AutoCloner

Multiple sequence alignment - TraesCS1A01G309100

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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	TraesCS1A01G309100	chr1A	100.000	3067	0	0	1	3067	499928619	499925553	0.000000e+00	5664
1	TraesCS1A01G309100	chr1A	82.945	1331	135	46	399	1672	499809708	499808413	0.000000e+00	1116
2	TraesCS1A01G309100	chr1A	84.028	576	35	21	1776	2324	499808230	499807685	4.570000e-138	501
3	TraesCS1A01G309100	chr1A	91.262	103	8	1	1	102	565354932	565354830	4.120000e-29	139
4	TraesCS1A01G309100	chr1D	90.075	1340	76	31	400	1696	404261582	404260257	0.000000e+00	1685
5	TraesCS1A01G309100	chr1D	82.291	1327	116	56	399	1663	404240548	404239279	0.000000e+00	1038
6	TraesCS1A01G309100	chr1D	88.196	449	21	13	1780	2217	404239175	404238748	9.810000e-140	507
7	TraesCS1A01G309100	chr1D	87.980	391	22	8	1779	2169	404260214	404259849	3.630000e-119	438
8	TraesCS1A01G309100	chr1D	86.920	237	23	5	2502	2733	404259659	404259426	3.030000e-65	259
9	TraesCS1A01G309100	chr1D	92.121	165	10	3	2446	2607	404238443	404238279	2.380000e-56	230
10	TraesCS1A01G309100	chr1D	89.634	164	15	2	170	333	493221758	493221919	1.110000e-49	207
11	TraesCS1A01G309100	chr1D	82.412	199	21	6	2639	2836	404236575	404236390	8.800000e-36	161
12	TraesCS1A01G309100	chr1B	82.294	1683	178	65	590	2217	543741404	543739787	0.000000e+00	1347
13	TraesCS1A01G309100	chr1B	78.825	2229	202	125	481	2590	543581685	543579608	0.000000e+00	1253
14	TraesCS1A01G309100	chr1B	85.934	391	26	12	2284	2650	543739784	543739399	1.030000e-104	390
15	TraesCS1A01G309100	chr1B	90.123	162	15	1	171	332	40182193	40182353	3.100000e-50	209
16	TraesCS1A01G309100	chr1B	89.091	110	11	1	1	109	247087187	247087078	5.330000e-28	135
17	TraesCS1A01G309100	chr7B	89.157	166	16	2	168	332	339685605	339685441	4.010000e-49	206
18	TraesCS1A01G309100	chr7B	88.623	167	18	1	166	332	443741562	443741397	5.190000e-48	202
19	TraesCS1A01G309100	chr7B	89.024	164	17	1	170	333	460995606	460995768	5.190000e-48	202
20	TraesCS1A01G309100	chr7A	89.091	165	16	2	170	333	606634147	606634310	1.440000e-48	204
21	TraesCS1A01G309100	chr7A	91.589	107	7	2	1	106	610088887	610088992	2.460000e-31	147
22	TraesCS1A01G309100	chr7A	90.741	108	8	2	1	107	671128884	671128990	3.190000e-30	143
23	TraesCS1A01G309100	chr5A	88.554	166	18	1	167	332	653299437	653299601	1.870000e-47	200
24	TraesCS1A01G309100	chr5A	92.453	106	7	1	1	105	436885215	436885110	1.910000e-32	150
25	TraesCS1A01G309100	chr5A	92.233	103	7	1	1	102	645397416	645397314	8.860000e-31	145
26	TraesCS1A01G309100	chr3D	87.719	171	20	1	162	332	552772347	552772516	6.710000e-47	198
27	TraesCS1A01G309100	chr6A	87.719	171	18	3	164	333	27786394	27786226	2.410000e-46	196
28	TraesCS1A01G309100	chr5B	93.396	106	6	1	1	105	478325177	478325072	4.090000e-34	156
29	TraesCS1A01G309100	chr7D	91.262	103	8	1	1	102	169823789	169823891	4.120000e-29	139
30	TraesCS1A01G309100	chr4A	90.291	103	9	1	1	102	46310352	46310454	1.920000e-27	134

