AutoCloner

Multiple sequence alignment - TraesCS2D01G389100

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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	TraesCS2D01G389100	chr2D	100.000	4883	0	0	1	4883	495406010	495401128	0.000000e+00	9018.0
1	TraesCS2D01G389100	chr2D	79.167	168	27	6	4506	4672	620203533	620203373	5.170000e-20	110.0
2	TraesCS2D01G389100	chr2D	100.000	29	0	0	1243	1271	495404681	495404653	2.000000e-03	54.7
3	TraesCS2D01G389100	chr2D	100.000	29	0	0	1330	1358	495404768	495404740	2.000000e-03	54.7
4	TraesCS2D01G389100	chr2B	96.344	4076	106	15	819	4883	583068784	583064741	0.000000e+00	6661.0
5	TraesCS2D01G389100	chr2B	90.149	538	27	13	208	739	583069672	583069155	0.000000e+00	676.0
6	TraesCS2D01G389100	chr2B	93.750	160	10	0	1	160	583070121	583069962	1.760000e-59	241.0
7	TraesCS2D01G389100	chr2B	95.455	132	6	0	1079	1210	762867262	762867131	1.380000e-50	211.0
8	TraesCS2D01G389100	chr2B	88.764	89	9	1	4584	4672	759892470	759892383	1.860000e-19	108.0
9	TraesCS2D01G389100	chr2B	100.000	29	0	0	1243	1271	583068264	583068236	2.000000e-03	54.7
10	TraesCS2D01G389100	chr2B	100.000	29	0	0	1330	1358	583068351	583068323	2.000000e-03	54.7
11	TraesCS2D01G389100	chr2A	97.939	3299	59	5	1588	4883	638306318	638309610	0.000000e+00	5707.0
12	TraesCS2D01G389100	chr2A	92.652	1742	73	20	1	1726	638304616	638306318	0.000000e+00	2457.0
13	TraesCS2D01G389100	chr2A	96.875	32	1	0	1327	1358	638305832	638305863	2.000000e-03	54.7
14	TraesCS2D01G389100	chr7D	98.732	473	5	1	734	1206	100648851	100649322	0.000000e+00	839.0
15	TraesCS2D01G389100	chr7D	89.655	87	8	1	4590	4676	148142072	148141987	5.170000e-20	110.0
16	TraesCS2D01G389100	chr7D	92.683	41	3	0	4525	4565	205242431	205242471	5.280000e-05	60.2
17	TraesCS2D01G389100	chr6D	97.886	473	8	2	734	1206	262759910	262760380	0.000000e+00	817.0
18	TraesCS2D01G389100	chr6D	98.936	188	1	1	1019	1206	159023492	159023306	7.830000e-88	335.0
19	TraesCS2D01G389100	chr3D	87.619	105	10	2	4568	4670	3002965	3003068	8.590000e-23	119.0
20	TraesCS2D01G389100	chr5D	86.792	106	9	4	4565	4668	44603278	44603380	3.990000e-21	113.0
21	TraesCS2D01G389100	chrUn	87.234	94	12	0	4568	4661	32136901	32136994	1.860000e-19	108.0
22	TraesCS2D01G389100	chr5B	87.912	91	9	2	4579	4668	43984342	43984431	6.680000e-19	106.0
23	TraesCS2D01G389100	chr5B	86.667	60	8	0	4506	4565	685214602	685214543	3.150000e-07	67.6
24	TraesCS2D01G389100	chr4B	81.250	128	13	6	4449	4565	2210903	2210776	5.200000e-15	93.5
25	TraesCS2D01G389100	chr4B	81.250	128	13	6	4449	4565	2240893	2240766	5.200000e-15	93.5
26	TraesCS2D01G389100	chr4D	80.769	130	12	7	4448	4565	1643099	1642971	6.730000e-14	89.8

