AutoCloner

Multiple sequence alignment - TraesCS2A01G322500

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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	TraesCS2A01G322500	chr2A	100.000	3820	0	0	1	3820	551720520	551724339	0.000000e+00	7055.0
1	TraesCS2A01G322500	chr2A	97.167	706	19	1	3115	3820	407427275	407426571	0.000000e+00	1192.0
2	TraesCS2A01G322500	chr2A	97.163	705	20	0	3114	3818	512119094	512118390	0.000000e+00	1192.0
3	TraesCS2A01G322500	chr2A	80.844	924	159	13	994	1911	12702349	12701438	0.000000e+00	710.0
4	TraesCS2A01G322500	chr2A	84.908	709	98	4	2183	2882	12701013	12700305	0.000000e+00	708.0
5	TraesCS2A01G322500	chr2A	82.252	755	119	11	2154	2894	12577660	12576907	4.160000e-179	638.0
6	TraesCS2A01G322500	chr2A	79.968	624	121	4	2188	2809	772219429	772218808	1.250000e-124	457.0
7	TraesCS2A01G322500	chr2A	95.122	41	2	0	448	488	214902112	214902152	8.860000e-07	65.8
8	TraesCS2A01G322500	chr2D	93.423	1338	65	14	669	1994	435072940	435071614	0.000000e+00	1962.0
9	TraesCS2A01G322500	chr2D	94.901	961	37	4	2114	3063	435071152	435070193	0.000000e+00	1493.0
10	TraesCS2A01G322500	chr2D	79.550	1022	182	17	994	2001	11964719	11963711	0.000000e+00	704.0
11	TraesCS2A01G322500	chr2D	83.929	728	105	6	2183	2898	11963385	11962658	0.000000e+00	686.0
12	TraesCS2A01G322500	chr2D	78.509	912	170	17	1001	1905	650656232	650655340	3.310000e-160	575.0
13	TraesCS2A01G322500	chr2D	78.098	936	165	28	994	1906	4029546	4028628	1.200000e-154	556.0
14	TraesCS2A01G322500	chr2D	77.671	936	169	27	994	1906	3971951	3971033	5.620000e-148	534.0
15	TraesCS2A01G322500	chr2D	93.294	343	12	7	1	340	435074382	435074048	2.650000e-136	496.0
16	TraesCS2A01G322500	chr2D	80.609	624	117	4	2188	2809	650654781	650654160	2.670000e-131	479.0
17	TraesCS2A01G322500	chr2D	90.028	351	18	10	341	677	435073772	435073425	4.530000e-119	438.0
18	TraesCS2A01G322500	chr2D	88.095	126	11	2	1974	2096	435071599	435071475	3.080000e-31	147.0
19	TraesCS2A01G322500	chr2D	90.196	51	4	1	441	491	579191490	579191539	8.860000e-07	65.8
20	TraesCS2A01G322500	chr2B	95.794	1070	37	5	994	2062	513481223	513480161	0.000000e+00	1720.0
21	TraesCS2A01G322500	chr2B	93.139	962	53	11	2108	3063	513480158	513479204	0.000000e+00	1399.0
22	TraesCS2A01G322500	chr2B	80.831	626	112	8	2188	2809	787819015	787818394	5.740000e-133	484.0
23	TraesCS2A01G322500	chr2B	96.400	250	3	3	1	244	513496898	513496649	1.280000e-109	407.0
24	TraesCS2A01G322500	chr2B	88.235	204	13	2	695	888	513481595	513481393	2.290000e-57	233.0
25	TraesCS2A01G322500	chr5A	97.592	706	16	1	3115	3820	595444242	595444946	0.000000e+00	1208.0
26	TraesCS2A01G322500	chr5A	97.309	706	19	0	3115	3820	26007147	26006442	0.000000e+00	1199.0
27	TraesCS2A01G322500	chr5A	97.167	706	19	1	3115	3820	534426660	534427364	0.000000e+00	1192.0
28	TraesCS2A01G322500	chr5A	89.041	73	4	4	3046	3114	569658293	569658365	1.890000e-13	87.9
29	TraesCS2A01G322500	chr3A	97.328	711	18	1	3110	3820	733145226	733144517	0.000000e+00	1206.0
30	TraesCS2A01G322500	chr7A	97.309	706	19	0	3115	3820	234272770	234273475	0.000000e+00	1199.0
