AutoCloner

Multiple sequence alignment - TraesCS6D01G119000

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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	TraesCS6D01G119000	chr6D	100.000	2915	0	0	1	2915	84225382	84222468	0.000000e+00	5384.0
1	TraesCS6D01G119000	chr6D	86.152	2123	272	9	814	2915	84232004	84229883	0.000000e+00	2272.0
2	TraesCS6D01G119000	chr6D	86.792	2014	248	5	917	2915	84631063	84629053	0.000000e+00	2230.0
3	TraesCS6D01G119000	chr6D	84.745	2137	271	30	814	2915	84620200	84618084	0.000000e+00	2089.0
4	TraesCS6D01G119000	chr6D	83.640	2121	316	21	814	2915	84474199	84472091	0.000000e+00	1965.0
5	TraesCS6D01G119000	chr6D	83.724	2003	289	26	925	2902	85608143	85610133	0.000000e+00	1858.0
6	TraesCS6D01G119000	chr6A	95.669	2909	85	8	24	2915	101555698	101552814	0.000000e+00	4636.0
7	TraesCS6D01G119000	chr6A	85.620	2121	280	15	814	2915	101562820	101560706	0.000000e+00	2204.0
8	TraesCS6D01G119000	chr6A	85.302	2116	265	35	814	2905	101865544	101863451	0.000000e+00	2143.0
9	TraesCS6D01G119000	chr6A	86.275	1887	246	9	1031	2915	101844918	101843043	0.000000e+00	2037.0
10	TraesCS6D01G119000	chr6A	80.539	334	39	14	952	1266	101868678	101868352	1.750000e-57	233.0
11	TraesCS6D01G119000	chr6A	91.566	83	7	0	833	915	101845485	101845403	6.600000e-22	115.0
12	TraesCS6D01G119000	chr6B	86.076	2133	259	24	814	2915	160683301	160681176	0.000000e+00	2259.0
13	TraesCS6D01G119000	chr6B	86.395	2014	256	3	917	2915	160717021	160715011	0.000000e+00	2185.0
14	TraesCS6D01G119000	chr6B	84.840	2124	273	33	814	2915	160905069	160902973	0.000000e+00	2093.0
15	TraesCS6D01G119000	chr6B	83.658	2001	277	25	952	2915	160912174	160910187	0.000000e+00	1838.0
16	TraesCS6D01G119000	chr6B	89.448	417	44	0	2499	2915	160685827	160685411	7.150000e-146	527.0
17	TraesCS6D01G119000	chrUn	88.889	63	7	0	626	688	79391500	79391438	8.660000e-11	78.7

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	TraesCS6D01G119000	chr6D	84222468	84225382	2914	True	5384	5384	100.0000	1	2915	1	chr6D.!!$R1	2914
1	TraesCS6D01G119000	chr6D	84229883	84232004	2121	True	2272	2272	86.1520	814	2915	1	chr6D.!!$R2	2101
2	TraesCS6D01G119000	chr6D	84629053	84631063	2010	True	2230	2230	86.7920	917	2915	1	chr6D.!!$R5	1998
3	TraesCS6D01G119000	chr6D	84618084	84620200	2116	True	2089	2089	84.7450	814	2915	1	chr6D.!!$R4	2101
4	TraesCS6D01G119000	chr6D	84472091	84474199	2108	True	1965	1965	83.6400	814	2915	1	chr6D.!!$R3	2101
5	TraesCS6D01G119000	chr6D	85608143	85610133	1990	False	1858	1858	83.7240	925	2902	1	chr6D.!!$F1	1977
