AutoCloner

Multiple sequence alignment - TraesCS5D01G554600

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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	TraesCS5D01G554600	chr5D	100.000	4326	0	0	2479	6804	558717597	558721922	0.000000e+00	7989.0
1	TraesCS5D01G554600	chr5D	100.000	2127	0	0	1	2127	558715119	558717245	0.000000e+00	3928.0
2	TraesCS5D01G554600	chr5D	77.358	2460	452	79	3583	5983	555449269	555446856	0.000000e+00	1360.0
3	TraesCS5D01G554600	chr5D	80.090	1557	281	24	4273	5810	556007875	556006329	0.000000e+00	1131.0
4	TraesCS5D01G554600	chr5D	81.577	1129	187	14	3764	4878	559982685	559983806	0.000000e+00	913.0
5	TraesCS5D01G554600	chr5D	84.014	882	123	13	983	1860	559915693	559916560	0.000000e+00	832.0
6	TraesCS5D01G554600	chr5D	80.600	866	147	15	1010	1869	555456615	555455765	0.000000e+00	649.0
7	TraesCS5D01G554600	chr5D	80.274	877	159	9	997	1866	559981532	559982401	0.000000e+00	649.0
8	TraesCS5D01G554600	chr5D	77.604	192	28	15	5548	5732	555068544	555068361	1.210000e-17	102.0
9	TraesCS5D01G554600	chr5D	84.000	75	10	2	5643	5716	555041462	555041389	3.400000e-08	71.3
10	TraesCS5D01G554600	chr5B	90.592	2519	171	32	3568	6074	704107079	704104615	0.000000e+00	3278.0
11	TraesCS5D01G554600	chr5B	89.765	1534	131	16	364	1887	704110623	704109106	0.000000e+00	1940.0
12	TraesCS5D01G554600	chr5B	77.860	2299	421	68	3722	5973	695950976	695953233	0.000000e+00	1345.0
13	TraesCS5D01G554600	chr5B	78.099	1936	370	48	3710	5619	695550391	695552298	0.000000e+00	1177.0
14	TraesCS5D01G554600	chr5B	77.113	1822	364	36	3815	5601	696230474	696232277	0.000000e+00	1005.0
15	TraesCS5D01G554600	chr5B	76.314	1959	401	57	3788	5711	695991001	695992931	0.000000e+00	989.0
16	TraesCS5D01G554600	chr5B	77.628	1627	324	37	3788	5389	695704711	695706322	0.000000e+00	952.0
17	TraesCS5D01G554600	chr5B	80.714	1177	214	12	3763	4935	710344209	710345376	0.000000e+00	904.0
18	TraesCS5D01G554600	chr5B	82.520	881	144	6	988	1866	710342736	710343608	0.000000e+00	765.0
19	TraesCS5D01G554600	chr5B	79.538	865	158	12	1007	1866	695947512	695948362	3.510000e-167	599.0
20	TraesCS5D01G554600	chr5B	92.391	184	12	1	6119	6302	704104475	704104294	1.880000e-65	261.0
21	TraesCS5D01G554600	chr5B	81.533	287	51	2	1579	1864	695548739	695549024	1.140000e-57	235.0
22	TraesCS5D01G554600	chr5B	85.463	227	19	12	43	268	704111179	704110966	2.470000e-54	224.0
23	TraesCS5D01G554600	chr5B	88.095	168	18	1	6638	6803	598439800	598439967	1.500000e-46	198.0
24	TraesCS5D01G554600	chr5B	86.747	166	21	1	6639	6803	21036584	21036419	4.190000e-42	183.0
25	TraesCS5D01G554600	chr5B	88.406	69	8	0	5541	5609	695964776	695964844	4.370000e-12	84.2
26	TraesCS5D01G554600	chr4A	80.948	1160	203	15	3784	4936	604849250	604848102	0.000000e+00	902.0
27	TraesCS5D01G554600	chr4A	83.744	892	128	12	973	1860	604772889	604773767	0.000000e+00	828.0
28	TraesCS5D01G554600	chr4A	90.419	167	15	1	6638	6803	439055916	439056082	1.150000e-52	219.0
