AutoCloner

Multiple sequence alignment - TraesCS3B01G462000

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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	TraesCS3B01G462000	chr3B	100.000	6446	0	0	1	6446	705134861	705141306	0.000000e+00	11904.0
1	TraesCS3B01G462000	chr3B	87.356	348	39	4	177	522	705033505	705033849	1.680000e-105	394.0
2	TraesCS3B01G462000	chr3B	84.814	349	45	6	3461	3801	821888038	821888386	1.720000e-90	344.0
3	TraesCS3B01G462000	chr3B	81.098	164	28	3	148	310	178540632	178540793	1.890000e-25	128.0
4	TraesCS3B01G462000	chr3B	94.667	75	4	0	1785	1859	705136582	705136656	4.080000e-22	117.0
5	TraesCS3B01G462000	chr3B	94.667	75	4	0	1722	1796	705136645	705136719	4.080000e-22	117.0
6	TraesCS3B01G462000	chr3B	92.500	40	1	1	1796	1835	4524672	4524709	1.000000e-03	56.5
7	TraesCS3B01G462000	chr3A	89.261	1760	142	26	4137	5875	668553022	668554755	0.000000e+00	2159.0
8	TraesCS3B01G462000	chr3A	90.654	1605	98	17	107	1701	668550232	668551794	0.000000e+00	2085.0
9	TraesCS3B01G462000	chr3A	90.877	1129	85	8	4827	5941	668212831	668213955	0.000000e+00	1498.0
10	TraesCS3B01G462000	chr3A	85.560	464	47	7	338	798	668067621	668068067	9.790000e-128	468.0
11	TraesCS3B01G462000	chr3A	88.372	387	34	5	441	826	668210796	668211172	7.620000e-124	455.0
12	TraesCS3B01G462000	chr3A	90.000	360	25	7	1621	1974	668551796	668552150	7.620000e-124	455.0
13	TraesCS3B01G462000	chr3A	85.301	415	49	5	4827	5233	668206034	668206444	1.000000e-112	418.0
14	TraesCS3B01G462000	chr3A	82.341	487	67	13	5968	6445	496031946	496031470	7.780000e-109	405.0
15	TraesCS3B01G462000	chr3A	84.971	346	49	2	3459	3801	730801757	730802102	1.330000e-91	348.0
16	TraesCS3B01G462000	chr3A	84.419	353	46	5	998	1343	668211339	668211689	8.010000e-89	339.0
17	TraesCS3B01G462000	chr3A	83.377	379	40	6	449	826	668090158	668090514	4.820000e-86	329.0
18	TraesCS3B01G462000	chr3A	87.547	265	23	7	1360	1617	668211675	668211936	1.360000e-76	298.0
19	TraesCS3B01G462000	chr3A	86.192	239	21	4	107	343	668023414	668023642	1.390000e-61	248.0
20	TraesCS3B01G462000	chr3A	84.043	188	30	0	5086	5273	667951065	667951252	1.430000e-41	182.0
21	TraesCS3B01G462000	chr3A	94.068	118	4	3	6	122	171016272	171016157	6.640000e-40	176.0
22	TraesCS3B01G462000	chr3D	91.248	1154	80	8	4790	5941	532856744	532857878	0.000000e+00	1552.0
23	TraesCS3B01G462000	chr3D	91.610	1037	65	12	320	1343	532854603	532855630	0.000000e+00	1413.0
24	TraesCS3B01G462000	chr3D	88.166	338	24	5	1975	2301	558269744	558269412	7.840000e-104	388.0
