AutoCloner

Multiple sequence alignment - TraesCS4A01G154800

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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	TraesCS4A01G154800	chr4A	100.000	2162	0	0	1	2162	310738086	310740247	0.000000e+00	3993
1	TraesCS4A01G154800	chr5D	96.115	2162	66	6	1	2162	503217725	503219868	0.000000e+00	3511
2	TraesCS4A01G154800	chr5D	95.745	2162	74	6	1	2162	503278719	503276576	0.000000e+00	3467
3	TraesCS4A01G154800	chr3B	96.022	2162	68	6	1	2162	201526531	201528674	0.000000e+00	3500
4	TraesCS4A01G154800	chr1A	96.022	2162	68	6	1	2162	554511755	554513898	0.000000e+00	3500
5	TraesCS4A01G154800	chr6D	95.791	2162	73	6	1	2162	168254433	168256576	0.000000e+00	3472
6	TraesCS4A01G154800	chr3D	95.791	2162	70	8	1	2162	589280035	589277895	0.000000e+00	3469
7	TraesCS4A01G154800	chr3A	95.745	2162	73	7	1	2162	672910500	672908358	0.000000e+00	3465
8	TraesCS4A01G154800	chrUn	95.654	2163	73	9	1	2162	216519095	216516953	0.000000e+00	3454
9	TraesCS4A01G154800	chrUn	96.044	2022	61	6	1	2022	93410124	93408122	0.000000e+00	3273
10	TraesCS4A01G154800	chrUn	95.570	2009	71	6	154	2162	346596834	346594844	0.000000e+00	3201
11	TraesCS4A01G154800	chrUn	95.232	755	18	5	1	755	216522483	216521747	0.000000e+00	1179
12	TraesCS4A01G154800	chrUn	94.523	493	9	5	1	493	216521271	216521745	0.000000e+00	745
13	TraesCS4A01G154800	chrUn	94.444	360	2	5	1	360	396205853	396205512	2.440000e-149	538

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	TraesCS4A01G154800	chr4A	310738086	310740247	2161	False	3993.0	3993	100.000	1	2162	1	chr4A.!!$F1	2161
1	TraesCS4A01G154800	chr5D	503217725	503219868	2143	False	3511.0	3511	96.115	1	2162	1	chr5D.!!$F1	2161
2	TraesCS4A01G154800	chr5D	503276576	503278719	2143	True	3467.0	3467	95.745	1	2162	1	chr5D.!!$R1	2161
3	TraesCS4A01G154800	chr3B	201526531	201528674	2143	False	3500.0	3500	96.022	1	2162	1	chr3B.!!$F1	2161
4	TraesCS4A01G154800	chr1A	554511755	554513898	2143	False	3500.0	3500	96.022	1	2162	1	chr1A.!!$F1	2161
5	TraesCS4A01G154800	chr6D	168254433	168256576	2143	False	3472.0	3472	95.791	1	2162	1	chr6D.!!$F1	2161
6	TraesCS4A01G154800	chr3D	589277895	589280035	2140	True	3469.0	3469	95.791	1	2162	1	chr3D.!!$R1	2161
7	TraesCS4A01G154800	chr3A	672908358	672910500	2142	True	3465.0	3465	95.745	1	2162	1	chr3A.!!$R1	2161
8	TraesCS4A01G154800	chrUn	93408122	93410124	2002	True	3273.0	3273	96.044	1	2022	1	chrUn.!!$R1	2021
9	TraesCS4A01G154800	chrUn	346594844	346596834	1990	True	3201.0	3201	95.570	154	2162	1	chrUn.!!$R2	2008
10	TraesCS4A01G154800	chrUn	216516953	216522483	5530	True	2316.5	3454	95.443	1	2162	2	chrUn.!!$R4	2161

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
260	261	0.57259	CGAATCGCTCATGTTCCGTC	59.427	55.0	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2133	5523	0.589223	TAAGCGCAACGAAAAGGGTG	59.411	50.0	11.47	0.0	0.0	4.61	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