29	TraesCS5D01G554600	chr1B	75.128	1954	432	43	3788	5710	597535589	597537519	0.000000e+00	867.0
30	TraesCS5D01G554600	chr1B	79.904	836	148	15	1007	1835	597534290	597535112	4.540000e-166	595.0
31	TraesCS5D01G554600	chr1B	76.841	842	168	14	1007	1835	26426522	26427349	3.740000e-122	449.0
32	TraesCS5D01G554600	chr1B	75.776	838	173	19	1010	1835	25896841	25896022	4.950000e-106	396.0
33	TraesCS5D01G554600	chr1B	76.393	754	167	8	1083	1835	25945845	25945102	4.950000e-106	396.0
34	TraesCS5D01G554600	chr7B	92.982	171	10	2	6634	6803	168632461	168632630	1.470000e-61	248.0
35	TraesCS5D01G554600	chr2D	92.727	165	12	0	6638	6802	605386715	605386879	8.820000e-59	239.0
36	TraesCS5D01G554600	chr3B	91.617	167	13	1	6638	6803	805521061	805521227	5.310000e-56	230.0
37	TraesCS5D01G554600	chr1A	92.667	150	11	0	6638	6787	9536135	9536284	4.130000e-52	217.0
38	TraesCS5D01G554600	chr6B	87.571	177	19	2	6629	6803	20742256	20742081	1.160000e-47	202.0
39	TraesCS5D01G554600	chr6B	93.701	127	8	0	6638	6764	316123705	316123579	2.500000e-44	191.0
40	TraesCS5D01G554600	chr2A	85.799	169	13	2	6635	6803	24956726	24956883	1.170000e-37	169.0
41	TraesCS5D01G554600	chrUn	97.143	35	0	1	2897	2931	68775951	68775984	2.650000e-04	58.4

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	TraesCS5D01G554600	chr5D	558715119	558721922	6803	False	5958.50	7989	100.00000	1	6804	2	chr5D.!!$F2	6803
1	TraesCS5D01G554600	chr5D	555446856	555449269	2413	True	1360.00	1360	77.35800	3583	5983	1	chr5D.!!$R3	2400
2	TraesCS5D01G554600	chr5D	556006329	556007875	1546	True	1131.00	1131	80.09000	4273	5810	1	chr5D.!!$R5	1537
3	TraesCS5D01G554600	chr5D	559915693	559916560	867	False	832.00	832	84.01400	983	1860	1	chr5D.!!$F1	877
4	TraesCS5D01G554600	chr5D	559981532	559983806	2274	False	781.00	913	80.92550	997	4878	2	chr5D.!!$F3	3881
5	TraesCS5D01G554600	chr5D	555455765	555456615	850	True	649.00	649	80.60000	1010	1869	1	chr5D.!!$R4	859
6	TraesCS5D01G554600	chr5B	704104294	704111179	6885	True	1425.75	3278	89.55275	43	6302	4	chr5B.!!$R2	6259
7	TraesCS5D01G554600	chr5B	696230474	696232277	1803	False	1005.00	1005	77.11300	3815	5601	1	chr5B.!!$F5	1786
8	TraesCS5D01G554600	chr5B	695991001	695992931	1930	False	989.00	989	76.31400	3788	5711	1	chr5B.!!$F4	1923
9	TraesCS5D01G554600	chr5B	695947512	695953233	5721	False	972.00	1345	78.69900	1007	5973	2	chr5B.!!$F7	4966
10	TraesCS5D01G554600	chr5B	695704711	695706322	1611	False	952.00	952	77.62800	3788	5389	1	chr5B.!!$F2	1601
11	TraesCS5D01G554600	chr5B	710342736	710345376	2640	False	834.50	904	81.61700	988	4935	2	chr5B.!!$F8	3947
12	TraesCS5D01G554600	chr5B	695548739	695552298	3559	False	706.00	1177	79.81600	1579	5619	2	chr5B.!!$F6	4040
13	TraesCS5D01G554600	chr4A	604848102	604849250	1148	True	902.00	902	80.94800	3784	4936	1	chr4A.!!$R1	1152
14	TraesCS5D01G554600	chr4A	604772889	604773767	878	False	828.00	828	83.74400	973	1860	1	chr4A.!!$F2	887
