AutoCloner

Multiple sequence alignment - TraesCS2D01G090900

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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	TraesCS2D01G090900	chr2D	100.000	2462	0	0	1	2462	43251940	43254401	0.000000e+00	4547.0
1	TraesCS2D01G090900	chr2D	86.441	590	47	12	1126	1683	40784174	40784762	1.250000e-172	616.0
2	TraesCS2D01G090900	chr2D	93.247	385	21	4	700	1084	40783184	40783563	1.650000e-156	562.0
3	TraesCS2D01G090900	chr2D	91.951	410	15	5	319	711	40782557	40782965	2.140000e-155	558.0
4	TraesCS2D01G090900	chr2D	90.536	317	20	3	1	317	40780276	40780582	6.340000e-111	411.0
5	TraesCS2D01G090900	chr2D	93.258	89	6	0	1677	1765	40785166	40785254	5.520000e-27	132.0
6	TraesCS2D01G090900	chr2D	93.333	45	3	0	1776	1820	40789926	40789970	1.580000e-07	67.6
7	TraesCS2D01G090900	chr2A	93.524	1606	81	9	330	1917	44797208	44798808	0.000000e+00	2368.0
8	TraesCS2D01G090900	chr2A	95.072	345	12	1	1	345	44796206	44796545	2.790000e-149	538.0
9	TraesCS2D01G090900	chr2A	80.814	344	50	11	896	1232	44719896	44720230	3.140000e-64	255.0
10	TraesCS2D01G090900	chr2B	86.704	1414	135	28	489	1871	67963607	67964998	0.000000e+00	1520.0
11	TraesCS2D01G090900	chr2B	90.493	284	19	3	1931	2208	184955080	184954799	3.870000e-98	368.0
12	TraesCS2D01G090900	chr2B	91.667	264	20	2	1931	2194	444844021	444843760	5.000000e-97	364.0
13	TraesCS2D01G090900	chr2B	88.614	202	11	5	2264	2462	184954614	184954422	4.090000e-58	235.0
14	TraesCS2D01G090900	chr2B	87.624	202	9	9	2264	2462	444843565	444843377	1.150000e-53	220.0
15	TraesCS2D01G090900	chr2B	89.759	166	17	0	7	172	67357017	67356852	1.920000e-51	213.0
16	TraesCS2D01G090900	chr2B	79.394	330	36	16	626	936	67908699	67909015	1.150000e-48	204.0
17	TraesCS2D01G090900	chr2B	89.655	116	12	0	239	354	67963340	67963455	5.490000e-32	148.0
18	TraesCS2D01G090900	chr2B	94.118	85	1	2	2211	2294	184954751	184954670	2.570000e-25	126.0
19	TraesCS2D01G090900	chr2B	94.118	85	1	2	2211	2294	444843702	444843621	2.570000e-25	126.0
20	TraesCS2D01G090900	chr5A	96.276	537	14	2	1931	2462	436607558	436608093	0.000000e+00	876.0
21	TraesCS2D01G090900	chr4A	93.097	536	21	9	1932	2462	735399951	735400475	0.000000e+00	771.0
22	TraesCS2D01G090900	chr3B	90.164	549	25	15	1931	2462	32768833	32769369	0.000000e+00	688.0
23	TraesCS2D01G090900	chr4D	89.796	539	32	16	1931	2460	450657255	450657779	0.000000e+00	669.0
24	TraesCS2D01G090900	chr7A	96.154	390	10	1	2078	2462	715247691	715247302	1.240000e-177	632.0
25	TraesCS2D01G090900	chr7A	86.837	547	39	13	1931	2457	677448477	677447944	4.560000e-162	580.0
26	TraesCS2D01G090900	chr5D	86.941	559	33	9	1931	2462	437744274	437744819	2.110000e-165	592.0
27	TraesCS2D01G090900	chr5D	90.909	187	16	1	12	198	423259881	423259696	1.460000e-62	250.0
28	TraesCS2D01G090900	chr5D	85.279	197	24	3	3	198	264075574	264075382	5.370000e-47	198.0
