AutoCloner

Multiple sequence alignment - TraesCS5D01G108100

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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	TraesCS5D01G108100	chr5D	100.000	2312	0	0	1	2312	121295418	121297729	0.000000e+00	4270.0
1	TraesCS5D01G108100	chr5D	88.737	1172	78	27	700	1850	121073087	121071949	0.000000e+00	1384.0
2	TraesCS5D01G108100	chr5D	91.705	434	22	7	288	708	121074717	121074285	7.110000e-165	590.0
3	TraesCS5D01G108100	chr5D	86.042	480	46	16	1849	2311	57376768	57377243	1.600000e-136	496.0
4	TraesCS5D01G108100	chr5D	89.691	97	6	2	1	97	121075004	121074912	1.120000e-23	121.0
5	TraesCS5D01G108100	chr5D	100.000	47	0	0	124	170	121074796	121074750	1.140000e-13	87.9
6	TraesCS5D01G108100	chr5B	92.433	1652	78	25	167	1792	134542603	134544233	0.000000e+00	2314.0
7	TraesCS5D01G108100	chr5B	93.138	1195	52	13	374	1546	134121469	134120283	0.000000e+00	1725.0
8	TraesCS5D01G108100	chr5B	83.072	319	51	3	999	1314	133893507	133893189	1.050000e-73	287.0
9	TraesCS5D01G108100	chr5B	83.190	232	17	10	125	343	134121689	134121467	2.340000e-45	193.0
10	TraesCS5D01G108100	chr5B	93.478	92	6	0	1760	1851	134544235	134544326	1.110000e-28	137.0
11	TraesCS5D01G108100	chr5B	89.691	97	10	0	1	97	134121939	134121843	8.670000e-25	124.0
12	TraesCS5D01G108100	chr5A	88.339	1638	96	43	273	1851	132093059	132091458	0.000000e+00	1879.0
13	TraesCS5D01G108100	chr5A	90.155	1158	53	20	1	1126	132970648	132971776	0.000000e+00	1450.0
14	TraesCS5D01G108100	chr5A	90.369	758	42	18	1124	1851	132975455	132976211	0.000000e+00	966.0
15	TraesCS5D01G108100	chr5A	86.667	120	6	3	125	234	132093179	132093060	8.670000e-25	124.0
16	TraesCS5D01G108100	chr4D	89.849	463	31	2	1849	2311	449861413	449861859	4.280000e-162	580.0
17	TraesCS5D01G108100	chr4D	94.444	306	16	1	1849	2154	291587842	291588146	9.670000e-129	470.0
18	TraesCS5D01G108100	chr7D	86.345	476	47	16	1849	2311	17323869	17324339	9.530000e-139	503.0
19	TraesCS5D01G108100	chr7D	94.498	309	17	0	1846	2154	633893910	633894218	5.780000e-131	477.0
20	TraesCS5D01G108100	chr7D	94.444	306	17	0	1849	2154	605477998	605477693	2.690000e-129	472.0
21	TraesCS5D01G108100	chr7D	94.118	306	18	0	1849	2154	92767601	92767906	1.250000e-127	466.0
22	TraesCS5D01G108100	chr7D	94.118	306	17	1	1849	2154	10799843	10799539	4.500000e-127	464.0
23	TraesCS5D01G108100	chr7D	94.928	138	6	1	2174	2311	633894303	633894439	5.000000e-52	215.0
24	TraesCS5D01G108100	chr7D	88.889	171	17	1	2143	2311	49039384	49039214	2.330000e-50	209.0