15	TraesCS5D01G554600	chr1B	597534290	597537519	3229	False	731.00	867	77.51600	1007	5710	2	chr1B.!!$F2	4703
16	TraesCS5D01G554600	chr1B	26426522	26427349	827	False	449.00	449	76.84100	1007	1835	1	chr1B.!!$F1	828
17	TraesCS5D01G554600	chr1B	25896022	25896841	819	True	396.00	396	75.77600	1010	1835	1	chr1B.!!$R1	825
18	TraesCS5D01G554600	chr1B	25945102	25945845	743	True	396.00	396	76.39300	1083	1835	1	chr1B.!!$R2	752

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
278	280	0.036875	GGCCTCCAAGTTGTAGCAGT	59.963	55.0	0.00	0.00	0.00	4.40	F
894	1180	0.103026	CGTCCTTGGATCGATGCAGA	59.897	55.0	19.31	11.80	0.00	4.26	F
2066	3762	0.033405	AGCAAGCCCATGAGCAGATT	60.033	50.0	0.76	0.00	34.23	2.40	F
2533	4229	0.041684	TCTCAGCCTCCAGGACATCA	59.958	55.0	0.00	0.00	37.39	3.07	F
2608	4304	0.322546	ATCACCCCTCAAAACCGCTC	60.323	55.0	0.00	0.00	0.00	5.03	F
2616	4312	0.326595	TCAAAACCGCTCCTGCCATA	59.673	50.0	0.00	0.00	35.36	2.74	F
3406	6889	0.575390	GCGTGGCACATATGTACGAC	59.425	55.0	26.07	18.77	44.52	4.34	F
5353	9793	0.473694	TGGCTGAACTGAGGGAGGAA	60.474	55.0	0.00	0.00	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2047	3743	0.033405	AATCTGCTCATGGGCTTGCT	60.033	50.000	20.42	0.11	0.00	3.91	R
2663	4359	0.033503	CCGCCTCCCTATGGGTTTTT	60.034	55.000	2.25	0.00	44.74	1.94	R
3129	6602	0.246635	CGGGGTGAACTAGTCTGTGG	59.753	60.000	0.00	0.00	0.00	4.17	R
3936	8341	3.827008	ACATGCGGTCATCAGTATTCT	57.173	42.857	0.00	0.00	0.00	2.40	R
4560	8967	3.372822	TCGCCGAATAAAACCTTGATGAC	59.627	43.478	0.00	0.00	0.00	3.06	R
4817	9224	2.523245	TGATGGTGGCTTTGTTATGCA	58.477	42.857	0.00	0.00	0.00	3.96	R
5494	9943	0.036388	TGGACCCTTTCGTGAGCATC	60.036	55.000	0.00	0.00	0.00	3.91	R
6507	11082	0.033601	TTGTTGGGCAGAACACCAGT	60.034	50.000	1.16	0.00	38.16	4.00	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
84	85	6.709846	GCAGATATTGAATCAGTAGCCTCTTT	59.290	38.462	0.00	0.00	0.00	2.52
92	94	9.912634	TTGAATCAGTAGCCTCTTTTATTTTTG	57.087	29.630	0.00	0.00	0.00	2.44
98	100	8.999431	CAGTAGCCTCTTTTATTTTTGTGACTA	58.001	33.333	0.00	0.00	0.00	2.59
99	101	9.000486	AGTAGCCTCTTTTATTTTTGTGACTAC	58.000	33.333	0.00	0.00	0.00	2.73
140	142	4.994907	ATCATTGCAGCAGCTAAATGAA	57.005	36.364	25.57	15.19	42.66	2.57
143	145	5.106442	TCATTGCAGCAGCTAAATGAAATG	58.894	37.500	22.08	15.08	39.06	2.32
147	149	3.855950	GCAGCAGCTAAATGAAATGTGTC	59.144	43.478	0.00	0.00	37.91	3.67
167	169	9.719355	ATGTGTCAGTGTTAATGAAATACTACA	57.281	29.630	0.00	0.00	37.43	2.74
168	170	9.203421	TGTGTCAGTGTTAATGAAATACTACAG	57.797	33.333	0.00	0.00	37.43	2.74
174	176	9.396022	AGTGTTAATGAAATACTACAGGAATGG	57.604	33.333	0.00	0.00	37.73	3.16
179	181	7.986085	ATGAAATACTACAGGAATGGCATAC	57.014	36.000	0.00	0.00	0.00	2.39
198	200	6.418226	GGCATACATACTCAGAAGACTAAACG	59.582	42.308	0.00	0.00	0.00	3.60
199	201	6.074782	GCATACATACTCAGAAGACTAAACGC	60.075	42.308	0.00	0.00	0.00	4.84
201	203	5.403246	ACATACTCAGAAGACTAAACGCTG	58.597	41.667	0.00	0.00	0.00	5.18
