AutoCloner

Multiple sequence alignment - TraesCS6D01G172600

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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	TraesCS6D01G172600	chr6D	100.000	4389	0	0	1	4389	159514506	159518894	0.000000e+00	8106.0
1	TraesCS6D01G172600	chr6D	93.853	423	13	1	504	926	364439342	364438933	3.730000e-175	625.0
2	TraesCS6D01G172600	chr6A	91.147	1299	64	26	934	2222	217769416	217770673	0.000000e+00	1714.0
3	TraesCS6D01G172600	chr6A	90.091	1100	45	23	2471	3534	217770731	217771802	0.000000e+00	1369.0
4	TraesCS6D01G172600	chr6A	86.640	509	45	11	1	502	584247814	584247322	3.860000e-150	542.0
5	TraesCS6D01G172600	chr6A	86.004	493	48	16	19	502	559461079	559461559	3.920000e-140	508.0
6	TraesCS6D01G172600	chr6A	85.396	493	52	16	19	502	559476307	559476788	1.100000e-135	494.0
7	TraesCS6D01G172600	chr6A	90.598	234	17	3	19	249	559491673	559491904	5.510000e-79	305.0
8	TraesCS6D01G172600	chr6A	86.782	174	17	6	335	502	559491950	559492123	5.790000e-44	189.0
9	TraesCS6D01G172600	chr4D	94.522	858	34	5	3544	4389	469602687	469601831	0.000000e+00	1312.0
10	TraesCS6D01G172600	chr4D	93.685	871	43	5	3531	4389	310477021	310477891	0.000000e+00	1293.0
11	TraesCS6D01G172600	chr4D	77.694	399	64	19	113	502	345251448	345251830	2.050000e-53	220.0
12	TraesCS6D01G172600	chr5A	91.830	869	59	6	3532	4389	457518822	457517955	0.000000e+00	1201.0
13	TraesCS6D01G172600	chr5A	91.734	871	56	8	3532	4389	313885384	313886251	0.000000e+00	1195.0
14	TraesCS6D01G172600	chr7D	91.724	870	60	4	3532	4389	556246306	556245437	0.000000e+00	1197.0
15	TraesCS6D01G172600	chr7D	96.897	419	13	0	505	923	23501924	23501506	0.000000e+00	702.0
16	TraesCS6D01G172600	chr7D	96.659	419	14	0	505	923	83854674	83854256	0.000000e+00	697.0
17	TraesCS6D01G172600	chr7D	87.222	180	20	3	116	294	540641848	540641671	7.440000e-48	202.0
18	TraesCS6D01G172600	chr7D	89.655	58	5	1	79	135	22523778	22523835	6.090000e-09	73.1
19	TraesCS6D01G172600	chr7D	100.000	29	0	0	478	506	454164671	454164699	2.000000e-03	54.7
20	TraesCS6D01G172600	chr2A	91.801	866	60	5	3534	4389	66525570	66524706	0.000000e+00	1195.0
21	TraesCS6D01G172600	chr2A	91.580	867	62	4	3534	4389	528822405	528821539	0.000000e+00	1186.0
22	TraesCS6D01G172600	chr2A	100.000	151	0	0	2286	2436	410888293	410888443	3.340000e-71	279.0
23	TraesCS6D01G172600	chr2A	93.671	158	9	1	2279	2436	758916238	758916394	7.340000e-58	235.0
24	TraesCS6D01G172600	chr2A	79.037	353	43	15	113	457	100205011	100205340	3.440000e-51	213.0
25	TraesCS6D01G172600	chr2A	92.157	51	1	2	1432	1479	748465491	748465441	7.880000e-08	69.4
26	TraesCS6D01G172600	chr3D	91.590	868	63	4	3532	4389	415644758	415645625	0.000000e+00	1190.0
27	TraesCS6D01G172600	chr5D	91.504	871	60	8	3531	4389	296996475	296997343	0.000000e+00	1186.0
28	TraesCS6D01G172600	chr5D	97.375	419	11	0	505	923	446273360	446272942	0.000000e+00	713.0
29	TraesCS6D01G172600	chr5D	90.141	426	22	5	505	923	531505379	531504967	1.800000e-148	536.0
30	TraesCS6D01G172600	chr6B	91.716	845	30	18	991	1808	289782217	289783048	0.000000e+00	1136.0