25	TraesCS5D01G108100	chr7D	88.304	171	18	1	2143	2311	60246388	60246218	1.080000e-48	204.0
26	TraesCS5D01G108100	chr7D	87.719	171	19	1	2143	2311	43681246	43681076	5.040000e-47	198.0
27	TraesCS5D01G108100	chr3D	94.118	306	18	0	1849	2154	611707239	611707544	1.250000e-127	466.0
28	TraesCS5D01G108100	chr3D	86.857	175	17	2	2143	2311	24656000	24655826	8.430000e-45	191.0
29	TraesCS5D01G108100	chr6D	94.891	137	5	2	2143	2278	31969553	31969688	1.800000e-51	213.0
30	TraesCS5D01G108100	chr2D	88.268	179	17	3	2137	2311	646509141	646509319	6.470000e-51	211.0
31	TraesCS5D01G108100	chr2D	87.719	171	19	1	2143	2311	58695585	58695415	5.040000e-47	198.0
32	TraesCS5D01G108100	chr1D	88.304	171	17	2	2143	2311	468112952	468113121	3.900000e-48	202.0

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	TraesCS5D01G108100	chr5D	121295418	121297729	2311	False	4270.000000	4270	100.00000	1	2312	1	chr5D.!!$F2	2311
1	TraesCS5D01G108100	chr5D	121071949	121075004	3055	True	545.725000	1384	92.53325	1	1850	4	chr5D.!!$R1	1849
2	TraesCS5D01G108100	chr5B	134542603	134544326	1723	False	1225.500000	2314	92.95550	167	1851	2	chr5B.!!$F1	1684
3	TraesCS5D01G108100	chr5B	134120283	134121939	1656	True	680.666667	1725	88.67300	1	1546	3	chr5B.!!$R2	1545
4	TraesCS5D01G108100	chr5A	132970648	132976211	5563	False	1208.000000	1450	90.26200	1	1851	2	chr5A.!!$F1	1850
5	TraesCS5D01G108100	chr5A	132091458	132093179	1721	True	1001.500000	1879	87.50300	125	1851	2	chr5A.!!$R1	1726
6	TraesCS5D01G108100	chr7D	633893910	633894439	529	False	346.000000	477	94.71300	1846	2311	2	chr7D.!!$F3	465

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
517	733	0.741221	GATCAGAACACGGCTCCACC	60.741	60.0	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
1806	6993	0.389391	CCGCTCCACCACATACCTAG	59.611	60.0	0.0	0.0	0.0	3.02	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
170	308	3.733337	CTTGGGCGCTTTGAGATAGTAT	58.267	45.455	7.64	0.00	0.00	2.12
237	375	1.834188	TCTACTCGATGCACTGGTGA	58.166	50.000	4.79	0.00	0.00	4.02
245	399	4.574892	TCGATGCACTGGTGAATCTTAAA	58.425	39.130	16.76	1.27	42.29	1.52
246	400	5.185454	TCGATGCACTGGTGAATCTTAAAT	58.815	37.500	16.76	0.00	42.29	1.40
247	401	5.294306	TCGATGCACTGGTGAATCTTAAATC	59.706	40.000	16.76	0.00	42.29	2.17
248	402	5.295292	CGATGCACTGGTGAATCTTAAATCT	59.705	40.000	16.76	0.00	42.29	2.40
249	403	5.885230	TGCACTGGTGAATCTTAAATCTG	57.115	39.130	4.79	0.00	0.00	2.90
250	404	5.316167	TGCACTGGTGAATCTTAAATCTGT	58.684	37.500	4.79	0.00	0.00	3.41
