AutoCloner

Multiple sequence alignment - TraesCS4A01G153600

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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	TraesCS4A01G153600	chr4A	100.000	2766	0	0	1	2766	309515772	309513007	0.000000e+00	5108
1	TraesCS4A01G153600	chr3D	96.387	2768	86	9	1	2766	589278902	589281657	0.000000e+00	4545
2	TraesCS4A01G153600	chr5D	96.279	2768	91	9	1	2766	503277584	503280341	0.000000e+00	4530
3	TraesCS4A01G153600	chr5D	96.208	2769	92	9	1	2766	6189582	6186824	0.000000e+00	4519
4	TraesCS4A01G153600	chr5D	95.451	2770	109	13	1	2766	432402855	432405611	0.000000e+00	4401
5	TraesCS4A01G153600	chr5D	96.562	2094	68	3	1	2093	503218860	503216770	0.000000e+00	3465
6	TraesCS4A01G153600	chr1D	96.172	2769	94	8	1	2766	254397467	254400226	0.000000e+00	4516
7	TraesCS4A01G153600	chr1A	96.172	2769	86	9	1	2766	554512890	554510139	0.000000e+00	4508
8	TraesCS4A01G153600	chr5A	95.340	2768	118	8	1	2766	607275042	607272284	0.000000e+00	4386
9	TraesCS4A01G153600	chr6D	96.659	2095	65	4	1	2093	168255568	168253477	0.000000e+00	3476
10	TraesCS4A01G153600	chr6D	96.045	1593	49	9	1179	2766	45519037	45517454	0.000000e+00	2580
11	TraesCS4A01G153600	chrUn	96.611	2095	65	5	1	2093	93408989	93411079	0.000000e+00	3470
12	TraesCS4A01G153600	chrUn	96.641	923	24	4	1845	2766	239345464	239346380	0.000000e+00	1526
13	TraesCS4A01G153600	chr7B	87.333	1050	105	18	1724	2766	719442377	719441349	0.000000e+00	1177
14	TraesCS4A01G153600	chr2B	94.981	259	12	1	2080	2337	755374055	755374313	3.320000e-109	405

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	TraesCS4A01G153600	chr4A	309513007	309515772	2765	True	5108	5108	100.000	1	2766	1	chr4A.!!$R1	2765
1	TraesCS4A01G153600	chr3D	589278902	589281657	2755	False	4545	4545	96.387	1	2766	1	chr3D.!!$F1	2765
2	TraesCS4A01G153600	chr5D	503277584	503280341	2757	False	4530	4530	96.279	1	2766	1	chr5D.!!$F2	2765
3	TraesCS4A01G153600	chr5D	6186824	6189582	2758	True	4519	4519	96.208	1	2766	1	chr5D.!!$R1	2765
4	TraesCS4A01G153600	chr5D	432402855	432405611	2756	False	4401	4401	95.451	1	2766	1	chr5D.!!$F1	2765
5	TraesCS4A01G153600	chr5D	503216770	503218860	2090	True	3465	3465	96.562	1	2093	1	chr5D.!!$R2	2092
6	TraesCS4A01G153600	chr1D	254397467	254400226	2759	False	4516	4516	96.172	1	2766	1	chr1D.!!$F1	2765
7	TraesCS4A01G153600	chr1A	554510139	554512890	2751	True	4508	4508	96.172	1	2766	1	chr1A.!!$R1	2765
8	TraesCS4A01G153600	chr5A	607272284	607275042	2758	True	4386	4386	95.340	1	2766	1	chr5A.!!$R1	2765
9	TraesCS4A01G153600	chr6D	168253477	168255568	2091	True	3476	3476	96.659	1	2093	1	chr6D.!!$R2	2092
