AutoCloner

Multiple sequence alignment - TraesCS1B01G178500

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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	TraesCS1B01G178500	chr1B	100.000	3410	0	0	1	3410	323633585	323636994	0.000000e+00	6298
1	TraesCS1B01G178500	chr1B	90.984	366	30	3	1919	2283	572288732	572288369	1.100000e-134	490
2	TraesCS1B01G178500	chr1B	98.507	134	2	0	2945	3078	522748672	522748805	1.580000e-58	237
3	TraesCS1B01G178500	chr1D	90.855	1181	79	22	1599	2770	224141153	224142313	0.000000e+00	1555
4	TraesCS1B01G178500	chr1D	83.594	896	85	34	480	1322	224138905	224139791	0.000000e+00	784
5	TraesCS1B01G178500	chr1D	97.561	164	4	0	3247	3410	224144136	224144299	7.200000e-72	281
6	TraesCS1B01G178500	chr1D	90.710	183	3	5	3073	3255	224142517	224142685	7.360000e-57	231
7	TraesCS1B01G178500	chr1A	91.565	818	46	12	1730	2528	290555263	290556076	0.000000e+00	1107
8	TraesCS1B01G178500	chr1A	87.481	663	37	27	746	1370	290554227	290554881	0.000000e+00	723
9	TraesCS1B01G178500	chr1A	91.803	366	23	6	2516	2875	290556525	290556889	1.410000e-138	503
10	TraesCS1B01G178500	chr1A	89.617	366	35	3	1919	2283	518954223	518953860	2.400000e-126	462
11	TraesCS1B01G178500	chr1A	86.849	365	44	4	1919	2282	111988536	111988175	4.100000e-109	405
12	TraesCS1B01G178500	chr1A	80.357	560	81	15	1	556	290553467	290554001	6.860000e-107	398
13	TraesCS1B01G178500	chr1A	89.641	251	22	3	3149	3398	290591786	290592033	1.970000e-82	316
14	TraesCS1B01G178500	chr1A	97.761	134	3	0	2945	3078	108916588	108916721	7.360000e-57	231
15	TraesCS1B01G178500	chr1A	92.405	79	6	0	1368	1446	396462065	396461987	2.780000e-21	113
16	TraesCS1B01G178500	chr1A	93.421	76	5	0	1368	1443	590462264	590462339	2.780000e-21	113
17	TraesCS1B01G178500	chr1A	91.358	81	5	2	1368	1447	230209892	230209813	3.600000e-20	110
18	TraesCS1B01G178500	chr2A	90.164	366	33	3	1919	2283	780743732	780743369	1.110000e-129	473
19	TraesCS1B01G178500	chr2A	99.248	133	1	0	2946	3078	647751928	647752060	1.220000e-59	241
20	TraesCS1B01G178500	chr2A	94.928	138	7	0	2945	3082	205193365	205193502	2.060000e-52	217
21	TraesCS1B01G178500	chr2A	92.683	82	6	0	1365	1446	745064562	745064481	5.980000e-23	119
22	TraesCS1B01G178500	chr2B	90.137	365	33	3	1919	2282	776687567	776687929	3.980000e-129	472
23	TraesCS1B01G178500	chr2D	89.344	366	36	3	1919	2283	633593395	633593758	1.120000e-124	457
24	TraesCS1B01G178500	chr2D	94.928	138	7	0	2945	3082	539450262	539450399	2.060000e-52	217
25	TraesCS1B01G178500	chr3B	87.123	365	43	4	1919	2282	646715265	646714904	8.810000e-111	411
26	TraesCS1B01G178500	chr7B	98.529	136	2	0	2948	3083	210805379	210805244	1.220000e-59	241
27	TraesCS1B01G178500	chr7B	97.778	135	2	1	2948	3081	542985694	542985560	7.360000e-57	231
28	TraesCS1B01G178500	chr5A	97.810	137	2	1	2948	3083	104976984	104977120	5.690000e-58	235
29	TraesCS1B01G178500	chr6A	95.556	135	6	0	2948	3082	586992440	586992306	2.060000e-52	217
30	TraesCS1B01G178500	chr7A	94.681	94	5	0	1368	1461	86246529	86246622	2.740000e-31	147
31	TraesCS1B01G178500	chr7A	93.590	78	5	0	1366	1443	605411432	605411509	2.150000e-22	117
32	TraesCS1B01G178500	chr6B	97.183	71	2	0	1365	1435	13491298	13491228	1.660000e-23	121
33	TraesCS1B01G178500	chr4A	97.183	71	2	0	1365	1435	154922128	154922198	1.660000e-23	121
34	TraesCS1B01G178500	chr3A	93.590	78	5	0	1366	1443	743184785	743184862	2.150000e-22	117

