AutoCloner

Multiple sequence alignment - TraesCS5A01G094900

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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	TraesCS5A01G094900	chr5A	100.000	2312	0	0	1	2312	132093323	132091012	0.000000e+00	4270.0
1	TraesCS5A01G094900	chr5A	90.315	857	45	15	1124	1954	132975455	132976299	0.000000e+00	1088.0
2	TraesCS5A01G094900	chr5A	90.052	774	54	9	362	1126	132971017	132971776	0.000000e+00	981.0
3	TraesCS5A01G094900	chr5A	90.164	122	12	0	143	264	132970766	132970887	2.380000e-35	159.0
4	TraesCS5A01G094900	chr5A	75.079	317	78	1	1000	1316	40813296	40813611	1.850000e-31	147.0
5	TraesCS5A01G094900	chr5A	90.476	63	4	1	271	333	132970952	132971012	5.290000e-12	82.4
6	TraesCS5A01G094900	chr5B	89.474	1748	83	49	265	1956	134542714	134544416	0.000000e+00	2115.0
7	TraesCS5A01G094900	chr5B	94.141	1280	45	14	373	1640	134121469	134120208	0.000000e+00	1921.0
8	TraesCS5A01G094900	chr5B	91.304	345	25	3	1968	2312	134118706	134118367	1.250000e-127	466.0
9	TraesCS5A01G094900	chr5B	96.000	250	8	1	14	261	134121822	134121573	2.770000e-109	405.0
10	TraesCS5A01G094900	chr5B	90.759	303	7	5	1656	1958	134119888	134119607	3.600000e-103	385.0
11	TraesCS5A01G094900	chr5B	82.132	319	54	3	999	1314	133893507	133893189	1.050000e-68	270.0
12	TraesCS5A01G094900	chr5B	97.917	96	2	0	14	109	134542105	134542200	1.420000e-37	167.0
13	TraesCS5A01G094900	chr5D	94.263	1255	48	11	707	1959	121073087	121071855	0.000000e+00	1897.0
14	TraesCS5A01G094900	chr5D	88.339	1638	96	44	265	1866	121295690	121297268	0.000000e+00	1879.0
15	TraesCS5A01G094900	chr5D	92.906	437	17	7	286	715	121074714	121074285	7.010000e-175	623.0
16	TraesCS5A01G094900	chr5D	93.143	350	20	3	1966	2312	121069788	121069440	5.700000e-141	510.0
17	TraesCS5A01G094900	chr5D	95.833	96	4	0	14	109	121074892	121074797	3.080000e-34	156.0
18	TraesCS5A01G094900	chr5D	75.564	266	65	0	1034	1299	51637556	51637821	5.180000e-27	132.0
19	TraesCS5A01G094900	chr5D	74.522	314	66	11	1000	1306	51675302	51675608	8.670000e-25	124.0
20	TraesCS5A01G094900	chr5D	86.667	120	6	3	145	264	121295542	121295651	8.670000e-25	124.0
21	TraesCS5A01G094900	chr5D	92.000	75	5	1	145	218	121074795	121074721	1.130000e-18	104.0
22	TraesCS5A01G094900	chr4A	81.915	94	12	5	2005	2095	728448148	728448057	8.860000e-10	75.0
23	TraesCS5A01G094900	chr6B	94.286	35	2	0	1976	2010	679565282	679565248	1.000000e-03	54.7
24	TraesCS5A01G094900	chr6B	94.286	35	1	1	1976	2010	679550402	679550369	4.000000e-03	52.8

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	TraesCS5A01G094900	chr5A	132091012	132093323	2311	True	4270.00	4270	100.00000	1	2312	1	chr5A.!!$R1	2311