256	257	3.079960	TCTACCGAATCGCTCATGTTC	57.920	47.619	0.00	0.00	0.00	3.18
257	258	2.128035	CTACCGAATCGCTCATGTTCC	58.872	52.381	0.00	0.00	0.00	3.62
259	260	0.806102	CCGAATCGCTCATGTTCCGT	60.806	55.000	0.00	0.00	0.00	4.69
260	261	0.572590	CGAATCGCTCATGTTCCGTC	59.427	55.000	0.00	0.00	0.00	4.79
261	262	1.640428	GAATCGCTCATGTTCCGTCA	58.360	50.000	0.00	0.00	0.00	4.35
262	263	2.205074	GAATCGCTCATGTTCCGTCAT	58.795	47.619	0.00	0.00	0.00	3.06
263	264	2.315925	ATCGCTCATGTTCCGTCATT	57.684	45.000	0.00	0.00	0.00	2.57
264	265	2.093306	TCGCTCATGTTCCGTCATTT	57.907	45.000	0.00	0.00	0.00	2.32
265	266	1.731709	TCGCTCATGTTCCGTCATTTG	59.268	47.619	0.00	0.00	0.00	2.32
266	267	1.202065	CGCTCATGTTCCGTCATTTGG	60.202	52.381	0.00	0.00	0.00	3.28
267	268	1.468054	GCTCATGTTCCGTCATTTGGC	60.468	52.381	0.00	0.00	0.00	4.52
268	269	2.086869	CTCATGTTCCGTCATTTGGCT	58.913	47.619	0.00	0.00	0.00	4.75
269	270	2.489329	CTCATGTTCCGTCATTTGGCTT	59.511	45.455	0.00	0.00	0.00	4.35
270	271	3.680490	TCATGTTCCGTCATTTGGCTTA	58.320	40.909	0.00	0.00	0.00	3.09
271	272	4.269183	TCATGTTCCGTCATTTGGCTTAT	58.731	39.130	0.00	0.00	0.00	1.73
272	273	4.096231	TCATGTTCCGTCATTTGGCTTATG	59.904	41.667	0.00	0.00	0.00	1.90
273	274	2.752354	TGTTCCGTCATTTGGCTTATGG	59.248	45.455	0.00	0.00	0.00	2.74
274	275	1.388547	TCCGTCATTTGGCTTATGGC	58.611	50.000	0.00	0.00	40.90	4.40
275	276	1.064758	TCCGTCATTTGGCTTATGGCT	60.065	47.619	3.78	0.00	41.46	4.75
276	277	1.750778	CCGTCATTTGGCTTATGGCTT	59.249	47.619	3.78	0.00	41.46	4.35
279	280	4.539870	CGTCATTTGGCTTATGGCTTATG	58.460	43.478	3.78	7.10	41.46	1.90
390	391	9.042450	TCGATACTTCCACATATTATGGGTAAT	57.958	33.333	8.48	0.00	37.85	1.89
414	415	2.707554	GGAGACATCCCTATTTCCCCT	58.292	52.381	0.00	0.00	40.03	4.79
417	418	2.090719	AGACATCCCTATTTCCCCTCGA	60.091	50.000	0.00	0.00	0.00	4.04
493	494	1.138464	GTGAATAACCCGTCCTCCTCC	59.862	57.143	0.00	0.00	0.00	4.30
494	495	1.273381	TGAATAACCCGTCCTCCTCCA	60.273	52.381	0.00	0.00	0.00	3.86
498	499	1.073098	AACCCGTCCTCCTCCATTTT	58.927	50.000	0.00	0.00	0.00	1.82
634	635	4.824537	TGCTGCCATTACTCAACAGTTTTA	59.175	37.500	0.00	0.00	33.62	1.52
650	651	7.690256	AACAGTTTTATGTTGAGGTCTATCCT	58.310	34.615	0.00	0.00	41.76	3.24
663	664	4.040706	AGGTCTATCCTGTAGAGGTAGTCG	59.959	50.000	5.71	0.00	46.19	4.18
759	4148	2.103432	TCAAACCGCACTCAAAGGTAGA	59.897	45.455	0.00	0.00	37.26	2.59
789	4178	8.893563	TTCCCATTGATATAGGAACTTTTGTT	57.106	30.769	0.00	0.00	46.75	2.83
895	4284	5.376854	AATGTATGCATTTCGATTAGGGC	57.623	39.130	3.54	0.00	42.19	5.19
897	4286	2.363306	ATGCATTTCGATTAGGGCCA	57.637	45.000	6.18	0.00	0.00	5.36
1138	4527	5.921408	GGTGTTTTGTATAAATGTTTCGCCA	59.079	36.000	0.00	0.00	0.00	5.69
1202	4592	5.446260	AGTGGAATAGAATAACCCGGTTT	57.554	39.130	8.44	0.00	0.00	3.27
