AutoCloner

Multiple sequence alignment - TraesCS2D01G139400

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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	TraesCS2D01G139400	chr2D	100.000	6056	0	0	1	6056	82186194	82180139	0.000000e+00	11184
1	TraesCS2D01G139400	chr2D	83.077	1430	148	38	1672	3028	82189287	82187879	0.000000e+00	1214
2	TraesCS2D01G139400	chr2D	85.014	694	61	17	4607	5284	82186300	82185634	0.000000e+00	665
3	TraesCS2D01G139400	chr2D	85.026	581	50	13	6	561	82181479	82180911	1.910000e-154	556
4	TraesCS2D01G139400	chr2D	87.810	443	49	5	3684	4122	82187159	82186718	1.160000e-141	514
5	TraesCS2D01G139400	chr2D	78.059	711	67	39	934	1594	82189993	82189322	3.450000e-97	366
6	TraesCS2D01G139400	chr2D	88.421	95	7	4	4179	4271	96798682	96798774	1.780000e-20	111
7	TraesCS2D01G139400	chr2A	94.064	4801	165	47	698	5468	82349742	82345032	0.000000e+00	7177
8	TraesCS2D01G139400	chr2A	82.463	1437	155	43	1672	3028	82353740	82352321	0.000000e+00	1168
9	TraesCS2D01G139400	chr2A	91.453	702	23	4	1	699	82350507	82349840	0.000000e+00	929
10	TraesCS2D01G139400	chr2A	85.754	723	74	12	4600	5315	82350620	82349920	0.000000e+00	737
11	TraesCS2D01G139400	chr2A	86.043	652	68	15	3043	3680	82352334	82351692	0.000000e+00	678
12	TraesCS2D01G139400	chr2A	92.841	447	17	10	5549	5981	82344896	82344451	8.560000e-178	634
13	TraesCS2D01G139400	chr2A	87.945	506	58	3	3684	4186	82351582	82351077	1.450000e-165	593
14	TraesCS2D01G139400	chr2A	82.961	716	59	39	962	1654	82354811	82354136	6.760000e-164	588
15	TraesCS2D01G139400	chr2A	83.681	576	58	14	6	557	82345785	82345222	1.510000e-140	510
16	TraesCS2D01G139400	chr2A	94.667	75	4	0	5982	6056	82344415	82344341	3.840000e-22	117
17	TraesCS2D01G139400	chr2B	92.189	2010	88	30	3978	5981	134045749	134043803	0.000000e+00	2778
18	TraesCS2D01G139400	chr2B	94.281	1836	72	12	1201	3005	134049017	134047184	0.000000e+00	2778
19	TraesCS2D01G139400	chr2B	96.472	992	26	2	2996	3980	134046899	134045910	0.000000e+00	1629
20	TraesCS2D01G139400	chr2B	87.828	723	61	10	4600	5314	134090703	134090000	0.000000e+00	822
21	TraesCS2D01G139400	chr2B	91.930	570	30	6	1	561	134090591	134090029	0.000000e+00	784
22	TraesCS2D01G139400	chr2B	85.423	686	74	14	3043	3710	134092351	134091674	0.000000e+00	689
23	TraesCS2D01G139400	chr2B	86.823	554	55	12	1672	2214	134093715	134093169	2.410000e-168	603
24	TraesCS2D01G139400	chr2B	80.220	819	92	37	2269	3028	134093145	134092338	8.870000e-153	551
25	TraesCS2D01G139400	chr2B	84.201	576	55	14	6	557	134045032	134044469	1.500000e-145	527
26	TraesCS2D01G139400	chr2B	81.006	716	66	37	973	1655	134094834	134094156	7.010000e-139	505
27	TraesCS2D01G139400	chr4D	91.579	95	3	5	4186	4278	34660035	34659944	6.370000e-25	126
28	TraesCS2D01G139400	chr6B	91.954	87	7	0	4185	4271	124550588	124550502	8.240000e-24	122
29	TraesCS2D01G139400	chr1A	91.765	85	6	1	4192	4275	343398331	343398415	3.840000e-22	117
30	TraesCS2D01G139400	chr5D	89.888	89	5	4	4186	4272	278271122	278271036	1.780000e-20	111
31	TraesCS2D01G139400	chr1B	89.888	89	5	4	4186	4272	288805396	288805482	1.780000e-20	111
32	TraesCS2D01G139400	chr1B	93.878	49	3	0	722	770	578093855	578093807	2.340000e-09	75
33	TraesCS2D01G139400	chr4A	87.234	94	8	4	4180	4271	581944255	581944346	2.990000e-18	104

