AutoCloner

Multiple sequence alignment - TraesCS7B01G006900

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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	TraesCS7B01G006900	chr7B	100.000	4088	0	0	1	4088	3845939	3850026	0.000000e+00	7550
1	TraesCS7B01G006900	chr7B	95.264	549	22	3	1	547	3800087	3800633	0.000000e+00	867
2	TraesCS7B01G006900	chr7B	93.967	547	30	3	1	547	563011690	563012233	0.000000e+00	824
3	TraesCS7B01G006900	chr7B	92.153	548	36	5	1	547	563036421	563036962	0.000000e+00	767
4	TraesCS7B01G006900	chr7B	89.855	552	40	10	1	547	318822117	318822657	0.000000e+00	695
5	TraesCS7B01G006900	chr7D	95.127	3468	127	10	546	3979	63442001	63445460	0.000000e+00	5430
6	TraesCS7B01G006900	chr7D	82.672	479	34	32	3254	3717	63451377	63451821	2.980000e-101	379
7	TraesCS7B01G006900	chr7D	90.132	152	12	3	2225	2373	63451248	63451399	1.160000e-45	195
8	TraesCS7B01G006900	chr7D	94.949	99	5	0	3980	4078	63445492	63445590	5.470000e-34	156
9	TraesCS7B01G006900	chr7A	96.369	2341	82	3	857	3197	66232634	66234971	0.000000e+00	3849
10	TraesCS7B01G006900	chr7A	96.092	563	20	1	3247	3807	66234974	66235536	0.000000e+00	917
11	TraesCS7B01G006900	chr7A	92.353	340	25	1	542	881	66231952	66232290	2.210000e-132	483
12	TraesCS7B01G006900	chr7A	94.495	109	6	0	3980	4088	66235944	66236052	7.030000e-38	169
13	TraesCS7B01G006900	chr7A	97.500	80	2	0	3900	3979	66235833	66235912	1.980000e-28	137
14	TraesCS7B01G006900	chrUn	93.333	555	25	5	1	549	305935999	305935451	0.000000e+00	809
15	TraesCS7B01G006900	chrUn	93.333	555	25	5	1	549	305940264	305939716	0.000000e+00	809
16	TraesCS7B01G006900	chrUn	93.333	555	25	5	1	549	317871800	317871252	0.000000e+00	809
17	TraesCS7B01G006900	chr4B	90.164	549	42	5	1	547	431609660	431609122	0.000000e+00	704
18	TraesCS7B01G006900	chr4B	89.580	547	45	5	1	547	431647079	431646545	0.000000e+00	684

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	TraesCS7B01G006900	chr7B	3845939	3850026	4087	False	7550	7550	100.0000	1	4088	1	chr7B.!!$F2	4087
1	TraesCS7B01G006900	chr7B	3800087	3800633	546	False	867	867	95.2640	1	547	1	chr7B.!!$F1	546
2	TraesCS7B01G006900	chr7B	563011690	563012233	543	False	824	824	93.9670	1	547	1	chr7B.!!$F4	546
3	TraesCS7B01G006900	chr7B	563036421	563036962	541	False	767	767	92.1530	1	547	1	chr7B.!!$F5	546
4	TraesCS7B01G006900	chr7B	318822117	318822657	540	False	695	695	89.8550	1	547	1	chr7B.!!$F3	546
5	TraesCS7B01G006900	chr7D	63442001	63445590	3589	False	2793	5430	95.0380	546	4078	2	chr7D.!!$F1	3532
