AutoCloner

Multiple sequence alignment - TraesCS5B01G443800

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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	TraesCS5B01G443800	chr5B	100.000	2498	0	0	1	2498	616331941	616334438	0.000000e+00	4614
1	TraesCS5B01G443800	chr5B	92.568	2395	115	27	1	2365	616309573	616311934	0.000000e+00	3378
2	TraesCS5B01G443800	chr5B	92.526	2395	116	27	1	2365	616321209	616323570	0.000000e+00	3373
3	TraesCS5B01G443800	chr5B	92.317	2395	121	27	1	2365	616275645	616278006	0.000000e+00	3345
4	TraesCS5B01G443800	chr5B	92.282	2397	118	30	1	2365	616264724	616267085	0.000000e+00	3339
5	TraesCS5B01G443800	chr5B	92.205	2386	121	29	1	2356	616244961	616247311	0.000000e+00	3315
6	TraesCS5B01G443800	chr5B	92.079	2386	123	30	1	2356	616298643	616300992	0.000000e+00	3299
7	TraesCS5B01G443800	chr5B	90.974	1673	108	21	701	2365	616223107	616224744	0.000000e+00	2213
8	TraesCS5B01G443800	chr5B	93.610	1158	63	8	1	1154	616103275	616104425	0.000000e+00	1718
9	TraesCS5B01G443800	chr5B	93.733	1133	61	7	1	1130	615965934	615964809	0.000000e+00	1690
10	TraesCS5B01G443800	chrUn	90.461	1845	110	27	701	2498	345125408	345127233	0.000000e+00	2372
11	TraesCS5B01G443800	chrUn	91.716	1690	99	17	701	2368	335556040	335554370	0.000000e+00	2307
12	TraesCS5B01G443800	chrUn	87.194	1062	81	22	1475	2498	391883988	391882944	0.000000e+00	1157
13	TraesCS5B01G443800	chrUn	95.157	702	29	4	1	701	335556767	335556070	0.000000e+00	1103
14	TraesCS5B01G443800	chrUn	84.211	418	30	14	2103	2498	461819503	461819906	8.440000e-100	374
15	TraesCS5B01G443800	chrUn	91.729	133	11	0	2366	2498	361546277	361546145	4.240000e-43	185
16	TraesCS5B01G443800	chr5A	86.389	1778	151	42	701	2434	621444001	621445731	0.000000e+00	1858
17	TraesCS5B01G443800	chr5D	87.123	1095	89	15	1439	2498	497367789	497366712	0.000000e+00	1194

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	TraesCS5B01G443800	chr5B	616331941	616334438	2497	False	4614	4614	100.0000	1	2498	1	chr5B.!!$F9	2497
1	TraesCS5B01G443800	chr5B	616309573	616311934	2361	False	3378	3378	92.5680	1	2365	1	chr5B.!!$F7	2364
2	TraesCS5B01G443800	chr5B	616321209	616323570	2361	False	3373	3373	92.5260	1	2365	1	chr5B.!!$F8	2364
3	TraesCS5B01G443800	chr5B	616275645	616278006	2361	False	3345	3345	92.3170	1	2365	1	chr5B.!!$F5	2364
4	TraesCS5B01G443800	chr5B	616264724	616267085	2361	False	3339	3339	92.2820	1	2365	1	chr5B.!!$F4	2364
5	TraesCS5B01G443800	chr5B	616244961	616247311	2350	False	3315	3315	92.2050	1	2356	1	chr5B.!!$F3	2355
6	TraesCS5B01G443800	chr5B	616298643	616300992	2349	False	3299	3299	92.0790	1	2356	1	chr5B.!!$F6	2355
7	TraesCS5B01G443800	chr5B	616223107	616224744	1637	False	2213	2213	90.9740	701	2365	1	chr5B.!!$F2	1664
8	TraesCS5B01G443800	chr5B	616103275	616104425	1150	False	1718	1718	93.6100	1	1154	1	chr5B.!!$F1	1153
