AutoCloner

Multiple sequence alignment - TraesCS1D01G046300

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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	TraesCS1D01G046300	chr1D	100.000	2796	0	0	1	2796	25955796	25953001	0.000000e+00	5164.0
1	TraesCS1D01G046300	chr1D	100.000	538	0	0	3153	3690	25952644	25952107	0.000000e+00	994.0
2	TraesCS1D01G046300	chr1D	89.249	493	27	13	3200	3690	25817163	25816695	8.820000e-166	593.0
3	TraesCS1D01G046300	chr1D	89.862	217	15	4	2073	2288	2852882	2853092	4.700000e-69	272.0
4	TraesCS1D01G046300	chr1D	90.909	66	6	0	1	66	452347549	452347614	5.080000e-14	89.8
5	TraesCS1D01G046300	chr1D	90.000	60	6	0	2728	2787	25827942	25827883	1.100000e-10	78.7
6	TraesCS1D01G046300	chr1B	86.388	1102	56	34	1172	2207	41450165	41449092	0.000000e+00	1118.0
7	TraesCS1D01G046300	chr1B	90.542	719	46	10	1	709	41642198	41641492	0.000000e+00	931.0
8	TraesCS1D01G046300	chr1B	94.715	492	22	2	3200	3687	41444420	41443929	0.000000e+00	761.0
9	TraesCS1D01G046300	chr1B	88.843	484	36	9	2124	2604	41640478	41640010	2.470000e-161	579.0
10	TraesCS1D01G046300	chr1B	90.376	426	29	4	2215	2640	41446318	41445905	1.940000e-152	549.0
11	TraesCS1D01G046300	chr1B	92.350	366	23	3	1752	2114	632752171	632752534	1.960000e-142	516.0
12	TraesCS1D01G046300	chr1B	82.581	465	47	17	1329	1768	41641232	41640777	2.690000e-101	379.0
13	TraesCS1D01G046300	chr1B	89.803	304	8	3	1805	2085	41640782	41640479	5.820000e-98	368.0
14	TraesCS1D01G046300	chr1B	76.538	439	56	24	2379	2787	41597914	41597493	2.910000e-46	196.0
15	TraesCS1D01G046300	chr1B	92.000	75	6	0	2703	2777	41445885	41445811	5.040000e-19	106.0
16	TraesCS1D01G046300	chr1B	89.394	66	7	0	1	66	622180127	622180062	2.360000e-12	84.2
17	TraesCS1D01G046300	chr1B	90.741	54	5	0	1433	1486	41450184	41450131	5.110000e-09	73.1
18	TraesCS1D01G046300	chr1B	82.609	69	8	4	715	781	23632066	23632132	1.430000e-04	58.4
19	TraesCS1D01G046300	chr1A	91.751	497	34	3	3200	3690	27203215	27202720	0.000000e+00	684.0
20	TraesCS1D01G046300	chr1A	87.396	603	47	19	2207	2796	27204160	27203574	0.000000e+00	665.0
21	TraesCS1D01G046300	chr1A	85.149	606	63	19	2	593	27260352	27260944	2.450000e-166	595.0
22	TraesCS1D01G046300	chr1A	89.394	66	7	0	1	66	547276547	547276612	2.360000e-12	84.2
23	TraesCS1D01G046300	chr4B	88.364	550	43	10	1752	2288	342969126	342968585	3.110000e-180	641.0
24	TraesCS1D01G046300	chr3B	92.077	366	23	3	1752	2114	569597353	569597715	9.140000e-141	510.0
25	TraesCS1D01G046300	chr3B	86.059	373	37	9	710	1069	465714726	465714356	1.610000e-103	387.0
26	TraesCS1D01G046300	chr3B	83.436	326	22	7	717	1010	465727537	465727212	1.310000e-69	274.0
27	TraesCS1D01G046300	chr3A	90.591	372	30	3	1752	2120	295950609	295950240	4.280000e-134	488.0
28	TraesCS1D01G046300	chr3A	89.552	67	7	0	1	67	740078176	740078110	6.570000e-13	86.1
29	TraesCS1D01G046300	chr7A	89.891	366	32	3	1752	2114	690659631	690659994	2.010000e-127	466.0
30	TraesCS1D01G046300	chr7A	82.741	394	42	19	1	375	721586033	721585647	9.880000e-86	327.0
31	TraesCS1D01G046300	chr7A	82.741	394	42	19	1	375	721660687	721660301	9.880000e-86	327.0
32	TraesCS1D01G046300	chr2D	89.071	366	34	6	1752	2114	229311392	229311754	2.020000e-122	449.0
33	TraesCS1D01G046300	chr2D	86.735	294	9	11	709	972	2632492	2632785	2.150000e-77	300.0
34	TraesCS1D01G046300	chr2D	84.589	292	15	10	711	972	2626825	2627116	2.830000e-66	263.0
35	TraesCS1D01G046300	chr7B	80.328	610	74	26	1	592	725854735	725855316	1.580000e-113	420.0
36	TraesCS1D01G046300	chr7D	81.395	516	54	26	1	492	626050907	626050410	2.080000e-102	383.0
37	TraesCS1D01G046300	chr7D	88.168	262	24	4	2028	2288	292420101	292420356	4.630000e-79	305.0
38	TraesCS1D01G046300	chr6D	91.367	278	8	3	710	971	151945420	151945143	2.090000e-97	366.0
39	TraesCS1D01G046300	chr6D	91.450	269	7	3	719	971	151949505	151949237	4.530000e-94	355.0
40	TraesCS1D01G046300	chr6B	88.043	276	26	4	2014	2288	575574537	575574268	1.650000e-83	320.0
41	TraesCS1D01G046300	chr6B	80.263	304	31	15	3356	3652	37956809	37957090	6.250000e-48	202.0
42	TraesCS1D01G046300	chr3D	89.552	67	7	0	1	67	607666586	607666520	6.570000e-13	86.1
43	TraesCS1D01G046300	chr6A	83.099	71	11	1	718	788	615718790	615718721	3.080000e-06	63.9
44	TraesCS1D01G046300	chrUn	82.609	69	8	4	715	781	2722431	2722365	1.430000e-04	58.4
45	TraesCS1D01G046300	chrUn	82.609	69	8	4	715	781	2727726	2727660	1.430000e-04	58.4

