AutoCloner

Multiple sequence alignment - TraesCS7D01G159300

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	TraesCS7D01G159300	chr7D	100.000	2411	0	0	1	2411	108411537	108413947	0.000000e+00	4453.0
1	TraesCS7D01G159300	chr7D	91.169	838	56	7	598	1426	108085192	108086020	0.000000e+00	1122.0
2	TraesCS7D01G159300	chr7D	91.019	412	37	0	1000	1411	91699844	91699433	7.530000e-155	556.0
3	TraesCS7D01G159300	chr7D	89.627	241	18	6	1777	2012	108086046	108086284	1.400000e-77	300.0
4	TraesCS7D01G159300	chr7D	98.936	94	1	0	1770	1863	108413212	108413305	4.120000e-38	169.0
5	TraesCS7D01G159300	chr7D	98.936	94	1	0	1676	1769	108413306	108413399	4.120000e-38	169.0
6	TraesCS7D01G159300	chr7D	90.083	121	8	2	1653	1770	108086016	108086135	1.150000e-33	154.0
7	TraesCS7D01G159300	chr7D	93.333	90	5	1	1433	1522	187108040	187108128	5.410000e-27	132.0
8	TraesCS7D01G159300	chr7D	95.349	43	2	0	2286	2328	108413658	108413700	4.300000e-08	69.4
9	TraesCS7D01G159300	chr7D	95.349	43	2	0	2122	2164	108413822	108413864	4.300000e-08	69.4
10	TraesCS7D01G159300	chr7A	92.063	1134	73	12	284	1413	113370326	113371446	0.000000e+00	1580.0
11	TraesCS7D01G159300	chr7A	91.019	412	37	0	1000	1411	93260964	93260553	7.530000e-155	556.0
12	TraesCS7D01G159300	chr7A	94.604	278	12	3	1776	2052	113371459	113371734	6.160000e-116	427.0
13	TraesCS7D01G159300	chr7A	88.780	205	17	3	1	199	113369772	113369976	1.850000e-61	246.0
14	TraesCS7D01G159300	chr7A	100.000	88	0	0	1682	1769	113371459	113371546	1.920000e-36	163.0
15	TraesCS7D01G159300	chr7B	86.020	1216	128	24	221	1426	66977963	66979146	0.000000e+00	1266.0
16	TraesCS7D01G159300	chr7B	90.909	605	37	10	819	1415	67807999	67808593	0.000000e+00	797.0
17	TraesCS7D01G159300	chr7B	91.262	412	36	0	1000	1411	63934979	63935390	1.620000e-156	562.0
18	TraesCS7D01G159300	chr7B	85.965	171	12	9	1777	1945	67808623	67808783	3.190000e-39	172.0
19	TraesCS7D01G159300	chr7B	81.982	222	21	10	1772	1990	66979167	66979372	1.150000e-38	171.0
20	TraesCS7D01G159300	chr7B	90.435	115	9	1	1656	1770	67808596	67808708	1.490000e-32	150.0
21	TraesCS7D01G159300	chr7B	95.294	85	4	0	1436	1520	74816675	74816591	4.180000e-28	135.0
22	TraesCS7D01G159300	chr7B	95.294	85	4	0	1436	1520	647685435	647685351	4.180000e-28	135.0
23	TraesCS7D01G159300	chr7B	85.470	117	8	2	1653	1769	66979142	66979249	1.960000e-21	113.0
24	TraesCS7D01G159300	chr6A	91.041	413	35	2	1000	1411	144528860	144528449	7.530000e-155	556.0
25	TraesCS7D01G159300	chr6A	91.579	95	7	1	1433	1527	614480026	614480119	1.950000e-26	130.0
26	TraesCS7D01G159300	chr1B	91.337	404	33	2	1000	1402	434409085	434409487	3.500000e-153	551.0
27	TraesCS7D01G159300	chr1B	94.444	90	4	1	1433	1522	448264339	448264427	1.160000e-28	137.0
28	TraesCS7D01G159300	chr1A	94.565	92	4	1	1436	1527	360459963	360460053	8.990000e-30	141.0
29	TraesCS7D01G159300	chr2D	95.402	87	4	0	1434	1520	633559827	633559741	3.230000e-29	139.0
30	TraesCS7D01G159300	chr2D	88.073	109	12	1	2304	2411	429087075	429086967	7.000000e-26	128.0
31	TraesCS7D01G159300	chr1D	93.617	94	5	1	1434	1527	413308842	413308934	3.230000e-29	139.0
32	TraesCS7D01G159300	chr2A	93.333	90	6	0	1433	1522	104780395	104780484	1.500000e-27	134.0
33	TraesCS7D01G159300	chr6B	80.916	131	11	5	1527	1643	278342743	278342613	9.180000e-15	91.6
34	TraesCS7D01G159300	chr2B	80.597	134	12	7	1524	1643	92602767	92602900	9.180000e-15	91.6

