AutoCloner

Multiple sequence alignment - TraesCS6D01G327200

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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	TraesCS6D01G327200	chr6D	100.000	3082	0	0	1	3082	432673276	432670195	0.000000e+00	5692.0
1	TraesCS6D01G327200	chr6D	86.558	1659	157	29	606	2250	432810606	432812212	0.000000e+00	1768.0
2	TraesCS6D01G327200	chr6D	97.555	777	17	2	2308	3082	331249201	331248425	0.000000e+00	1328.0
3	TraesCS6D01G327200	chr6D	88.535	314	28	4	3	315	97806501	97806807	1.040000e-99	374.0
4	TraesCS6D01G327200	chr6D	86.219	283	36	3	1911	2190	432815739	432816021	1.390000e-78	303.0
5	TraesCS6D01G327200	chr6A	97.155	1652	31	3	599	2250	578701654	578700019	0.000000e+00	2776.0
6	TraesCS6D01G327200	chr6A	87.539	1589	164	21	647	2208	578926108	578927689	0.000000e+00	1807.0
7	TraesCS6D01G327200	chr6A	90.654	321	22	4	3	319	578703167	578702851	1.320000e-113	420.0
8	TraesCS6D01G327200	chr6A	98.013	151	2	1	317	467	578702378	578702229	8.480000e-66	261.0
9	TraesCS6D01G327200	chr6A	100.000	35	0	0	478	512	578702231	578702197	7.130000e-07	65.8
10	TraesCS6D01G327200	chr6B	92.519	1671	85	10	599	2250	652522658	652521009	0.000000e+00	2357.0
11	TraesCS6D01G327200	chr6B	85.697	811	75	21	986	1786	652890404	652891183	0.000000e+00	817.0
12	TraesCS6D01G327200	chr6B	92.523	321	17	2	3	319	652523711	652523394	1.300000e-123	453.0
13	TraesCS6D01G327200	chr6B	83.962	424	54	6	1784	2194	652902935	652903357	8.010000e-106	394.0
14	TraesCS6D01G327200	chr6B	86.735	196	4	7	331	521	652523105	652522927	6.740000e-47	198.0
15	TraesCS6D01G327200	chr6B	100.000	68	0	0	537	604	652522940	652522873	3.230000e-25	126.0
16	TraesCS6D01G327200	chr5D	98.077	780	12	3	2305	3082	97251254	97252032	0.000000e+00	1354.0
17	TraesCS6D01G327200	chr5D	98.072	778	13	2	2307	3082	50855561	50854784	0.000000e+00	1352.0
18	TraesCS6D01G327200	chr5D	97.190	783	13	4	2308	3082	319614456	319615237	0.000000e+00	1315.0
19	TraesCS6D01G327200	chr5D	79.385	325	38	14	7	318	559365620	559365928	5.210000e-48	202.0
20	TraesCS6D01G327200	chr5D	75.179	419	82	16	670	1074	321670049	321670459	8.780000e-41	178.0
21	TraesCS6D01G327200	chr7D	98.072	778	11	4	2308	3082	43234722	43235498	0.000000e+00	1351.0
22	TraesCS6D01G327200	chr7D	97.812	777	14	3	2308	3082	582181012	582181787	0.000000e+00	1338.0
23	TraesCS6D01G327200	chr3D	97.695	781	11	4	2308	3082	19992358	19993137	0.000000e+00	1336.0
24	TraesCS6D01G327200	chr1D	97.561	779	15	3	2308	3082	230717256	230716478	0.000000e+00	1330.0
25	TraesCS6D01G327200	chr1D	78.722	1612	243	56	667	2242	198167374	198168921	0.000000e+00	985.0
26	TraesCS6D01G327200	chr1D	87.975	316	25	9	3	316	222737710	222737406	8.120000e-96	361.0
27	TraesCS6D01G327200	chr1D	87.261	314	30	6	3	315	328875886	328875582	1.760000e-92	350.0
