AutoCloner

Multiple sequence alignment - TraesCS1D01G395600

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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	TraesCS1D01G395600	chr1D	100.000	3938	0	0	1	3938	464138444	464142381	0.000000e+00	7273.0
1	TraesCS1D01G395600	chr1A	95.087	3969	123	33	2	3912	556296312	556300266	0.000000e+00	6183.0
2	TraesCS1D01G395600	chr1B	93.776	3085	106	31	109	3119	640153815	640156887	0.000000e+00	4554.0
3	TraesCS1D01G395600	chr1B	95.477	619	25	2	3154	3769	640156882	640157500	0.000000e+00	985.0
4	TraesCS1D01G395600	chr1B	95.238	147	7	0	3792	3938	640157492	640157638	2.370000e-57	233.0
5	TraesCS1D01G395600	chr1B	94.958	119	5	1	1	119	640153657	640153774	6.720000e-43	185.0
6	TraesCS1D01G395600	chr7A	88.824	170	17	2	3558	3726	85734993	85735161	1.430000e-49	207.0
7	TraesCS1D01G395600	chr7D	98.592	71	1	0	1707	1777	107135331	107135261	4.130000e-25	126.0
8	TraesCS1D01G395600	chr6D	97.183	71	2	0	1707	1777	421182432	421182502	1.920000e-23	121.0
9	TraesCS1D01G395600	chr4D	97.183	71	2	0	1707	1777	177515047	177514977	1.920000e-23	121.0
10	TraesCS1D01G395600	chr6B	95.775	71	3	0	1707	1777	7162436	7162506	8.940000e-22	115.0
11	TraesCS1D01G395600	chr2B	95.775	71	3	0	1707	1777	754437614	754437544	8.940000e-22	115.0
12	TraesCS1D01G395600	chr2A	95.775	71	3	0	1707	1777	635080912	635080842	8.940000e-22	115.0
13	TraesCS1D01G395600	chr2A	95.349	43	2	0	340	382	759752837	759752879	7.060000e-08	69.4
14	TraesCS1D01G395600	chr2A	95.349	43	0	1	350	390	706284759	706284717	2.540000e-07	67.6
15	TraesCS1D01G395600	chr2A	85.965	57	6	1	329	383	695980213	695980269	4.250000e-05	60.2
16	TraesCS1D01G395600	chr7B	94.366	71	4	0	1707	1777	644282211	644282281	4.160000e-20	110.0
17	TraesCS1D01G395600	chr3A	93.333	60	2	1	332	389	646133713	646133772	1.950000e-13	87.9
18	TraesCS1D01G395600	chr4B	94.231	52	1	1	332	381	618330491	618330542	1.170000e-10	78.7
19	TraesCS1D01G395600	chr4A	95.349	43	1	1	348	389	663145316	663145358	2.540000e-07	67.6

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	TraesCS1D01G395600	chr1D	464138444	464142381	3937	False	7273.00	7273	100.00000	1	3938	1	chr1D.!!$F1	3937
1	TraesCS1D01G395600	chr1A	556296312	556300266	3954	False	6183.00	6183	95.08700	2	3912	1	chr1A.!!$F1	3910
2	TraesCS1D01G395600	chr1B	640153657	640157638	3981	False	1489.25	4554	94.86225	1	3938	4	chr1B.!!$F1	3937

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
