AutoCloner

Multiple sequence alignment - TraesCS4D01G337900

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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	TraesCS4D01G337900	chr4D	100.000	2528	0	0	1	2528	495637644	495640171	0.000000e+00	4669.0
1	TraesCS4D01G337900	chr4D	87.456	574	45	17	307	874	495519402	495519954	9.860000e-179	636.0
2	TraesCS4D01G337900	chr4D	92.386	394	19	4	910	1303	495520283	495520665	3.680000e-153	551.0
3	TraesCS4D01G337900	chr4D	85.678	398	33	13	1712	2101	495521052	495521433	5.070000e-107	398.0
4	TraesCS4D01G337900	chr4D	88.843	242	16	5	1300	1530	495520692	495520933	1.140000e-73	287.0
5	TraesCS4D01G337900	chr4D	77.914	489	69	18	1081	1530	495074507	495074995	4.150000e-68	268.0
6	TraesCS4D01G337900	chr4D	82.168	286	39	6	995	1280	495129587	495129860	4.200000e-58	235.0
7	TraesCS4D01G337900	chr4D	87.222	180	20	2	2270	2449	495521556	495521732	4.260000e-48	202.0
8	TraesCS4D01G337900	chr5A	91.128	1285	38	21	1300	2528	675154990	675153726	0.000000e+00	1672.0
9	TraesCS4D01G337900	chr5A	88.491	1312	89	28	1	1304	675320587	675319330	0.000000e+00	1530.0
10	TraesCS4D01G337900	chr5A	87.283	692	41	17	553	1226	675161157	675160495	0.000000e+00	747.0
11	TraesCS4D01G337900	chr5A	84.517	549	64	13	1	544	675189952	675189420	8.010000e-145	523.0
12	TraesCS4D01G337900	chr5A	86.073	438	33	10	1721	2142	675318865	675318440	1.780000e-121	446.0
13	TraesCS4D01G337900	chr5A	84.821	336	28	14	1300	1617	675319304	675318974	1.460000e-82	316.0
14	TraesCS4D01G337900	chr5A	81.029	311	45	8	995	1304	674937364	674937661	4.200000e-58	235.0
15	TraesCS4D01G337900	chr5A	76.626	492	73	23	1081	1530	674852078	674852569	1.510000e-57	233.0
16	TraesCS4D01G337900	chr5A	76.626	492	73	23	1081	1530	674893290	674893781	1.510000e-57	233.0
17	TraesCS4D01G337900	chr5A	85.135	222	24	5	2237	2449	675318339	675318118	4.230000e-53	219.0
18	TraesCS4D01G337900	chr4B	90.590	797	45	13	1712	2493	635461254	635462035	0.000000e+00	1029.0
19	TraesCS4D01G337900	chr4B	90.469	640	42	10	677	1304	635460238	635460870	0.000000e+00	826.0
20	TraesCS4D01G337900	chr4B	90.154	518	42	6	1	513	635459398	635459911	0.000000e+00	665.0
21	TraesCS4D01G337900	chr4B	89.167	240	17	4	1300	1530	635460896	635461135	8.850000e-75	291.0
22	TraesCS4D01G337900	chr4B	97.297	37	1	0	2492	2528	635462580	635462616	2.100000e-06	63.9
23	TraesCS4D01G337900	chrUn	76.626	492	73	23	1081	1530	283623737	283624228	1.510000e-57	233.0
24	TraesCS4D01G337900	chr2D	86.036	222	20	8	1716	1931	334150303	334150087	7.040000e-56	228.0

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	TraesCS4D01G337900	chr4D	495637644	495640171	2527	False	4669.00	4669	100.0000	1	2528	1	chr4D.!!$F3	2527
1	TraesCS4D01G337900	chr4D	495519402	495521732	2330	False	414.80	636	88.3170	307	2449	5	chr4D.!!$F4	2142