31	TraesCS2A01G322500	chr1A	97.309	706	18	1	3115	3820	440252430	440251726	0.000000e+00	1197.0
32	TraesCS2A01G322500	chr1A	97.030	707	20	1	3114	3820	275004477	275003772	0.000000e+00	1188.0
33	TraesCS2A01G322500	chr1A	96.078	51	2	0	3062	3112	442631644	442631594	2.450000e-12	84.2
34	TraesCS2A01G322500	chr5D	84.679	966	132	8	1000	1960	522761631	522760677	0.000000e+00	950.0
35	TraesCS2A01G322500	chr5D	86.838	623	82	0	2181	2803	522759645	522759023	0.000000e+00	697.0
36	TraesCS2A01G322500	chr7D	79.878	820	139	23	1097	1906	591207002	591207805	9.200000e-161	577.0
37	TraesCS2A01G322500	chr7D	78.132	942	173	20	994	1915	263889984	263890912	5.540000e-158	568.0
38	TraesCS2A01G322500	chr7D	96.226	53	1	1	3063	3114	47186525	47186473	6.800000e-13	86.1
39	TraesCS2A01G322500	chr7D	92.857	42	1	2	450	491	439236350	439236311	4.120000e-05	60.2
40	TraesCS2A01G322500	chr6B	96.154	52	2	0	3063	3114	416909775	416909826	6.800000e-13	86.1
41	TraesCS2A01G322500	chr6B	94.231	52	3	0	3063	3114	506544220	506544169	3.160000e-11	80.5
42	TraesCS2A01G322500	chr6B	94.231	52	3	0	3063	3114	518592872	518592923	3.160000e-11	80.5
43	TraesCS2A01G322500	chr6B	94.231	52	3	0	3063	3114	626216567	626216516	3.160000e-11	80.5
44	TraesCS2A01G322500	chr4B	89.706	68	6	1	3059	3125	311202838	311202771	6.800000e-13	86.1
45	TraesCS2A01G322500	chr3B	91.228	57	3	2	3056	3112	463487605	463487659	4.090000e-10	76.8
46	TraesCS2A01G322500	chr4D	90.196	51	3	2	442	491	416070623	416070672	8.860000e-07	65.8
47	TraesCS2A01G322500	chr4D	93.182	44	2	1	448	491	218516286	218516244	3.190000e-06	63.9
48	TraesCS2A01G322500	chr6A	95.122	41	1	1	451	491	39864174	39864213	3.190000e-06	63.9
49	TraesCS2A01G322500	chr1D	91.304	46	2	2	447	491	366474150	366474106	1.150000e-05	62.1

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	TraesCS2A01G322500	chr2A	551720520	551724339	3819	False	7055.000000	7055	100.000000	1	3820	1	chr2A.!!$F2	3819
1	TraesCS2A01G322500	chr2A	407426571	407427275	704	True	1192.000000	1192	97.167000	3115	3820	1	chr2A.!!$R2	705
2	TraesCS2A01G322500	chr2A	512118390	512119094	704	True	1192.000000	1192	97.163000	3114	3818	1	chr2A.!!$R3	704
3	TraesCS2A01G322500	chr2A	12700305	12702349	2044	True	709.000000	710	82.876000	994	2882	2	chr2A.!!$R5	1888
4	TraesCS2A01G322500	chr2A	12576907	12577660	753	True	638.000000	638	82.252000	2154	2894	1	chr2A.!!$R1	740
5	TraesCS2A01G322500	chr2A	772218808	772219429	621	True	457.000000	457	79.968000	2188	2809	1	chr2A.!!$R4	621
6	TraesCS2A01G322500	chr2D	435070193	435074382	4189	True	907.200000	1962	91.948200	1	3063	5	chr2D.!!$R4	3062
7	TraesCS2A01G322500	chr2D	11962658	11964719	2061	True	695.000000	704	81.739500	994	2898	2	chr2D.!!$R3	1904
8	TraesCS2A01G322500	chr2D	4028628	4029546	918	True	556.000000	556	78.098000	994	1906	1	chr2D.!!$R2	912
9	TraesCS2A01G322500	chr2D	3971033	3971951	918	True	534.000000	534	77.671000	994	1906	1	chr2D.!!$R1	912
10	TraesCS2A01G322500	chr2D	650654160	650656232	2072	True	527.000000	575	79.559000	1001	2809	2	chr2D.!!$R5	1808
