AutoCloner

Multiple sequence alignment - TraesCS7D01G305900

Loading Multiple Alignment...

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	TraesCS7D01G305900	chr7D	100.000	6730	0	0	1	6730	387218329	387225058	0.000000e+00	12429.0
1	TraesCS7D01G305900	chr7D	97.098	448	12	1	1	447	568933271	568932824	0.000000e+00	754.0
2	TraesCS7D01G305900	chr7D	96.205	448	16	1	1	447	46410079	46410526	0.000000e+00	732.0
3	TraesCS7D01G305900	chr7D	87.586	145	12	4	4489	4630	509615289	509615430	5.400000e-36	163.0
4	TraesCS7D01G305900	chr7A	91.614	3148	152	60	456	3530	437066330	437069438	0.000000e+00	4248.0
5	TraesCS7D01G305900	chr7A	94.086	1691	53	20	5055	6730	437071123	437072781	0.000000e+00	2525.0
6	TraesCS7D01G305900	chr7A	88.241	1063	77	30	3653	4700	437069465	437070494	0.000000e+00	1227.0
7	TraesCS7D01G305900	chr7A	94.928	138	7	0	4739	4876	437070607	437070744	4.090000e-52	217.0
8	TraesCS7D01G305900	chr7B	95.286	2694	85	25	1739	4414	382277452	382280121	0.000000e+00	4233.0
9	TraesCS7D01G305900	chr7B	94.360	1720	58	16	5017	6730	382282052	382283738	0.000000e+00	2603.0
10	TraesCS7D01G305900	chr7B	90.943	1325	68	29	456	1741	382275821	382277132	0.000000e+00	1735.0
11	TraesCS7D01G305900	chr7B	85.784	204	21	6	4492	4688	382280129	382280331	6.840000e-50	209.0
12	TraesCS7D01G305900	chr3D	96.652	448	14	1	1	447	29858078	29857631	0.000000e+00	743.0
13	TraesCS7D01G305900	chr3D	95.536	448	19	1	1	447	43571585	43572032	0.000000e+00	715.0
14	TraesCS7D01G305900	chr3D	94.420	448	24	1	1	447	552431201	552430754	0.000000e+00	688.0
15	TraesCS7D01G305900	chr3D	90.541	74	3	1	3543	3616	157099442	157099373	2.000000e-15	95.3
16	TraesCS7D01G305900	chr3D	97.959	49	1	0	3543	3591	105428601	105428553	1.200000e-12	86.1
17	TraesCS7D01G305900	chr4A	95.536	448	19	1	1	447	667057386	667056939	0.000000e+00	715.0
18	TraesCS7D01G305900	chr4A	87.000	100	10	2	4523	4622	534164750	534164846	7.140000e-20	110.0
19	TraesCS7D01G305900	chr2B	94.866	448	22	1	1	447	731222978	731223425	0.000000e+00	699.0
20	TraesCS7D01G305900	chr3B	94.420	448	24	1	1	447	449842903	449842456	0.000000e+00	688.0
21	TraesCS7D01G305900	chr3B	100.000	49	0	0	3543	3591	252558303	252558351	2.580000e-14	91.6
22	TraesCS7D01G305900	chr6A	94.209	449	24	1	1	447	616077938	616077490	0.000000e+00	684.0
23	TraesCS7D01G305900	chr4B	84.672	137	10	7	4488	4622	92547347	92547220	7.090000e-25	126.0
24	TraesCS7D01G305900	chr6D	90.541	74	3	2	3543	3616	319255392	319255323	2.000000e-15	95.3
25	TraesCS7D01G305900	chr6D	86.667	75	6	3	3542	3616	2490441	2490371	5.590000e-11	80.5
26	TraesCS7D01G305900	chr6D	90.323	62	2	2	3543	3604	128098180	128098123	2.010000e-10	78.7
27	TraesCS7D01G305900	chr6B	89.189	74	4	3	3543	3616	226869132	226869063	9.300000e-14	89.8
28	TraesCS7D01G305900	chr4D	84.884	86	6	5	3533	3616	71072743	71072823	5.590000e-11	80.5
29	TraesCS7D01G305900	chr5A	79.688	128	9	11	4489	4611	29135958	29136073	7.240000e-10	76.8

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	TraesCS7D01G305900	chr7D	387218329	387225058	6729	False	12429.00	12429	100.00000	1	6730	1	chr7D.!!$F2	6729
1	TraesCS7D01G305900	chr7A	437066330	437072781	6451	False	2054.25	4248	92.21725	456	6730	4	chr7A.!!$F1	6274
2	TraesCS7D01G305900	chr7B	382275821	382283738	7917	False	2195.00	4233	91.59325	456	6730	4	chr7B.!!$F1	6274