2	TraesCS4D01G337900	chr5A	675153726	675154990	1264	True	1672.00	1672	91.1280	1300	2528	1	chr5A.!!$R1	1228
3	TraesCS4D01G337900	chr5A	675160495	675161157	662	True	747.00	747	87.2830	553	1226	1	chr5A.!!$R2	673
4	TraesCS4D01G337900	chr5A	675318118	675320587	2469	True	627.75	1530	86.1300	1	2449	4	chr5A.!!$R4	2448
5	TraesCS4D01G337900	chr5A	675189420	675189952	532	True	523.00	523	84.5170	1	544	1	chr5A.!!$R3	543
6	TraesCS4D01G337900	chr4B	635459398	635462616	3218	False	574.98	1029	91.5354	1	2528	5	chr4B.!!$F1	2527

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
50	51	0.588252	CCCATACTATGCTTGTGCGC	59.412	55.0	0.0	0.0	43.34	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1957	2602	2.159071	AGCCGTTATTACATGCGGTACA	60.159	45.455	8.64	0.0	45.3	2.9	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
36	37	3.451178	CGAAAGTCCTTCTTCCTCCCATA	59.549	47.826	0.00	0.00	35.02	2.74
43	44	3.906846	CCTTCTTCCTCCCATACTATGCT	59.093	47.826	0.00	0.00	0.00	3.79
48	49	2.104792	TCCTCCCATACTATGCTTGTGC	59.895	50.000	0.00	0.00	40.20	4.57
50	51	0.588252	CCCATACTATGCTTGTGCGC	59.412	55.000	0.00	0.00	43.34	6.09
83	84	2.431454	CTTCTGAGGAAACTGCCCTTC	58.569	52.381	0.00	0.00	44.43	3.46
93	94	5.010282	GGAAACTGCCCTTCATCTTTTCTA	58.990	41.667	0.00	0.00	0.00	2.10
215	216	4.163427	TCCACCTAAATTTGCCATGGAAA	58.837	39.130	18.40	9.10	31.90	3.13
243	244	7.016170	TGTTAGTATGGCTTGCTGGAATATCTA	59.984	37.037	1.22	0.00	0.00	1.98
244	245	6.633325	AGTATGGCTTGCTGGAATATCTAT	57.367	37.500	0.00	0.00	0.00	1.98
245	246	6.413052	AGTATGGCTTGCTGGAATATCTATG	58.587	40.000	0.00	0.00	0.00	2.23
252	253	3.578282	TGCTGGAATATCTATGCGGAGAA	59.422	43.478	0.00	0.00	0.00	2.87
286	291	4.010349	CAAACCTAAGTCACCTTCCATCC	58.990	47.826	0.00	0.00	31.89	3.51
294	299	1.487976	TCACCTTCCATCCTCTCATGC	59.512	52.381	0.00	0.00	0.00	4.06
304	309	4.100653	CCATCCTCTCATGCAAGAGACTAA	59.899	45.833	17.33	6.59	44.67	2.24
347	352	6.732531	TGTCAAGCATAGAATCAACAGAAG	57.267	37.500	0.00	0.00	0.00	2.85
374	379	4.283722	TCAAGAGACCTTCCTTAACTGGAC	59.716	45.833	0.00	0.00	35.58	4.02
381	386	4.597507	ACCTTCCTTAACTGGACTGATCAA	59.402	41.667	0.00	0.00	35.58	2.57
429	434	9.755122	AATATTTTAGGCTTTCCTAGAACTTGT	57.245	29.630	0.00	0.00	45.21	3.16
467	472	3.742882	GGTTCATTTTGAGCTTTTGAGCC	59.257	43.478	0.00	0.00	34.90	4.70
637	655	8.865590	TTATCTTGCTAAACTGGAAAACAAAC	57.134	30.769	0.00	0.00	0.00	2.93
638	656	6.524101	TCTTGCTAAACTGGAAAACAAACT	57.476	33.333	0.00	0.00	0.00	2.66
703	917	6.203723	GGATCAGATTCGTCCAAATAGAAAGG	59.796	42.308	0.00	0.00	32.23	3.11
744	958	6.877236	CAATTTTGCATAATTGTAGGACCCT	58.123	36.000	25.59	0.00	39.52	4.34
768	982	0.820074	TACTGCACCGGTTGTTTGGG	60.820	55.000	2.97	0.00	0.00	4.12
793	1007	3.131709	TCTTTCAAGCACTTCCTCCAG	57.868	47.619	0.00	0.00	0.00	3.86
794	1008	2.157738	CTTTCAAGCACTTCCTCCAGG	58.842	52.381	0.00	0.00	0.00	4.45
844	1058	5.874810	ACTCGCTTGACTTTAATATCTGCAA	59.125	36.000	0.00	0.00	0.00	4.08
