AutoCloner

Multiple sequence alignment - TraesCS1D01G341400

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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	TraesCS1D01G341400	chr1D	100.000	2273	0	0	1	2273	431515447	431517719	0.000000e+00	4198
1	TraesCS1D01G341400	chr5D	97.928	1303	25	1	1	1301	240523349	240522047	0.000000e+00	2255
2	TraesCS1D01G341400	chr3D	97.771	1301	27	1	1	1299	406417575	406418875	0.000000e+00	2241
3	TraesCS1D01G341400	chr3D	97.021	1309	34	4	1	1307	570309814	570311119	0.000000e+00	2196
4	TraesCS1D01G341400	chr2D	97.320	1306	33	1	1	1304	650478413	650477108	0.000000e+00	2217
5	TraesCS1D01G341400	chr7D	96.705	1305	41	1	1	1303	554425497	554426801	0.000000e+00	2170
6	TraesCS1D01G341400	chr5A	92.781	1316	91	3	1	1313	415261550	415260236	0.000000e+00	1901
7	TraesCS1D01G341400	chr2B	87.360	1250	150	7	58	1303	109881558	109880313	0.000000e+00	1426
8	TraesCS1D01G341400	chrUn	85.911	1306	178	5	1	1302	336409522	336410825	0.000000e+00	1387
9	TraesCS1D01G341400	chr6B	84.862	1308	186	8	1	1304	67339747	67341046	0.000000e+00	1308
10	TraesCS1D01G341400	chr1A	88.866	988	45	27	1306	2270	529784768	529785713	0.000000e+00	1155
11	TraesCS1D01G341400	chr1B	85.542	581	51	20	1306	1859	582686815	582687389	5.440000e-161	577
12	TraesCS1D01G341400	chr1B	94.340	159	8	1	1306	1464	582674257	582674414	2.260000e-60	243

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	TraesCS1D01G341400	chr1D	431515447	431517719	2272	False	4198	4198	100.000	1	2273	1	chr1D.!!$F1	2272
1	TraesCS1D01G341400	chr5D	240522047	240523349	1302	True	2255	2255	97.928	1	1301	1	chr5D.!!$R1	1300
2	TraesCS1D01G341400	chr3D	406417575	406418875	1300	False	2241	2241	97.771	1	1299	1	chr3D.!!$F1	1298
3	TraesCS1D01G341400	chr3D	570309814	570311119	1305	False	2196	2196	97.021	1	1307	1	chr3D.!!$F2	1306
4	TraesCS1D01G341400	chr2D	650477108	650478413	1305	True	2217	2217	97.320	1	1304	1	chr2D.!!$R1	1303
5	TraesCS1D01G341400	chr7D	554425497	554426801	1304	False	2170	2170	96.705	1	1303	1	chr7D.!!$F1	1302
6	TraesCS1D01G341400	chr5A	415260236	415261550	1314	True	1901	1901	92.781	1	1313	1	chr5A.!!$R1	1312
7	TraesCS1D01G341400	chr2B	109880313	109881558	1245	True	1426	1426	87.360	58	1303	1	chr2B.!!$R1	1245
8	TraesCS1D01G341400	chrUn	336409522	336410825	1303	False	1387	1387	85.911	1	1302	1	chrUn.!!$F1	1301
9	TraesCS1D01G341400	chr6B	67339747	67341046	1299	False	1308	1308	84.862	1	1304	1	chr6B.!!$F1	1303
10	TraesCS1D01G341400	chr1A	529784768	529785713	945	False	1155	1155	88.866	1306	2270	1	chr1A.!!$F1	964
11	TraesCS1D01G341400	chr1B	582686815	582687389	574	False	577	577	85.542	1306	1859	1	chr1B.!!$F2	553

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
129	132	1.20002	CGTCAGAATTTCTTGCACCCC	59.8	52.381	0.0	0.0	0.0	4.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1555	1563	0.030908	GGCCTCTCTACAACGATCCG	59.969	60.0	0.0	0.0	0.0	4.18	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
