AutoCloner

Multiple sequence alignment - TraesCS5B01G090700

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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	TraesCS5B01G090700	chr5B	100.000	2716	0	0	1	2716	117897482	117894767	0.000000e+00	5016.0
1	TraesCS5B01G090700	chrUn	97.846	1764	23	5	960	2716	305945868	305947623	0.000000e+00	3033.0
2	TraesCS5B01G090700	chrUn	94.444	126	6	1	834	959	305945784	305945908	2.760000e-45	193.0
3	TraesCS5B01G090700	chrUn	97.059	34	1	0	1981	2014	305946982	305947015	1.050000e-04	58.4
4	TraesCS5B01G090700	chr7A	92.248	1793	68	22	960	2716	5206980	5205223	0.000000e+00	2475.0
5	TraesCS5B01G090700	chr7A	91.500	1800	98	19	960	2716	377638047	377639834	0.000000e+00	2425.0
6	TraesCS5B01G090700	chr7A	86.174	311	29	7	978	1281	511879427	511879124	9.380000e-85	324.0
7	TraesCS5B01G090700	chr7A	90.598	117	10	1	833	949	5207065	5206950	1.300000e-33	154.0
8	TraesCS5B01G090700	chr7A	91.111	90	6	1	1810	1897	477225605	477225694	1.320000e-23	121.0
9	TraesCS5B01G090700	chr2B	93.101	1174	34	10	960	2097	521325946	521324784	0.000000e+00	1676.0
10	TraesCS5B01G090700	chr2B	91.429	350	8	2	2388	2716	521324788	521324440	6.850000e-126	460.0
11	TraesCS5B01G090700	chr2B	87.339	387	20	4	2351	2716	141002379	141002001	1.500000e-112	416.0
12	TraesCS5B01G090700	chr2B	91.765	255	18	1	2320	2574	113270475	113270726	4.300000e-93	351.0
13	TraesCS5B01G090700	chr2B	85.185	324	31	8	960	1276	467554906	467554593	1.570000e-82	316.0
14	TraesCS5B01G090700	chr2B	80.159	126	24	1	834	959	467554990	467554866	2.880000e-15	93.5
15	TraesCS5B01G090700	chr5A	95.102	837	27	6	1	835	110662819	110661995	0.000000e+00	1306.0
16	TraesCS5B01G090700	chr5A	81.061	132	16	7	832	959	596570839	596570965	2.230000e-16	97.1
17	TraesCS5B01G090700	chr5A	91.803	61	5	0	899	959	490831386	490831446	4.820000e-13	86.1
18	TraesCS5B01G090700	chr5D	94.970	835	23	6	1	835	107778258	107777443	0.000000e+00	1291.0
19	TraesCS5B01G090700	chr4A	88.563	647	60	8	1013	1646	556470207	556469562	0.000000e+00	773.0
20	TraesCS5B01G090700	chr4A	96.491	171	6	0	1949	2119	556469323	556469153	1.590000e-72	283.0
21	TraesCS5B01G090700	chr4A	89.773	176	16	2	2541	2716	738713149	738712976	9.790000e-55	224.0
22	TraesCS5B01G090700	chr7D	89.570	604	46	3	1060	1646	227551519	227552122	0.000000e+00	750.0
23	TraesCS5B01G090700	chr7D	87.519	665	58	7	1006	1646	261515594	261516257	0.000000e+00	745.0
24	TraesCS5B01G090700	chr7D	94.143	461	17	4	2114	2574	227552606	227553056	0.000000e+00	693.0
25	TraesCS5B01G090700	chr7D	93.059	461	20	5	2114	2574	261516741	261517189	0.000000e+00	664.0