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	TraesCS1A01G309100	chr1A	499925553	499928619	3066	True	5664.0	5664	100.0000	1	3067	1	chr1A.!!$R1	3066
1	TraesCS1A01G309100	chr1A	499807685	499809708	2023	True	808.5	1116	83.4865	399	2324	2	chr1A.!!$R3	1925
2	TraesCS1A01G309100	chr1D	404259426	404261582	2156	True	794.0	1685	88.3250	400	2733	3	chr1D.!!$R2	2333
3	TraesCS1A01G309100	chr1D	404236390	404240548	4158	True	484.0	1038	86.2550	399	2836	4	chr1D.!!$R1	2437
4	TraesCS1A01G309100	chr1B	543579608	543581685	2077	True	1253.0	1253	78.8250	481	2590	1	chr1B.!!$R2	2109
5	TraesCS1A01G309100	chr1B	543739399	543741404	2005	True	868.5	1347	84.1140	590	2650	2	chr1B.!!$R3	2060

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
286	287	0.323302	TTTGCTCCGCATGTAGTCCA	59.677	50.0	0.0	0.0	38.76	4.02	F
1710	1890	0.035317	TCAAGCGTCCAGTTGCTCAT	59.965	50.0	0.0	0.0	41.46	2.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1955	2214	0.035881	TGCTTGAGAGGTTCCTGCAG	59.964	55.0	6.78	6.78	32.07	4.41	R
2777	4901	0.039798	CACAGCACAACAGACATGCC	60.040	55.0	0.00	0.00	40.33	4.40	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
78	79	4.969816	CTTTGACCAAAGCTAATACGTGG	58.030	43.478	9.25	0.00	40.94	4.94
79	80	3.965379	TGACCAAAGCTAATACGTGGA	57.035	42.857	0.00	0.00	33.39	4.02
80	81	3.857052	TGACCAAAGCTAATACGTGGAG	58.143	45.455	0.00	0.00	33.39	3.86
81	82	3.259876	TGACCAAAGCTAATACGTGGAGT	59.740	43.478	0.00	0.00	33.39	3.85
82	83	4.463539	TGACCAAAGCTAATACGTGGAGTA	59.536	41.667	0.00	0.00	40.03	2.59
83	84	5.047164	TGACCAAAGCTAATACGTGGAGTAA	60.047	40.000	0.00	0.00	39.04	2.24
84	85	5.797051	ACCAAAGCTAATACGTGGAGTAAA	58.203	37.500	0.00	0.00	39.04	2.01
85	86	6.412214	ACCAAAGCTAATACGTGGAGTAAAT	58.588	36.000	0.00	0.00	39.04	1.40
86	87	7.558604	ACCAAAGCTAATACGTGGAGTAAATA	58.441	34.615	0.00	0.00	39.04	1.40
87	88	8.042515	ACCAAAGCTAATACGTGGAGTAAATAA	58.957	33.333	0.00	0.00	39.04	1.40
88	89	8.548721	CCAAAGCTAATACGTGGAGTAAATAAG	58.451	37.037	0.00	0.00	39.04	1.73
89	90	9.309516	CAAAGCTAATACGTGGAGTAAATAAGA	57.690	33.333	0.00	0.00	39.04	2.10
90	91	9.880157	AAAGCTAATACGTGGAGTAAATAAGAA	57.120	29.630	0.00	0.00	39.04	2.52
91	92	8.868635	AGCTAATACGTGGAGTAAATAAGAAC	57.131	34.615	0.00	0.00	39.04	3.01
92	93	7.646922	AGCTAATACGTGGAGTAAATAAGAACG	59.353	37.037	0.00	0.00	39.04	3.95
93	94	7.096312	GCTAATACGTGGAGTAAATAAGAACGG	60.096	40.741	0.00	0.00	39.04	4.44
94	95	4.789012	ACGTGGAGTAAATAAGAACGGA	57.211	40.909	0.00	0.00	34.06	4.69
95	96	5.334724	ACGTGGAGTAAATAAGAACGGAT	57.665	39.130	0.00	0.00	34.06	4.18
96	97	5.107133	ACGTGGAGTAAATAAGAACGGATG	58.893	41.667	0.00	0.00	34.06	3.51
97	98	4.506654	CGTGGAGTAAATAAGAACGGATGG	59.493	45.833	0.00	0.00	0.00	3.51
98	99	5.667466	GTGGAGTAAATAAGAACGGATGGA	58.333	41.667	0.00	0.00	0.00	3.41
99	100	5.753921	GTGGAGTAAATAAGAACGGATGGAG	59.246	44.000	0.00	0.00	0.00	3.86
100	101	5.424252	TGGAGTAAATAAGAACGGATGGAGT	59.576	40.000	0.00	0.00	0.00	3.85
101	102	6.608405	TGGAGTAAATAAGAACGGATGGAGTA	59.392	38.462	0.00	0.00	0.00	2.59
102	103	7.146648	GGAGTAAATAAGAACGGATGGAGTAG	58.853	42.308	0.00	0.00	0.00	2.57