1221	4611	5.221106	CGGTTTAAGGGTAGTGATCATACGA	60.221	44.000	0.00	0.00	0.00	3.43
1222	4612	6.516194	CGGTTTAAGGGTAGTGATCATACGAT	60.516	42.308	0.00	0.00	33.31	3.73
1239	4629	8.376889	TCATACGATTGTAATGCATTGTATGT	57.623	30.769	27.39	18.92	39.11	2.29
1342	4732	5.476945	AGTTCGACCCAATGCTTTATTTCTT	59.523	36.000	0.00	0.00	0.00	2.52
1345	4735	5.102313	CGACCCAATGCTTTATTTCTTTCC	58.898	41.667	0.00	0.00	0.00	3.13
1349	4739	6.381133	ACCCAATGCTTTATTTCTTTCCTAGG	59.619	38.462	0.82	0.82	0.00	3.02
1438	4828	6.748333	ATACTGCATATTTGATTCCATCCG	57.252	37.500	0.00	0.00	0.00	4.18
1463	4853	2.467880	TCGACTTTCCCTCCTATGCTT	58.532	47.619	0.00	0.00	0.00	3.91
1600	4990	5.885912	GCCAGTTCCAATAGACTTATGGAAA	59.114	40.000	18.22	5.59	39.92	3.13
1620	5010	2.024868	TTCCCGTTCGTGTGCATCG	61.025	57.895	7.73	7.73	0.00	3.84
1636	5026	2.877168	GCATCGAGCAGGAATTGAATCT	59.123	45.455	0.00	0.00	44.79	2.40
1676	5066	1.544246	GTTGGGCGCTTTAACCATTCT	59.456	47.619	7.64	0.00	33.63	2.40
1791	5181	3.077359	GGAGATGGCAAATATTCGGAGG	58.923	50.000	0.00	0.00	0.00	4.30
1822	5212	0.396417	ACACCTCTCTGGATCCTCGG	60.396	60.000	14.23	8.36	39.71	4.63
1854	5244	6.042322	AGAGAGATTGAGAGGGATCAAGAATG	59.958	42.308	0.00	0.00	42.20	2.67
2014	5404	8.632679	GGCATTGATAACAAGGATCTAATGAAA	58.367	33.333	1.20	0.00	39.71	2.69
2060	5450	9.745880	CTTTAGCAGAAAGACGTATATTCCTTA	57.254	33.333	5.42	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
256	257	1.392589	AGCCATAAGCCAAATGACGG	58.607	50.000	0.00	0.00	45.47	4.79
257	258	4.036734	ACATAAGCCATAAGCCAAATGACG	59.963	41.667	0.00	0.00	45.47	4.35
259	260	5.893255	AGAACATAAGCCATAAGCCAAATGA	59.107	36.000	0.00	0.00	45.47	2.57
260	261	6.152932	AGAACATAAGCCATAAGCCAAATG	57.847	37.500	0.00	0.00	45.47	2.32
261	262	6.833416	TGTAGAACATAAGCCATAAGCCAAAT	59.167	34.615	0.00	0.00	45.47	2.32
262	263	6.184068	TGTAGAACATAAGCCATAAGCCAAA	58.816	36.000	0.00	0.00	45.47	3.28
263	264	5.750524	TGTAGAACATAAGCCATAAGCCAA	58.249	37.500	0.00	0.00	45.47	4.52
264	265	5.366482	TGTAGAACATAAGCCATAAGCCA	57.634	39.130	0.00	0.00	45.47	4.75
265	266	5.412904	GGATGTAGAACATAAGCCATAAGCC	59.587	44.000	0.00	0.00	40.03	4.35
266	267	6.234177	AGGATGTAGAACATAAGCCATAAGC	58.766	40.000	0.00	0.00	39.27	3.09
267	268	8.037758	CCTAGGATGTAGAACATAAGCCATAAG	58.962	40.741	1.05	0.00	39.27	1.73
268	269	7.512746	ACCTAGGATGTAGAACATAAGCCATAA	59.487	37.037	17.98	0.00	39.27	1.90
269	270	7.016914	ACCTAGGATGTAGAACATAAGCCATA	58.983	38.462	17.98	0.00	39.27	2.74
270	271	5.846714	ACCTAGGATGTAGAACATAAGCCAT	59.153	40.000	17.98	0.00	39.27	4.40
271	272	5.216622	ACCTAGGATGTAGAACATAAGCCA	58.783	41.667	17.98	0.00	39.27	4.75
272	273	5.540719	AGACCTAGGATGTAGAACATAAGCC	59.459	44.000	17.98	0.00	39.27	4.35
273	274	6.492087	AGAGACCTAGGATGTAGAACATAAGC	59.508	42.308	17.98	0.00	39.27	3.09
274	275	7.504238	ACAGAGACCTAGGATGTAGAACATAAG	59.496	40.741	17.98	0.00	39.27	1.73