26	TraesCS5B01G090700	chr7D	97.358	265	7	0	1946	2210	227552358	227552622	4.120000e-123	451.0
27	TraesCS5B01G090700	chr7D	96.604	265	9	0	1946	2210	261516493	261516757	8.930000e-120	440.0
28	TraesCS5B01G090700	chr7D	93.617	235	14	1	1641	1875	227552160	227552393	1.550000e-92	350.0
29	TraesCS5B01G090700	chr7D	100.000	28	0	0	2004	2031	66994312	66994339	5.000000e-03	52.8
30	TraesCS5B01G090700	chr4D	93.878	392	14	4	2059	2450	34598823	34598442	1.400000e-162	582.0
31	TraesCS5B01G090700	chr4D	87.319	276	14	1	2447	2701	34595702	34595427	2.040000e-76	296.0
32	TraesCS5B01G090700	chr4D	97.059	34	1	0	1981	2014	34598807	34598774	1.050000e-04	58.4
33	TraesCS5B01G090700	chr2D	88.172	465	34	5	2126	2580	634860913	634860460	3.980000e-148	534.0
34	TraesCS5B01G090700	chr2D	91.892	111	9	0	1865	1975	234356560	234356450	3.620000e-34	156.0
35	TraesCS5B01G090700	chr2D	96.512	86	3	0	1854	1939	234356496	234356411	2.820000e-30	143.0
36	TraesCS5B01G090700	chr3A	81.425	716	76	29	978	1646	2147984	2147279	1.430000e-147	532.0
37	TraesCS5B01G090700	chr3A	81.198	718	76	38	978	1646	3084922	3084215	8.620000e-145	523.0
38	TraesCS5B01G090700	chr3A	79.456	735	80	31	961	1646	426657997	426658709	3.190000e-124	455.0
39	TraesCS5B01G090700	chr3A	92.157	255	17	1	2320	2574	426666566	426666817	9.250000e-95	357.0
40	TraesCS5B01G090700	chr3A	96.591	88	3	0	2627	2714	160866103	160866190	2.180000e-31	147.0
41	TraesCS5B01G090700	chr3A	96.512	86	3	0	1854	1939	160865959	160866044	2.820000e-30	143.0
42	TraesCS5B01G090700	chr3A	90.323	93	7	1	1810	1900	12991059	12990967	1.320000e-23	121.0
43	TraesCS5B01G090700	chr3A	81.250	128	19	5	834	959	596920647	596920771	6.190000e-17	99.0
44	TraesCS5B01G090700	chr3A	96.429	56	2	0	1688	1743	1971419	1971364	2.880000e-15	93.5
45	TraesCS5B01G090700	chr3A	80.800	125	19	5	834	956	596869663	596869784	2.880000e-15	93.5
46	TraesCS5B01G090700	chr3A	80.315	127	22	3	834	959	649830554	649830678	2.880000e-15	93.5
47	TraesCS5B01G090700	chr3A	89.231	65	7	0	1911	1975	160865941	160866005	6.230000e-12	82.4
48	TraesCS5B01G090700	chr3D	78.322	715	93	38	960	1646	89271786	89272466	3.260000e-109	405.0
49	TraesCS5B01G090700	chr1B	95.181	249	12	0	2320	2568	253046609	253046857	7.050000e-106	394.0
50	TraesCS5B01G090700	chr6A	84.078	358	43	5	1300	1646	18708077	18707723	1.560000e-87	333.0
51	TraesCS5B01G090700	chr6D	87.676	284	26	1	1300	1574	18013010	18013293	3.370000e-84	322.0

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	TraesCS5B01G090700	chr5B	117894767	117897482	2715	True	5016.000000	5016	100.000000	1	2716	1	chr5B.!!$R1	2715
