AutoCloner

Multiple sequence alignment - TraesCS5B01G072500

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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	TraesCS5B01G072500	chr5B	100.000	2390	0	0	1	2390	84664769	84667158	0.000000e+00	4414.0
1	TraesCS5B01G072500	chr5A	94.256	1828	71	15	1	1814	71456705	71458512	0.000000e+00	2763.0
2	TraesCS5B01G072500	chr5A	92.096	291	18	2	2067	2352	71458730	71459020	2.860000e-109	405.0
3	TraesCS5B01G072500	chr5A	92.818	181	8	2	1891	2066	71458515	71458695	8.480000e-65	257.0
4	TraesCS5B01G072500	chr5A	100.000	28	0	0	2363	2390	71459018	71459045	4.000000e-03	52.8
5	TraesCS5B01G072500	chr5D	94.737	1558	52	11	79	1630	76003048	76004581	0.000000e+00	2396.0
6	TraesCS5B01G072500	chr5D	90.331	393	18	5	1632	2006	76023164	76023554	4.590000e-137	497.0
7	TraesCS5B01G072500	chr5D	92.121	165	6	4	2231	2390	76024139	76024301	2.390000e-55	226.0
8	TraesCS5B01G072500	chr5D	90.164	122	5	2	2048	2163	76023708	76023828	4.110000e-33	152.0
9	TraesCS5B01G072500	chr5D	95.556	90	3	1	2158	2247	76023927	76024015	2.480000e-30	143.0
10	TraesCS5B01G072500	chr5D	93.651	63	4	0	2004	2066	76023636	76023698	7.030000e-16	95.3
11	TraesCS5B01G072500	chr5D	97.727	44	1	0	1	44	76003005	76003048	2.550000e-10	76.8
12	TraesCS5B01G072500	chr2D	81.663	1527	199	48	163	1637	21911843	21910346	0.000000e+00	1194.0
13	TraesCS5B01G072500	chr2D	82.872	578	84	10	1067	1632	22107909	22107335	2.740000e-139	505.0
14	TraesCS5B01G072500	chr6A	80.017	1206	162	40	251	1417	86400252	86399087	0.000000e+00	819.0
15	TraesCS5B01G072500	chr6D	78.099	1452	200	62	194	1584	68848944	68847550	0.000000e+00	811.0
16	TraesCS5B01G072500	chr6D	87.288	118	14	1	431	548	68843208	68843092	1.490000e-27	134.0
17	TraesCS5B01G072500	chr6B	82.532	790	97	23	827	1584	143751306	143750526	0.000000e+00	656.0
18	TraesCS5B01G072500	chr2A	94.937	79	4	0	1111	1189	23937001	23936923	8.970000e-25	124.0

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	TraesCS5B01G072500	chr5B	84664769	84667158	2389	False	4414.00	4414	100.0000	1	2390	1	chr5B.!!$F1	2389
1	TraesCS5B01G072500	chr5A	71456705	71459045	2340	False	869.45	2763	94.7925	1	2390	4	chr5A.!!$F1	2389
2	TraesCS5B01G072500	chr5D	76003005	76004581	1576	False	1236.40	2396	96.2320	1	1630	2	chr5D.!!$F1	1629
3	TraesCS5B01G072500	chr5D	76023164	76024301	1137	False	222.66	497	92.3646	1632	2390	5	chr5D.!!$F2	758
4	TraesCS5B01G072500	chr2D	21910346	21911843	1497	True	1194.00	1194	81.6630	163	1637	1	chr2D.!!$R1	1474
