AutoCloner

Multiple sequence alignment - TraesCS2D01G158400

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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	TraesCS2D01G158400	chr2D	100.000	5363	0	0	1	5363	102086724	102081362	0.000000e+00	9904.0
1	TraesCS2D01G158400	chr2D	83.710	442	28	20	4907	5345	537490969	537491369	1.410000e-100	377.0
2	TraesCS2D01G158400	chr2B	90.717	2413	155	28	2536	4912	153225648	153223269	0.000000e+00	3151.0
3	TraesCS2D01G158400	chr2B	88.660	2037	130	50	564	2539	153227670	153225674	0.000000e+00	2388.0
4	TraesCS2D01G158400	chr2B	90.749	454	35	4	4912	5362	725732165	725732614	2.760000e-167	599.0
5	TraesCS2D01G158400	chr2B	90.030	331	16	8	90	410	153228088	153227765	3.870000e-111	412.0
6	TraesCS2D01G158400	chr2B	82.759	87	11	4	5171	5255	751333229	751333145	2.070000e-09	75.0
7	TraesCS2D01G158400	chr2A	90.746	2172	122	23	2539	4684	101096096	101093978	0.000000e+00	2824.0
8	TraesCS2D01G158400	chr2A	90.596	1276	61	21	1294	2539	101097371	101096125	0.000000e+00	1637.0
9	TraesCS2D01G158400	chr2A	84.350	754	40	29	485	1215	101098200	101097502	0.000000e+00	667.0
10	TraesCS2D01G158400	chr2A	91.414	198	7	2	4725	4912	101093975	101093778	4.120000e-66	263.0
11	TraesCS2D01G158400	chr2A	78.696	230	17	12	271	492	101098715	101098510	2.030000e-24	124.0
12	TraesCS2D01G158400	chr1B	91.247	457	33	5	4909	5362	416580296	416580748	2.740000e-172	616.0
13	TraesCS2D01G158400	chr7B	90.426	470	34	8	4900	5362	245853060	245853525	4.590000e-170	608.0
14	TraesCS2D01G158400	chr6B	90.949	453	36	3	4912	5362	490207611	490207162	5.940000e-169	604.0
15	TraesCS2D01G158400	chr6B	90.566	53	4	1	4897	4948	564989754	564989702	9.640000e-08	69.4
16	TraesCS2D01G158400	chrUn	88.136	472	30	11	4912	5361	9993411	9992944	6.110000e-149	538.0
17	TraesCS2D01G158400	chr7D	93.594	281	12	4	4912	5190	213792535	213792811	1.070000e-111	414.0
18	TraesCS2D01G158400	chr4A	90.036	281	22	4	4912	5190	231098371	231098647	5.110000e-95	359.0
19	TraesCS2D01G158400	chr5A	83.704	270	39	4	4945	5210	429122523	429122791	3.210000e-62	250.0

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	TraesCS2D01G158400	chr2D	102081362	102086724	5362	True	9904.000000	9904	100.000000	1	5363	1	chr2D.!!$R1	5362
1	TraesCS2D01G158400	chr2B	153223269	153228088	4819	True	1983.666667	3151	89.802333	90	4912	3	chr2B.!!$R2	4822
2	TraesCS2D01G158400	chr2A	101093778	101098715	4937	True	1103.000000	2824	87.160400	271	4912	5	chr2A.!!$R1	4641

