AutoCloner

Multiple sequence alignment - TraesCS4D01G034100

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	evalue	bitscore
0	TraesCS4D01G034100	chr4D	100.000	4384	0	0	1	4384	15551122	15555505	0.000000e+00	8096.0
1	TraesCS4D01G034100	chr4D	100.000	2947	0	0	4627	7573	15555748	15558694	0.000000e+00	5443.0
2	TraesCS4D01G034100	chr4D	93.856	651	40	0	6921	7571	242938234	242938884	0.000000e+00	981.0
3	TraesCS4D01G034100	chr4D	93.548	651	42	0	6921	7571	443841433	443840783	0.000000e+00	970.0
4	TraesCS4D01G034100	chr4D	87.029	239	28	3	1369	1606	43054307	43054543	4.500000e-67	267.0
5	TraesCS4D01G034100	chr4B	95.183	4090	137	28	337	4384	26485928	26489999	0.000000e+00	6407.0
6	TraesCS4D01G034100	chr4B	94.166	2331	83	19	4629	6923	26490059	26492372	0.000000e+00	3502.0
7	TraesCS4D01G034100	chr4B	92.553	94	4	1	35	125	373351676	373351583	1.710000e-26	132.0
8	TraesCS4D01G034100	chr4B	85.075	134	9	3	154	287	26485792	26485914	7.980000e-25	126.0
9	TraesCS4D01G034100	chr4A	92.821	4109	151	51	329	4384	585034008	585029991	0.000000e+00	5821.0
10	TraesCS4D01G034100	chr4A	93.865	2331	102	18	4634	6926	585029922	585027595	0.000000e+00	3474.0
11	TraesCS4D01G034100	chr4A	86.441	236	30	2	1369	1604	556840535	556840302	2.710000e-64	257.0
12	TraesCS4D01G034100	chr4A	96.970	99	3	0	216	314	585034210	585034112	4.700000e-37	167.0
13	TraesCS4D01G034100	chr3B	94.000	650	39	0	6922	7571	342877301	342876652	0.000000e+00	985.0
14	TraesCS4D01G034100	chr3B	93.702	651	41	0	6921	7571	275341368	275342018	0.000000e+00	976.0
15	TraesCS4D01G034100	chr5A	93.712	652	41	0	6920	7571	410512761	410512110	0.000000e+00	977.0
16	TraesCS4D01G034100	chr5A	93.702	651	41	0	6921	7571	421824520	421825170	0.000000e+00	976.0
17	TraesCS4D01G034100	chr5A	86.122	245	28	6	1369	1610	651989220	651988979	7.540000e-65	259.0
18	TraesCS4D01G034100	chr7B	93.702	651	41	0	6921	7571	469536637	469535987	0.000000e+00	976.0
19	TraesCS4D01G034100	chr7B	88.393	112	8	3	44	151	624951820	624951710	6.170000e-26	130.0
20	TraesCS4D01G034100	chr7B	83.333	102	17	0	6777	6878	30794975	30794874	2.250000e-15	95.3
21	TraesCS4D01G034100	chr7B	82.692	104	18	0	6775	6878	31464005	31463902	8.090000e-15	93.5
22	TraesCS4D01G034100	chr6A	93.548	651	42	0	6921	7571	410902244	410901594	0.000000e+00	970.0
23	TraesCS4D01G034100	chr1D	93.548	651	42	0	6921	7571	247479554	247478904	0.000000e+00	970.0
24	TraesCS4D01G034100	chr2B	88.525	244	26	2	1363	1606	216454374	216454615	2.070000e-75	294.0
25	TraesCS4D01G034100	chr2A	88.525	244	27	1	1363	1606	170458234	170458476	2.070000e-75	294.0
26	TraesCS4D01G034100	chr5B	86.920	237	31	0	1370	1606	647792685	647792449	4.500000e-67	267.0
27	TraesCS4D01G034100	chr3D	85.892	241	32	2	1369	1609	469807010	469806772	9.750000e-64	255.0
28	TraesCS4D01G034100	chr7A	88.816	152	15	2	4995	5144	148483558	148483709	1.300000e-42	185.0
29	TraesCS4D01G034100	chr7A	85.950	121	12	3	11	127	689269255	689269374	2.870000e-24	124.0
30	TraesCS4D01G034100	chrUn	92.553	94	4	1	35	125	325927174	325927267	1.710000e-26	132.0
31	TraesCS4D01G034100	chr2D	88.991	109	8	2	39	144	555911010	555911117	1.710000e-26	132.0
32	TraesCS4D01G034100	chr1A	92.553	94	4	1	35	125	272648122	272648029	1.710000e-26	132.0
33	TraesCS4D01G034100	chr6D	90.909	99	5	2	34	129	464673603	464673700	6.170000e-26	130.0
34	TraesCS4D01G034100	chr5D	90.909	99	5	2	37	132	182800832	182800929	6.170000e-26	130.0
35	TraesCS4D01G034100	chr5D	76.613	124	22	7	2260	2376	361662569	361662446	2.280000e-05	62.1
36	TraesCS4D01G034100	chr1B	90.099	101	6	2	36	132	681293854	681293954	2.220000e-25	128.0
37	TraesCS4D01G034100	chr7D	81.905	105	13	3	6777	6878	82462481	82462380	4.870000e-12	84.2