5	TraesCS5B01G072500	chr2D	22107335	22107909	574	True	505.00	505	82.8720	1067	1632	1	chr2D.!!$R2	565
6	TraesCS5B01G072500	chr6A	86399087	86400252	1165	True	819.00	819	80.0170	251	1417	1	chr6A.!!$R1	1166
7	TraesCS5B01G072500	chr6D	68847550	68848944	1394	True	811.00	811	78.0990	194	1584	1	chr6D.!!$R2	1390
8	TraesCS5B01G072500	chr6B	143750526	143751306	780	True	656.00	656	82.5320	827	1584	1	chr6B.!!$R1	757

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
211	212	0.526211	GTTCTGATTTTGGGTCGGCC	59.474	55.000	0.0	0.0	0.0	6.13	F
866	915	1.531883	GCCTTGATTCGTTGCGGATTC	60.532	52.381	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1330	1384	0.321653	GTCCGGTTGTCCAGCTTGAT	60.322	55.0	0.00	0.0	0.00	2.57	R
1978	2105	0.813610	TCAACTGGTTGTCACGGCTG	60.814	55.0	12.34	0.0	41.16	4.85	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
47	48	9.559732	CCAAAGTTGTTCATCCTGTGATATATA	57.440	33.333	0.00	0.00	36.54	0.86
116	117	7.604545	CCCATGGTTTAACGGTGAATTAAATTT	59.395	33.333	11.73	0.00	34.81	1.82
148	149	2.693069	AGTGCCGCATATAGCTGATTC	58.307	47.619	0.00	0.00	42.61	2.52
211	212	0.526211	GTTCTGATTTTGGGTCGGCC	59.474	55.000	0.00	0.00	0.00	6.13
266	267	6.601741	TCCAATTGATTTTGCTTCAACAAC	57.398	33.333	7.12	0.00	36.02	3.32
274	275	6.648310	TGATTTTGCTTCAACAACAAACAGAA	59.352	30.769	0.00	0.00	33.29	3.02
276	277	4.511617	TGCTTCAACAACAAACAGAACA	57.488	36.364	0.00	0.00	0.00	3.18
287	288	6.183360	ACAACAAACAGAACAGTGTTATCTGG	60.183	38.462	22.83	11.79	43.79	3.86
288	289	4.821805	ACAAACAGAACAGTGTTATCTGGG	59.178	41.667	22.83	15.93	43.79	4.45
289	290	3.059352	ACAGAACAGTGTTATCTGGGC	57.941	47.619	22.83	5.45	43.79	5.36
290	291	2.371841	ACAGAACAGTGTTATCTGGGCA	59.628	45.455	22.83	0.00	43.79	5.36
291	292	3.009473	ACAGAACAGTGTTATCTGGGCAT	59.991	43.478	22.83	5.34	43.79	4.40
477	491	2.037687	TTGGGGCTTGATGCTGGG	59.962	61.111	0.00	0.00	42.39	4.45
478	492	2.855770	TTGGGGCTTGATGCTGGGT	61.856	57.895	0.00	0.00	42.39	4.51
796	844	5.306419	CCCAGATCTGATATTCCAGAGTCAA	59.694	44.000	24.62	0.00	45.27	3.18
866	915	1.531883	GCCTTGATTCGTTGCGGATTC	60.532	52.381	0.00	0.00	0.00	2.52
967	1021	8.204836	AGAGTTAACACTTCTTAGTTGTGATGT	58.795	33.333	8.61	0.00	35.83	3.06
1102	1156	2.600173	TTGCGGCCAAGGGAAAGG	60.600	61.111	2.24	0.00	0.00	3.11
1165	1219	4.023450	TCAGCAAAGAAATGAAGAGCACAG	60.023	41.667	0.00	0.00	0.00	3.66
1330	1384	5.175859	CCTATGAAGACCAGAAGCGTTTTA	58.824	41.667	0.00	0.00	0.00	1.52
