AutoCloner

Multiple sequence alignment - TraesCS2D01G448900

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	TraesCS2D01G448900	chr2D	100.000	5476	0	0	1	5476	558799194	558804669	0.000000e+00	10113.0
1	TraesCS2D01G448900	chr2D	93.333	270	16	2	2166	2433	315858988	315859257	1.110000e-106	398.0
2	TraesCS2D01G448900	chr2D	93.585	265	15	1	2165	2429	194819109	194818847	1.430000e-105	394.0
3	TraesCS2D01G448900	chr2A	91.200	3159	165	46	1999	5101	699512487	699515588	0.000000e+00	4189.0
4	TraesCS2D01G448900	chr2A	92.550	1490	54	19	514	1973	699511030	699512492	0.000000e+00	2084.0
5	TraesCS2D01G448900	chr2A	93.600	250	16	0	5227	5476	699515960	699516209	1.860000e-99	374.0
6	TraesCS2D01G448900	chr2A	94.079	152	9	0	359	510	725349677	725349828	1.190000e-56	231.0
7	TraesCS2D01G448900	chr2A	96.269	134	1	1	5100	5233	699515669	699515798	3.320000e-52	217.0
8	TraesCS2D01G448900	chr2B	92.167	1698	72	26	3414	5101	667416303	667417949	0.000000e+00	2342.0
9	TraesCS2D01G448900	chr2B	93.745	1295	51	15	545	1822	667413416	667414697	0.000000e+00	1916.0
10	TraesCS2D01G448900	chr2B	91.486	552	21	11	2425	2960	667415141	667415682	0.000000e+00	736.0
11	TraesCS2D01G448900	chr2B	94.872	312	14	2	1859	2170	667414831	667415140	2.290000e-133	486.0
12	TraesCS2D01G448900	chr2B	96.774	279	8	1	3033	3311	667415715	667415992	1.070000e-126	464.0
13	TraesCS2D01G448900	chr2B	94.079	152	9	0	360	511	386595249	386595098	1.190000e-56	231.0
14	TraesCS2D01G448900	chr2B	80.000	275	21	22	5236	5476	667418347	667418621	7.290000e-39	172.0
15	TraesCS2D01G448900	chr2B	95.283	106	5	0	3313	3418	667416077	667416182	9.430000e-38	169.0
16	TraesCS2D01G448900	chr6B	83.287	1077	94	38	1146	2169	560650359	560651402	0.000000e+00	913.0
17	TraesCS2D01G448900	chr6B	85.572	402	33	15	2424	2824	560651398	560651775	1.110000e-106	398.0
18	TraesCS2D01G448900	chr6B	93.284	268	16	2	2165	2431	214870607	214870341	1.430000e-105	394.0
19	TraesCS2D01G448900	chr6B	89.333	150	16	0	359	508	584581184	584581333	7.240000e-44	189.0
20	TraesCS2D01G448900	chr6B	88.172	93	4	4	963	1055	560650269	560650354	2.700000e-18	104.0
21	TraesCS2D01G448900	chr6B	100.000	37	0	0	1405	1441	96474642	96474606	9.840000e-08	69.4
22	TraesCS2D01G448900	chr5D	94.737	266	14	0	2166	2431	202399607	202399342	1.100000e-111	414.0
23	TraesCS2D01G448900	chr5D	93.916	263	16	0	2165	2427	279293132	279292870	1.110000e-106	398.0
24	TraesCS2D01G448900	chr5D	88.158	152	18	0	358	509	320417701	320417852	1.210000e-41	182.0
25	TraesCS2D01G448900	chr6D	94.007	267	16	0	2166	2432	410373780	410373514	6.600000e-109	405.0
26	TraesCS2D01G448900	chr6D	95.420	131	6	0	359	489	292962742	292962872	5.560000e-50	209.0
27	TraesCS2D01G448900	chr6D	86.154	65	5	2	1377	1440	41443356	41443417	3.540000e-07	67.6
28	TraesCS2D01G448900	chr4A	93.561	264	17	0	2163	2426	674616791	674617054	1.430000e-105	394.0
29	TraesCS2D01G448900	chr7A	92.058	277	19	2	2166	2439	329488540	329488264	2.390000e-103	387.0
30	TraesCS2D01G448900	chr7A	97.436	156	3	1	354	509	732938616	732938462	1.170000e-66	265.0
31	TraesCS2D01G448900	chr7D	97.386	153	4	0	357	509	519108185	519108337	1.510000e-65	261.0
32	TraesCS2D01G448900	chr1D	96.078	153	6	0	357	509	143175875	143175723	3.270000e-62	250.0
33	TraesCS2D01G448900	chr5B	90.196	153	11	2	359	510	137409194	137409045	4.330000e-46	196.0
34	TraesCS2D01G448900	chr6A	87.500	64	4	2	1379	1441	51919768	51919828	2.740000e-08	71.3

