AutoCloner

Multiple sequence alignment - TraesCS5A01G133100

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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	TraesCS5A01G133100	chr5A	100.000	4710	0	0	1	4710	299614775	299619484	0.000000e+00	8698
1	TraesCS5A01G133100	chr5A	96.842	475	12	1	4	475	48742156	48741682	0.000000e+00	791
2	TraesCS5A01G133100	chr7A	97.815	4714	86	4	1	4710	46896193	46900893	0.000000e+00	8118
3	TraesCS5A01G133100	chr3D	96.029	2946	94	9	1779	4710	146280527	146283463	0.000000e+00	4771
4	TraesCS5A01G133100	chr3D	96.085	1967	57	8	2595	4547	12137953	12139913	0.000000e+00	3188
5	TraesCS5A01G133100	chr3D	96.121	1289	36	2	496	1784	146275786	146277060	0.000000e+00	2091
6	TraesCS5A01G133100	chr3D	97.405	655	17	0	1131	1785	12135810	12136464	0.000000e+00	1116
7	TraesCS5A01G133100	chr3D	95.563	586	12	2	496	1081	12135240	12135811	0.000000e+00	926
8	TraesCS5A01G133100	chr3D	97.048	542	15	1	1779	2320	12137410	12137950	0.000000e+00	911
9	TraesCS5A01G133100	chr2D	96.327	2777	80	9	1788	4547	36499621	36496850	0.000000e+00	4543
10	TraesCS5A01G133100	chr2D	96.592	1115	26	2	673	1787	36501687	36500585	0.000000e+00	1838
11	TraesCS5A01G133100	chr2D	90.860	186	4	1	496	681	36503244	36503072	2.190000e-58	237
12	TraesCS5A01G133100	chr2D	84.507	213	12	7	496	706	44087507	44087314	1.730000e-44	191
13	TraesCS5A01G133100	chr7D	96.263	2783	81	8	1779	4547	168795742	168792969	0.000000e+00	4542
14	TraesCS5A01G133100	chr7D	95.789	2541	77	8	2184	4710	32510526	32513050	0.000000e+00	4072
15	TraesCS5A01G133100	chr7D	96.006	1252	37	1	536	1787	32507006	32508244	0.000000e+00	2023
16	TraesCS5A01G133100	chr7D	95.272	994	42	4	1779	2772	32509543	32510531	0.000000e+00	1570
17	TraesCS5A01G133100	chr7D	97.108	657	14	1	1131	1787	168797352	168796701	0.000000e+00	1103
18	TraesCS5A01G133100	chr7D	95.734	586	11	2	496	1081	168797922	168797351	0.000000e+00	931
19	TraesCS5A01G133100	chr1D	96.002	2151	68	6	2400	4536	46474794	46472648	0.000000e+00	3480
20	TraesCS5A01G133100	chr1D	97.348	641	17	0	1131	1771	46478952	46478312	0.000000e+00	1090
21	TraesCS5A01G133100	chr1D	95.563	586	12	2	496	1081	46479522	46478951	0.000000e+00	926
22	TraesCS5A01G133100	chr1D	96.781	497	15	1	1779	2275	46477344	46476849	0.000000e+00	828
23	TraesCS5A01G133100	chr1D	92.836	335	23	1	1	335	420023937	420024270	7.090000e-133	484
24	TraesCS5A01G133100	chr1D	94.220	173	7	1	326	495	420050540	420050712	1.300000e-65	261
25	TraesCS5A01G133100	chr1D	96.190	105	4	0	2310	2414	46476846	46476742	6.270000e-39	172
26	TraesCS5A01G133100	chr4D	97.070	1604	30	5	2958	4547	462827759	462829359	0.000000e+00	2686
27	TraesCS5A01G133100	chr4D	95.254	1180	54	2	1779	2958	462822071	462823248	0.000000e+00	1868
28	TraesCS5A01G133100	chr4D	97.869	657	14	0	1131	1787	462820458	462821114	0.000000e+00	1136
29	TraesCS5A01G133100	chr4D	95.392	586	13	2	496	1081	462819888	462820459	0.000000e+00	920
30	TraesCS5A01G133100	chr6B	91.120	1295	75	13	496	1787	7314209	7315466	0.000000e+00	1718
31	TraesCS5A01G133100	chr6B	91.776	535	29	7	2670	3203	7315625	7316145	0.000000e+00	730
