AutoCloner

Multiple sequence alignment - TraesCS1D01G440700

Loading Multiple Alignment...

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	bitscore
0	TraesCS1D01G440700	chr1D	100.000	2512	0	0	869	3380	486116061	486118572	4639
1	TraesCS1D01G440700	chr1D	84.792	2525	352	19	873	3380	19341173	19343682	2507
2	TraesCS1D01G440700	chr1D	100.000	486	0	0	1	486	486115193	486115678	898
3	TraesCS1D01G440700	chr1B	88.038	2508	279	10	873	3373	676810081	676812574	2950
4	TraesCS1D01G440700	chr1B	87.267	2521	289	18	873	3380	676949811	676952312	2848
5	TraesCS1D01G440700	chr1B	86.820	2519	304	18	873	3380	676851819	676854320	2787
6	TraesCS1D01G440700	chr1B	84.822	2385	347	10	993	3371	29823975	29826350	2385
7	TraesCS1D01G440700	chr1B	83.776	2410	362	18	993	3380	29898388	29900790	2257
8	TraesCS1D01G440700	chr1B	83.464	1536	238	14	1836	3364	29085866	29087392	1415
9	TraesCS1D01G440700	chrUn	83.859	2441	373	19	950	3380	116819362	116821791	2305
10	TraesCS1D01G440700	chrUn	83.849	2328	339	23	1079	3380	180337352	180339668	2182
11	TraesCS1D01G440700	chr1A	83.664	1359	200	11	873	2218	21075516	21076865	1260
12	TraesCS1D01G440700	chr1A	82.517	1184	182	15	2220	3380	21076955	21078136	1016

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	TraesCS1D01G440700	chr1D	486115193	486118572	3379	False	2768.5	4639	100.0000	1	3380	2	chr1D.!!$F2	3379
1	TraesCS1D01G440700	chr1D	19341173	19343682	2509	False	2507.0	2507	84.7920	873	3380	1	chr1D.!!$F1	2507
2	TraesCS1D01G440700	chr1B	676810081	676812574	2493	False	2950.0	2950	88.0380	873	3373	1	chr1B.!!$F4	2500
3	TraesCS1D01G440700	chr1B	676949811	676952312	2501	False	2848.0	2848	87.2670	873	3380	1	chr1B.!!$F6	2507
4	TraesCS1D01G440700	chr1B	676851819	676854320	2501	False	2787.0	2787	86.8200	873	3380	1	chr1B.!!$F5	2507
5	TraesCS1D01G440700	chr1B	29823975	29826350	2375	False	2385.0	2385	84.8220	993	3371	1	chr1B.!!$F2	2378
6	TraesCS1D01G440700	chr1B	29898388	29900790	2402	False	2257.0	2257	83.7760	993	3380	1	chr1B.!!$F3	2387
7	TraesCS1D01G440700	chr1B	29085866	29087392	1526	False	1415.0	1415	83.4640	1836	3364	1	chr1B.!!$F1	1528
8	TraesCS1D01G440700	chrUn	116819362	116821791	2429	False	2305.0	2305	83.8590	950	3380	1	chrUn.!!$F1	2430
9	TraesCS1D01G440700	chrUn	180337352	180339668	2316	False	2182.0	2182	83.8490	1079	3380	1	chrUn.!!$F2	2301
10	TraesCS1D01G440700	chr1A	21075516	21078136	2620	False	1138.0	1260	83.0905	873	3380	2	chr1A.!!$F1	2507