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	TraesCS2D01G448900	chr2D	558799194	558804669	5475	False	10113.000000	10113	100.000000	1	5476	1	chr2D.!!$F2	5475
1	TraesCS2D01G448900	chr2A	699511030	699516209	5179	False	1716.000000	4189	93.404750	514	5476	4	chr2A.!!$F2	4962
2	TraesCS2D01G448900	chr2B	667413416	667418621	5205	False	897.857143	2342	92.046714	545	5476	7	chr2B.!!$F1	4931
3	TraesCS2D01G448900	chr6B	560650269	560651775	1506	False	471.666667	913	85.677000	963	2824	3	chr6B.!!$F2	1861

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
292	293	0.030101	GAGGAGATCGGACGCAGAAG	59.970	60.0	0.00	0.00	2.85	F
309	310	0.037326	AAGATGGCGTTCGCTCAGAA	60.037	50.0	16.40	36.31	3.02	F
310	311	0.037326	AGATGGCGTTCGCTCAGAAA	60.037	50.0	16.40	41.10	2.52	F
314	315	0.164002	GGCGTTCGCTCAGAAAACTC	59.836	55.0	16.40	41.10	3.01	F
470	471	0.179108	GGCCCTGCTACTTCGTACAG	60.179	60.0	0.00	0.00	2.74	F
1414	1467	0.391793	CGTGAAGAAGAAGAGGGGGC	60.392	60.0	0.00	0.00	5.80	F
2831	3049	0.179702	GCTGCTGATCCACAGGATGA	59.820	55.0	2.74	45.30	2.92	F
3385	3698	0.036952	TTCTGTAGCCTGCACTCTGC	60.037	55.0	0.00	45.29	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1672	1728	2.890311	TGGTGGCAAACATGTAGAAAGG	59.110	45.455	0.00	0.00	0.00	3.11	R
1994	2166	4.055710	TGATACTCCTATATTGCCCGGA	57.944	45.455	0.73	0.00	0.00	5.14	R
1995	2167	4.162320	ACATGATACTCCTATATTGCCCGG	59.838	45.833	0.00	0.00	0.00	5.73	R
2186	2390	4.953667	TCAGCCAACTCTAATATGCAGAG	58.046	43.478	11.37	11.37	44.28	3.35	R
2456	2660	0.037697	AACAACCAGAGCACGCGATA	60.038	50.000	15.93	0.00	0.00	2.92	R
3075	3305	1.159285	TCGAAGCAACATCCTGCAAG	58.841	50.000	0.00	0.00	45.18	4.01	R
4391	4868	0.249447	CCGGAGCATATGAAGCGTGA	60.249	55.000	6.97	0.00	37.01	4.35	R
4481	4958	0.394938	TGAAGCTGCTGTAAACCGGA	59.605	50.000	9.46	0.00	0.00	5.14	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	3.412722	ACAACGGTGAGAATTGCCA	57.587	47.368	7.88	0.00	0.00	4.92
19	20	1.909700	ACAACGGTGAGAATTGCCAT	58.090	45.000	7.88	0.00	0.00	4.40
20	21	1.541147	ACAACGGTGAGAATTGCCATG	59.459	47.619	7.88	0.00	0.00	3.66
21	22	0.527565	AACGGTGAGAATTGCCATGC	59.472	50.000	0.00	0.00	0.00	4.06
22	23	0.322816	ACGGTGAGAATTGCCATGCT	60.323	50.000	0.00	0.00	0.00	3.79
23	24	1.065491	ACGGTGAGAATTGCCATGCTA	60.065	47.619	0.00	0.00	0.00	3.49
24	25	2.224606	CGGTGAGAATTGCCATGCTAT	58.775	47.619	0.00	0.00	0.00	2.97
25	26	3.181455	ACGGTGAGAATTGCCATGCTATA	60.181	43.478	0.00	0.00	0.00	1.31
26	27	3.434641	CGGTGAGAATTGCCATGCTATAG	59.565	47.826	0.00	0.00	0.00	1.31
27	28	4.392940	GGTGAGAATTGCCATGCTATAGT	58.607	43.478	0.84	0.00	0.00	2.12
28	29	5.551233	GGTGAGAATTGCCATGCTATAGTA	58.449	41.667	0.84	0.00	0.00	1.82
29	30	5.997746	GGTGAGAATTGCCATGCTATAGTAA	59.002	40.000	0.84	0.00	0.00	2.24
30	31	6.148480	GGTGAGAATTGCCATGCTATAGTAAG	59.852	42.308	0.84	0.00	0.00	2.34
31	32	6.931281	GTGAGAATTGCCATGCTATAGTAAGA	59.069	38.462	0.84	0.00	0.00	2.10
32	33	7.442364	GTGAGAATTGCCATGCTATAGTAAGAA	59.558	37.037	0.84	0.00	0.00	2.52
33	34	7.992608	TGAGAATTGCCATGCTATAGTAAGAAA	59.007	33.333	0.84	0.00	0.00	2.52
34	35	8.159344	AGAATTGCCATGCTATAGTAAGAAAC	57.841	34.615	0.84	0.00	0.00	2.78
35	36	7.995488	AGAATTGCCATGCTATAGTAAGAAACT	59.005	33.333	0.84	0.00	42.62	2.66
36	37	8.525290	AATTGCCATGCTATAGTAAGAAACTT	57.475	30.769	0.84	0.00	39.80	2.66
37	38	7.938140	TTGCCATGCTATAGTAAGAAACTTT	57.062	32.000	0.84	0.00	39.80	2.66
38	39	7.553881	TGCCATGCTATAGTAAGAAACTTTC	57.446	36.000	0.84	0.00	39.80	2.62
39	40	7.109501	TGCCATGCTATAGTAAGAAACTTTCA	58.890	34.615	0.84	0.00	39.80	2.69
40	41	7.775093	TGCCATGCTATAGTAAGAAACTTTCAT	59.225	33.333	0.84	0.00	39.80	2.57
41	42	9.273016	GCCATGCTATAGTAAGAAACTTTCATA	57.727	33.333	0.84	0.00	39.80	2.15
45	46	9.314321	TGCTATAGTAAGAAACTTTCATACTGC	57.686	33.333	21.67	17.95	42.29	4.40