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	TraesCS4D01G034100	chr4D	15551122	15558694	7572	False	6769.5	8096	100.000000	1	7573	2	chr4D.!!$F3	7572
1	TraesCS4D01G034100	chr4D	242938234	242938884	650	False	981.0	981	93.856000	6921	7571	1	chr4D.!!$F2	650
2	TraesCS4D01G034100	chr4D	443840783	443841433	650	True	970.0	970	93.548000	6921	7571	1	chr4D.!!$R1	650
3	TraesCS4D01G034100	chr4B	26485792	26492372	6580	False	3345.0	6407	91.474667	154	6923	3	chr4B.!!$F1	6769
4	TraesCS4D01G034100	chr4A	585027595	585034210	6615	True	3154.0	5821	94.552000	216	6926	3	chr4A.!!$R2	6710
5	TraesCS4D01G034100	chr3B	342876652	342877301	649	True	985.0	985	94.000000	6922	7571	1	chr3B.!!$R1	649
6	TraesCS4D01G034100	chr3B	275341368	275342018	650	False	976.0	976	93.702000	6921	7571	1	chr3B.!!$F1	650
7	TraesCS4D01G034100	chr5A	410512110	410512761	651	True	977.0	977	93.712000	6920	7571	1	chr5A.!!$R1	651
8	TraesCS4D01G034100	chr5A	421824520	421825170	650	False	976.0	976	93.702000	6921	7571	1	chr5A.!!$F1	650
9	TraesCS4D01G034100	chr7B	469535987	469536637	650	True	976.0	976	93.702000	6921	7571	1	chr7B.!!$R3	650
10	TraesCS4D01G034100	chr6A	410901594	410902244	650	True	970.0	970	93.548000	6921	7571	1	chr6A.!!$R1	650
11	TraesCS4D01G034100	chr1D	247478904	247479554	650	True	970.0	970	93.548000	6921	7571	1	chr1D.!!$R1	650