6	TraesCS6D01G119000	chr6A	101552814	101555698	2884	True	4636	4636	95.6690	24	2915	1	chr6A.!!$R1	2891
7	TraesCS6D01G119000	chr6A	101560706	101562820	2114	True	2204	2204	85.6200	814	2915	1	chr6A.!!$R2	2101
8	TraesCS6D01G119000	chr6A	101863451	101868678	5227	True	1188	2143	82.9205	814	2905	2	chr6A.!!$R4	2091
9	TraesCS6D01G119000	chr6A	101843043	101845485	2442	True	1076	2037	88.9205	833	2915	2	chr6A.!!$R3	2082
10	TraesCS6D01G119000	chr6B	160715011	160717021	2010	True	2185	2185	86.3950	917	2915	1	chr6B.!!$R1	1998
11	TraesCS6D01G119000	chr6B	160902973	160905069	2096	True	2093	2093	84.8400	814	2915	1	chr6B.!!$R2	2101
12	TraesCS6D01G119000	chr6B	160910187	160912174	1987	True	1838	1838	83.6580	952	2915	1	chr6B.!!$R3	1963
13	TraesCS6D01G119000	chr6B	160681176	160685827	4651	True	1393	2259	87.7620	814	2915	2	chr6B.!!$R4	2101

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
580	581	0.394762	CCTGAGCAAGCCAAGCCATA	60.395	55.0	0.00	0.0	0.0	2.74	F
830	4021	0.667993	CATTTGTGCACCAACCGACT	59.332	50.0	15.69	0.0	31.2	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1904	5484	0.654683	GCTCAGAGTTTATGGCAGCG	59.345	55.0	0.00	0.0	0.00	5.18	R
2563	6156	1.067295	AGACCAAGGTCAATGAGGCA	58.933	50.0	20.52	0.0	46.76	4.75	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
19	20	1.770957	TCATACATCATCAGTCGCGC	58.229	50.000	0.00	0.00	0.00	6.86
20	21	1.338020	TCATACATCATCAGTCGCGCT	59.662	47.619	5.56	0.00	0.00	5.92
21	22	1.718178	CATACATCATCAGTCGCGCTC	59.282	52.381	5.56	0.00	0.00	5.03
103	104	0.815734	AGGATGACCAACCGTACTCG	59.184	55.000	0.00	0.00	38.94	4.18
108	109	3.751246	CCAACCGTACTCGCCCGA	61.751	66.667	0.00	0.00	35.54	5.14
110	111	4.107051	AACCGTACTCGCCCGACG	62.107	66.667	0.00	0.00	45.62	5.12
121	122	2.508439	CCCGACGATGACCAACCG	60.508	66.667	0.00	0.00	0.00	4.44
122	123	2.260434	CCGACGATGACCAACCGT	59.740	61.111	0.00	0.00	39.41	4.83
123	124	1.507630	CCGACGATGACCAACCGTA	59.492	57.895	0.00	0.00	36.60	4.02
176	177	4.612279	AATTGCCCACCACCGCCA	62.612	61.111	0.00	0.00	0.00	5.69
242	243	1.078072	AGCCACGACACCACAAACA	60.078	52.632	0.00	0.00	0.00	2.83
276	277	5.495640	GAGAGGTCAAGTCTCCAAAATGAT	58.504	41.667	0.00	0.00	35.35	2.45
356	357	3.593442	TGGTTTTCACTGGGAGACAAT	57.407	42.857	0.00	0.00	0.00	2.71
362	363	5.497464	TTTCACTGGGAGACAATACATCA	57.503	39.130	0.00	0.00	0.00	3.07
392	393	0.398318	AGGTGTCAGAACTCCTTGGC	59.602	55.000	0.00	0.00	45.03	4.52
407	408	0.467844	TTGGCAGGTGTTGTCAGCAT	60.468	50.000	0.00	0.00	43.45	3.79
431	432	1.734465	CATCCAGCAAGACTTTCGTCC	59.266	52.381	0.00	0.00	41.16	4.79
