AutoCloner

Multiple sequence alignment - TraesCS3B01G139000

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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	TraesCS3B01G139000	chr3B	100.000	3466	0	0	1	3466	125550731	125554196	0.000000e+00	6401.0
1	TraesCS3B01G139000	chr3B	91.827	1505	95	19	1060	2557	125778973	125780456	0.000000e+00	2073.0
2	TraesCS3B01G139000	chr3B	91.829	1334	99	8	1057	2385	125524360	125523032	0.000000e+00	1851.0
3	TraesCS3B01G139000	chr3B	87.027	555	26	19	2906	3459	726438349	726438858	4.980000e-163	584.0
4	TraesCS3B01G139000	chr3B	80.814	172	14	6	835	1001	125778727	125778884	2.190000e-22	117.0
5	TraesCS3B01G139000	chr3B	90.000	60	6	0	745	804	125778663	125778722	1.030000e-10	78.7
6	TraesCS3B01G139000	chr3D	89.744	2974	219	40	1	2905	79426969	79429925	0.000000e+00	3723.0
7	TraesCS3B01G139000	chr3D	91.413	1514	83	23	1060	2557	79504249	79505731	0.000000e+00	2032.0
8	TraesCS3B01G139000	chr3D	91.742	1332	104	3	1057	2385	79421376	79420048	0.000000e+00	1845.0
9	TraesCS3B01G139000	chr3D	91.667	60	5	0	745	804	79503945	79504004	2.220000e-12	84.2
10	TraesCS3B01G139000	chr3A	88.392	2481	206	53	1	2425	93262662	93265116	0.000000e+00	2911.0
11	TraesCS3B01G139000	chr3A	87.161	2547	240	66	413	2907	93336708	93339219	0.000000e+00	2811.0
12	TraesCS3B01G139000	chr3A	92.042	1332	100	3	1057	2385	93042878	93041550	0.000000e+00	1868.0
13	TraesCS3B01G139000	chr3A	92.795	347	25	0	2113	2459	93265663	93266009	1.440000e-138	503.0
14	TraesCS3B01G139000	chr3A	90.909	176	8	4	2451	2622	93309888	93310059	2.690000e-56	230.0
15	TraesCS3B01G139000	chr3A	94.444	90	5	0	1902	1991	468728529	468728440	4.660000e-29	139.0
16	TraesCS3B01G139000	chr3A	91.579	95	8	0	2618	2712	93319510	93319604	7.810000e-27	132.0
17	TraesCS3B01G139000	chrUn	87.543	578	42	12	2907	3459	67438059	67437487	2.920000e-180	641.0
18	TraesCS3B01G139000	chrUn	84.076	157	17	3	3304	3459	35361572	35361423	1.000000e-30	145.0
19	TraesCS3B01G139000	chrUn	84.076	157	17	3	3304	3459	263319811	263319662	1.000000e-30	145.0
20	TraesCS3B01G139000	chr4D	85.802	486	51	12	2951	3421	401625200	401624718	1.860000e-137	499.0
21	TraesCS3B01G139000	chr6A	75.871	402	68	19	7	390	449807582	449807192	9.890000e-41	178.0
22	TraesCS3B01G139000	chr2D	81.152	191	31	3	14	201	28560891	28560703	7.750000e-32	148.0
23	TraesCS3B01G139000	chr2D	72.917	384	82	18	20	385	145737133	145736754	2.830000e-21	113.0
24	TraesCS3B01G139000	chr5A	87.288	118	15	0	14	131	476636944	476637061	6.030000e-28	135.0
25	TraesCS3B01G139000	chr7D	74.084	382	73	23	1086	1458	452998127	452997763	2.170000e-27	134.0
26	TraesCS3B01G139000	chr4B	74.324	370	65	18	42	384	387391312	387390946	2.810000e-26	130.0
27	TraesCS3B01G139000	chr5D	84.921	126	19	0	14	139	420980888	420980763	1.010000e-25	128.0
28	TraesCS3B01G139000	chr5D	74.044	366	59	19	42	383	534016768	534016415	2.190000e-22	117.0
29	TraesCS3B01G139000	chr7A	87.619	105	11	2	3110	3213	2720819	2720716	1.690000e-23	121.0
30	TraesCS3B01G139000	chr1D	79.268	164	29	4	42	201	364609495	364609333	3.660000e-20	110.0
31	TraesCS3B01G139000	chr6B	77.174	184	33	7	14	192	522528316	522528137	7.920000e-17	99.0
32	TraesCS3B01G139000	chr7B	77.692	130	22	4	257	379	527861589	527861718	4.800000e-09	73.1