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
609	727	0.407139	AGCAAGGCTCAGATGGGTTT	59.593	50.000	0.00	0.0	30.62	3.27	F
697	817	0.595095	GGAACACTGCTTCTGCTTGG	59.405	55.000	0.00	0.0	40.48	3.61	F
1390	1543	0.822164	ACCTCCGTCCTGGTTTATCG	59.178	55.000	0.00	0.0	39.52	2.92	F
2730	2903	1.021202	TGGTTTCCGTGCAAGTTCTG	58.979	50.000	0.00	0.0	0.00	3.02	F
2734	2907	1.581934	TTCCGTGCAAGTTCTGTGAG	58.418	50.000	0.00	0.0	0.00	3.51	F
4022	4199	1.471676	GCCTTGATAGTCCGTGTCCTG	60.472	57.143	0.00	0.0	0.00	3.86	F
5614	5815	0.817229	GGGCTTATCTGCAGGCTGTC	60.817	60.000	17.16	9.1	37.02	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1749	1905	2.855963	GCAATCAAATCGATGTTGCCTG	59.144	45.455	19.21	15.30	33.47	4.85	R
2426	2595	4.768448	TCTCTCCGTACATGTAAACTTCCA	59.232	41.667	7.25	0.00	0.00	3.53	R
3293	3470	1.270550	GGGTGGCAGACTTGTGAATTG	59.729	52.381	0.00	0.00	0.00	2.32	R
4001	4178	0.535335	GGACACGGACTATCAAGGCA	59.465	55.000	0.00	0.00	29.10	4.75	R
4263	4440	2.393646	GCCTAGGAAGTGGTCTCAGAT	58.606	52.381	14.75	0.00	0.00	2.90	R
5864	6068	0.242825	GGTTGGTTAGAAAAGCCGGC	59.757	55.000	21.89	21.89	31.91	6.13	R
7229	7448	0.248498	ACATACGCATCTCCGTCACG	60.248	55.000	0.00	0.00	42.20	4.35	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
52	53	5.632034	ATCCAACATTTACTACTCCCTCC	57.368	43.478	0.00	0.00	0.00	4.30
53	54	3.449737	TCCAACATTTACTACTCCCTCCG	59.550	47.826	0.00	0.00	0.00	4.63
54	55	3.197116	CCAACATTTACTACTCCCTCCGT	59.803	47.826	0.00	0.00	0.00	4.69
55	56	4.403432	CCAACATTTACTACTCCCTCCGTA	59.597	45.833	0.00	0.00	0.00	4.02
56	57	5.105228	CCAACATTTACTACTCCCTCCGTAA	60.105	44.000	0.00	0.00	0.00	3.18
57	58	6.400568	CAACATTTACTACTCCCTCCGTAAA	58.599	40.000	0.00	0.00	36.59	2.01
58	59	5.970592	ACATTTACTACTCCCTCCGTAAAC	58.029	41.667	0.00	0.00	35.45	2.01
59	60	5.718607	ACATTTACTACTCCCTCCGTAAACT	59.281	40.000	0.00	0.00	35.45	2.66
60	61	6.891908	ACATTTACTACTCCCTCCGTAAACTA	59.108	38.462	0.00	0.00	35.45	2.24
61	62	7.562821	ACATTTACTACTCCCTCCGTAAACTAT	59.437	37.037	0.00	0.00	35.45	2.12
62	63	9.071276	CATTTACTACTCCCTCCGTAAACTATA	57.929	37.037	0.00	0.00	35.45	1.31
63	64	9.646522	ATTTACTACTCCCTCCGTAAACTATAA	57.353	33.333	0.00	0.00	35.45	0.98
64	65	8.682936	TTACTACTCCCTCCGTAAACTATAAG	57.317	38.462	0.00	0.00	0.00	1.73
65	66	6.904626	ACTACTCCCTCCGTAAACTATAAGA	58.095	40.000	0.00	0.00	0.00	2.10
66	67	6.997476	ACTACTCCCTCCGTAAACTATAAGAG	59.003	42.308	0.00	0.00	0.00	2.85
67	68	5.764432	ACTCCCTCCGTAAACTATAAGAGT	58.236	41.667	0.00	0.00	41.56	3.24
68	69	5.593502	ACTCCCTCCGTAAACTATAAGAGTG	59.406	44.000	0.00	0.00	38.87	3.51
69	70	5.513233	TCCCTCCGTAAACTATAAGAGTGT	58.487	41.667	0.00	0.00	38.87	3.55
70	71	5.954150	TCCCTCCGTAAACTATAAGAGTGTT	59.046	40.000	0.00	0.00	38.87	3.32
71	72	6.438425	TCCCTCCGTAAACTATAAGAGTGTTT	59.562	38.462	0.00	0.00	38.87	2.83
72	73	7.615365	TCCCTCCGTAAACTATAAGAGTGTTTA	59.385	37.037	0.00	0.00	38.87	2.01
73	74	7.919621	CCCTCCGTAAACTATAAGAGTGTTTAG	59.080	40.741	0.00	0.00	38.87	1.85
74	75	8.680903	CCTCCGTAAACTATAAGAGTGTTTAGA	58.319	37.037	0.00	0.00	38.87	2.10
119	120	9.915629	AAACGCTCTTATATTATCTTACAGAGG	57.084	33.333	0.00	0.00	0.00	3.69
120	121	8.057536	ACGCTCTTATATTATCTTACAGAGGG	57.942	38.462	8.36	8.36	42.53	4.30

