AutoCloner

Multiple sequence alignment - TraesCS4B01G352500

Loading Multiple Alignment...

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	TraesCS4B01G352500	chr4B	100.000	2264	0	0	1	2264	644496818	644494555	0.000000e+00	4181.0
1	TraesCS4B01G352500	chr4B	90.983	987	76	10	1	975	111310987	111310002	0.000000e+00	1317.0
2	TraesCS4B01G352500	chr4B	90.836	993	71	11	1	976	241125365	241126354	0.000000e+00	1312.0
3	TraesCS4B01G352500	chr2B	88.352	1305	117	16	975	2264	71642504	71641220	0.000000e+00	1535.0
4	TraesCS4B01G352500	chr2B	87.811	1247	119	24	975	2197	292848383	292849620	0.000000e+00	1430.0
5	TraesCS4B01G352500	chr2B	90.539	909	83	1	975	1883	15207531	15206626	0.000000e+00	1199.0
6	TraesCS4B01G352500	chr2B	89.486	428	30	7	1345	1764	465663749	465663329	5.540000e-146	527.0
7	TraesCS4B01G352500	chr2B	79.109	359	52	15	1835	2191	71641301	71641638	2.260000e-55	226.0
8	TraesCS4B01G352500	chr1B	87.966	1313	110	18	975	2264	449941868	449943155	0.000000e+00	1506.0
9	TraesCS4B01G352500	chr1B	82.749	371	42	16	1838	2194	449943071	449942709	6.070000e-81	311.0
10	TraesCS4B01G352500	chr7B	93.103	986	57	7	1	975	103807351	103808336	0.000000e+00	1434.0
11	TraesCS4B01G352500	chr3B	90.198	1061	83	11	975	2021	548880065	548881118	0.000000e+00	1363.0
12	TraesCS4B01G352500	chrUn	90.323	992	76	13	1	977	228649025	228650011	0.000000e+00	1282.0
13	TraesCS4B01G352500	chrUn	90.222	992	76	14	1	977	197452663	197453648	0.000000e+00	1275.0
14	TraesCS4B01G352500	chr1D	90.323	992	76	13	1	977	489368191	489369177	0.000000e+00	1282.0
15	TraesCS4B01G352500	chr1D	93.205	780	52	1	975	1753	198509559	198510338	0.000000e+00	1146.0
16	TraesCS4B01G352500	chr5D	90.336	983	77	13	4	975	315591318	315590343	0.000000e+00	1273.0
17	TraesCS4B01G352500	chr3D	89.394	990	79	15	977	1943	116062491	116063477	0.000000e+00	1223.0
18	TraesCS4B01G352500	chr6D	88.889	990	92	8	1	975	375659229	375660215	0.000000e+00	1203.0
19	TraesCS4B01G352500	chr6D	91.435	829	63	5	975	1795	471961950	471962778	0.000000e+00	1131.0
20	TraesCS4B01G352500	chr6D	91.435	829	63	5	975	1795	472012129	472012957	0.000000e+00	1131.0
21	TraesCS4B01G352500	chr6D	100.000	28	0	0	2126	2153	471945826	471945799	4.000000e-03	52.8
22	TraesCS4B01G352500	chr5B	87.792	983	97	11	1	975	134341906	134340939	0.000000e+00	1129.0
23	TraesCS4B01G352500	chr6A	82.982	758	76	19	1226	1942	466153196	466153941	8.820000e-179	636.0
