	0.00	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2295	3002	0.536006	GTGCACTTCCCAGTTCAGCT	60.536	55.000	10.32	0.0	25.39	4.24	R
3076	6268	2.910977	ACACGACCCCCTCTAAATTTCT	59.089	45.455	0.00	0.0	0.00	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
158	188	0.517316	CCGTTTTTCGCTTCTCCTGG	59.483	55.000	0.00	0.00	38.35	4.45
189	227	1.376812	GCGTTGGTTCCCCGATTCT	60.377	57.895	2.95	0.00	0.00	2.40
205	243	4.417506	CGATTCTACATGTACACGGTTGA	58.582	43.478	0.08	3.63	0.00	3.18
212	251	4.778904	ACATGTACACGGTTGATTTTTCG	58.221	39.130	0.00	0.00	0.00	3.46
214	253	5.180492	ACATGTACACGGTTGATTTTTCGAT	59.820	36.000	0.00	0.00	0.00	3.59
215	254	5.676532	TGTACACGGTTGATTTTTCGATT	57.323	34.783	0.00	0.00	0.00	3.34
216	255	5.681880	TGTACACGGTTGATTTTTCGATTC	58.318	37.500	0.00	0.00	0.00	2.52
271	324	9.534565	CGGTAGTATCATCCATAGATTTAATGG	57.465	37.037	0.00	0.00	44.51	3.16
303	545	8.554490	AAGCCATTCTTCTAGGTAGAATTAGA	57.446	34.615	14.57	0.00	39.65	2.10
304	546	8.554490	AGCCATTCTTCTAGGTAGAATTAGAA	57.446	34.615	14.57	1.86	39.65	2.10
305	547	8.993424	AGCCATTCTTCTAGGTAGAATTAGAAA	58.007	33.333	14.57	0.00	39.65	2.52
306	548	9.267084	GCCATTCTTCTAGGTAGAATTAGAAAG	57.733	37.037	14.57	0.00	39.65	2.62
311	553	9.134055	TCTTCTAGGTAGAATTAGAAAGTAGCC	57.866	37.037	0.00	0.00	41.12	3.93
356	717	3.264450	AGGGTTGCAGCAAATACTACTCT	59.736	43.478	10.11	0.00	0.00	3.24
357	718	4.469945	AGGGTTGCAGCAAATACTACTCTA	59.530	41.667	10.11	0.00	0.00	2.43
358	719	4.571176	GGGTTGCAGCAAATACTACTCTAC	59.429	45.833	10.11	0.00	0.00	2.59
359	720	5.420409	GGTTGCAGCAAATACTACTCTACT	58.580	41.667	10.11	0.00	0.00	2.57
360	721	5.520649	GGTTGCAGCAAATACTACTCTACTC	59.479	44.000	10.11	0.00	0.00	2.59
468	955	8.311109	GGCAAAATGATTTCCCTACTTTCTTTA	58.689	33.333	0.00	0.00	0.00	1.85
640	1159	2.284514	GCGTCAATTCTAGCTCGTTTCG	60.285	50.000	0.00	0.00	0.00	3.46
679	1291	2.189594	TCATTGTTCAGGCTCTGGTG	57.810	50.000	2.86	0.00	31.51	4.17
789	1437	8.151596	GGTGCTAGCTACTTTAATAAATCTCCT	58.848	37.037	17.23	0.00	0.00	3.69
881	1555	0.389296	CAATGAGTGTCGCCGGTGTA	60.389	55.000	16.01	2.50	0.00	2.90
960	1644	4.334481	TCTTCGGTTGTTTTCTGAACCTTC	59.666	41.667	0.00	0.00	39.69	3.46
967	1655	9.104965	CGGTTGTTTTCTGAACCTTCATATATA	57.895	33.333	0.00	0.00	39.69	0.86
1311	2007	2.414481	CTCGCTGATTGACCTCACTTTG	59.586	50.000	0.00	0.00	0.00	2.77
1316	2012	3.668447	TGATTGACCTCACTTTGAGCTC	58.332	45.455	6.82	6.82	42.98	4.09