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	TraesCS1B01G178500	chr1B	323633585	323636994	3409	False	6298.00	6298	100.0000	1	3410	1	chr1B.!!$F1	3409
1	TraesCS1B01G178500	chr1D	224138905	224144299	5394	False	712.75	1555	90.6800	480	3410	4	chr1D.!!$F1	2930
2	TraesCS1B01G178500	chr1A	290553467	290556889	3422	False	682.75	1107	87.8015	1	2875	4	chr1A.!!$F4	2874

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
361	363	0.040958	GCAGAGCGTGTTGAGGTTTG	60.041	55.0	0.0	0.0	0.0	2.93	F
1401	2496	0.103876	AGGGAGGGTTTGGAGAGGTT	60.104	55.0	0.0	0.0	0.0	3.50	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1778	3088	0.036765	GTTGTGCGGTCAGGTATGGA	60.037	55.0	0.0	0.0	0.00	3.41	R
3055	4996	0.107831	CCTTGTTCGGTTGACAGGGA	59.892	55.0	0.0	0.0	44.49	4.20	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
29	30	7.696017	ACAATTAAAGCTAGGGTTTCTCCTTA	58.304	34.615	0.00	0.00	38.30	2.69
40	41	4.348168	GGGTTTCTCCTTAGCCATCATCTA	59.652	45.833	0.00	0.00	36.25	1.98
46	47	3.576118	TCCTTAGCCATCATCTACTCTGC	59.424	47.826	0.00	0.00	0.00	4.26
50	51	1.043816	CCATCATCTACTCTGCCGGT	58.956	55.000	1.90	0.00	0.00	5.28
51	52	1.000283	CCATCATCTACTCTGCCGGTC	60.000	57.143	1.90	0.00	0.00	4.79
55	57	0.683504	ATCTACTCTGCCGGTCCGTT	60.684	55.000	11.06	0.00	0.00	4.44
74	76	2.824041	GTGTGGGTATGCGGGCAG	60.824	66.667	0.00	0.00	0.00	4.85
87	89	1.819632	GGGCAGCACCAATCTACCG	60.820	63.158	0.00	0.00	42.05	4.02
90	92	0.940126	GCAGCACCAATCTACCGATG	59.060	55.000	0.00	0.00	0.00	3.84
91	93	1.473257	GCAGCACCAATCTACCGATGA	60.473	52.381	0.00	0.00	0.00	2.92
95	97	1.414181	CACCAATCTACCGATGAGGCT	59.586	52.381	0.00	0.00	46.52	4.58
96	98	2.119495	ACCAATCTACCGATGAGGCTT	58.881	47.619	0.00	0.00	46.52	4.35
104	106	2.795329	ACCGATGAGGCTTGTCATTTT	58.205	42.857	0.00	0.00	46.52	1.82
113	115	2.291217	GGCTTGTCATTTTCCCCTCTCT	60.291	50.000	0.00	0.00	0.00	3.10
128	130	0.758734	TCTCTGGGTCGGGCAATATG	59.241	55.000	0.00	0.00	0.00	1.78
136	138	1.072331	GTCGGGCAATATGGTCTCCAT	59.928	52.381	6.52	6.52	46.99	3.41
142	144	2.487805	GCAATATGGTCTCCATGCCTCA	60.488	50.000	11.04	0.00	44.84	3.86
148	150	1.204146	GTCTCCATGCCTCACCCTTA	58.796	55.000	0.00	0.00	0.00	2.69
177	179	5.126396	TGATGCTTACTCGTATCATCAGG	57.874	43.478	13.64	0.00	38.70	3.86
178	180	4.827284	TGATGCTTACTCGTATCATCAGGA	59.173	41.667	13.64	0.00	38.70	3.86
179	181	4.837896	TGCTTACTCGTATCATCAGGAG	57.162	45.455	0.00	0.00	36.67	3.69
180	182	3.570125	TGCTTACTCGTATCATCAGGAGG	59.430	47.826	0.00	0.00	35.27	4.30
181	183	3.057174	GCTTACTCGTATCATCAGGAGGG	60.057	52.174	0.00	0.00	35.27	4.30
182	184	2.757894	ACTCGTATCATCAGGAGGGT	57.242	50.000	0.00	0.00	35.27	4.34
183	185	2.311463	ACTCGTATCATCAGGAGGGTG	58.689	52.381	0.00	0.00	35.27	4.61