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
516	882	0.036388	CCCCGAAAAGCTAGCACTGA	60.036	55.000	18.83	0.0	0.00	3.41	F
564	930	0.178992	CTGAGCTTTTCACCACCCCA	60.179	55.000	0.00	0.0	0.00	4.96	F
1536	2041	0.182299	GATCTAGCCTTGCCTTGCCT	59.818	55.000	0.00	0.0	0.00	4.75	F
1538	2043	0.322816	TCTAGCCTTGCCTTGCCTTG	60.323	55.000	0.00	0.0	0.00	3.61	F
1757	2263	0.445436	CGGTGCTGAACTGCTGATTC	59.555	55.000	0.00	0.0	0.00	2.52	F
2736	3278	1.202302	GCTTCAGGCCTTTATTTCCGC	60.202	52.381	0.00	0.0	34.27	5.54	F
3945	4504	0.250338	ACGCTGTGAAGGGTTTCTCC	60.250	55.000	0.00	0.0	34.31	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1814	2321	0.605319	TCCAAAGCAGTTGCCGGTAG	60.605	55.000	1.90	0.0	43.38	3.18	R
2109	2619	1.816224	GGCATTTACAATCCGTGGTGT	59.184	47.619	0.00	0.0	0.00	4.16	R
2772	3314	0.904394	AACGCATTCCTTGGGCCATT	60.904	50.000	7.26	0.0	41.83	3.16	R
2874	3417	1.562475	GGGCCTGGTGGTATCAAGTTA	59.438	52.381	0.84	0.0	35.27	2.24	R
3544	4099	2.970324	GGCAACACGTTCTGCGGA	60.970	61.111	11.43	0.0	46.52	5.54	R
3969	4528	1.069973	TGCGCGAAACAAGAGTTGATG	60.070	47.619	12.10	0.0	38.17	3.07	R
4912	5508	0.102481	ACGCACGGGCATTCTACTAG	59.898	55.000	11.77	0.0	41.24	2.57	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
47	48	4.875544	TTTCGGAAGCATGTATAGTTGC	57.124	40.909	0.00	0.00	39.17	4.17
48	49	2.833794	TCGGAAGCATGTATAGTTGCC	58.166	47.619	0.00	0.00	39.72	4.52
49	50	2.169561	TCGGAAGCATGTATAGTTGCCA	59.830	45.455	0.00	0.00	39.72	4.92
50	51	2.287915	CGGAAGCATGTATAGTTGCCAC	59.712	50.000	0.00	0.00	39.72	5.01
51	52	3.545703	GGAAGCATGTATAGTTGCCACT	58.454	45.455	0.00	0.00	39.72	4.00
52	53	4.703897	GGAAGCATGTATAGTTGCCACTA	58.296	43.478	0.00	0.00	39.72	2.74
53	54	5.123227	GGAAGCATGTATAGTTGCCACTAA	58.877	41.667	1.22	0.00	39.05	2.24
54	55	5.007724	GGAAGCATGTATAGTTGCCACTAAC	59.992	44.000	1.22	3.22	39.05	2.34
55	56	5.097742	AGCATGTATAGTTGCCACTAACA	57.902	39.130	1.22	8.20	39.05	2.41
56	57	5.496556	AGCATGTATAGTTGCCACTAACAA	58.503	37.500	1.22	0.00	39.05	2.83
57	58	5.943416	AGCATGTATAGTTGCCACTAACAAA	59.057	36.000	1.22	0.00	39.05	2.83
58	59	6.027749	GCATGTATAGTTGCCACTAACAAAC	58.972	40.000	1.22	0.12	39.05	2.93
59	60	6.348950	GCATGTATAGTTGCCACTAACAAACA	60.349	38.462	1.22	5.30	39.05	2.83
60	61	6.795098	TGTATAGTTGCCACTAACAAACAG	57.205	37.500	1.22	0.00	39.05	3.16
61	62	5.703592	TGTATAGTTGCCACTAACAAACAGG	59.296	40.000	1.22	0.00	39.05	4.00
62	63	3.012934	AGTTGCCACTAACAAACAGGT	57.987	42.857	0.00	0.00	33.02	4.00
63	64	2.949644	AGTTGCCACTAACAAACAGGTC	59.050	45.455	0.00	0.00	33.02	3.85
64	65	2.685897	GTTGCCACTAACAAACAGGTCA	59.314	45.455	0.00	0.00	0.00	4.02
65	66	2.571212	TGCCACTAACAAACAGGTCAG	58.429	47.619	0.00	0.00	0.00	3.51
66	67	2.092646	TGCCACTAACAAACAGGTCAGT	60.093	45.455	0.00	0.00	0.00	3.41
67	68	3.134985	TGCCACTAACAAACAGGTCAGTA	59.865	43.478	0.00	0.00	0.00	2.74
68	69	4.131596	GCCACTAACAAACAGGTCAGTAA	58.868	43.478	0.00	0.00	0.00	2.24
69	70	4.024302	GCCACTAACAAACAGGTCAGTAAC	60.024	45.833	0.00	0.00	0.00	2.50
70	71	5.365619	CCACTAACAAACAGGTCAGTAACT	58.634	41.667	0.00	0.00	0.00	2.24
71	72	6.518493	CCACTAACAAACAGGTCAGTAACTA	58.482	40.000	0.00	0.00	0.00	2.24

