AutoCloner

Multiple sequence alignment - TraesCS4B01G185900

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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	TraesCS4B01G185900	chr4B	100.000	2276	0	0	1	2276	405633105	405635380	0.000000e+00	4204
1	TraesCS4B01G185900	chr2B	96.865	1244	38	1	1	1244	675289812	675291054	0.000000e+00	2080
2	TraesCS4B01G185900	chr1B	93.928	1301	77	2	1	1301	63071070	63072368	0.000000e+00	1964
3	TraesCS4B01G185900	chr1B	97.969	1083	22	0	1	1083	16126539	16125457	0.000000e+00	1879
4	TraesCS4B01G185900	chr1B	98.817	169	2	0	1133	1301	16125460	16125292	3.670000e-78	302
5	TraesCS4B01G185900	chr5B	92.690	1327	74	6	2	1307	35291991	35290667	0.000000e+00	1892
6	TraesCS4B01G185900	chr5B	93.956	1241	74	1	1	1240	605231283	605230043	0.000000e+00	1875
7	TraesCS4B01G185900	chr5B	93.750	96	6	0	1206	1301	605225857	605225762	6.550000e-31	145
8	TraesCS4B01G185900	chr7A	91.194	1306	103	5	1	1301	47684831	47686129	0.000000e+00	1764
9	TraesCS4B01G185900	chr7D	90.323	1302	120	6	2	1301	52029850	52028553	0.000000e+00	1701
10	TraesCS4B01G185900	chr4D	88.659	820	75	10	1467	2276	325360628	325361439	0.000000e+00	983
11	TraesCS4B01G185900	chr4D	91.908	173	11	1	1297	1466	325360409	325360581	2.920000e-59	239
12	TraesCS4B01G185900	chr4A	86.967	821	85	13	1467	2276	145882095	145881286	0.000000e+00	904
13	TraesCS4B01G185900	chr6A	89.323	384	37	1	1	380	53084093	53084476	1.580000e-131	479
14	TraesCS4B01G185900	chr7B	96.167	287	11	0	898	1184	712642938	712643224	9.520000e-129	470
15	TraesCS4B01G185900	chr6D	87.430	358	44	1	296	652	291241542	291241899	5.850000e-111	411
16	TraesCS4B01G185900	chr5A	89.062	256	19	5	1050	1301	632359514	632359264	2.200000e-80	309

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	TraesCS4B01G185900	chr4B	405633105	405635380	2275	False	4204.0	4204	100.0000	1	2276	1	chr4B.!!$F1	2275
1	TraesCS4B01G185900	chr2B	675289812	675291054	1242	False	2080.0	2080	96.8650	1	1244	1	chr2B.!!$F1	1243
2	TraesCS4B01G185900	chr1B	63071070	63072368	1298	False	1964.0	1964	93.9280	1	1301	1	chr1B.!!$F1	1300
3	TraesCS4B01G185900	chr1B	16125292	16126539	1247	True	1090.5	1879	98.3930	1	1301	2	chr1B.!!$R1	1300
4	TraesCS4B01G185900	chr5B	35290667	35291991	1324	True	1892.0	1892	92.6900	2	1307	1	chr5B.!!$R1	1305
5	TraesCS4B01G185900	chr5B	605230043	605231283	1240	True	1875.0	1875	93.9560	1	1240	1	chr5B.!!$R3	1239
6	TraesCS4B01G185900	chr7A	47684831	47686129	1298	False	1764.0	1764	91.1940	1	1301	1	chr7A.!!$F1	1300
7	TraesCS4B01G185900	chr7D	52028553	52029850	1297	True	1701.0	1701	90.3230	2	1301	1	chr7D.!!$R1	1299
8	TraesCS4B01G185900	chr4D	325360409	325361439	1030	False	611.0	983	90.2835	1297	2276	2	chr4D.!!$F1	979
9	TraesCS4B01G185900	chr4A	145881286	145882095	809	True	904.0	904	86.9670	1467	2276	1	chr4A.!!$R1	809

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