6	TraesCS7B01G006900	chr7D	63451248	63451821	573	False	287	379	86.4020	2225	3717	2	chr7D.!!$F2	1492
7	TraesCS7B01G006900	chr7A	66231952	66236052	4100	False	1111	3849	95.3618	542	4088	5	chr7A.!!$F1	3546
8	TraesCS7B01G006900	chrUn	305935451	305940264	4813	True	809	809	93.3330	1	549	2	chrUn.!!$R2	548
9	TraesCS7B01G006900	chrUn	317871252	317871800	548	True	809	809	93.3330	1	549	1	chrUn.!!$R1	548
10	TraesCS7B01G006900	chr4B	431609122	431609660	538	True	704	704	90.1640	1	547	1	chr4B.!!$R1	546
11	TraesCS7B01G006900	chr4B	431646545	431647079	534	True	684	684	89.5800	1	547	1	chr4B.!!$R2	546

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	Hairpin	End Stability	Orientation
491	4762	0.253160	TAGGCAGGGGGTGTGATCTT	60.253	55.0	0.00	0.00	2.40	F
1992	6636	0.318441	TCCGGATGAATGAGATCGCC	59.682	55.0	0.00	0.00	5.54	F
2812	7456	0.467290	GCATTGCCGGGGAGGAAATA	60.467	55.0	2.18	46.79	1.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2034	6678	1.448365	TGCGAGCAATGCGTCATCT	60.448	52.632	0.00	0.00	34.24	2.90	R
3012	7656	1.012486	CAGCGTCCACGTTACCTTCC	61.012	60.000	0.36	0.00	42.22	3.46	R
3717	8380	1.487452	CGTAATGCCATCGACCGGTG	61.487	60.000	14.63	4.45	0.00	4.94	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
68	69	4.805744	AGGACCGACTTTAGTCAGGATAT	58.194	43.478	20.05	5.47	44.99	1.63
75	76	6.207213	CGACTTTAGTCAGGATATGTGTACC	58.793	44.000	10.27	0.00	44.99	3.34
266	4533	0.824759	AGGCGACTGAACTCCCATAC	59.175	55.000	0.00	0.00	41.13	2.39
314	4581	1.214062	CTCGCGAGGCTGTTCTTCT	59.786	57.895	28.40	0.00	0.00	2.85
339	4608	0.693049	ACTATTCATCATCGGCCCCC	59.307	55.000	0.00	0.00	0.00	5.40
383	4652	4.710375	CACACTGGAGTAGGGTATTACACT	59.290	45.833	3.67	3.67	42.52	3.55
384	4653	4.710375	ACACTGGAGTAGGGTATTACACTG	59.290	45.833	8.90	0.00	42.62	3.66
491	4762	0.253160	TAGGCAGGGGGTGTGATCTT	60.253	55.000	0.00	0.00	0.00	2.40
514	4785	0.534203	GTGCACCCCAGAGTTCGAAA	60.534	55.000	5.22	0.00	0.00	3.46
522	4793	2.037251	CCCAGAGTTCGAAACTTGAGGA	59.963	50.000	0.00	0.00	43.03	3.71
534	4805	0.539051	CTTGAGGATCTGCCGGAACT	59.461	55.000	5.05	0.00	43.43	3.01
550	4821	2.618053	GAACTCGAAATCCGACACCAT	58.382	47.619	0.00	0.00	43.23	3.55
566	4837	3.202151	ACACCATCTACAACCTTATGGGG	59.798	47.826	0.00	0.00	46.41	4.96
609	4880	3.021695	TGGTATTCTGTACTCCTGACCG	58.978	50.000	0.00	0.00	0.00	4.79
635	4906	7.863877	GGTGACTTTTATGTAACAATCGGTTTT	59.136	33.333	0.00	0.00	40.96	2.43