275	276	7.285629	CACAGAGACCTAGGATGTAGAACATAA	59.714	40.741	17.98	0.00	39.27	1.90
276	277	6.773200	CACAGAGACCTAGGATGTAGAACATA	59.227	42.308	17.98	0.00	39.27	2.29
279	280	4.951094	ACACAGAGACCTAGGATGTAGAAC	59.049	45.833	17.98	0.00	0.00	3.01
390	391	4.232091	GGGAAATAGGGATGTCTCCTACA	58.768	47.826	0.00	0.00	43.86	2.74
432	433	5.184671	AGAGGCAAATTGAAAGCTAAGAAGG	59.815	40.000	0.00	0.00	0.00	3.46
435	436	5.182001	GTCAGAGGCAAATTGAAAGCTAAGA	59.818	40.000	0.00	0.00	0.00	2.10
493	494	2.741759	AGCGCCCCTTGTTTAAAATG	57.258	45.000	2.29	0.00	0.00	2.32
494	495	2.028476	GGAAGCGCCCCTTGTTTAAAAT	60.028	45.455	2.29	0.00	32.78	1.82
498	499	1.673009	CGGAAGCGCCCCTTGTTTA	60.673	57.895	2.29	0.00	32.78	2.01
650	651	5.198207	TGATCCAATTCGACTACCTCTACA	58.802	41.667	0.00	0.00	0.00	2.74
663	664	6.857777	AGAAATCGATCACTGATCCAATTC	57.142	37.500	12.58	9.23	35.83	2.17
721	4110	6.898189	GCGGTTTGAACTATTGATTTACGTAG	59.102	38.462	0.00	0.00	0.00	3.51
895	4284	8.528643	TGGTAGAATCGTAACCATAGAATATGG	58.471	37.037	13.15	13.15	44.54	2.74
897	4286	9.529823	TCTGGTAGAATCGTAACCATAGAATAT	57.470	33.333	5.80	0.00	42.23	1.28
958	4347	2.561419	GAGGTCATAAGCGCCTATACCA	59.439	50.000	18.62	0.00	31.89	3.25
1202	4592	6.971726	ACAATCGTATGATCACTACCCTTA	57.028	37.500	0.00	0.00	32.24	2.69
1210	4600	7.355017	ACAATGCATTACAATCGTATGATCAC	58.645	34.615	12.53	0.00	32.24	3.06
1221	4611	6.128486	TCTGGGACATACAATGCATTACAAT	58.872	36.000	12.53	3.14	38.20	2.71
1222	4612	5.504853	TCTGGGACATACAATGCATTACAA	58.495	37.500	12.53	0.60	38.20	2.41
1267	4657	1.115467	AGCCATCGACTACCTGGAAG	58.885	55.000	6.18	0.00	31.38	3.46
1342	4732	1.968493	CGAATCGGGATTCCCTAGGAA	59.032	52.381	19.63	3.05	46.39	3.36
1438	4828	4.750598	GCATAGGAGGGAAAGTCGATTTAC	59.249	45.833	0.00	0.00	0.00	2.01
1463	4853	7.648112	CGAATTCTTATCGATACTGGAACTCAA	59.352	37.037	4.16	0.00	42.76	3.02
1536	4926	7.557875	TCTCATCCATCATCCATACATAACA	57.442	36.000	0.00	0.00	0.00	2.41
1600	4990	0.949105	GATGCACACGAACGGGAACT	60.949	55.000	2.83	0.00	0.00	3.01
1634	5024	8.034215	CCAACTCATAATTGGTAAATTTGCAGA	58.966	33.333	8.59	0.00	41.55	4.26
1636	5026	7.102346	CCCAACTCATAATTGGTAAATTTGCA	58.898	34.615	8.59	0.00	44.46	4.08
1676	5066	1.685803	CCCTGTTAAGCATCCATGGCA	60.686	52.381	6.96	0.00	0.00	4.92
1770	5160	3.077359	CCTCCGAATATTTGCCATCTCC	58.923	50.000	0.00	0.00	0.00	3.71
1791	5181	4.932200	CCAGAGAGGTGTTTTCATAGTCAC	59.068	45.833	0.00	0.00	0.00	3.67
1822	5212	6.232581	TCCCTCTCAATCTCTCTTTCAATC	57.767	41.667	0.00	0.00	0.00	2.67
1854	5244	5.470098	TCCATTCCAAATAGCGAGAATTAGC	59.530	40.000	0.00	0.00	0.00	3.09
1957	5347	6.070424	GGTATCATAAGTAAATGGATCCCGGA	60.070	42.308	9.90	0.00	0.00	5.14
2060	5450	9.553064	GGAATAAGTGATTGTCTGATAATGAGT	57.447	33.333	4.27	0.00	0.00	3.41
2133	5523	0.589223	TAAGCGCAACGAAAAGGGTG	59.411	50.000	11.47	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.