24	TraesCS4B01G352500	chr6B	86.667	105	12	2	2088	2191	702990495	702990598	5.110000e-22	115.0

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	TraesCS4B01G352500	chr4B	644494555	644496818	2263	True	4181	4181	100.000	1	2264	1	chr4B.!!$R2	2263
1	TraesCS4B01G352500	chr4B	111310002	111310987	985	True	1317	1317	90.983	1	975	1	chr4B.!!$R1	974
2	TraesCS4B01G352500	chr4B	241125365	241126354	989	False	1312	1312	90.836	1	976	1	chr4B.!!$F1	975
3	TraesCS4B01G352500	chr2B	71641220	71642504	1284	True	1535	1535	88.352	975	2264	1	chr2B.!!$R2	1289
4	TraesCS4B01G352500	chr2B	292848383	292849620	1237	False	1430	1430	87.811	975	2197	1	chr2B.!!$F2	1222
5	TraesCS4B01G352500	chr2B	15206626	15207531	905	True	1199	1199	90.539	975	1883	1	chr2B.!!$R1	908
6	TraesCS4B01G352500	chr1B	449941868	449943155	1287	False	1506	1506	87.966	975	2264	1	chr1B.!!$F1	1289
7	TraesCS4B01G352500	chr7B	103807351	103808336	985	False	1434	1434	93.103	1	975	1	chr7B.!!$F1	974
8	TraesCS4B01G352500	chr3B	548880065	548881118	1053	False	1363	1363	90.198	975	2021	1	chr3B.!!$F1	1046
9	TraesCS4B01G352500	chrUn	228649025	228650011	986	False	1282	1282	90.323	1	977	1	chrUn.!!$F2	976
10	TraesCS4B01G352500	chrUn	197452663	197453648	985	False	1275	1275	90.222	1	977	1	chrUn.!!$F1	976
11	TraesCS4B01G352500	chr1D	489368191	489369177	986	False	1282	1282	90.323	1	977	1	chr1D.!!$F2	976
12	TraesCS4B01G352500	chr1D	198509559	198510338	779	False	1146	1146	93.205	975	1753	1	chr1D.!!$F1	778
13	TraesCS4B01G352500	chr5D	315590343	315591318	975	True	1273	1273	90.336	4	975	1	chr5D.!!$R1	971
14	TraesCS4B01G352500	chr3D	116062491	116063477	986	False	1223	1223	89.394	977	1943	1	chr3D.!!$F1	966
15	TraesCS4B01G352500	chr6D	375659229	375660215	986	False	1203	1203	88.889	1	975	1	chr6D.!!$F1	974
16	TraesCS4B01G352500	chr6D	471961950	471962778	828	False	1131	1131	91.435	975	1795	1	chr6D.!!$F2	820
17	TraesCS4B01G352500	chr6D	472012129	472012957	828	False	1131	1131	91.435	975	1795	1	chr6D.!!$F3	820
18	TraesCS4B01G352500	chr5B	134340939	134341906	967	True	1129	1129	87.792	1	975	1	chr5B.!!$R1	974
19	TraesCS4B01G352500	chr6A	466153196	466153941	745	False	636	636	82.982	1226	1942	1	chr6A.!!$F1	716

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