514	515	1.915614	GAGCCGACATGCCTTGTGTG	61.916	60.000	0.00	0.00	39.18	3.82
547	548	2.031163	GTCTTGGAGCACAGCCGT	59.969	61.111	0.00	0.00	0.00	5.68
555	556	2.964925	GCACAGCCGTCAACGTCA	60.965	61.111	1.48	0.00	37.74	4.35
580	581	0.394762	CCTGAGCAAGCCAAGCCATA	60.395	55.000	0.00	0.00	0.00	2.74
627	628	0.821711	CCACAAGGAAAGGAACGCCA	60.822	55.000	0.00	0.00	36.89	5.69
799	805	1.342819	CTTCAAGGGGCGAGGAGATAG	59.657	57.143	0.00	0.00	0.00	2.08
830	4021	0.667993	CATTTGTGCACCAACCGACT	59.332	50.000	15.69	0.00	31.20	4.18
1009	4570	1.303236	CACCGGTCAATGCCTTCCA	60.303	57.895	2.59	0.00	0.00	3.53
1436	5013	1.219393	GGCCTCTGCAGGTACTCAC	59.781	63.158	15.13	0.00	42.74	3.51
1543	5120	1.559682	ACAGCTTCACCGGGAACATAT	59.440	47.619	6.32	0.00	0.00	1.78
1702	5279	2.622436	GGACTCTCCCTGTTGAAATCG	58.378	52.381	0.00	0.00	0.00	3.34
1904	5484	3.380320	GGTAACAATAACATGTCTGGGGC	59.620	47.826	0.00	0.00	31.81	5.80
1982	5564	3.845860	ACAACTTCAGTGGAGACCTAGA	58.154	45.455	5.11	0.00	0.00	2.43
2155	5737	4.194640	GAGAATAGGCAATCTGAAGCACA	58.805	43.478	7.59	0.00	0.00	4.57
2274	5856	3.442977	GCAGAAACTTCATGAATGAGGCT	59.557	43.478	8.96	0.73	37.40	4.58
2332	5914	3.071457	TCTTCAGTTTCTCTCCATGTGCA	59.929	43.478	0.00	0.00	0.00	4.57
2540	6133	7.637229	CAGATGCCACTGTTAAAATCAGATAG	58.363	38.462	0.00	0.00	36.81	2.08
2563	6156	2.024080	ACTGGCATGTATTTGGACCCAT	60.024	45.455	0.00	0.00	0.00	4.00
2802	6395	1.340889	CTGCAGAGGCTAGATCTGTCC	59.659	57.143	20.34	6.23	44.92	4.02
2815	6408	6.817641	GCTAGATCTGTCCAATAATCATCTGG	59.182	42.308	5.18	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	1.338020	TGAGCGCGACTGATGATGTAT	59.662	47.619	12.10	0.00	0.00	2.29
3	4	0.738389	TGAGCGCGACTGATGATGTA	59.262	50.000	12.10	0.00	0.00	2.29
4	5	0.103755	ATGAGCGCGACTGATGATGT	59.896	50.000	12.10	0.00	0.00	3.06
5	6	0.507358	CATGAGCGCGACTGATGATG	59.493	55.000	19.33	8.29	42.11	3.07
8	9	1.805261	CGTCATGAGCGCGACTGATG	61.805	60.000	12.10	16.43	41.00	3.07
9	10	1.587350	CGTCATGAGCGCGACTGAT	60.587	57.895	12.10	3.06	0.00	2.90
10	11	2.202479	CGTCATGAGCGCGACTGA	60.202	61.111	12.10	0.07	0.00	3.41
11	12	3.906649	GCGTCATGAGCGCGACTG	61.907	66.667	21.00	0.05	45.36	3.51
19	20	1.226802	CTCTCACCGGCGTCATGAG	60.227	63.158	20.61	20.61	41.06	2.90
20	21	1.248101	TTCTCTCACCGGCGTCATGA	61.248	55.000	6.01	5.85	0.00	3.07
21	22	0.803768	CTTCTCTCACCGGCGTCATG	60.804	60.000	6.01	0.94	0.00	3.07
29	30	0.534412	AGACATGCCTTCTCTCACCG	59.466	55.000	0.00	0.00	0.00	4.94
103	104	2.818274	GGTTGGTCATCGTCGGGC	60.818	66.667	0.00	0.00	0.00	6.13
108	109	0.169672	CGAGTACGGTTGGTCATCGT	59.830	55.000	0.00	0.00	40.40	3.73
