AutoCloner

Multiple sequence alignment - TraesCS1D01G000700

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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	TraesCS1D01G000700	chr1D	100.000	2741	0	0	1	2741	211267	208527	0.000000e+00	5062.0
1	TraesCS1D01G000700	chr1D	93.373	166	11	0	2576	2741	122222	122057	2.110000e-61	246.0
2	TraesCS1D01G000700	chr1D	86.905	84	7	2	2527	2607	122313	122231	1.050000e-14	91.6
3	TraesCS1D01G000700	chr1A	93.314	1705	89	11	381	2075	4052548	4054237	0.000000e+00	2494.0
4	TraesCS1D01G000700	chr1A	86.636	651	43	17	2134	2741	4054234	4054883	0.000000e+00	680.0
5	TraesCS1D01G000700	chr1A	73.184	537	106	20	1211	1738	4049931	4050438	2.830000e-35	159.0
6	TraesCS1D01G000700	chr1B	92.221	1337	73	18	587	1909	5175116	5176435	0.000000e+00	1864.0
7	TraesCS1D01G000700	chr1B	85.082	858	52	20	1907	2741	5176692	5177496	0.000000e+00	806.0
8	TraesCS1D01G000700	chr1B	84.884	258	37	1	342	599	5174843	5175098	2.710000e-65	259.0
9	TraesCS1D01G000700	chr1B	97.222	36	1	0	2068	2103	112354572	112354607	8.200000e-06	62.1
10	TraesCS1D01G000700	chr7B	91.979	187	13	2	17	202	643480952	643481137	7.530000e-66	261.0
11	TraesCS1D01G000700	chr7B	97.222	36	1	0	2068	2103	485475450	485475415	8.200000e-06	62.1
12	TraesCS1D01G000700	chr7D	90.050	201	18	2	3	202	15771447	15771646	2.710000e-65	259.0
13	TraesCS1D01G000700	chr7D	89.340	197	16	4	4	199	400193098	400192906	2.730000e-60	243.0
14	TraesCS1D01G000700	chr4B	89.055	201	20	2	3	202	446767883	446767684	5.860000e-62	248.0
15	TraesCS1D01G000700	chr2B	87.273	220	21	6	1	218	702720795	702721009	7.580000e-61	244.0
16	TraesCS1D01G000700	chr2B	88.060	201	20	4	3	202	199405412	199405215	4.560000e-58	235.0
17	TraesCS1D01G000700	chr2A	88.557	201	20	3	3	202	762186985	762186787	9.810000e-60	241.0
18	TraesCS1D01G000700	chr6D	88.060	201	21	3	3	202	343124504	343124702	4.560000e-58	235.0
19	TraesCS1D01G000700	chr4D	88.060	201	21	3	3	202	447335185	447334987	4.560000e-58	235.0
20	TraesCS1D01G000700	chr6B	82.051	78	8	3	2067	2138	114836286	114836363	8.200000e-06	62.1
21	TraesCS1D01G000700	chr6B	97.222	36	1	0	2068	2103	267798658	267798623	8.200000e-06	62.1
22	TraesCS1D01G000700	chr2D	97.222	36	1	0	2068	2103	549418167	549418202	8.200000e-06	62.1
23	TraesCS1D01G000700	chrUn	92.857	42	2	1	2060	2101	110290435	110290475	2.950000e-05	60.2
24	TraesCS1D01G000700	chrUn	92.857	42	2	1	2060	2101	187683144	187683184	2.950000e-05	60.2
25	TraesCS1D01G000700	chrUn	92.857	42	2	1	2060	2101	307658760	307658720	2.950000e-05	60.2

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	TraesCS1D01G000700	chr1D	208527	211267	2740	True	5062.000000	5062	100.000000	1	2741	1	chr1D.!!$R1	2740
1	TraesCS1D01G000700	chr1A	4049931	4054883	4952	False	1111.000000	2494	84.378000	381	2741	3	chr1A.!!$F1	2360
2	TraesCS1D01G000700	chr1B	5174843	5177496	2653	False	976.333333	1864	87.395667	342	2741	3	chr1B.!!$F2	2399

