AutoCloner

Multiple sequence alignment - TraesCS3B01G364300

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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	TraesCS3B01G364300	chr3B	100.000	3530	0	0	1	3530	575841734	575838205	0.000000e+00	6519
1	TraesCS3B01G364300	chr3B	96.630	3531	113	6	1	3530	483331222	483334747	0.000000e+00	5856
2	TraesCS3B01G364300	chr6A	96.856	3530	109	2	1	3530	155855308	155858835	0.000000e+00	5903
3	TraesCS3B01G364300	chr6A	96.545	3531	119	2	1	3530	375862752	375859224	0.000000e+00	5842
4	TraesCS3B01G364300	chr7B	97.848	3300	69	2	1	3300	742950729	742947432	0.000000e+00	5699
5	TraesCS3B01G364300	chr7B	97.637	3301	74	4	1	3300	716782616	716785913	0.000000e+00	5661
6	TraesCS3B01G364300	chr7A	97.758	3300	72	2	1	3300	60170758	60167461	0.000000e+00	5683
7	TraesCS3B01G364300	chr5A	97.667	3300	74	3	1	3300	420183712	420187008	0.000000e+00	5664
8	TraesCS3B01G364300	chr4B	97.020	3356	98	2	175	3530	209240740	209244093	0.000000e+00	5642
9	TraesCS3B01G364300	chr4A	95.524	3530	154	3	1	3530	350170251	350173776	0.000000e+00	5640
10	TraesCS3B01G364300	chrUn	97.041	338	10	0	3193	3530	171017238	171017575	1.420000e-158	569
11	TraesCS3B01G364300	chrUn	97.041	338	9	1	3193	3530	45101032	45101368	5.110000e-158	568
12	TraesCS3B01G364300	chrUn	97.041	338	9	1	3193	3530	365030897	365030561	5.110000e-158	568

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	TraesCS3B01G364300	chr3B	575838205	575841734	3529	True	6519	6519	100.000	1	3530	1	chr3B.!!$R1	3529
1	TraesCS3B01G364300	chr3B	483331222	483334747	3525	False	5856	5856	96.630	1	3530	1	chr3B.!!$F1	3529
2	TraesCS3B01G364300	chr6A	155855308	155858835	3527	False	5903	5903	96.856	1	3530	1	chr6A.!!$F1	3529
3	TraesCS3B01G364300	chr6A	375859224	375862752	3528	True	5842	5842	96.545	1	3530	1	chr6A.!!$R1	3529
4	TraesCS3B01G364300	chr7B	742947432	742950729	3297	True	5699	5699	97.848	1	3300	1	chr7B.!!$R1	3299
5	TraesCS3B01G364300	chr7B	716782616	716785913	3297	False	5661	5661	97.637	1	3300	1	chr7B.!!$F1	3299
6	TraesCS3B01G364300	chr7A	60167461	60170758	3297	True	5683	5683	97.758	1	3300	1	chr7A.!!$R1	3299
7	TraesCS3B01G364300	chr5A	420183712	420187008	3296	False	5664	5664	97.667	1	3300	1	chr5A.!!$F1	3299
8	TraesCS3B01G364300	chr4B	209240740	209244093	3353	False	5642	5642	97.020	175	3530	1	chr4B.!!$F1	3355
9	TraesCS3B01G364300	chr4A	350170251	350173776	3525	False	5640	5640	95.524	1	3530	1	chr4A.!!$F1	3529

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
203	204	0.669932	GATGCGGCATCTGGCTCTAG	60.670	60.0	30.48	0.0	44.01	2.43	F
1034	1037	0.888619	AGAGATGCGGAACTCACGAA	59.111	50.0	16.20	0.0	35.83	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1718	1722	0.911045	TTGCAGAGGAGCAGGATCCA	60.911	55.0	15.82	0.0	46.54	3.41	R
3020	3025	0.250234	AGCAATTGTAGCAGCTCCGA	59.750	50.0	7.40	0.0	30.05	4.55	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