264	315	0.109723	AACCTCAGCCGCCTAAAACA	59.890	50.000	0.00	0.00	0.00	2.83	F
273	324	0.163788	CGCCTAAAACACAGCTGACG	59.836	55.000	23.35	13.56	0.00	4.35	F
630	704	0.179084	CCGGTGAAGTGTGACAGTGT	60.179	55.000	0.00	0.00	0.00	3.55	F
985	1071	0.460987	CCGAGGAGCTTAACTGGCTG	60.461	60.000	0.00	0.00	40.40	4.85	F
1858	1964	1.669440	GACGACTGGCTTACCACCA	59.331	57.895	0.00	0.00	42.67	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1323	1423	1.212751	GAACATGGCGTTGAAGGGC	59.787	57.895	4.38	4.38	38.19	5.19	R
1836	1942	1.288127	GGTAAGCCAGTCGTCGTGT	59.712	57.895	0.00	0.00	34.09	4.49	R
2415	2526	3.295273	AGCAGCGACGACCTCACA	61.295	61.111	0.00	0.00	0.00	3.58	R
2781	2895	1.135888	TCCGTCGTGTCGATGTACTTG	60.136	52.381	9.84	0.00	40.74	3.16	R
3483	3636	0.036732	TCTTGCATCCGCTGGTTCTT	59.963	50.000	0.00	0.00	39.64	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
132	182	5.617187	GCATAACTAAAATTGCGAGACGATG	59.383	40.000	0.00	0.00	0.00	3.84
133	183	4.600012	AACTAAAATTGCGAGACGATGG	57.400	40.909	0.00	0.00	0.00	3.51
262	313	1.883926	GAAAACCTCAGCCGCCTAAAA	59.116	47.619	0.00	0.00	0.00	1.52
264	315	0.109723	AACCTCAGCCGCCTAAAACA	59.890	50.000	0.00	0.00	0.00	2.83
265	316	0.605589	ACCTCAGCCGCCTAAAACAC	60.606	55.000	0.00	0.00	0.00	3.32
273	324	0.163788	CGCCTAAAACACAGCTGACG	59.836	55.000	23.35	13.56	0.00	4.35
311	362	6.203145	GGCCGAAGAAAGAATATTAGGAGAAC	59.797	42.308	0.00	0.00	0.00	3.01
475	530	6.218746	CAGATGACATCCGTGAAATATCTGA	58.781	40.000	11.92	0.00	41.53	3.27
514	572	9.340695	TCAATGACATTTATGAAACGTTGAATC	57.659	29.630	0.00	0.00	35.09	2.52
551	619	1.007154	GCTTACGAGCTCGGGATCC	60.007	63.158	36.93	18.50	45.65	3.36
579	647	2.224784	GTCCGGAAGCAAACACGTTTAT	59.775	45.455	5.23	0.00	0.00	1.40
630	704	0.179084	CCGGTGAAGTGTGACAGTGT	60.179	55.000	0.00	0.00	0.00	3.55
897	979	3.680786	CTGCCCAGACACCGACGA	61.681	66.667	0.00	0.00	0.00	4.20
898	980	3.633094	CTGCCCAGACACCGACGAG	62.633	68.421	0.00	0.00	0.00	4.18
924	1009	1.563879	CTCTCTCTCCCTCTCTGACCA	59.436	57.143	0.00	0.00	0.00	4.02
985	1071	0.460987	CCGAGGAGCTTAACTGGCTG	60.461	60.000	0.00	0.00	40.40	4.85
1302	1402	2.356313	AACCAGTCGCTGTCGCTG	60.356	61.111	6.19	0.00	38.57	5.18
1845	1951	4.736896	GGGCAGGGACACGACGAC	62.737	72.222	0.00	0.00	0.00	4.34
1851	1957	2.338984	GGACACGACGACTGGCTT	59.661	61.111	0.00	0.00	0.00	4.35
1858	1964	1.669440	GACGACTGGCTTACCACCA	59.331	57.895	0.00	0.00	42.67	4.17