254	413	4.016444	TGGTGAATCTTAAATCTGTGGCC	58.984	43.478	0.00	0.00	0.00	5.36
385	591	7.112779	AGCTTAACAAACAGCCAATAGATAGT	58.887	34.615	0.00	0.00	36.62	2.12
433	641	6.206829	TCCATAGGCATATATACGAGATTCCG	59.793	42.308	0.00	0.00	0.00	4.30
453	665	3.502920	CGTCTAGCTAGGTCAACACTTG	58.497	50.000	20.58	0.00	0.00	3.16
517	733	0.741221	GATCAGAACACGGCTCCACC	60.741	60.000	0.00	0.00	0.00	4.61
531	747	2.289694	GCTCCACCCGTGCATTATCTAT	60.290	50.000	0.00	0.00	0.00	1.98
594	812	0.751277	CCAATGGCGCCAATACCAGA	60.751	55.000	36.33	7.40	39.88	3.86
605	828	3.813443	CCAATACCAGACATGCTAGCTT	58.187	45.455	17.23	6.81	0.00	3.74
610	833	1.483827	CCAGACATGCTAGCTTGGAGA	59.516	52.381	28.29	4.16	0.00	3.71
618	841	6.359804	ACATGCTAGCTTGGAGATTTCATTA	58.640	36.000	28.29	0.00	0.00	1.90
837	2270	1.244019	CCCCTGTGCTAGCAAACCAC	61.244	60.000	21.29	7.20	0.00	4.16
1062	2498	2.103153	TCTTCACCCTGAGTTCCTGT	57.897	50.000	0.00	0.00	0.00	4.00
1140	6257	0.251653	ACGAGCTAGACCAAGACCCA	60.252	55.000	0.00	0.00	0.00	4.51
1242	6359	2.029964	GTCGGCGGGACAAACAGA	59.970	61.111	7.21	0.00	45.36	3.41
1342	6460	4.020307	CAGGTGCCACTTGGGAAAATAAAT	60.020	41.667	0.00	0.00	40.01	1.40
1668	6805	9.499585	GTATAGTTGCATTGCATATTGATCATC	57.500	33.333	12.95	0.00	38.76	2.92
1690	6827	5.121105	TCGTAGTTTATCATCGTCTCCTGA	58.879	41.667	0.00	0.00	0.00	3.86
1694	6831	6.227298	AGTTTATCATCGTCTCCTGATTGT	57.773	37.500	0.00	0.00	34.14	2.71
1698	6843	8.328864	GTTTATCATCGTCTCCTGATTGTTTAC	58.671	37.037	0.00	0.00	34.14	2.01
1700	6845	5.410924	TCATCGTCTCCTGATTGTTTACTG	58.589	41.667	0.00	0.00	0.00	2.74
1785	6972	2.361104	GCTGTTCGGGGGATGCAA	60.361	61.111	0.00	0.00	0.00	4.08
1792	6979	0.258484	TCGGGGGATGCAACATCAAT	59.742	50.000	9.60	0.00	0.00	2.57
1875	7062	3.123804	CAGAATAACTGCTTACGCCGAT	58.876	45.455	0.00	0.00	39.86	4.18
1890	7077	0.392193	CCGATGGCCTCATCTATGCC	60.392	60.000	3.32	0.00	45.66	4.40
1893	7080	4.683432	GGCCTCATCTATGCCGAC	57.317	61.111	0.00	0.00	35.08	4.79
1924	7111	2.551270	GGCATAGATGGACCTATCCCA	58.449	52.381	0.00	0.00	45.59	4.37
1979	7166	4.602006	CCGTCGGCATATGTCTATCTATG	58.398	47.826	5.65	0.00	0.00	2.23
2024	7211	4.471726	CCGTCGGGACCGTTCGAG	62.472	72.222	23.18	14.10	40.74	4.04
2189	7441	0.596083	CTCTGCCACGTCATCGATCC	60.596	60.000	0.00	0.00	40.62	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	9.247861	ACTCATTTCTACTTAATTGAAAGGCAT	57.752	29.630	0.00	0.00	35.84	4.40
170	308	7.285629	GGAATATGGACCTCATCATCGATAGTA	59.714	40.741	0.00	0.00	37.30	1.82
186	324	5.485209	AATAAGGAGGTCGGAATATGGAC	57.515	43.478	0.00	0.00	0.00	4.02