32	TraesCS5A01G133100	chr6B	83.673	392	42	11	496	884	157479660	157479288	2.700000e-92	350
33	TraesCS5A01G133100	chr6B	94.030	67	4	0	4644	4710	7316826	7316892	8.340000e-18	102
34	TraesCS5A01G133100	chr7B	94.703	774	38	3	3749	4519	700522075	700521302	0.000000e+00	1199
35	TraesCS5A01G133100	chr7B	92.205	526	30	4	2675	3200	700512915	700512401	0.000000e+00	734
36	TraesCS5A01G133100	chr7B	86.164	477	51	8	20	482	8908289	8908764	7.040000e-138	501
37	TraesCS5A01G133100	chr5B	96.988	498	11	2	1	495	6607882	6608378	0.000000e+00	833
38	TraesCS5A01G133100	chr6A	97.071	478	11	1	1	475	39947602	39947125	0.000000e+00	802
39	TraesCS5A01G133100	chr1A	96.444	478	14	1	1	475	5989984	5989507	0.000000e+00	785
40	TraesCS5A01G133100	chr1A	95.188	478	20	1	1	475	50495714	50496191	0.000000e+00	752
41	TraesCS5A01G133100	chr3B	90.760	487	25	10	4	485	61545306	61544835	2.390000e-177	632
42	TraesCS5A01G133100	chr3B	90.000	130	13	0	4515	4644	28319365	28319236	8.110000e-38	169
43	TraesCS5A01G133100	chr4B	83.333	468	57	11	3354	3803	158268047	158268511	3.390000e-111	412
44	TraesCS5A01G133100	chr1B	86.765	272	28	4	1855	2118	398144968	398145239	3.560000e-76	296
45	TraesCS5A01G133100	chr1B	88.298	94	7	3	4554	4645	67540306	67540397	4.980000e-20	110
46	TraesCS5A01G133100	chr2B	84.643	280	23	11	496	772	94927245	94927507	1.300000e-65	261
47	TraesCS5A01G133100	chr2A	86.458	192	9	8	493	684	61286957	61287131	1.340000e-45	195
48	TraesCS5A01G133100	chr2A	93.233	133	5	4	4515	4646	341628358	341628229	4.810000e-45	193
49	TraesCS5A01G133100	chr4A	93.846	130	5	3	4515	4643	565745561	565745688	4.810000e-45	193

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	TraesCS5A01G133100	chr5A	299614775	299619484	4709	False	8698.00	8698	100.000000	1	4710	1	chr5A.!!$F1	4709
1	TraesCS5A01G133100	chr7A	46896193	46900893	4700	False	8118.00	8118	97.815000	1	4710	1	chr7A.!!$F1	4709
2	TraesCS5A01G133100	chr3D	146275786	146283463	7677	False	3431.00	4771	96.075000	496	4710	2	chr3D.!!$F2	4214
3	TraesCS5A01G133100	chr3D	12135240	12139913	4673	False	1535.25	3188	96.525250	496	4547	4	chr3D.!!$F1	4051
4	TraesCS5A01G133100	chr2D	36496850	36503244	6394	True	2206.00	4543	94.593000	496	4547	3	chr2D.!!$R2	4051
5	TraesCS5A01G133100	chr7D	32507006	32513050	6044	False	2555.00	4072	95.689000	536	4710	3	chr7D.!!$F1	4174
6	TraesCS5A01G133100	chr7D	168792969	168797922	4953	True	2192.00	4542	96.368333	496	4547	3	chr7D.!!$R1	4051
7	TraesCS5A01G133100	chr1D	46472648	46479522	6874	True	1299.20	3480	96.376800	496	4536	5	chr1D.!!$R1	4040
8	TraesCS5A01G133100	chr4D	462827759	462829359	1600	False	2686.00	2686	97.070000	2958	4547	1	chr4D.!!$F1	1589
9	TraesCS5A01G133100	chr4D	462819888	462823248	3360	False	1308.00	1868	96.171667	496	2958	3	chr4D.!!$F2	2462
10	TraesCS5A01G133100	chr6B	7314209	7316892	2683	False	850.00	1718	92.308667	496	4710	3	chr6B.!!$F1	4214
11	TraesCS5A01G133100	chr7B	700521302	700522075	773	True	1199.00	1199	94.703000	3749	4519	1	chr7B.!!$R2	770