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	TraesCS3B01G139000	chr3B	125550731	125554196	3465	False	6401.000000	6401	100.0000	1	3466	1	chr3B.!!$F1	3465
1	TraesCS3B01G139000	chr3B	125523032	125524360	1328	True	1851.000000	1851	91.8290	1057	2385	1	chr3B.!!$R1	1328
2	TraesCS3B01G139000	chr3B	125778663	125780456	1793	False	756.233333	2073	87.5470	745	2557	3	chr3B.!!$F3	1812
3	TraesCS3B01G139000	chr3B	726438349	726438858	509	False	584.000000	584	87.0270	2906	3459	1	chr3B.!!$F2	553
4	TraesCS3B01G139000	chr3D	79426969	79429925	2956	False	3723.000000	3723	89.7440	1	2905	1	chr3D.!!$F1	2904
5	TraesCS3B01G139000	chr3D	79420048	79421376	1328	True	1845.000000	1845	91.7420	1057	2385	1	chr3D.!!$R1	1328
6	TraesCS3B01G139000	chr3D	79503945	79505731	1786	False	1058.100000	2032	91.5400	745	2557	2	chr3D.!!$F2	1812
7	TraesCS3B01G139000	chr3A	93336708	93339219	2511	False	2811.000000	2811	87.1610	413	2907	1	chr3A.!!$F3	2494
8	TraesCS3B01G139000	chr3A	93041550	93042878	1328	True	1868.000000	1868	92.0420	1057	2385	1	chr3A.!!$R1	1328
9	TraesCS3B01G139000	chr3A	93262662	93266009	3347	False	1707.000000	2911	90.5935	1	2459	2	chr3A.!!$F4	2458
10	TraesCS3B01G139000	chrUn	67437487	67438059	572	True	641.000000	641	87.5430	2907	3459	1	chrUn.!!$R2	552

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	Hairpin	End Stability	Orientation
357	365	0.108329	CAGAGGTCGGGCGTGTATTT	60.108	55.0	0.00	1.40	F
358	366	0.108329	AGAGGTCGGGCGTGTATTTG	60.108	55.0	0.00	2.32	F
572	603	0.322456	TTCCCCTCGGAAATGTGCAG	60.322	55.0	45.54	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1888	2032	1.079750	GAAGCAGAGGTGGACGGTC	60.080	63.158	0.00	0.00	4.79	R
1972	2116	1.208259	CGCGCATGATGTAGTAGCAA	58.792	50.000	8.75	0.00	3.91	R
2565	2772	1.892474	GAGCCCCTTGCATTGTACAAA	59.108	47.619	13.23	44.83	2.83	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
37	38	2.011947	CTTGATGAAGGCATTGCTCGA	58.988	47.619	8.82	34.11	4.04
46	47	1.336240	GGCATTGCTCGAAGTTTGCTT	60.336	47.619	8.82	37.71	3.91
49	50	1.674359	TTGCTCGAAGTTTGCTTGGA	58.326	45.000	0.00	37.16	3.53
94	95	5.243954	CCCATGATCTGACCTTCGATAGTTA	59.756	44.000	0.00	37.40	2.24
102	103	3.819902	GACCTTCGATAGTTAGATCCGGT	59.180	47.826	0.00	37.40	5.28
105	106	4.320348	CCTTCGATAGTTAGATCCGGTGAC	60.320	50.000	0.00	37.40	3.67
131	132	1.893168	GCTTGCGCGTCGTTTCCTTA	61.893	55.000	8.43	0.00	2.69
159	164	3.388024	GGCCTTTTGGAGAACCTTTTCTT	59.612	43.478	0.00	42.53	2.52
160	165	4.587262	GGCCTTTTGGAGAACCTTTTCTTA	59.413	41.667	0.00	42.53	2.10
225	230	4.393062	CCACTGTCACTGTATTTCATCACC	59.607	45.833	0.00	0.00	4.02
236	244	0.895530	TTCATCACCTCGGGAGTGTC	59.104	55.000	4.19	0.00	3.67
266	274	1.146041	ATTCGCGGGCATAGCTTCA	59.854	52.632	6.13	0.00	3.02
307	315	3.551454	CCTTGCAGGTGTGATCTTTTGTG	60.551	47.826	0.00	0.00	3.33
311	319	3.563808	GCAGGTGTGATCTTTTGTGTGTA	59.436	43.478	0.00	0.00	2.90
318	326	3.496884	TGATCTTTTGTGTGTAGGTTCGC	59.503	43.478	0.00	0.00	4.70
319	327	2.215196	TCTTTTGTGTGTAGGTTCGCC	58.785	47.619	0.00	37.60	5.54
348	356	4.336889	TTCTAATTATGCAGAGGTCGGG	57.663	45.455	0.00	0.00	5.14
349	357	2.037251	TCTAATTATGCAGAGGTCGGGC	59.963	50.000	0.00	0.00	6.13
355	363	3.077519	GCAGAGGTCGGGCGTGTAT	62.078	63.158	0.00	0.00	2.29
357	365	0.108329	CAGAGGTCGGGCGTGTATTT	60.108	55.000	0.00	0.00	1.40
358	366	0.108329	AGAGGTCGGGCGTGTATTTG	60.108	55.000	0.00	0.00	2.32
387	395	8.420374	TGATTGTATTCCTTGATTCTACGTTC	57.580	34.615	0.00	0.00	3.95
396	421	6.535150	TCCTTGATTCTACGTTCTGCTTTATG	59.465	38.462	0.00	0.00	1.90
397	422	6.535150	CCTTGATTCTACGTTCTGCTTTATGA	59.465	38.462	0.00	0.00	2.15
398	423	7.064609	CCTTGATTCTACGTTCTGCTTTATGAA	59.935	37.037	0.00	0.00	2.57

