AutoCloner

Multiple sequence alignment - TraesCS4B01G330600

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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	TraesCS4B01G330600	chr4B	100.000	4233	0	0	1	4233	621666260	621670492	0.000000e+00	7817.0
1	TraesCS4B01G330600	chr4B	92.075	265	17	4	1510	1772	453764832	453764570	1.860000e-98	370.0
2	TraesCS4B01G330600	chr4B	95.000	40	0	2	92	131	25264356	25264393	1.270000e-05	62.1
3	TraesCS4B01G330600	chr5A	90.053	1709	140	20	1810	3495	667127913	667126212	0.000000e+00	2187.0
4	TraesCS4B01G330600	chr5A	90.189	1060	51	19	462	1512	667128930	667127915	0.000000e+00	1332.0
5	TraesCS4B01G330600	chr5A	86.258	946	124	4	2297	3237	524408603	524409547	0.000000e+00	1022.0
6	TraesCS4B01G330600	chr5A	84.830	1002	144	7	2259	3255	524403135	524404133	0.000000e+00	1002.0
7	TraesCS4B01G330600	chr5A	88.514	444	49	2	999	1441	524406889	524407331	1.730000e-148	536.0
8	TraesCS4B01G330600	chr5A	86.577	447	58	2	996	1441	524402270	524402715	3.800000e-135	492.0
9	TraesCS4B01G330600	chr5A	91.284	218	15	3	192	406	667129461	667129245	1.150000e-75	294.0
10	TraesCS4B01G330600	chr5A	95.455	66	3	0	405	470	667129205	667129140	5.790000e-19	106.0
11	TraesCS4B01G330600	chr5A	88.060	67	8	0	138	204	556685577	556685643	3.510000e-11	80.5
12	TraesCS4B01G330600	chr4D	95.485	1196	48	4	2306	3495	486911476	486910281	0.000000e+00	1905.0
13	TraesCS4B01G330600	chr4D	92.802	1028	41	13	427	1445	486913099	486912096	0.000000e+00	1458.0
14	TraesCS4B01G330600	chr4D	85.238	420	47	8	1799	2205	486911992	486911575	6.550000e-113	418.0
15	TraesCS4B01G330600	chr4D	100.000	51	0	0	3594	3644	486910096	486910046	1.250000e-15	95.3
16	TraesCS4B01G330600	chr4D	94.444	36	1	1	103	138	6170555	6170589	2.000000e-03	54.7
17	TraesCS4B01G330600	chr5D	85.832	967	135	2	2271	3235	412459676	412460642	0.000000e+00	1026.0
18	TraesCS4B01G330600	chr5D	83.626	1081	158	13	2270	3335	412465971	412467047	0.000000e+00	998.0
19	TraesCS4B01G330600	chr5D	86.313	811	100	8	2274	3075	412471326	412472134	0.000000e+00	872.0
20	TraesCS4B01G330600	chr5D	87.919	447	52	2	996	1441	412458784	412459229	3.750000e-145	525.0
21	TraesCS4B01G330600	chr5D	87.838	444	52	2	999	1441	412464918	412465360	1.740000e-143	520.0
22	TraesCS4B01G330600	chr5D	86.547	446	56	3	999	1440	412469295	412469740	4.920000e-134	488.0
23	TraesCS4B01G330600	chr5D	96.721	61	2	0	3015	3075	412584238	412584298	7.490000e-18	102.0
24	TraesCS4B01G330600	chr5B	85.862	969	131	6	2271	3235	496817479	496818445	0.000000e+00	1026.0
25	TraesCS4B01G330600	chr5B	83.859	1078	155	12	2270	3335	496829298	496830368	0.000000e+00	1009.0
26	TraesCS4B01G330600	chr5B	87.838	444	52	2	999	1441	496828241	496828683	1.740000e-143	520.0
27	TraesCS4B01G330600	chr5B	87.472	447	54	2	996	1441	496816597	496817042	8.120000e-142	514.0
28	TraesCS4B01G330600	chr5B	86.981	361	45	2	2304	2663	496959950	496960309	5.100000e-109	405.0
29	TraesCS4B01G330600	chr5B	88.710	62	4	2	136	195	702626034	702625974	5.870000e-09	73.1
30	TraesCS4B01G330600	chr5B	88.710	62	4	2	136	195	702758274	702758214	5.870000e-09	73.1