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
442	443	0.102300	GCAGAACCGTGGTTTTTGCT	59.898	50.000	23.64	9.07	41.43	3.91	F
1179	1249	1.301716	GCCTTCACACTCGCCAAGA	60.302	57.895	0.00	0.00	0.00	3.02	F
1607	1683	1.134694	GACCAAATGCTCGAACCGC	59.865	57.895	0.00	0.00	0.00	5.68	F
2669	3076	1.092345	GCAGAAGAATCCAGTCCCGC	61.092	60.000	0.00	0.00	0.00	6.13	F
3981	4427	1.171308	GGTACAGACGTCCTGCTACA	58.829	55.000	13.01	0.00	46.81	2.74	F
4567	5026	0.464036	TCGCTCATTTCAGCCCGTAT	59.536	50.000	0.00	0.00	35.84	3.06	F
5009	6603	0.172578	TGGACGAGATGGTTACAGCG	59.827	55.000	0.00	0.00	38.25	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1272	1342	0.689412	TGTCACCACACTGGACTCCA	60.689	55.000	0.00	0.0	40.96	3.86	R
2032	2430	1.203523	TCGCCCACACAAATATTTGGC	59.796	47.619	27.43	20.4	42.34	4.52	R
3191	3613	1.489230	AGGTGAAAAGTGTTCCCTCGT	59.511	47.619	0.00	0.0	0.00	4.18	R
4448	4901	0.661020	CAAGACGTTTTTGCGGAGGT	59.339	50.000	0.00	0.0	35.98	3.85	R
4802	5380	0.033228	CTCCATGATCACGAGCTCCC	59.967	60.000	8.47	0.0	0.00	4.30	R
5453	7540	0.035881	CAGGCTCTTCCACTGCTTCA	59.964	55.000	0.00	0.0	37.29	3.02	R
6576	8676	0.036952	ATGTCAGGAAGAGTGGTGCG	60.037	55.000	0.00	0.0	0.00	5.34	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.093835	AATCCATTCGGGCCGGGA	61.094	61.111	27.98	24.58	36.21	5.14
18	19	3.120086	AATCCATTCGGGCCGGGAG	62.120	63.158	27.98	15.36	36.21	4.30
47	48	3.988379	TTTTTCATCTGCGATATGGCC	57.012	42.857	7.29	0.00	0.00	5.36
48	49	2.936919	TTTCATCTGCGATATGGCCT	57.063	45.000	3.32	0.00	0.00	5.19
49	50	2.936919	TTCATCTGCGATATGGCCTT	57.063	45.000	3.32	0.00	0.00	4.35
50	51	4.350368	TTTCATCTGCGATATGGCCTTA	57.650	40.909	3.32	1.49	0.00	2.69
51	52	4.350368	TTCATCTGCGATATGGCCTTAA	57.650	40.909	3.32	0.00	0.00	1.85
52	53	4.350368	TCATCTGCGATATGGCCTTAAA	57.650	40.909	3.32	0.00	0.00	1.52
53	54	4.065088	TCATCTGCGATATGGCCTTAAAC	58.935	43.478	3.32	0.33	0.00	2.01
54	55	3.552132	TCTGCGATATGGCCTTAAACA	57.448	42.857	3.32	1.57	0.00	2.83
55	56	3.202906	TCTGCGATATGGCCTTAAACAC	58.797	45.455	3.32	0.00	0.00	3.32
56	57	2.290641	CTGCGATATGGCCTTAAACACC	59.709	50.000	3.32	0.00	0.00	4.16
57	58	2.092646	TGCGATATGGCCTTAAACACCT	60.093	45.455	3.32	0.00	0.00	4.00
58	59	2.548480	GCGATATGGCCTTAAACACCTC	59.452	50.000	3.32	0.00	0.00	3.85
59	60	3.744530	GCGATATGGCCTTAAACACCTCT	60.745	47.826	3.32	0.00	0.00	3.69
60	61	4.451900	CGATATGGCCTTAAACACCTCTT	58.548	43.478	3.32	0.00	0.00	2.85
61	62	4.881850	CGATATGGCCTTAAACACCTCTTT	59.118	41.667	3.32	0.00	0.00	2.52
62	63	5.007724	CGATATGGCCTTAAACACCTCTTTC	59.992	44.000	3.32	0.00	0.00	2.62
63	64	3.876309	TGGCCTTAAACACCTCTTTCT	57.124	42.857	3.32	0.00	0.00	2.52
64	65	3.751518	TGGCCTTAAACACCTCTTTCTC	58.248	45.455	3.32	0.00	0.00	2.87
65	66	3.137544	TGGCCTTAAACACCTCTTTCTCA	59.862	43.478	3.32	0.00	0.00	3.27
66	67	3.753797	GGCCTTAAACACCTCTTTCTCAG	59.246	47.826	0.00	0.00	0.00	3.35
67	68	4.505039	GGCCTTAAACACCTCTTTCTCAGA	60.505	45.833	0.00	0.00	0.00	3.27
68	69	5.063880	GCCTTAAACACCTCTTTCTCAGAA	58.936	41.667	0.00	0.00	0.00	3.02
69	70	5.531287	GCCTTAAACACCTCTTTCTCAGAAA	59.469	40.000	0.00	0.00	0.00	2.52