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	TraesCS2D01G389100	chr2D	495401128	495406010	4882	True	3042.466667	9018	100.0000	1	4883	3	chr2D.!!$R2	4882
1	TraesCS2D01G389100	chr2B	583064741	583070121	5380	True	1537.480000	6661	96.0486	1	4883	5	chr2B.!!$R3	4882
2	TraesCS2D01G389100	chr2A	638304616	638309610	4994	False	2739.566667	5707	95.8220	1	4883	3	chr2A.!!$F1	4882

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
498	745	0.103026	CGGTTCCGCTCATCATCAGA	59.897	55.000	0.00	0.00	3.27	F
501	748	0.103026	TTCCGCTCATCATCAGACGG	59.897	55.000	0.00	41.92	4.79	F
505	752	0.249657	GCTCATCATCAGACGGGGTC	60.250	60.000	0.00	0.00	4.46	F
1657	2365	0.462937	CACCGGTGCCGAAATGGATA	60.463	55.000	24.02	42.00	2.59	F
2408	3116	2.025605	AGAAAGCCATCAGATCCTTGCA	60.026	45.455	0.00	0.00	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1657	2365	0.468029	CTGGACTTGCCCAAACCACT	60.468	55.000	0.00	35.47	4.00	R
1735	2443	2.283966	ACCGCTGTAGTCTGGCCT	60.284	61.111	3.32	0.00	5.19	R
2081	2789	2.301346	GGAACCTCCATGGCACTATTG	58.699	52.381	6.96	40.22	1.90	R
2637	3345	3.254960	ACCATCCTCCTTCCTGATATGG	58.745	50.000	0.00	35.41	2.74	R
4136	4844	0.811281	GAGAGGTTGCCGGAAAATGG	59.189	55.000	5.05	0.00	3.16	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
154	155	2.593725	CAGCGATGCCCCATCCAG	60.594	66.667	0.00	0.00	37.57	3.86
168	169	0.915872	ATCCAGTGGCCAGTCATCCA	60.916	55.000	11.12	0.00	0.00	3.41
193	194	2.363359	CCCAAAATAGCAGGCCTTGATC	59.637	50.000	0.00	0.00	0.00	2.92
232	475	6.233430	ACAAACGAGTCTCATTTGAATCTG	57.767	37.500	24.14	1.88	36.91	2.90
233	476	5.760253	ACAAACGAGTCTCATTTGAATCTGT	59.240	36.000	24.14	2.48	36.91	3.41
272	517	5.596361	TGGCACTCCACTTTTGAGATTAAAA	59.404	36.000	0.00	0.00	37.47	1.52
278	523	9.667107	ACTCCACTTTTGAGATTAAAATCGATA	57.333	29.630	0.00	0.00	40.35	2.92
310	555	2.540101	GTCTGAATTTATCTGACCGCCG	59.460	50.000	4.66	0.00	45.99	6.46
330	575	6.073765	CCGCCGCATTTATATCCATTCTATAC	60.074	42.308	0.00	0.00	0.00	1.47
403	650	0.250234	CCGAGTGGAGCTGGAATCAA	59.750	55.000	0.00	0.00	37.49	2.57
404	651	1.134280	CCGAGTGGAGCTGGAATCAAT	60.134	52.381	0.00	0.00	37.49	2.57
405	652	2.208431	CGAGTGGAGCTGGAATCAATC	58.792	52.381	0.00	0.00	0.00	2.67
406	653	2.419159	CGAGTGGAGCTGGAATCAATCA	60.419	50.000	0.00	0.00	0.00	2.57
412	659	0.659957	GCTGGAATCAATCACGCCTC	59.340	55.000	0.00	0.00	0.00	4.70
417	664	3.126831	GGAATCAATCACGCCTCTACAG	58.873	50.000	0.00	0.00	0.00	2.74
434	681	1.349688	ACAGATTCGTAAACCAGCCCA	59.650	47.619	0.00	0.00	0.00	5.36
440	687	2.706890	TCGTAAACCAGCCCAGAATTC	58.293	47.619	0.00	0.00	0.00	2.17
471	718	1.078708	ACACGCCCACCCTAAATCG	60.079	57.895	0.00	0.00	0.00	3.34
480	727	0.672342	ACCCTAAATCGATCGACCCG	59.328	55.000	22.06	9.10	0.00	5.28