1	TraesCS5B01G090700	chrUn	305945784	305947623	1839	False	1094.800000	3033	96.449667	834	2716	3	chrUn.!!$F1	1882
2	TraesCS5B01G090700	chr7A	377638047	377639834	1787	False	2425.000000	2425	91.500000	960	2716	1	chr7A.!!$F1	1756
3	TraesCS5B01G090700	chr7A	5205223	5207065	1842	True	1314.500000	2475	91.423000	833	2716	2	chr7A.!!$R2	1883
4	TraesCS5B01G090700	chr2B	521324440	521325946	1506	True	1068.000000	1676	92.265000	960	2716	2	chr2B.!!$R3	1756
5	TraesCS5B01G090700	chr5A	110661995	110662819	824	True	1306.000000	1306	95.102000	1	835	1	chr5A.!!$R1	834
6	TraesCS5B01G090700	chr5D	107777443	107778258	815	True	1291.000000	1291	94.970000	1	835	1	chr5D.!!$R1	834
7	TraesCS5B01G090700	chr4A	556469153	556470207	1054	True	528.000000	773	92.527000	1013	2119	2	chr4A.!!$R2	1106
8	TraesCS5B01G090700	chr7D	261515594	261517189	1595	False	616.333333	745	92.394000	1006	2574	3	chr7D.!!$F3	1568
9	TraesCS5B01G090700	chr7D	227551519	227553056	1537	False	561.000000	750	93.672000	1060	2574	4	chr7D.!!$F2	1514
10	TraesCS5B01G090700	chr4D	34595427	34598823	3396	True	312.133333	582	92.752000	1981	2701	3	chr4D.!!$R1	720
11	TraesCS5B01G090700	chr3A	2147279	2147984	705	True	532.000000	532	81.425000	978	1646	1	chr3A.!!$R2	668
12	TraesCS5B01G090700	chr3A	3084215	3084922	707	True	523.000000	523	81.198000	978	1646	1	chr3A.!!$R3	668
13	TraesCS5B01G090700	chr3A	426657997	426658709	712	False	455.000000	455	79.456000	961	1646	1	chr3A.!!$F1	685
14	TraesCS5B01G090700	chr3D	89271786	89272466	680	False	405.000000	405	78.322000	960	1646	1	chr3D.!!$F1	686

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
818	821	0.250338	GCTCCTGGTTTCGTTCACCT	60.25	55.0	0.0	0.0	35.07	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1758	1931	0.321919	GCATCCTGTTGGCTGTCTCA	60.322	55.0	0.0	0.0	32.39	3.27	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	115	2.284921	CCTCCAGCTCCAGGACCA	60.285	66.667	1.55	0.00	30.32	4.02
194	195	4.529731	GAATCCTGCCCCTGCCCC	62.530	72.222	0.00	0.00	36.33	5.80
269	270	2.437396	CCCTTGCCCCCATGATTGC	61.437	63.158	0.00	0.00	0.00	3.56
283	284	5.009410	CCCATGATTGCTGAGATTTAGGAAC	59.991	44.000	0.00	0.00	0.00	3.62
316	317	3.568007	TCACAACAGGTAGGCAAATGAAC	59.432	43.478	0.00	0.00	0.00	3.18
325	326	6.375455	CAGGTAGGCAAATGAACTATTTCAGT	59.625	38.462	1.80	0.00	45.07	3.41
517	520	5.837437	AGCGTGTGATTGTTAATTTTTCCA	58.163	33.333	0.00	0.00	0.00	3.53
521	524	7.043059	GCGTGTGATTGTTAATTTTTCCAAAGA	60.043	33.333	0.00	0.00	0.00	2.52