9	TraesCS5B01G443800	chr5B	615964809	615965934	1125	True	1690	1690	93.7330	1	1130	1	chr5B.!!$R1	1129
10	TraesCS5B01G443800	chrUn	345125408	345127233	1825	False	2372	2372	90.4610	701	2498	1	chrUn.!!$F1	1797
11	TraesCS5B01G443800	chrUn	335554370	335556767	2397	True	1705	2307	93.4365	1	2368	2	chrUn.!!$R3	2367
12	TraesCS5B01G443800	chrUn	391882944	391883988	1044	True	1157	1157	87.1940	1475	2498	1	chrUn.!!$R2	1023
13	TraesCS5B01G443800	chr5A	621444001	621445731	1730	False	1858	1858	86.3890	701	2434	1	chr5A.!!$F1	1733
14	TraesCS5B01G443800	chr5D	497366712	497367789	1077	True	1194	1194	87.1230	1439	2498	1	chr5D.!!$R1	1059

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
783	820	1.007336	CAGGCCGCGGACGATTATAC	61.007	60.0	33.48	7.28	43.93	1.47	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1948	2023	0.03213	GCGATCGAAGTGGCCTATGA	59.968	55.0	21.57	0.0	0.0	2.15	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
123	124	1.586154	CGAAAAAGCTCACGCCCCAT	61.586	55.000	0.00	0.00	36.60	4.00
205	206	5.030936	GGTTAAATCAATCTCGCTTGAAGC	58.969	41.667	7.20	7.20	38.55	3.86
461	464	6.266323	AGCTACTCATATATTATCGCCAACG	58.734	40.000	0.00	0.00	42.01	4.10
783	820	1.007336	CAGGCCGCGGACGATTATAC	61.007	60.000	33.48	7.28	43.93	1.47
910	947	1.402613	CAATCGATCATGTGCAGGCAA	59.597	47.619	0.00	0.00	0.00	4.52
1216	1256	1.001860	GCCAGCTGATCCATACTCCTC	59.998	57.143	17.39	0.00	0.00	3.71
1647	1711	6.169557	TGACGCCATATATTGTTTAGACCT	57.830	37.500	0.00	0.00	0.00	3.85
1757	1829	3.079960	ACTGAGTATGGTATTCGTGCG	57.920	47.619	0.00	0.00	0.00	5.34
1758	1830	1.787155	CTGAGTATGGTATTCGTGCGC	59.213	52.381	0.00	0.00	0.00	6.09
1759	1831	0.776451	GAGTATGGTATTCGTGCGCG	59.224	55.000	14.79	14.79	39.92	6.86
1762	1834	0.311477	TATGGTATTCGTGCGCGCTA	59.689	50.000	33.29	16.09	38.14	4.26
1763	1835	0.319555	ATGGTATTCGTGCGCGCTAT	60.320	50.000	33.29	20.72	38.14	2.97
1765	1837	1.487231	GTATTCGTGCGCGCTATGG	59.513	57.895	33.29	17.85	38.14	2.74
1766	1838	0.937699	GTATTCGTGCGCGCTATGGA	60.938	55.000	33.29	19.87	38.14	3.41
1770	1843	2.860628	CGTGCGCGCTATGGAGAAC	61.861	63.158	33.29	17.93	0.00	3.01
1774	1849	0.446222	GCGCGCTATGGAGAACAAAA	59.554	50.000	26.67	0.00	0.00	2.44
1784	1859	4.829064	TGGAGAACAAAACAGCATACAC	57.171	40.909	0.00	0.00	0.00	2.90
1798	1873	6.446318	ACAGCATACACAAAAACCACTAATG	58.554	36.000	0.00	0.00	0.00	1.90
1817	1892	8.233190	CACTAATGAAAGTGTCTTTCTTCCATC	58.767	37.037	18.64	0.00	41.63	3.51
1844	1919	5.809562	GTCATCTCACACTTGTTCTCTATGG	59.190	44.000	0.00	0.00	0.00	2.74
1853	1928	6.874134	ACACTTGTTCTCTATGGTGTGTATTC	59.126	38.462	0.00	0.00	36.70	1.75
1878	1953	4.735662	TTTTTGAATCCCAACTCGTACG	57.264	40.909	9.53	9.53	33.85	3.67
1900	1975	3.128242	GGACAAACGGAGTAGATCTCGAA	59.872	47.826	0.00	0.00	45.00	3.71
1906	1981	1.341852	GGAGTAGATCTCGAAAGGGCC	59.658	57.143	0.00	0.00	43.60	5.80
