AutoCloner

Multiple sequence alignment - TraesCS2B01G327700

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	TraesCS2B01G327700	chr2B	100.000	2534	0	0	1	2534	469614883	469612350	0.000000e+00	4680.0
1	TraesCS2B01G327700	chr2B	89.231	65	6	1	2253	2317	53754198	53754135	2.090000e-11	80.5
2	TraesCS2B01G327700	chr2D	91.693	2215	119	27	367	2534	396426146	396423950	0.000000e+00	3011.0
3	TraesCS2B01G327700	chr2D	97.159	352	9	1	1	352	396427697	396427347	6.040000e-166	593.0
4	TraesCS2B01G327700	chr2A	91.475	2217	105	11	367	2532	534319290	534317107	0.000000e+00	2970.0
5	TraesCS2B01G327700	chr2A	98.028	355	7	0	1	355	534320792	534320438	3.580000e-173	617.0
6	TraesCS2B01G327700	chr4D	79.032	248	42	9	1909	2148	423407553	423407798	7.250000e-36	161.0
7	TraesCS2B01G327700	chr4D	75.248	303	52	17	1929	2210	101500887	101501187	3.420000e-24	122.0
8	TraesCS2B01G327700	chr1A	78.800	250	39	11	1908	2148	578755699	578755943	3.380000e-34	156.0
9	TraesCS2B01G327700	chr4B	79.221	231	30	15	1929	2148	519814226	519814449	7.310000e-31	145.0
10	TraesCS2B01G327700	chr5D	78.138	247	37	15	1907	2142	391360557	391360317	9.450000e-30	141.0
11	TraesCS2B01G327700	chr1D	80.226	177	26	8	1969	2137	443463673	443463498	9.520000e-25	124.0
12	TraesCS2B01G327700	chr7D	74.483	290	50	11	2261	2534	54233794	54234075	1.240000e-18	104.0
13	TraesCS2B01G327700	chr7D	87.640	89	8	3	2063	2150	229792064	229791978	1.600000e-17	100.0
14	TraesCS2B01G327700	chrUn	88.406	69	6	2	2253	2321	24932115	24932049	5.810000e-12	82.4
15	TraesCS2B01G327700	chr6D	79.825	114	21	2	1053	1165	428650033	428649921	5.810000e-12	82.4
16	TraesCS2B01G327700	chr6B	79.825	114	21	2	1053	1165	645359829	645359717	5.810000e-12	82.4
17	TraesCS2B01G327700	chr6A	79.825	114	21	2	1053	1165	573414239	573414127	5.810000e-12	82.4

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	TraesCS2B01G327700	chr2B	469612350	469614883	2533	True	4680.0	4680	100.0000	1	2534	1	chr2B.!!$R2	2533
1	TraesCS2B01G327700	chr2D	396423950	396427697	3747	True	1802.0	3011	94.4260	1	2534	2	chr2D.!!$R1	2533
2	TraesCS2B01G327700	chr2A	534317107	534320792	3685	True	1793.5	2970	94.7515	1	2532	2	chr2A.!!$R1	2531