28	TraesCS6D01G327200	chr1D	86.392	316	17	8	3	317	416844938	416845228	3.830000e-84	322.0
29	TraesCS6D01G327200	chr1B	96.671	781	19	6	2308	3082	621609423	621610202	0.000000e+00	1291.0
30	TraesCS6D01G327200	chr1B	77.910	335	68	5	743	1074	288171683	288171352	1.450000e-48	204.0
31	TraesCS6D01G327200	chr3B	79.677	1609	237	46	667	2242	463458300	463456749	0.000000e+00	1077.0
32	TraesCS6D01G327200	chr3B	82.209	815	112	16	667	1471	455509616	455510407	0.000000e+00	671.0
33	TraesCS6D01G327200	chr7A	80.119	1006	136	33	667	1646	471814348	471813381	0.000000e+00	691.0
34	TraesCS6D01G327200	chr4B	76.358	1197	227	37	659	1834	477371553	477370392	2.650000e-165	592.0
35	TraesCS6D01G327200	chr4B	76.274	1197	228	37	659	1834	477389492	477388331	1.230000e-163	586.0
36	TraesCS6D01G327200	chr4B	86.000	150	17	3	153	302	404777632	404777487	1.140000e-34	158.0
37	TraesCS6D01G327200	chr4D	89.809	314	23	5	3	315	310115868	310115563	8.010000e-106	394.0
38	TraesCS6D01G327200	chr2B	88.679	318	26	8	3	317	800132685	800132995	2.240000e-101	379.0
39	TraesCS6D01G327200	chr2B	100.000	28	0	0	1963	1990	775769784	775769757	6.000000e-03	52.8
40	TraesCS6D01G327200	chr2D	89.180	305	24	6	3	302	540321631	540321331	3.750000e-99	372.0
41	TraesCS6D01G327200	chr1A	87.821	312	30	4	4	314	514138840	514139144	2.920000e-95	359.0
42	TraesCS6D01G327200	chr1A	87.066	317	30	6	3	318	425710974	425710668	6.330000e-92	348.0
43	TraesCS6D01G327200	chr1A	87.891	256	23	6	49	302	557927678	557927927	8.360000e-76	294.0
44	TraesCS6D01G327200	chr7B	85.050	301	38	4	3	302	117014840	117015134	1.800000e-77	300.0
45	TraesCS6D01G327200	chr5B	75.772	421	76	15	670	1074	372567268	372567678	4.060000e-44	189.0
46	TraesCS6D01G327200	chr2A	100.000	28	0	0	1963	1990	759589080	759589053	6.000000e-03	52.8

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	TraesCS6D01G327200	chr6D	432670195	432673276	3081	True	5692.0	5692	100.00000	1	3082	1	chr6D.!!$R2	3081
1	TraesCS6D01G327200	chr6D	331248425	331249201	776	True	1328.0	1328	97.55500	2308	3082	1	chr6D.!!$R1	774
2	TraesCS6D01G327200	chr6D	432810606	432816021	5415	False	1035.5	1768	86.38850	606	2250	2	chr6D.!!$F2	1644
3	TraesCS6D01G327200	chr6A	578926108	578927689	1581	False	1807.0	1807	87.53900	647	2208	1	chr6A.!!$F1	1561
4	TraesCS6D01G327200	chr6A	578700019	578703167	3148	True	880.7	2776	96.45550	3	2250	4	chr6A.!!$R1	2247
5	TraesCS6D01G327200	chr6B	652890404	652891183	779	False	817.0	817	85.69700	986	1786	1	chr6B.!!$F1	800
6	TraesCS6D01G327200	chr6B	652521009	652523711	2702	True	783.5	2357	92.94425	3	2250	4	chr6B.!!$R1	2247
7	TraesCS6D01G327200	chr5D	97251254	97252032	778	False	1354.0	1354	98.07700	2305	3082	1	chr5D.!!$F1	777
8	TraesCS6D01G327200	chr5D	50854784	50855561	777	True	1352.0	1352	98.07200	2307	3082	1	chr5D.!!$R1	775
9	TraesCS6D01G327200	chr5D	319614456	319615237	781	False	1315.0	1315	97.19000	2308	3082	1	chr5D.!!$F2	774
