AutoCloner

Multiple sequence alignment - TraesCS2D01G341200

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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	TraesCS2D01G341200	chr2D	100.000	4775	0	0	1	4775	435924149	435928923	0.000000e+00	8818
1	TraesCS2D01G341200	chr2D	78.663	2662	420	82	1242	3854	582503752	582501190	0.000000e+00	1633
2	TraesCS2D01G341200	chr2D	77.652	1414	227	51	2153	3535	545727778	545726423	0.000000e+00	778
3	TraesCS2D01G341200	chr2D	77.273	1364	240	28	2185	3519	580971906	580973228	0.000000e+00	737
4	TraesCS2D01G341200	chr2D	77.159	1401	231	43	2153	3519	584235982	584237327	0.000000e+00	732
5	TraesCS2D01G341200	chr2D	75.022	1125	202	38	860	1947	545729045	545727963	9.430000e-122	448
6	TraesCS2D01G341200	chr2D	80.455	440	65	10	310	738	582546791	582546362	2.770000e-82	316
7	TraesCS2D01G341200	chr2B	98.597	4135	29	8	1	4108	515051505	515047373	0.000000e+00	7287
8	TraesCS2D01G341200	chr2B	79.093	2602	404	73	984	3528	701503281	701500763	0.000000e+00	1663
9	TraesCS2D01G341200	chr2B	77.914	1390	243	26	2153	3519	700207014	700208362	0.000000e+00	808
10	TraesCS2D01G341200	chr2B	77.516	1401	226	45	2153	3519	703351236	703352581	0.000000e+00	760
11	TraesCS2D01G341200	chr2B	94.266	436	16	5	4226	4653	515047179	515046745	0.000000e+00	658
12	TraesCS2D01G341200	chr2B	77.049	793	126	27	874	1632	700205675	700206445	5.750000e-109	405
13	TraesCS2D01G341200	chr2B	82.534	292	32	9	213	499	701506853	701506576	6.180000e-59	239
14	TraesCS2D01G341200	chr2B	92.063	126	7	2	4650	4775	515046268	515046146	1.770000e-39	174
15	TraesCS2D01G341200	chr2B	98.936	94	1	0	4106	4199	515047270	515047177	8.220000e-38	169
16	TraesCS2D01G341200	chr2A	77.581	1414	228	53	2153	3535	687314251	687315606	0.000000e+00	773
17	TraesCS2D01G341200	chr2A	75.311	1126	199	39	860	1949	687312962	687314044	2.600000e-127	466
18	TraesCS2D01G341200	chr5B	72.752	745	166	25	2625	3355	710941856	710942577	2.890000e-52	217

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	TraesCS2D01G341200	chr2D	435924149	435928923	4774	False	8818.0	8818	100.0000	1	4775	1	chr2D.!!$F1	4774
1	TraesCS2D01G341200	chr2D	582501190	582503752	2562	True	1633.0	1633	78.6630	1242	3854	1	chr2D.!!$R1	2612
2	TraesCS2D01G341200	chr2D	580971906	580973228	1322	False	737.0	737	77.2730	2185	3519	1	chr2D.!!$F2	1334
3	TraesCS2D01G341200	chr2D	584235982	584237327	1345	False	732.0	732	77.1590	2153	3519	1	chr2D.!!$F3	1366
4	TraesCS2D01G341200	chr2D	545726423	545729045	2622	True	613.0	778	76.3370	860	3535	2	chr2D.!!$R3	2675
5	TraesCS2D01G341200	chr2B	515046146	515051505	5359	True	2072.0	7287	95.9655	1	4775	4	chr2B.!!$R1	4774
6	TraesCS2D01G341200	chr2B	701500763	701506853	6090	True	951.0	1663	80.8135	213	3528	2	chr2B.!!$R2	3315
7	TraesCS2D01G341200	chr2B	703351236	703352581	1345	False	760.0	760	77.5160	2153	3519	1	chr2B.!!$F1	1366
8	TraesCS2D01G341200	chr2B	700205675	700208362	2687	False	606.5	808	77.4815	874	3519	2	chr2B.!!$F2	2645