Showing 1 to 25 of 440 entries

Previous1 2 3 4 5…18Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.093835	TCCCGGCCCGAATGGATT	61.094	61.111	3.71	0.00	37.49	3.01
1	2	3.560251	CTCCCGGCCCGAATGGAT	61.560	66.667	3.71	0.00	37.49	3.41
27	28	3.554934	AGGCCATATCGCAGATGAAAAA	58.445	40.909	5.01	0.00	45.12	1.94
28	29	3.213206	AGGCCATATCGCAGATGAAAA	57.787	42.857	5.01	0.00	45.12	2.29
29	30	2.936919	AGGCCATATCGCAGATGAAA	57.063	45.000	5.01	0.00	45.12	2.69
30	31	2.936919	AAGGCCATATCGCAGATGAA	57.063	45.000	5.01	0.00	45.12	2.57
31	32	4.065088	GTTTAAGGCCATATCGCAGATGA	58.935	43.478	5.01	0.00	45.12	2.92
32	33	3.814842	TGTTTAAGGCCATATCGCAGATG	59.185	43.478	5.01	0.00	45.12	2.90
33	34	3.815401	GTGTTTAAGGCCATATCGCAGAT	59.185	43.478	5.01	0.00	45.12	2.90
34	35	3.202906	GTGTTTAAGGCCATATCGCAGA	58.797	45.455	5.01	0.00	45.75	4.26
35	36	2.290641	GGTGTTTAAGGCCATATCGCAG	59.709	50.000	5.01	0.00	0.00	5.18
36	37	2.092646	AGGTGTTTAAGGCCATATCGCA	60.093	45.455	5.01	0.00	0.00	5.10
37	38	2.548480	GAGGTGTTTAAGGCCATATCGC	59.452	50.000	5.01	0.58	0.00	4.58
38	39	4.073293	AGAGGTGTTTAAGGCCATATCG	57.927	45.455	5.01	0.00	0.00	2.92
39	40	6.122964	AGAAAGAGGTGTTTAAGGCCATATC	58.877	40.000	5.01	0.00	0.00	1.63
40	41	6.079712	AGAAAGAGGTGTTTAAGGCCATAT	57.920	37.500	5.01	0.00	0.00	1.78
41	42	5.013704	TGAGAAAGAGGTGTTTAAGGCCATA	59.986	40.000	5.01	0.00	0.00	2.74
42	43	4.202567	TGAGAAAGAGGTGTTTAAGGCCAT	60.203	41.667	5.01	0.00	0.00	4.40
43	44	3.137544	TGAGAAAGAGGTGTTTAAGGCCA	59.862	43.478	5.01	0.00	0.00	5.36
44	45	3.751518	TGAGAAAGAGGTGTTTAAGGCC	58.248	45.455	0.00	0.00	0.00	5.19
45	46	4.642429	TCTGAGAAAGAGGTGTTTAAGGC	58.358	43.478	0.00	0.00	0.00	4.35
46	47	7.568199	TTTTCTGAGAAAGAGGTGTTTAAGG	57.432	36.000	7.76	0.00	35.91	2.69
47	48	8.131731	CCTTTTTCTGAGAAAGAGGTGTTTAAG	58.868	37.037	27.46	15.94	36.45	1.85
48	49	7.832187	TCCTTTTTCTGAGAAAGAGGTGTTTAA	59.168	33.333	31.50	16.69	36.45	1.52
49	50	7.343357	TCCTTTTTCTGAGAAAGAGGTGTTTA	58.657	34.615	31.50	17.25	36.45	2.01

Showing 1 to 25 of 461 entries

Previous1 2 3 4 5…19Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.