10	TraesCS4A01G153600	chr6D	45517454	45519037	1583	True	2580	2580	96.045	1179	2766	1	chr6D.!!$R1	1587
11	TraesCS4A01G153600	chrUn	93408989	93411079	2090	False	3470	3470	96.611	1	2093	1	chrUn.!!$F1	2092
12	TraesCS4A01G153600	chrUn	239345464	239346380	916	False	1526	1526	96.641	1845	2766	1	chrUn.!!$F2	921
13	TraesCS4A01G153600	chr7B	719441349	719442377	1028	True	1177	1177	87.333	1724	2766	1	chr7B.!!$R1	1042

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
656	658	1.25084	GGAAGCGCCCCTTGTTTCAT	61.251	55.0	2.29	0.0	32.78	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1960	1970	0.530288	AATTCCCCCAATTTGCGACG	59.47	50.0	0.0	0.0	29.6	5.12	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
113	114	6.777091	TCCACGAAATAATTTGATCCATGGAT	59.223	34.615	27.66	27.66	37.59	3.41
142	143	5.239963	CCGTTGTGGTAAAGGTTGTAATTCT	59.760	40.000	0.00	0.00	0.00	2.40
266	267	9.096823	TCATAACCATAGAATACGACCCTAATT	57.903	33.333	0.00	0.00	0.00	1.40
310	311	2.505819	ACACTATGGGGATGGTGAGAAC	59.494	50.000	5.65	0.00	36.65	3.01
480	482	7.608153	TGACAAAACCTAGAAATCGATCACTA	58.392	34.615	0.00	4.95	0.00	2.74
499	501	6.650120	TCACTAATCCAATTTGACTACCTCC	58.350	40.000	0.00	0.00	0.00	4.30
525	527	5.783360	TGGGATAGACCTCAACAGAAAACTA	59.217	40.000	0.00	0.00	38.98	2.24
536	538	7.384115	CCTCAACAGAAAACTATTGAGTAACGA	59.616	37.037	14.28	0.00	44.28	3.85
630	632	2.193306	AAGTTGTTTGAAGCACGCAG	57.807	45.000	0.00	0.00	0.00	5.18
656	658	1.250840	GGAAGCGCCCCTTGTTTCAT	61.251	55.000	2.29	0.00	32.78	2.57
668	670	4.657969	CCCTTGTTTCATAGAGAGGAGGAT	59.342	45.833	0.00	0.00	0.00	3.24
712	714	3.831323	TGGTCAGAGGCAAATTGAAAGA	58.169	40.909	0.00	0.00	0.00	2.52
737	739	4.702196	AGTAGTGGTAATTAAGACCCCCA	58.298	43.478	6.83	0.00	35.99	4.96
841	843	5.116180	TGCTACATGTAGAACATAAGCCAC	58.884	41.667	32.39	12.97	41.94	5.01
877	879	6.442952	CAGAAACCTAGGATGTAGAAGATCG	58.557	44.000	17.98	0.00	0.00	3.69
892	894	5.352284	AGAAGATCGTAACATGAGCGATTT	58.648	37.500	18.67	13.35	44.06	2.17
914	916	2.432146	GGCAGATTTGGATTCCTTTCCC	59.568	50.000	3.95	0.00	34.67	3.97
1079	1082	2.622064	ACTTCAACCGATATGCCCTC	57.378	50.000	0.00	0.00	0.00	4.30
1119	1122	5.147330	ACATAGAAATCACACGTGGAAGA	57.853	39.130	21.57	14.78	0.00	2.87
1199	1202	6.541278	GGTAAATCGGCCACTTTAAGATTACT	59.459	38.462	2.24	0.00	32.05	2.24
1237	1240	6.149807	CCGTTTAGTATCCCAAAACTGCTTAA	59.850	38.462	0.00	0.00	32.25	1.85
1305	1308	1.000052	GGTAGAGCCGGATCTAAGTGC	60.000	57.143	29.95	17.47	33.66	4.40
1503	1509	7.781548	ATTCTTCGTTGCCGTAAGTAAATAT	57.218	32.000	0.00	0.00	35.01	1.28
1623	1629	1.656652	CCTTGATCCACTTGGCTACG	58.343	55.000	0.00	0.00	34.44	3.51
1865	1875	4.040706	AGAAACAATAGTAACGTGGTCCCA	59.959	41.667	0.00	0.00	0.00	4.37