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	TraesCS7D01G159300	chr7D	108411537	108413947	2410	False	985.960000	4453	97.714000	1	2411	5	chr7D.!!$F3	2410
1	TraesCS7D01G159300	chr7D	108085192	108086284	1092	False	525.333333	1122	90.293000	598	2012	3	chr7D.!!$F2	1414
2	TraesCS7D01G159300	chr7A	113369772	113371734	1962	False	604.000000	1580	93.861750	1	2052	4	chr7A.!!$F1	2051
3	TraesCS7D01G159300	chr7B	66977963	66979372	1409	False	516.666667	1266	84.490667	221	1990	3	chr7B.!!$F2	1769
4	TraesCS7D01G159300	chr7B	67807999	67808783	784	False	373.000000	797	89.103000	819	1945	3	chr7B.!!$F3	1126

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
215	222	0.031314	CACGCACACACACTCTCTCT	59.969	55.0	0.0	0.0	0.0	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1484	1789	0.040425	CGGTGCTTCAGAAAAACCCG	60.04	55.0	7.91	3.09	0.0	5.28	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	Hairpin	End Stability
30	31	1.221840	CGGTGAGCCTGTGCCTATT	59.778	57.895	0.00	38.69	1.73
32	33	0.749454	GGTGAGCCTGTGCCTATTGG	60.749	60.000	0.00	38.69	3.16
39	40	3.459598	AGCCTGTGCCTATTGGATTAAGA	59.540	43.478	0.00	38.69	2.10
46	47	5.049129	GTGCCTATTGGATTAAGAGCATCAC	60.049	44.000	0.00	33.68	3.06
69	71	1.608425	CAATTCCCTAACCCCTCCCT	58.392	55.000	0.00	0.00	4.20
81	83	1.133482	CCCCTCCCTTTGAGTGTGTTT	60.133	52.381	0.00	39.65	2.83
93	99	4.134563	TGAGTGTGTTTAAGGGCTCTTTC	58.865	43.478	2.94	34.59	2.62
125	131	1.838568	GAGTTTCACGGGTGTTCGGC	61.839	60.000	0.00	0.00	5.54
131	137	2.205152	ACGGGTGTTCGGCTGTAGT	61.205	57.895	0.00	0.00	2.73
136	142	2.934553	GGGTGTTCGGCTGTAGTAATTC	59.065	50.000	0.00	0.00	2.17
138	144	2.601763	GTGTTCGGCTGTAGTAATTCCG	59.398	50.000	0.00	41.30	4.30
139	145	1.591619	GTTCGGCTGTAGTAATTCCGC	59.408	52.381	0.00	39.90	5.54
141	147	1.066605	TCGGCTGTAGTAATTCCGCTC	59.933	52.381	0.00	39.90	5.03
166	173	4.625607	ACCTCTTCCCAAACTAAGACTG	57.374	45.455	0.00	0.00	3.51
205	212	4.041617	GTGGATCACACGCACACA	57.958	55.556	0.00	40.85	3.72
206	213	1.569493	GTGGATCACACGCACACAC	59.431	57.895	0.00	40.85	3.82
207	214	1.144936	TGGATCACACGCACACACA	59.855	52.632	0.00	0.00	3.72
208	215	1.157257	TGGATCACACGCACACACAC	61.157	55.000	0.00	0.00	3.82
209	216	0.880278	GGATCACACGCACACACACT	60.880	55.000	0.00	0.00	3.55
210	217	0.508641	GATCACACGCACACACACTC	59.491	55.000	0.00	0.00	3.51
211	218	0.104855	ATCACACGCACACACACTCT	59.895	50.000	0.00	0.00	3.24
212	219	0.527600	TCACACGCACACACACTCTC	60.528	55.000	0.00	0.00	3.20
213	220	0.528466	CACACGCACACACACTCTCT	60.528	55.000	0.00	0.00	3.10
214	221	0.249073	ACACGCACACACACTCTCTC	60.249	55.000	0.00	0.00	3.20
215	222	0.031314	CACGCACACACACTCTCTCT	59.969	55.000	0.00	0.00	3.10