Showing 1 to 25 of 361 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	4.643463	TCCACGTATTAGCTTTGGTCAAA	58.357	39.130	0.00	0.00	0.00	2.69
58	59	4.250464	CTCCACGTATTAGCTTTGGTCAA	58.750	43.478	0.00	0.00	0.00	3.18
59	60	3.259876	ACTCCACGTATTAGCTTTGGTCA	59.740	43.478	0.00	0.00	0.00	4.02
60	61	3.858247	ACTCCACGTATTAGCTTTGGTC	58.142	45.455	0.00	0.00	0.00	4.02
61	62	3.975168	ACTCCACGTATTAGCTTTGGT	57.025	42.857	0.00	0.00	0.00	3.67
62	63	6.920569	ATTTACTCCACGTATTAGCTTTGG	57.079	37.500	0.00	0.00	0.00	3.28
63	64	9.309516	TCTTATTTACTCCACGTATTAGCTTTG	57.690	33.333	0.00	0.00	0.00	2.77
64	65	9.880157	TTCTTATTTACTCCACGTATTAGCTTT	57.120	29.630	0.00	0.00	0.00	3.51
65	66	9.310716	GTTCTTATTTACTCCACGTATTAGCTT	57.689	33.333	0.00	0.00	0.00	3.74
66	67	7.646922	CGTTCTTATTTACTCCACGTATTAGCT	59.353	37.037	0.00	0.00	0.00	3.32
67	68	7.096312	CCGTTCTTATTTACTCCACGTATTAGC	60.096	40.741	0.00	0.00	0.00	3.09
68	69	8.131100	TCCGTTCTTATTTACTCCACGTATTAG	58.869	37.037	0.00	0.00	0.00	1.73
69	70	7.995289	TCCGTTCTTATTTACTCCACGTATTA	58.005	34.615	0.00	0.00	0.00	0.98
70	71	6.866480	TCCGTTCTTATTTACTCCACGTATT	58.134	36.000	0.00	0.00	0.00	1.89
71	72	6.455360	TCCGTTCTTATTTACTCCACGTAT	57.545	37.500	0.00	0.00	0.00	3.06
72	73	5.895636	TCCGTTCTTATTTACTCCACGTA	57.104	39.130	0.00	0.00	0.00	3.57
73	74	4.789012	TCCGTTCTTATTTACTCCACGT	57.211	40.909	0.00	0.00	0.00	4.49
74	75	4.506654	CCATCCGTTCTTATTTACTCCACG	59.493	45.833	0.00	0.00	0.00	4.94
75	76	5.667466	TCCATCCGTTCTTATTTACTCCAC	58.333	41.667	0.00	0.00	0.00	4.02
76	77	5.424252	ACTCCATCCGTTCTTATTTACTCCA	59.576	40.000	0.00	0.00	0.00	3.86
77	78	5.915175	ACTCCATCCGTTCTTATTTACTCC	58.085	41.667	0.00	0.00	0.00	3.85
78	79	7.714703	ACTACTCCATCCGTTCTTATTTACTC	58.285	38.462	0.00	0.00	0.00	2.59
79	80	7.657023	ACTACTCCATCCGTTCTTATTTACT	57.343	36.000	0.00	0.00	0.00	2.24
80	81	9.978044	ATAACTACTCCATCCGTTCTTATTTAC	57.022	33.333	0.00	0.00	0.00	2.01
82	83	9.901172	AAATAACTACTCCATCCGTTCTTATTT	57.099	29.630	0.00	0.00	0.00	1.40

Showing 1 to 25 of 386 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.