110	111	0.804933	GGCGAGTACGGTTGGTCATC	60.805	60.000	0.00	0.00	40.15	2.92
111	112	1.217244	GGCGAGTACGGTTGGTCAT	59.783	57.895	0.00	0.00	40.15	3.06
112	113	2.652530	GGCGAGTACGGTTGGTCA	59.347	61.111	0.00	0.00	40.15	4.02
113	114	2.125793	GGGCGAGTACGGTTGGTC	60.126	66.667	0.00	0.00	40.15	4.02
114	115	4.060038	CGGGCGAGTACGGTTGGT	62.060	66.667	0.00	0.00	40.15	3.67
115	116	3.751246	TCGGGCGAGTACGGTTGG	61.751	66.667	0.00	0.00	40.15	3.77
166	167	4.704833	CTGGGACTGGCGGTGGTG	62.705	72.222	2.25	0.00	0.00	4.17
176	177	0.828022	TGTTGTGTTCGTCTGGGACT	59.172	50.000	0.00	0.00	0.00	3.85
276	277	4.586421	TGGCATTGTTACTTTGGTGAATCA	59.414	37.500	0.00	0.00	0.00	2.57
305	306	2.951745	CAGCTCGACGATGGCGAC	60.952	66.667	0.00	0.00	41.64	5.19
356	357	3.107601	CACCTCTCCCTTCCTTGATGTA	58.892	50.000	0.00	0.00	0.00	2.29
362	363	1.150135	TCTGACACCTCTCCCTTCCTT	59.850	52.381	0.00	0.00	0.00	3.36
392	393	1.915614	GCCGATGCTGACAACACCTG	61.916	60.000	0.00	0.00	33.53	4.00
407	408	0.036732	AAAGTCTTGCTGGATGCCGA	59.963	50.000	0.00	0.00	42.00	5.54
427	428	3.505464	AGATGTTTAGTTCTCCGGACG	57.495	47.619	0.00	0.00	0.00	4.79
431	432	3.114065	GGCGTAGATGTTTAGTTCTCCG	58.886	50.000	0.00	0.00	0.00	4.63
514	515	2.930562	ACCAGGGAGTGTGGAGCC	60.931	66.667	0.00	0.00	38.57	4.70
580	581	1.826054	CGATCCCTGCTCCGAGACT	60.826	63.158	0.00	0.00	0.00	3.24
691	692	0.392595	ACCCTAAAACTGCCGCTAGC	60.393	55.000	4.06	4.06	44.14	3.42
830	4021	2.066340	CTTAGTGTCCTGGGCCACA	58.934	57.895	0.00	0.00	33.99	4.17
1009	4570	1.056660	ACAACTGGAGGAACGGTGAT	58.943	50.000	0.00	0.00	0.00	3.06
1436	5013	2.486982	CTGAACTGGTTGCTTGAGATGG	59.513	50.000	0.00	0.00	0.00	3.51
1543	5120	0.891373	CCAAGGCAGAGAGAAGACGA	59.109	55.000	0.00	0.00	0.00	4.20
1702	5279	4.129737	TAGCGAGGCAGCGTGGAC	62.130	66.667	0.70	0.00	43.00	4.02
1904	5484	0.654683	GCTCAGAGTTTATGGCAGCG	59.345	55.000	0.00	0.00	0.00	5.18
1982	5564	1.601166	GGTGGCGAAGTTTACCTTGT	58.399	50.000	0.00	0.00	32.03	3.16
2155	5737	7.496346	TTCTAACAAGTGACAGGAAGGATAT	57.504	36.000	0.00	0.00	0.00	1.63
2251	5833	3.442977	GCCTCATTCATGAAGTTTCTGCT	59.557	43.478	14.54	0.00	36.18	4.24
2274	5856	6.458615	CGTCAATGATTTCATCTTGTGGCATA	60.459	38.462	0.00	0.00	35.10	3.14
2332	5914	3.214696	CCTTCCAGTCAAGGAACACTT	57.785	47.619	0.00	0.00	45.41	3.16
2540	6133	2.024414	GGTCCAAATACATGCCAGTCC	58.976	52.381	0.00	0.00	0.00	3.85
2563	6156	1.067295	AGACCAAGGTCAATGAGGCA	58.933	50.000	20.52	0.00	46.76	4.75
2802	6395	1.267806	GCACCCGCCAGATGATTATTG	59.732	52.381	0.00	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.