28	29	1.597027	CGACCGCACTGAAACCCTT	60.597	57.895	0.00	0.00	0.00	3.95
129	132	1.200020	CGTCAGAATTTCTTGCACCCC	59.800	52.381	0.00	0.00	0.00	4.95
165	168	7.112779	CCATCCTAAATATACCACTCAATCCC	58.887	42.308	0.00	0.00	0.00	3.85
220	223	4.164796	TGGAGAAGTCGGGTATCTACACTA	59.835	45.833	0.00	0.00	29.11	2.74
285	288	3.231818	CTCTTTAGAGGAAGGGGCGATA	58.768	50.000	0.00	0.00	38.48	2.92
379	382	4.019231	GGGTATTTTGGTGGAGAGTTCTCT	60.019	45.833	8.89	1.67	42.48	3.10
674	677	2.162208	CACGGAACAATTGGACTCATGG	59.838	50.000	10.83	0.44	0.00	3.66
796	799	1.229496	TGGAGGCCACCTGAAGCTA	60.229	57.895	20.77	0.00	31.76	3.32
817	820	6.666546	AGCTAGTTGGGTCACTATAAACACTA	59.333	38.462	0.00	0.00	0.00	2.74
1083	1086	2.149578	GCTGCGCCTATCTTGAATGAT	58.850	47.619	4.18	0.00	0.00	2.45
1259	1262	1.664151	GCGGGCTGATTGTAACACTAC	59.336	52.381	0.00	0.00	0.00	2.73
1263	1266	4.498513	CGGGCTGATTGTAACACTACGATA	60.499	45.833	0.00	0.00	33.01	2.92
1455	1463	4.988598	CGGAAGCAGCACCACCGT	62.989	66.667	8.93	0.00	38.97	4.83
1509	1517	2.714991	CGCCACCTGAGCTCAGCTA	61.715	63.158	34.09	4.66	39.88	3.32
1524	1532	4.430007	CTCAGCTACATTTTAGGCGTGTA	58.570	43.478	0.00	0.00	0.00	2.90
1550	1558	7.094762	ACACTATCTTGATTTCGGTTTCCTTTC	60.095	37.037	0.00	0.00	0.00	2.62
1555	1563	7.645402	TCTTGATTTCGGTTTCCTTTCTTAAC	58.355	34.615	0.00	0.00	0.00	2.01
1573	1581	0.739561	ACGGATCGTTGTAGAGAGGC	59.260	55.000	0.00	0.00	36.35	4.70
1603	1650	3.191791	AGGCTCTCTACTTCGTTTGAGAC	59.808	47.826	0.00	0.00	32.86	3.36
1605	1652	4.321378	GGCTCTCTACTTCGTTTGAGACTT	60.321	45.833	0.00	0.00	32.86	3.01
1646	1694	2.445654	CCTGCCCTCTCCTCCTCC	60.446	72.222	0.00	0.00	0.00	4.30
1647	1695	2.445654	CTGCCCTCTCCTCCTCCC	60.446	72.222	0.00	0.00	0.00	4.30
1707	1755	3.489398	GCTCGGGCCGATCTTGTATATAG	60.489	52.174	31.23	13.99	34.61	1.31
1709	1757	4.084287	TCGGGCCGATCTTGTATATAGTT	58.916	43.478	27.46	0.00	0.00	2.24
1753	1801	3.564027	GCGTATGGCCTCGTGTGC	61.564	66.667	3.32	0.00	34.80	4.57
1781	1829	2.581354	CTTCTCACCGGAGCAGGG	59.419	66.667	9.46	0.00	41.13	4.45
1819	1867	0.470341	GGCCTTGTCCTCCTCATACC	59.530	60.000	0.00	0.00	0.00	2.73
1852	1901	0.958876	GCTCGGTGGGTTAGGGTTTG	60.959	60.000	0.00	0.00	0.00	2.93
1859	1908	4.384427	CGGTGGGTTAGGGTTTGTGTATAT	60.384	45.833	0.00	0.00	0.00	0.86
1860	1909	5.512298	GGTGGGTTAGGGTTTGTGTATATT	58.488	41.667	0.00	0.00	0.00	1.28
1861	1910	6.632219	CGGTGGGTTAGGGTTTGTGTATATTA	60.632	42.308	0.00	0.00	0.00	0.98
1862	1911	7.292319	GGTGGGTTAGGGTTTGTGTATATTAT	58.708	38.462	0.00	0.00	0.00	1.28
1863	1912	8.439172	GGTGGGTTAGGGTTTGTGTATATTATA	58.561	37.037	0.00	0.00	0.00	0.98
1930	1982	1.938861	GTCGTGCCGAGCAAAAAGA	59.061	52.632	0.00	0.00	41.47	2.52
1990	2042	2.493278	CAATGGTTTAGCAGGAACCCAG	59.507	50.000	11.77	1.21	44.73	4.45
2008	2060	3.303938	CCAGAGGTGTCTACATCATCCT	58.696	50.000	0.00	0.00	39.96	3.24