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	TraesCS1D01G046300	chr1D	25952107	25955796	3689	True	3079.00	5164	100.00000	1	3690	2	chr1D.!!$R3	3689
1	TraesCS1D01G046300	chr1B	41640010	41642198	2188	True	564.25	931	87.94225	1	2604	4	chr1B.!!$R4	2603
2	TraesCS1D01G046300	chr1B	41443929	41450184	6255	True	521.42	1118	90.84400	1172	3687	5	chr1B.!!$R3	2515
3	TraesCS1D01G046300	chr1A	27202720	27204160	1440	True	674.50	684	89.57350	2207	3690	2	chr1A.!!$R1	1483
4	TraesCS1D01G046300	chr1A	27260352	27260944	592	False	595.00	595	85.14900	2	593	1	chr1A.!!$F1	591
5	TraesCS1D01G046300	chr4B	342968585	342969126	541	True	641.00	641	88.36400	1752	2288	1	chr4B.!!$R1	536
6	TraesCS1D01G046300	chr7B	725854735	725855316	581	False	420.00	420	80.32800	1	592	1	chr7B.!!$F1	591
7	TraesCS1D01G046300	chr6D	151945143	151949505	4362	True	360.50	366	91.40850	710	971	2	chr6D.!!$R1	261

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
523	559	0.398696	AGTATGTTTGTGGTCGGCCA	59.601	50.0	3.51	3.51	43.73	5.36	F
1090	1146	0.112995	ACACCCACGTACACCTAGGA	59.887	55.0	17.98	0.00	0.00	2.94	F
1431	1641	0.178938	TTCATTTTGAGCAGGCCCCA	60.179	50.0	0.00	0.00	0.00	4.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2221	5802	0.179018	AGGACCCTGCACAACAAGAC	60.179	55.0	0.0	0.00	0.00	3.01	R
2565	8208	0.250234	TGGCCAGCGATATATGCTCC	59.750	55.0	0.0	7.09	41.72	4.70	R
2713	8404	0.531974	TGTGCTCGTGTTTCCTCCAC	60.532	55.0	0.0	0.00	0.00	4.02	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
54	55	2.544685	GAGTGGTTCTCCATCATCACG	58.455	52.381	0.00	0.00	46.20	4.35
67	68	2.193127	TCATCACGACCCCCAAGTAAT	58.807	47.619	0.00	0.00	0.00	1.89
68	69	2.574369	TCATCACGACCCCCAAGTAATT	59.426	45.455	0.00	0.00	0.00	1.40
71	72	4.411256	TCACGACCCCCAAGTAATTATC	57.589	45.455	0.00	0.00	0.00	1.75
74	75	4.101119	CACGACCCCCAAGTAATTATCTCT	59.899	45.833	0.00	0.00	0.00	3.10
75	76	4.101119	ACGACCCCCAAGTAATTATCTCTG	59.899	45.833	0.00	0.00	0.00	3.35
76	77	4.344102	CGACCCCCAAGTAATTATCTCTGA	59.656	45.833	0.00	0.00	0.00	3.27
78	79	6.631766	CGACCCCCAAGTAATTATCTCTGAAA	60.632	42.308	0.00	0.00	0.00	2.69
79	80	6.424032	ACCCCCAAGTAATTATCTCTGAAAC	58.576	40.000	0.00	0.00	0.00	2.78
80	81	5.828328	CCCCCAAGTAATTATCTCTGAAACC	59.172	44.000	0.00	0.00	0.00	3.27
81	82	5.527582	CCCCAAGTAATTATCTCTGAAACCG	59.472	44.000	0.00	0.00	0.00	4.44
82	83	6.113411	CCCAAGTAATTATCTCTGAAACCGT	58.887	40.000	0.00	0.00	0.00	4.83
83	84	6.598064	CCCAAGTAATTATCTCTGAAACCGTT	59.402	38.462	0.00	0.00	0.00	4.44
84	85	7.414098	CCCAAGTAATTATCTCTGAAACCGTTG	60.414	40.741	0.00	0.00	0.00	4.10
85	86	6.663944	AGTAATTATCTCTGAAACCGTTGC	57.336	37.500	0.00	0.00	0.00	4.17
87	88	1.355971	TATCTCTGAAACCGTTGCGC	58.644	50.000	0.00	0.00	0.00	6.09
97	103	2.125991	CGTTGCGCCCATTGCATT	60.126	55.556	4.18	0.00	42.84	3.56
284	313	4.136978	TCCAAGAGGCTGGACTCC	57.863	61.111	0.00	0.00	40.71	3.85
423	457	1.133513	AGCTGGTGGTGGTTTTCATCA	60.134	47.619	0.00	0.00	33.36	3.07
490	525	3.069016	TGTTAGTGTCAGGTCATCGTTGT	59.931	43.478	0.00	0.00	0.00	3.32
493	528	2.872245	AGTGTCAGGTCATCGTTGTTTG	59.128	45.455	0.00	0.00	0.00	2.93
499	535	3.431912	CAGGTCATCGTTGTTTGAATCGA	59.568	43.478	0.00	0.00	36.77	3.59
500	536	3.679980	AGGTCATCGTTGTTTGAATCGAG	59.320	43.478	0.00	0.00	35.85	4.04
501	537	3.432252	GGTCATCGTTGTTTGAATCGAGT	59.568	43.478	0.00	0.00	35.85	4.18
506	542	4.116961	TCGTTGTTTGAATCGAGTTGAGT	58.883	39.130	0.00	0.00	0.00	3.41