1379	1434	4.348863	AAGAGAACAATGCTCTCACAGT	57.651	40.909	15.09	0.00	41.66	3.55
1398	1453	4.189639	AGTTAAGAACTGATCGGGACAC	57.810	45.455	6.47	0.00	41.01	3.67
1464	1562	8.925161	TTTTGGTAATAATGTAGCATTGAAGC	57.075	30.769	4.78	0.00	31.88	3.86
1521	1623	8.081633	CCAGCAAAATAGTTTGTCATGTTCTTA	58.918	33.333	16.26	0.00	45.06	2.10
1543	1645	8.999431	TCTTATGAAGATTTAACTTGTGTGTCC	58.001	33.333	0.00	0.00	31.20	4.02
1546	1648	6.119536	TGAAGATTTAACTTGTGTGTCCTGT	58.880	36.000	0.00	0.00	0.00	4.00
1741	1862	5.353956	CAGTGGATAATCACCGACATTTCAA	59.646	40.000	0.00	0.00	38.34	2.69
1742	1863	5.586243	AGTGGATAATCACCGACATTTCAAG	59.414	40.000	0.00	0.00	38.34	3.02
1743	1864	4.335315	TGGATAATCACCGACATTTCAAGC	59.665	41.667	0.00	0.00	0.00	4.01
1744	1865	4.335315	GGATAATCACCGACATTTCAAGCA	59.665	41.667	0.00	0.00	0.00	3.91
1789	1916	4.957759	ATACTTCCGTGCATTAAACCAC	57.042	40.909	0.00	0.19	0.00	4.16
1795	1922	1.067915	CGTGCATTAAACCACCAAGGG	60.068	52.381	0.00	0.00	43.89	3.95
1814	1941	3.190535	AGGGTTTGTTATGCTTGCTAACG	59.809	43.478	0.00	0.00	32.83	3.18
1816	1943	3.498082	GTTTGTTATGCTTGCTAACGGG	58.502	45.455	0.00	0.00	32.83	5.28
1847	1974	3.928375	TCCTCGCGACAACTTAATTTACC	59.072	43.478	3.71	0.00	0.00	2.85
1883	2010	7.304735	GTTTGATTTGCCATGGTTAAAAATCC	58.695	34.615	25.14	15.21	36.74	3.01
1886	2013	3.859411	TGCCATGGTTAAAAATCCGAC	57.141	42.857	14.67	0.00	0.00	4.79
1926	2053	2.678336	CCGATTAGAAAGTGAGGCAACC	59.322	50.000	0.00	0.00	37.17	3.77
1978	2105	1.069227	GTGAACGGTTTGCCAGATGTC	60.069	52.381	0.00	0.00	34.09	3.06
2002	2129	3.659786	CCGTGACAACCAGTTGAGAATA	58.340	45.455	17.06	0.00	42.93	1.75
2011	2222	8.974060	ACAACCAGTTGAGAATAACTTTTCTA	57.026	30.769	17.06	0.00	42.93	2.10
2070	2315	1.789506	TGCACCGGCTTTTATTTTGC	58.210	45.000	0.00	0.08	41.91	3.68
2095	2340	2.634982	TGCGAAATGGCATCAAGTTC	57.365	45.000	0.00	0.00	38.17	3.01
2126	2371	7.564793	AGGTTATACATGCAGTTCATTCTACA	58.435	34.615	0.00	0.00	31.79	2.74
2173	2522	6.201997	GCTCTACTAAGTACTACCGAGGTTAC	59.798	46.154	0.00	0.00	0.00	2.50
2175	2524	7.268586	TCTACTAAGTACTACCGAGGTTACAG	58.731	42.308	0.00	0.00	0.00	2.74
2217	2566	5.181690	TGGTCAAATAGAACAGTGCAAAC	57.818	39.130	0.00	0.00	39.57	2.93
2295	2782	7.316544	TGACATCATAATATCATGCATCAGC	57.683	36.000	0.00	0.00	42.57	4.26
2307	2794	3.513909	TGCATCAGCCCTAATGCTATT	57.486	42.857	5.11	0.00	46.64	1.73
2311	2798	5.104617	GCATCAGCCCTAATGCTATTAGCA	61.105	45.833	20.06	20.06	45.47	3.49