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
382	383	0.035317	AGCACAATCGAGTGAGCCAA	59.965	50.0	27.21	0.0	42.05	4.52	F
1062	1093	0.977395	ACAAGGTGTCCAGCTACCTC	59.023	55.0	6.37	0.0	46.28	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1754	1788	0.238289	CAATGCCTTGTCACGGTCAC	59.762	55.0	0.00	0.00	0.0	3.67	R
2772	2923	0.313987	GGTGTTGTAAGTGCCTTGGC	59.686	55.0	4.43	4.43	0.0	4.52	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	Hairpin	End Stability
23	24	5.964958	ACTTCTCACATGGTAAATTGGTG	57.035	39.130	0.00	0.00	4.17
24	25	5.630121	ACTTCTCACATGGTAAATTGGTGA	58.370	37.500	0.00	37.02	4.02
25	26	6.248433	ACTTCTCACATGGTAAATTGGTGAT	58.752	36.000	0.00	37.79	3.06
26	27	6.151648	ACTTCTCACATGGTAAATTGGTGATG	59.848	38.462	0.00	37.79	3.07
27	28	5.814481	TCTCACATGGTAAATTGGTGATGA	58.186	37.500	0.00	37.79	2.92
28	29	6.425735	TCTCACATGGTAAATTGGTGATGAT	58.574	36.000	0.00	37.79	2.45
29	30	6.319405	TCTCACATGGTAAATTGGTGATGATG	59.681	38.462	0.00	37.79	3.07
30	31	5.951148	TCACATGGTAAATTGGTGATGATGT	59.049	36.000	0.00	33.88	3.06
31	32	7.115414	TCACATGGTAAATTGGTGATGATGTA	58.885	34.615	0.00	33.88	2.29
32	33	7.066887	TCACATGGTAAATTGGTGATGATGTAC	59.933	37.037	0.00	33.88	2.90
33	34	6.321181	ACATGGTAAATTGGTGATGATGTACC	59.679	38.462	0.00	37.48	3.34
34	35	6.073447	TGGTAAATTGGTGATGATGTACCT	57.927	37.500	4.78	37.84	3.08
35	36	6.489603	TGGTAAATTGGTGATGATGTACCTT	58.510	36.000	4.78	37.84	3.50
36	37	7.634718	TGGTAAATTGGTGATGATGTACCTTA	58.365	34.615	4.78	37.84	2.69
37	38	8.278639	TGGTAAATTGGTGATGATGTACCTTAT	58.721	33.333	4.78	37.84	1.73
38	39	9.131791	GGTAAATTGGTGATGATGTACCTTATT	57.868	33.333	0.00	37.84	1.40
39	40	9.950680	GTAAATTGGTGATGATGTACCTTATTG	57.049	33.333	0.00	37.84	1.90
40	41	8.593945	AAATTGGTGATGATGTACCTTATTGT	57.406	30.769	0.00	37.84	2.71
41	42	7.807977	ATTGGTGATGATGTACCTTATTGTC	57.192	36.000	0.00	37.84	3.18
42	43	6.560003	TGGTGATGATGTACCTTATTGTCT	57.440	37.500	0.00	37.84	3.41
43	44	6.957631	TGGTGATGATGTACCTTATTGTCTT	58.042	36.000	0.00	37.84	3.01
44	45	6.823182	TGGTGATGATGTACCTTATTGTCTTG	59.177	38.462	0.00	37.84	3.02
45	46	7.047891	GGTGATGATGTACCTTATTGTCTTGA	58.952	38.462	0.00	34.11	3.02
46	47	7.225538	GGTGATGATGTACCTTATTGTCTTGAG	59.774	40.741	0.00	34.11	3.02
47	48	7.981789	GTGATGATGTACCTTATTGTCTTGAGA	59.018	37.037	0.00	0.00	3.27

Showing 1 to 25 of 398 entries

Previous1 2 3 4 5…16Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
3	4	6.244654	TCATCACCAATTTACCATGTGAGAA	58.755	36.000	0.00	39.12	2.87
4	5	5.814481	TCATCACCAATTTACCATGTGAGA	58.186	37.500	0.00	39.12	3.27
5	6	6.095860	ACATCATCACCAATTTACCATGTGAG	59.904	38.462	0.00	39.12	3.51
7	8	6.211587	ACATCATCACCAATTTACCATGTG	57.788	37.500	0.00	0.00	3.21
8	9	6.321181	GGTACATCATCACCAATTTACCATGT	59.679	38.462	0.00	34.77	3.21
9	10	6.547141	AGGTACATCATCACCAATTTACCATG	59.453	38.462	0.00	37.28	3.66
10	11	6.672593	AGGTACATCATCACCAATTTACCAT	58.327	36.000	0.00	37.28	3.55
11	12	6.073447	AGGTACATCATCACCAATTTACCA	57.927	37.500	0.00	37.28	3.25
12	13	8.691661	ATAAGGTACATCATCACCAATTTACC	57.308	34.615	0.00	37.28	2.85
13	14	9.950680	CAATAAGGTACATCATCACCAATTTAC	57.049	33.333	0.00	37.28	2.01
14	15	9.693739	ACAATAAGGTACATCATCACCAATTTA	57.306	29.630	0.00	37.28	1.40
15	16	8.593945	ACAATAAGGTACATCATCACCAATTT	57.406	30.769	0.00	37.28	1.82
16	17	8.055181	AGACAATAAGGTACATCATCACCAATT	58.945	33.333	0.00	37.28	2.32
17	18	7.577303	AGACAATAAGGTACATCATCACCAAT	58.423	34.615	0.00	37.28	3.16
18	19	6.957631	AGACAATAAGGTACATCATCACCAA	58.042	36.000	0.00	37.28	3.67
19	20	6.560003	AGACAATAAGGTACATCATCACCA	57.440	37.500	0.00	37.28	4.17
20	21	7.047891	TCAAGACAATAAGGTACATCATCACC	58.952	38.462	0.00	34.86	4.02
21	22	7.981789	TCTCAAGACAATAAGGTACATCATCAC	59.018	37.037	0.00	0.00	3.06
22	23	8.078060	TCTCAAGACAATAAGGTACATCATCA	57.922	34.615	0.00	0.00	3.07
23	24	9.202273	GATCTCAAGACAATAAGGTACATCATC	57.798	37.037	0.00	0.00	2.92
24	25	8.932610	AGATCTCAAGACAATAAGGTACATCAT	58.067	33.333	0.00	0.00	2.45
25	26	8.311395	AGATCTCAAGACAATAAGGTACATCA	57.689	34.615	0.00	0.00	3.07
26	27	7.593273	CGAGATCTCAAGACAATAAGGTACATC	59.407	40.741	22.31	0.00	3.06
27	28	7.285629	TCGAGATCTCAAGACAATAAGGTACAT	59.714	37.037	22.31	0.00	2.29
28	29	6.602009	TCGAGATCTCAAGACAATAAGGTACA	59.398	38.462	22.31	0.00	2.90

Showing 1 to 25 of 402 entries

Previous1 2 3 4 5…17Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.