205	207	1.728971	CAGAAGACTAAACGCTGGCTG	59.271	52.381	0.00	0.00	0.00	4.85
209	211	2.245714	GACTAAACGCTGGCTGCAGC	62.246	60.000	30.88	30.88	44.25	5.25
210	212	2.032528	TAAACGCTGGCTGCAGCT	59.967	55.556	35.82	18.34	45.43	4.24
211	213	1.580845	CTAAACGCTGGCTGCAGCTT	61.581	55.000	35.82	23.53	45.43	3.74
212	214	1.855213	TAAACGCTGGCTGCAGCTTG	61.855	55.000	35.82	27.64	45.43	4.01
213	215	4.631247	ACGCTGGCTGCAGCTTGA	62.631	61.111	35.82	19.87	45.43	3.02
214	216	3.800863	CGCTGGCTGCAGCTTGAG	61.801	66.667	35.82	27.55	45.43	3.02
215	217	4.117661	GCTGGCTGCAGCTTGAGC	62.118	66.667	35.82	31.90	44.31	4.26
223	225	1.139095	GCAGCTTGAGCCTTGATGC	59.861	57.895	0.00	0.00	43.38	3.91
226	228	1.103803	AGCTTGAGCCTTGATGCATG	58.896	50.000	2.46	0.00	43.38	4.06
245	247	5.530543	TGCATGTCATTGTCAAGTAACAGAA	59.469	36.000	0.00	0.00	0.00	3.02

Showing 1 to 25 of 780 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	8.397906	GCTTCAATAATGCACTTGTGAATAGTA	58.602	33.333	4.79	0.00	0.00	1.82
35	36	7.094248	TGCTTCAATAATGCACTTGTGAATAGT	60.094	33.333	4.79	0.00	0.00	2.12
36	37	7.252708	TGCTTCAATAATGCACTTGTGAATAG	58.747	34.615	4.79	0.00	0.00	1.73
37	38	7.121020	TCTGCTTCAATAATGCACTTGTGAATA	59.879	33.333	4.79	0.00	32.91	1.75
38	39	6.028146	TGCTTCAATAATGCACTTGTGAAT	57.972	33.333	4.79	0.00	0.00	2.57
39	40	5.241285	TCTGCTTCAATAATGCACTTGTGAA	59.759	36.000	4.79	0.00	32.91	3.18
40	41	4.761227	TCTGCTTCAATAATGCACTTGTGA	59.239	37.500	4.79	0.00	32.91	3.58
41	42	5.050644	TCTGCTTCAATAATGCACTTGTG	57.949	39.130	0.00	0.00	32.91	3.33
106	108	7.308169	GCTGCTGCAATGATAGTGACATATTTA	60.308	37.037	11.11	0.00	39.41	1.40
110	112	3.811497	GCTGCTGCAATGATAGTGACATA	59.189	43.478	11.11	0.00	39.41	2.29
117	119	5.684550	TCATTTAGCTGCTGCAATGATAG	57.315	39.130	24.17	8.89	36.97	2.08
125	127	3.841643	ACACATTTCATTTAGCTGCTGC	58.158	40.909	13.43	7.62	40.05	5.25
128	130	4.855388	CACTGACACATTTCATTTAGCTGC	59.145	41.667	0.00	0.00	0.00	5.25
143	145	8.656849	CCTGTAGTATTTCATTAACACTGACAC	58.343	37.037	0.00	0.00	0.00	3.67
164	166	5.838521	TCTGAGTATGTATGCCATTCCTGTA	59.161	40.000	0.00	0.00	34.86	2.74
166	168	5.219343	TCTGAGTATGTATGCCATTCCTG	57.781	43.478	0.00	0.00	34.86	3.86
167	169	5.604231	TCTTCTGAGTATGTATGCCATTCCT	59.396	40.000	0.00	0.00	34.86	3.36
168	170	5.698545	GTCTTCTGAGTATGTATGCCATTCC	59.301	44.000	0.00	0.00	34.86	3.01
174	176	6.074782	GCGTTTAGTCTTCTGAGTATGTATGC	60.075	42.308	0.00	0.00	0.00	3.14
179	181	4.800993	CCAGCGTTTAGTCTTCTGAGTATG	59.199	45.833	0.00	0.00	0.00	2.39
205	207	1.139095	GCATCAAGGCTCAAGCTGC	59.861	57.895	1.46	0.00	41.70	5.25
209	211	2.089201	TGACATGCATCAAGGCTCAAG	58.911	47.619	0.00	0.00	34.04	3.02
210	212	2.203470	TGACATGCATCAAGGCTCAA	57.797	45.000	0.00	0.00	34.04	3.02
211	213	2.425668	CAATGACATGCATCAAGGCTCA	59.574	45.455	0.00	0.00	35.78	4.26
212	214	2.426024	ACAATGACATGCATCAAGGCTC	59.574	45.455	0.00	0.00	35.78	4.70

Showing 1 to 25 of 708 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.