25	TraesCS3B01G462000	chr3D	86.707	331	32	10	1360	1687	532855616	532855937	2.210000e-94	357.0
26	TraesCS3B01G462000	chr3D	91.045	201	15	2	138	336	532854388	532854587	1.070000e-67	268.0
27	TraesCS3B01G462000	chr3D	86.100	259	22	3	1975	2224	37370364	37370617	3.830000e-67	267.0
28	TraesCS3B01G462000	chr3D	90.769	195	15	2	3790	3981	557630875	557631069	2.310000e-64	257.0
29	TraesCS3B01G462000	chr3D	84.043	188	30	0	5086	5273	532777309	532777496	1.430000e-41	182.0
30	TraesCS3B01G462000	chr3D	85.542	83	9	2	4650	4732	532856575	532856654	4.140000e-12	84.2
31	TraesCS3B01G462000	chr7D	91.710	953	59	10	2363	3314	569578533	569577600	0.000000e+00	1304.0
32	TraesCS3B01G462000	chr7D	88.316	291	17	6	3745	4020	40197551	40197839	3.720000e-87	333.0
33	TraesCS3B01G462000	chr7D	92.746	193	13	1	3790	3981	565058459	565058651	1.770000e-70	278.0
34	TraesCS3B01G462000	chr7D	88.053	226	20	2	2001	2224	565058187	565058407	1.780000e-65	261.0
35	TraesCS3B01G462000	chr7D	94.737	114	6	0	1	114	24542463	24542350	1.850000e-40	178.0
36	TraesCS3B01G462000	chr7D	94.017	117	5	1	3310	3424	569577554	569577438	6.640000e-40	176.0
37	TraesCS3B01G462000	chr6B	90.282	957	65	12	2363	3314	706068113	706069046	0.000000e+00	1227.0
38	TraesCS3B01G462000	chr6B	88.270	341	37	1	3461	3801	685253993	685254330	7.780000e-109	405.0
39	TraesCS3B01G462000	chr6D	84.708	497	54	16	5968	6445	177797215	177796722	1.630000e-130	477.0
40	TraesCS3B01G462000	chr6D	85.837	233	18	3	3803	4020	468580890	468581122	3.890000e-57	233.0
41	TraesCS3B01G462000	chr5D	84.454	476	50	14	5973	6439	6527630	6527170	1.270000e-121	448.0
42	TraesCS3B01G462000	chr5D	90.295	237	10	2	3797	4020	533607809	533607573	1.360000e-76	298.0
43	TraesCS3B01G462000	chr2D	83.265	490	55	18	5978	6445	399345379	399345863	5.970000e-115	425.0
44	TraesCS3B01G462000	chr2D	89.752	322	25	3	2001	2320	7218008	7217693	7.780000e-109	405.0
45	TraesCS3B01G462000	chr1D	82.992	488	63	12	5968	6445	163409676	163410153	2.150000e-114	424.0
46	TraesCS3B01G462000	chr1D	93.173	249	9	5	2363	2611	478742722	478742962	6.150000e-95	359.0
47	TraesCS3B01G462000	chr1D	86.667	285	21	5	3757	4027	40933037	40932756	3.780000e-77	300.0
48	TraesCS3B01G462000	chr5B	82.887	485	63	13	5970	6445	524327601	524327128	1.000000e-112	418.0
49	TraesCS3B01G462000	chr5B	86.455	347	37	6	3464	3801	192661304	192660959	7.890000e-99	372.0
50	TraesCS3B01G462000	chr5B	85.801	331	32	7	2001	2322	140959480	140959156	2.880000e-88	337.0
51	TraesCS3B01G462000	chr4D	83.090	479	59	14	5976	6445	51849462	51848997	3.600000e-112	416.0