587	590	4.715297	ACGGAGTTGATTAAGTACTGGGAT	59.285	41.667	0.00	0.00	37.78	3.85
681	684	3.751175	CGGTACATGAAAGTTGGTGTCAT	59.249	43.478	0.00	0.00	32.17	3.06
712	715	1.480954	TCCGTTGACTGGAAGATAGGC	59.519	52.381	0.00	0.00	37.43	3.93
751	754	9.912634	ATTGACTTCTTTTGTACAATATGGTTG	57.087	29.630	9.56	0.26	0.00	3.77
818	821	0.250338	GCTCCTGGTTTCGTTCACCT	60.250	55.000	0.00	0.00	35.07	4.00
835	838	7.977853	TCGTTCACCTAATCTTTTGATAGGTAC	59.022	37.037	3.57	0.00	39.07	3.34
836	839	7.980099	CGTTCACCTAATCTTTTGATAGGTACT	59.020	37.037	3.57	0.00	39.07	2.73
837	840	9.315525	GTTCACCTAATCTTTTGATAGGTACTC	57.684	37.037	3.57	0.00	39.07	2.59
838	841	8.019656	TCACCTAATCTTTTGATAGGTACTCC	57.980	38.462	3.57	0.00	39.07	3.85
848	851	3.053095	TGATAGGTACTCCCTTCCGTCTT	60.053	47.826	0.00	0.00	42.73	3.01
909	912	1.095807	GCTAATTCCCGACACAGCCC	61.096	60.000	0.00	0.00	0.00	5.19
949	952	3.749064	GACACTCCGCCGCTCTGA	61.749	66.667	0.00	0.00	0.00	3.27
951	954	4.056125	CACTCCGCCGCTCTGACA	62.056	66.667	0.00	0.00	0.00	3.58
952	955	3.071206	ACTCCGCCGCTCTGACAT	61.071	61.111	0.00	0.00	0.00	3.06
953	956	1.753078	ACTCCGCCGCTCTGACATA	60.753	57.895	0.00	0.00	0.00	2.29
954	957	1.007964	CTCCGCCGCTCTGACATAG	60.008	63.158	0.00	0.00	0.00	2.23
955	958	2.028190	CCGCCGCTCTGACATAGG	59.972	66.667	0.00	0.00	0.00	2.57
956	959	2.659897	CGCCGCTCTGACATAGGC	60.660	66.667	0.00	0.00	44.00	3.93
957	960	2.659897	GCCGCTCTGACATAGGCG	60.660	66.667	9.01	9.01	42.17	5.52
958	961	2.659897	CCGCTCTGACATAGGCGC	60.660	66.667	0.00	0.00	41.60	6.53
968	971	1.038130	ACATAGGCGCCGTCTTCTCT	61.038	55.000	23.20	2.71	0.00	3.10
972	975	2.048127	GCGCCGTCTTCTCTGGTT	60.048	61.111	0.00	0.00	0.00	3.67
1005	1008	0.104855	TCTGACATAGGCGCATGGAC	59.895	55.000	10.83	5.10	0.00	4.02
1006	1009	1.217585	CTGACATAGGCGCATGGACG	61.218	60.000	10.83	0.00	0.00	4.79
1148	1160	2.239907	CCTCCCGAATCTTCCCTCTTTT	59.760	50.000	0.00	0.00	0.00	2.27
1758	1931	2.242043	CCAGCCCAAAGTTGATGAAGT	58.758	47.619	0.00	0.00	0.00	3.01
1780	1953	2.036098	CAGCCAACAGGATGCCCA	59.964	61.111	0.00	0.00	42.53	5.36
1845	2018	4.659111	TTAGACTGAGTGTTCACCGAAA	57.341	40.909	0.00	0.00	0.00	3.46
2104	2294	1.202177	CGAACAAGGTGCATATGCCAC	60.202	52.381	24.54	20.14	41.18	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	115	3.760035	CCGCGCTCCCTGTACACT	61.760	66.667	5.56	0.00	0.00	3.55
153	154	0.182537	TGACAAAGTGACCACCAGGG	59.817	55.000	0.00	0.00	44.81	4.45
210	211	3.454858	AGAATTAGGAACTGGAGCTGGA	58.545	45.455	0.00	0.00	41.52	3.86
213	214	4.141914	CGGTAAGAATTAGGAACTGGAGCT	60.142	45.833	0.00	0.00	41.52	4.09