31	TraesCS4B01G330600	chr5B	94.286	35	1	1	104	138	28479799	28479766	8.000000e-03	52.8
32	TraesCS4B01G330600	chr5B	100.000	28	0	0	105	132	594925360	594925387	8.000000e-03	52.8
33	TraesCS4B01G330600	chr6D	92.803	264	17	2	1510	1771	24007135	24007398	8.590000e-102	381.0
34	TraesCS4B01G330600	chr6D	92.188	64	5	0	136	199	454824161	454824224	1.620000e-14	91.6
35	TraesCS4B01G330600	chr3B	91.729	266	18	4	1510	1772	590629000	590629264	2.400000e-97	366.0
36	TraesCS4B01G330600	chr3B	93.370	181	10	2	4054	4233	494713509	494713330	2.510000e-67	267.0
37	TraesCS4B01G330600	chr3B	87.013	77	7	3	136	211	473860766	473860692	2.710000e-12	84.2
38	TraesCS4B01G330600	chr3B	88.235	68	5	2	136	201	4226189	4226123	1.260000e-10	78.7
39	TraesCS4B01G330600	chr3B	97.222	36	0	1	96	131	45447523	45447557	4.570000e-05	60.2
40	TraesCS4B01G330600	chr3B	94.118	34	2	0	104	137	733895154	733895121	8.000000e-03	52.8
41	TraesCS4B01G330600	chr6B	90.357	280	24	3	1505	1781	131732035	131732314	8.650000e-97	364.0
42	TraesCS4B01G330600	chr6B	87.879	66	8	0	138	203	117589798	117589863	1.260000e-10	78.7
43	TraesCS4B01G330600	chr6B	91.111	45	2	2	65	108	499006818	499006775	4.570000e-05	60.2
44	TraesCS4B01G330600	chr7D	91.667	264	19	3	1510	1770	18847292	18847555	3.110000e-96	363.0
45	TraesCS4B01G330600	chr7D	91.011	89	7	1	3969	4057	69205586	69205499	7.440000e-23	119.0
46	TraesCS4B01G330600	chr1B	91.011	267	21	3	1509	1773	240431424	240431159	1.450000e-94	357.0
47	TraesCS4B01G330600	chr1B	92.982	57	3	1	140	196	373606262	373606317	9.750000e-12	82.4
48	TraesCS4B01G330600	chr1B	89.796	49	3	2	85	131	492367925	492367973	1.270000e-05	62.1
49	TraesCS4B01G330600	chr1B	94.118	34	2	0	104	137	596886824	596886791	8.000000e-03	52.8
50	TraesCS4B01G330600	chr7B	90.909	264	22	2	1510	1771	544466689	544466426	1.870000e-93	353.0
51	TraesCS4B01G330600	chr7B	94.872	39	2	0	93	131	293170297	293170335	1.270000e-05	62.1
52	TraesCS4B01G330600	chr7B	94.286	35	1	1	103	137	85140222	85140189	8.000000e-03	52.8
53	TraesCS4B01G330600	chr2B	90.943	265	21	3	1503	1765	3922438	3922701	1.870000e-93	353.0
54	TraesCS4B01G330600	chr2B	90.943	265	21	3	1503	1765	4192172	4192435	1.870000e-93	353.0
55	TraesCS4B01G330600	chr2B	88.557	201	22	1	3857	4057	235071407	235071606	4.230000e-60	243.0
56	TraesCS4B01G330600	chr2B	82.803	157	23	4	3899	4053	186383238	186383084	2.050000e-28	137.0
57	TraesCS4B01G330600	chr2B	90.698	43	1	2	89	131	681216903	681216942	2.000000e-03	54.7
58	TraesCS4B01G330600	chr2D	86.740	181	21	3	3878	4057	611890541	611890719	9.280000e-47	198.0
59	TraesCS4B01G330600	chr2D	88.235	68	4	3	136	201	612994339	612994404	1.260000e-10	78.7
60	TraesCS4B01G330600	chr2D	86.154	65	5	3	132	194	296162004	296161942	2.730000e-07	67.6
61	TraesCS4B01G330600	chr2D	100.000	29	0	0	104	132	441766357	441766329	2.000000e-03	54.7
62	TraesCS4B01G330600	chr2A	84.091	176	28	0	4054	4229	726166469	726166294	2.020000e-38	171.0
63	TraesCS4B01G330600	chr2A	100.000	29	0	0	103	131	31440141	31440113	2.000000e-03	54.7
64	TraesCS4B01G330600	chr3D	81.765	170	28	3	3886	4053	266397291	266397123	5.710000e-29	139.0