464	477	0.90961	TCGGAGAGGCCTTGGTGATT	60.91	55.0	6.77	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1888	2027	0.252375	AACAACCTACCGCTAGGGGA	60.252	55.0	31.0	14.1	43.87	4.81	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
31	32	8.446714	AGATGACATGATGTAGAGGGATAAAT	57.553	34.615	0.00	0.00	0.00	1.40
74	75	4.446311	CCCCATCTTTTTATCCTCGATGGT	60.446	45.833	13.64	0.00	46.05	3.55
305	307	4.594970	TCATAAACCCACAATTCATCGGT	58.405	39.130	0.00	0.00	0.00	4.69
464	477	0.909610	TCGGAGAGGCCTTGGTGATT	60.910	55.000	6.77	0.00	0.00	2.57
520	533	2.358737	AGCACCGGAAAAGGCTCG	60.359	61.111	9.46	0.00	33.69	5.03
592	605	2.790433	GTGGTGCTCCTGGATGTTTTA	58.210	47.619	6.34	0.00	34.23	1.52
606	621	7.421382	CCTGGATGTTTTAGGGGTATGTAGATT	60.421	40.741	0.00	0.00	0.00	2.40
731	754	1.249407	GACGTCCACTCCAAGTCTCT	58.751	55.000	3.51	0.00	0.00	3.10
855	883	2.543797	AATTCGGGTTGGGCCTCCA	61.544	57.895	17.27	0.00	42.25	3.86
1061	1090	1.538512	CCAAGAAGACATGCCACACAG	59.461	52.381	0.00	0.00	0.00	3.66
1149	1179	4.072131	GAGATGTTTGCAAGGTGAAGGTA	58.928	43.478	0.00	0.00	0.00	3.08
1191	1221	2.385803	TGGACGGAAGGAAGGAGATAC	58.614	52.381	0.00	0.00	0.00	2.24
1211	1241	4.316025	ACTTTGTATGCCCCAACTATGT	57.684	40.909	0.00	0.00	0.00	2.29
1319	1350	6.832520	ACACTACATCCATTTTGTATGCAA	57.167	33.333	0.00	0.00	0.00	4.08
1326	1357	3.761218	TCCATTTTGTATGCAATCACCGT	59.239	39.130	0.00	0.00	34.18	4.83
1337	1368	2.362397	GCAATCACCGTCTCCTCTATGA	59.638	50.000	0.00	0.00	0.00	2.15
1363	1394	7.002250	AGTACTTCACATGGATAGATCATGG	57.998	40.000	0.00	0.00	44.42	3.66
1504	1535	1.816863	AAGCAACGCGAGGAGGAGAA	61.817	55.000	15.93	0.00	0.00	2.87
1507	1538	1.304217	AACGCGAGGAGGAGAAGGA	60.304	57.895	15.93	0.00	0.00	3.36
1550	1584	0.988063	AGGAGGAGAGGGCAAGAAAC	59.012	55.000	0.00	0.00	0.00	2.78
1553	1587	0.695347	AGGAGAGGGCAAGAAACCTG	59.305	55.000	0.00	0.00	37.18	4.00
1583	1617	1.298014	CAAGGCACCTGAGGAGGAC	59.702	63.158	4.99	0.00	42.93	3.85
1610	1644	2.105821	ACGTGACAAGAAGGGGAAATGA	59.894	45.455	0.00	0.00	0.00	2.57
1650	1684	0.250295	CCTTCGCTTTGGTGGACTCA	60.250	55.000	0.00	0.00	0.00	3.41
1678	1712	2.484062	CGGATGAAGCCATGCCACC	61.484	63.158	0.00	0.00	37.79	4.61
1697	1731	8.481492	TGCCACCTTTATCATTTATCATGAAT	57.519	30.769	0.00	0.00	0.00	2.57
1806	1915	6.974048	TGTCAACAATTTCTGTGATTTGTCAG	59.026	34.615	0.00	0.00	38.67	3.51
1809	1918	6.092955	ACAATTTCTGTGATTTGTCAGCAT	57.907	33.333	0.00	0.00	36.69	3.79