54	55	6.949352	ATGCCTCTCGTAATTGATTGAAAT	57.051	33.333	0.00	0.00	0.00	2.17
63	64	4.445452	AATTGATTGAAATGTGCTCGCT	57.555	36.364	0.00	0.00	0.00	4.93
203	204	0.669932	GATGCGGCATCTGGCTCTAG	60.670	60.000	30.48	0.00	44.01	2.43
348	349	9.467258	CATAACACTTATTCAAAATGGGCTATG	57.533	33.333	0.00	0.00	0.00	2.23
359	360	1.131638	TGGGCTATGCGAAAGAGGAT	58.868	50.000	0.00	0.00	0.00	3.24
360	361	1.070758	TGGGCTATGCGAAAGAGGATC	59.929	52.381	0.00	0.00	0.00	3.36
542	543	2.971598	ATTCTCACGGCCACCCCAG	61.972	63.158	2.24	0.00	0.00	4.45
585	587	5.007921	CCAATCGATCATCACTTGCATACAA	59.992	40.000	0.00	0.00	0.00	2.41
796	799	1.543802	TCGTTTTCGGTATGGGTACGT	59.456	47.619	0.00	0.00	44.25	3.57
847	850	4.640690	ACCAGGGAGCAGGACCGT	62.641	66.667	0.00	0.00	0.00	4.83
1034	1037	0.888619	AGAGATGCGGAACTCACGAA	59.111	50.000	16.20	0.00	35.83	3.85
1264	1267	8.521176	GTGATACCGCTATTAAAGAAGGAGATA	58.479	37.037	0.00	0.00	0.00	1.98
1382	1385	1.469251	GGCTCTAAGCGATCACGAACA	60.469	52.381	0.00	0.00	43.62	3.18
1546	1550	5.945784	ACTGGAAAAACTGCAATAGCTATCA	59.054	36.000	6.72	0.65	42.74	2.15
1665	1669	6.348132	CGACTGTGGCACAATTAGTTCAAATA	60.348	38.462	22.31	0.00	44.16	1.40
1718	1722	1.228124	TTGTAGCAGCCACCGCTTT	60.228	52.632	0.00	0.00	45.55	3.51
1783	1788	2.757606	GCCATGGGGGAATATTTCTGCT	60.758	50.000	15.13	0.00	40.01	4.24
1850	1855	0.730265	GCGGTGGCATATCGACAAAA	59.270	50.000	11.00	0.00	39.62	2.44
1900	1905	0.045623	TGAGGCTTTCCCAGGGGATA	59.954	55.000	8.12	2.32	44.74	2.59
2020	2025	1.200252	CTGGAGACGTATCGGCCTATG	59.800	57.143	3.77	0.00	34.11	2.23
2041	2046	0.921896	CCCCACCAATGTGATCTCCT	59.078	55.000	0.00	0.00	45.76	3.69
2121	2126	6.037172	CAGCTATTAACGTTGGCTTATCTGTT	59.963	38.462	11.99	0.00	0.00	3.16
2128	2133	3.259064	GTTGGCTTATCTGTTAGTCGCA	58.741	45.455	0.00	0.00	0.00	5.10
2212	2217	0.107897	ACAATATCGCGAAGTGGCCA	60.108	50.000	15.24	0.00	39.32	5.36
2249	2254	2.355513	GGTCAGACCTTGATGCTGTGAT	60.356	50.000	12.94	0.00	38.29	3.06
2469	2474	5.934935	TCTTAGAAAAAGGTGGCTTAACG	57.065	39.130	0.00	0.00	0.00	3.18
2560	2565	1.302993	GGTTGCCCCTTACTCGCAA	60.303	57.895	0.00	0.00	40.06	4.85
2657	2662	2.572191	AGATTTTCGTGCCATGCATG	57.428	45.000	20.19	20.19	45.79	4.06
3020	3025	6.067217	AGAAGGTGCTAAATCAATAGGTGT	57.933	37.500	0.00	0.00	0.00	4.16
3045	3050	3.350833	AGCTGCTACAATTGCTTTAGCT	58.649	40.909	20.79	19.00	42.66	3.32
3070	3075	2.295909	GCTGCTGTTGGTATTGGAAACA	59.704	45.455	0.00	0.00	39.83	2.83
3213	3218	5.474876	AGCCTTTCTGATCTCATTCGTTTTT	59.525	36.000	0.00	0.00	0.00	1.94
3325	3330	2.923035	ATGGGGCGTCCTATCCGG	60.923	66.667	5.77	0.00	36.20	5.14
3344	3349	2.050144	GGTGGATGAATGAGGAGCCTA	58.950	52.381	0.00	0.00	0.00	3.93
3422	3427	1.442769	GATTCAAGCCAAGAGTGCGA	58.557	50.000	0.00	0.00	0.00	5.10
3449	3454	4.442192	CCTTAAGAGCGGTCAAAGCTAGAT	60.442	45.833	18.15	0.00	46.13	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	0.109272	CGGAACTAGAAGCGAGCACA	60.109	55.000	0.00	0.00	0.00	4.57