494	741	2.311688	GACCCGGTTCCGCTCATCAT	62.312	60.000	0.00	0.00	0.00	2.45
495	742	1.595382	CCCGGTTCCGCTCATCATC	60.595	63.158	0.00	0.00	0.00	2.92
496	743	1.143838	CCGGTTCCGCTCATCATCA	59.856	57.895	5.66	0.00	0.00	3.07
497	744	0.877649	CCGGTTCCGCTCATCATCAG	60.878	60.000	5.66	0.00	0.00	2.90
498	745	0.103026	CGGTTCCGCTCATCATCAGA	59.897	55.000	0.00	0.00	0.00	3.27
499	746	1.576356	GGTTCCGCTCATCATCAGAC	58.424	55.000	0.00	0.00	0.00	3.51
500	747	1.203928	GTTCCGCTCATCATCAGACG	58.796	55.000	0.00	0.00	0.00	4.18
501	748	0.103026	TTCCGCTCATCATCAGACGG	59.897	55.000	0.00	0.00	41.92	4.79
502	749	1.300465	CCGCTCATCATCAGACGGG	60.300	63.158	0.00	0.00	37.04	5.28
503	750	1.300465	CGCTCATCATCAGACGGGG	60.300	63.158	0.00	0.00	0.00	5.73
504	751	1.826024	GCTCATCATCAGACGGGGT	59.174	57.895	0.00	0.00	0.00	4.95
505	752	0.249657	GCTCATCATCAGACGGGGTC	60.250	60.000	0.00	0.00	0.00	4.46
506	753	1.114627	CTCATCATCAGACGGGGTCA	58.885	55.000	0.00	0.00	34.60	4.02
507	754	0.824109	TCATCATCAGACGGGGTCAC	59.176	55.000	0.00	0.00	34.60	3.67
508	755	0.528466	CATCATCAGACGGGGTCACG	60.528	60.000	0.00	0.00	34.60	4.35
682	938	2.230653	CCATCCAGTCACCCACCCA	61.231	63.158	0.00	0.00	0.00	4.51
684	940	2.231380	ATCCAGTCACCCACCCACC	61.231	63.158	0.00	0.00	0.00	4.61
686	942	2.854032	CAGTCACCCACCCACCCT	60.854	66.667	0.00	0.00	0.00	4.34
687	943	2.529389	AGTCACCCACCCACCCTC	60.529	66.667	0.00	0.00	0.00	4.30
688	944	2.852075	GTCACCCACCCACCCTCA	60.852	66.667	0.00	0.00	0.00	3.86
689	945	2.852075	TCACCCACCCACCCTCAC	60.852	66.667	0.00	0.00	0.00	3.51
690	946	3.966543	CACCCACCCACCCTCACC	61.967	72.222	0.00	0.00	0.00	4.02
691	947	4.202030	ACCCACCCACCCTCACCT	62.202	66.667	0.00	0.00	0.00	4.00
692	948	3.330720	CCCACCCACCCTCACCTC	61.331	72.222	0.00	0.00	0.00	3.85
693	949	3.330720	CCACCCACCCTCACCTCC	61.331	72.222	0.00	0.00	0.00	4.30
694	950	3.330720	CACCCACCCTCACCTCCC	61.331	72.222	0.00	0.00	0.00	4.30
695	951	3.869934	ACCCACCCTCACCTCCCA	61.870	66.667	0.00	0.00	0.00	4.37
871	1425	0.477597	TCCTCCACCCACCCAATCTT	60.478	55.000	0.00	0.00	0.00	2.40
887	1441	2.541233	TCTTTCTCTCTCCCCCTCTG	57.459	55.000	0.00	0.00	0.00	3.35
1273	1843	1.078848	AGTGCGACCATGAAGAGGC	60.079	57.895	0.00	0.00	0.00	4.70
1418	1988	4.047834	CAGTGCGACTGCCAAGAA	57.952	55.556	3.83	0.00	39.62	2.52
1435	2005	3.629142	AGAACTCCGATGGGGTTAAAG	57.371	47.619	0.08	0.00	37.00	1.85
1444	2014	3.558321	CGATGGGGTTAAAGTGGAGAACA	60.558	47.826	0.00	0.00	0.00	3.18
1565	2135	1.831580	AGCAGTGCTGGAAAGGATTC	58.168	50.000	18.98	0.00	37.57	2.52
1657	2365	0.462937	CACCGGTGCCGAAATGGATA	60.463	55.000	24.02	0.00	42.00	2.59
1735	2443	3.072915	TGGAGGAGATTGCTGTTTTGAGA	59.927	43.478	0.00	0.00	0.00	3.27
1783	2491	7.120285	TGAGAGATGAACATGTCCAGAATTTTC	59.880	37.037	0.00	0.00	32.06	2.29