10	TraesCS6D01G327200	chr7D	43234722	43235498	776	False	1351.0	1351	98.07200	2308	3082	1	chr7D.!!$F1	774
11	TraesCS6D01G327200	chr7D	582181012	582181787	775	False	1338.0	1338	97.81200	2308	3082	1	chr7D.!!$F2	774
12	TraesCS6D01G327200	chr3D	19992358	19993137	779	False	1336.0	1336	97.69500	2308	3082	1	chr3D.!!$F1	774
13	TraesCS6D01G327200	chr1D	230716478	230717256	778	True	1330.0	1330	97.56100	2308	3082	1	chr1D.!!$R2	774
14	TraesCS6D01G327200	chr1D	198167374	198168921	1547	False	985.0	985	78.72200	667	2242	1	chr1D.!!$F1	1575
15	TraesCS6D01G327200	chr1B	621609423	621610202	779	False	1291.0	1291	96.67100	2308	3082	1	chr1B.!!$F1	774
16	TraesCS6D01G327200	chr3B	463456749	463458300	1551	True	1077.0	1077	79.67700	667	2242	1	chr3B.!!$R1	1575
17	TraesCS6D01G327200	chr3B	455509616	455510407	791	False	671.0	671	82.20900	667	1471	1	chr3B.!!$F1	804
18	TraesCS6D01G327200	chr7A	471813381	471814348	967	True	691.0	691	80.11900	667	1646	1	chr7A.!!$R1	979
19	TraesCS6D01G327200	chr4B	477370392	477371553	1161	True	592.0	592	76.35800	659	1834	1	chr4B.!!$R2	1175
20	TraesCS6D01G327200	chr4B	477388331	477389492	1161	True	586.0	586	76.27400	659	1834	1	chr4B.!!$R3	1175

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
473	993	2.019951	GAAACGCAAGAGTCGCCGA	61.020	57.895	7.04	0.0	43.62	5.54	F
535	1055	2.107953	GCGTGCTCCCATCTCCTC	59.892	66.667	0.00	0.0	0.00	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2041	3125	0.391263	GCGTGGAATCCGAAGTTCCT	60.391	55.0	12.51	0.0	44.36	3.36	R
2140	3224	0.818296	AAGCCGTGCCTAGTGTCTAG	59.182	55.0	0.00	0.0	0.00	2.43	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
87	88	3.315521	CTTCGACGGCTGATCGCG	61.316	66.667	0.00	0.00	39.46	5.87
128	129	2.507058	TGCTGATATCAAGGAGTTGGCT	59.493	45.455	6.90	0.00	34.09	4.75
137	138	2.618709	CAAGGAGTTGGCTTCGTTCTTT	59.381	45.455	0.00	0.00	0.00	2.52
172	177	6.795114	CGCTTTAGTCATGTAAATCGTTTGTT	59.205	34.615	0.00	0.00	30.56	2.83
295	300	9.208022	TCTGATTATACTTGATCAATAAAGCGG	57.792	33.333	8.96	8.80	32.33	5.52
308	313	9.832445	GATCAATAAAGCGGGATATTATTCCTA	57.168	33.333	0.00	0.00	35.97	2.94
471	991	2.470286	CGAAACGCAAGAGTCGCC	59.530	61.111	0.00	0.00	39.41	5.54
472	992	2.470286	GAAACGCAAGAGTCGCCG	59.530	61.111	0.00	0.00	43.62	6.46
473	993	2.019951	GAAACGCAAGAGTCGCCGA	61.020	57.895	7.04	0.00	43.62	5.54
533	1053	4.899239	CGGCGTGCTCCCATCTCC	62.899	72.222	0.00	0.00	0.00	3.71
534	1054	3.474570	GGCGTGCTCCCATCTCCT	61.475	66.667	0.00	0.00	0.00	3.69
535	1055	2.107953	GCGTGCTCCCATCTCCTC	59.892	66.667	0.00	0.00	0.00	3.71
536	1056	2.415010	CGTGCTCCCATCTCCTCG	59.585	66.667	0.00	0.00	0.00	4.63
537	1057	2.107953	GTGCTCCCATCTCCTCGC	59.892	66.667	0.00	0.00	0.00	5.03
680	1656	2.676471	GCAAATCGGTGGCTGGGT	60.676	61.111	0.00	0.00	0.00	4.51