2349	2853	9.214957	CGAGTATGCAACCCATAAATTAGATTA	57.785	33.333	0.00	0.00	38.11	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	6.004574	GGTTTGAGTCTCCTAAAAACCTCAT	58.995	40.000	18.69	0.00	40.78	2.90
48	49	5.374071	GGTTTGAGTCTCCTAAAAACCTCA	58.626	41.667	18.69	0.00	40.78	3.86
49	50	4.760715	GGGTTTGAGTCTCCTAAAAACCTC	59.239	45.833	22.41	13.96	43.36	3.85
50	51	4.726583	GGGTTTGAGTCTCCTAAAAACCT	58.273	43.478	22.41	0.00	43.36	3.50
51	52	4.726583	AGGGTTTGAGTCTCCTAAAAACC	58.273	43.478	18.11	18.11	46.05	3.27
66	67	1.474077	GCTGCACCTGATAAGGGTTTG	59.526	52.381	0.00	0.00	34.44	2.93
116	117	0.742990	GCGGCACTACATGGTTAGCA	60.743	55.000	0.00	0.00	0.00	3.49
266	267	4.320494	GCCCAGATAACACTGTTCTGTTTG	60.320	45.833	0.00	0.00	36.06	2.93
274	275	4.460382	CAGAAAATGCCCAGATAACACTGT	59.540	41.667	0.00	0.00	36.30	3.55
276	277	4.019174	CCAGAAAATGCCCAGATAACACT	58.981	43.478	0.00	0.00	0.00	3.55
287	288	0.244721	GGTGCAGACCAGAAAATGCC	59.755	55.000	0.00	0.00	42.59	4.40
288	289	1.251251	AGGTGCAGACCAGAAAATGC	58.749	50.000	0.00	0.00	45.98	3.56
289	290	3.571401	AGAAAGGTGCAGACCAGAAAATG	59.429	43.478	0.00	0.00	45.98	2.32
290	291	3.823304	GAGAAAGGTGCAGACCAGAAAAT	59.177	43.478	0.00	0.00	45.98	1.82
291	292	3.214328	GAGAAAGGTGCAGACCAGAAAA	58.786	45.455	0.00	0.00	45.98	2.29
477	491	7.324178	AGTCCTGAAGAACATCAACACTATAC	58.676	38.462	0.00	0.00	0.00	1.47
478	492	7.482169	AGTCCTGAAGAACATCAACACTATA	57.518	36.000	0.00	0.00	0.00	1.31
541	556	6.738114	TCATCTAAAGGTTCTTGCAAAAGTG	58.262	36.000	0.00	0.00	0.00	3.16
967	1021	3.980646	ATTTTAGCTGCACACGTCAAA	57.019	38.095	1.02	0.00	0.00	2.69
1102	1156	3.062466	GCCACCTTTTCCGCCCTC	61.062	66.667	0.00	0.00	0.00	4.30
1165	1219	1.404035	GATATTCGCCCCAAACACACC	59.596	52.381	0.00	0.00	0.00	4.16
1330	1384	0.321653	GTCCGGTTGTCCAGCTTGAT	60.322	55.000	0.00	0.00	0.00	2.57
1359	1413	4.348863	AACTGTGAGAGCATTGTTCTCT	57.651	40.909	24.97	11.64	43.11	3.10
1379	1434	4.087182	AGAGTGTCCCGATCAGTTCTTAA	58.913	43.478	0.00	0.00	0.00	1.85
1392	1447	4.832266	ACTATGATGAGATGAGAGTGTCCC	59.168	45.833	0.00	0.00	0.00	4.46
1398	1453	7.514784	AGAAGACACTATGATGAGATGAGAG	57.485	40.000	0.00	0.00	0.00	3.20
1464	1562	2.949451	ACATTCTACTGTGAGCTCGG	57.051	50.000	9.64	4.45	0.00	4.63
1521	1623	6.772716	ACAGGACACACAAGTTAAATCTTCAT	59.227	34.615	0.00	0.00	0.00	2.57
1560	1668	1.180029	CAGGAGCATGGGAAACTTGG	58.820	55.000	0.00	0.00	0.00	3.61
1647	1756	7.986085	ACCAATAATAGGTATCATCACAAGC	57.014	36.000	0.00	0.00	37.67	4.01
1741	1862	4.609018	AGTTCACGCACCGCTGCT	62.609	61.111	0.54	0.00	41.77	4.24
