AutoCloner

Multiple sequence alignment - TraesCS6B01G435700

Loading Multiple Alignment...

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	TraesCS6B01G435700	chr6B	100.000	2726	0	0	1	2726	703414760	703412035	0.000000e+00	5035
1	TraesCS6B01G435700	chr6B	97.824	1241	20	7	1492	2726	703486937	703485698	0.000000e+00	2135
2	TraesCS6B01G435700	chr6B	97.375	1181	13	3	1	1181	703488099	703486937	0.000000e+00	1993
3	TraesCS6B01G435700	chr6B	95.248	484	18	4	2244	2726	6137676	6138155	0.000000e+00	761
4	TraesCS6B01G435700	chr6B	94.606	482	25	1	2246	2726	480831916	480832397	0.000000e+00	745
5	TraesCS6B01G435700	chr6B	94.179	481	26	1	2246	2726	1950228	1949750	0.000000e+00	732
6	TraesCS6B01G435700	chr6B	93.763	481	29	1	2247	2726	307176518	307176998	0.000000e+00	721
7	TraesCS6B01G435700	chr6B	93.776	482	25	3	2245	2725	73340109	73339632	0.000000e+00	719
8	TraesCS6B01G435700	chr6A	88.170	1361	141	12	892	2243	608401408	608400059	0.000000e+00	1604
9	TraesCS6B01G435700	chr6A	76.571	700	144	14	892	1588	608292088	608291406	1.540000e-97	366
10	TraesCS6B01G435700	chr6A	89.362	94	8	2	753	844	420829771	420829864	1.720000e-22	117
11	TraesCS6B01G435700	chr5A	95.000	480	23	1	2247	2726	219276051	219276529	0.000000e+00	752
12	TraesCS6B01G435700	chr5A	93.582	483	29	2	2243	2724	225243874	225244355	0.000000e+00	719
13	TraesCS6B01G435700	chr1B	92.872	491	33	2	2238	2726	329300269	329299779	0.000000e+00	712
14	TraesCS6B01G435700	chr4D	92.308	91	5	2	752	841	320026963	320027052	7.920000e-26	128
15	TraesCS6B01G435700	chr1A	92.308	91	5	2	753	841	436259647	436259737	7.920000e-26	128
16	TraesCS6B01G435700	chr7D	90.426	94	7	2	753	844	103820626	103820533	3.690000e-24	122
17	TraesCS6B01G435700	chr2B	90.426	94	7	2	753	844	793544973	793544880	3.690000e-24	122
18	TraesCS6B01G435700	chr5D	92.857	84	5	1	759	841	197147100	197147183	1.330000e-23	121
19	TraesCS6B01G435700	chr2D	89.362	94	8	2	753	844	610470842	610470749	1.720000e-22	117
20	TraesCS6B01G435700	chr2D	89.362	94	8	2	753	844	610493505	610493412	1.720000e-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	TraesCS6B01G435700	chr6B	703412035	703414760	2725	True	5035	5035	100.0000	1	2726	1	chr6B.!!$R3	2725
1	TraesCS6B01G435700	chr6B	703485698	703488099	2401	True	2064	2135	97.5995	1	2726	2	chr6B.!!$R4	2725
2	TraesCS6B01G435700	chr6A	608400059	608401408	1349	True	1604	1604	88.1700	892	2243	1	chr6A.!!$R2	1351
3	TraesCS6B01G435700	chr6A	608291406	608292088	682	True	366	366	76.5710	892	1588	1	chr6A.!!$R1	696

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
379	380	1.593196	TTTCAGAGCTTGTGGAACCG	58.407	50.0	0.0	0.0	34.36	4.44	F
1227	1229	0.173255	GTTTGATGCCCACCAATCGG	59.827	55.0	0.0	0.0	38.77	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1263	1268	0.693049	ACATCCAGGAACGGAAAGCT	59.307	50.0	0.00	0.0	38.95	3.74	R
2474	2487	0.753262	AGCGCGGGATATCTTCAACT	59.247	50.0	8.83	0.0	0.00	3.16	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	2.361357	CCACTCCGGGTCTCGTCT	60.361	66.667	0.00	0.00	37.11	4.18
128	129	2.269241	GTAGAGGGGTGGCAGCAC	59.731	66.667	19.48	15.96	0.00	4.40