9	TraesCS2D01G341200	chr2A	687312962	687315606	2644	False	619.5	773	76.4460	860	3535	2	chr2A.!!$F1	2675
10	TraesCS2D01G341200	chr5B	710941856	710942577	721	False	217.0	217	72.7520	2625	3355	1	chr5B.!!$F1	730

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
143	144	5.745312	TTTCTTGTGAGCTAGAGAATGGA	57.255	39.130	0.00	0.00	0.00	3.41	F
1746	4622	0.250901	AAGAGGCGGCATTTGAGTGT	60.251	50.000	13.08	0.00	0.00	3.55	F
2292	5300	4.990426	CCCCTTGTGATGAAATTTGTTCAC	59.010	41.667	17.35	17.35	39.11	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1949	4879	0.996762	TCCTCCTCCTCCTCCTCCTC	60.997	65.000	0.00	3.71	R
2599	5616	6.743773	GCATCCTCTCTATAACCTCTTGCAAT	60.744	42.308	0.00	3.56	R
4128	7332	0.922032	GGCTTTACGCTCTACTTCGC	59.078	55.000	39.13	4.70	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
143	144	5.745312	TTTCTTGTGAGCTAGAGAATGGA	57.255	39.130	0.00	0.00	0.00	3.41
600	689	6.899089	TCAATCCCTATTTGAGACAGCATTA	58.101	36.000	0.00	0.00	0.00	1.90
857	3262	7.307694	TGCTGATTGACTCATTTGAATGTAAC	58.692	34.615	3.85	0.00	37.65	2.50
1139	3961	5.772672	TCCTAGGTTTATCATCTCAGCTCTC	59.227	44.000	9.08	0.00	0.00	3.20
1746	4622	0.250901	AAGAGGCGGCATTTGAGTGT	60.251	50.000	13.08	0.00	0.00	3.55
1941	4856	9.710900	GAAGAAGAAGAAGAAGAAGAAGAAGAT	57.289	33.333	0.00	0.00	0.00	2.40
1949	4879	8.096414	AGAAGAAGAAGAAGAAGATGAAGAAGG	58.904	37.037	0.00	0.00	0.00	3.46
2292	5300	4.990426	CCCCTTGTGATGAAATTTGTTCAC	59.010	41.667	17.35	17.35	39.11	3.18
2595	5612	8.531982	TCCATTGAAGTGTATGGAGCTATATAC	58.468	37.037	11.17	11.17	44.04	1.47
2685	5708	5.131977	TGTTAAGCCTCTTATTGATGCCCTA	59.868	40.000	0.00	0.00	37.07	3.53
2800	5823	9.283768	TGAGCAACATTGAAGAACTAGAAATTA	57.716	29.630	0.00	0.00	0.00	1.40
2899	5928	5.022122	TGTCATCAGATGAGAGGAAGAACT	58.978	41.667	13.78	0.00	40.53	3.01
3065	6097	0.721718	GACAATCCTACTGCACGTGC	59.278	55.000	33.11	33.11	42.50	5.34
3750	6838	9.108284	TCAGAGCGATTAATTGTATTGATGAAA	57.892	29.630	4.60	0.00	0.00	2.69
3792	6885	5.412594	GCAGTGATGAGGAACTAAATTGTGA	59.587	40.000	0.00	0.00	41.55	3.58
4128	7332	9.549078	GAGGTAAAACTCTAATATTGGAGAAGG	57.451	37.037	29.34	9.48	37.94	3.46
4199	7403	2.132762	CCGCTTGGATCACCGTATAAC	58.867	52.381	0.00	0.00	39.42	1.89
4200	7404	2.223971	CCGCTTGGATCACCGTATAACT	60.224	50.000	0.00	0.00	39.42	2.24
4201	7405	3.454375	CGCTTGGATCACCGTATAACTT	58.546	45.455	0.00	0.00	39.42	2.66
4202	7406	3.869246	CGCTTGGATCACCGTATAACTTT	59.131	43.478	0.00	0.00	39.42	2.66
4203	7407	4.025979	CGCTTGGATCACCGTATAACTTTC	60.026	45.833	0.00	0.00	39.42	2.62
4204	7408	4.272748	GCTTGGATCACCGTATAACTTTCC	59.727	45.833	0.00	0.00	39.42	3.13
4205	7409	5.423704	TTGGATCACCGTATAACTTTCCA	57.576	39.130	0.00	0.00	39.42	3.53
4206	7410	5.623956	TGGATCACCGTATAACTTTCCAT	57.376	39.130	0.00	0.00	39.42	3.41
4207	7411	5.607477	TGGATCACCGTATAACTTTCCATC	58.393	41.667	0.00	0.00	39.42	3.51
4208	7412	5.365605	TGGATCACCGTATAACTTTCCATCT	59.634	40.000	0.00	0.00	39.42	2.90
