AutoCloner

Multiple sequence alignment - TraesCS2D01G277100

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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	TraesCS2D01G277100	chr2D	100.000	5611	0	0	1	5611	347453753	347459363	0.000000e+00	10362.0
1	TraesCS2D01G277100	chr2D	93.548	93	5	1	3774	3865	75255018	75255110	2.730000e-28	137.0
2	TraesCS2D01G277100	chr2B	97.159	4189	96	13	1439	5611	412744815	412748996	0.000000e+00	7055.0
3	TraesCS2D01G277100	chr2B	93.380	1420	52	9	20	1408	412743413	412744821	0.000000e+00	2063.0
4	TraesCS2D01G277100	chr2A	93.667	2179	75	14	1	2126	461028335	461030503	0.000000e+00	3201.0
5	TraesCS2D01G277100	chr2A	94.427	1615	73	6	2163	3775	461030621	461032220	0.000000e+00	2468.0
6	TraesCS2D01G277100	chr2A	94.603	1260	45	12	3857	5108	461032219	461033463	0.000000e+00	1929.0
7	TraesCS2D01G277100	chr5B	94.382	89	5	0	3774	3862	35382455	35382367	2.730000e-28	137.0
8	TraesCS2D01G277100	chr3A	95.349	86	4	0	3773	3858	489193084	489193169	2.730000e-28	137.0
9	TraesCS2D01G277100	chr3B	94.186	86	5	0	3773	3858	478078354	478078439	1.270000e-26	132.0
10	TraesCS2D01G277100	chr7D	93.023	86	6	0	3774	3859	474349146	474349061	5.900000e-25	126.0
11	TraesCS2D01G277100	chr7D	87.805	82	6	2	3201	3282	63446949	63446872	5.990000e-15	93.5
12	TraesCS2D01G277100	chr5D	91.304	92	8	0	3771	3862	434549309	434549400	5.900000e-25	126.0
13	TraesCS2D01G277100	chr1A	93.103	87	5	1	3773	3859	63515491	63515406	5.900000e-25	126.0
14	TraesCS2D01G277100	chr1A	92.941	85	6	0	3774	3858	16377817	16377733	2.120000e-24	124.0
15	TraesCS2D01G277100	chr7B	82.812	128	16	4	3201	3327	3851049	3850927	5.940000e-20	110.0
16	TraesCS2D01G277100	chr7A	83.740	123	13	5	3201	3322	66237048	66236932	5.940000e-20	110.0

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	TraesCS2D01G277100	chr2D	347453753	347459363	5610	False	10362.000000	10362	100.000000	1	5611	1	chr2D.!!$F2	5610
1	TraesCS2D01G277100	chr2B	412743413	412748996	5583	False	4559.000000	7055	95.269500	20	5611	2	chr2B.!!$F1	5591
2	TraesCS2D01G277100	chr2A	461028335	461033463	5128	False	2532.666667	3201	94.232333	1	5108	3	chr2A.!!$F1	5107

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
160	163	0.322098	CCGCACACTAAATCCACCCA	60.322	55.000	0.0	0.00	4.51	F
170	173	1.381867	AATCCACCCATCCTGTCCAA	58.618	50.000	0.0	0.00	3.53	F
275	283	3.295093	TGCACTCCTGTTCAAAAATCCA	58.705	40.909	0.0	0.00	3.41	F
2167	2321	3.628032	TGTTCGGTTAACAACAGATGCAA	59.372	39.130	8.1	45.11	4.08	F
3198	3362	4.445832	TGCAAGCAGGCATTCCAT	57.554	50.000	0.0	39.25	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1357	1412	1.081442	GCCTTTGCTGTAACGCCAC	60.081	57.895	33.53	5.01	R