849	1063	5.871465	TGACTTTAATATCTGCAACGCAA	57.129	34.783	0.00	0.00	38.41	4.85
986	1499	7.491682	CAGCTACCTTGGCATACAAAAATATT	58.508	34.615	0.00	0.00	38.91	1.28
987	1500	8.629158	CAGCTACCTTGGCATACAAAAATATTA	58.371	33.333	0.00	0.00	38.91	0.98
988	1501	8.630037	AGCTACCTTGGCATACAAAAATATTAC	58.370	33.333	0.00	0.00	38.91	1.89
1017	1530	2.284625	ATGGAGAGGGCCACGACA	60.285	61.111	6.18	4.56	41.56	4.35
1212	1725	1.301716	GTTCCTCAAGTCGCAGGCA	60.302	57.895	0.00	0.00	0.00	4.75
1254	1767	4.880537	CGCAAGGATCGCCTCGCT	62.881	66.667	0.00	0.00	46.28	4.93
1286	1799	1.337447	CGACCCCTACAACAACGACAT	60.337	52.381	0.00	0.00	0.00	3.06
1292	1805	1.990563	CTACAACAACGACATCCCGTC	59.009	52.381	0.00	0.00	42.54	4.79
1481	2027	2.673523	CTGGTCAAGGGCCTCTGG	59.326	66.667	6.46	0.00	0.00	3.86
1710	2339	2.890945	AGCTCACTTTTTATTTGCGGGT	59.109	40.909	0.00	0.00	0.00	5.28
1840	2471	2.882876	GTCGGCTGCTCTCGGTAA	59.117	61.111	0.00	0.00	0.00	2.85
1957	2602	3.972950	CGAGTCCTCGTACATCAATCT	57.027	47.619	8.50	0.00	46.99	2.40
2127	2866	4.021981	TGCAGACGATTGATCTATAGGTGG	60.022	45.833	0.00	0.00	0.00	4.61
2235	3012	0.797542	CTCTGCTGCTTCTTCTGCAC	59.202	55.000	0.00	0.00	36.27	4.57
2370	3166	0.038251	GGCCGATCGACATATGCTCA	60.038	55.000	18.66	0.00	0.00	4.26
2462	3258	0.040067	CTTTGTTCTCTTGCCCGCAC	60.040	55.000	0.00	0.00	0.00	5.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.623811	TGGGAGGAAGAAGGACTTTCG	59.376	52.381	0.00	0.00	39.01	3.46
19	20	4.262678	GCATAGTATGGGAGGAAGAAGGAC	60.263	50.000	12.07	0.00	0.00	3.85
36	37	0.940126	GCATAGCGCACAAGCATAGT	59.060	50.000	11.47	0.00	42.27	2.12
70	71	3.829026	AGAAAAGATGAAGGGCAGTTTCC	59.171	43.478	0.00	0.00	31.28	3.13
73	74	4.289672	TCCTAGAAAAGATGAAGGGCAGTT	59.710	41.667	0.00	0.00	0.00	3.16
215	216	4.235079	TCCAGCAAGCCATACTAACAAT	57.765	40.909	0.00	0.00	0.00	2.71
243	244	6.817765	TTGAAAATCTTAGTTTCTCCGCAT	57.182	33.333	2.13	0.00	36.22	4.73
244	245	6.435428	GTTTGAAAATCTTAGTTTCTCCGCA	58.565	36.000	2.13	0.00	36.22	5.69
245	246	5.856986	GGTTTGAAAATCTTAGTTTCTCCGC	59.143	40.000	2.13	0.00	36.22	5.54
252	253	8.847196	GGTGACTTAGGTTTGAAAATCTTAGTT	58.153	33.333	8.62	0.00	38.63	2.24
274	279	1.487976	GCATGAGAGGATGGAAGGTGA	59.512	52.381	0.00	0.00	0.00	4.02
286	291	5.068855	TCCTGATTAGTCTCTTGCATGAGAG	59.931	44.000	27.48	18.72	42.91	3.20
294	299	6.232581	AGGTCATTCCTGATTAGTCTCTTG	57.767	41.667	0.00	0.00	46.19	3.02
324	329	5.645067	CCTTCTGTTGATTCTATGCTTGACA	59.355	40.000	0.00	0.00	0.00	3.58
347	352	5.877564	CAGTTAAGGAAGGTCTCTTGATTCC	59.122	44.000	0.00	0.00	41.29	3.01
374	379	8.370940	TGGGAGCTTAAGTAAGATATTGATCAG	58.629	37.037	4.02	0.00	35.33	2.90
427	432	6.085555	TGAACCAAACTTAACAAACACACA	57.914	33.333	0.00	0.00	0.00	3.72
428	433	7.589574	AATGAACCAAACTTAACAAACACAC	57.410	32.000	0.00	0.00	0.00	3.82
429	434	8.499162	CAAAATGAACCAAACTTAACAAACACA	58.501	29.630	0.00	0.00	0.00	3.72