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
322	323	0.322366	TGATGAAACGCCTGGATGCA	60.322	50.0	0.00	0.00	0.0	3.96	F
1329	3607	0.322456	TGGTAATGTGGGAGCAGTGC	60.322	55.0	7.13	7.13	0.0	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1480	3758	0.909610	TGGCTAGAACCCAGACCCTG	60.910	60.000	0.00	0.00	0.00	4.45	R
2304	4882	1.068055	GCAACCAATCAGAGTGGCTTG	60.068	52.381	17.11	18.64	40.02	4.01	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.553079	TTGAAGCGCGAACAACTTTT	57.447	40.000	12.10	0.00	0.00	2.27
20	21	2.553079	TGAAGCGCGAACAACTTTTT	57.447	40.000	12.10	0.00	0.00	1.94
21	22	3.677190	TGAAGCGCGAACAACTTTTTA	57.323	38.095	12.10	0.00	0.00	1.52
22	23	4.017380	TGAAGCGCGAACAACTTTTTAA	57.983	36.364	12.10	0.00	0.00	1.52
24	25	4.497608	TGAAGCGCGAACAACTTTTTAAAG	59.502	37.500	12.10	0.80	41.73	1.85
25	26	2.787129	AGCGCGAACAACTTTTTAAAGC	59.213	40.909	12.10	0.00	39.63	3.51
26	27	2.532317	GCGCGAACAACTTTTTAAAGCA	59.468	40.909	12.10	0.00	39.63	3.91
27	28	3.598447	GCGCGAACAACTTTTTAAAGCAC	60.598	43.478	12.10	0.00	39.63	4.40
28	29	3.061469	CGCGAACAACTTTTTAAAGCACC	60.061	43.478	0.00	0.00	39.63	5.01
29	30	3.061469	GCGAACAACTTTTTAAAGCACCG	60.061	43.478	2.23	1.82	39.63	4.94
30	31	4.344448	CGAACAACTTTTTAAAGCACCGA	58.656	39.130	2.23	0.00	39.63	4.69
32	33	4.705337	ACAACTTTTTAAAGCACCGACA	57.295	36.364	2.23	0.00	39.63	4.35
33	34	5.257082	ACAACTTTTTAAAGCACCGACAT	57.743	34.783	2.23	0.00	39.63	3.06
34	35	5.656480	ACAACTTTTTAAAGCACCGACATT	58.344	33.333	2.23	0.00	39.63	2.71
35	36	6.103330	ACAACTTTTTAAAGCACCGACATTT	58.897	32.000	2.23	0.00	39.63	2.32
36	37	6.592220	ACAACTTTTTAAAGCACCGACATTTT	59.408	30.769	2.23	0.00	39.63	1.82
37	38	7.118535	ACAACTTTTTAAAGCACCGACATTTTT	59.881	29.630	2.23	0.00	39.63	1.94
65	66	9.425577	AGTTTTGAGAACAAATTTTTAAACGGA	57.574	25.926	0.00	0.00	43.99	4.69
66	67	9.683651	GTTTTGAGAACAAATTTTTAAACGGAG	57.316	29.630	0.00	0.00	43.99	4.63
67	68	9.640963	TTTTGAGAACAAATTTTTAAACGGAGA	57.359	25.926	0.00	0.00	43.99	3.71
68	69	9.640963	TTTGAGAACAAATTTTTAAACGGAGAA	57.359	25.926	0.00	0.00	40.47	2.87
70	71	8.244802	TGAGAACAAATTTTTAAACGGAGAACA	58.755	29.630	0.00	0.00	0.00	3.18
72	73	9.594478	AGAACAAATTTTTAAACGGAGAACAAT	57.406	25.926	0.00	0.00	0.00	2.71
84	85	7.477144	AACGGAGAACAATTTTGAAAAATCC	57.523	32.000	0.00	0.00	37.62	3.01
86	87	5.118510	CGGAGAACAATTTTGAAAAATCCCG	59.881	40.000	0.00	0.00	37.62	5.14

