AutoCloner

Multiple sequence alignment - TraesCS2A01G256100

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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	TraesCS2A01G256100	chr2A	100.000	6457	0	0	1	6457	392723405	392729861	0.000000e+00	11924.0
1	TraesCS2A01G256100	chr2D	93.583	3226	99	51	2677	5858	325363069	325359908	0.000000e+00	4711.0
2	TraesCS2A01G256100	chr2D	89.860	2495	103	56	262	2679	325365596	325363175	0.000000e+00	3068.0
3	TraesCS2A01G256100	chr2D	88.276	145	10	5	71	210	325365759	325365617	4.000000e-37	167.0
4	TraesCS2A01G256100	chr2B	95.320	2372	61	26	3495	5858	394361954	394359625	0.000000e+00	3720.0
5	TraesCS2A01G256100	chr2B	90.604	1937	72	45	381	2286	394365006	394363149	0.000000e+00	2468.0
6	TraesCS2A01G256100	chr2B	85.676	1117	27	40	2296	3357	394363108	394362070	0.000000e+00	1053.0
7	TraesCS2A01G256100	chr2B	81.215	181	26	7	5959	6135	109330857	109331033	8.730000e-29	139.0
8	TraesCS2A01G256100	chr2B	93.478	92	2	2	104	192	394365574	394365484	4.060000e-27	134.0
9	TraesCS2A01G256100	chr2B	89.286	56	5	1	5961	6015	779309040	779308985	1.160000e-07	69.4
10	TraesCS2A01G256100	chr6B	91.618	346	21	4	5973	6318	132949625	132949962	7.580000e-129	472.0
11	TraesCS2A01G256100	chr6B	82.464	211	37	0	1156	1366	574460723	574460933	1.110000e-42	185.0
12	TraesCS2A01G256100	chr6B	76.610	295	67	2	3544	3837	61224420	61224713	1.860000e-35	161.0
13	TraesCS2A01G256100	chr3A	93.706	286	16	2	5973	6257	159996537	159996821	1.660000e-115	427.0
14	TraesCS2A01G256100	chr3A	95.192	208	3	3	6256	6457	159997059	159997265	8.080000e-84	322.0
15	TraesCS2A01G256100	chr5B	83.878	459	54	10	6009	6457	498834209	498833761	2.780000e-113	420.0
16	TraesCS2A01G256100	chr6A	83.412	211	35	0	1156	1366	526115974	526116184	5.110000e-46	196.0
17	TraesCS2A01G256100	chr6A	77.365	296	63	4	3544	3837	33584217	33584510	8.610000e-39	172.0
18	TraesCS2A01G256100	chr6A	78.210	257	56	0	3544	3800	33541690	33541434	1.440000e-36	165.0
19	TraesCS2A01G256100	chr6D	82.464	211	37	0	1156	1366	384218667	384218877	1.110000e-42	185.0
20	TraesCS2A01G256100	chr6D	78.327	263	57	0	3538	3800	28999646	28999908	3.100000e-38	171.0
21	TraesCS2A01G256100	chr6D	78.138	247	52	2	3544	3789	28941829	28941584	8.670000e-34	156.0
22	TraesCS2A01G256100	chr7B	78.889	180	32	5	5958	6135	66969847	66970022	4.090000e-22	117.0
23	TraesCS2A01G256100	chr3B	91.228	57	3	2	5972	6026	42602669	42602613	6.940000e-10	76.8
24	TraesCS2A01G256100	chr3B	90.909	55	5	0	5962	6016	130471079	130471133	2.500000e-09	75.0
25	TraesCS2A01G256100	chr1A	95.556	45	2	0	5971	6015	137874078	137874122	8.980000e-09	73.1
26	TraesCS2A01G256100	chr4D	90.566	53	4	1	5964	6015	51993122	51993174	1.160000e-07	69.4

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	TraesCS2A01G256100	chr2A	392723405	392729861	6456	False	11924.000000	11924	100.0000	1	6457	1	chr2A.!!$F1	6456
1	TraesCS2A01G256100	chr2D	325359908	325365759	5851	True	2648.666667	4711	90.5730	71	5858	3	chr2D.!!$R1	5787
2	TraesCS2A01G256100	chr2B	394359625	394365574	5949	True	1843.750000	3720	91.2695	104	5858	4	chr2B.!!$R2	5754
3	TraesCS2A01G256100	chr3A	159996537	159997265	728	False	374.500000	427	94.4490	5973	6457	2	chr3A.!!$F1	484