31	TraesCS6D01G172600	chr6B	91.124	845	35	18	991	1808	289767459	289768290	0.000000e+00	1109.0
32	TraesCS6D01G172600	chr6B	90.307	815	38	14	2472	3281	289785062	289785840	0.000000e+00	1029.0
33	TraesCS6D01G172600	chr6B	90.074	816	40	11	2471	3281	289770331	289771110	0.000000e+00	1020.0
34	TraesCS6D01G172600	chr6B	89.963	817	30	16	2472	3281	289824215	289824986	0.000000e+00	1007.0
35	TraesCS6D01G172600	chr6B	94.012	668	26	10	991	1647	289821396	289822060	0.000000e+00	1000.0
36	TraesCS6D01G172600	chr6B	95.047	424	21	0	504	927	696083754	696083331	0.000000e+00	667.0
37	TraesCS6D01G172600	chr6B	91.232	479	22	8	1813	2285	289784579	289785043	6.190000e-178	634.0
38	TraesCS6D01G172600	chr6B	93.632	424	26	1	504	926	357275510	357275087	2.230000e-177	632.0
39	TraesCS6D01G172600	chr6B	91.023	479	23	8	1813	2285	289769849	289770313	2.880000e-176	628.0
40	TraesCS6D01G172600	chr6B	91.042	480	22	9	1813	2285	289823731	289824196	2.880000e-176	628.0
41	TraesCS6D01G172600	chr6B	100.000	151	0	0	2286	2436	354218002	354217852	3.340000e-71	279.0
42	TraesCS6D01G172600	chr6B	87.156	218	20	3	3320	3533	289771202	289771415	1.580000e-59	241.0
43	TraesCS6D01G172600	chr6B	100.000	41	0	0	3176	3216	289772137	289772177	4.710000e-10	76.8
44	TraesCS6D01G172600	chr6B	97.561	41	1	0	3176	3216	289786888	289786928	2.190000e-08	71.3
45	TraesCS6D01G172600	chr3A	95.181	415	20	0	513	927	74439938	74439524	0.000000e+00	656.0
46	TraesCS6D01G172600	chr3A	87.424	493	43	15	19	502	638773145	638773627	2.310000e-152	549.0
47	TraesCS6D01G172600	chr3A	88.021	192	18	5	113	302	19037623	19037435	5.710000e-54	222.0
48	TraesCS6D01G172600	chr7B	94.145	427	23	2	505	930	157807547	157807972	0.000000e+00	649.0
49	TraesCS6D01G172600	chr7B	100.000	151	0	0	2286	2436	595991933	595991783	3.340000e-71	279.0
50	TraesCS6D01G172600	chr7B	87.435	191	22	2	113	302	692783415	692783226	7.390000e-53	219.0
51	TraesCS6D01G172600	chr3B	94.131	426	24	1	504	928	414826666	414826241	0.000000e+00	647.0
52	TraesCS6D01G172600	chr1A	92.974	427	27	3	500	923	482825895	482826321	1.730000e-173	619.0
53	TraesCS6D01G172600	chr1B	85.802	486	30	19	1	477	603100339	603100794	3.070000e-131	479.0
54	TraesCS6D01G172600	chr1B	95.652	46	1	1	1427	1471	61893046	61893091	6.090000e-09	73.1
55	TraesCS6D01G172600	chr7A	100.000	151	0	0	2286	2436	109839657	109839807	3.340000e-71	279.0
56	TraesCS6D01G172600	chr7A	94.231	156	8	1	2282	2437	709897710	709897864	2.040000e-58	237.0
57	TraesCS6D01G172600	chr4B	100.000	151	0	0	2286	2436	640535082	640535232	3.340000e-71	279.0
58	TraesCS6D01G172600	chr4B	97.484	159	3	1	2280	2437	22220081	22220239	2.010000e-68	270.0
59	TraesCS6D01G172600	chr4B	97.368	152	4	0	2286	2437	502415823	502415672	4.350000e-65	259.0
60	TraesCS6D01G172600	chr1D	78.195	399	62	18	113	502	473585694	473586076	9.490000e-57	231.0
61	TraesCS6D01G172600	chr5B	77.722	395	62	13	113	502	450616666	450617039	7.390000e-53	219.0
62	TraesCS6D01G172600	chr2D	87.500	192	19	5	113	302	89616165	89616353	2.660000e-52	217.0