2012	2064	6.299922	CAGAGGTGTCTACATCATCCTAGTA	58.700	44.000	0.00	0.00	39.96	1.82
2023	2075	7.437713	ACATCATCCTAGTAAAATCCAGTCA	57.562	36.000	0.00	0.00	0.00	3.41
2040	2100	4.263243	CCAGTCAATCAGTTCCCTCTTTCT	60.263	45.833	0.00	0.00	0.00	2.52
2068	2128	1.203928	CATCTCGAGTCGCCAATCAC	58.796	55.000	13.13	0.00	0.00	3.06
2090	2150	1.208535	TGCCTGGTACTGAAATACGGG	59.791	52.381	0.00	0.00	0.00	5.28
2091	2151	1.483415	GCCTGGTACTGAAATACGGGA	59.517	52.381	0.00	0.00	0.00	5.14
2098	2158	5.644636	TGGTACTGAAATACGGGATTTGAAC	59.355	40.000	2.18	0.00	37.90	3.18
2100	2160	6.317893	GGTACTGAAATACGGGATTTGAACAT	59.682	38.462	2.18	0.00	37.90	2.71
2120	2180	3.708563	TTTTGGCTTCACTTTCCTTCG	57.291	42.857	0.00	0.00	0.00	3.79
2123	2183	2.925724	TGGCTTCACTTTCCTTCGAAA	58.074	42.857	0.00	0.00	36.55	3.46
2128	2188	5.586643	GGCTTCACTTTCCTTCGAAATATCT	59.413	40.000	0.00	0.00	37.36	1.98
2168	2228	6.843752	TGACCTTTATTTTTCAGGGTCTACA	58.156	36.000	10.58	0.00	42.37	2.74
2242	2305	5.007332	CAGTCGATTGATCTGCAAATGATGA	59.993	40.000	0.86	0.00	40.48	2.92
2247	2310	2.626266	TGATCTGCAAATGATGATGGCC	59.374	45.455	0.00	0.00	0.00	5.36
2270	2333	1.134159	CAGCAGAAAGGGATAGCAGCT	60.134	52.381	0.00	0.00	0.00	4.24
2271	2334	1.563410	AGCAGAAAGGGATAGCAGCTT	59.437	47.619	0.00	0.00	0.00	3.74
2272	2335	2.025510	AGCAGAAAGGGATAGCAGCTTT	60.026	45.455	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
129	132	2.067091	TTAGGATGGCTACCGCGTCG	62.067	60.000	4.92	0.00	36.88	5.12
165	168	0.108329	AAGTATCTTCACCACCCGCG	60.108	55.000	0.00	0.00	0.00	6.46
220	223	4.938080	AGAGAACGATACGCTGATTTCAT	58.062	39.130	0.00	0.00	0.00	2.57
285	288	4.645535	TGTTAGCTGATGAAGTTTCTGCT	58.354	39.130	12.03	12.03	46.20	4.24
379	382	2.775960	TCGAGTCAGGTAGTATCCCTCA	59.224	50.000	0.00	0.00	0.00	3.86
796	799	6.161381	CGTTAGTGTTTATAGTGACCCAACT	58.839	40.000	0.00	0.00	0.00	3.16
817	820	0.668096	TCGACATTAAGTGCGCCGTT	60.668	50.000	4.18	0.00	0.00	4.44
1083	1086	5.514500	AGGTAGCACCAATTTCCTCTAAA	57.486	39.130	7.86	0.00	41.95	1.85
1259	1262	9.507280	TTCAGGAACTTTATTAACGTAGTATCG	57.493	33.333	0.00	0.00	35.77	2.92
1263	1266	8.866956	CGAATTCAGGAACTTTATTAACGTAGT	58.133	33.333	6.22	0.00	40.06	2.73
1304	1307	2.035961	GGGAAAGTGAAAGGCAAGTTCC	59.964	50.000	0.00	0.00	39.39	3.62
1455	1463	2.309528	AGATCGACGCAAGCCAAATA	57.690	45.000	0.00	0.00	45.62	1.40
1509	1517	5.974108	AGATAGTGTACACGCCTAAAATGT	58.026	37.500	19.93	1.50	36.20	2.71
1524	1532	5.805728	AGGAAACCGAAATCAAGATAGTGT	58.194	37.500	0.00	0.00	0.00	3.55
1555	1563	0.030908	GGCCTCTCTACAACGATCCG	59.969	60.000	0.00	0.00	0.00	4.18
1573	1581	0.749649	AGTAGAGAGCCTCGCAATGG	59.250	55.000	0.00	0.00	35.36	3.16
1603	1650	4.393990	GGGTAAAGTGGTAAACCGATCAAG	59.606	45.833	0.00	0.00	39.43	3.02
1605	1652	3.307621	GGGGTAAAGTGGTAAACCGATCA	60.308	47.826	0.00	0.00	39.43	2.92
1707	1755	4.576053	ACGGAAGTACAAACCTAAACCAAC	59.424	41.667	0.00	0.00	46.88	3.77