4209	7413	5.696724	GGATCACCGTATAACTTTCCATCTG	59.303	44.000	0.00	0.00	0.00	2.90
4210	7414	4.439057	TCACCGTATAACTTTCCATCTGC	58.561	43.478	0.00	0.00	0.00	4.26
4211	7415	4.081365	TCACCGTATAACTTTCCATCTGCA	60.081	41.667	0.00	0.00	0.00	4.41
4212	7416	4.816385	CACCGTATAACTTTCCATCTGCAT	59.184	41.667	0.00	0.00	0.00	3.96
4213	7417	5.296780	CACCGTATAACTTTCCATCTGCATT	59.703	40.000	0.00	0.00	0.00	3.56
4214	7418	5.885912	ACCGTATAACTTTCCATCTGCATTT	59.114	36.000	0.00	0.00	0.00	2.32
4215	7419	6.377146	ACCGTATAACTTTCCATCTGCATTTT	59.623	34.615	0.00	0.00	0.00	1.82
4216	7420	7.554835	ACCGTATAACTTTCCATCTGCATTTTA	59.445	33.333	0.00	0.00	0.00	1.52
4217	7421	8.567948	CCGTATAACTTTCCATCTGCATTTTAT	58.432	33.333	0.00	0.00	0.00	1.40
4222	7426	7.944729	ACTTTCCATCTGCATTTTATACACT	57.055	32.000	0.00	0.00	0.00	3.55
4223	7427	8.353423	ACTTTCCATCTGCATTTTATACACTT	57.647	30.769	0.00	0.00	0.00	3.16
4224	7428	8.246180	ACTTTCCATCTGCATTTTATACACTTG	58.754	33.333	0.00	0.00	0.00	3.16
4225	7429	7.701539	TTCCATCTGCATTTTATACACTTGT	57.298	32.000	0.00	0.00	0.00	3.16
4226	7430	8.800370	TTCCATCTGCATTTTATACACTTGTA	57.200	30.769	0.00	0.00	34.67	2.41
4227	7431	8.800370	TCCATCTGCATTTTATACACTTGTAA	57.200	30.769	0.00	0.00	33.76	2.41
4262	7466	4.871557	TCATAAAGAAACCGGTGGAATACG	59.128	41.667	8.52	0.00	0.00	3.06
4282	7488	2.418197	CGCGTAAGAGAATTCCCCTTCA	60.418	50.000	12.34	0.95	40.82	3.02
4347	7558	1.227263	CCATTCCCCTAGCACGACG	60.227	63.158	0.00	0.00	0.00	5.12
4389	7600	2.020559	GCTGCGAGTTTGCGATCG	59.979	61.111	11.69	11.69	41.79	3.69
4417	7628	1.270839	CCCTCAGCTTCCTCGTTTCAA	60.271	52.381	0.00	0.00	0.00	2.69
4479	7690	2.725221	ATCCACTTCATCTTCCTGCC	57.275	50.000	0.00	0.00	0.00	4.85
4487	7698	1.377725	ATCTTCCTGCCACGCCAAG	60.378	57.895	0.00	0.00	0.00	3.61
4553	7764	2.213499	GGACAAGAGCAACATATCCGG	58.787	52.381	0.00	0.00	0.00	5.14
4554	7765	1.599542	GACAAGAGCAACATATCCGGC	59.400	52.381	0.00	0.00	0.00	6.13
4589	7800	1.132844	CCTCGTCGTCTGTCTCACG	59.867	63.158	0.00	0.00	38.67	4.35
4640	7851	2.004733	TCTGTTTGCGCATCTCATCTG	58.995	47.619	12.75	0.00	0.00	2.90
4645	7856	0.249615	TGCGCATCTCATCTGTAGCC	60.250	55.000	5.66	0.00	0.00	3.93
4648	7859	0.948141	GCATCTCATCTGTAGCCGCC	60.948	60.000	0.00	0.00	0.00	6.13
4654	8346	3.396822	ATCTGTAGCCGCCCCTCCT	62.397	63.158	0.00	0.00	0.00	3.69
4692	8384	1.299468	CCGCGCTCTGAGATACACC	60.299	63.158	9.28	0.00	0.00	4.16
4693	8385	1.655654	CGCGCTCTGAGATACACCG	60.656	63.158	9.28	2.28	0.00	4.94
4704	8396	1.434622	GATACACCGCGTCTCTCCGA	61.435	60.000	4.92	0.00	0.00	4.55
4719	8411	4.240103	CGATGGATGAGCCGGCCA	62.240	66.667	26.15	21.45	40.66	5.36
4720	8412	2.281345	GATGGATGAGCCGGCCAG	60.281	66.667	26.15	0.00	40.66	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
143	144	5.034200	TCTCTACCTCACTAGAGAGAACCT	58.966	45.833	17.70	1.41	42.55	3.50
459	460	7.290014	AGGGAAAATTGATGGATAAATGGGTAC	59.710	37.037	0.00	0.00	0.00	3.34
1746	4622	4.350368	TCTGGATGCAACTACAACAAGA	57.650	40.909	0.00	0.00	0.00	3.02