664	4935	6.038603	CACCGTGAATCCATCTCATACAAATT	59.961	38.462	0.00	0.00	0.00	1.82
764	5035	6.403866	ACCACAGTTTCAATAATTCAGCAA	57.596	33.333	0.00	0.00	0.00	3.91
772	5043	6.899393	TTCAATAATTCAGCAAGGACTTGT	57.101	33.333	13.08	0.00	42.31	3.16
807	5078	1.291033	ACTAGGGTCAGGGCTCACATA	59.709	52.381	0.00	0.00	0.00	2.29
1752	6396	1.669760	GGTGTTCGACGGAATGGCA	60.670	57.895	0.00	0.00	34.05	4.92
1870	6514	3.103742	GAGATGTCTCAGAAAGGGGTCT	58.896	50.000	5.18	0.00	42.42	3.85
1875	6519	2.125512	CAGAAAGGGGTCTCGCCG	60.126	66.667	0.00	0.00	41.60	6.46
1961	6605	2.593978	CCTGGTGGGGCAGATGAG	59.406	66.667	0.00	0.00	0.00	2.90
1992	6636	0.318441	TCCGGATGAATGAGATCGCC	59.682	55.000	0.00	0.00	0.00	5.54
2010	6654	2.482664	CGCCTTCACAGCACTGATAGAT	60.483	50.000	4.31	0.00	0.00	1.98
2034	6678	2.831685	TCTGCAAGAACGGCTTCTTA	57.168	45.000	10.29	0.00	43.70	2.10
2169	6813	3.181479	CGAGGGAGTTGGTCGATGAAATA	60.181	47.826	0.00	0.00	35.70	1.40
2211	6855	4.442350	TGACGTCGTGACATATAGTACG	57.558	45.455	11.62	0.00	37.85	3.67
2216	6860	5.078084	CGTCGTGACATATAGTACGATTCC	58.922	45.833	9.68	0.04	45.66	3.01
2219	6863	5.532032	TCGTGACATATAGTACGATTCCCAA	59.468	40.000	0.00	0.00	40.21	4.12
2268	6912	4.844998	TTCTGCATTTGAATTGAACCGA	57.155	36.364	0.00	0.00	0.00	4.69
2397	7041	2.584835	TGCTTCAACTTGGCCTACAT	57.415	45.000	3.32	0.00	0.00	2.29
2494	7138	6.256539	TCTGCACGATGAGATGATAAAGAAAC	59.743	38.462	0.00	0.00	0.00	2.78
2605	7249	3.641434	AGCTGTACTACGAAGACCCTA	57.359	47.619	0.00	0.00	0.00	3.53
2691	7335	3.054361	TGGTGGCTCTTCTTAAGGGATTC	60.054	47.826	1.85	0.00	0.00	2.52
2736	7380	3.131396	AGCTGACAAAGTTTACCAGTCG	58.869	45.455	14.24	5.42	32.08	4.18
2760	7404	3.181440	TGTTGGACAGAGATTGGAAGCTT	60.181	43.478	0.00	0.00	0.00	3.74
2763	7407	3.006247	GGACAGAGATTGGAAGCTTGAC	58.994	50.000	2.10	0.00	0.00	3.18
2784	7428	2.353011	CGGTTCGGTGTATGGTGTACTT	60.353	50.000	0.00	0.00	0.00	2.24
2799	7443	4.499696	GGTGTACTTATTCATGGGCATTGC	60.500	45.833	0.00	0.00	0.00	3.56
2812	7456	0.467290	GCATTGCCGGGGAGGAAATA	60.467	55.000	2.18	0.00	46.79	1.40
2892	7536	6.012658	TCAACAAGCACTATTTCATTGGTC	57.987	37.500	0.00	0.00	0.00	4.02
3012	7656	5.407995	GGCTCTTATTGATCTCAATCGGAAG	59.592	44.000	8.63	7.82	44.67	3.46
3249	7893	4.828939	TGAAGTTTCTTCTTCATGCCACAT	59.171	37.500	10.21	0.00	45.62	3.21
3381	8026	6.599638	AGGTTAGAAGAATGGTTATTGCTGTC	59.400	38.462	0.00	0.00	0.00	3.51
3440	8085	3.193691	AGGACACTAGAAGACCACGATTG	59.806	47.826	0.00	0.00	0.00	2.67
3708	8371	4.904466	GACACTACGCCGTCCAAT	57.096	55.556	0.00	0.00	0.00	3.16