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
388	1598	0.040425	CGCGGTTCTTTTTCAGGGTG	60.04	55.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2251	3531	1.281867	TGGCCACCGAATTGAAGATCT	59.718	47.619	0.0	0.0	0.0	2.75	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
338	339	2.693797	GCTACATGCCAATCAATCGG	57.306	50.000	0.00	0.00	35.15	4.18
352	353	2.362397	TCAATCGGCCTAAGCTAGTCAG	59.638	50.000	0.00	0.00	39.73	3.51
355	356	2.295885	TCGGCCTAAGCTAGTCAGTAC	58.704	52.381	0.00	0.00	39.73	2.73
358	359	3.250521	CGGCCTAAGCTAGTCAGTACTAC	59.749	52.174	0.00	0.00	39.73	2.73
360	361	4.888823	GGCCTAAGCTAGTCAGTACTACTT	59.111	45.833	0.00	0.00	39.73	2.24
363	364	6.767423	GCCTAAGCTAGTCAGTACTACTTAGT	59.233	42.308	19.53	0.00	41.38	2.24
364	365	7.930865	GCCTAAGCTAGTCAGTACTACTTAGTA	59.069	40.741	19.53	0.00	41.38	1.82
365	366	9.480053	CCTAAGCTAGTCAGTACTACTTAGTAG	57.520	40.741	16.96	16.96	41.38	2.57
388	1598	0.040425	CGCGGTTCTTTTTCAGGGTG	60.040	55.000	0.00	0.00	0.00	4.61
434	1644	0.110373	CGGCTTGTAACCAAACTCGC	60.110	55.000	0.00	0.00	0.00	5.03
496	1706	7.075741	CGTGAATTCCTTCTTTAAACGACAAT	58.924	34.615	2.27	0.00	31.22	2.71
715	1933	0.178068	ATGCATGTACACTCGGTCCC	59.822	55.000	0.00	0.00	0.00	4.46
744	1976	0.946221	GGAGTGGTCAGACTGCAACG	60.946	60.000	0.00	0.00	34.59	4.10
771	2003	2.213499	GATCCATCGTCCATTCCACAC	58.787	52.381	0.00	0.00	0.00	3.82
774	2006	0.729116	CATCGTCCATTCCACACTGC	59.271	55.000	0.00	0.00	0.00	4.40
863	2095	3.435566	CAGCGTACGTATGAAGTGACAT	58.564	45.455	18.93	0.00	0.00	3.06
932	2164	1.605710	CCCACAAAGATCGCATCCATC	59.394	52.381	0.00	0.00	0.00	3.51
972	2204	2.014857	TCTTCGATCATCTCCGTCGTT	58.985	47.619	0.00	0.00	36.77	3.85
974	2206	3.813724	TCTTCGATCATCTCCGTCGTTAT	59.186	43.478	0.00	0.00	36.77	1.89
991	2223	5.583069	CGTTATACGTTGGGCAAGAAGCG	62.583	52.174	0.00	0.00	39.69	4.68
1128	2360	3.134127	GGCACCAAGACCCGCATC	61.134	66.667	0.00	0.00	0.00	3.91
1690	2923	1.207089	TCACGGGGCTACTCAGAATTG	59.793	52.381	0.00	0.00	0.00	2.32
1696	2929	1.576356	GCTACTCAGAATTGGCCTCG	58.424	55.000	3.32	0.00	0.00	4.63
1831	3064	6.571731	CGCAGATAATCCGGGATTCTAAGTTA	60.572	42.308	24.90	7.05	33.95	2.24
1836	3069	6.749036	AATCCGGGATTCTAAGTTACTCAT	57.251	37.500	16.53	0.00	0.00	2.90
1865	3098	6.774656	AGTGATCCTTTGAGCTTATTTATGGG	59.225	38.462	0.00	0.00	0.00	4.00
1901	3134	1.381191	TCGAGCTCACATGCCCCTA	60.381	57.895	15.40	0.00	0.00	3.53
2006	3266	7.199766	TGAAATGACATTTGTGGAAGTTGTAC	58.800	34.615	18.00	0.04	31.47	2.90
2057	3318	9.308318	GCTTTTGAAAGTAGTATTTTTGAACCA	57.692	29.630	5.47	0.00	38.28	3.67
2112	3375	3.916761	TCCATGATGAAACTTTGCAAGC	58.083	40.909	0.00	0.00	0.00	4.01
2121	3384	4.993584	TGAAACTTTGCAAGCACTCAAAAA	59.006	33.333	0.00	0.00	32.55	1.94
2218	3498	6.681729	AAGATACTCCGCATCCCTTATTTA	57.318	37.500	0.00	0.00	0.00	1.40
2251	3531	7.389803	TGATTGAATAGCGGAAAAAGAATCA	57.610	32.000	0.00	0.00	0.00	2.57
2268	3548	5.121811	AGAATCAGATCTTCAATTCGGTGG	58.878	41.667	12.96	0.00	34.17	4.61
2271	3551	1.281867	AGATCTTCAATTCGGTGGCCA	59.718	47.619	0.00	0.00	0.00	5.36
2343	3625	2.089980	GGATGCAAGATGCTTGAGTGT	58.910	47.619	11.08	0.00	45.31	3.55
2350	3632	1.930908	GATGCTTGAGTGTGGCAGGC	61.931	60.000	0.00	0.00	39.38	4.85
2351	3633	2.595463	GCTTGAGTGTGGCAGGCA	60.595	61.111	0.00	0.00	38.14	4.75
2384	3666	9.778993	AAATTTCATGACTAAATGACATTCGAG	57.221	29.630	0.05	4.98	36.43	4.04
2423	3705	8.785329	AAAAAGACAAAATTAGCTCCAAACAA	57.215	26.923	0.00	0.00	0.00	2.83
2446	3728	9.165035	ACAATGTTGTTTTCAAATGTTTCTCAT	57.835	25.926	0.00	0.00	41.76	2.90
2462	3744	9.739276	ATGTTTCTCATAGGTCTGAAATTTGTA	57.261	29.630	0.00	0.00	34.67	2.41
2489	3771	3.743521	TGCTGAGTGCTACTGAAATGTT	58.256	40.909	0.00	0.00	43.37	2.71
2503	3785	5.168526	TGAAATGTTCAAACTCCACGAAG	57.831	39.130	0.00	0.00	36.59	3.79
2514	3796	2.051345	CACGAAGTTTGGCACGGC	60.051	61.111	0.00	0.00	41.61	5.68