29	TraesCS2D01G090900	chrUn	86.141	469	31	17	1931	2375	132137640	132137182	2.220000e-130	475.0
30	TraesCS2D01G090900	chr3A	92.045	264	19	2	1931	2194	594497880	594497619	1.080000e-98	370.0
31	TraesCS2D01G090900	chr3A	87.129	202	10	9	2264	2462	594497424	594497236	5.330000e-52	215.0
32	TraesCS2D01G090900	chr1D	87.817	197	21	2	3	199	60314089	60314282	6.850000e-56	228.0
33	TraesCS2D01G090900	chr5B	85.930	199	25	2	3	199	658521833	658521636	2.480000e-50	209.0
34	TraesCS2D01G090900	chr6A	87.363	182	19	4	12	192	572592753	572592575	3.210000e-49	206.0
35	TraesCS2D01G090900	chr3D	82.805	221	31	2	3	223	14139115	14139328	8.990000e-45	191.0

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	TraesCS2D01G090900	chr2D	43251940	43254401	2461	False	4547.000000	4547	100.000000	1	2462	1	chr2D.!!$F2	2461
1	TraesCS2D01G090900	chr2D	40780276	40785254	4978	False	455.800000	616	91.086600	1	1765	5	chr2D.!!$F3	1764
2	TraesCS2D01G090900	chr2A	44796206	44798808	2602	False	1453.000000	2368	94.298000	1	1917	2	chr2A.!!$F2	1916
3	TraesCS2D01G090900	chr2B	67963340	67964998	1658	False	834.000000	1520	88.179500	239	1871	2	chr2B.!!$F2	1632
4	TraesCS2D01G090900	chr2B	184954422	184955080	658	True	243.000000	368	91.075000	1931	2462	3	chr2B.!!$R2	531
5	TraesCS2D01G090900	chr2B	444843377	444844021	644	True	236.666667	364	91.136333	1931	2462	3	chr2B.!!$R3	531
6	TraesCS2D01G090900	chr5A	436607558	436608093	535	False	876.000000	876	96.276000	1931	2462	1	chr5A.!!$F1	531
7	TraesCS2D01G090900	chr4A	735399951	735400475	524	False	771.000000	771	93.097000	1932	2462	1	chr4A.!!$F1	530
8	TraesCS2D01G090900	chr3B	32768833	32769369	536	False	688.000000	688	90.164000	1931	2462	1	chr3B.!!$F1	531
9	TraesCS2D01G090900	chr4D	450657255	450657779	524	False	669.000000	669	89.796000	1931	2460	1	chr4D.!!$F1	529
10	TraesCS2D01G090900	chr7A	677447944	677448477	533	True	580.000000	580	86.837000	1931	2457	1	chr7A.!!$R1	526
11	TraesCS2D01G090900	chr5D	437744274	437744819	545	False	592.000000	592	86.941000	1931	2462	1	chr5D.!!$F1	531
12	TraesCS2D01G090900	chr3A	594497236	594497880	644	True	292.500000	370	89.587000	1931	2462	2	chr3A.!!$R1	531

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
617	3320	0.243907	ACTACATCTTGCGTGCTCGT	59.756	50.0	10.18	0.0	39.49	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2139	6129	0.034756	CACACCTTGTGGACGGATCA	59.965	55.0	0.0	0.0	44.27	2.92	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
80	81	2.351253	CGGTCGGTTTGCATGAATTTCA	60.351	45.455	0.75	0.75	0.00	2.69
218	219	0.532573	TTTTTGCAGGTTGCCGTTGA	59.467	45.000	0.00	0.00	44.23	3.18
227	228	2.007608	GGTTGCCGTTGAAGATACCTC	58.992	52.381	0.00	0.00	0.00	3.85
271	272	2.543848	CGTCCATGACAATTACATCCCG	59.456	50.000	0.00	0.00	32.09	5.14
272	273	3.541632	GTCCATGACAATTACATCCCGT	58.458	45.455	0.00	0.00	32.09	5.28
298	299	5.849510	TGTCAATTCCTAACTCGAACAGAA	58.150	37.500	0.00	0.00	0.00	3.02