179	180	4.465512	GCCATGCGCAAGGTGTCG	62.466	66.667	30.29	7.46	37.47	4.35
180	181	3.803082	CCATGCGCAAGGTGTCGG	61.803	66.667	23.20	7.25	38.28	4.79
181	182	3.803082	CATGCGCAAGGTGTCGGG	61.803	66.667	17.11	0.00	38.28	5.14
335	336	4.180057	CACTACATCAAGGAGCTCTCAAC	58.820	47.826	14.64	0.00	0.00	3.18
379	380	1.593196	TTTCAGAGCTTGTGGAACCG	58.407	50.000	0.00	0.00	34.36	4.44
573	574	8.595362	TCCTGATATTTGTCTACTCAAGAGAA	57.405	34.615	3.73	0.00	35.78	2.87
814	815	7.421955	GCAAGTTGTTTAGTTTGCAAAAATG	57.578	32.000	14.67	1.33	43.93	2.32
836	837	5.647230	TGTCTTATATTATGGGACGGAGGA	58.353	41.667	0.00	0.00	0.00	3.71
1066	1068	0.948623	TTCGTCGCACCCTCAACATG	60.949	55.000	0.00	0.00	0.00	3.21
1076	1078	4.445448	GCACCCTCAACATGAAGATATCCT	60.445	45.833	0.00	0.00	0.00	3.24
1165	1167	1.226030	GGTGTTGTTCGTTCCCTCCG	61.226	60.000	0.00	0.00	0.00	4.63
1227	1229	0.173255	GTTTGATGCCCACCAATCGG	59.827	55.000	0.00	0.00	38.77	4.18
1263	1268	4.894784	AGTATGACGAAAAGAAGGAGCAA	58.105	39.130	0.00	0.00	0.00	3.91
1306	1311	1.179152	TCTGGCATCATTGGTTGCTG	58.821	50.000	10.82	6.27	39.24	4.41
1309	1314	1.592743	GCATCATTGGTTGCTGCCA	59.407	52.632	0.00	0.00	40.75	4.92
1314	1319	0.892755	CATTGGTTGCTGCCATCACT	59.107	50.000	0.00	0.00	38.48	3.41
1323	1328	2.244436	CTGCCATCACTTTCACCGCG	62.244	60.000	0.00	0.00	0.00	6.46
1326	1331	1.375396	CATCACTTTCACCGCGGGA	60.375	57.895	31.76	20.83	0.00	5.14
1332	1337	2.709125	CTTTCACCGCGGGACTCACA	62.709	60.000	31.76	5.49	0.00	3.58
1341	1346	4.699522	GGACTCACACCACCCGGC	62.700	72.222	0.00	0.00	34.57	6.13
1386	1391	2.872028	CAACAAGTTCGTTGCTGGC	58.128	52.632	5.60	0.00	39.82	4.85
1635	1640	0.937304	TCGTTCTTGTGCTTGCACTC	59.063	50.000	23.53	10.01	0.00	3.51
1919	1926	8.851541	TTGTATTTGTAACTACGGGAGAAAAT	57.148	30.769	0.00	0.00	0.00	1.82
1969	1978	9.391006	TCCTATTATGTTGGATGAACTTGTAAC	57.609	33.333	0.00	0.00	35.37	2.50
2243	2256	1.651240	GAGACAGCGCATGCCACATT	61.651	55.000	13.15	0.00	44.31	2.71
2436	2449	8.630037	CGGCTGGTAAAATAAAGATAGGAAAAT	58.370	33.333	0.00	0.00	0.00	1.82
2472	2485	1.240256	TACATGACCGCCAACCAAAC	58.760	50.000	0.00	0.00	0.00	2.93
2474	2487	1.152652	ATGACCGCCAACCAAACCA	60.153	52.632	0.00	0.00	0.00	3.67
2507	2520	1.299468	GCGCTACCATCTCTCACCG	60.299	63.158	0.00	0.00	0.00	4.94
2536	2549	0.036306	AGTAACCAAACGCTCCCTGG	59.964	55.000	0.00	0.00	36.24	4.45
2558	2571	0.679002	TCCGTCGGAGTGAGTAAGGG	60.679	60.000	10.71	0.00	0.00	3.95
2559	2572	1.139095	CGTCGGAGTGAGTAAGGGC	59.861	63.158	0.00	0.00	0.00	5.19
2695	2708	8.565416	CATACACTCCTACACGAATATGTCTAA	58.435	37.037	0.00	0.00	33.85	2.10
2711	2724	9.570468	AATATGTCTAACTGTATCGGACTCTAA	57.430	33.333	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	3.191162	CGGCAGAACAAGATCCAAATTCA	59.809	43.478	0.00	0.00	0.00	2.57
170	171	2.113139	AGTTGCCCCGACACCTTG	59.887	61.111	0.00	0.00	0.00	3.61
171	172	1.412453	TACAGTTGCCCCGACACCTT	61.412	55.000	0.00	0.00	0.00	3.50
172	173	1.412453	TTACAGTTGCCCCGACACCT	61.412	55.000	0.00	0.00	0.00	4.00
173	174	1.071814	TTACAGTTGCCCCGACACC	59.928	57.895	0.00	0.00	0.00	4.16