1	TraesCS5A01G094900	chr5A	132970766	132976299	5533	False	577.60	1088	90.25175	143	1954	4	chr5A.!!$F2	1811
2	TraesCS5A01G094900	chr5B	134542105	134544416	2311	False	1141.00	2115	93.69550	14	1956	2	chr5B.!!$F1	1942
3	TraesCS5A01G094900	chr5B	134118367	134121822	3455	True	794.25	1921	93.05100	14	2312	4	chr5B.!!$R2	2298
4	TraesCS5A01G094900	chr5D	121295542	121297268	1726	False	1001.50	1879	87.50300	145	1866	2	chr5D.!!$F3	1721
5	TraesCS5A01G094900	chr5D	121069440	121074892	5452	True	658.00	1897	93.62900	14	2312	5	chr5D.!!$R1	2298

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
960	2605	0.933796	GCTTAGAGATCCGTGCAAGC	59.066	55.0	0.0	0.0	32.51	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2031	9805	0.035534	AGGCGTATGTTGATGTGGCA	60.036	50.0	0.0	0.0	0.0	4.92	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
198	515	5.333645	GCGTTTTGAGATAGTATGCATGAGG	60.334	44.000	10.16	0.00	0.00	3.86
202	519	6.484364	TTGAGATAGTATGCATGAGGACAA	57.516	37.500	10.16	4.69	0.00	3.18
253	570	5.816258	CCTTCTTACTTTCCGGATTTCTACC	59.184	44.000	4.15	0.00	0.00	3.18
264	581	2.158957	GGATTTCTACCCGATGCACTGA	60.159	50.000	0.00	0.00	0.00	3.41
266	583	4.262463	GGATTTCTACCCGATGCACTGATA	60.262	45.833	0.00	0.00	0.00	2.15
268	585	2.945456	TCTACCCGATGCACTGATAGT	58.055	47.619	0.00	0.00	0.00	2.12
278	654	3.396560	TGCACTGATAGTATGCATGAGC	58.603	45.455	10.16	1.33	44.17	4.26
327	707	8.380742	TCCAAGTCTTAATTAGTTCTCCTGAT	57.619	34.615	0.00	0.00	0.00	2.90
374	790	1.786579	CGTGCAAGCTTAAAAACAGCC	59.213	47.619	0.00	0.00	38.09	4.85
386	802	9.413734	AGCTTAAAAACAGCCAATAGATAGATT	57.586	29.630	0.00	0.00	38.09	2.40
453	875	4.098196	CCCTCTAGCTAGGTCAACACTTAC	59.902	50.000	20.58	0.00	34.56	2.34
488	910	1.852067	ATTCCAGTCGCGTGTTTGGC	61.852	55.000	5.77	0.00	0.00	4.52
551	973	7.789202	TTATCTAATCTGATCTCCTCTTGGG	57.211	40.000	0.00	0.00	0.00	4.12
584	1008	7.172875	CCAATATGCTTTTGAACAAACCAATGA	59.827	33.333	0.00	0.00	0.00	2.57
592	1016	2.437200	ACAAACCAATGACGCCAATG	57.563	45.000	0.00	0.00	0.00	2.82
787	2431	6.234177	AGCTAGTGCATAGAAAGAAACACTT	58.766	36.000	0.00	0.00	42.74	3.16
841	2485	1.908619	TCTGCTAGCAAACCATCCAGA	59.091	47.619	19.86	6.14	0.00	3.86
921	2566	6.070656	TCCATCACATTTCAAAGTCCTCTTT	58.929	36.000	0.00	0.00	43.66	2.52
958	2603	1.134699	CAGGCTTAGAGATCCGTGCAA	60.135	52.381	0.00	0.00	0.00	4.08
960	2605	0.933796	GCTTAGAGATCCGTGCAAGC	59.066	55.000	0.00	0.00	32.51	4.01
1022	2668	0.807667	GATCGCGTGATGAAGCTGGT	60.808	55.000	17.73	0.00	34.09	4.00
1182	6509	1.397672	CTCTCCTCAAGATGCTCGGA	58.602	55.000	0.00	0.00	32.19	4.55
1350	6678	7.571892	CCACTTGGGAAAATAAAATTTTGTCG	58.428	34.615	13.76	0.00	40.01	4.35
1362	6690	8.782533	ATAAAATTTTGTCGAAGAGTGTGAAC	57.217	30.769	13.76	0.00	36.95	3.18
1363	6691	6.436843	AAATTTTGTCGAAGAGTGTGAACT	57.563	33.333	0.00	0.00	36.95	3.01