Showing 1 to 25 of 211 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	5.888982	TCAGAGATAATTACTTGGGGGTC	57.111	43.478	0.00	0.00	0.00	4.46
67	68	1.730064	GCGCAACGGTTTCAGAGATAA	59.270	47.619	0.30	0.00	0.00	1.75
68	69	1.355971	GCGCAACGGTTTCAGAGATA	58.644	50.000	0.30	0.00	0.00	1.98
71	72	2.556287	GGCGCAACGGTTTCAGAG	59.444	61.111	10.83	0.00	0.00	3.35
74	75	2.196925	AATGGGCGCAACGGTTTCA	61.197	52.632	10.83	0.00	0.00	2.69
75	76	1.732683	CAATGGGCGCAACGGTTTC	60.733	57.895	10.83	0.00	0.00	2.78
76	77	2.338257	CAATGGGCGCAACGGTTT	59.662	55.556	10.83	0.00	0.00	3.27
87	88	6.698008	TGAAATACAGAGTAATGCAATGGG	57.302	37.500	0.00	0.00	0.00	4.00
130	153	4.398044	ACACACAAAACGGTTTCAGAGATT	59.602	37.500	6.57	0.00	0.00	2.40
135	158	1.917303	GCACACACAAAACGGTTTCAG	59.083	47.619	6.57	5.61	0.00	3.02
141	164	1.588667	GGCTGCACACACAAAACGG	60.589	57.895	0.50	0.00	0.00	4.44
284	313	0.392461	TGGGGGCGAAGAAAATCTCG	60.392	55.000	0.00	0.00	0.00	4.04
423	457	5.543507	AAGATAGATTCGCAGAGGTGATT	57.456	39.130	0.00	0.00	38.43	2.57
463	498	4.800993	CGATGACCTGACACTAACATTCTC	59.199	45.833	0.00	0.00	0.00	2.87
490	525	7.351981	CACAAACATACTCAACTCGATTCAAA	58.648	34.615	0.00	0.00	0.00	2.69
493	528	5.408604	ACCACAAACATACTCAACTCGATTC	59.591	40.000	0.00	0.00	0.00	2.52
499	535	3.399330	CCGACCACAAACATACTCAACT	58.601	45.455	0.00	0.00	0.00	3.16
500	536	2.095919	GCCGACCACAAACATACTCAAC	60.096	50.000	0.00	0.00	0.00	3.18
501	537	2.147958	GCCGACCACAAACATACTCAA	58.852	47.619	0.00	0.00	0.00	3.02
517	553	3.767673	AGTTCTCATACTAGTTTGGCCGA	59.232	43.478	12.61	0.00	0.00	5.54
523	559	8.043113	TGCATTCATCAGTTCTCATACTAGTTT	58.957	33.333	0.00	0.00	0.00	2.66
525	561	7.117285	TGCATTCATCAGTTCTCATACTAGT	57.883	36.000	0.00	0.00	0.00	2.57
528	564	6.202379	CGATTGCATTCATCAGTTCTCATACT	59.798	38.462	9.14	0.00	0.00	2.12
531	567	5.121105	TCGATTGCATTCATCAGTTCTCAT	58.879	37.500	9.14	0.00	0.00	2.90
613	649	2.287788	ACAGAAAAGAAGCACGCCAATG	60.288	45.455	0.00	0.00	0.00	2.82

Showing 1 to 25 of 201 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.