1970	3054	4.796606	ACGTATGTAGGAGTAAAGGGCTA	58.203	43.478	0.00	0.00	0.00	3.93
2041	3125	6.068010	TCAAGAAAATAAGGGCACAAGAGAA	58.932	36.000	0.00	0.00	0.00	2.87
2114	3198	4.436050	CGCCATGTTTCACATTACTCACTC	60.436	45.833	0.00	0.00	36.53	3.51
2155	3243	0.179134	GCCACTAGACACTAGGCACG	60.179	60.000	0.00	0.00	44.59	5.34
2168	3256	0.605589	AGGCACGGCTTCTTACAACC	60.606	55.000	0.00	0.00	0.00	3.77
2173	3261	1.792006	CGGCTTCTTACAACCGTCTT	58.208	50.000	0.00	0.00	40.77	3.01
2194	3283	3.651562	AGTTGACGTTTTTGAGTCACG	57.348	42.857	0.00	0.00	45.71	4.35
2196	3285	0.299300	TGACGTTTTTGAGTCACGCG	59.701	50.000	3.53	3.53	41.81	6.01
2197	3286	0.382636	GACGTTTTTGAGTCACGCGG	60.383	55.000	12.47	0.00	37.44	6.46
2208	3297	1.077089	GTCACGCGGCTTCTAACCTC	61.077	60.000	12.47	0.00	0.00	3.85
2213	3302	1.291132	GCGGCTTCTAACCTCACATC	58.709	55.000	0.00	0.00	0.00	3.06
2295	3384	5.733620	ATTTGACTGATGCACTTTCCAAT	57.266	34.783	0.00	0.00	0.00	3.16
2303	3392	6.265196	ACTGATGCACTTTCCAATTTGTAGAA	59.735	34.615	0.00	0.00	0.00	2.10
2930	5865	2.067013	GGTAGAGACCGCTGAACAAAC	58.933	52.381	0.00	0.00	35.52	2.93

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.189287	CCTTGAAAATCCTTCCTCACGTG	59.811	47.826	9.94	9.94	0.00	4.49
1	2	3.412386	CCTTGAAAATCCTTCCTCACGT	58.588	45.455	0.00	0.00	0.00	4.49
57	58	1.201812	CGTCGAAGCAATTGGTTCTCG	60.202	52.381	34.86	32.17	46.88	4.04
90	91	2.284625	AGTGATGAGCCCCACCGA	60.285	61.111	0.00	0.00	34.00	4.69
92	93	2.439156	GCAGTGATGAGCCCCACC	60.439	66.667	0.00	0.00	34.00	4.61
128	129	2.034339	GCGAACAGACGAAAAGAACGAA	60.034	45.455	0.00	0.00	35.09	3.85
137	138	3.358707	TGACTAAAGCGAACAGACGAA	57.641	42.857	0.00	0.00	35.09	3.85
172	177	0.599991	GGATATGTGCCGCGACATCA	60.600	55.000	15.76	8.23	37.70	3.07
392	912	2.782222	CGCTCGGAATCGGAAGGGA	61.782	63.158	0.00	0.00	36.95	4.20
464	984	2.655685	GGCTCGATTCGGCGACTC	60.656	66.667	10.16	13.88	36.17	3.36
465	985	2.501223	TTTGGCTCGATTCGGCGACT	62.501	55.000	10.16	3.40	36.17	4.18
466	986	1.429148	ATTTGGCTCGATTCGGCGAC	61.429	55.000	10.16	0.00	36.17	5.19
467	987	0.742990	AATTTGGCTCGATTCGGCGA	60.743	50.000	4.99	4.99	38.74	5.54
468	988	0.316196	GAATTTGGCTCGATTCGGCG	60.316	55.000	0.00	0.00	0.00	6.46
469	989	0.732571	TGAATTTGGCTCGATTCGGC	59.267	50.000	6.18	8.44	35.53	5.54
470	990	1.267532	CGTGAATTTGGCTCGATTCGG	60.268	52.381	6.18	0.00	35.53	4.30
471	991	1.267532	CCGTGAATTTGGCTCGATTCG	60.268	52.381	0.00	0.00	35.53	3.34
472	992	1.064060	CCCGTGAATTTGGCTCGATTC	59.936	52.381	0.00	0.00	33.83	2.52
473	993	1.094785	CCCGTGAATTTGGCTCGATT	58.905	50.000	0.00	0.00	0.00	3.34
516	1036	4.899239	GGAGATGGGAGCACGCCG	62.899	72.222	0.00	0.00	0.00	6.46
517	1037	3.453070	GAGGAGATGGGAGCACGCC	62.453	68.421	0.00	0.00	0.00	5.68
518	1038	2.107953	GAGGAGATGGGAGCACGC	59.892	66.667	0.00	0.00	0.00	5.34
519	1039	2.415010	CGAGGAGATGGGAGCACG	59.585	66.667	0.00	0.00	0.00	5.34