1364	6692	4.857871	TTTTGTCGAAGAGTGTGAACTG	57.142	40.909	0.00	0.00	36.95	3.16
1365	6693	3.520290	TTGTCGAAGAGTGTGAACTGT	57.480	42.857	0.00	0.00	36.95	3.55
1366	6694	2.809446	TGTCGAAGAGTGTGAACTGTG	58.191	47.619	0.00	0.00	36.95	3.66
1367	6695	2.425668	TGTCGAAGAGTGTGAACTGTGA	59.574	45.455	0.00	0.00	36.95	3.58
1368	6696	3.119280	TGTCGAAGAGTGTGAACTGTGAA	60.119	43.478	0.00	0.00	36.95	3.18
1369	6697	3.487574	GTCGAAGAGTGTGAACTGTGAAG	59.512	47.826	0.00	0.00	36.95	3.02
1370	6698	3.130516	TCGAAGAGTGTGAACTGTGAAGT	59.869	43.478	0.00	0.00	0.00	3.01
1371	6699	4.337274	TCGAAGAGTGTGAACTGTGAAGTA	59.663	41.667	0.00	0.00	0.00	2.24
1372	6700	4.441415	CGAAGAGTGTGAACTGTGAAGTAC	59.559	45.833	0.00	0.00	0.00	2.73
1380	6712	6.805271	GTGTGAACTGTGAAGTACGTATATGT	59.195	38.462	0.00	2.56	0.00	2.29
1617	6978	2.086094	TGATGCGTGCACATCTTCAAT	58.914	42.857	18.64	0.00	45.51	2.57
1630	7284	7.116662	TGCACATCTTCAATCTACAAATTTTGC	59.883	33.333	9.04	0.00	0.00	3.68
1802	7491	2.891936	GTCGGCGATGCAGCATCA	60.892	61.111	30.49	12.04	40.54	3.07
1803	7492	2.109593	TCGGCGATGCAGCATCAT	59.890	55.556	30.49	0.85	40.54	2.45
1804	7493	1.957695	TCGGCGATGCAGCATCATC	60.958	57.895	30.49	21.66	40.54	2.92
1845	7543	0.916086	TATGTGGTGGAGCGGGAATT	59.084	50.000	0.00	0.00	0.00	2.17
1896	7594	2.365617	CCATCGGCCTCTACTACAATGT	59.634	50.000	0.00	0.00	0.00	2.71
1932	7630	0.525029	TGCGTACGACGTGTTGAACA	60.525	50.000	21.65	0.00	44.73	3.18
1959	7661	0.879765	ATGACGTTCGACTCTCCGTT	59.120	50.000	0.00	0.00	33.03	4.44
1960	7662	0.040692	TGACGTTCGACTCTCCGTTG	60.041	55.000	0.00	0.00	33.03	4.10
1961	7663	0.040603	GACGTTCGACTCTCCGTTGT	60.041	55.000	0.00	0.00	33.03	3.32
1962	7664	0.383231	ACGTTCGACTCTCCGTTGTT	59.617	50.000	0.00	0.00	0.00	2.83
1963	7665	0.776451	CGTTCGACTCTCCGTTGTTG	59.224	55.000	0.00	0.00	0.00	3.33
1964	7666	1.849097	GTTCGACTCTCCGTTGTTGT	58.151	50.000	0.00	0.00	0.00	3.32
2053	9827	3.070302	TGCCACATCAACATACGCCTATA	59.930	43.478	0.00	0.00	0.00	1.31
2098	9873	2.973694	GCATCATGCATGGGAAAAGT	57.026	45.000	25.97	1.98	44.26	2.66
2240	10015	9.197694	CTCATAGTACTAGCCAATATGTTTCAC	57.802	37.037	8.85	0.00	0.00	3.18
2241	10016	8.700973	TCATAGTACTAGCCAATATGTTTCACA	58.299	33.333	8.85	0.00	0.00	3.58

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	9.786105	CCTTGTCGGTTTTTACTTTTTACTTAA	57.214	29.630	0.00	0.00	0.00	1.85
5	6	9.171877	TCCTTGTCGGTTTTTACTTTTTACTTA	57.828	29.630	0.00	0.00	0.00	2.24
6	7	7.970061	GTCCTTGTCGGTTTTTACTTTTTACTT	59.030	33.333	0.00	0.00	0.00	2.24
7	8	7.415541	GGTCCTTGTCGGTTTTTACTTTTTACT	60.416	37.037	0.00	0.00	0.00	2.24
8	9	6.692681	GGTCCTTGTCGGTTTTTACTTTTTAC	59.307	38.462	0.00	0.00	0.00	2.01
9	10	6.376581	TGGTCCTTGTCGGTTTTTACTTTTTA	59.623	34.615	0.00	0.00	0.00	1.52