52	TraesCS3B01G462000	chr1B	81.928	498	65	17	5968	6445	636471043	636471535	1.300000e-106	398.0
53	TraesCS3B01G462000	chr1B	86.040	351	39	3	3461	3801	48850898	48851248	1.020000e-97	368.0
54	TraesCS3B01G462000	chr1A	82.402	483	59	18	5977	6445	105915691	105915221	1.300000e-106	398.0
55	TraesCS3B01G462000	chr1A	85.303	347	42	3	3464	3801	258200831	258200485	3.700000e-92	350.0
56	TraesCS3B01G462000	chr5A	87.390	341	42	1	3461	3801	609404296	609403957	2.180000e-104	390.0
57	TraesCS3B01G462000	chr5A	97.196	107	2	1	6	112	302275437	302275542	5.130000e-41	180.0
58	TraesCS3B01G462000	chr5A	95.575	113	2	3	6	118	328284535	328284426	1.850000e-40	178.0
59	TraesCS3B01G462000	chr6A	88.704	301	22	7	2002	2300	596781534	596781824	2.210000e-94	357.0
60	TraesCS3B01G462000	chr6A	88.655	238	14	3	3796	4020	596781867	596782104	1.770000e-70	278.0
61	TraesCS3B01G462000	chr6A	86.740	181	17	2	3803	3981	592453285	592453110	1.830000e-45	195.0
62	TraesCS3B01G462000	chr6A	98.095	105	2	0	6	110	114043749	114043853	3.970000e-42	183.0
63	TraesCS3B01G462000	chr7B	84.000	375	33	14	1962	2317	685995291	685995657	1.040000e-87	335.0
64	TraesCS3B01G462000	chr7B	84.571	350	33	11	3464	3801	122318440	122318100	1.730000e-85	327.0
65	TraesCS3B01G462000	chr7B	83.747	363	35	12	2001	2356	269801832	269802177	8.060000e-84	322.0
66	TraesCS3B01G462000	chr4A	86.928	306	30	3	3505	3801	735993228	735992924	1.040000e-87	335.0
67	TraesCS3B01G462000	chr7A	88.672	256	23	2	2001	2255	17715469	17715719	2.260000e-79	307.0
68	TraesCS3B01G462000	chr7A	83.051	354	27	9	2001	2349	682260145	682259820	2.270000e-74	291.0
69	TraesCS3B01G462000	chr7A	79.325	237	42	6	3025	3256	497738626	497738392	6.690000e-35	159.0
70	TraesCS3B01G462000	chr2A	84.483	290	30	5	1971	2251	736459846	736460129	8.240000e-69	272.0
71	TraesCS3B01G462000	chr2B	98.113	106	2	0	1	106	490904683	490904578	1.100000e-42	185.0
72	TraesCS3B01G462000	chr2B	96.429	112	2	2	2	111	582572429	582572540	3.970000e-42	183.0
73	TraesCS3B01G462000	chr4B	97.196	107	3	0	1	107	145998424	145998530	1.430000e-41	182.0
74	TraesCS3B01G462000	chr4B	97.222	108	1	1	1	108	166792375	166792270	1.430000e-41	182.0

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	TraesCS3B01G462000	chr3B	705134861	705141306	6445	False	11904.000000	11904	100.000000	1	6446	1	chr3B.!!$F4	6445
1	TraesCS3B01G462000	chr3A	668550232	668554755	4523	False	1566.333333	2159	89.971667	107	5875	3	chr3A.!!$F8	5768
2	TraesCS3B01G462000	chr3A	668210796	668213955	3159	False	647.500000	1498	87.803750	441	5941	4	chr3A.!!$F7	5500