524	531	9.699410	TTCTATTTGAACCATGAACCATAGAAT	57.301	29.630	0.00	0.00	30.56	2.40
530	537	5.048083	GTGCTTCTATTTGAACCATGAACCA	60.048	40.000	0.00	0.00	0.00	3.67
546	553	4.524053	TCTTCCTCGACATAGTGCTTCTA	58.476	43.478	0.00	0.00	0.00	2.10
547	554	3.357203	TCTTCCTCGACATAGTGCTTCT	58.643	45.455	0.00	0.00	0.00	2.85
548	555	3.784701	TCTTCCTCGACATAGTGCTTC	57.215	47.619	0.00	0.00	0.00	3.86
614	632	7.112452	AGTTTGTTTTCCAGTTTAGCAAGAT	57.888	32.000	0.00	0.00	0.00	2.40
616	634	6.811170	TCAAGTTTGTTTTCCAGTTTAGCAAG	59.189	34.615	0.00	0.00	0.00	4.01
651	673	2.238646	ACTCAGAGTTTGTTGTCCACCA	59.761	45.455	0.00	0.00	0.00	4.17
703	917	4.558538	AATTGCATCTCGGATTTGCTAC	57.441	40.909	11.90	0.00	37.28	3.58
744	958	0.394938	ACAACCGGTGCAGTACATGA	59.605	50.000	8.52	0.00	0.00	3.07
768	982	5.010012	TGGAGGAAGTGCTTGAAAGAAAATC	59.990	40.000	0.00	0.00	0.00	2.17
793	1007	2.420890	CCGGAGAGCAGCTCATCC	59.579	66.667	24.64	23.09	45.81	3.51
794	1008	2.420890	CCCGGAGAGCAGCTCATC	59.579	66.667	24.64	17.08	45.81	2.92
849	1063	0.893447	GGTTCTACAGTAGTGCGGGT	59.107	55.000	7.50	0.00	0.00	5.28
920	1429	1.964223	AGCGGCGATCCTATATATGGG	59.036	52.381	12.98	8.81	0.00	4.00
1017	1530	2.593148	TGCGCATGGAACCACGTT	60.593	55.556	5.66	0.00	0.00	3.99
1125	1638	2.661537	CACACCGTCTGCGCTTGA	60.662	61.111	9.73	3.98	36.67	3.02
1245	1758	4.742649	AGGACTCCAGCGAGGCGA	62.743	66.667	0.00	0.00	46.26	5.54
1465	2011	3.650950	GCCAGAGGCCCTTGACCA	61.651	66.667	0.00	0.00	44.06	4.02
1710	2339	9.515226	ACAAAGTTGGTTAATTGAGCTAGATTA	57.485	29.630	0.00	0.00	0.00	1.75
1840	2471	6.446318	ACAATATCACGCAAGAACACAAATT	58.554	32.000	0.00	0.00	43.62	1.82
1936	2581	7.208724	TACAGATTGATGTACGAGGACTCGC	62.209	48.000	20.46	6.98	44.15	5.03
1937	2582	4.272748	TACAGATTGATGTACGAGGACTCG	59.727	45.833	19.13	19.13	44.95	4.18
1938	2583	4.640789	ACAGATTGATGTACGAGGACTC	57.359	45.455	0.00	0.00	0.00	3.36
1939	2584	5.502153	GTACAGATTGATGTACGAGGACT	57.498	43.478	1.64	0.00	44.30	3.85
1957	2602	2.159071	AGCCGTTATTACATGCGGTACA	60.159	45.455	8.64	0.00	45.30	2.90
2105	2844	4.021894	ACCACCTATAGATCAATCGTCTGC	60.022	45.833	0.00	0.00	0.00	4.26
2127	2866	9.961265	AAAACCTACAGCAGTAAAAATAAGAAC	57.039	29.630	0.00	0.00	0.00	3.01
2160	2905	2.098934	ACATGAGCTTGTGACGCAAAAA	59.901	40.909	0.00	0.00	36.53	1.94
2161	2906	1.675483	ACATGAGCTTGTGACGCAAAA	59.325	42.857	0.00	0.00	36.53	2.44
2162	2907	1.308047	ACATGAGCTTGTGACGCAAA	58.692	45.000	0.00	0.00	36.53	3.68
2163	2908	1.798223	GTACATGAGCTTGTGACGCAA	59.202	47.619	0.00	0.77	35.50	4.85
2164	2909	1.428448	GTACATGAGCTTGTGACGCA	58.572	50.000	0.00	0.00	0.00	5.24
2235	3012	2.435422	TCACATGGGTGCAGTAACATG	58.565	47.619	14.63	14.63	44.87	3.21
2414	3210	3.695060	TCGGTCCAAAACTAAGCAAACAA	59.305	39.130	0.00	0.00	0.00	2.83
2462	3258	9.988350	AATCTATAAAAAGCATTTCGTAGTGTG	57.012	29.630	0.00	0.00	37.28	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.