Showing 1 to 25 of 225 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.553079	AAAAAGTTGTTCGCGCTTCA	57.447	40.000	5.56	0.00	0.00	3.02
2	3	4.603173	GCTTTAAAAAGTTGTTCGCGCTTC	60.603	41.667	5.56	0.00	38.28	3.86
5	6	2.532317	TGCTTTAAAAAGTTGTTCGCGC	59.468	40.909	0.00	0.00	38.28	6.86
6	7	3.061469	GGTGCTTTAAAAAGTTGTTCGCG	60.061	43.478	0.00	0.00	38.28	5.87
7	8	3.061469	CGGTGCTTTAAAAAGTTGTTCGC	60.061	43.478	4.50	0.00	38.28	4.70
8	9	4.203563	GTCGGTGCTTTAAAAAGTTGTTCG	59.796	41.667	4.50	3.11	38.28	3.95
9	10	5.096849	TGTCGGTGCTTTAAAAAGTTGTTC	58.903	37.500	4.50	0.00	38.28	3.18
11	12	4.705337	TGTCGGTGCTTTAAAAAGTTGT	57.295	36.364	4.50	0.00	38.28	3.32
13	14	7.603963	AAAAATGTCGGTGCTTTAAAAAGTT	57.396	28.000	4.50	0.00	38.28	2.66
39	40	9.425577	TCCGTTTAAAAATTTGTTCTCAAAACT	57.574	25.926	0.00	0.00	44.97	2.66
40	41	9.683651	CTCCGTTTAAAAATTTGTTCTCAAAAC	57.316	29.630	0.00	0.00	44.97	2.43
41	42	9.640963	TCTCCGTTTAAAAATTTGTTCTCAAAA	57.359	25.926	0.00	0.00	44.97	2.44
43	44	9.078753	GTTCTCCGTTTAAAAATTTGTTCTCAA	57.921	29.630	0.00	0.00	0.00	3.02
44	45	8.244802	TGTTCTCCGTTTAAAAATTTGTTCTCA	58.755	29.630	0.00	0.00	0.00	3.27
45	46	8.623310	TGTTCTCCGTTTAAAAATTTGTTCTC	57.377	30.769	0.00	0.00	0.00	2.87
46	47	8.989653	TTGTTCTCCGTTTAAAAATTTGTTCT	57.010	26.923	0.00	0.00	0.00	3.01
59	60	7.011950	GGGATTTTTCAAAATTGTTCTCCGTTT	59.988	33.333	0.00	0.00	38.64	3.60
61	62	5.989168	GGGATTTTTCAAAATTGTTCTCCGT	59.011	36.000	0.00	0.00	38.64	4.69
63	64	6.220201	TCGGGATTTTTCAAAATTGTTCTCC	58.780	36.000	0.00	0.00	38.64	3.71
64	65	7.707774	TTCGGGATTTTTCAAAATTGTTCTC	57.292	32.000	0.00	0.00	38.64	2.87
65	66	8.499403	TTTTCGGGATTTTTCAAAATTGTTCT	57.501	26.923	0.00	0.00	38.64	3.01
88	89	5.641636	ACAAAGTTCACGCTTCCAAATTTTT	59.358	32.000	0.00	0.00	0.00	1.94
92	93	4.385358	AACAAAGTTCACGCTTCCAAAT	57.615	36.364	0.00	0.00	0.00	2.32
93	94	3.859411	AACAAAGTTCACGCTTCCAAA	57.141	38.095	0.00	0.00	0.00	3.28
94	95	3.859411	AAACAAAGTTCACGCTTCCAA	57.141	38.095	0.00	0.00	0.00	3.53

Showing 1 to 25 of 227 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.