3	TraesCS3B01G462000	chr3D	532854388	532857878	3490	False	734.840000	1552	89.230400	138	5941	5	chr3D.!!$F4	5803
4	TraesCS3B01G462000	chr7D	569577438	569578533	1095	True	740.000000	1304	92.863500	2363	3424	2	chr7D.!!$R2	1061
5	TraesCS3B01G462000	chr6B	706068113	706069046	933	False	1227.000000	1227	90.282000	2363	3314	1	chr6B.!!$F2	951
6	TraesCS3B01G462000	chr6A	596781534	596782104	570	False	317.500000	357	88.679500	2002	4020	2	chr6A.!!$F2	2018

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
810	857	0.318441	GTATGAGCTGGCTATGCGGA	59.682	55.0	0.00	0.00	35.28	5.54	F
1710	1903	0.035439	AGGAATAAGCCACCGTGGTG	60.035	55.0	18.95	12.17	45.02	4.17	F
3147	3350	0.035152	ACTCCGGATGAGCAATGCAA	60.035	50.0	3.57	0.00	45.61	4.08	F
3506	3762	0.036388	TCTTGCAAGATCCACCGACC	60.036	55.0	25.16	0.00	0.00	4.79	F
3998	4267	0.039618	GGAAGGCAAGACCCAATGGA	59.960	55.0	0.00	0.00	40.58	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2240	2439	0.179001	AGGGGTTGGTTTGACCTTCG	60.179	55.0	0.00	0.00	39.58	3.79	R
3487	3743	0.036388	GGTCGGTGGATCTTGCAAGA	60.036	55.0	30.23	30.23	39.78	3.02	R
4985	6462	0.039708	GCTGAAGTCCAGTTTGCAGC	60.040	55.0	0.00	0.00	44.71	5.25	R
5194	6682	0.179936	GTTCTGAGCCTGGATGGAGG	59.820	60.0	0.00	0.00	38.35	4.30	R
5956	7452	0.323725	AGCGGACAAGGGATTGCAAT	60.324	50.0	12.83	12.83	0.00	3.56	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
25	26	8.865590	GTTGTTAAAATCTGCCAAGAACTAAA	57.134	30.769	0.00	0.00	35.59	1.85
26	27	9.308318	GTTGTTAAAATCTGCCAAGAACTAAAA	57.692	29.630	0.00	0.00	35.59	1.52
30	31	7.967890	AAAATCTGCCAAGAACTAAAATTGG	57.032	32.000	0.00	0.00	45.16	3.16
31	32	5.665916	ATCTGCCAAGAACTAAAATTGGG	57.334	39.130	5.43	0.00	43.06	4.12
32	33	4.735369	TCTGCCAAGAACTAAAATTGGGA	58.265	39.130	5.43	1.58	43.06	4.37
33	34	5.144100	TCTGCCAAGAACTAAAATTGGGAA	58.856	37.500	5.43	0.00	42.82	3.97
34	35	5.600484	TCTGCCAAGAACTAAAATTGGGAAA	59.400	36.000	5.43	0.00	42.82	3.13
35	36	6.098982	TCTGCCAAGAACTAAAATTGGGAAAA	59.901	34.615	5.43	0.00	42.82	2.29
36	37	6.287525	TGCCAAGAACTAAAATTGGGAAAAG	58.712	36.000	5.43	0.00	40.87	2.27
37	38	5.700832	GCCAAGAACTAAAATTGGGAAAAGG	59.299	40.000	5.43	0.00	43.06	3.11
38	39	6.687901	GCCAAGAACTAAAATTGGGAAAAGGT	60.688	38.462	5.43	0.00	43.06	3.50
39	40	7.279615	CCAAGAACTAAAATTGGGAAAAGGTT	58.720	34.615	0.00	0.00	39.87	3.50
40	41	8.425703	CCAAGAACTAAAATTGGGAAAAGGTTA	58.574	33.333	0.00	0.00	39.87	2.85
41	42	9.825109	CAAGAACTAAAATTGGGAAAAGGTTAA	57.175	29.630	0.00	0.00	0.00	2.01
43	44	9.209048	AGAACTAAAATTGGGAAAAGGTTAAGT	57.791	29.630	0.00	0.00	0.00	2.24
44	45	9.826574	GAACTAAAATTGGGAAAAGGTTAAGTT	57.173	29.630	0.00	0.00	0.00	2.66