Showing 1 to 25 of 381 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	5.392595	GGCAACTATACATGCTTCCGAAAAA	60.393	40.000	0.00	0.00	42.20	1.94
25	26	4.095782	GGCAACTATACATGCTTCCGAAAA	59.904	41.667	0.00	0.00	42.20	2.29
26	27	3.625764	GGCAACTATACATGCTTCCGAAA	59.374	43.478	0.00	0.00	42.20	3.46
27	28	3.202906	GGCAACTATACATGCTTCCGAA	58.797	45.455	0.00	0.00	42.20	4.30
28	29	2.169561	TGGCAACTATACATGCTTCCGA	59.830	45.455	0.00	0.00	42.20	4.55
29	30	2.287915	GTGGCAACTATACATGCTTCCG	59.712	50.000	0.00	0.00	42.20	4.30
30	31	3.545703	AGTGGCAACTATACATGCTTCC	58.454	45.455	0.00	0.00	42.20	3.46
31	32	5.584649	TGTTAGTGGCAACTATACATGCTTC	59.415	40.000	0.65	0.79	42.20	3.86
32	33	5.496556	TGTTAGTGGCAACTATACATGCTT	58.503	37.500	0.65	0.00	42.20	3.91
33	34	5.097742	TGTTAGTGGCAACTATACATGCT	57.902	39.130	0.65	0.00	42.20	3.79
34	35	5.811399	TTGTTAGTGGCAACTATACATGC	57.189	39.130	0.65	0.00	38.69	4.06
35	36	7.139896	TGTTTGTTAGTGGCAACTATACATG	57.860	36.000	0.65	0.00	38.69	3.21
36	37	6.374333	CCTGTTTGTTAGTGGCAACTATACAT	59.626	38.462	0.65	0.00	38.69	2.29
37	38	5.703592	CCTGTTTGTTAGTGGCAACTATACA	59.296	40.000	0.65	6.94	38.69	2.29
38	39	5.704053	ACCTGTTTGTTAGTGGCAACTATAC	59.296	40.000	0.65	4.47	38.69	1.47
39	40	5.871834	ACCTGTTTGTTAGTGGCAACTATA	58.128	37.500	0.65	0.00	38.69	1.31
40	41	4.725490	ACCTGTTTGTTAGTGGCAACTAT	58.275	39.130	0.65	0.00	38.69	2.12
41	42	4.131596	GACCTGTTTGTTAGTGGCAACTA	58.868	43.478	0.00	0.00	37.88	2.24
42	43	2.949644	GACCTGTTTGTTAGTGGCAACT	59.050	45.455	0.00	0.00	40.67	3.16
43	44	2.685897	TGACCTGTTTGTTAGTGGCAAC	59.314	45.455	0.00	0.00	0.00	4.17
44	45	2.948979	CTGACCTGTTTGTTAGTGGCAA	59.051	45.455	0.00	0.00	0.00	4.52
45	46	2.092646	ACTGACCTGTTTGTTAGTGGCA	60.093	45.455	0.00	0.00	34.20	4.92
46	47	2.572290	ACTGACCTGTTTGTTAGTGGC	58.428	47.619	0.00	0.00	34.20	5.01
47	48	5.365619	AGTTACTGACCTGTTTGTTAGTGG	58.634	41.667	0.00	0.00	36.00	4.00
48	49	8.603242	ATTAGTTACTGACCTGTTTGTTAGTG	57.397	34.615	0.00	0.00	36.00	2.74

Showing 1 to 25 of 348 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.