1814	1887	6.690530	TGCATGAACAAAAGAGAATTAAGGG	58.309	36.000	0.00	3.95	R
2673	2836	7.282585	AGCAAGAATATACTATGAAACCTGCA	58.717	34.615	0.00	4.41	R
3298	3462	0.107017	GGATGCAAGCAGGAGCCTAA	60.107	55.000	41.48	2.69	R
5047	5223	0.608856	TCGCATGGTTGATGGTTGCT	60.609	50.000	31.99	3.91	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
46	49	4.123506	GCTTCCTTTGGCTACATCTAGTC	58.876	47.826	0.00	0.00	0.00	2.59
107	110	2.014857	CTCGATCGGTGTCAGTTAGGA	58.985	52.381	16.41	0.00	0.00	2.94
114	117	2.618053	GGTGTCAGTTAGGATGAACGG	58.382	52.381	0.00	0.00	34.36	4.44
140	143	0.942252	GTTCAACTGAACCCACGTCC	59.058	55.000	10.87	0.00	46.42	4.79
160	163	0.322098	CCGCACACTAAATCCACCCA	60.322	55.000	0.00	0.00	0.00	4.51
170	173	1.381867	AATCCACCCATCCTGTCCAA	58.618	50.000	0.00	0.00	0.00	3.53
238	246	9.667107	TTCCAAGTAGAAACGAATCATATTCTT	57.333	29.630	0.00	0.00	34.24	2.52
274	282	3.858503	GCTGCACTCCTGTTCAAAAATCC	60.859	47.826	0.00	0.00	0.00	3.01
275	283	3.295093	TGCACTCCTGTTCAAAAATCCA	58.705	40.909	0.00	0.00	0.00	3.41
504	529	5.106987	GGATTGGTTACGTCGTTGTACAAAT	60.107	40.000	10.51	5.34	0.00	2.32
534	559	7.531857	TTTCATTTGCCTTTATGTGTAGGAA	57.468	32.000	0.00	0.00	33.13	3.36
644	689	9.693739	TTATCCCAATACTTTTCTGAAATAGCA	57.306	29.630	3.31	0.00	0.00	3.49
975	1030	8.604640	TGTAGGATACGTGTTGAATTTTGTAA	57.395	30.769	0.00	0.00	46.99	2.41
986	1041	8.011106	GTGTTGAATTTTGTAATTGATTGCCAG	58.989	33.333	0.00	0.00	34.16	4.85
991	1046	9.807649	GAATTTTGTAATTGATTGCCAGTAGAT	57.192	29.630	0.00	0.00	34.16	1.98
1062	1117	5.039333	GCCACATCATCAAGTGCTTTTATC	58.961	41.667	0.00	0.00	34.48	1.75
1086	1141	5.582269	CGGATCTAGCTTTGTGATCAAGAAA	59.418	40.000	0.00	0.00	38.55	2.52
1814	1887	7.548097	TCTGGTGAACTGATAGTAGAATGTTC	58.452	38.462	0.00	0.00	35.68	3.18
1970	2043	8.025445	CGATGGAAAGAAAGATTGATTCAGTTT	58.975	33.333	0.00	0.00	0.00	2.66
2141	2214	4.571919	ACCATCAATGCTGGTTTGAAATG	58.428	39.130	2.47	0.00	44.67	2.32
2167	2321	3.628032	TGTTCGGTTAACAACAGATGCAA	59.372	39.130	8.10	0.00	45.11	4.08
2459	2613	6.710295	ACAAAACATGCTGTGTCATTCTACTA	59.290	34.615	0.00	0.00	41.14	1.82
2673	2836	9.448438	TTTGACATGCAACTATAATCTGTACTT	57.552	29.630	0.00	0.00	35.91	2.24
2850	3013	6.126409	ACCAGGACTTGAGTTGTTCAAATTA	58.874	36.000	0.00	0.00	44.84	1.40
3198	3362	4.445832	TGCAAGCAGGCATTCCAT	57.554	50.000	0.00	0.00	39.25	3.41
3361	3526	8.869109	CAATGGTTGTAATTCCCATGGTAATAT	58.131	33.333	11.73	0.95	38.93	1.28
3380	3545	9.391006	GGTAATATGTCTGTTAACAAAGGATGA	57.609	33.333	10.03	0.00	31.81	2.92
3391	3556	4.895668	ACAAAGGATGATTGCCAATTGT	57.104	36.364	4.43	0.00	34.76	2.71
3400	3565	5.925506	TGATTGCCAATTGTCATTCATCT	57.074	34.783	9.35	0.00	0.00	2.90
3401	3566	5.656480	TGATTGCCAATTGTCATTCATCTG	58.344	37.500	9.35	0.00	0.00	2.90