53	54	8.966069	TGGGAAAAGGTTAAGTTTTTATTTGG	57.034	30.769	0.00	0.00	0.00	3.28
54	55	8.549731	TGGGAAAAGGTTAAGTTTTTATTTGGT	58.450	29.630	0.00	0.00	0.00	3.67
55	56	9.048446	GGGAAAAGGTTAAGTTTTTATTTGGTC	57.952	33.333	0.00	0.00	0.00	4.02
56	57	9.602568	GGAAAAGGTTAAGTTTTTATTTGGTCA	57.397	29.630	0.00	0.00	0.00	4.02
71	72	9.444600	TTTATTTGGTCAAGTAGTCTAATCACC	57.555	33.333	2.72	2.72	0.00	4.02
72	73	5.416271	TTGGTCAAGTAGTCTAATCACCC	57.584	43.478	6.13	0.00	0.00	4.61
73	74	3.773119	TGGTCAAGTAGTCTAATCACCCC	59.227	47.826	6.13	0.00	0.00	4.95
74	75	3.134262	GGTCAAGTAGTCTAATCACCCCC	59.866	52.174	0.00	0.00	0.00	5.40
98	99	3.563223	CCCCCTCTAGACATACTTTCGA	58.437	50.000	0.00	0.00	0.00	3.71

Showing 1 to 25 of 917 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	8.865590	TTTAGTTCTTGGCAGATTTTAACAAC	57.134	30.769	0.00	3.32
4	5	9.487790	CCAATTTTAGTTCTTGGCAGATTTTAA	57.512	29.630	33.59	1.52
5	6	8.093927	CCCAATTTTAGTTCTTGGCAGATTTTA	58.906	33.333	38.47	1.52
6	7	6.936335	CCCAATTTTAGTTCTTGGCAGATTTT	59.064	34.615	38.47	1.82
7	8	6.269769	TCCCAATTTTAGTTCTTGGCAGATTT	59.730	34.615	38.47	2.17
8	9	5.779771	TCCCAATTTTAGTTCTTGGCAGATT	59.220	36.000	38.47	2.40
9	10	5.332743	TCCCAATTTTAGTTCTTGGCAGAT	58.667	37.500	38.47	2.90
10	11	4.735369	TCCCAATTTTAGTTCTTGGCAGA	58.265	39.130	38.47	4.26
11	12	5.467035	TTCCCAATTTTAGTTCTTGGCAG	57.533	39.130	38.47	4.85
12	13	5.878406	TTTCCCAATTTTAGTTCTTGGCA	57.122	34.783	38.47	4.92
13	14	5.700832	CCTTTTCCCAATTTTAGTTCTTGGC	59.299	40.000	38.47	4.52
14	15	6.826668	ACCTTTTCCCAATTTTAGTTCTTGG	58.173	36.000	39.31	3.61
15	16	9.825109	TTAACCTTTTCCCAATTTTAGTTCTTG	57.175	29.630	0.00	3.02
17	18	9.209048	ACTTAACCTTTTCCCAATTTTAGTTCT	57.791	29.630	0.00	3.01
18	19	9.826574	AACTTAACCTTTTCCCAATTTTAGTTC	57.173	29.630	0.00	3.01
27	28	9.397280	CCAAATAAAAACTTAACCTTTTCCCAA	57.603	29.630	0.00	4.12
28	29	8.549731	ACCAAATAAAAACTTAACCTTTTCCCA	58.450	29.630	0.00	4.37
29	30	8.967664	ACCAAATAAAAACTTAACCTTTTCCC	57.032	30.769	0.00	3.97
30	31	9.602568	TGACCAAATAAAAACTTAACCTTTTCC	57.397	29.630	0.00	3.13
45	46	9.444600	GGTGATTAGACTACTTGACCAAATAAA	57.555	33.333	0.00	1.40
46	47	8.044908	GGGTGATTAGACTACTTGACCAAATAA	58.955	37.037	0.00	1.40
47	48	7.365295	GGGGTGATTAGACTACTTGACCAAATA	60.365	40.741	0.00	1.40
48	49	6.415573	GGGTGATTAGACTACTTGACCAAAT	58.584	40.000	0.00	2.32
49	50	5.280317	GGGGTGATTAGACTACTTGACCAAA	60.280	44.000	0.00	3.28
50	51	4.224370	GGGGTGATTAGACTACTTGACCAA	59.776	45.833	0.00	3.67

Showing 1 to 25 of 862 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.