Showing 1 to 25 of 470 entries

Previous1 2 3 4 5…19Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.541147	CATGGCAATTCTCACCGTTGT	59.459	47.619	0.00	0.00	0.00	3.32
1	2	1.733389	GCATGGCAATTCTCACCGTTG	60.733	52.381	0.00	0.00	0.00	4.10
2	3	0.527565	GCATGGCAATTCTCACCGTT	59.472	50.000	0.00	0.00	0.00	4.44
3	4	0.322816	AGCATGGCAATTCTCACCGT	60.323	50.000	0.00	0.00	0.00	4.83
4	5	1.667236	TAGCATGGCAATTCTCACCG	58.333	50.000	0.00	0.00	0.00	4.94
5	6	4.392940	ACTATAGCATGGCAATTCTCACC	58.607	43.478	0.00	0.00	0.00	4.02
6	7	6.931281	TCTTACTATAGCATGGCAATTCTCAC	59.069	38.462	0.00	0.00	0.00	3.51
7	8	7.066307	TCTTACTATAGCATGGCAATTCTCA	57.934	36.000	0.00	0.00	0.00	3.27
8	9	7.969536	TTCTTACTATAGCATGGCAATTCTC	57.030	36.000	0.00	0.00	0.00	2.87
9	10	7.995488	AGTTTCTTACTATAGCATGGCAATTCT	59.005	33.333	0.00	0.00	34.56	2.40
10	11	8.159344	AGTTTCTTACTATAGCATGGCAATTC	57.841	34.615	0.00	0.00	34.56	2.17
11	12	8.525290	AAGTTTCTTACTATAGCATGGCAATT	57.475	30.769	0.00	0.00	35.54	2.32
12	13	8.525290	AAAGTTTCTTACTATAGCATGGCAAT	57.475	30.769	0.00	0.00	35.54	3.56
13	14	7.609918	TGAAAGTTTCTTACTATAGCATGGCAA	59.390	33.333	16.33	0.00	35.54	4.52
14	15	7.109501	TGAAAGTTTCTTACTATAGCATGGCA	58.890	34.615	16.33	0.00	35.54	4.92
15	16	7.553881	TGAAAGTTTCTTACTATAGCATGGC	57.446	36.000	16.33	0.00	35.54	4.40
19	20	9.314321	GCAGTATGAAAGTTTCTTACTATAGCA	57.686	33.333	29.47	6.37	44.21	3.49
20	21	9.314321	TGCAGTATGAAAGTTTCTTACTATAGC	57.686	33.333	29.47	27.60	44.21	2.97
23	24	9.502091	TGTTGCAGTATGAAAGTTTCTTACTAT	57.498	29.630	29.47	15.86	44.21	2.12
24	25	8.896320	TGTTGCAGTATGAAAGTTTCTTACTA	57.104	30.769	29.47	19.41	44.21	1.82
25	26	7.801716	TGTTGCAGTATGAAAGTTTCTTACT	57.198	32.000	26.70	26.70	45.83	2.24
26	27	7.913297	TGTTGTTGCAGTATGAAAGTTTCTTAC	59.087	33.333	24.11	24.11	31.26	2.34
27	28	7.990917	TGTTGTTGCAGTATGAAAGTTTCTTA	58.009	30.769	16.33	11.45	31.26	2.10
28	29	6.862209	TGTTGTTGCAGTATGAAAGTTTCTT	58.138	32.000	16.33	12.42	31.26	2.52
29	30	6.318648	TCTGTTGTTGCAGTATGAAAGTTTCT	59.681	34.615	16.33	5.22	31.26	2.52

Showing 1 to 25 of 486 entries

Previous1 2 3 4 5…20Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.