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
217	222	0.104304	CCCGACTGAATCTTACCCCG	59.896	60.0	0.00	0.00	0.00	5.73	F
993	1305	0.112606	ATCTAGCCGGCTGGTAGCTA	59.887	55.0	38.98	19.88	43.35	3.32	F
1484	1813	0.588233	CGTACGTACGCTGCACCTAG	60.588	60.0	32.36	5.42	43.14	3.02	F
1680	2010	0.724453	GCCGTACGTGCATGTGTTTG	60.724	55.0	21.92	8.35	0.00	2.93	F
2933	3481	0.523072	ACGCAGTGATGAAATGGTGC	59.477	50.0	0.00	0.00	42.51	5.01	F
3524	4115	0.038526	GACTGACGGACGGATGTTGT	60.039	55.0	0.00	0.00	0.00	3.32	F
4565	5156	0.173708	GGCTCTTCTACACGGACCTG	59.826	60.0	0.00	0.00	0.00	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1375	1702	0.460987	AGCGAGGAAGGAAATCTGCG	60.461	55.0	0.00	0.00	5.18	R
2566	2972	0.043334	AGAGACCTACCTGCCCACAT	59.957	55.0	0.00	0.00	3.21	R
2579	2985	0.173708	CGGCTGGACTACAAGAGACC	59.826	60.0	0.00	40.14	3.85	R
3505	4096	0.038526	ACAACATCCGTCCGTCAGTC	60.039	55.0	0.00	0.00	3.51	R
4602	5193	1.123077	TGGATGGACGGGATCTTCTG	58.877	55.0	0.00	0.00	3.02	R
4926	5517	1.208642	TGCATCGTCATCGTCATCGC	61.209	55.0	0.00	38.33	4.58	R
5969	6575	0.037605	GCGCGGGTATGGCTAGTTAT	60.038	55.0	8.83	0.00	1.89	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
36	37	9.793259	AAAAAGAGGATATGTCAGTGTTCTAAA	57.207	29.630	0.00	0.00	0.00	1.85
37	38	9.793259	AAAAGAGGATATGTCAGTGTTCTAAAA	57.207	29.630	0.00	0.00	0.00	1.52
38	39	9.442047	AAAGAGGATATGTCAGTGTTCTAAAAG	57.558	33.333	0.00	0.00	0.00	2.27
39	40	7.560368	AGAGGATATGTCAGTGTTCTAAAAGG	58.440	38.462	0.00	0.00	0.00	3.11
40	41	7.400339	AGAGGATATGTCAGTGTTCTAAAAGGA	59.600	37.037	0.00	0.00	0.00	3.36
41	42	8.095452	AGGATATGTCAGTGTTCTAAAAGGAT	57.905	34.615	0.00	0.00	0.00	3.24
42	43	9.213777	AGGATATGTCAGTGTTCTAAAAGGATA	57.786	33.333	0.00	0.00	0.00	2.59
43	44	9.262358	GGATATGTCAGTGTTCTAAAAGGATAC	57.738	37.037	0.00	0.00	0.00	2.24
90	91	1.524621	CCTGTATGGCGCTTCCTGG	60.525	63.158	7.64	2.98	35.26	4.45
97	98	1.143401	GGCGCTTCCTGGGTACTAC	59.857	63.158	7.64	0.00	0.00	2.73
98	99	1.226888	GCGCTTCCTGGGTACTACG	60.227	63.158	0.00	0.00	0.00	3.51
102	105	1.134877	GCTTCCTGGGTACTACGTTCC	60.135	57.143	0.00	0.00	0.00	3.62
124	127	5.596836	CTAGCTGAGGAAGAAGAGATTGT	57.403	43.478	0.00	0.00	0.00	2.71
126	129	7.106439	CTAGCTGAGGAAGAAGAGATTGTAA	57.894	40.000	0.00	0.00	0.00	2.41
127	130	5.976458	AGCTGAGGAAGAAGAGATTGTAAG	58.024	41.667	0.00	0.00	0.00	2.34
128	131	5.719085	AGCTGAGGAAGAAGAGATTGTAAGA	59.281	40.000	0.00	0.00	0.00	2.10
129	132	6.042143	GCTGAGGAAGAAGAGATTGTAAGAG	58.958	44.000	0.00	0.00	0.00	2.85
130	133	5.971763	TGAGGAAGAAGAGATTGTAAGAGC	58.028	41.667	0.00	0.00	0.00	4.09
131	134	5.481824	TGAGGAAGAAGAGATTGTAAGAGCA	59.518	40.000	0.00	0.00	0.00	4.26
134	139	7.725251	AGGAAGAAGAGATTGTAAGAGCATAG	58.275	38.462	0.00	0.00	0.00	2.23
137	142	9.677567	GAAGAAGAGATTGTAAGAGCATAGTAG	57.322	37.037	0.00	0.00	0.00	2.57
192	197	4.780021	AGATAAAGGCCAGACAGAAGAGAA	59.220	41.667	5.01	0.00	0.00	2.87
196	201	2.147150	GGCCAGACAGAAGAGAAACAC	58.853	52.381	0.00	0.00	0.00	3.32
200	205	1.700186	AGACAGAAGAGAAACACCCCC	59.300	52.381	0.00	0.00	0.00	5.40
201	206	0.396811	ACAGAAGAGAAACACCCCCG	59.603	55.000	0.00	0.00	0.00	5.73