409	3061	4.547532	CGTGATTCTTACCCCTAATCTCG	58.452	47.826	0.00	0.00	39.03	4.04
493	3195	5.892119	AGAAAACGACAGACAGGGATATCTA	59.108	40.000	2.05	0.00	0.00	1.98
593	3296	8.737168	ATAGCATTGTACAAGACATACACATT	57.263	30.769	14.65	0.00	38.07	2.71
615	3318	6.583912	TTATTTACTACATCTTGCGTGCTC	57.416	37.500	0.00	0.00	0.00	4.26
617	3320	0.243907	ACTACATCTTGCGTGCTCGT	59.756	50.000	10.18	0.00	39.49	4.18
618	3321	0.917259	CTACATCTTGCGTGCTCGTC	59.083	55.000	10.18	3.07	39.49	4.20
622	3336	3.414700	CTTGCGTGCTCGTCCCAC	61.415	66.667	10.18	0.00	39.49	4.61
624	3338	4.662961	TGCGTGCTCGTCCCACAG	62.663	66.667	10.18	0.00	39.49	3.66
639	3353	4.573607	GTCCCACAGTCCGAATAATTAACC	59.426	45.833	0.00	0.00	0.00	2.85
656	3375	2.504681	CGCAAATGGCTCGGTTGC	60.505	61.111	0.00	0.00	43.32	4.17
690	3409	3.353557	TGGCGTTCTGATACTGTACTCT	58.646	45.455	0.00	0.00	0.00	3.24
742	3690	9.562583	GACATACAGTTCGGCAAATTAAAAATA	57.437	29.630	0.00	0.00	0.00	1.40
819	3767	3.375299	GTGCATAAAAGCGAGAGAATGGT	59.625	43.478	0.00	0.00	37.31	3.55
826	3774	8.993121	CATAAAAGCGAGAGAATGGTTATACAT	58.007	33.333	0.00	0.00	0.00	2.29
855	3803	2.607602	CCCTCTACTACCCGGCCT	59.392	66.667	0.00	0.00	0.00	5.19
936	3884	2.298729	ACACTCAGCTCTCTCAAGTTCC	59.701	50.000	0.00	0.00	0.00	3.62
947	3895	4.020751	TCTCTCAAGTTCCCATCTCAAGTG	60.021	45.833	0.00	0.00	0.00	3.16
1156	4676	4.024143	GCCAACACATGCGACGCA	62.024	61.111	26.68	26.68	44.86	5.24
1307	4827	3.551496	ATGTGTGGTGCCTCCGTGG	62.551	63.158	0.00	0.00	39.52	4.94
1414	4937	1.349026	CCATATGGGAGAGCCAATCGT	59.651	52.381	14.52	0.00	40.01	3.73
1419	4942	1.330655	GGGAGAGCCAATCGTCCAGA	61.331	60.000	0.00	0.00	35.15	3.86
1662	5216	8.469200	AGTGCAAATTTCAAGCAGCTATAATAA	58.531	29.630	0.00	0.00	39.21	1.40
1691	5655	9.923143	TTATAAGACATCTTCTTCGTTTCTTCA	57.077	29.630	0.00	0.00	44.02	3.02
1826	5797	2.481289	AGAGAAAAGAAGGAAGGGCG	57.519	50.000	0.00	0.00	0.00	6.13
1831	5802	0.329596	AAAGAAGGAAGGGCGAGCAT	59.670	50.000	0.00	0.00	0.00	3.79
1832	5803	0.393537	AAGAAGGAAGGGCGAGCATG	60.394	55.000	0.00	0.00	0.00	4.06
1842	5816	1.131315	GGGCGAGCATGAAAGTTTCTC	59.869	52.381	16.33	5.04	0.00	2.87
1919	5894	9.525409	AAGCTTTATTGATTAGCTAAAATGCAG	57.475	29.630	19.57	13.14	44.05	4.41
1920	5895	8.139989	AGCTTTATTGATTAGCTAAAATGCAGG	58.860	33.333	19.57	8.12	43.08	4.85
1921	5896	7.383300	GCTTTATTGATTAGCTAAAATGCAGGG	59.617	37.037	10.85	0.48	34.99	4.45
1922	5897	4.654091	TTGATTAGCTAAAATGCAGGGC	57.346	40.909	10.85	0.00	34.99	5.19
1923	5898	2.958355	TGATTAGCTAAAATGCAGGGCC	59.042	45.455	10.85	0.00	34.99	5.80
1924	5899	1.388547	TTAGCTAAAATGCAGGGCCG	58.611	50.000	2.97	0.00	34.99	6.13
1925	5900	0.254747	TAGCTAAAATGCAGGGCCGT	59.745	50.000	0.00	0.00	34.99	5.68
1926	5901	1.032114	AGCTAAAATGCAGGGCCGTC	61.032	55.000	0.00	0.00	34.99	4.79
1927	5902	2.004808	GCTAAAATGCAGGGCCGTCC	62.005	60.000	0.00	0.00	0.00	4.79
1928	5903	0.679640	CTAAAATGCAGGGCCGTCCA	60.680	55.000	0.00	0.00	38.24	4.02
1929	5904	0.251386	TAAAATGCAGGGCCGTCCAA	60.251	50.000	0.00	0.00	38.24	3.53