432	433	0.038166	ACCGCCACATCAGGACAATT	59.962	50.0	0.0	0.0	0.0	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1833	1920	0.249155	CAAAGGTGGCAGCAACACAG	60.249	55.0	20.04	0.0	40.54	3.66	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
52	53	0.534873	TCTCGGCAATGATCCGTTGA	59.465	50.000	11.01	0.00	46.49	3.18
125	126	1.270625	TGTCAGGCGGAATTTTCTCGT	60.271	47.619	0.00	0.00	0.00	4.18
302	303	2.033049	CGGTATCGGAGACTTCATCGTT	59.967	50.000	2.47	0.00	42.51	3.85
432	433	0.038166	ACCGCCACATCAGGACAATT	59.962	50.000	0.00	0.00	0.00	2.32
482	483	1.078848	AGGACTTGATGCACGCTCC	60.079	57.895	0.00	0.00	0.00	4.70
736	737	5.641209	GCAAGAGATGACTTGTCAGTATTGT	59.359	40.000	17.08	0.58	45.98	2.71
835	836	0.630134	TGATGGGGCCATTGACATGA	59.370	50.000	4.39	0.00	36.70	3.07
1044	1050	3.003763	AACCTCTGGACCTCGGGC	61.004	66.667	0.00	0.00	0.00	6.13
1124	1130	2.060050	TTTGCCTCCTTTTCGGTTCA	57.940	45.000	0.00	0.00	0.00	3.18
1293	1323	5.183904	GCAATAAAGATCCCTGTTCTGTGTT	59.816	40.000	0.00	0.00	0.00	3.32
1359	1389	6.179906	TCAATTTGTTTGGGCAGGATAAAA	57.820	33.333	0.00	0.00	35.92	1.52
1423	1456	7.255836	GGGAAGAGTTATTGTTAGGTTGCTTTT	60.256	37.037	0.00	0.00	0.00	2.27
1432	1465	1.029681	AGGTTGCTTTTCCCGACAAC	58.970	50.000	0.00	0.00	41.26	3.32
1491	1570	5.571784	ATCAAGGATGCACACAATAACAG	57.428	39.130	0.00	0.00	0.00	3.16
1492	1571	4.650734	TCAAGGATGCACACAATAACAGA	58.349	39.130	0.00	0.00	0.00	3.41
1493	1572	5.069318	TCAAGGATGCACACAATAACAGAA	58.931	37.500	0.00	0.00	0.00	3.02
1494	1573	5.534278	TCAAGGATGCACACAATAACAGAAA	59.466	36.000	0.00	0.00	0.00	2.52
1495	1574	6.040278	TCAAGGATGCACACAATAACAGAAAA	59.960	34.615	0.00	0.00	0.00	2.29
1562	1641	4.104102	TCAACAACTCCACCTTCCTTACAT	59.896	41.667	0.00	0.00	0.00	2.29
1578	1657	1.800805	ACATCACAAGAGTTGCGAGG	58.199	50.000	0.00	0.00	30.61	4.63
1598	1677	2.615493	GGAAGGCTCTCCGAAATCAACA	60.615	50.000	0.00	0.00	37.47	3.33
1600	1679	1.087501	GGCTCTCCGAAATCAACACC	58.912	55.000	0.00	0.00	0.00	4.16
1642	1722	4.939915	CCCGTCGTCGCGAGATCG	62.940	72.222	10.24	10.68	45.19	3.69
1680	1767	0.944386	TTTCACCAAAGAGAGCACGC	59.056	50.000	0.00	0.00	0.00	5.34
1701	1788	3.131755	GCCTTAGCAGATTCCAAAGCAAT	59.868	43.478	0.00	0.00	39.53	3.56
1702	1789	4.382362	GCCTTAGCAGATTCCAAAGCAATT	60.382	41.667	0.00	0.00	39.53	2.32
1723	1810	7.857569	CAATTTTGCTTTGACAAAGACATGAT	58.142	30.769	28.15	17.60	40.43	2.45
1833	1920	3.574614	CACCACCAAATCGAAAACATCC	58.425	45.455	0.00	0.00	0.00	3.51
1881	1968	6.784031	AGAAGATGAAAGTACATGGAAAGGT	58.216	36.000	0.00	0.00	0.00	3.50
1904	1992	1.362768	CACACACCATGATCACGGAG	58.637	55.000	16.14	9.54	0.00	4.63
1906	1994	1.623311	ACACACCATGATCACGGAGAA	59.377	47.619	16.14	0.00	0.00	2.87
1907	1995	2.002586	CACACCATGATCACGGAGAAC	58.997	52.381	16.14	0.00	0.00	3.01
1949	2037	7.548196	TGTCGCATTAATTTTTAGAGGTAGG	57.452	36.000	0.00	0.00	0.00	3.18
1950	2038	7.332557	TGTCGCATTAATTTTTAGAGGTAGGA	58.667	34.615	0.00	0.00	0.00	2.94