1791	2499	2.105821	TGTCCAGAATTTTCGGACTGGT	59.894	45.455	22.65	0.00	46.68	4.00
2408	3116	2.025605	AGAAAGCCATCAGATCCTTGCA	60.026	45.455	0.00	0.00	0.00	4.08
2637	3345	1.677820	CCACACCGGTTAGGGATTGAC	60.678	57.143	2.97	0.00	46.96	3.18
2773	3481	8.358895	CAGCTACAATGAATCAGAAGATAGAGA	58.641	37.037	0.00	0.00	33.08	3.10
3114	3822	4.818642	ACTCAATATCTGATGAGCATCCG	58.181	43.478	7.92	2.13	45.50	4.18
3279	3987	7.683578	TCAATGATAAAGGCTGTATCATAGCT	58.316	34.615	31.07	18.44	44.31	3.32
3411	4119	2.035626	ATGGGTTGGGGCGTGAAG	59.964	61.111	0.00	0.00	0.00	3.02
3438	4146	6.780901	TCTCGACTATATACCATCTGGAAGT	58.219	40.000	2.55	0.00	38.94	3.01
3808	4516	6.006275	ACAACTATGCCATAGATCAGGTTT	57.994	37.500	18.38	0.00	36.68	3.27
4089	4797	6.521162	TGTAGTTCTAGCTTTCAACATGACA	58.479	36.000	0.00	0.00	0.00	3.58
4102	4810	9.350357	CTTTCAACATGACAATAATTCTTGGAG	57.650	33.333	0.00	0.00	0.00	3.86
4172	4880	4.763793	ACCTCTCATTTGGTTCAGTGATTG	59.236	41.667	0.00	0.00	31.62	2.67
4296	5006	8.831715	AATTGCGATATCATGATGTACACTTA	57.168	30.769	18.72	0.00	0.00	2.24
4638	5348	8.721478	GTTGCATGTTGAGAGAATTAGAGTTAA	58.279	33.333	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
182	183	1.826385	AAAGGTTCGATCAAGGCCTG	58.174	50.000	5.69	0.00	0.00	4.85
193	194	5.512473	TCGTTTGTTAATGGAAAAGGTTCG	58.488	37.500	0.00	0.00	34.28	3.95
232	475	1.293963	GCCACGGACGGAAAAGGTAC	61.294	60.000	0.00	0.00	0.00	3.34
233	476	1.004679	GCCACGGACGGAAAAGGTA	60.005	57.895	0.00	0.00	0.00	3.08
272	517	6.378710	TTCAGACTCGACTTGAATATCGAT	57.621	37.500	2.16	2.16	45.63	3.59
278	523	8.253810	TCAGATAAATTCAGACTCGACTTGAAT	58.746	33.333	7.94	7.94	0.00	2.57
350	595	2.048877	TTCGGCTTCGGTTCGGAC	60.049	61.111	0.00	0.00	34.13	4.79
403	650	2.025155	ACGAATCTGTAGAGGCGTGAT	58.975	47.619	9.88	0.00	36.74	3.06
404	651	1.460504	ACGAATCTGTAGAGGCGTGA	58.539	50.000	9.88	0.00	36.74	4.35
405	652	3.416119	TTACGAATCTGTAGAGGCGTG	57.584	47.619	16.81	0.00	37.95	5.34
406	653	3.428589	GGTTTACGAATCTGTAGAGGCGT	60.429	47.826	13.64	13.64	39.71	5.68
412	659	3.195661	GGGCTGGTTTACGAATCTGTAG	58.804	50.000	0.00	0.00	0.00	2.74
417	664	2.396590	TCTGGGCTGGTTTACGAATC	57.603	50.000	0.00	0.00	0.00	2.52
453	700	1.078708	CGATTTAGGGTGGGCGTGT	60.079	57.895	0.00	0.00	0.00	4.49
454	701	0.179056	ATCGATTTAGGGTGGGCGTG	60.179	55.000	0.00	0.00	0.00	5.34
471	718	3.769875	GAGCGGAACCGGGTCGATC	62.770	68.421	14.69	13.37	40.19	3.69
480	727	1.576356	GTCTGATGATGAGCGGAACC	58.424	55.000	0.00	0.00	0.00	3.62
503	750	2.804828	CTTTGCCTCTCCCCCGTGAC	62.805	65.000	0.00	0.00	0.00	3.67
504	751	2.528127	TTTGCCTCTCCCCCGTGA	60.528	61.111	0.00	0.00	0.00	4.35
505	752	2.045926	CTTTGCCTCTCCCCCGTG	60.046	66.667	0.00	0.00	0.00	4.94