2002	2012	2.677971	CCTACTCGGCATTTCACGG	58.322	57.895	0.00	0.00	0.00	4.94
2153	2164	8.533569	TGGGTATTTCTGTCTTTTCTTTCTTT	57.466	30.769	0.00	0.00	0.00	2.52
2291	2303	4.997395	GGTTAGCACGGTTGATGATATCAT	59.003	41.667	18.21	18.21	39.39	2.45
2329	2343	4.096311	CGTGACCTTGACTATCAACTACG	58.904	47.826	0.00	0.00	32.21	3.51
2330	2344	4.379186	CGTGACCTTGACTATCAACTACGT	60.379	45.833	0.00	0.00	32.21	3.57
2333	2347	7.256286	GTGACCTTGACTATCAACTACGTATT	58.744	38.462	0.00	0.00	32.21	1.89
2334	2348	7.220300	GTGACCTTGACTATCAACTACGTATTG	59.780	40.741	0.00	3.74	32.21	1.90
2335	2349	6.570692	ACCTTGACTATCAACTACGTATTGG	58.429	40.000	13.93	0.46	32.21	3.16
2336	2350	6.154021	ACCTTGACTATCAACTACGTATTGGT	59.846	38.462	13.93	11.09	32.21	3.67
2337	2351	7.039882	CCTTGACTATCAACTACGTATTGGTT	58.960	38.462	13.93	5.66	32.21	3.67
2338	2352	7.010183	CCTTGACTATCAACTACGTATTGGTTG	59.990	40.741	16.14	16.14	40.87	3.77
2410	2424	2.237392	AGCAGTGAACCAGATTCCTACC	59.763	50.000	0.00	0.00	36.36	3.18
2445	2459	5.296780	CAGCCAAGAAGAAGTGTAAAGAACA	59.703	40.000	0.00	0.00	35.06	3.18
2581	2596	8.655935	ATTCATTTTCAGTAGTTTCCCTGATT	57.344	30.769	0.00	0.00	37.54	2.57
2596	2611	8.319881	GTTTCCCTGATTAAACTAGAGGTTACT	58.680	37.037	0.00	0.00	37.12	2.24
2665	2680	3.085952	ACACCTAACATGTGGAATGGG	57.914	47.619	9.12	2.82	38.05	4.00
2688	2703	3.012518	GCATAAGGATGTTGTGCTCTGT	58.987	45.455	0.00	0.00	35.30	3.41
2744	2759	6.101734	AGAGATTCCTAAAGGCATACCATCAA	59.898	38.462	0.00	0.00	39.06	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	5.071250	TGCTCGGGATAGGTGTTTTGTATAT	59.929	40.000	0.00	0.00	0.00	0.86
134	135	7.152645	GCGGTAATGATTCCTCTAGAATTACA	58.847	38.462	18.02	6.82	45.52	2.41
142	143	3.494398	GCCTTGCGGTAATGATTCCTCTA	60.494	47.826	0.00	0.00	0.00	2.43
171	172	0.466739	TAGGCGCTTATGACCTCCGA	60.467	55.000	7.64	0.00	34.92	4.55
172	173	0.603569	ATAGGCGCTTATGACCTCCG	59.396	55.000	11.70	0.00	34.92	4.63
242	243	9.096823	TCAATTAGGGTCGTATTCTATGGTTAT	57.903	33.333	0.00	0.00	0.00	1.89
310	311	8.986991	AGCCCTCTAGGATGTAAAATATATCTG	58.013	37.037	0.00	0.00	38.24	2.90
404	406	5.732647	CGTAAATCAATAGTTCAAACCGCAG	59.267	40.000	0.00	0.00	0.00	5.18
455	457	6.464222	AGTGATCGATTTCTAGGTTTTGTCA	58.536	36.000	0.00	0.00	0.00	3.58
480	482	5.203528	CCATGGAGGTAGTCAAATTGGATT	58.796	41.667	5.56	0.00	0.00	3.01
499	501	4.760530	TTCTGTTGAGGTCTATCCCATG	57.239	45.455	0.00	0.00	36.75	3.66
525	527	3.990092	TCACTTGCTGTCGTTACTCAAT	58.010	40.909	0.00	0.00	0.00	2.57
536	538	3.813443	ACTGAACTCAATCACTTGCTGT	58.187	40.909	0.00	0.00	32.11	4.40
600	602	5.163612	GCTTCAAACAACTTTGTCTTCTCCT	60.164	40.000	0.00	0.00	41.31	3.69
613	615	1.330521	TCTCTGCGTGCTTCAAACAAC	59.669	47.619	0.00	0.00	0.00	3.32