1908	2014	1.811266	CTTCGTGCCCATCACCTCG	60.811	63.158	0.00	0.00	42.69	4.63
2241	2352	2.526873	ACGGCCAAGGTGGACTCT	60.527	61.111	2.24	0.00	45.79	3.24
2247	2358	2.936032	AAGGTGGACTCTGGGGGC	60.936	66.667	0.00	0.00	0.00	5.80
2415	2526	4.194720	CGCGCCTACTTCGAGCCT	62.195	66.667	0.00	0.00	0.00	4.58
2781	2895	2.825836	CCCGTGCAGAAGATGGCC	60.826	66.667	0.00	0.00	0.00	5.36
2847	2961	1.538135	GGGGTACTGGGTGGTCACT	60.538	63.158	0.93	0.00	0.00	3.41
2954	3068	5.711506	AGGTTTGAATCAGTTGTGCATATCA	59.288	36.000	0.00	0.00	0.00	2.15
2985	3107	1.594862	GCGCACATACATCAAGAGGTC	59.405	52.381	0.30	0.00	0.00	3.85
3042	3170	6.049955	TCTTGTAAATCAGGACCAGTTAGG	57.950	41.667	0.00	0.00	45.67	2.69
3064	3211	3.676646	GGCTGTGAGATGTTGAAATTTGC	59.323	43.478	0.00	0.00	0.00	3.68
3121	3271	3.726557	ATTCCCTTGCTGAAGATGTCA	57.273	42.857	0.00	0.00	34.17	3.58
3126	3276	1.329906	CTTGCTGAAGATGTCATCCGC	59.670	52.381	9.29	7.88	35.07	5.54
3129	3279	2.168313	TGCTGAAGATGTCATCCGCTTA	59.832	45.455	9.29	0.00	35.07	3.09
3131	3281	3.001736	GCTGAAGATGTCATCCGCTTAAC	59.998	47.826	9.29	0.00	35.07	2.01
3132	3282	4.183865	CTGAAGATGTCATCCGCTTAACA	58.816	43.478	9.29	0.10	35.07	2.41
3188	3340	2.026729	TGAACCAGCATCCACCGATTTA	60.027	45.455	0.00	0.00	0.00	1.40
3189	3341	2.038387	ACCAGCATCCACCGATTTAC	57.962	50.000	0.00	0.00	0.00	2.01
3210	3363	3.181491	ACATCACAAAACCCAACAGAACG	60.181	43.478	0.00	0.00	0.00	3.95
3396	3549	1.005748	CACACGCTGCCTCTTCTCA	60.006	57.895	0.00	0.00	0.00	3.27
3437	3590	2.470362	CCGCCTCATTCAGCTGCAG	61.470	63.158	10.11	10.11	0.00	4.41
3483	3636	0.927537	CAGTCACGCTTCAAACGACA	59.072	50.000	0.00	0.00	0.00	4.35
3561	3714	2.359900	GGTTCATGAAGAAGGTGCGAT	58.640	47.619	8.80	0.00	36.78	4.58
3712	3867	1.208614	GCAGCAAAGAACAGCTCCG	59.791	57.895	0.00	0.00	39.50	4.63
3799	3954	4.326504	AACTTCAGAGCAAACATTTGGG	57.673	40.909	6.49	0.00	38.57	4.12
3872	4027	6.251376	GCAACGAACTCCAAATTAATGATGAC	59.749	38.462	0.00	0.00	0.00	3.06
3877	4032	9.045223	CGAACTCCAAATTAATGATGACAGATA	57.955	33.333	3.66	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	3.745975	CAGTCTGATGTTCGCTGGTTAAA	59.254	43.478	0.00	0.00	0.00	1.52
163	213	3.508845	AATTATAATGCTCGCTGGGGT	57.491	42.857	0.00	0.00	0.00	4.95
254	305	0.163788	CGTCAGCTGTGTTTTAGGCG	59.836	55.000	14.67	0.00	0.00	5.52
262	313	2.920645	CGGTCTCCGTCAGCTGTGT	61.921	63.158	14.67	0.00	42.73	3.72
264	315	3.374402	CCGGTCTCCGTCAGCTGT	61.374	66.667	14.67	0.00	46.80	4.40