11	TraesCS2A01G322500	chr2B	513479204	513481595	2391	True	1117.333333	1720	92.389333	695	3063	3	chr2B.!!$R3	2368
12	TraesCS2A01G322500	chr2B	787818394	787819015	621	True	484.000000	484	80.831000	2188	2809	1	chr2B.!!$R2	621
13	TraesCS2A01G322500	chr5A	595444242	595444946	704	False	1208.000000	1208	97.592000	3115	3820	1	chr5A.!!$F3	705
14	TraesCS2A01G322500	chr5A	26006442	26007147	705	True	1199.000000	1199	97.309000	3115	3820	1	chr5A.!!$R1	705
15	TraesCS2A01G322500	chr5A	534426660	534427364	704	False	1192.000000	1192	97.167000	3115	3820	1	chr5A.!!$F1	705
16	TraesCS2A01G322500	chr3A	733144517	733145226	709	True	1206.000000	1206	97.328000	3110	3820	1	chr3A.!!$R1	710
17	TraesCS2A01G322500	chr7A	234272770	234273475	705	False	1199.000000	1199	97.309000	3115	3820	1	chr7A.!!$F1	705
18	TraesCS2A01G322500	chr1A	440251726	440252430	704	True	1197.000000	1197	97.309000	3115	3820	1	chr1A.!!$R2	705
19	TraesCS2A01G322500	chr1A	275003772	275004477	705	True	1188.000000	1188	97.030000	3114	3820	1	chr1A.!!$R1	706
20	TraesCS2A01G322500	chr5D	522759023	522761631	2608	True	823.500000	950	85.758500	1000	2803	2	chr5D.!!$R1	1803
21	TraesCS2A01G322500	chr7D	591207002	591207805	803	False	577.000000	577	79.878000	1097	1906	1	chr7D.!!$F2	809
22	TraesCS2A01G322500	chr7D	263889984	263890912	928	False	568.000000	568	78.132000	994	1915	1	chr7D.!!$F1	921

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	Hairpin	End Stability	Orientation
822	1617	0.392863	CGTGATCCATCAGGCAACCA	60.393	55.000	37.51	3.67	F
944	1765	0.541863	CATGTTCTTCTACCCCGGCT	59.458	55.000	0.00	5.52	F
959	1780	1.202417	CCGGCTGGCTATATATCCGTG	60.202	57.143	35.52	4.94	F
1286	2163	1.676014	GGAGGTGATGAAGACCAACGG	60.676	57.143	35.76	4.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1702	2588	1.143183	GGATCCTCTTTACGCGGCA	59.857	57.895	12.47	0.00	5.69	R
2414	4579	1.270826	CAGTCTTCTCTGGTCTTGCGA	59.729	52.381	0.00	0.00	5.10	R
2723	4889	3.684788	ACCCGAATTTCTCAGACAAATCG	59.315	43.478	0.00	0.00	3.34	R
3072	5258	0.403271	AGCCAGCTGTGTTGGATCTT	59.597	50.000	13.81	35.94	2.40	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
55	56	3.262420	CCACCATACCGAACTTCTTCTG	58.738	50.000	0.00	0.00	0.00	3.02
56	57	3.306780	CCACCATACCGAACTTCTTCTGT	60.307	47.826	0.00	0.00	0.00	3.41
58	59	4.389077	CACCATACCGAACTTCTTCTGTTC	59.611	45.833	0.00	0.00	40.05	3.18
68	71	6.702282	CGAACTTCTTCTGTTCCTAGTCTTTT	59.298	38.462	0.00	0.00	40.26	2.27
77	80	1.825474	TCCTAGTCTTTTCTGAGCCGG	59.175	52.381	0.00	0.00	0.00	6.13
202	205	5.923204	TGTTTTTAAATTGCTGTCCATGGT	58.077	33.333	12.58	0.00	0.00	3.55
217	220	4.746611	GTCCATGGTTTTCTGCTTTTGAAG	59.253	41.667	12.58	0.00	0.00	3.02
220	223	6.097554	TCCATGGTTTTCTGCTTTTGAAGTTA	59.902	34.615	12.58	0.00	0.00	2.24
221	224	6.200854	CCATGGTTTTCTGCTTTTGAAGTTAC	59.799	38.462	2.57	0.00	0.00	2.50
226	229	7.330946	GGTTTTCTGCTTTTGAAGTTACTTGTT	59.669	33.333	0.93	0.00	0.00	2.83
227	230	7.810766	TTTCTGCTTTTGAAGTTACTTGTTG	57.189	32.000	0.93	0.00	0.00	3.33
228	231	6.509418	TCTGCTTTTGAAGTTACTTGTTGT	57.491	33.333	0.93	0.00	0.00	3.32