1957	2045	9.920946	ATTAATTTTTAGAGGTAGGATCTTGCA	57.079	29.630	0.00	0.00	0.00	4.08
1970	2058	1.179152	TCTTGCATGCACATCCTTGG	58.821	50.000	22.58	3.58	0.00	3.61
1989	2077	0.792640	GCGTGGAGATCACAACACAG	59.207	55.000	0.00	0.00	46.36	3.66
1996	2085	5.009010	GTGGAGATCACAACACAGTCAAATT	59.991	40.000	0.00	0.00	45.39	1.82
2005	2094	6.641723	CACAACACAGTCAAATTTATGCATGA	59.358	34.615	10.16	0.00	0.00	3.07
2007	2096	5.713025	ACACAGTCAAATTTATGCATGACC	58.287	37.500	10.16	0.00	42.39	4.02
2046	2135	3.126001	TGTGGAGAGTTGAAAATCGCT	57.874	42.857	0.00	0.00	0.00	4.93
2047	2136	4.265904	TGTGGAGAGTTGAAAATCGCTA	57.734	40.909	0.00	0.00	0.00	4.26
2070	2159	1.230635	GCCATCTCAAGTGCACGTGT	61.231	55.000	28.05	10.24	0.00	4.49
2071	2160	1.939381	GCCATCTCAAGTGCACGTGTA	60.939	52.381	28.05	19.26	0.00	2.90
2085	2174	5.352016	GTGCACGTGTACCAAAATTCCTATA	59.648	40.000	24.26	0.00	0.00	1.31
2104	2193	2.338620	CAGAGGCCGACAACGACA	59.661	61.111	0.00	0.00	42.66	4.35
2119	2208	1.805945	GACACCGAGACATGGCGAC	60.806	63.158	0.00	0.00	0.00	5.19
2157	2246	2.703798	GCCGTAGTCGCACTACCCA	61.704	63.158	16.03	0.00	46.27	4.51
2158	2247	1.885157	CCGTAGTCGCACTACCCAA	59.115	57.895	16.03	0.00	46.27	4.12
2159	2248	0.457337	CCGTAGTCGCACTACCCAAC	60.457	60.000	16.03	0.72	46.27	3.77
2160	2249	0.457337	CGTAGTCGCACTACCCAACC	60.457	60.000	16.03	0.00	46.27	3.77
2162	2251	0.542467	TAGTCGCACTACCCAACCCA	60.542	55.000	0.00	0.00	0.00	4.51
2172	2263	1.378382	CCCAACCCATCGATGCACA	60.378	57.895	20.25	0.00	0.00	4.57
2179	2270	2.019249	CCCATCGATGCACATTTCTGT	58.981	47.619	20.25	0.00	35.44	3.41
2242	2333	1.227263	CCCGATCCGCCACTGTTAG	60.227	63.158	0.00	0.00	0.00	2.34
2243	2334	1.672854	CCCGATCCGCCACTGTTAGA	61.673	60.000	0.00	0.00	0.00	2.10
2272	2363	6.208988	TGTACTCCATGCGAGATATTATCC	57.791	41.667	15.51	0.00	41.63	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	8.969260	TGATCAATAAGCTCAGACACAAATAT	57.031	30.769	0.00	0.00	0.00	1.28
302	303	3.554337	GGTCGACCAAAGCTGTTTCTCTA	60.554	47.826	29.75	0.00	35.64	2.43
432	433	5.969741	GATTTACATAAATCGCACGTAGCA	58.030	37.500	8.27	0.00	41.24	3.49
482	483	1.001068	TTGCATGGGAACAATGCACTG	59.999	47.619	10.63	0.00	46.77	3.66
736	737	0.668535	CGACGATCCTGTGGCATAGA	59.331	55.000	13.32	0.00	0.00	1.98
1124	1130	6.787170	ACATTAGCATCCCTCATAACATGAT	58.213	36.000	0.00	0.00	38.85	2.45
1390	1420	9.725206	ACCTAACAATAACTCTTCCCTATAAGA	57.275	33.333	0.00	0.00	34.39	2.10
1404	1437	5.048573	TCGGGAAAAGCAACCTAACAATAAC	60.049	40.000	0.00	0.00	0.00	1.89
1406	1439	4.456566	GTCGGGAAAAGCAACCTAACAATA	59.543	41.667	0.00	0.00	0.00	1.90
1418	1451	3.190535	ACATACATGTTGTCGGGAAAAGC	59.809	43.478	2.30	0.00	37.90	3.51
1511	1590	2.175202	TGCAAGTCTTTGGGTGTGTTT	58.825	42.857	0.00	0.00	34.79	2.83
1562	1641	1.270305	CCTTCCTCGCAACTCTTGTGA	60.270	52.381	0.00	0.00	46.95	3.58
1578	1657	2.416893	GTGTTGATTTCGGAGAGCCTTC	59.583	50.000	0.00	0.00	38.43	3.46
1600	1679	4.108699	TGAGTGTTGTTGCCTTTTGAAG	57.891	40.909	0.00	0.00	0.00	3.02