1709	1757	4.420522	ACGGAAGTACAAACCTAAACCA	57.579	40.909	0.00	0.00	46.88	3.67
1727	1775	3.713963	GCCATACGCCACTAACGG	58.286	61.111	0.00	0.00	34.00	4.44
1751	1799	1.279271	GTGAGAAGCTCCCTAAAGGCA	59.721	52.381	0.00	0.00	34.51	4.75
1752	1800	1.407575	GGTGAGAAGCTCCCTAAAGGC	60.408	57.143	0.00	0.00	34.51	4.35
1753	1801	1.134670	CGGTGAGAAGCTCCCTAAAGG	60.135	57.143	0.00	0.00	0.00	3.11
1754	1802	1.134670	CCGGTGAGAAGCTCCCTAAAG	60.135	57.143	0.00	0.00	0.00	1.85
1806	1854	1.797211	CGAGGCGGTATGAGGAGGAC	61.797	65.000	0.00	0.00	0.00	3.85
1819	1867	4.213700	GAGCTTATCGACGAGGCG	57.786	61.111	3.01	0.00	0.00	5.52
1863	1912	9.811995	TCGACTGTGCTTAAAATAATACAGTAT	57.188	29.630	14.73	0.00	46.01	2.12
1864	1913	9.642327	TTCGACTGTGCTTAAAATAATACAGTA	57.358	29.630	14.73	0.00	46.01	2.74
1866	1915	8.656849	ACTTCGACTGTGCTTAAAATAATACAG	58.343	33.333	0.00	0.00	40.84	2.74
1867	1916	8.542497	ACTTCGACTGTGCTTAAAATAATACA	57.458	30.769	0.00	0.00	0.00	2.29
1868	1917	8.653338	TGACTTCGACTGTGCTTAAAATAATAC	58.347	33.333	0.00	0.00	0.00	1.89
1869	1918	8.766000	TGACTTCGACTGTGCTTAAAATAATA	57.234	30.769	0.00	0.00	0.00	0.98
1870	1919	7.667043	TGACTTCGACTGTGCTTAAAATAAT	57.333	32.000	0.00	0.00	0.00	1.28
1871	1920	7.225931	AGTTGACTTCGACTGTGCTTAAAATAA	59.774	33.333	0.00	0.00	39.07	1.40
1915	1967	2.704725	TCAATCTTTTTGCTCGGCAC	57.295	45.000	0.00	0.00	38.71	5.01
1930	1982	8.892723	TCAGCGTATTCTTGTGAATAAATCAAT	58.107	29.630	0.76	0.00	44.04	2.57
1990	2042	7.584122	TTTACTAGGATGATGTAGACACCTC	57.416	40.000	0.00	0.00	0.00	3.85
2008	2060	7.037586	AGGGAACTGATTGACTGGATTTTACTA	60.038	37.037	0.00	0.00	41.13	1.82
2012	2064	5.003096	AGGGAACTGATTGACTGGATTTT	57.997	39.130	0.00	0.00	41.13	1.82
2023	2075	4.599241	TGGAAGAGAAAGAGGGAACTGATT	59.401	41.667	0.00	0.00	44.43	2.57
2040	2100	1.950216	CGACTCGAGATGGATGGAAGA	59.050	52.381	21.68	0.00	0.00	2.87
2068	2128	2.936498	CCGTATTTCAGTACCAGGCAAG	59.064	50.000	0.00	0.00	0.00	4.01
2090	2150	6.849588	AAGTGAAGCCAAAATGTTCAAATC	57.150	33.333	0.00	0.00	32.15	2.17
2091	2151	6.260714	GGAAAGTGAAGCCAAAATGTTCAAAT	59.739	34.615	0.00	0.00	32.15	2.32
2098	2158	3.983344	CGAAGGAAAGTGAAGCCAAAATG	59.017	43.478	0.00	0.00	0.00	2.32
2100	2160	3.283751	TCGAAGGAAAGTGAAGCCAAAA	58.716	40.909	0.00	0.00	0.00	2.44
2123	2183	8.535335	AGGTCAATGATATTTACTCGCAGATAT	58.465	33.333	0.00	0.00	33.89	1.63
2128	2188	8.902540	ATAAAGGTCAATGATATTTACTCGCA	57.097	30.769	5.41	0.00	0.00	5.10
2162	2222	7.148052	ACAGTCACCAGTATGTAGATTGTAGAC	60.148	40.741	0.00	0.00	36.62	2.59
2168	2228	5.717178	ACTCACAGTCACCAGTATGTAGATT	59.283	40.000	0.00	0.00	0.00	2.40
2215	2278	5.587443	TCATTTGCAGATCAATCGACTGAAT	59.413	36.000	0.00	0.00	34.12	2.57
2242	2305	1.377725	CCTTTCTGCTGTCGGCCAT	60.378	57.895	2.24	0.00	40.92	4.40
2247	2310	1.134699	TGCTATCCCTTTCTGCTGTCG	60.135	52.381	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.