174	175	0.533308	TGTTACAGTTGCCCCGACAC	60.533	55.000	0.00	0.00	0.00	3.67
175	176	0.398696	ATGTTACAGTTGCCCCGACA	59.601	50.000	0.00	0.00	0.00	4.35
176	177	1.467342	GAATGTTACAGTTGCCCCGAC	59.533	52.381	0.00	0.00	0.00	4.79
177	178	1.349688	AGAATGTTACAGTTGCCCCGA	59.650	47.619	0.00	0.00	0.00	5.14
178	179	1.821216	AGAATGTTACAGTTGCCCCG	58.179	50.000	0.00	0.00	0.00	5.73
179	180	3.421844	AGAAGAATGTTACAGTTGCCCC	58.578	45.455	0.00	0.00	0.00	5.80
180	181	4.518970	TGAAGAAGAATGTTACAGTTGCCC	59.481	41.667	0.00	0.00	0.00	5.36
181	182	5.452777	GTGAAGAAGAATGTTACAGTTGCC	58.547	41.667	0.00	0.00	0.00	4.52
182	183	5.452777	GGTGAAGAAGAATGTTACAGTTGC	58.547	41.667	0.00	0.00	0.00	4.17
183	184	5.679906	CGGTGAAGAAGAATGTTACAGTTG	58.320	41.667	0.00	0.00	0.00	3.16
184	185	4.213482	GCGGTGAAGAAGAATGTTACAGTT	59.787	41.667	0.00	0.00	0.00	3.16
185	186	3.746492	GCGGTGAAGAAGAATGTTACAGT	59.254	43.478	0.00	0.00	0.00	3.55
335	336	2.815647	GCCAAGGGAAGCTCGTCG	60.816	66.667	0.00	0.00	0.00	5.12
379	380	1.288752	CACCACCCGCAACCAATTC	59.711	57.895	0.00	0.00	0.00	2.17
814	815	6.210984	ACTTCCTCCGTCCCATAATATAAGAC	59.789	42.308	0.00	0.00	0.00	3.01
836	837	6.825213	GGAACGAAAACCCCTGTAATATACTT	59.175	38.462	0.00	0.00	0.00	2.24
1066	1068	7.362229	CGGACTATGGTCACTAAGGATATCTTC	60.362	44.444	11.67	0.00	43.77	2.87
1076	1078	3.965379	TTTGCGGACTATGGTCACTAA	57.035	42.857	11.67	3.31	43.77	2.24
1244	1246	2.485814	GCTTGCTCCTTCTTTTCGTCAT	59.514	45.455	0.00	0.00	0.00	3.06
1263	1268	0.693049	ACATCCAGGAACGGAAAGCT	59.307	50.000	0.00	0.00	38.95	3.74
1297	1302	1.340889	GAAAGTGATGGCAGCAACCAA	59.659	47.619	7.17	0.00	44.65	3.67
1306	1311	2.480555	CGCGGTGAAAGTGATGGC	59.519	61.111	0.00	0.00	0.00	4.40
1309	1314	1.375523	GTCCCGCGGTGAAAGTGAT	60.376	57.895	26.12	0.00	0.00	3.06
1314	1319	2.029964	GTGAGTCCCGCGGTGAAA	59.970	61.111	26.12	3.21	0.00	2.69
1323	1328	4.016706	CCGGGTGGTGTGAGTCCC	62.017	72.222	0.00	0.00	36.82	4.46
1355	1360	2.980568	ACTTGTTGTCCTTGTCGTCAA	58.019	42.857	0.00	0.00	0.00	3.18
1356	1361	2.684001	ACTTGTTGTCCTTGTCGTCA	57.316	45.000	0.00	0.00	0.00	4.35
1386	1391	1.349627	GTCACGCATGATTGGCTCG	59.650	57.895	0.00	0.00	37.14	5.03
1800	1806	4.478371	CAGGCAGGCCGCTGATGA	62.478	66.667	17.07	0.00	41.91	2.92
1919	1926	9.658799	GGAGATACTAATGATTAGCAATAGCAA	57.341	33.333	11.92	0.00	45.49	3.91
2005	2017	5.126545	GGGTACTCGGCTAAAATGGAAATTT	59.873	40.000	0.00	0.00	0.00	1.82
2267	2280	3.035173	TTCTGATGCAGAGGCCGGG	62.035	63.158	2.18	0.00	41.75	5.73
2406	2419	6.993902	CCTATCTTTATTTTACCAGCCGGTTA	59.006	38.462	1.90	0.00	46.31	2.85
2436	2449	7.822334	CGGTCATGTAATAGGATAGGCAATTAA	59.178	37.037	0.00	0.00	0.00	1.40
2472	2485	1.502231	CGCGGGATATCTTCAACTGG	58.498	55.000	0.00	0.00	0.00	4.00
2474	2487	0.753262	AGCGCGGGATATCTTCAACT	59.247	50.000	8.83	0.00	0.00	3.16
2507	2520	3.000727	CGTTTGGTTACTGGATCTGTCC	58.999	50.000	0.00	0.00	45.31	4.02
2558	2571	2.598632	GCGCTGATCCGTATGTGGC	61.599	63.158	0.00	0.00	0.00	5.01
2559	2572	1.956170	GGCGCTGATCCGTATGTGG	60.956	63.158	7.64	0.00	0.00	4.17
2695	2708	3.377253	TGGGTTAGAGTCCGATACAGT	57.623	47.619	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.