63	TraesCS6D01G172600	chr4A	100.000	29	0	0	478	506	140301906	140301934	2.000000e-03	54.7

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	TraesCS6D01G172600	chr6D	159514506	159518894	4388	False	8106.000000	8106	100.000000	1	4389	1	chr6D.!!$F1	4388
1	TraesCS6D01G172600	chr6A	217769416	217771802	2386	False	1541.500000	1714	90.619000	934	3534	2	chr6A.!!$F3	2600
2	TraesCS6D01G172600	chr4D	469601831	469602687	856	True	1312.000000	1312	94.522000	3544	4389	1	chr4D.!!$R1	845
3	TraesCS6D01G172600	chr4D	310477021	310477891	870	False	1293.000000	1293	93.685000	3531	4389	1	chr4D.!!$F1	858
4	TraesCS6D01G172600	chr5A	457517955	457518822	867	True	1201.000000	1201	91.830000	3532	4389	1	chr5A.!!$R1	857
5	TraesCS6D01G172600	chr5A	313885384	313886251	867	False	1195.000000	1195	91.734000	3532	4389	1	chr5A.!!$F1	857
6	TraesCS6D01G172600	chr7D	556245437	556246306	869	True	1197.000000	1197	91.724000	3532	4389	1	chr7D.!!$R4	857
7	TraesCS6D01G172600	chr2A	66524706	66525570	864	True	1195.000000	1195	91.801000	3534	4389	1	chr2A.!!$R1	855
8	TraesCS6D01G172600	chr2A	528821539	528822405	866	True	1186.000000	1186	91.580000	3534	4389	1	chr2A.!!$R2	855
9	TraesCS6D01G172600	chr3D	415644758	415645625	867	False	1190.000000	1190	91.590000	3532	4389	1	chr3D.!!$F1	857
10	TraesCS6D01G172600	chr5D	296996475	296997343	868	False	1186.000000	1186	91.504000	3531	4389	1	chr5D.!!$F1	858
11	TraesCS6D01G172600	chr6B	289821396	289824986	3590	False	878.333333	1007	91.672333	991	3281	3	chr6B.!!$F3	2290
12	TraesCS6D01G172600	chr6B	289782217	289786928	4711	False	717.575000	1136	92.704000	991	3281	4	chr6B.!!$F2	2290
13	TraesCS6D01G172600	chr6B	289767459	289772177	4718	False	614.960000	1109	91.875400	991	3533	5	chr6B.!!$F1	2542

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
744	745	0.029834	GCATGCAGCCGTAATTCCAG	59.970	55.0	14.21	0.0	37.23	3.86	F
2294	3912	0.038159	CCCGAGAGAACGAAACTGCT	60.038	55.0	0.00	0.0	35.09	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2358	3976	0.033781	GCCGTTGGTGTGTGGTAGTA	59.966	55.0	0.0	0.0	0.0	1.82	R
3511	5203	0.108472	TCAAGCCACGAGATCAGCAG	60.108	55.0	0.0	0.0	0.0	4.24	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
22	23	2.096248	TGGCCGACCAAATTTGATACC	58.904	47.619	19.86	12.80	45.37	2.73
23	24	2.291282	TGGCCGACCAAATTTGATACCT	60.291	45.455	19.86	0.00	45.37	3.08
24	25	2.357952	GGCCGACCAAATTTGATACCTC	59.642	50.000	19.86	5.05	35.26	3.85
25	26	3.013921	GCCGACCAAATTTGATACCTCA	58.986	45.455	19.86	0.00	0.00	3.86
26	27	3.442273	GCCGACCAAATTTGATACCTCAA	59.558	43.478	19.86	0.00	39.62	3.02
27	28	7.067210	GGCCGACCAAATTTGATACCTCAAA	62.067	44.000	19.86	3.50	44.31	2.69
28	29	8.458484	GGCCGACCAAATTTGATACCTCAAAA	62.458	42.308	19.86	0.00	43.86	2.44
29	30	9.667866	GGCCGACCAAATTTGATACCTCAAAAT	62.668	40.741	19.86	0.00	43.86	1.82
81	82	7.513371	TTTTTCATTTACTATTCACACGGGT	57.487	32.000	0.00	0.00	0.00	5.28
82	83	6.489127	TTTCATTTACTATTCACACGGGTG	57.511	37.500	12.84	12.84	46.66	4.61
83	84	3.936453	TCATTTACTATTCACACGGGTGC	59.064	43.478	14.50	0.00	44.87	5.01