229	232	6.321717	TCTGCTTTTGAAGTTACTTGTTGTG	58.678	36.000	0.93	0.00	0.00	3.33
230	233	5.406649	TGCTTTTGAAGTTACTTGTTGTGG	58.593	37.500	0.93	0.00	0.00	4.17
231	234	5.184096	TGCTTTTGAAGTTACTTGTTGTGGA	59.816	36.000	0.93	0.00	0.00	4.02
232	235	5.515270	GCTTTTGAAGTTACTTGTTGTGGAC	59.485	40.000	0.93	0.00	0.00	4.02
233	236	4.868450	TTGAAGTTACTTGTTGTGGACG	57.132	40.909	0.93	0.00	0.00	4.79
261	264	1.540267	TATGTTTTCGTGGCCTTGGG	58.460	50.000	3.32	0.00	0.00	4.12
300	303	4.697352	GTGAGATGGCAGAACACAAATAGT	59.303	41.667	13.15	0.00	0.00	2.12
301	304	5.874810	GTGAGATGGCAGAACACAAATAGTA	59.125	40.000	13.15	0.00	0.00	1.82
302	305	6.036517	GTGAGATGGCAGAACACAAATAGTAG	59.963	42.308	13.15	0.00	0.00	2.57
324	327	3.130693	GGAGTAGCTCACAATACGGAAGT	59.869	47.826	0.00	0.00	39.26	3.01
337	340	2.104859	GGAAGTTACCGCGGAAGGC	61.105	63.158	35.90	18.22	38.69	4.35
340	343	1.823169	AAGTTACCGCGGAAGGCTCA	61.823	55.000	35.90	3.68	40.44	4.26
342	345	2.575893	TTACCGCGGAAGGCTCACA	61.576	57.895	35.90	0.72	40.44	3.58

Showing 1 to 25 of 111 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	3.073209	TGGTAAAGACAGCATGGGTGTAA	59.927	43.478	0.54	0.00	44.55	2.41
55	56	3.254892	CGGCTCAGAAAAGACTAGGAAC	58.745	50.000	0.00	0.00	0.00	3.62
56	57	2.233922	CCGGCTCAGAAAAGACTAGGAA	59.766	50.000	0.00	0.00	0.00	3.36
58	59	1.825474	TCCGGCTCAGAAAAGACTAGG	59.175	52.381	0.00	0.00	0.00	3.02
68	71	0.758734	CCATACCATTCCGGCTCAGA	59.241	55.000	0.00	0.00	39.03	3.27
77	80	4.282703	ACACTCCGGTATACCATACCATTC	59.717	45.833	21.76	0.00	37.44	2.67
202	205	7.870445	ACAACAAGTAACTTCAAAAGCAGAAAA	59.130	29.630	0.00	0.00	0.00	2.29
217	220	4.114794	ACTACACGTCCACAACAAGTAAC	58.885	43.478	0.00	0.00	0.00	2.50
220	223	2.973694	ACTACACGTCCACAACAAGT	57.026	45.000	0.00	0.00	0.00	3.16
221	224	6.588756	ACATATTACTACACGTCCACAACAAG	59.411	38.462	0.00	0.00	0.00	3.16
226	229	6.308524	CGAAAACATATTACTACACGTCCACA	59.691	38.462	0.00	0.00	0.00	4.17
227	230	6.308766	ACGAAAACATATTACTACACGTCCAC	59.691	38.462	0.00	0.00	0.00	4.02
228	231	6.308524	CACGAAAACATATTACTACACGTCCA	59.691	38.462	0.00	0.00	0.00	4.02
229	232	6.237648	CCACGAAAACATATTACTACACGTCC	60.238	42.308	0.00	0.00	0.00	4.79
230	233	6.689547	CCACGAAAACATATTACTACACGTC	58.310	40.000	0.00	0.00	0.00	4.34
231	234	5.062558	GCCACGAAAACATATTACTACACGT	59.937	40.000	0.00	0.00	0.00	4.49
232	235	5.486706	GCCACGAAAACATATTACTACACG	58.513	41.667	0.00	0.00	0.00	4.49
233	236	5.583457	AGGCCACGAAAACATATTACTACAC	59.417	40.000	5.01	0.00	0.00	2.90
261	264	1.139853	CTCACCTTGGACAGCCCTATC	59.860	57.143	0.00	0.00	35.38	2.08
268	271	0.325933	TGCCATCTCACCTTGGACAG	59.674	55.000	0.00	0.00	34.81	3.51
300	303	4.160642	TCCGTATTGTGAGCTACTCCTA	57.839	45.455	0.00	0.00	0.00	2.94
301	304	3.014304	TCCGTATTGTGAGCTACTCCT	57.986	47.619	0.00	0.00	0.00	3.69
302	305	3.130693	ACTTCCGTATTGTGAGCTACTCC	59.869	47.826	0.00	0.00	0.00	3.85
324	327	2.102109	TTGTGAGCCTTCCGCGGTAA	62.102	55.000	27.15	16.74	44.76	2.85
337	340	6.382869	AAAGGAAAACAGATGAGTTGTGAG	57.617	37.500	0.00	0.00	0.00	3.51

Showing 1 to 25 of 132 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.