1617	1697	4.052229	CGACGACGGGGCTTGAGT	62.052	66.667	0.00	0.00	35.72	3.41
1660	1740	1.334149	GCGTGCTCTCTTTGGTGAAAC	60.334	52.381	0.00	0.00	0.00	2.78
1680	1767	4.996788	ATTGCTTTGGAATCTGCTAAGG	57.003	40.909	0.00	0.00	0.00	2.69
1701	1788	5.234757	GCATCATGTCTTTGTCAAAGCAAAA	59.765	36.000	18.80	12.49	37.82	2.44
1702	1789	4.746115	GCATCATGTCTTTGTCAAAGCAAA	59.254	37.500	18.80	12.76	38.39	3.68
1741	1828	3.849951	CGATGGCTACACCCGGCT	61.850	66.667	0.00	0.00	37.83	5.52
1763	1850	1.092348	GGTGAAAACCCTATGTCCGC	58.908	55.000	0.00	0.00	0.00	5.54
1806	1893	1.808411	TCGATTTGGTGGTGCTCTTC	58.192	50.000	0.00	0.00	0.00	2.87
1833	1920	0.249155	CAAAGGTGGCAGCAACACAG	60.249	55.000	20.04	0.00	40.54	3.66
1856	1943	6.881602	ACCTTTCCATGTACTTTCATCTTCTC	59.118	38.462	0.00	0.00	0.00	2.87
1881	1968	2.158971	CCGTGATCATGGTGTGTGGATA	60.159	50.000	23.76	0.00	32.81	2.59
1937	2025	5.126067	GCATGCAAGATCCTACCTCTAAAA	58.874	41.667	14.21	0.00	0.00	1.52
1949	2037	2.223735	CCAAGGATGTGCATGCAAGATC	60.224	50.000	24.58	24.08	0.00	2.75
1950	2038	1.754803	CCAAGGATGTGCATGCAAGAT	59.245	47.619	24.58	17.43	0.00	2.40
1957	2045	2.048023	CCACGCCAAGGATGTGCAT	61.048	57.895	0.00	0.00	32.32	3.96
1989	2077	3.768406	TGCGGTCATGCATAAATTTGAC	58.232	40.909	0.00	2.71	40.62	3.18
2005	2094	0.392706	TCTGTGACATTCTGTGCGGT	59.607	50.000	0.00	0.00	0.00	5.68
2007	2096	2.481568	ACATTCTGTGACATTCTGTGCG	59.518	45.455	0.00	0.00	0.00	5.34
2023	2112	4.154918	AGCGATTTTCAACTCTCCACATTC	59.845	41.667	0.00	0.00	0.00	2.67
2046	2135	2.675032	CGTGCACTTGAGATGGCTCTTA	60.675	50.000	16.19	0.00	41.84	2.10
2047	2136	1.818642	GTGCACTTGAGATGGCTCTT	58.181	50.000	10.32	0.00	41.84	2.85
2070	2159	5.456186	GGCCTCTGCTATAGGAATTTTGGTA	60.456	44.000	1.04	0.00	36.08	3.25
2071	2160	4.464947	GCCTCTGCTATAGGAATTTTGGT	58.535	43.478	1.04	0.00	36.08	3.67
2085	2174	3.303135	TCGTTGTCGGCCTCTGCT	61.303	61.111	0.00	0.00	37.74	4.24
2104	2193	1.374252	GTTGTCGCCATGTCTCGGT	60.374	57.895	0.00	0.00	0.00	4.69
2119	2208	2.991190	GCTTGCATCAAACATGAGGTTG	59.009	45.455	0.00	0.78	40.35	3.77
2123	2212	1.200716	ACGGCTTGCATCAAACATGAG	59.799	47.619	0.00	0.00	0.00	2.90
2157	2246	2.424601	CAGAAATGTGCATCGATGGGTT	59.575	45.455	26.00	0.00	0.00	4.11
2158	2247	2.019249	CAGAAATGTGCATCGATGGGT	58.981	47.619	26.00	0.00	0.00	4.51
2159	2248	2.019249	ACAGAAATGTGCATCGATGGG	58.981	47.619	26.00	2.75	0.00	4.00
2160	2249	2.421073	ACACAGAAATGTGCATCGATGG	59.579	45.455	26.00	9.00	43.13	3.51
2162	2251	4.094887	GGTAACACAGAAATGTGCATCGAT	59.905	41.667	8.24	0.00	43.13	3.59
2172	2263	5.833131	ACAATGACAAGGGTAACACAGAAAT	59.167	36.000	0.00	0.00	39.74	2.17
2179	2270	6.514212	CGAAAATGACAATGACAAGGGTAACA	60.514	38.462	0.00	0.00	39.74	2.41
2183	2274	3.888930	ACGAAAATGACAATGACAAGGGT	59.111	39.130	0.00	0.00	0.00	4.34
2187	2278	3.550561	GCGACGAAAATGACAATGACAA	58.449	40.909	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.