3721	3889	8.130307	AGTTTGTGTTGCATAAAAGAAATGAC	57.870	30.769	0.00	0.00	0.00	3.06
3794	3962	7.093640	TGAGCTACTCCTTCCGTAAAGAAATAA	60.094	37.037	0.00	0.00	37.12	1.40
3814	3982	6.663944	ATAAAAGAGCGTTTGGATCACTAC	57.336	37.500	0.00	0.00	32.03	2.73
3815	3983	3.963428	AAGAGCGTTTGGATCACTACT	57.037	42.857	0.00	0.00	32.03	2.57
3816	3984	3.963428	AGAGCGTTTGGATCACTACTT	57.037	42.857	0.00	0.00	32.03	2.24
4221	4390	5.890424	TTTTCTAGTTAGGCATTTTCCCG	57.110	39.130	0.00	0.00	0.00	5.14
4291	4460	7.543172	TGAAAATGTGTTCACTACGATACTACC	59.457	37.037	4.59	0.00	32.56	3.18
4845	5016	6.422776	AGGAATCGTTGCTGTAATGTTAAG	57.577	37.500	0.00	0.00	0.00	1.85
4874	5045	5.705609	ATTATGCCAAGAGTTGACGTTTT	57.294	34.783	0.00	0.00	0.00	2.43
4875	5046	6.811253	ATTATGCCAAGAGTTGACGTTTTA	57.189	33.333	0.00	0.00	0.00	1.52
4947	5118	5.251601	TGATATTCGACCGTAATGTGTCA	57.748	39.130	0.00	0.00	0.00	3.58
5047	5223	6.524101	AGTGGAGTTTTTGCTTGTTTAGAA	57.476	33.333	0.00	0.00	0.00	2.10
5174	5351	4.722220	AGCACATGCCATCAATATGTAGT	58.278	39.130	0.00	0.00	43.38	2.73
5178	5355	5.049198	CACATGCCATCAATATGTAGTCACC	60.049	44.000	0.00	0.00	33.57	4.02
5194	5371	2.236644	GTCACCTTTTCCCCCTACTCTC	59.763	54.545	0.00	0.00	0.00	3.20
5195	5372	2.113777	TCACCTTTTCCCCCTACTCTCT	59.886	50.000	0.00	0.00	0.00	3.10
5287	5464	8.668510	AATAGCAGAAACATATCGAATTGTCT	57.331	30.769	4.32	0.86	0.00	3.41
5288	5465	6.992063	AGCAGAAACATATCGAATTGTCTT	57.008	33.333	4.32	2.52	0.00	3.01
5357	5535	3.714798	AGAAAAGCTCGGGGTATGGATAA	59.285	43.478	0.00	0.00	0.00	1.75
5482	5660	8.862325	TTGTTTATGTCTTTAGATCATGTGGT	57.138	30.769	0.00	0.00	0.00	4.16
5493	5671	5.443185	AGATCATGTGGTTTTTCAGTGTG	57.557	39.130	0.00	0.00	0.00	3.82
5497	5675	3.162202	TGTGGTTTTTCAGTGTGCATG	57.838	42.857	0.00	0.00	0.00	4.06
5498	5676	2.757314	TGTGGTTTTTCAGTGTGCATGA	59.243	40.909	0.00	0.00	0.00	3.07
5557	5735	8.737168	ATGACATGCAATTAAACTAGAAGCTA	57.263	30.769	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	49	2.893637	AGTAAGCACGTAGGCAATCTG	58.106	47.619	0.36	0.00	35.83	2.90
107	110	1.684450	GTTGAACCCCAAACCGTTCAT	59.316	47.619	3.69	0.00	45.66	2.57
140	143	1.029947	GGGTGGATTTAGTGTGCGGG	61.030	60.000	0.00	0.00	0.00	6.13
238	246	1.587547	TGCAGCACACACAAATCGTA	58.412	45.000	0.00	0.00	0.00	3.43
274	282	4.278419	AGAAATTCTCAAAACGGGGTTCTG	59.722	41.667	0.00	0.00	0.00	3.02
275	283	4.278419	CAGAAATTCTCAAAACGGGGTTCT	59.722	41.667	0.00	0.00	0.00	3.01
311	319	3.421844	ACTCCACTAATTTGCTGAACCC	58.578	45.455	0.00	0.00	0.00	4.11
439	463	3.605634	TCACCCCAAATGTCTTATGTCG	58.394	45.455	0.00	0.00	0.00	4.35
444	468	4.955450	CCATCATTCACCCCAAATGTCTTA	59.045	41.667	0.00	0.00	35.92	2.10
504	529	8.121305	ACACATAAAGGCAAATGAAATGACTA	57.879	30.769	1.44	0.00	34.20	2.59