12	TraesCS5A01G133100	chr7B	700512401	700512915	514	True	734.00	734	92.205000	2675	3200	1	chr7B.!!$R1	525

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
676	2073	0.469070	CAGGAGAGATTGGCTCAGGG	59.531	60.000	0.00	0.00	46.45	4.45	F
1200	2651	1.227734	GCCGGCCGGTACATATGTT	60.228	57.895	42.53	0.00	37.65	2.71	F
1501	2953	4.098894	TCCTACCCAAATCCGAGTACTTT	58.901	43.478	0.00	0.00	0.00	2.66	F
2024	7286	1.231958	GGCGATTGTTGGTCGGTTGA	61.232	55.000	0.00	0.00	39.38	3.18	F
2181	7443	1.371337	GCGAGCTGATGCATCCACAA	61.371	55.000	23.67	4.23	42.74	3.33	F
2780	10587	2.101575	GCTCATCGTACACGCCGA	59.898	61.111	0.00	0.00	39.60	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2006	7268	0.165944	CTCAACCGACCAACAATCGC	59.834	55.000	0.00	38.27	4.58	R
2024	7286	1.963338	GCTCGTGTTGCAAGCTCCT	60.963	57.895	0.00	33.23	3.69	R
3419	11228	2.522185	TGTAAGGGAGCTTCGTGTACT	58.478	47.619	0.00	0.00	2.73	R
3421	11230	3.555586	GGTTTGTAAGGGAGCTTCGTGTA	60.556	47.826	0.00	0.00	2.90	R
3490	11299	5.431420	TTTGCTTACGTGTTTGATGTGAT	57.569	34.783	0.00	0.00	3.06	R
4194	12019	5.725362	AGGAAGTAGAATAAGTGTCACTGC	58.275	41.667	6.18	0.00	4.40	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	0.472471	ATGTGGTTCGGTGGTCAACT	59.528	50.000	0.00	0.00	0.00	3.16
153	154	4.158764	TCTGATCCGAACCTTCTTCTCTTC	59.841	45.833	0.00	0.00	0.00	2.87
221	222	3.075884	GAGGTGTTCGAGTAGTCTGTCT	58.924	50.000	0.00	0.00	0.00	3.41
231	232	2.781431	TAGTCTGTCTCGGGGCTGCA	62.781	60.000	0.50	0.00	0.00	4.41
300	301	1.847328	CCGGCTGGGGTTCTTATTTT	58.153	50.000	2.57	0.00	0.00	1.82
334	335	1.074775	GCAACTGGGACCATGGTGA	59.925	57.895	25.52	4.78	0.00	4.02
362	363	2.519541	CCTCTCCGGCTGGATCGA	60.520	66.667	16.52	9.15	45.33	3.59
388	389	7.176690	ACAGTCTATCCACCCAGTAAATTTTTG	59.823	37.037	0.00	0.00	0.00	2.44
588	592	2.569404	GACCCTCTCTGACCAGTTTGAT	59.431	50.000	0.00	0.00	0.00	2.57
649	653	3.326297	GCTAGCAGGGAGAGGAATATTGT	59.674	47.826	10.63	0.00	0.00	2.71
676	2073	0.469070	CAGGAGAGATTGGCTCAGGG	59.531	60.000	0.00	0.00	46.45	4.45
728	2127	9.994432	CTATTTCCTCACATAGTTTGATTTGTC	57.006	33.333	0.00	0.00	0.00	3.18
888	2287	1.626654	CGTGCCATGTCGAGTTGGAC	61.627	60.000	15.97	10.36	34.81	4.02
935	2334	7.761704	TCTTGTAGTCAAATTAGTGAGATGCTC	59.238	37.037	0.00	0.00	32.87	4.26
1200	2651	1.227734	GCCGGCCGGTACATATGTT	60.228	57.895	42.53	0.00	37.65	2.71
1501	2953	4.098894	TCCTACCCAAATCCGAGTACTTT	58.901	43.478	0.00	0.00	0.00	2.66
1733	3185	7.962441	TGATCTGTGCTGGCTATAGTTTATTA	58.038	34.615	0.84	0.00	0.00	0.98
1824	7086	9.847224	TCTAATTTCCTGAAAGTTGTTAGTCTT	57.153	29.630	0.00	0.00	33.32	3.01
2006	7268	4.477975	GACCGGAGACTGTCGCGG	62.478	72.222	9.46	16.16	41.95	6.46
2024	7286	1.231958	GGCGATTGTTGGTCGGTTGA	61.232	55.000	0.00	0.00	39.38	3.18
2181	7443	1.371337	GCGAGCTGATGCATCCACAA	61.371	55.000	23.67	4.23	42.74	3.33
2293	7555	5.506982	GCCGTGTTTAATATCCTACTCGTCT	60.507	44.000	0.00	0.00	0.00	4.18
2491	9715	3.756434	GGCATGTTAGGCTTGTTGTAGAA	59.244	43.478	0.00	0.00	0.00	2.10
2543	9767	8.859236	ATTGCTAGATGTGCTATGATTGTTAT	57.141	30.769	0.00	0.00	0.00	1.89