10	11	5.185442	TGGTCCTTGTCGGTTTTTACTTTTT	59.815	36.000	0.00	0.00	0.00	1.94
11	12	4.705991	TGGTCCTTGTCGGTTTTTACTTTT	59.294	37.500	0.00	0.00	0.00	2.27
12	13	4.271661	TGGTCCTTGTCGGTTTTTACTTT	58.728	39.130	0.00	0.00	0.00	2.66
29	30	4.097892	ACAAACAGATGAACAACTTGGTCC	59.902	41.667	4.31	0.00	31.76	4.46
126	129	4.871933	ACGAAATTCCAAGGCAGATTTT	57.128	36.364	0.00	0.00	0.00	1.82
177	493	6.888105	TGTCCTCATGCATACTATCTCAAAA	58.112	36.000	0.00	0.00	0.00	2.44
202	519	8.854117	TCGGAATATGAATCTCATCATCGATAT	58.146	33.333	0.00	0.00	40.44	1.63
253	570	3.030668	TGCATACTATCAGTGCATCGG	57.969	47.619	0.00	0.00	43.30	4.18
266	583	8.737175	CAATCTTATAATTGGCTCATGCATACT	58.263	33.333	0.00	0.00	41.91	2.12
268	585	8.733458	GTCAATCTTATAATTGGCTCATGCATA	58.267	33.333	0.00	0.00	38.06	3.14
278	654	5.705400	AGGGGTGGTCAATCTTATAATTGG	58.295	41.667	0.00	0.00	37.27	3.16
386	802	4.074970	GAGAGGTCCTGCTTTTGAAATCA	58.925	43.478	0.00	0.00	0.00	2.57
488	910	4.074259	TGTTGGTTCTGATCAACATGGAG	58.926	43.478	17.35	0.00	45.40	3.86
514	936	2.588027	TAGATAATGCACGCGTGGAA	57.412	45.000	36.42	22.31	33.77	3.53
551	973	6.451393	TGTTCAAAAGCATATTGGTTGGTAC	58.549	36.000	0.00	0.00	38.20	3.34
638	1065	4.152938	GCACAAAGAGCAATTTGGATTTCC	59.847	41.667	15.47	0.00	43.10	3.13
639	1066	4.751098	TGCACAAAGAGCAATTTGGATTTC	59.249	37.500	15.47	3.66	43.10	2.17
841	2485	3.030291	TGTGTTGTGCCAAAGAGGAAAT	58.970	40.909	0.00	0.00	41.22	2.17
921	2566	3.384467	AGCCTGCTTTGCTTTGAAGTTTA	59.616	39.130	0.00	0.00	34.87	2.01
958	2603	4.568072	TCTAATGGGTTATGTGTGTGCT	57.432	40.909	0.00	0.00	0.00	4.40
960	2605	6.655003	AGTTCTTCTAATGGGTTATGTGTGTG	59.345	38.462	0.00	0.00	0.00	3.82
1022	2668	3.062466	CCACCGCTCTCTCCGACA	61.062	66.667	0.00	0.00	0.00	4.35
1182	6509	1.534697	TGGAACAGACGGGCCTTTT	59.465	52.632	0.84	0.00	0.00	2.27
1272	6599	1.684248	GCATTCCTCAGCATTGGGACT	60.684	52.381	0.00	0.00	0.00	3.85
1350	6678	4.441415	CGTACTTCACAGTTCACACTCTTC	59.559	45.833	0.00	0.00	34.06	2.87
1601	6962	2.672874	TGTAGATTGAAGATGTGCACGC	59.327	45.455	13.13	6.90	0.00	5.34
1630	7284	7.368059	ACTATGATCAATATGCAATGCAACTG	58.632	34.615	13.45	9.99	43.62	3.16
1825	7514	0.180406	ATTCCCGCTCCACCACATAC	59.820	55.000	0.00	0.00	0.00	2.39
1845	7543	1.674322	GGCAAGCCAAAGCCGTAGA	60.674	57.895	6.14	0.00	41.70	2.59
1896	7594	1.668793	CATGCACGTGCCACAGAGA	60.669	57.895	35.72	17.31	41.18	3.10
2031	9805	0.035534	AGGCGTATGTTGATGTGGCA	60.036	50.000	0.00	0.00	0.00	4.92
2098	9873	0.961019	GGTTGCATGCTGAGGTGAAA	59.039	50.000	20.33	0.00	0.00	2.69
2270	10045	3.184178	CCCATGCGTTGTTGTGAAAATTC	59.816	43.478	0.00	0.00	0.00	2.17
2276	10051	0.108774	TACCCCATGCGTTGTTGTGA	59.891	50.000	0.00	0.00	0.00	3.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.