3717	8380	1.705337	CGCCGTCCAATGGTGTCATC	61.705	60.000	0.00	0.00	32.24	2.92
3816	8486	1.701031	TTCCTTCCAGGCGTTCCACA	61.701	55.000	0.00	0.00	34.61	4.17
3821	8491	0.327924	TCCAGGCGTTCCACAATGAT	59.672	50.000	0.00	0.00	33.74	2.45
3824	8494	2.355197	CAGGCGTTCCACAATGATACA	58.645	47.619	0.00	0.00	33.74	2.29
3837	8507	0.975887	TGATACACAGCACAGCAGGA	59.024	50.000	0.00	0.00	0.00	3.86
3861	8543	2.945008	CTGCTCTGTTCCTTGTTTGTCA	59.055	45.455	0.00	0.00	0.00	3.58
4013	8918	5.050490	CCCTTGTATATTGGTCTTGACTCG	58.950	45.833	0.61	0.00	0.00	4.18
4016	8921	5.006153	TGTATATTGGTCTTGACTCGTGG	57.994	43.478	0.61	0.00	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	2.038863	AGGGGAACATCTGGTACACA	57.961	50.000	0.00	0.00	0.00	3.72
75	76	3.368739	GCCATTTTGAAGGGGAACATCTG	60.369	47.826	0.00	0.00	31.67	2.90
193	194	1.519455	CCGACTTCAGGTGCGGATC	60.519	63.158	0.00	0.00	39.32	3.36
266	4533	2.401766	GGCTGGTGCGATGAACTGG	61.402	63.158	0.00	0.00	40.82	4.00
314	4581	4.262463	GGGCCGATGATGAATAGTACAAGA	60.262	45.833	0.00	0.00	0.00	3.02
339	4608	0.962356	GGTGTGGTGGATTGCCTCTG	60.962	60.000	0.00	0.00	34.31	3.35
383	4652	1.907807	GGTTCAGGCCACCATTGCA	60.908	57.895	5.01	0.00	34.04	4.08
384	4653	1.880819	CTGGTTCAGGCCACCATTGC	61.881	60.000	13.53	0.00	43.60	3.56
514	4785	0.250513	GTTCCGGCAGATCCTCAAGT	59.749	55.000	0.00	0.00	0.00	3.16
522	4793	1.473434	GGATTTCGAGTTCCGGCAGAT	60.473	52.381	0.00	0.00	39.14	2.90
534	4805	2.756207	TGTAGATGGTGTCGGATTTCGA	59.244	45.455	0.00	0.00	46.77	3.71
550	4821	1.843851	CCTGCCCCATAAGGTTGTAGA	59.156	52.381	0.00	0.00	0.00	2.59
566	4837	4.503741	TTGTTTTGTGATCTTAGCCTGC	57.496	40.909	0.00	0.00	0.00	4.85
609	4880	6.490566	ACCGATTGTTACATAAAAGTCACC	57.509	37.500	0.00	0.00	0.00	4.02
635	4906	4.014569	TGAGATGGATTCACGGTGAAAA	57.985	40.909	25.64	15.29	40.12	2.29
640	4911	4.753516	TTGTATGAGATGGATTCACGGT	57.246	40.909	0.00	0.00	0.00	4.83
664	4935	5.195146	TGGATGACCTAGGGTTAGAGTTAGA	59.805	44.000	14.81	0.00	35.25	2.10
764	5035	8.753497	AGTTTTGAAGATTTCTTACAAGTCCT	57.247	30.769	0.00	0.00	36.11	3.85
772	5043	7.883311	CCTGACCCTAGTTTTGAAGATTTCTTA	59.117	37.037	0.00	0.00	36.11	2.10
825	5096	4.036971	CGATTTGGTTGGTTGGAGTTGTAA	59.963	41.667	0.00	0.00	0.00	2.41
826	5097	3.566322	CGATTTGGTTGGTTGGAGTTGTA	59.434	43.478	0.00	0.00	0.00	2.41
1408	6052	1.931007	ATGGAGCCCTCAAGGAAGCC	61.931	60.000	0.00	0.00	38.24	4.35
1870	6514	2.431771	CGTCACAACATCCGGCGA	60.432	61.111	9.30	0.00	0.00	5.54