65	TraesCS4B01G330600	chr3A	81.176	170	29	3	3886	4053	114562136	114561968	2.660000e-27	134.0
66	TraesCS4B01G330600	chr1A	90.476	63	6	0	136	198	5198021	5198083	2.710000e-12	84.2
67	TraesCS4B01G330600	chr1A	100.000	28	0	0	104	131	385024648	385024675	8.000000e-03	52.8
68	TraesCS4B01G330600	chr4A	89.062	64	7	0	139	202	636312721	636312784	3.510000e-11	80.5
69	TraesCS4B01G330600	chr7A	97.368	38	1	0	94	131	320981160	320981197	9.820000e-07	65.8
70	TraesCS4B01G330600	chr7A	89.130	46	3	2	83	128	521817685	521817728	5.910000e-04	56.5

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	TraesCS4B01G330600	chr4B	621666260	621670492	4232	False	7817.000	7817	100.00000	1	4233	1	chr4B.!!$F2	4232
1	TraesCS4B01G330600	chr5A	667126212	667129461	3249	True	979.750	2187	91.74525	192	3495	4	chr5A.!!$R1	3303
2	TraesCS4B01G330600	chr5A	524402270	524409547	7277	False	763.000	1022	86.54475	996	3255	4	chr5A.!!$F2	2259
3	TraesCS4B01G330600	chr4D	486910046	486913099	3053	True	969.075	1905	93.38125	427	3644	4	chr4D.!!$R1	3217
4	TraesCS4B01G330600	chr5D	412458784	412460642	1858	False	775.500	1026	86.87550	996	3235	2	chr5D.!!$F2	2239
5	TraesCS4B01G330600	chr5D	412464918	412472134	7216	False	719.500	998	86.08100	999	3335	4	chr5D.!!$F3	2336
6	TraesCS4B01G330600	chr5B	496816597	496818445	1848	False	770.000	1026	86.66700	996	3235	2	chr5B.!!$F3	2239
7	TraesCS4B01G330600	chr5B	496828241	496830368	2127	False	764.500	1009	85.84850	999	3335	2	chr5B.!!$F4	2336

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
798	1067	0.246635	CCAACTCTTCCGTCCGTCAT	59.753	55.0	0.00	0.0	0.00	3.06	F
930	1199	0.898789	AGCAAGCAAGCAAGCCATCT	60.899	50.0	3.19	0.0	36.85	2.90	F
2560	8588	0.887836	AGTGCACAGGAGACGACGTA	60.888	55.0	21.04	0.0	0.00	3.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2560	8588	0.532862	CCGGCGGAGTTGATAGCATT	60.533	55.000	24.41	0.0	0.00	3.56	R
2689	8717	2.359107	CACCGCCACATGACAGCT	60.359	61.111	0.00	0.0	0.00	4.24	R
4038	14343	0.031857	CTCCAACATGCCGTGCAAAA	59.968	50.000	2.68	0.0	43.62	2.44	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
116	117	9.021807	TCAATATTTAAGATACTACTCCCTCCG	57.978	37.037	0.00	0.00	0.00	4.63
117	118	8.804204	CAATATTTAAGATACTACTCCCTCCGT	58.196	37.037	0.00	0.00	0.00	4.69
118	119	8.953223	ATATTTAAGATACTACTCCCTCCGTT	57.047	34.615	0.00	0.00	0.00	4.44
119	120	6.705863	TTTAAGATACTACTCCCTCCGTTC	57.294	41.667	0.00	0.00	0.00	3.95
120	121	3.226682	AGATACTACTCCCTCCGTTCC	57.773	52.381	0.00	0.00	0.00	3.62
121	122	2.784682	AGATACTACTCCCTCCGTTCCT	59.215	50.000	0.00	0.00	0.00	3.36
122	123	3.979347	AGATACTACTCCCTCCGTTCCTA	59.021	47.826	0.00	0.00	0.00	2.94
123	124	4.414846	AGATACTACTCCCTCCGTTCCTAA	59.585	45.833	0.00	0.00	0.00	2.69
124	125	3.463048	ACTACTCCCTCCGTTCCTAAA	57.537	47.619	0.00	0.00	0.00	1.85
125	126	3.991683	ACTACTCCCTCCGTTCCTAAAT	58.008	45.455	0.00	0.00	0.00	1.40
126	127	5.134725	ACTACTCCCTCCGTTCCTAAATA	57.865	43.478	0.00	0.00	0.00	1.40
127	128	5.713807	ACTACTCCCTCCGTTCCTAAATAT	58.286	41.667	0.00	0.00	0.00	1.28
128	129	6.141790	ACTACTCCCTCCGTTCCTAAATATT	58.858	40.000	0.00	0.00	0.00	1.28