2107	2813	0.804989	CTGCCCAATTCGTGTTCTCC	59.195	55.000	0.00	0.00	0.00	3.71
2295	3002	8.544622	TGTCATAAGGTTACTGATGTTGGATTA	58.455	33.333	0.00	0.00	36.96	1.75
2308	3015	3.073798	TGTTGGATTAGCTGAACTGGGAA	59.926	43.478	0.00	0.00	0.00	3.97
2525	3256	1.945387	AGGCTGTGCATTATCAGACG	58.055	50.000	6.25	0.00	43.68	4.18
2606	3386	9.378551	CTGTATGAAACTTTTATAGTAGGCACA	57.621	33.333	0.00	0.00	35.54	4.57
2674	3459	2.952978	ACCGCTGTTTTGTAATCCACAA	59.047	40.909	0.00	0.00	45.49	3.33
2692	3477	4.263243	CCACAAAAATTGGCCCCAAGATTA	60.263	41.667	0.00	0.00	39.47	1.75
2721	3522	6.524101	TTTTGCTGTTTGGTTTCTACTCTT	57.476	33.333	0.00	0.00	0.00	2.85
2733	3534	6.872020	TGGTTTCTACTCTTAAGAAATGTCGG	59.128	38.462	6.63	0.00	43.01	4.79
2756	3561	4.637534	GGAACCCTTTTTACTACGGGATTC	59.362	45.833	0.00	1.08	39.08	2.52
2779	5787	5.600069	TCTGAAGACATGTATATCTGCCTGT	59.400	40.000	0.00	0.00	0.00	4.00
2845	5900	4.154918	GTCAATGTTTCACATGGAGACCTC	59.845	45.833	0.00	0.00	39.10	3.85
3074	6266	5.175859	TGTGTGCTAATTACAGGCTTCTAC	58.824	41.667	0.00	0.00	0.00	2.59
3075	6267	5.046591	TGTGTGCTAATTACAGGCTTCTACT	60.047	40.000	0.00	0.00	0.00	2.57
3076	6268	6.153851	TGTGTGCTAATTACAGGCTTCTACTA	59.846	38.462	0.00	0.00	0.00	1.82
3314	9358	8.367911	ACAACTGTGTATATCTGAAAGTGAGAA	58.632	33.333	0.00	0.00	35.72	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
158	188	3.284449	AACGCAACGAACAGGGGC	61.284	61.111	0.00	0.00	0.00	5.80
189	227	5.695363	TCGAAAAATCAACCGTGTACATGTA	59.305	36.000	13.91	0.08	0.00	2.29
205	243	7.928307	TCAATCAAGAGAGGAATCGAAAAAT	57.072	32.000	0.00	0.00	0.00	1.82
216	255	5.372373	GTTTCCCCTATCAATCAAGAGAGG	58.628	45.833	0.00	0.00	44.67	3.69
271	324	8.639761	TCTACCTAGAAGAATGGCTTTATACAC	58.360	37.037	0.00	0.00	36.83	2.90
299	541	4.216257	CAGCTGCAAAAGGCTACTTTCTAA	59.784	41.667	0.00	0.00	45.85	2.10
301	543	2.555757	CAGCTGCAAAAGGCTACTTTCT	59.444	45.455	0.00	0.00	45.85	2.52
302	544	2.554032	TCAGCTGCAAAAGGCTACTTTC	59.446	45.455	9.47	0.00	45.85	2.62
304	546	2.157738	CTCAGCTGCAAAAGGCTACTT	58.842	47.619	9.47	0.00	45.15	2.24
305	547	1.612726	CCTCAGCTGCAAAAGGCTACT	60.613	52.381	9.47	0.00	45.15	2.57
306	548	0.807496	CCTCAGCTGCAAAAGGCTAC	59.193	55.000	9.47	0.00	45.15	3.58
307	549	0.692476	TCCTCAGCTGCAAAAGGCTA	59.308	50.000	9.47	0.00	45.15	3.93
311	553	1.736681	GCTAGTCCTCAGCTGCAAAAG	59.263	52.381	9.47	0.28	36.07	2.27
356	717	9.399797	TCTGTTCAACTAGAAATATACGGAGTA	57.600	33.333	0.00	0.00	42.68	2.59