656	658	5.148502	GTGAATAACCCATCCTCCTCTCTA	58.851	45.833	0.00	0.00	0.00	2.43
668	670	8.820831	ACCATCAAATTAAATGTGAATAACCCA	58.179	29.630	0.00	0.00	0.00	4.51
712	714	6.910290	TGGGGGTCTTAATTACCACTACTTAT	59.090	38.462	8.78	0.00	40.51	1.73
737	739	3.056832	GGAGACATCCCTATTTTCCCCT	58.943	50.000	0.00	0.00	40.03	4.79
827	829	3.449377	TCCGTCATGTGGCTTATGTTCTA	59.551	43.478	0.00	0.00	0.00	2.10
841	843	0.165944	GGTTTCTGCGTTCCGTCATG	59.834	55.000	0.00	0.00	0.00	3.07
857	859	6.832384	TGTTACGATCTTCTACATCCTAGGTT	59.168	38.462	9.08	0.00	0.00	3.50
877	879	2.677836	TCTGCCAAATCGCTCATGTTAC	59.322	45.455	0.00	0.00	0.00	2.50
892	894	3.099141	GGAAAGGAATCCAAATCTGCCA	58.901	45.455	0.61	0.00	39.42	4.92
1119	1122	1.141858	GCTCTAGCTAATTGCCCACCT	59.858	52.381	0.00	0.00	44.23	4.00
1199	1202	2.023695	ACTAAACGGACCTCCCCAGATA	60.024	50.000	0.00	0.00	0.00	1.98
1237	1240	1.005450	ACCCACTTGTCCAACTGTTGT	59.995	47.619	18.38	0.00	0.00	3.32
1245	1248	2.489985	CCCAACATTACCCACTTGTCCA	60.490	50.000	0.00	0.00	0.00	4.02
1488	1494	8.236585	TCCTAGTTACATATTTACTTACGGCA	57.763	34.615	0.00	0.00	0.00	5.69
1503	1509	8.815565	TGCAATTTTCCATATTCCTAGTTACA	57.184	30.769	0.00	0.00	0.00	2.41
1623	1629	1.119574	TAGCTGGATAAGGGGCGGAC	61.120	60.000	0.00	0.00	0.00	4.79
1778	1788	7.707624	AAATGATGAGCTACAAAAGGATTCA	57.292	32.000	0.00	0.00	0.00	2.57
1834	1844	8.943002	CCACGTTACTATTGTTTCTTTATCCTT	58.057	33.333	0.00	0.00	0.00	3.36
1839	1849	6.650390	GGGACCACGTTACTATTGTTTCTTTA	59.350	38.462	0.00	0.00	0.00	1.85
1865	1875	2.370189	GTGGGTAGAATGCTAGATGCCT	59.630	50.000	0.00	0.00	42.00	4.75
1937	1947	8.652810	ACGTACCATAGGATTTGTTATGTAAC	57.347	34.615	0.00	0.00	36.74	2.50
1960	1970	0.530288	AATTCCCCCAATTTGCGACG	59.470	50.000	0.00	0.00	29.60	5.12
2002	2012	8.470002	AGTATCCTTTCTTGCATTTTCATAACC	58.530	33.333	0.00	0.00	0.00	2.85
2291	2303	6.549433	AGGTCACGTTATTAATACTTGGGA	57.451	37.500	0.00	0.00	0.00	4.37
2309	2321	7.255569	CAATACGTAGTTGATAGTCAAGGTCA	58.744	38.462	0.08	0.00	37.78	4.02
2329	2343	7.254624	GGTTTCAATTTCAACCACAACCAATAC	60.255	37.037	9.76	0.00	41.97	1.89
2330	2344	6.763610	GGTTTCAATTTCAACCACAACCAATA	59.236	34.615	9.76	0.00	41.97	1.90
2333	2347	4.020218	TGGTTTCAATTTCAACCACAACCA	60.020	37.500	12.46	0.00	46.16	3.67
2334	2348	4.508662	TGGTTTCAATTTCAACCACAACC	58.491	39.130	12.46	0.00	46.16	3.77
2445	2459	7.665559	TCCAATATGCTAGTTTCAACAACTCTT	59.334	33.333	0.00	0.00	0.00	2.85
2581	2596	8.755977	CATGGTTCCTTAGTAACCTCTAGTTTA	58.244	37.037	8.17	0.00	45.53	2.01
2596	2611	3.199727	TCAGTGCTATGCATGGTTCCTTA	59.800	43.478	10.16	0.00	41.91	2.69
2665	2680	3.012518	AGAGCACAACATCCTTATGCAC	58.987	45.455	0.00	0.00	38.79	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.