63	64	3.760693	GCATCTGCCGGAACTAGAA	57.239	52.632	5.05	0.00	34.31	2.10
203	204	0.817013	TTCCCATTGCTTTCATCGCC	59.183	50.000	0.00	0.00	0.00	5.54
348	349	5.760253	TGGAATTATTGAGATCCTCTTTCGC	59.240	40.000	0.00	0.00	33.02	4.70
359	360	9.964354	CCCATATTGATAGTGGAATTATTGAGA	57.036	33.333	0.00	0.00	34.94	3.27
360	361	9.745018	ACCCATATTGATAGTGGAATTATTGAG	57.255	33.333	0.00	0.00	34.94	3.02
704	707	2.552155	CCAAACAAGACCGAGATTCCCA	60.552	50.000	0.00	0.00	0.00	4.37
991	994	5.878116	TGGGTGAGAATTCCATACTTTAACG	59.122	40.000	0.65	0.00	0.00	3.18
1019	1022	3.735237	ATAGATTCGTGAGTTCCGCAT	57.265	42.857	0.00	0.00	0.00	4.73
1264	1267	1.089920	GATCCAGTGCGCTTGACAAT	58.910	50.000	9.73	2.27	0.00	2.71
1382	1385	2.284417	GCTTTCACTTCGACACGTCTTT	59.716	45.455	0.00	0.00	0.00	2.52
1686	1690	5.767168	GGCTGCTACAAGAATGGAATATTCT	59.233	40.000	14.95	0.00	39.82	2.40
1718	1722	0.911045	TTGCAGAGGAGCAGGATCCA	60.911	55.000	15.82	0.00	46.54	3.41
1850	1855	3.192466	GGTCGGCGTAACAATAATGACT	58.808	45.455	6.85	0.00	0.00	3.41
2020	2025	1.408822	GGAGATCACATTGGTGGGGAC	60.409	57.143	0.00	0.00	45.32	4.46
2079	2084	2.029828	AGCTGGTCTAATTCCGCGATAG	60.030	50.000	8.23	4.74	32.79	2.08
2121	2126	2.782222	GGCAGACCCGATGCGACTA	61.782	63.158	0.00	0.00	44.80	2.59
2212	2217	1.202879	TGACCCAAATTGAGCGAAGGT	60.203	47.619	0.00	0.00	46.54	3.50
2249	2254	5.674525	CACCTCTATTGAGTAATGCCTGAA	58.325	41.667	3.47	0.00	38.61	3.02
2439	2444	6.209589	AGCCACCTTTTTCTAAGAAGGATTTC	59.790	38.462	16.55	5.22	44.15	2.17
2469	2474	4.755123	TCTGGTTCCATCTTTCTTTCGTTC	59.245	41.667	0.00	0.00	0.00	3.95
2560	2565	4.938226	CGAGAAAAGCCTTCTTCCTACATT	59.062	41.667	0.51	0.00	0.00	2.71
2657	2662	1.001860	AGACTCTCAGCAGCTTGGTTC	59.998	52.381	0.00	0.00	0.00	3.62
2787	2792	5.988310	TGAGCTGTGGATTGAAAATCATT	57.012	34.783	0.00	0.00	0.00	2.57
2983	2988	3.119459	GCACCTTCTAACATCTCGAGTCA	60.119	47.826	13.13	0.00	0.00	3.41
3020	3025	0.250234	AGCAATTGTAGCAGCTCCGA	59.750	50.000	7.40	0.00	30.05	4.55
3045	3050	1.614051	CCAATACCAACAGCAGCTCCA	60.614	52.381	0.00	0.00	0.00	3.86
3057	3062	4.927267	ACTGAGGATGTTTCCAATACCA	57.073	40.909	0.00	0.00	45.30	3.25
3070	3075	5.587844	CGGAATGAATCAAAGAACTGAGGAT	59.412	40.000	0.00	0.00	0.00	3.24
3188	3193	3.529533	ACGAATGAGATCAGAAAGGCTG	58.470	45.455	0.00	0.00	46.31	4.85
3189	3194	3.902881	ACGAATGAGATCAGAAAGGCT	57.097	42.857	0.00	0.00	0.00	4.58
3213	3218	5.348164	TCTCATGACTTTTTATGCGATCGA	58.652	37.500	21.57	4.34	0.00	3.59
3245	3250	7.482169	TCTGTAACTACATCCTCACATTTCT	57.518	36.000	0.00	0.00	35.36	2.52
3302	3307	2.180276	GATAGGACGCCCCATCTATGT	58.820	52.381	0.00	0.00	37.41	2.29
3325	3330	3.072184	ACATAGGCTCCTCATTCATCCAC	59.928	47.826	0.00	0.00	0.00	4.02
3344	3349	6.961360	TCCTATCATTTCACTACTCGACAT	57.039	37.500	0.00	0.00	0.00	3.06
3422	3427	0.685097	TTGACCGCTCTTAAGGTGCT	59.315	50.000	15.61	2.68	41.51	4.40
3449	3454	4.635223	GTTCCAGCAGTCATGATATAGCA	58.365	43.478	0.00	0.00	0.00	3.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.