84	85	3.404224	TTTACTATTCACACGGGTGCA	57.596	42.857	14.50	1.30	44.87	4.57
85	86	2.373540	TACTATTCACACGGGTGCAC	57.626	50.000	14.50	8.80	44.87	4.57
86	87	0.669318	ACTATTCACACGGGTGCACG	60.669	55.000	14.50	2.44	44.87	5.34
93	94	4.922026	ACGGGTGCACGTGGAACC	62.922	66.667	32.25	32.25	46.64	3.62
94	95	4.920112	CGGGTGCACGTGGAACCA	62.920	66.667	38.27	16.56	44.25	3.67
95	96	2.282180	GGGTGCACGTGGAACCAT	60.282	61.111	36.03	0.00	43.42	3.55
96	97	2.625823	GGGTGCACGTGGAACCATG	61.626	63.158	36.03	11.02	43.42	3.66
97	98	1.896660	GGTGCACGTGGAACCATGT	60.897	57.895	15.03	12.29	45.93	3.21
98	99	1.574428	GTGCACGTGGAACCATGTC	59.426	57.895	18.88	10.76	43.50	3.06
99	100	1.599518	TGCACGTGGAACCATGTCC	60.600	57.895	18.88	7.84	43.50	4.02
100	101	1.599518	GCACGTGGAACCATGTCCA	60.600	57.895	18.88	0.95	45.72	4.02
106	107	1.993956	TGGAACCATGTCCACCTTTG	58.006	50.000	0.95	0.00	42.97	2.77
107	108	1.216678	TGGAACCATGTCCACCTTTGT	59.783	47.619	0.95	0.00	42.97	2.83
108	109	2.443632	TGGAACCATGTCCACCTTTGTA	59.556	45.455	0.95	0.00	42.97	2.41

Showing 1 to 25 of 823 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.132111	GGTATCAAATTTGGTCGGCCATT	59.868	43.478	10.94	0.00	45.56	3.16
1	2	2.693074	GGTATCAAATTTGGTCGGCCAT	59.307	45.455	10.94	0.00	45.56	4.40
3	4	2.357952	GAGGTATCAAATTTGGTCGGCC	59.642	50.000	17.90	13.40	0.00	6.13
4	5	3.013921	TGAGGTATCAAATTTGGTCGGC	58.986	45.455	17.90	5.36	30.61	5.54
57	58	7.364200	CACCCGTGTGAATAGTAAATGAAAAA	58.636	34.615	0.00	0.00	45.76	1.94
58	59	6.568844	GCACCCGTGTGAATAGTAAATGAAAA	60.569	38.462	0.90	0.00	45.76	2.29
59	60	5.106475	GCACCCGTGTGAATAGTAAATGAAA	60.106	40.000	0.90	0.00	45.76	2.69
60	61	4.393680	GCACCCGTGTGAATAGTAAATGAA	59.606	41.667	0.90	0.00	45.76	2.57
61	62	3.936453	GCACCCGTGTGAATAGTAAATGA	59.064	43.478	0.90	0.00	45.76	2.57
62	63	3.687212	TGCACCCGTGTGAATAGTAAATG	59.313	43.478	0.90	0.00	45.76	2.32
63	64	3.687698	GTGCACCCGTGTGAATAGTAAAT	59.312	43.478	5.22	0.00	45.76	1.40
64	65	3.068560	GTGCACCCGTGTGAATAGTAAA	58.931	45.455	5.22	0.00	45.76	2.01
65	66	2.690786	GTGCACCCGTGTGAATAGTAA	58.309	47.619	5.22	0.00	45.76	2.24
66	67	1.403116	CGTGCACCCGTGTGAATAGTA	60.403	52.381	12.15	0.00	45.76	1.82
67	68	0.669318	CGTGCACCCGTGTGAATAGT	60.669	55.000	12.15	0.00	45.76	2.12
68	69	0.669318	ACGTGCACCCGTGTGAATAG	60.669	55.000	12.15	0.00	45.76	1.73
69	70	1.368209	ACGTGCACCCGTGTGAATA	59.632	52.632	12.15	0.00	45.76	1.75
70	71	2.110213	ACGTGCACCCGTGTGAAT	59.890	55.556	12.15	0.00	45.76	2.57
76	77	4.922026	GGTTCCACGTGCACCCGT	62.922	66.667	19.67	3.46	42.87	5.28
77	78	4.920112	TGGTTCCACGTGCACCCG	62.920	66.667	24.73	2.69	0.00	5.28
78	79	2.282180	ATGGTTCCACGTGCACCC	60.282	61.111	24.73	17.02	0.00	4.61
79	80	1.852067	GACATGGTTCCACGTGCACC	61.852	60.000	22.29	22.29	0.00	5.01
80	81	1.574428	GACATGGTTCCACGTGCAC	59.426	57.895	10.91	6.82	0.00	4.57
81	82	1.599518	GGACATGGTTCCACGTGCA	60.600	57.895	10.91	2.60	35.49	4.57
82	83	1.599518	TGGACATGGTTCCACGTGC	60.600	57.895	10.91	2.81	41.00	5.34

Showing 1 to 25 of 865 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.