Showing 1 to 25 of 379 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
10	11	9.793259	TTTAGAACACTGACATATCCTCTTTTT	57.207	29.630	0.00	0.00	1.94
11	12	9.793259	TTTTAGAACACTGACATATCCTCTTTT	57.207	29.630	0.00	0.00	2.27
12	13	9.442047	CTTTTAGAACACTGACATATCCTCTTT	57.558	33.333	0.00	0.00	2.52
13	14	8.043710	CCTTTTAGAACACTGACATATCCTCTT	58.956	37.037	0.00	0.00	2.85
14	15	7.400339	TCCTTTTAGAACACTGACATATCCTCT	59.600	37.037	0.00	0.00	3.69
15	16	7.556844	TCCTTTTAGAACACTGACATATCCTC	58.443	38.462	0.00	0.00	3.71
16	17	7.496346	TCCTTTTAGAACACTGACATATCCT	57.504	36.000	0.00	0.00	3.24
17	18	9.262358	GTATCCTTTTAGAACACTGACATATCC	57.738	37.037	0.00	0.00	2.59
19	20	9.823647	CAGTATCCTTTTAGAACACTGACATAT	57.176	33.333	0.00	35.12	1.78
20	21	8.258007	CCAGTATCCTTTTAGAACACTGACATA	58.742	37.037	0.00	35.12	2.29
21	22	7.106239	CCAGTATCCTTTTAGAACACTGACAT	58.894	38.462	0.00	35.12	3.06
22	23	6.042781	ACCAGTATCCTTTTAGAACACTGACA	59.957	38.462	0.00	35.12	3.58
23	24	6.465084	ACCAGTATCCTTTTAGAACACTGAC	58.535	40.000	0.00	35.12	3.51
24	25	6.681729	ACCAGTATCCTTTTAGAACACTGA	57.318	37.500	0.00	35.12	3.41
25	26	9.449719	AATTACCAGTATCCTTTTAGAACACTG	57.550	33.333	0.00	33.40	3.66
37	38	9.628500	GTTTCCTTGATAAATTACCAGTATCCT	57.372	33.333	0.00	0.00	3.24
38	39	9.628500	AGTTTCCTTGATAAATTACCAGTATCC	57.372	33.333	0.00	0.00	2.59
48	49	9.660544	AGGCCATTATAGTTTCCTTGATAAATT	57.339	29.630	5.01	0.00	1.82
49	50	9.082313	CAGGCCATTATAGTTTCCTTGATAAAT	57.918	33.333	5.01	0.00	1.40
50	51	8.058847	ACAGGCCATTATAGTTTCCTTGATAAA	58.941	33.333	5.01	0.00	1.40
51	52	7.582719	ACAGGCCATTATAGTTTCCTTGATAA	58.417	34.615	5.01	0.00	1.75
52	53	7.149202	ACAGGCCATTATAGTTTCCTTGATA	57.851	36.000	5.01	0.00	2.15
53	54	6.018433	ACAGGCCATTATAGTTTCCTTGAT	57.982	37.500	5.01	0.00	2.57
54	55	5.450818	ACAGGCCATTATAGTTTCCTTGA	57.549	39.130	5.01	0.00	3.02
55	56	6.207417	CCATACAGGCCATTATAGTTTCCTTG	59.793	42.308	5.01	0.00	3.61

Showing 1 to 25 of 379 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.