129	130	5.970501	ACTCCCTCCGTTCCTAAATATTT	57.029	39.130	5.89	5.89	0.00	1.40
130	131	5.681639	ACTCCCTCCGTTCCTAAATATTTG	58.318	41.667	11.05	1.40	0.00	2.32
131	132	5.427481	ACTCCCTCCGTTCCTAAATATTTGA	59.573	40.000	11.05	0.00	0.00	2.69
132	133	6.069847	ACTCCCTCCGTTCCTAAATATTTGAA	60.070	38.462	11.05	4.12	0.00	2.69
133	134	6.723339	TCCCTCCGTTCCTAAATATTTGAAA	58.277	36.000	11.05	0.02	0.00	2.69
134	135	7.351166	TCCCTCCGTTCCTAAATATTTGAAAT	58.649	34.615	11.05	0.00	0.00	2.17
135	136	7.837187	TCCCTCCGTTCCTAAATATTTGAAATT	59.163	33.333	11.05	0.00	0.00	1.82
136	137	8.474831	CCCTCCGTTCCTAAATATTTGAAATTT	58.525	33.333	11.05	0.00	0.00	1.82
137	138	9.516314	CCTCCGTTCCTAAATATTTGAAATTTC	57.484	33.333	11.41	11.41	0.00	2.17
138	139	9.221775	CTCCGTTCCTAAATATTTGAAATTTCG	57.778	33.333	13.34	6.52	0.00	3.46
139	140	8.732531	TCCGTTCCTAAATATTTGAAATTTCGT	58.267	29.630	13.34	4.98	0.00	3.85
140	141	9.991388	CCGTTCCTAAATATTTGAAATTTCGTA	57.009	29.630	13.34	6.91	0.00	3.43

Showing 1 to 25 of 427 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
90	91	9.021807	CGGAGGGAGTAGTATCTTAAATATTGA	57.978	37.037	0.00	0.00	0.00	2.57
91	92	8.804204	ACGGAGGGAGTAGTATCTTAAATATTG	58.196	37.037	0.00	0.00	0.00	1.90
92	93	8.953223	ACGGAGGGAGTAGTATCTTAAATATT	57.047	34.615	0.00	0.00	0.00	1.28
93	94	8.953223	AACGGAGGGAGTAGTATCTTAAATAT	57.047	34.615	0.00	0.00	0.00	1.28
94	95	7.449704	GGAACGGAGGGAGTAGTATCTTAAATA	59.550	40.741	0.00	0.00	0.00	1.40
95	96	6.267242	GGAACGGAGGGAGTAGTATCTTAAAT	59.733	42.308	0.00	0.00	0.00	1.40
96	97	5.595952	GGAACGGAGGGAGTAGTATCTTAAA	59.404	44.000	0.00	0.00	0.00	1.52
97	98	5.103771	AGGAACGGAGGGAGTAGTATCTTAA	60.104	44.000	0.00	0.00	0.00	1.85
98	99	4.414846	AGGAACGGAGGGAGTAGTATCTTA	59.585	45.833	0.00	0.00	0.00	2.10
99	100	3.204831	AGGAACGGAGGGAGTAGTATCTT	59.795	47.826	0.00	0.00	0.00	2.40
100	101	2.784682	AGGAACGGAGGGAGTAGTATCT	59.215	50.000	0.00	0.00	0.00	1.98
101	102	3.226682	AGGAACGGAGGGAGTAGTATC	57.773	52.381	0.00	0.00	0.00	2.24
102	103	4.803329	TTAGGAACGGAGGGAGTAGTAT	57.197	45.455	0.00	0.00	0.00	2.12
103	104	4.591321	TTTAGGAACGGAGGGAGTAGTA	57.409	45.455	0.00	0.00	0.00	1.82
104	105	3.463048	TTTAGGAACGGAGGGAGTAGT	57.537	47.619	0.00	0.00	0.00	2.73
105	106	6.667558	AATATTTAGGAACGGAGGGAGTAG	57.332	41.667	0.00	0.00	0.00	2.57
106	107	6.612456	TCAAATATTTAGGAACGGAGGGAGTA	59.388	38.462	0.00	0.00	0.00	2.59
107	108	5.427481	TCAAATATTTAGGAACGGAGGGAGT	59.573	40.000	0.00	0.00	0.00	3.85
108	109	5.925509	TCAAATATTTAGGAACGGAGGGAG	58.074	41.667	0.00	0.00	0.00	4.30
109	110	5.961398	TCAAATATTTAGGAACGGAGGGA	57.039	39.130	0.00	0.00	0.00	4.20
110	111	7.582667	ATTTCAAATATTTAGGAACGGAGGG	57.417	36.000	0.00	0.00	0.00	4.30
111	112	9.516314	GAAATTTCAAATATTTAGGAACGGAGG	57.484	33.333	13.40	0.00	0.00	4.30
112	113	9.221775	CGAAATTTCAAATATTTAGGAACGGAG	57.778	33.333	17.99	0.00	0.00	4.63
113	114	8.732531	ACGAAATTTCAAATATTTAGGAACGGA	58.267	29.630	17.99	0.00	0.00	4.69
114	115	8.905103	ACGAAATTTCAAATATTTAGGAACGG	57.095	30.769	17.99	0.00	0.00	4.44

Showing 1 to 25 of 471 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.