Showing 1 to 25 of 101 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	5.859205	AAAGATCAAGTCCAAGCAAACTT	57.141	34.783	0.00	0.00	36.16	2.66
46	47	5.576563	TTTCACCCTAAAGATCAAGTCCA	57.423	39.130	0.00	0.00	0.00	4.02
74	75	6.431543	GGATCTAACTATCGAAGGTCAGATCA	59.568	42.308	23.64	0.00	38.44	2.92
75	76	6.402766	CGGATCTAACTATCGAAGGTCAGATC	60.403	46.154	18.40	18.40	37.27	2.75
94	95	2.815308	GCCATCGTCACCGGATCT	59.185	61.111	9.46	0.00	33.95	2.75
131	132	2.529632	GTTCTCCAAAAGGCCTCCAAT	58.470	47.619	5.23	0.00	0.00	3.16
192	197	1.768275	AGTGACAGTGGTGACCATCAA	59.232	47.619	7.94	0.00	35.28	2.57
225	230	3.669251	AAAAAGAGAGACACTCCCGAG	57.331	47.619	0.00	0.00	45.96	4.63
291	299	4.141482	ACCTACACACAAAAGATCACACCT	60.141	41.667	0.00	0.00	0.00	4.00
307	315	2.664436	GCACACGGCGAACCTACAC	61.664	63.158	16.62	0.00	0.00	2.90
348	356	8.342634	AGGAATACAATCATAACAAATACACGC	58.657	33.333	0.00	0.00	0.00	5.34
469	497	1.626654	CGTGCAGGTTAGGCGAGTTG	61.627	60.000	0.00	0.00	0.00	3.16
570	601	0.236711	CTTTGAGTGGCGACTTGCTG	59.763	55.000	1.83	0.00	45.43	4.41
572	603	0.235926	GACTTTGAGTGGCGACTTGC	59.764	55.000	1.83	0.00	45.38	4.01
607	638	3.202906	GCACGTCCATAGGCTTATTTCA	58.797	45.455	0.00	0.00	0.00	2.69
641	692	0.036858	AAGGCGGAAGAAGAGACAGC	60.037	55.000	0.00	0.00	0.00	4.40
642	693	2.464157	AAAGGCGGAAGAAGAGACAG	57.536	50.000	0.00	0.00	0.00	3.51
649	700	2.524300	CGTCGAAAAGGCGGAAGAA	58.476	52.632	0.00	0.00	45.57	2.52
664	715	4.389077	CCTAACAACTCCAAGATTGTCGTC	59.611	45.833	0.00	0.00	38.08	4.20
709	763	3.932710	CCAGCAGCTCACGTTCTTAATTA	59.067	43.478	0.00	0.00	0.00	1.40
768	823	1.021202	TCAAAAGGTGGTGAAGCGTG	58.979	50.000	0.00	0.00	0.00	5.34
774	829	1.149627	CGGGGTCAAAAGGTGGTGA	59.850	57.895	0.00	0.00	0.00	4.02
847	909	2.828868	AAGCTGACCGTGGCTTCA	59.171	55.556	0.00	0.00	44.18	3.02
938	1013	1.450312	ATTGAAGGGAGAAGCGCGG	60.450	57.895	8.83	0.00	34.07	6.46
977	1055	0.465287	CCTTGCTTGGCTTGGTTTGT	59.535	50.000	0.00	0.00	0.00	2.83

Showing 1 to 25 of 82 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.