1938	2013	0.411452	TTCCTGAGACTCCTGCTCCT	59.589	55.000	0.00	0.00	0.00	3.69
1939	2014	0.033601	TCCTGAGACTCCTGCTCCTC	60.034	60.000	0.00	0.00	0.00	3.71
1948	2023	3.790437	CTGCTCCTCCCACCGCAT	61.790	66.667	0.00	0.00	0.00	4.73
1960	2035	0.464373	CACCGCATCATAGGCCACTT	60.464	55.000	5.01	0.00	0.00	3.16
1964	2039	1.606480	CGCATCATAGGCCACTTCGAT	60.606	52.381	5.01	0.00	0.00	3.59
2024	2099	1.544825	CCTCCCAGGTTTCGCTCTGA	61.545	60.000	0.00	0.00	33.11	3.27
2030	2105	1.734465	CAGGTTTCGCTCTGAATCCAC	59.266	52.381	7.31	0.00	45.30	4.02
2036	2111	0.250234	CGCTCTGAATCCACCTCCAA	59.750	55.000	0.00	0.00	0.00	3.53
2041	2116	1.299976	GAATCCACCTCCAACCGCT	59.700	57.895	0.00	0.00	0.00	5.52
2144	2219	1.102222	GTAGATCTGGCCTCGACGGT	61.102	60.000	5.18	0.00	34.25	4.83
2155	2230	2.885644	CGACGGTGCGAATCCTGG	60.886	66.667	0.00	0.00	0.00	4.45
2157	2232	3.950794	GACGGTGCGAATCCTGGCA	62.951	63.158	0.00	0.00	36.70	4.92
2173	2248	1.153549	GCACGTGGAGAGTCATCCC	60.154	63.158	18.88	0.00	38.72	3.85
2174	2249	1.888436	GCACGTGGAGAGTCATCCCA	61.888	60.000	18.88	0.00	38.72	4.37
2175	2250	0.826715	CACGTGGAGAGTCATCCCAT	59.173	55.000	7.95	0.00	38.72	4.00
2176	2251	0.826715	ACGTGGAGAGTCATCCCATG	59.173	55.000	13.59	13.59	38.72	3.66
2177	2252	0.531532	CGTGGAGAGTCATCCCATGC	60.532	60.000	0.00	0.00	38.72	4.06
2210	2285	3.378512	TGCCTGTGATACTCCAGATCTT	58.621	45.455	0.00	0.00	0.00	2.40
2223	2298	2.124151	ATCTTGGCGCATCACCCC	60.124	61.111	10.83	0.00	0.00	4.95
2232	2307	1.224592	GCATCACCCCGGATTGAGT	59.775	57.895	0.73	0.00	0.00	3.41
2242	2317	0.108186	CGGATTGAGTAGCAGTGCCA	60.108	55.000	12.58	0.00	0.00	4.92
2263	2338	2.127271	AAATCCATCGTGGTCATGCA	57.873	45.000	0.00	0.00	39.03	3.96
2273	2348	2.821366	GTCATGCACTCCGCCCTG	60.821	66.667	0.00	0.00	41.33	4.45
2333	2409	4.966805	ACGGAGGTCTAATCCAAAGGAATA	59.033	41.667	0.00	0.00	36.57	1.75
2334	2410	5.070580	ACGGAGGTCTAATCCAAAGGAATAG	59.929	44.000	2.39	2.39	36.74	1.73
2442	2539	1.202290	CGCTTCAAAGGCAAGTGTTGT	60.202	47.619	0.00	0.00	0.00	3.32
2474	2571	7.122650	CCTTAGCAAACATTATTGGAGAAAGGA	59.877	37.037	0.00	0.00	31.06	3.36
2479	2576	4.922206	ACATTATTGGAGAAAGGACAGCA	58.078	39.130	0.00	0.00	0.00	4.41
2490	2587	2.548464	AGGACAGCAGAGATCCTCTT	57.452	50.000	0.00	0.00	38.55	2.85
2491	2588	2.387757	AGGACAGCAGAGATCCTCTTC	58.612	52.381	0.00	0.00	38.55	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
783	820	1.805945	GCGCGTTGAGGTAGTCAGG	60.806	63.158	8.43	0.00	36.21	3.86
910	947	6.702723	ACCATGCGTACGTTGTGTATTTATAT	59.297	34.615	17.90	0.00	35.02	0.86
1609	1673	3.711814	TCAAATCCGGCCGGCTGA	61.712	61.111	39.89	33.29	34.68	4.26
1647	1711	9.797556	GAATCATAACGGTACATATATACAGCA	57.202	33.333	0.00	0.00	0.00	4.41
1752	1824	2.582226	TTCTCCATAGCGCGCACG	60.582	61.111	35.10	20.25	44.07	5.34
1757	1829	2.729156	GCTGTTTTGTTCTCCATAGCGC	60.729	50.000	0.00	0.00	0.00	5.92
1758	1830	2.483877	TGCTGTTTTGTTCTCCATAGCG	59.516	45.455	0.00	0.00	32.88	4.26