Showing 1 to 25 of 405 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	0.678395	CGGCAGAGTAGATGATGGCT	59.322	55.000	0.00	0.00	36.18	4.75
34	35	1.101635	CGGACCGGCAGAGTAGATGA	61.102	60.000	5.81	0.00	0.00	2.92
40	41	4.003788	CCAACGGACCGGCAGAGT	62.004	66.667	20.00	0.00	0.00	3.24
50	51	1.003112	GCATACCCACACCAACGGA	60.003	57.895	0.00	0.00	0.00	4.69
51	52	2.395360	CGCATACCCACACCAACGG	61.395	63.158	0.00	0.00	0.00	4.44
55	57	4.418328	GCCCGCATACCCACACCA	62.418	66.667	0.00	0.00	0.00	4.17
74	76	1.871080	CCTCATCGGTAGATTGGTGC	58.129	55.000	0.00	0.00	34.23	5.01
75	77	1.414181	AGCCTCATCGGTAGATTGGTG	59.586	52.381	0.00	0.00	34.23	4.17
79	81	2.766263	TGACAAGCCTCATCGGTAGATT	59.234	45.455	0.00	0.00	34.23	2.40
87	89	2.428530	GGGGAAAATGACAAGCCTCATC	59.571	50.000	0.00	0.00	30.12	2.92
90	92	2.095461	GAGGGGAAAATGACAAGCCTC	58.905	52.381	0.00	0.00	0.00	4.70
91	93	1.713078	AGAGGGGAAAATGACAAGCCT	59.287	47.619	0.00	0.00	0.00	4.58
95	97	3.439857	CCAGAGAGGGGAAAATGACAA	57.560	47.619	0.00	0.00	0.00	3.18
113	115	0.986019	AGACCATATTGCCCGACCCA	60.986	55.000	0.00	0.00	0.00	4.51
120	122	1.251251	GGCATGGAGACCATATTGCC	58.749	55.000	15.08	15.08	45.79	4.52
128	130	1.566298	AAGGGTGAGGCATGGAGACC	61.566	60.000	0.00	0.00	0.00	3.85
136	138	2.503765	TCATCGAAATAAGGGTGAGGCA	59.496	45.455	0.00	0.00	0.00	4.75
142	144	5.930135	AGTAAGCATCATCGAAATAAGGGT	58.070	37.500	0.00	0.00	0.00	4.34
148	150	6.447162	TGATACGAGTAAGCATCATCGAAAT	58.553	36.000	8.15	2.41	38.50	2.17
175	177	2.225650	ACACTATCTTCCACACCCTCCT	60.226	50.000	0.00	0.00	0.00	3.69
176	178	2.093447	CACACTATCTTCCACACCCTCC	60.093	54.545	0.00	0.00	0.00	4.30
177	179	2.567615	ACACACTATCTTCCACACCCTC	59.432	50.000	0.00	0.00	0.00	4.30
178	180	2.567615	GACACACTATCTTCCACACCCT	59.432	50.000	0.00	0.00	0.00	4.34
179	181	2.567615	AGACACACTATCTTCCACACCC	59.432	50.000	0.00	0.00	0.00	4.61
180	182	3.963428	AGACACACTATCTTCCACACC	57.037	47.619	0.00	0.00	0.00	4.16

Showing 1 to 25 of 438 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.