506	753	3.330720	CCTTTGCCTCTCCCCCGT	61.331	66.667	0.00	0.00	0.00	5.28
507	754	4.803908	GCCTTTGCCTCTCCCCCG	62.804	72.222	0.00	0.00	0.00	5.73
508	755	4.803908	CGCCTTTGCCTCTCCCCC	62.804	72.222	0.00	0.00	0.00	5.40
674	930	4.202030	AGGTGAGGGTGGGTGGGT	62.202	66.667	0.00	0.00	0.00	4.51
682	938	4.677151	GGGGTGGGAGGTGAGGGT	62.677	72.222	0.00	0.00	0.00	4.34
684	940	3.330720	GTGGGGTGGGAGGTGAGG	61.331	72.222	0.00	0.00	0.00	3.86
686	942	4.995058	GGGTGGGGTGGGAGGTGA	62.995	72.222	0.00	0.00	0.00	4.02
791	1052	1.689582	GTGGAGGAGGTGGGTAGGG	60.690	68.421	0.00	0.00	0.00	3.53
871	1425	0.033991	CGACAGAGGGGGAGAGAGAA	60.034	60.000	0.00	0.00	0.00	2.87
1041	1602	3.400054	GCCTTGTACCTCCGCCCT	61.400	66.667	0.00	0.00	0.00	5.19
1239	1809	2.313172	ACTGCGCGTGCTTCTCTTG	61.313	57.895	23.16	5.99	43.34	3.02
1418	1988	1.280998	CCACTTTAACCCCATCGGAGT	59.719	52.381	0.00	0.00	34.64	3.85
1435	2005	3.426568	GCAGGCGCTGTTCTCCAC	61.427	66.667	7.64	0.00	33.43	4.02
1565	2135	3.191371	GTGTGTGCCTCTCTTTATTTGGG	59.809	47.826	0.00	0.00	0.00	4.12
1657	2365	0.468029	CTGGACTTGCCCAAACCACT	60.468	55.000	0.00	0.00	35.47	4.00
1735	2443	2.283966	ACCGCTGTAGTCTGGCCT	60.284	61.111	3.32	0.00	0.00	5.19
1783	2491	4.988598	AACGCTGCCACCAGTCCG	62.989	66.667	0.00	0.00	41.26	4.79
1899	2607	4.258543	CGTTGCTCTTTAACCTATTCCCA	58.741	43.478	0.00	0.00	0.00	4.37
1906	2614	5.007724	CAGAAGAAACGTTGCTCTTTAACCT	59.992	40.000	9.83	2.92	32.01	3.50
2081	2789	2.301346	GGAACCTCCATGGCACTATTG	58.699	52.381	6.96	0.00	40.22	1.90
2142	2850	5.253330	GGAGTTTCAAGTGATCCACCATTA	58.747	41.667	0.00	0.00	34.49	1.90
2408	3116	7.696992	TTCTTGTAAATTAAGCGGAAATCCT	57.303	32.000	0.00	0.00	0.00	3.24
2637	3345	3.254960	ACCATCCTCCTTCCTGATATGG	58.745	50.000	0.00	0.00	35.41	2.74
2773	3481	4.623932	TCTTCAGTGCAAGATTGGTACT	57.376	40.909	0.00	0.00	0.00	2.73
3114	3822	5.734786	GCGAGACATGTAGATATAGGGCATC	60.735	48.000	0.00	0.00	0.00	3.91
3411	4119	6.408035	TCCAGATGGTATATAGTCGAGAGTC	58.592	44.000	0.00	0.00	36.34	3.36
3438	4146	4.006989	CCCCAATGTATTCACAGACGAAA	58.993	43.478	0.00	0.00	38.30	3.46
3808	4516	9.551734	CTTCTTGATGTTACCATTCTCATCATA	57.448	33.333	7.37	0.00	43.57	2.15
4136	4844	0.811281	GAGAGGTTGCCGGAAAATGG	59.189	55.000	5.05	0.00	0.00	3.16
4172	4880	5.983540	AGGAGTTGAAGGACACAGAATATC	58.016	41.667	0.00	0.00	0.00	1.63
4296	5006	7.560368	CACAGGGTATCATCTCTAGTTTTCTT	58.440	38.462	0.00	0.00	0.00	2.52
4515	5225	3.572632	ACTATGCCAACTCATCATGCT	57.427	42.857	0.00	0.00	0.00	3.79
4638	5348	5.674958	ACATACCTAAATAGTTGACCCCCAT	59.325	40.000	0.00	0.00	0.00	4.00
4717	5427	6.869315	TGATGACCAAACGAAATTACTGAA	57.131	33.333	0.00	0.00	0.00	3.02
4718	5428	7.447374	AATGATGACCAAACGAAATTACTGA	57.553	32.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.