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
338	339	6.767423	ACTAAGTAGTACTGACTAGCTTAGGC	59.233	42.308	21.93	0.00	43.54	3.93
355	356	3.373439	AGAACCGCGTGACTACTAAGTAG	59.627	47.826	4.92	0.00	41.43	2.57
358	359	2.915738	AGAACCGCGTGACTACTAAG	57.084	50.000	4.92	0.00	0.00	2.18
360	361	3.648339	AAAAGAACCGCGTGACTACTA	57.352	42.857	4.92	0.00	0.00	1.82
363	364	2.798283	CTGAAAAAGAACCGCGTGACTA	59.202	45.455	4.92	0.00	0.00	2.59
364	365	1.597663	CTGAAAAAGAACCGCGTGACT	59.402	47.619	4.92	0.00	0.00	3.41
365	366	1.333791	CCTGAAAAAGAACCGCGTGAC	60.334	52.381	4.92	0.00	0.00	3.67
388	1598	1.331756	CCAGATTAACTGCGTGATGCC	59.668	52.381	0.00	0.00	45.60	4.40
434	1644	3.000322	GTGCAATTAGTCGTCGATCCTTG	60.000	47.826	0.00	2.19	0.00	3.61
496	1706	6.072230	TCGGTTGTTGCAATGAAGAAATATCA	60.072	34.615	0.59	0.00	0.00	2.15
548	1766	4.243270	ACTACTTGCGAAACAGACCATAC	58.757	43.478	0.00	0.00	0.00	2.39
639	1857	7.648142	CAAAGGACACTCAAAAGTAATTAGCA	58.352	34.615	0.00	0.00	33.25	3.49
715	1933	0.608130	TGACCACTCCACATCTTCGG	59.392	55.000	0.00	0.00	0.00	4.30
763	1995	0.038599	TGGCAGATGCAGTGTGGAAT	59.961	50.000	7.19	0.00	44.36	3.01
765	1997	1.002990	CTGGCAGATGCAGTGTGGA	60.003	57.895	9.42	0.00	44.36	4.02
771	2003	4.237445	CCTTCCTGGCAGATGCAG	57.763	61.111	17.94	5.69	44.36	4.41
889	2121	4.141914	GCTTATATAGGAGACGGGGAATGG	60.142	50.000	0.00	0.00	0.00	3.16
892	2124	3.438183	GGCTTATATAGGAGACGGGGAA	58.562	50.000	0.00	0.00	0.00	3.97
898	2130	6.420913	TCTTTGTGGGCTTATATAGGAGAC	57.579	41.667	0.00	0.00	0.00	3.36
932	2164	0.454600	GTGTGGGATGCAATGCAGAG	59.545	55.000	14.98	0.00	43.65	3.35
972	2204	1.066716	ACGCTTCTTGCCCAACGTATA	60.067	47.619	0.00	0.00	38.78	1.47
974	2206	0.533308	AACGCTTCTTGCCCAACGTA	60.533	50.000	0.00	0.00	38.78	3.57
1025	2257	0.250901	GGAGGAGCTTGAGTTTGGCA	60.251	55.000	0.00	0.00	0.00	4.92
1377	2609	2.035940	AACTCCTCGTCGCTCCCT	59.964	61.111	0.00	0.00	0.00	4.20
1696	2929	4.000557	CACACTCGCGCACACACC	62.001	66.667	8.75	0.00	0.00	4.16
1831	3064	4.383552	GCTCAAAGGATCACTACCATGAGT	60.384	45.833	2.62	0.00	41.39	3.41
1836	3069	5.957771	ATAAGCTCAAAGGATCACTACCA	57.042	39.130	0.00	0.00	0.00	3.25
1865	3098	4.502645	GCTCGAGCTAAGAAGATGACTTTC	59.497	45.833	29.88	0.00	35.80	2.62
1948	3207	5.512753	TTGCAGCACTCAAAACTTTCATA	57.487	34.783	0.00	0.00	0.00	2.15
2081	3344	9.642327	CAAAGTTTCATCATGGAATAACATTCA	57.358	29.630	0.00	0.00	0.00	2.57
2121	3384	4.958509	TGTGTGGCAAACATTGATGAATT	58.041	34.783	6.35	0.00	41.97	2.17
2189	3469	1.789464	GATGCGGAGTATCTTTGCTCG	59.211	52.381	0.00	0.00	46.14	5.03
2218	3498	6.239217	TCCGCTATTCAATCATATAGCCAT	57.761	37.500	0.00	0.00	43.97	4.40
2251	3531	1.281867	TGGCCACCGAATTGAAGATCT	59.718	47.619	0.00	0.00	0.00	2.75
2268	3548	1.900498	GGGTGCATATGAGCCTGGC	60.900	63.158	11.65	11.65	0.00	4.85
2271	3551	2.072487	ACCGGGTGCATATGAGCCT	61.072	57.895	6.32	0.00	0.00	4.58
2350	3632	3.187478	AGTCATGAAATTTCGCACGTG	57.813	42.857	12.28	12.28	0.00	4.49
2351	3633	5.351233	TTTAGTCATGAAATTTCGCACGT	57.649	34.783	13.34	1.21	0.00	4.49
2357	3639	9.773328	TCGAATGTCATTTAGTCATGAAATTTC	57.227	29.630	11.41	11.41	40.04	2.17
2423	3705	9.480053	CCTATGAGAAACATTTGAAAACAACAT	57.520	29.630	0.00	0.00	40.07	2.71
2465	3747	9.020990	TGAACATTTCAGTAGCACTCAGCAAAA	62.021	37.037	0.00	0.00	39.45	2.44
2475	3757	5.008613	GTGGAGTTTGAACATTTCAGTAGCA	59.991	40.000	0.00	0.00	41.38	3.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.