1854	1993	2.356125	GCTAAGATGAGGGGCAGAACAA	60.356	50.000	0.00	0.00	0.00	2.83
1862	2001	2.570302	GAGGGGCAGAACAAAGTAGGTA	59.430	50.000	0.00	0.00	0.00	3.08
1888	2027	7.034967	TCTATTTTAAACCCTACCACCACAT	57.965	36.000	0.00	0.00	0.00	3.21
1894	2033	0.030501	CCCTACCACCACATCCCCTA	60.031	60.000	0.00	0.00	0.00	3.53
1918	2057	4.563404	GGTTGTTGAACCCGACCA	57.437	55.556	7.47	0.00	45.48	4.02
1943	2082	3.416880	CCATGGCGGTAAGGGGGT	61.417	66.667	0.00	0.00	0.00	4.95
1945	2084	3.416880	ATGGCGGTAAGGGGGTGG	61.417	66.667	0.00	0.00	0.00	4.61
1949	2088	3.642503	CGGTAAGGGGGTGGCACA	61.643	66.667	20.82	0.00	0.00	4.57
1951	2090	2.228480	GGTAAGGGGGTGGCACAGA	61.228	63.158	20.82	0.00	41.80	3.41
1952	2091	1.571773	GGTAAGGGGGTGGCACAGAT	61.572	60.000	20.82	3.03	41.80	2.90
1953	2092	1.209621	GTAAGGGGGTGGCACAGATA	58.790	55.000	20.82	2.03	41.80	1.98
1954	2093	1.141053	GTAAGGGGGTGGCACAGATAG	59.859	57.143	20.82	0.00	41.80	2.08
1955	2094	0.550147	AAGGGGGTGGCACAGATAGT	60.550	55.000	20.82	0.00	41.80	2.12
1976	2115	5.850614	AGTGTTTCGGTACTGTAACAAGAT	58.149	37.500	23.49	12.86	32.84	2.40
1977	2116	6.285990	AGTGTTTCGGTACTGTAACAAGATT	58.714	36.000	23.49	10.60	32.84	2.40
1981	2123	8.767085	TGTTTCGGTACTGTAACAAGATTAAAG	58.233	33.333	20.68	0.00	0.00	1.85
2022	2170	2.203771	CCCTACCGCCAGAGCCTAG	61.204	68.421	0.00	0.00	34.57	3.02
2024	2172	1.455959	CTACCGCCAGAGCCTAGGT	60.456	63.158	11.31	0.00	34.92	3.08
2025	2173	1.001248	TACCGCCAGAGCCTAGGTT	59.999	57.895	11.31	3.54	33.05	3.50
2028	2183	1.448540	CGCCAGAGCCTAGGTTGTG	60.449	63.158	15.02	15.02	34.57	3.33
2035	2190	0.252742	AGCCTAGGTTGTGCCCTACT	60.253	55.000	11.31	0.00	38.26	2.57
2067	2222	5.394993	GGGGCTTTAATCTCGTTACACTACT	60.395	44.000	0.00	0.00	0.00	2.57
2075	2230	4.966249	TCTCGTTACACTACTGATTCACG	58.034	43.478	0.00	0.00	0.00	4.35
2079	2234	0.108804	ACACTACTGATTCACGCCCG	60.109	55.000	0.00	0.00	0.00	6.13
2081	2236	1.883084	CTACTGATTCACGCCCGGC	60.883	63.158	0.00	0.00	0.00	6.13
2156	2311	2.433004	GGTGTGGCGGTAGGGTTT	59.567	61.111	0.00	0.00	0.00	3.27
2163	2318	2.821378	GTGGCGGTAGGGTTTAAAACAT	59.179	45.455	5.45	0.00	0.00	2.71
2166	2321	3.065786	GGCGGTAGGGTTTAAAACATAGC	59.934	47.826	15.26	15.26	0.00	2.97
2184	2339	2.061220	CACCTCCTCTGTTCTGCCA	58.939	57.895	0.00	0.00	0.00	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	8.954834	ATGGGGTTTATATCATATTGCTTGAA	57.045	30.769	0.00	0.00	0.00	2.69