265	316	4.135153	CCCGGTCTCCGTCAGCTG	62.135	72.222	7.63	7.63	46.80	4.24
311	362	1.889170	GTTTGCTTCCTCCCTTTCCTG	59.111	52.381	0.00	0.00	0.00	3.86
514	572	5.757850	AAGCTCAGGTGAACAGTAAAAAG	57.242	39.130	0.00	0.00	0.00	2.27
551	619	1.492319	TTTGCTTCCGGACACGTTCG	61.492	55.000	1.83	0.00	38.78	3.95
579	647	5.296151	ACAAGAATCCAAGTCTTCTGTCA	57.704	39.130	0.00	0.00	32.96	3.58
621	695	8.345565	AGTAGAAAATCAATCAAACACTGTCAC	58.654	33.333	0.00	0.00	0.00	3.67
630	704	5.856126	ACGCGAGTAGAAAATCAATCAAA	57.144	34.783	15.93	0.00	46.88	2.69
897	979	2.277404	GGGAGAGAGAGGCCGTCT	59.723	66.667	10.23	10.23	38.71	4.18
898	980	1.826487	GAGGGAGAGAGAGGCCGTC	60.826	68.421	0.00	0.00	0.00	4.79
924	1009	1.133976	AGCTGTGCTTTGTGGAGAAGT	60.134	47.619	0.00	0.00	33.89	3.01
985	1071	4.864334	CATCCCCGCTCCACCAGC	62.864	72.222	0.00	0.00	45.85	4.85
1323	1423	1.212751	GAACATGGCGTTGAAGGGC	59.787	57.895	4.38	4.38	38.19	5.19
1836	1942	1.288127	GGTAAGCCAGTCGTCGTGT	59.712	57.895	0.00	0.00	34.09	4.49
1851	1957	3.845259	GAGGCGGCGATGGTGGTA	61.845	66.667	12.98	0.00	0.00	3.25
1929	2035	3.621805	TGGTTGAGGAAGCCGCGA	61.622	61.111	8.23	0.00	0.00	5.87
2346	2457	4.849329	GCCTCGCCGACGACGATT	62.849	66.667	6.73	0.00	45.12	3.34
2415	2526	3.295273	AGCAGCGACGACCTCACA	61.295	61.111	0.00	0.00	0.00	3.58
2781	2895	1.135888	TCCGTCGTGTCGATGTACTTG	60.136	52.381	9.84	0.00	40.74	3.16
2954	3068	3.070748	TGTATGTGCGCACTTTGTACAT	58.929	40.909	37.59	24.00	36.15	2.29
2961	3075	2.674852	CTCTTGATGTATGTGCGCACTT	59.325	45.455	37.59	33.00	0.00	3.16
2985	3107	6.510478	GCACTCTCTAATCTACAGTCTGTACG	60.510	46.154	8.70	5.98	0.00	3.67
3042	3170	3.676646	GCAAATTTCAACATCTCACAGCC	59.323	43.478	0.00	0.00	0.00	4.85
3104	3254	2.295885	GGATGACATCTTCAGCAAGGG	58.704	52.381	14.95	0.00	42.92	3.95
3121	3271	5.815740	CAGTTACCAGTAATGTTAAGCGGAT	59.184	40.000	0.00	0.00	0.00	4.18
3188	3340	3.181491	CGTTCTGTTGGGTTTTGTGATGT	60.181	43.478	0.00	0.00	0.00	3.06
3189	3341	3.371168	CGTTCTGTTGGGTTTTGTGATG	58.629	45.455	0.00	0.00	0.00	3.07
3210	3363	6.156602	AGGATGATGATGATATCAGAGGTTCC	59.843	42.308	11.78	12.04	43.53	3.62
3437	3590	2.669391	CGAGGAAACAAATGCCTCTTGC	60.669	50.000	0.00	0.00	44.73	4.01
3483	3636	0.036732	TCTTGCATCCGCTGGTTCTT	59.963	50.000	0.00	0.00	39.64	2.52
3799	3954	0.459759	CCCGCTTAACTTCCCTCGAC	60.460	60.000	0.00	0.00	0.00	4.20
3877	4032	9.643693	CAATGTTCCTTTTAGCATTTGAATACT	57.356	29.630	0.00	0.00	30.17	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.