237	375	7.500559	GTGATAGAAGGCCACAGATTTAAGATT	59.499	37.037	5.01	0.00	0.00	2.40
245	399	1.771255	GGGTGATAGAAGGCCACAGAT	59.229	52.381	5.01	0.00	32.79	2.90
246	400	1.204146	GGGTGATAGAAGGCCACAGA	58.796	55.000	5.01	0.00	32.79	3.41
247	401	0.911769	TGGGTGATAGAAGGCCACAG	59.088	55.000	5.01	0.00	32.79	3.66
248	402	1.595311	ATGGGTGATAGAAGGCCACA	58.405	50.000	5.01	0.00	32.79	4.17
249	403	2.736670	AATGGGTGATAGAAGGCCAC	57.263	50.000	5.01	0.00	0.00	5.01
250	404	2.441750	GGTAATGGGTGATAGAAGGCCA	59.558	50.000	5.01	0.00	0.00	5.36
254	413	6.428159	GCAACTATGGTAATGGGTGATAGAAG	59.572	42.308	0.00	0.00	33.96	2.85
385	591	3.486383	AGGTCCTGCTTTTGAAATCGAA	58.514	40.909	0.00	0.00	0.00	3.71
433	641	3.510360	TCCAAGTGTTGACCTAGCTAGAC	59.490	47.826	22.70	15.19	0.00	2.59
517	733	5.809562	GGAGATGAGAATAGATAATGCACGG	59.190	44.000	0.00	0.00	0.00	4.94
594	812	4.226427	TGAAATCTCCAAGCTAGCATGT	57.774	40.909	18.83	0.00	0.00	3.21
837	2270	0.178964	TGCCAAAGAGGAAACCTGGG	60.179	55.000	0.00	0.00	41.22	4.45
1056	2492	2.040330	GTGGCACATGCAACAGGAA	58.960	52.632	13.86	0.00	44.29	3.36
1062	2498	2.518112	ACGGTGTGGCACATGCAA	60.518	55.556	24.95	0.00	44.52	4.08
1140	6257	2.046447	TCTCTCCATCTCCTTTCCCCTT	59.954	50.000	0.00	0.00	0.00	3.95
1242	6359	2.745482	GCTGAGATGCATGGACATGACT	60.745	50.000	15.99	10.64	41.20	3.41
1381	6514	6.037940	GCTAACCAGGCCATTAGTTAAGTTAC	59.962	42.308	17.79	1.65	32.07	2.50
1438	6571	5.296151	AGCTATAAGCCTTGCTATTGTCA	57.704	39.130	0.00	0.00	43.77	3.58
1550	6687	4.273318	AGCTCTTTGAGAAAAGGTTGTGT	58.727	39.130	0.00	0.00	0.00	3.72
1617	6754	6.742718	CACAATTTTTAGGTTAGAGATGTGCG	59.257	38.462	0.00	0.00	0.00	5.34
1668	6805	5.419760	TCAGGAGACGATGATAAACTACG	57.580	43.478	0.00	0.00	0.00	3.51
1735	6883	2.585247	GTACCGGCCAGATCACGC	60.585	66.667	0.00	0.00	0.00	5.34
1750	6898	2.717044	CCGCTGGACCATCACCGTA	61.717	63.158	0.00	0.00	0.00	4.02
1757	6907	2.045926	GAACAGCCGCTGGACCAT	60.046	61.111	24.03	5.11	35.51	3.55
1785	6972	3.195002	CGTCGCCGCCATTGATGT	61.195	61.111	0.00	0.00	0.00	3.06
1806	6993	0.389391	CCGCTCCACCACATACCTAG	59.611	60.000	0.00	0.00	0.00	3.02
1899	7086	1.664965	GGTCCATCTATGCCGACGC	60.665	63.158	0.00	0.00	0.00	5.19
1968	7155	1.244816	CCCGTCGGCATAGATAGACA	58.755	55.000	5.50	0.00	33.56	3.41
1991	7178	3.052081	GGCCTCGTCTATGCCGAT	58.948	61.111	0.00	0.00	35.08	4.18
2189	7441	4.742201	CGGAGGTGCAGTCCCACG	62.742	72.222	9.08	2.71	36.59	4.94
2273	7525	9.838339	GCATACCTCTGCCATAAATAGTATAAT	57.162	33.333	0.00	0.00	36.10	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.