74	75	4.938832	AGCAAGGCACGTATTGTATTGTTA	59.061	37.500	8.55	0.00	0.00	2.41
305	307	0.460459	TGCGGTGTGTTTGTCGAGAA	60.460	50.000	0.00	0.00	0.00	2.87
464	477	3.511540	CGATCATGGAGGGCTTCTACATA	59.488	47.826	5.27	0.00	45.02	2.29
520	533	1.123928	ACCCGTGAGATCCCATCTTC	58.876	55.000	0.00	0.00	40.38	2.87
592	605	8.927059	TTGCCTATATAAATCTACATACCCCT	57.073	34.615	0.00	0.00	0.00	4.79
606	621	6.880484	TGACCGACTTCTTTTGCCTATATAA	58.120	36.000	0.00	0.00	0.00	0.98
616	631	1.348036	CTCCCCTGACCGACTTCTTTT	59.652	52.381	0.00	0.00	0.00	2.27
677	700	4.643387	GCCACGAGGGTGCAAGGT	62.643	66.667	0.00	0.00	43.00	3.50
701	724	1.689273	AGTGGACGTCAAGAAGAAGCT	59.311	47.619	18.91	0.00	0.00	3.74
705	728	1.699730	TGGAGTGGACGTCAAGAAGA	58.300	50.000	18.91	0.00	0.00	2.87
776	799	0.034896	ATCAAACGGAGTCCAAGCGT	59.965	50.000	10.49	0.00	45.00	5.07
779	802	4.770795	AGGAATATCAAACGGAGTCCAAG	58.229	43.478	10.49	0.00	45.00	3.61
833	861	1.379309	GGCCCAACCCGAATTGCTA	60.379	57.895	0.00	0.00	0.00	3.49
855	883	7.981142	TCATTTTTGGGACTAACCTACTAACT	58.019	34.615	0.00	0.00	38.98	2.24
960	989	7.113658	AGATGTTAAGTGATACGTCTCCAAT	57.886	36.000	0.00	0.00	36.19	3.16
993	1022	1.602311	CAGATGAAGCCATGCCTACC	58.398	55.000	0.00	0.00	32.09	3.18
1061	1090	0.804989	CAAAGATGCGTTCTCCCACC	59.195	55.000	0.00	0.00	31.78	4.61
1149	1179	0.974383	ACTTCTTTCGGTCGGTGGAT	59.026	50.000	0.00	0.00	0.00	3.41
1191	1221	5.659440	AAACATAGTTGGGGCATACAAAG	57.341	39.130	0.00	0.00	0.00	2.77
1211	1241	2.017138	TGGAAGCGCACGATCATAAA	57.983	45.000	11.47	0.00	0.00	1.40
1319	1350	4.282496	ACTTTCATAGAGGAGACGGTGAT	58.718	43.478	0.00	0.00	0.00	3.06
1326	1357	7.147828	CCATGTGAAGTACTTTCATAGAGGAGA	60.148	40.741	19.50	0.00	46.85	3.71
1337	1368	7.935755	CCATGATCTATCCATGTGAAGTACTTT	59.064	37.037	10.02	0.00	39.66	2.66
1363	1394	2.479566	TTGGACATCTTCTGGCACTC	57.520	50.000	0.00	0.00	32.82	3.51
1504	1535	1.529244	AGCTTTGCTTGGCGTTCCT	60.529	52.632	0.00	0.00	33.89	3.36
1573	1607	2.888863	GTGCCTCGTCCTCCTCAG	59.111	66.667	0.00	0.00	0.00	3.35
1574	1608	3.062466	CGTGCCTCGTCCTCCTCA	61.062	66.667	0.00	0.00	34.52	3.86
1583	1617	1.284982	CCTTCTTGTCACGTGCCTCG	61.285	60.000	11.67	0.00	46.00	4.63
1610	1644	2.167900	GCTTTACTGAGTCATACGGGGT	59.832	50.000	0.00	0.00	0.00	4.95
1640	1674	2.093711	CGGTTACATGATGAGTCCACCA	60.094	50.000	0.00	0.00	0.00	4.17
1650	1684	2.172505	TGGCTTCATCCGGTTACATGAT	59.827	45.455	0.00	0.00	0.00	2.45