1759	1831	4.708726	ATGCTGTTTTGTTCTCCATAGC	57.291	40.909	0.00	0.00	0.00	2.97
1762	1834	4.826733	TGTGTATGCTGTTTTGTTCTCCAT	59.173	37.500	0.00	0.00	0.00	3.41
1763	1835	4.203226	TGTGTATGCTGTTTTGTTCTCCA	58.797	39.130	0.00	0.00	0.00	3.86
1765	1837	7.391016	GTTTTTGTGTATGCTGTTTTGTTCTC	58.609	34.615	0.00	0.00	0.00	2.87
1766	1838	6.312672	GGTTTTTGTGTATGCTGTTTTGTTCT	59.687	34.615	0.00	0.00	0.00	3.01
1770	1843	5.580297	AGTGGTTTTTGTGTATGCTGTTTTG	59.420	36.000	0.00	0.00	0.00	2.44
1774	1849	6.264292	TCATTAGTGGTTTTTGTGTATGCTGT	59.736	34.615	0.00	0.00	0.00	4.40
1798	1873	6.260936	TGACAAGATGGAAGAAAGACACTTTC	59.739	38.462	14.05	14.05	0.00	2.62
1817	1892	5.295950	AGAGAACAAGTGTGAGATGACAAG	58.704	41.667	0.00	0.00	0.00	3.16
1863	1938	1.259609	TGTCCGTACGAGTTGGGATT	58.740	50.000	18.76	0.00	0.00	3.01
1878	1953	2.681848	TCGAGATCTACTCCGTTTGTCC	59.318	50.000	0.00	0.00	42.18	4.02
1900	1975	2.764547	GAGACCTAGCGGGCCCTT	60.765	66.667	22.43	10.84	40.21	3.95
1906	1981	1.030488	TCAGGAACGAGACCTAGCGG	61.030	60.000	0.00	0.00	35.84	5.52
1931	2006	3.746949	GATGCGGTGGGAGGAGCAG	62.747	68.421	0.00	0.00	43.20	4.24
1938	2013	2.818169	GGCCTATGATGCGGTGGGA	61.818	63.158	0.00	0.00	0.00	4.37
1939	2014	2.281761	GGCCTATGATGCGGTGGG	60.282	66.667	0.00	0.00	0.00	4.61
1947	2022	1.337260	GCGATCGAAGTGGCCTATGAT	60.337	52.381	21.57	0.00	0.00	2.45
1948	2023	0.032130	GCGATCGAAGTGGCCTATGA	59.968	55.000	21.57	0.00	0.00	2.15
2024	2099	1.002134	CAGCGGTTGGAGGTGGATT	60.002	57.895	0.00	0.00	33.87	3.01
2030	2105	1.746615	CATGGACAGCGGTTGGAGG	60.747	63.158	0.00	0.00	0.00	4.30
2036	2111	2.982130	GAGACCATGGACAGCGGT	59.018	61.111	21.47	0.00	35.12	5.68
2041	2116	0.320683	CTTGCACGAGACCATGGACA	60.321	55.000	21.47	1.67	0.00	4.02
2144	2219	2.741985	CACGTGCCAGGATTCGCA	60.742	61.111	0.82	0.00	0.00	5.10
2155	2230	1.153549	GGGATGACTCTCCACGTGC	60.154	63.158	10.91	0.00	37.01	5.34
2157	2232	0.826715	CATGGGATGACTCTCCACGT	59.173	55.000	0.00	0.00	37.01	4.49
2160	2235	0.621280	TGGCATGGGATGACTCTCCA	60.621	55.000	0.00	0.00	39.69	3.86
2223	2298	0.108186	TGGCACTGCTACTCAATCCG	60.108	55.000	0.00	0.00	0.00	4.18
2232	2307	2.423185	CGATGGATTTTTGGCACTGCTA	59.577	45.455	0.00	0.00	0.00	3.49
2242	2317	2.824936	TGCATGACCACGATGGATTTTT	59.175	40.909	10.46	0.00	40.96	1.94
2263	2338	1.779061	AATGTTGACCAGGGCGGAGT	61.779	55.000	0.00	0.00	38.63	3.85
2333	2409	1.963338	GCTCCTTGCTTGTGCGTCT	60.963	57.895	0.00	0.00	43.34	4.18
2334	2410	2.558313	GCTCCTTGCTTGTGCGTC	59.442	61.111	0.00	0.00	43.34	5.19
2337	2413	1.509923	GATGGCTCCTTGCTTGTGC	59.490	57.895	0.00	0.00	42.39	4.57
2419	2516	2.259511	CTTGCCTTTGAAGCGGCC	59.740	61.111	0.00	0.00	45.71	6.13
2460	2557	4.532126	TCTCTGCTGTCCTTTCTCCAATAA	59.468	41.667	0.00	0.00	0.00	1.40
2463	2560	2.329267	TCTCTGCTGTCCTTTCTCCAA	58.671	47.619	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.