2583	9807	8.500773	GGTAACTACTGACGAATTTTGATTCAA	58.499	33.333	0.00	0.00	0.00	2.69
2780	10587	2.101575	GCTCATCGTACACGCCGA	59.898	61.111	0.00	0.00	39.60	5.54
3231	11040	5.407407	TCAGGTAAATCAGACCAAGACTC	57.593	43.478	0.00	0.00	39.65	3.36
3419	11228	7.857404	TGGGGGTTTTCAATTTATGAGTAAA	57.143	32.000	0.00	0.00	39.77	2.01
3421	11230	7.511028	TGGGGGTTTTCAATTTATGAGTAAAGT	59.489	33.333	0.00	0.00	39.77	2.66
3490	11299	3.255395	TGCATTTTTCTTCATCGGCTTCA	59.745	39.130	0.00	0.00	0.00	3.02
3765	11587	6.830324	TCTTTCTTCCATGGTGATTCCTATTG	59.170	38.462	12.58	0.00	37.07	1.90
4171	11996	2.607187	GTGCTAGCACTGACAACGTAT	58.393	47.619	35.25	0.00	43.12	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	2.342659	AGCCATACCATACTGCATCCT	58.657	47.619	0.00	0.00	0.00	3.24
153	154	3.725459	TTGGTGCGTGCATGAGCG	61.725	61.111	10.93	0.00	46.23	5.03
248	249	0.254178	AGCAATGGCAAGACGGAGAT	59.746	50.000	0.00	0.00	44.61	2.75
300	301	3.849951	GCGGAAGGCCTCGATGGA	61.850	66.667	17.43	0.00	38.35	3.41
334	335	1.698506	CCGGAGAGGAAGCTATCAGT	58.301	55.000	0.00	0.00	45.00	3.41
362	363	6.388619	AAATTTACTGGGTGGATAGACTGT	57.611	37.500	0.00	0.00	0.00	3.55
588	592	1.321474	CTTGGCCTCAAACTGAAGCA	58.679	50.000	3.32	0.00	35.60	3.91
649	653	1.493861	CAATCTCTCCTGCCTCCTCA	58.506	55.000	0.00	0.00	0.00	3.86
676	2073	3.438434	GGGCTCAAGTGAAAGTCATCTTC	59.562	47.826	0.00	0.00	32.90	2.87
728	2127	9.283768	TGTATTTCAGTACCAATATAATGCAGG	57.716	33.333	0.00	0.00	0.00	4.85
888	2287	0.179174	GAAAAATACGCCACCGCCAG	60.179	55.000	0.00	0.00	38.22	4.85
1200	2651	6.541907	AGAGTCTGAGATAGATGATGCACTA	58.458	40.000	0.00	0.00	37.83	2.74
1501	2953	1.136828	AGGTGTACAGTGCCTTGGAA	58.863	50.000	0.00	0.00	0.00	3.53
1733	3185	1.869767	CAAGACTTCGAAGCAAGCAGT	59.130	47.619	24.86	4.00	0.00	4.40
1824	7086	7.522073	GCATCTAGGAAAATAAATGCATCCGAA	60.522	37.037	0.00	0.00	39.36	4.30
2006	7268	0.165944	CTCAACCGACCAACAATCGC	59.834	55.000	0.00	0.00	38.27	4.58
2024	7286	1.963338	GCTCGTGTTGCAAGCTCCT	60.963	57.895	0.00	0.00	33.23	3.69
2181	7443	2.159184	AGATGCAGTCGACGATGATGTT	60.159	45.455	10.46	0.00	0.00	2.71
2293	7555	2.833121	TGCTCGAGATAGGCGGCA	60.833	61.111	18.75	1.38	34.36	5.69
2543	9767	5.421056	CAGTAGTTACCATTCCCACTGTCTA	59.579	44.000	0.00	0.00	0.00	2.59
2583	9807	9.953565	TGTTCTTGCTTATAGTAACTAACCAAT	57.046	29.630	0.00	0.00	0.00	3.16
2780	10587	2.949177	TAAGTTGAGCACCACCATGT	57.051	45.000	0.00	0.00	0.00	3.21
2905	10712	7.345914	AGAGTTAGCTTGTACTATTTCCTCCAT	59.654	37.037	0.00	0.00	0.00	3.41
3231	11040	4.839121	AGAGTGGCTATCTATAGTCTCCG	58.161	47.826	0.00	0.00	36.02	4.63
3289	11098	6.166279	GGAGATGTAGTCACTTCATTGTCAA	58.834	40.000	0.00	0.00	32.56	3.18
3419	11228	2.522185	TGTAAGGGAGCTTCGTGTACT	58.478	47.619	0.00	0.00	0.00	2.73
3421	11230	3.555586	GGTTTGTAAGGGAGCTTCGTGTA	60.556	47.826	0.00	0.00	0.00	2.90
3490	11299	5.431420	TTTGCTTACGTGTTTGATGTGAT	57.569	34.783	0.00	0.00	0.00	3.06
3765	11587	9.413048	GATAATCCTGCTAGTACAACTATGAAC	57.587	37.037	0.00	0.00	29.08	3.18
4194	12019	5.725362	AGGAAGTAGAATAAGTGTCACTGC	58.275	41.667	6.18	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.