Showing 1 to 25 of 562 entries

Previous1 2 3 4 5…23Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
30	31	2.168313	TGCTCGTGATGCTCTTAATCCA	59.832	45.455	0.00	0.00	3.41
32	33	5.415415	AATTGCTCGTGATGCTCTTAATC	57.585	39.130	0.00	0.00	1.75
39	40	0.254178	AGGGAATTGCTCGTGATGCT	59.746	50.000	0.00	0.00	3.79
46	47	0.546598	AGGGGTTAGGGAATTGCTCG	59.453	55.000	0.00	0.00	5.03
69	71	4.164843	AGAGCCCTTAAACACACTCAAA	57.835	40.909	0.00	0.00	2.69
112	118	1.736645	CTACAGCCGAACACCCGTG	60.737	63.158	0.00	0.00	4.94
125	131	5.903810	AGGTTTAGAGCGGAATTACTACAG	58.096	41.667	0.00	0.00	2.74
131	137	4.141779	GGGAAGAGGTTTAGAGCGGAATTA	60.142	45.833	0.00	0.00	1.40
136	142	0.902531	TGGGAAGAGGTTTAGAGCGG	59.097	55.000	0.00	0.00	5.52
138	144	4.022413	AGTTTGGGAAGAGGTTTAGAGC	57.978	45.455	0.00	0.00	4.09
139	145	6.874664	GTCTTAGTTTGGGAAGAGGTTTAGAG	59.125	42.308	0.00	32.43	2.43
141	147	6.651225	CAGTCTTAGTTTGGGAAGAGGTTTAG	59.349	42.308	0.00	32.43	1.85
180	187	1.702886	CGTGTGATCCACTGACAGAC	58.297	55.000	10.08	42.20	3.51
181	188	0.038251	GCGTGTGATCCACTGACAGA	60.038	55.000	10.08	42.20	3.41
199	206	0.037790	GGGAGAGAGAGTGTGTGTGC	60.038	60.000	0.00	0.00	4.57
201	208	0.543174	GGGGGAGAGAGAGTGTGTGT	60.543	60.000	0.00	0.00	3.72
202	209	0.252012	AGGGGGAGAGAGAGTGTGTG	60.252	60.000	0.00	0.00	3.82
203	210	0.040499	GAGGGGGAGAGAGAGTGTGT	59.960	60.000	0.00	0.00	3.72
204	211	0.334676	AGAGGGGGAGAGAGAGTGTG	59.665	60.000	0.00	0.00	3.82
205	212	0.629058	GAGAGGGGGAGAGAGAGTGT	59.371	60.000	0.00	0.00	3.55
206	213	0.926293	AGAGAGGGGGAGAGAGAGTG	59.074	60.000	0.00	0.00	3.51
207	214	2.512476	GTTAGAGAGGGGGAGAGAGAGT	59.488	54.545	0.00	0.00	3.24
208	215	2.486548	CGTTAGAGAGGGGGAGAGAGAG	60.487	59.091	0.00	0.00	3.20
209	216	1.491332	CGTTAGAGAGGGGGAGAGAGA	59.509	57.143	0.00	0.00	3.10
210	217	1.975660	CGTTAGAGAGGGGGAGAGAG	58.024	60.000	0.00	0.00	3.20

Showing 1 to 25 of 531 entries

Previous1 2 3 4 5…22Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.