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	TraesCS2D01G139400	chr2D	82180139	82186194	6055	True	11184.000000	11184	100.000000	1	6056	1	chr2D.!!$R1	6055
1	TraesCS2D01G139400	chr2D	82185634	82189993	4359	True	689.750000	1214	83.490000	934	5284	4	chr2D.!!$R3	4350
2	TraesCS2D01G139400	chr2D	82180911	82181479	568	True	556.000000	556	85.026000	6	561	1	chr2D.!!$R2	555
3	TraesCS2D01G139400	chr2A	82344341	82349742	5401	True	2642.666667	7177	93.857333	698	6056	3	chr2A.!!$R2	5358
4	TraesCS2D01G139400	chr2A	82349840	82354811	4971	True	782.166667	1168	86.103167	1	5315	6	chr2A.!!$R3	5314
5	TraesCS2D01G139400	chr2A	82345222	82345785	563	True	510.000000	510	83.681000	6	557	1	chr2A.!!$R1	551
6	TraesCS2D01G139400	chr2B	134043803	134049017	5214	True	1928.000000	2778	91.785750	6	5981	4	chr2B.!!$R1	5975
7	TraesCS2D01G139400	chr2B	134090000	134094834	4834	True	659.000000	822	85.538333	1	5314	6	chr2B.!!$R2	5313

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	Hairpin	End Stability	Orientation
169	170	0.036010	AGTTCCACCATCCGCAAGAG	60.036	55.000	0.00	43.02	2.85	F
1114	1124	0.036164	CCATCGAACCAACTGACCCA	59.964	55.000	0.00	0.00	4.51	F
1654	1723	0.254462	TCCCGCAGCCATGAATGTTA	59.746	50.000	0.00	0.00	2.41	F
1821	1890	3.119602	TCAAGGACTGCTGTGACGTATAC	60.120	47.826	0.00	0.00	1.47	F
3319	3775	1.145803	GCACGTTTAGTCAGTGGTCC	58.854	55.000	0.00	36.48	4.46	F
3451	3918	2.511600	GATTGCGAGGGTCGTGGG	60.512	66.667	0.00	42.81	4.61	F
3961	4512	4.221703	AGACAAGTGACCACAGAATAGAGG	59.778	45.833	2.78	0.00	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1375	1412	1.675641	GCAGCAGTTGACGGGGATT	60.676	57.895	0.00	0.00	0.00	3.01	R
2609	2731	2.375509	GGAAAGGAACTCCAGGGAGAAA	59.624	50.000	21.73	0.00	44.53	2.52	R
2943	3090	2.928334	ACTGGTCCATGAGATGAATGC	58.072	47.619	0.00	0.00	0.00	3.56	R
3451	3918	3.055385	TGCAAGTAGGACATGGTACCTTC	60.055	47.826	14.36	6.82	37.68	3.46	R
4437	5256	3.128764	GCCCTACTGGTTTGCTGATAAAC	59.871	47.826	0.00	0.00	39.28	2.01	R
4639	5512	4.276926	AGAAATTGCAAGTCAGACCAAGAC	59.723	41.667	4.94	0.00	36.26	3.01	R
5838	6827	0.442699	GACGATTCTTGGCCGTGTTC	59.557	55.000	0.00	0.00	36.60	3.18	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
18	19	3.394836	GGAGCTGCTTCGGTCCCT	61.395	66.667	2.53	0.00	43.94	4.20
19	20	2.125350	GAGCTGCTTCGGTCCCTG	60.125	66.667	2.53	0.00	0.00	4.45
21	22	2.435059	GCTGCTTCGGTCCCTGAC	60.435	66.667	0.00	0.00	0.00	3.51
22	23	2.125912	CTGCTTCGGTCCCTGACG	60.126	66.667	0.00	0.00	32.65	4.35
23	24	2.599281	TGCTTCGGTCCCTGACGA	60.599	61.111	0.00	0.00	37.33	4.20
24	25	2.154798	CTGCTTCGGTCCCTGACGAA	62.155	60.000	0.00	0.00	45.61	3.85
40	41	0.110644	CGAAGTTTTCCACAGAGCGC	60.111	55.000	0.00	0.00	0.00	5.92
41	42	0.944386	GAAGTTTTCCACAGAGCGCA	59.056	50.000	11.47	0.00	0.00	6.09
42	43	1.333619	GAAGTTTTCCACAGAGCGCAA	59.666	47.619	11.47	0.00	0.00	4.85
43	44	0.947244	AGTTTTCCACAGAGCGCAAG	59.053	50.000	11.47	0.19	43.44	4.01
44	45	0.040067	GTTTTCCACAGAGCGCAAGG	60.040	55.000	11.47	3.48	38.28	3.61
45	46	1.172180	TTTTCCACAGAGCGCAAGGG	61.172	55.000	11.47	3.45	38.28	3.95
46	47	3.551496	TTCCACAGAGCGCAAGGGG	62.551	63.158	11.47	9.74	38.28	4.79
72	73	5.751680	CAACTATGCAACATACAGGCATAC	58.248	41.667	0.00	0.00	45.72	2.39
73	74	4.389374	ACTATGCAACATACAGGCATACC	58.611	43.478	0.00	0.00	45.72	2.73
75	76	3.078891	TGCAACATACAGGCATACCAA	57.921	42.857	0.00	0.00	39.06	3.67
76	77	3.630168	TGCAACATACAGGCATACCAAT	58.370	40.909	0.00	0.00	39.06	3.16
77	78	3.380954	TGCAACATACAGGCATACCAATG	59.619	43.478	0.00	0.00	39.06	2.82
88	89	2.372264	CATACCAATGCACTCCAGCTT	58.628	47.619	0.00	0.00	34.99	3.74
89	90	2.584835	TACCAATGCACTCCAGCTTT	57.415	45.000	0.00	0.00	34.99	3.51
91	92	1.202976	ACCAATGCACTCCAGCTTTCT	60.203	47.619	0.00	0.00	34.99	2.52
92	93	1.891150	CCAATGCACTCCAGCTTTCTT	59.109	47.619	0.00	0.00	34.99	2.52
94	95	3.314553	CAATGCACTCCAGCTTTCTTTG	58.685	45.455	0.00	0.00	34.99	2.77
95	96	0.670162	TGCACTCCAGCTTTCTTTGC	59.330	50.000	0.00	0.00	34.99	3.68
96	97	0.038801	GCACTCCAGCTTTCTTTGCC	60.039	55.000	0.00	0.00	0.00	4.52