1992	6636	3.118482	ACCCATCTATCAGTGCTGTGAAG	60.118	47.826	0.00	0.00	0.00	3.02
2028	6672	3.060674	CGAGCAATGCGTCATCTAAGAAG	60.061	47.826	0.00	0.00	0.00	2.85
2034	6678	1.448365	TGCGAGCAATGCGTCATCT	60.448	52.632	0.00	0.00	34.24	2.90
2106	6750	4.655963	ACTTGCAGTAACCATTGATGAGT	58.344	39.130	0.00	0.00	0.00	3.41
2109	6753	5.647658	TCCTAACTTGCAGTAACCATTGATG	59.352	40.000	0.00	0.00	0.00	3.07
2216	6860	4.640201	CACCAATCTTACAGTACCCATTGG	59.360	45.833	16.52	16.52	43.98	3.16
2219	6863	5.975988	ATCACCAATCTTACAGTACCCAT	57.024	39.130	0.00	0.00	0.00	4.00
2494	7138	2.029020	TCACAACATCAGGGAGAACTCG	60.029	50.000	0.00	0.00	0.00	4.18
2605	7249	9.247861	GGCCTCATATTTAATATTGTCTGGAAT	57.752	33.333	0.00	0.00	0.00	3.01
2691	7335	4.643334	TCATTCATCAAGCCTTTCATGGAG	59.357	41.667	0.00	0.00	0.00	3.86
2736	7380	3.376546	GCTTCCAATCTCTGTCCAACATC	59.623	47.826	0.00	0.00	0.00	3.06
2760	7404	0.038067	CACCATACACCGAACCGTCA	60.038	55.000	0.00	0.00	0.00	4.35
2763	7407	1.203052	AGTACACCATACACCGAACCG	59.797	52.381	0.00	0.00	0.00	4.44
2769	7413	5.763204	CCCATGAATAAGTACACCATACACC	59.237	44.000	0.00	0.00	0.00	4.16
2799	7443	3.496870	CCTTCAGAATATTTCCTCCCCGG	60.497	52.174	0.00	0.00	0.00	5.73
2812	7456	3.328931	TGGAAGTTGAGAGCCTTCAGAAT	59.671	43.478	0.00	0.00	39.04	2.40
2892	7536	1.133668	CCCTCTTCAAATAGGCCCCTG	60.134	57.143	0.00	0.00	0.00	4.45
3012	7656	1.012486	CAGCGTCCACGTTACCTTCC	61.012	60.000	0.36	0.00	42.22	3.46
3249	7893	4.011966	ACTTGCTCACTTCACATCATCA	57.988	40.909	0.00	0.00	0.00	3.07
3289	7933	7.448420	ACTTGTATTCACATGATAGGATCTGG	58.552	38.462	0.00	0.00	33.76	3.86
3416	8061	4.232188	TCGTGGTCTTCTAGTGTCCTAT	57.768	45.455	0.00	0.00	0.00	2.57
3440	8085	8.548433	GAACTTTAATCAGTTCGCAAATATCC	57.452	34.615	4.67	0.00	42.48	2.59
3465	8110	2.530701	ACTGAGACCAGGGTACAAGAG	58.469	52.381	0.00	0.00	44.60	2.85
3717	8380	1.487452	CGTAATGCCATCGACCGGTG	61.487	60.000	14.63	4.45	0.00	4.94
3816	8486	2.026915	TCCTGCTGTGCTGTGTATCATT	60.027	45.455	0.00	0.00	0.00	2.57
3821	8491	1.625315	AGAATCCTGCTGTGCTGTGTA	59.375	47.619	0.00	0.00	0.00	2.90
3824	8494	3.244764	CAGAATCCTGCTGTGCTGT	57.755	52.632	0.00	0.00	33.07	4.40
3837	8507	4.210331	ACAAACAAGGAACAGAGCAGAAT	58.790	39.130	0.00	0.00	0.00	2.40
4013	8918	3.016736	CCCATGTAGACATTTGTCCCAC	58.983	50.000	7.07	6.59	45.85	4.61
4016	8921	2.722094	TGCCCATGTAGACATTTGTCC	58.278	47.619	7.07	0.00	45.85	4.02
4059	8964	8.729805	ACAATGAAAAACAAAAGGAGCAAATA	57.270	26.923	0.00	0.00	0.00	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.