1697	1731	8.357290	TGTCTTCTTGCCTTAGTAGTACATAA	57.643	34.615	2.52	0.00	0.00	1.90
1836	1975	2.108952	ACTTTGTTCTGCCCCTCATCTT	59.891	45.455	0.00	0.00	0.00	2.40
1862	2001	6.044637	TGTGGTGGTAGGGTTTAAAATAGAGT	59.955	38.462	0.00	0.00	0.00	3.24
1888	2027	0.252375	AACAACCTACCGCTAGGGGA	60.252	55.000	31.00	14.10	43.87	4.81
1914	2053	4.447342	CCATGGGCCCTGGTGGTC	62.447	72.222	25.70	0.00	38.35	4.02
1937	2076	1.082954	ACTATCTGTGCCACCCCCT	59.917	57.895	0.00	0.00	0.00	4.79
1947	2086	6.016024	TGTTACAGTACCGAAACACTATCTGT	60.016	38.462	0.00	0.00	38.26	3.41
1948	2087	6.384224	TGTTACAGTACCGAAACACTATCTG	58.616	40.000	0.00	0.00	0.00	2.90
1949	2088	6.579666	TGTTACAGTACCGAAACACTATCT	57.420	37.500	0.00	0.00	0.00	1.98
1951	2090	6.985117	TCTTGTTACAGTACCGAAACACTAT	58.015	36.000	4.51	0.00	31.92	2.12
1952	2091	6.389830	TCTTGTTACAGTACCGAAACACTA	57.610	37.500	4.51	0.00	31.92	2.74
1953	2092	5.266733	TCTTGTTACAGTACCGAAACACT	57.733	39.130	4.51	0.00	31.92	3.55
1954	2093	6.535274	AATCTTGTTACAGTACCGAAACAC	57.465	37.500	4.51	0.00	31.92	3.32
1955	2094	8.659925	TTTAATCTTGTTACAGTACCGAAACA	57.340	30.769	0.00	0.00	0.00	2.83
1957	2096	7.095102	GGCTTTAATCTTGTTACAGTACCGAAA	60.095	37.037	0.00	0.00	0.00	3.46
2000	2147	2.955881	GCTCTGGCGGTAGGGTGTT	61.956	63.158	0.00	0.00	0.00	3.32
2044	2199	5.519206	CAGTAGTGTAACGAGATTAAAGCCC	59.481	44.000	0.00	0.00	45.86	5.19
2045	2200	6.327934	TCAGTAGTGTAACGAGATTAAAGCC	58.672	40.000	0.00	0.00	45.86	4.35
2047	2202	9.569167	TGAATCAGTAGTGTAACGAGATTAAAG	57.431	33.333	0.00	0.00	45.86	1.85
2051	2206	6.028368	CGTGAATCAGTAGTGTAACGAGATT	58.972	40.000	0.00	0.00	45.86	2.40
2052	2207	5.570344	CGTGAATCAGTAGTGTAACGAGAT	58.430	41.667	0.00	0.00	45.86	2.75
2079	2234	4.796495	CAGTAAGGGGGTGGCGCC	62.796	72.222	22.73	22.73	35.60	6.53
2081	2236	4.796495	GGCAGTAAGGGGGTGGCG	62.796	72.222	0.00	0.00	0.00	5.69
2086	2241	2.603008	CCCATGGCAGTAAGGGGG	59.397	66.667	6.09	1.91	37.66	5.40
2156	2311	5.248477	AGAACAGAGGAGGTGCTATGTTTTA	59.752	40.000	12.03	0.00	31.44	1.52
2163	2318	0.898320	GCAGAACAGAGGAGGTGCTA	59.102	55.000	0.00	0.00	0.00	3.49
2166	2321	0.617413	ATGGCAGAACAGAGGAGGTG	59.383	55.000	0.00	0.00	0.00	4.00
2184	2339	5.663106	TGAGTTGAGTTAGGCCTTAGATGAT	59.337	40.000	12.58	0.00	0.00	2.45
2197	2353	8.094548	AGTTATGTATGTGCTTGAGTTGAGTTA	58.905	33.333	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.