Showing 1 to 25 of 382 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.394836	GGGACCGAAGCAGCTCCT	61.395	66.667	0.00	0.00	0.00	3.69
2	3	2.125350	CAGGGACCGAAGCAGCTC	60.125	66.667	0.00	0.00	0.00	4.09
3	4	2.604686	TCAGGGACCGAAGCAGCT	60.605	61.111	0.00	0.00	0.00	4.24
6	7	2.154798	CTTCGTCAGGGACCGAAGCA	62.155	60.000	8.60	0.00	36.89	3.91
7	8	1.446272	CTTCGTCAGGGACCGAAGC	60.446	63.158	8.60	0.00	36.89	3.86
8	9	0.317479	AACTTCGTCAGGGACCGAAG	59.683	55.000	17.31	17.31	42.58	3.79
10	11	0.754472	AAAACTTCGTCAGGGACCGA	59.246	50.000	0.00	0.00	0.00	4.69
13	14	1.871676	GTGGAAAACTTCGTCAGGGAC	59.128	52.381	0.00	0.00	0.00	4.46
14	15	1.487142	TGTGGAAAACTTCGTCAGGGA	59.513	47.619	0.00	0.00	0.00	4.20
15	16	1.873591	CTGTGGAAAACTTCGTCAGGG	59.126	52.381	0.00	0.00	31.91	4.45
16	17	2.802816	CTCTGTGGAAAACTTCGTCAGG	59.197	50.000	0.00	0.00	34.33	3.86
17	18	2.221981	GCTCTGTGGAAAACTTCGTCAG	59.778	50.000	0.00	0.00	34.62	3.51
18	19	2.210116	GCTCTGTGGAAAACTTCGTCA	58.790	47.619	0.00	0.00	0.00	4.35
19	20	1.192534	CGCTCTGTGGAAAACTTCGTC	59.807	52.381	0.00	0.00	0.00	4.20
21	22	0.110644	GCGCTCTGTGGAAAACTTCG	60.111	55.000	0.00	0.00	0.00	3.79
22	23	0.944386	TGCGCTCTGTGGAAAACTTC	59.056	50.000	9.73	0.00	0.00	3.01
23	24	1.334869	CTTGCGCTCTGTGGAAAACTT	59.665	47.619	9.73	0.00	0.00	2.66
24	25	0.947244	CTTGCGCTCTGTGGAAAACT	59.053	50.000	9.73	0.00	0.00	2.66
26	27	1.172180	CCCTTGCGCTCTGTGGAAAA	61.172	55.000	9.73	0.00	0.00	2.29
28	29	2.032528	CCCTTGCGCTCTGTGGAA	59.967	61.111	9.73	0.00	0.00	3.53
29	30	4.020617	CCCCTTGCGCTCTGTGGA	62.021	66.667	9.73	0.00	0.00	4.02
49	50	4.906065	ATGCCTGTATGTTGCATAGTTG	57.094	40.909	0.00	0.00	43.51	3.16
50	51	4.821805	GGTATGCCTGTATGTTGCATAGTT	59.178	41.667	3.84	0.00	45.64	2.24
51	52	4.141505	TGGTATGCCTGTATGTTGCATAGT	60.142	41.667	0.16	0.00	45.64	2.12
52	53	4.388485	TGGTATGCCTGTATGTTGCATAG	58.612	43.478	0.16	0.00	45.64	2.23

Showing 1 to 25 of 408 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.