692	747	9.632638	ACTAAGATGGCAATACAAGAACAATAT	57.367	29.630	0.00	0.00	0.00	1.28
768	823	7.336931	ACAGATATGCGTCCAAAGTCTTAAAAT	59.663	33.333	0.00	0.00	0.00	1.82
818	873	8.875168	CAGGTCCCTATAGAAATGTAGAAGAAT	58.125	37.037	0.00	0.00	0.00	2.40
1062	1117	4.686972	TCTTGATCACAAAGCTAGATCCG	58.313	43.478	0.00	6.97	37.86	4.18
1086	1141	1.897802	CCAGCTTTCTTCAGGCCAATT	59.102	47.619	5.01	0.00	0.00	2.32
1229	1284	9.693739	TCATGAGGGTAAAAAGCATAGATTAAA	57.306	29.630	0.00	0.00	0.00	1.52
1357	1412	1.081442	GCCTTTGCTGTAACGCCAC	60.081	57.895	0.00	0.00	33.53	5.01
1814	1887	6.690530	TGCATGAACAAAAGAGAATTAAGGG	58.309	36.000	0.00	0.00	0.00	3.95
2670	2833	9.113838	CAAGAATATACTATGAAACCTGCAAGT	57.886	33.333	0.00	0.00	0.00	3.16
2673	2836	7.282585	AGCAAGAATATACTATGAAACCTGCA	58.717	34.615	0.00	0.00	0.00	4.41
2850	3013	4.396166	CACTTCATCAGGGCGTTCTAAATT	59.604	41.667	0.00	0.00	0.00	1.82
3088	3251	0.177373	CTGTAGGTTAGGCCCCGAAC	59.823	60.000	0.00	0.99	38.26	3.95
3198	3362	9.688091	TTTTGATATACTTGTATGTGGGCTTTA	57.312	29.630	3.75	0.00	0.00	1.85
3298	3462	0.107017	GGATGCAAGCAGGAGCCTAA	60.107	55.000	0.00	0.00	41.48	2.69
3361	3526	5.048083	GGCAATCATCCTTTGTTAACAGACA	60.048	40.000	8.56	0.00	0.00	3.41
3380	3545	4.141801	CCCAGATGAATGACAATTGGCAAT	60.142	41.667	19.96	10.54	36.16	3.56
3391	3556	5.818887	TCAGAAAATGTCCCAGATGAATGA	58.181	37.500	0.00	0.00	0.00	2.57
3400	3565	6.601332	ACTTTACTTCTCAGAAAATGTCCCA	58.399	36.000	0.00	0.00	0.00	4.37
3401	3566	7.511959	AACTTTACTTCTCAGAAAATGTCCC	57.488	36.000	0.00	0.00	0.00	4.46
3794	3962	4.273148	AGTAGTGATCCAAACGCTCTTT	57.727	40.909	0.00	0.00	0.00	2.52
3814	3982	6.910536	ATAAGAGCGTTTGGATCACTAAAG	57.089	37.500	0.00	0.00	32.03	1.85
3815	3983	8.958119	AATATAAGAGCGTTTGGATCACTAAA	57.042	30.769	0.00	0.00	32.03	1.85
3816	3984	8.958119	AAATATAAGAGCGTTTGGATCACTAA	57.042	30.769	0.00	0.00	32.03	2.24
4211	4380	3.920412	GTCTTCATGAAACGGGAAAATGC	59.080	43.478	9.88	0.00	0.00	3.56
4221	4390	8.273780	ACTTCCATATCTTGTCTTCATGAAAC	57.726	34.615	9.88	10.89	32.81	2.78
4845	5016	6.523201	CGTCAACTCTTGGCATAATTAACAAC	59.477	38.462	0.00	0.00	34.15	3.32
4875	5046	9.628500	GGAATATAAGTGTTTCCCTAAACTGAT	57.372	33.333	3.01	0.00	44.44	2.90
5047	5223	0.608856	TCGCATGGTTGATGGTTGCT	60.609	50.000	0.00	0.00	31.99	3.91
5144	5321	4.169059	TGATGGCATGTGCTAGGTAAAT	57.831	40.909	3.81	0.00	41.70	1.40
5174	5351	2.113777	AGAGAGTAGGGGGAAAAGGTGA	59.886	50.000	0.00	0.00	0.00	4.02
5178	5355	5.506730	AAAGAAGAGAGTAGGGGGAAAAG	57.493	43.478	0.00	0.00	0.00	2.27
5194	5371	6.566197	ACAGAACTTCATAGGCAAAAGAAG	57.434	37.500	0.00	0.00	42.32	2.85
5195	5372	6.772716	AGAACAGAACTTCATAGGCAAAAGAA	59.227	34.615	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.