269	270	4.142665	TGACTCGACGTTCCTAAATCTCAG	60.143	45.833	0.00	0.00	0.00	3.35
283	284	1.721389	CCTGTTGTGAATGACTCGACG	59.279	52.381	0.00	0.00	31.30	5.12
325	326	7.108841	CCTGTACAGGCAGTAAACTAGAATA	57.891	40.000	28.48	0.00	42.44	1.75
435	436	3.512154	TACTGGTGACCCCGACCGT	62.512	63.158	0.00	0.00	36.12	4.83
484	487	0.676782	ATCACACGCTAAGGCCCAAC	60.677	55.000	0.00	0.00	34.44	3.77
517	520	2.162681	CCGAAGCAAGGGATGTTCTTT	58.837	47.619	0.00	0.00	0.00	2.52
521	524	0.400213	TCACCGAAGCAAGGGATGTT	59.600	50.000	0.00	0.00	0.00	2.71
587	590	4.612712	GCAAACACTACTAGCATTTTCGCA	60.613	41.667	0.00	0.00	0.00	5.10
639	642	9.499479	TGTACCGAATACCAACAAATAAGTAAA	57.501	29.630	0.00	0.00	32.16	2.01
640	643	9.669887	ATGTACCGAATACCAACAAATAAGTAA	57.330	29.630	0.00	0.00	32.16	2.24
681	684	2.160615	CAGTCAACGGAAACACAACACA	59.839	45.455	0.00	0.00	0.00	3.72
682	685	2.477189	CCAGTCAACGGAAACACAACAC	60.477	50.000	0.00	0.00	0.00	3.32
712	715	9.403110	CAAAAGAAGTCAATTATTCCTGACAAG	57.597	33.333	5.13	0.00	43.64	3.16
751	754	1.873863	GTACAAGGGCCTTCGTTGC	59.126	57.895	17.86	10.59	42.98	4.17
848	851	3.117701	TGACCATGAGGACAACTTTTCCA	60.118	43.478	0.00	0.00	36.64	3.53
909	912	1.137825	GGAGAAGACGAGGAGTGCG	59.862	63.158	0.00	0.00	0.00	5.34
949	952	1.038130	AGAGAAGACGGCGCCTATGT	61.038	55.000	26.68	15.78	0.00	2.29
951	954	1.736586	CAGAGAAGACGGCGCCTAT	59.263	57.895	26.68	13.07	0.00	2.57
952	955	2.415608	CCAGAGAAGACGGCGCCTA	61.416	63.158	26.68	0.00	0.00	3.93
953	956	3.764466	CCAGAGAAGACGGCGCCT	61.764	66.667	26.68	11.91	0.00	5.52
954	957	3.591254	AACCAGAGAAGACGGCGCC	62.591	63.158	19.07	19.07	0.00	6.53
955	958	2.048127	AACCAGAGAAGACGGCGC	60.048	61.111	6.90	0.00	0.00	6.53
956	959	1.009389	GTCAACCAGAGAAGACGGCG	61.009	60.000	4.80	4.80	0.00	6.46
957	960	0.033504	TGTCAACCAGAGAAGACGGC	59.966	55.000	0.00	0.00	33.83	5.68
958	961	1.341531	AGTGTCAACCAGAGAAGACGG	59.658	52.381	0.00	0.00	33.83	4.79
968	971	4.980805	GCGGCGGAGTGTCAACCA	62.981	66.667	9.78	0.00	0.00	3.67
972	975	4.056125	CAGAGCGGCGGAGTGTCA	62.056	66.667	9.78	0.00	0.00	3.58
1010	1013	3.917760	CAGGGGATCTCCGGCGAC	61.918	72.222	9.30	0.00	36.71	5.19
1158	1172	2.437413	GCGGGAGGAAGAAGAAACAAT	58.563	47.619	0.00	0.00	0.00	2.71
1454	1540	3.374402	CCTCGAGCACCGTGACCT	61.374	66.667	6.99	0.00	39.75	3.85
1758	1931	0.321919	GCATCCTGTTGGCTGTCTCA	60.322	55.000	0.00	0.00	32.39	3.27
1780	1953	4.178540	CCTTGCTCGAAATTGATTTGCAT	58.821	39.130	0.00	0.00	29.96	3.96
2104	2294	3.311322	TCAGTTTGCTGTTCGGTTTACAG	59.689	43.478	0.00	0.00	44.55	2.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.