520	1040	2.107953	GCGAGGAGATGGGAGCAC	59.892	66.667	0.00	0.00	0.00	4.40
521	1041	3.157252	GGCGAGGAGATGGGAGCA	61.157	66.667	0.00	0.00	0.00	4.26
522	1042	3.934962	GGGCGAGGAGATGGGAGC	61.935	72.222	0.00	0.00	0.00	4.70
523	1043	3.610669	CGGGCGAGGAGATGGGAG	61.611	72.222	0.00	0.00	0.00	4.30
524	1044	4.137615	TCGGGCGAGGAGATGGGA	62.138	66.667	0.00	0.00	0.00	4.37
525	1045	3.917760	GTCGGGCGAGGAGATGGG	61.918	72.222	0.00	0.00	0.00	4.00
526	1046	4.271816	CGTCGGGCGAGGAGATGG	62.272	72.222	0.00	0.00	44.77	3.51
527	1047	4.933064	GCGTCGGGCGAGGAGATG	62.933	72.222	6.02	0.00	44.77	2.90
800	1811	4.547367	GATTGGGGTCGCGGGGAG	62.547	72.222	6.13	0.00	0.00	4.30
802	1813	4.856801	CAGATTGGGGTCGCGGGG	62.857	72.222	6.13	0.00	0.00	5.73
1970	3054	6.726490	ATATAGTGGTACTCGTGGAACATT	57.274	37.500	0.00	0.00	44.52	2.71
2041	3125	0.391263	GCGTGGAATCCGAAGTTCCT	60.391	55.000	12.51	0.00	44.36	3.36
2048	3132	2.584970	GCGATGCGTGGAATCCGA	60.585	61.111	0.00	0.00	0.00	4.55
2140	3224	0.818296	AAGCCGTGCCTAGTGTCTAG	59.182	55.000	0.00	0.00	0.00	2.43
2155	3243	3.922910	ACTAAGACGGTTGTAAGAAGCC	58.077	45.455	0.00	0.00	0.00	4.35
2173	3261	3.000523	GCGTGACTCAAAAACGTCAACTA	59.999	43.478	0.00	0.00	41.35	2.24
2194	3283	1.291132	GATGTGAGGTTAGAAGCCGC	58.709	55.000	0.00	0.00	0.00	6.53
2196	3285	2.911484	CAGGATGTGAGGTTAGAAGCC	58.089	52.381	0.00	0.00	0.00	4.35
2254	3343	9.522804	AGTCAAATATGCAACTTTTCGTAAAAA	57.477	25.926	0.00	0.00	33.42	1.94
2255	3344	8.963130	CAGTCAAATATGCAACTTTTCGTAAAA	58.037	29.630	0.00	0.00	0.00	1.52
2256	3345	8.346300	TCAGTCAAATATGCAACTTTTCGTAAA	58.654	29.630	0.00	0.00	0.00	2.01
2258	3347	7.428282	TCAGTCAAATATGCAACTTTTCGTA	57.572	32.000	0.00	0.00	0.00	3.43
2259	3348	6.312399	TCAGTCAAATATGCAACTTTTCGT	57.688	33.333	0.00	0.00	0.00	3.85
2260	3349	6.237384	GCATCAGTCAAATATGCAACTTTTCG	60.237	38.462	0.00	0.00	44.27	3.46
2261	3350	6.986118	GCATCAGTCAAATATGCAACTTTTC	58.014	36.000	0.00	0.00	44.27	2.29
2262	3351	6.956299	GCATCAGTCAAATATGCAACTTTT	57.044	33.333	0.00	0.00	44.27	2.27
2269	3358	5.039333	GGAAAGTGCATCAGTCAAATATGC	58.961	41.667	0.00	0.00	44.94	3.14
2270	3359	6.198650	TGGAAAGTGCATCAGTCAAATATG	57.801	37.500	0.00	0.00	0.00	1.78
2271	3360	6.839124	TTGGAAAGTGCATCAGTCAAATAT	57.161	33.333	0.00	0.00	0.00	1.28
2272	3361	6.839124	ATTGGAAAGTGCATCAGTCAAATA	57.161	33.333	0.00	0.00	0.00	1.40
2273	3362	5.733620	ATTGGAAAGTGCATCAGTCAAAT	57.266	34.783	0.00	0.00	0.00	2.32
2274	3363	5.534207	AATTGGAAAGTGCATCAGTCAAA	57.466	34.783	0.00	0.00	0.00	2.69
2287	3376	9.846248	CTAAACAGGATTCTACAAATTGGAAAG	57.154	33.333	0.00	0.00	0.00	2.62
2303	3392	8.766476	TCTCTCAATCTCAATTCTAAACAGGAT	58.234	33.333	0.00	0.00	0.00	3.24
2323	3412	2.861147	TGTCTCTCGTTCCTCTCTCA	57.139	50.000	0.00	0.00	0.00	3.27
2930	5865	2.730090	GCAAGTCAAATCATGCGACTGG	60.730	50.000	7.41	6.21	39.86	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.