357	718	8.189460	GTCTGTTCAACTAGAAATATACGGAGT	58.811	37.037	0.00	0.00	41.09	3.85
358	719	8.188799	TGTCTGTTCAACTAGAAATATACGGAG	58.811	37.037	0.00	0.00	38.13	4.63
359	720	8.058667	TGTCTGTTCAACTAGAAATATACGGA	57.941	34.615	0.00	0.00	38.13	4.69
360	721	8.873215	ATGTCTGTTCAACTAGAAATATACGG	57.127	34.615	0.00	0.00	38.13	4.02
589	1104	1.166531	GCAAGAAGACCCACGTGCTT	61.167	55.000	10.91	8.41	38.17	3.91
640	1159	9.372369	ACAATGAACTAGCTAAGAGAATACAAC	57.628	33.333	0.00	0.00	0.00	3.32
789	1437	6.449635	AACTTGTGTGTTCTTCATAAGCAA	57.550	33.333	0.00	0.00	37.47	3.91
881	1555	5.748402	TGCATGTGAAGTTAGATGGAGATT	58.252	37.500	0.00	0.00	0.00	2.40
967	1655	5.804639	TCAGCTGTACAAATCAGGTAATGT	58.195	37.500	14.67	0.00	40.86	2.71
968	1656	6.741992	TTCAGCTGTACAAATCAGGTAATG	57.258	37.500	14.67	0.00	40.86	1.90
1170	1866	3.322706	GAACCGGGCGCACAATGAC	62.323	63.158	11.77	0.00	0.00	3.06
2107	2813	0.951558	AAGTTGGCGGTGTTTAGCAG	59.048	50.000	0.00	0.00	34.54	4.24
2295	3002	0.536006	GTGCACTTCCCAGTTCAGCT	60.536	55.000	10.32	0.00	25.39	4.24
2308	3015	5.934625	CCAAAGACTCTAACTTATGTGCACT	59.065	40.000	19.41	6.22	0.00	4.40
2525	3256	6.930731	AGAAAGTCCAGAGAAGTGAATCTAC	58.069	40.000	0.00	0.00	0.00	2.59
2606	3386	6.292703	GCAACAAGAATTACAGTACACGAGTT	60.293	38.462	0.00	0.00	0.00	3.01
2674	3459	3.802132	AGGTAATCTTGGGGCCAATTTT	58.198	40.909	4.39	0.00	35.20	1.82
2679	3464	4.618378	AAAATAGGTAATCTTGGGGCCA	57.382	40.909	4.39	0.00	0.00	5.36
2692	3477	6.233905	AGAAACCAAACAGCAAAAATAGGT	57.766	33.333	0.00	0.00	0.00	3.08
2721	3522	4.376225	AAAGGGTTCCCGACATTTCTTA	57.624	40.909	1.91	0.00	0.00	2.10
2733	3534	3.701205	TCCCGTAGTAAAAAGGGTTCC	57.299	47.619	0.00	0.00	44.13	3.62
2756	3561	5.851720	ACAGGCAGATATACATGTCTTCAG	58.148	41.667	0.00	0.00	0.00	3.02
2845	5900	2.893637	AGCATGTCGCCTTTGTAGTAG	58.106	47.619	0.00	0.00	44.04	2.57
2985	6168	6.407865	CCTCAACTTCCATGAGATGAGTACAT	60.408	42.308	15.90	0.00	45.74	2.29
3027	6210	4.202050	GCTATGTTATTTGCCTTCAGTGGG	60.202	45.833	0.00	0.00	0.00	4.61
3074	6266	4.161754	ACACGACCCCCTCTAAATTTCTAG	59.838	45.833	0.00	0.00	0.00	2.43
3075	6267	4.098894	ACACGACCCCCTCTAAATTTCTA	58.901	43.478	0.00	0.00	0.00	2.10
3076	6268	2.910977	ACACGACCCCCTCTAAATTTCT	59.089	45.455	0.00	0.00	0.00	2.52
3193	6389	4.432712	ACAATCACAACAAAAGTTCAGCC	58.567	39.130	0.00	0.00	0.00	4.85
3314	9358	6.403722	CTCGCAGAAGGAAAAACGTGTTTTT	61.404	40.000	20.05	20.05	45.25	1.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.