1742	1863	4.374702	CAGTTCACGCACCGCTGC	62.375	66.667	0.00	0.00	40.38	5.25
1743	1864	2.661537	TCAGTTCACGCACCGCTG	60.662	61.111	0.00	0.00	0.00	5.18
1744	1865	2.661866	GTCAGTTCACGCACCGCT	60.662	61.111	0.00	0.00	0.00	5.52
1789	1916	2.299867	AGCAAGCATAACAAACCCTTGG	59.700	45.455	0.00	0.00	36.82	3.61
1795	1922	3.189702	TCCCGTTAGCAAGCATAACAAAC	59.810	43.478	11.85	0.00	33.60	2.93
1814	1941	2.546494	CGCGAGGATGGCAATTCCC	61.546	63.158	0.00	0.00	41.24	3.97
1816	1943	1.089481	TGTCGCGAGGATGGCAATTC	61.089	55.000	10.24	0.00	41.24	2.17
1869	1996	4.390603	TCTGACGTCGGATTTTTAACCATG	59.609	41.667	23.11	0.00	0.00	3.66
1926	2053	1.726791	CTCCACGGTTGACTGAAATCG	59.273	52.381	0.00	0.00	0.00	3.34
1978	2105	0.813610	TCAACTGGTTGTCACGGCTG	60.814	55.000	12.34	0.00	41.16	4.85
2002	2129	9.319143	GTGTCATCAGCATACTATAGAAAAGTT	57.681	33.333	6.78	0.00	0.00	2.66
2095	2340	4.585955	ACTGCATGTATAACCTCGGTAG	57.414	45.455	0.00	0.00	0.00	3.18
2126	2371	6.058183	AGCTTGTTGTTCTGATAGAGTTTGT	58.942	36.000	0.00	0.00	0.00	2.83
2173	2522	9.525409	GACCATTTGGAATATTTTCTTCATCTG	57.475	33.333	3.01	0.00	38.94	2.90
2175	2524	9.874205	TTGACCATTTGGAATATTTTCTTCATC	57.126	29.630	3.01	0.00	38.94	2.92
2217	2566	9.069078	CATTGCTAGTTGTATGTTCAGATTTTG	57.931	33.333	0.00	0.00	0.00	2.44
2273	2760	5.593095	GGGCTGATGCATGATATTATGATGT	59.407	40.000	2.46	0.00	41.91	3.06
2307	2794	2.343101	ACTCGCGTGCTTATTTTGCTA	58.657	42.857	5.77	0.00	0.00	3.49
2311	2798	2.675844	TGCATACTCGCGTGCTTATTTT	59.324	40.909	18.50	0.00	41.78	1.82
2351	2855	9.577110	CTTTGCATGTAACTATGAATCACAAAT	57.423	29.630	0.00	0.00	0.00	2.32
2352	2856	7.541783	GCTTTGCATGTAACTATGAATCACAAA	59.458	33.333	0.00	0.00	0.00	2.83
2353	2857	7.028962	GCTTTGCATGTAACTATGAATCACAA	58.971	34.615	0.00	0.00	0.00	3.33
2354	2858	6.150809	TGCTTTGCATGTAACTATGAATCACA	59.849	34.615	0.00	0.00	31.71	3.58
2355	2859	6.554419	TGCTTTGCATGTAACTATGAATCAC	58.446	36.000	0.00	0.00	31.71	3.06
2356	2860	6.756299	TGCTTTGCATGTAACTATGAATCA	57.244	33.333	0.00	0.00	31.71	2.57
2357	2861	7.028962	TGTTGCTTTGCATGTAACTATGAATC	58.971	34.615	17.10	0.00	38.76	2.52
2358	2862	6.923012	TGTTGCTTTGCATGTAACTATGAAT	58.077	32.000	17.10	0.00	38.76	2.57
2359	2863	6.324561	TGTTGCTTTGCATGTAACTATGAA	57.675	33.333	17.10	0.77	38.76	2.57
2360	2864	5.956068	TGTTGCTTTGCATGTAACTATGA	57.044	34.783	17.10	1.05	38.76	2.15
2361	2865	6.089820	CCTTTGTTGCTTTGCATGTAACTATG	59.910	38.462	17.10	12.95	38.76	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.