Showing 1 to 25 of 150 entries

Previous1 2 3 4 5 6Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
26	27	8.218488	GGAGGGAGTAGTAAATGTTGGATATTT	58.782	37.037	0.00	0.00	1.40
27	28	7.472945	CGGAGGGAGTAGTAAATGTTGGATATT	60.473	40.741	0.00	0.00	1.28
28	29	6.014499	CGGAGGGAGTAGTAAATGTTGGATAT	60.014	42.308	0.00	0.00	1.63
29	30	5.303589	CGGAGGGAGTAGTAAATGTTGGATA	59.696	44.000	0.00	0.00	2.59
30	31	4.101119	CGGAGGGAGTAGTAAATGTTGGAT	59.899	45.833	0.00	0.00	3.41
31	32	3.449737	CGGAGGGAGTAGTAAATGTTGGA	59.550	47.826	0.00	0.00	3.53
32	33	3.197116	ACGGAGGGAGTAGTAAATGTTGG	59.803	47.826	0.00	0.00	3.77
33	34	4.467198	ACGGAGGGAGTAGTAAATGTTG	57.533	45.455	0.00	0.00	3.33
34	35	6.212187	AGTTTACGGAGGGAGTAGTAAATGTT	59.788	38.462	3.48	39.98	2.71
35	36	5.718607	AGTTTACGGAGGGAGTAGTAAATGT	59.281	40.000	3.48	39.98	2.71
36	37	6.218108	AGTTTACGGAGGGAGTAGTAAATG	57.782	41.667	3.48	39.98	2.32
37	38	9.646522	TTATAGTTTACGGAGGGAGTAGTAAAT	57.353	33.333	3.48	39.98	1.40
38	39	9.125026	CTTATAGTTTACGGAGGGAGTAGTAAA	57.875	37.037	0.00	36.91	2.01
39	40	8.494433	TCTTATAGTTTACGGAGGGAGTAGTAA	58.506	37.037	0.00	0.00	2.24
40	41	8.034313	TCTTATAGTTTACGGAGGGAGTAGTA	57.966	38.462	0.00	0.00	1.82
41	42	6.904626	TCTTATAGTTTACGGAGGGAGTAGT	58.095	40.000	0.00	0.00	2.73
42	43	6.997476	ACTCTTATAGTTTACGGAGGGAGTAG	59.003	42.308	0.00	33.35	2.57
43	44	6.769822	CACTCTTATAGTTTACGGAGGGAGTA	59.230	42.308	0.00	35.76	2.59
44	45	5.593502	CACTCTTATAGTTTACGGAGGGAGT	59.406	44.000	0.00	35.76	3.85
45	46	5.593502	ACACTCTTATAGTTTACGGAGGGAG	59.406	44.000	0.00	35.76	4.30
46	47	5.513233	ACACTCTTATAGTTTACGGAGGGA	58.487	41.667	0.00	35.76	4.20
47	48	5.848833	ACACTCTTATAGTTTACGGAGGG	57.151	43.478	0.00	35.76	4.30
48	49	8.680903	TCTAAACACTCTTATAGTTTACGGAGG	58.319	37.037	0.00	35.76	4.30
93	94	9.915629	CCTCTGTAAGATAATATAAGAGCGTTT	57.084	33.333	0.00	45.62	3.60
94	95	8.524487	CCCTCTGTAAGATAATATAAGAGCGTT	58.476	37.037	0.00	45.62	4.84

Showing 1 to 25 of 150 entries

Previous1 2 3 4 5 6Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.