1941	4856	1.007721	CCTCCTCCTCCTCCTTCTTCA	59.992	57.143	0.00	0.00	0.00	3.02
1949	4879	0.996762	TCCTCCTCCTCCTCCTCCTC	60.997	65.000	0.00	0.00	0.00	3.71
2292	5300	2.158900	ACTAGGCCCATTGATGTTCTCG	60.159	50.000	0.00	0.00	0.00	4.04
2595	5612	8.424918	TCCTCTCTATAACCTCTTGCAATAAAG	58.575	37.037	0.00	0.00	0.00	1.85
2599	5616	6.743773	GCATCCTCTCTATAACCTCTTGCAAT	60.744	42.308	0.00	0.00	0.00	3.56
2800	5823	8.216423	AGACATTAATCCAATAAGAGCATCACT	58.784	33.333	0.00	0.00	37.82	3.41
3750	6838	5.724854	TCACTGCCTACTAATAAACCCTTCT	59.275	40.000	0.00	0.00	0.00	2.85
4064	7163	4.642437	TCCAATCAAGCAAGTTTACACACA	59.358	37.500	0.00	0.00	0.00	3.72
4128	7332	0.922032	GGCTTTACGCTCTACTTCGC	59.078	55.000	0.00	0.00	39.13	4.70
4199	7403	8.246180	ACAAGTGTATAAAATGCAGATGGAAAG	58.754	33.333	0.00	0.00	0.00	2.62
4200	7404	8.121305	ACAAGTGTATAAAATGCAGATGGAAA	57.879	30.769	0.00	0.00	0.00	3.13
4201	7405	7.701539	ACAAGTGTATAAAATGCAGATGGAA	57.298	32.000	0.00	0.00	0.00	3.53
4202	7406	8.800370	TTACAAGTGTATAAAATGCAGATGGA	57.200	30.769	0.00	0.00	0.00	3.41
4216	7420	9.672673	ATGAGAGCAAGTAAATTACAAGTGTAT	57.327	29.630	5.89	0.00	0.00	2.29
4218	7422	7.986085	ATGAGAGCAAGTAAATTACAAGTGT	57.014	32.000	5.89	0.00	0.00	3.55
4226	7430	8.237267	CGGTTTCTTTATGAGAGCAAGTAAATT	58.763	33.333	0.00	0.00	35.37	1.82
4227	7431	7.148239	CCGGTTTCTTTATGAGAGCAAGTAAAT	60.148	37.037	0.00	0.00	35.37	1.40
4262	7466	3.261981	TGAAGGGGAATTCTCTTACGC	57.738	47.619	5.06	0.00	0.00	4.42
4282	7488	1.362224	TGCTTCCCAAGTAGCTCCTT	58.638	50.000	0.00	0.00	37.31	3.36
4347	7558	0.872388	ACGTCCGAGTTCAAAATGGC	59.128	50.000	0.00	0.00	0.00	4.40
4380	7591	0.249155	GGGGACGTATCGATCGCAAA	60.249	55.000	11.09	0.00	0.00	3.68
4385	7596	0.241481	GCTGAGGGGACGTATCGATC	59.759	60.000	0.00	0.00	0.00	3.69
4389	7600	0.389757	GGAAGCTGAGGGGACGTATC	59.610	60.000	0.00	0.00	0.00	2.24
4417	7628	3.733709	CTTGGAACCAAGGACAGCT	57.266	52.632	21.70	0.00	46.88	4.24
4430	7641	0.256752	CATCCATGCCCTGACTTGGA	59.743	55.000	2.12	2.12	45.03	3.53
4479	7690	2.108700	CGTTGACTTTTTCTTGGCGTG	58.891	47.619	0.00	0.00	0.00	5.34
4553	7764	3.797353	TTGCCCTGGAGATCCCGC	61.797	66.667	0.00	0.00	37.93	6.13
4554	7765	2.190578	GTTGCCCTGGAGATCCCG	59.809	66.667	0.00	0.00	37.93	5.14
4560	7771	2.266055	GACGAGGTTGCCCTGGAG	59.734	66.667	0.00	0.00	42.86	3.86
4565	7776	2.432628	CAGACGACGAGGTTGCCC	60.433	66.667	0.00	0.00	0.00	5.36
4581	7792	2.910479	ACACCGGAGCGTGAGACA	60.910	61.111	9.46	0.00	37.20	3.41
4675	8367	1.655654	CGGTGTATCTCAGAGCGCG	60.656	63.158	0.00	0.00	34.49	6.86
4692	8384	1.371022	CATCCATCGGAGAGACGCG	60.371	63.158	3.53	3.53	43.63	6.01
4693	8385	0.039617	CTCATCCATCGGAGAGACGC	60.040	60.000	0.00	0.00	43.63	5.19
4704	8396	3.882326	CCTGGCCGGCTCATCCAT	61.882	66.667	28.56	0.00	34.01	3.41
4719	8411	2.690510	GGCCTCTGCTTCCTCCCT	60.691	66.667	0.00	0.00	37.74	4.20
4720	8412	4.168291	CGGCCTCTGCTTCCTCCC	62.168	72.222	0.00	0.00	37.74	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.