2144	6134	0.105039	GGTGAGGACATCCGTGATCC	59.895	60.000	0.00	0.00	42.08	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	81	3.613030	ACCGCATTTTAACTAACCGGAT	58.387	40.909	9.46	0.00	37.76	4.18
227	228	6.637254	ACGAAGCAGTGAATACTACGATATTG	59.363	38.462	0.00	0.00	34.74	1.90
271	272	6.721321	TGTTCGAGTTAGGAATTGACAAAAC	58.279	36.000	0.00	0.00	0.00	2.43
272	273	6.764085	TCTGTTCGAGTTAGGAATTGACAAAA	59.236	34.615	0.00	0.00	0.00	2.44
298	299	7.827729	AGTAAAACAAACAAGTTAGACTCACCT	59.172	33.333	0.00	0.00	0.00	4.00
409	3061	3.923017	ACACTTCCAACTAAAGCATGC	57.077	42.857	10.51	10.51	0.00	4.06
493	3195	2.030562	CACAAGACGCTTCGGGGT	59.969	61.111	0.00	0.00	43.93	4.95
593	3296	4.738252	CGAGCACGCAAGATGTAGTAAATA	59.262	41.667	0.00	0.00	43.62	1.40
615	3318	2.596904	ATTATTCGGACTGTGGGACG	57.403	50.000	0.00	0.00	0.00	4.79
617	3320	4.681244	CGGTTAATTATTCGGACTGTGGGA	60.681	45.833	0.00	0.00	0.00	4.37
618	3321	3.558418	CGGTTAATTATTCGGACTGTGGG	59.442	47.826	0.00	0.00	0.00	4.61
622	3336	4.868450	TTGCGGTTAATTATTCGGACTG	57.132	40.909	9.12	0.85	0.00	3.51
624	3338	4.973663	CCATTTGCGGTTAATTATTCGGAC	59.026	41.667	9.12	0.00	0.00	4.79
656	3375	6.122850	TCAGAACGCCATATTTGATCTTTG	57.877	37.500	0.00	0.00	0.00	2.77
690	3409	0.252057	TCGATGGAGGACTGTGGGAA	60.252	55.000	0.00	0.00	0.00	3.97
742	3690	8.367911	TCGGTGATATCTATGAGTTGCTATTTT	58.632	33.333	3.98	0.00	0.00	1.82
826	3774	6.463331	CGGGTAGTAGAGGGCATAAAATTACA	60.463	42.308	0.00	0.00	0.00	2.41
855	3803	1.823470	GTGTGCAACCTGACTGGCA	60.823	57.895	0.00	0.00	40.22	4.92
936	3884	1.446907	GTGTCCTGCACTTGAGATGG	58.553	55.000	0.00	0.00	44.41	3.51
947	3895	1.475403	TGAGTAGCCTAGTGTCCTGC	58.525	55.000	0.00	0.00	0.00	4.85
1102	4515	2.923035	CCACCAGTCCAGGTCCGT	60.923	66.667	0.00	0.00	40.77	4.69
1264	4784	4.112341	GTAGTCGTGCTCGCCGGT	62.112	66.667	1.90	0.00	36.96	5.28
1290	4810	4.248842	CCACGGAGGCACCACACA	62.249	66.667	0.94	0.00	38.90	3.72
1307	4827	2.098842	GAAGCTGATGATGACGCCGC	62.099	60.000	0.00	0.00	0.00	6.53
1319	4839	2.235891	TGAAGTACTCACGGAAGCTGA	58.764	47.619	0.00	0.00	0.00	4.26
1414	4937	3.706373	GCGGCTCTTGGGTCTGGA	61.706	66.667	0.00	0.00	0.00	3.86
1419	4942	3.011517	ATGGAGCGGCTCTTGGGT	61.012	61.111	27.47	8.33	0.00	4.51
1676	5230	6.364945	AGACCTTTTGAAGAAACGAAGAAG	57.635	37.500	0.00	0.00	0.00	2.85
1972	5947	0.674534	ACTTCGTCGGTTCAGCTCTT	59.325	50.000	0.00	0.00	0.00	2.85
1973	5948	0.039074	CACTTCGTCGGTTCAGCTCT	60.039	55.000	0.00	0.00	0.00	4.09
2138	6128	0.034896	ACACCTTGTGGACGGATCAC	59.965	55.000	0.00	0.00	37.94	3.06
2139	6129	0.034756	CACACCTTGTGGACGGATCA	59.965	55.000	0.00	0.00	44.27	2.92
2209	6252	4.875536	TGATAAACTGAAGCGTATGCACAT	59.124	37.500	10.11	0.00	46.23	3.21
2259	6303	5.651576	ACTTGGTCAACTAGCCTAGTAGTAC	59.348	44.000	4.50	4.01	38.64	2.73
2336	6495	9.614792	AGGCTTATACAGTACCAAGATAAAAAG	57.385	33.333	7.63	0.00	0.00	2.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.