AutoCloner

Multiple sequence alignment - TraesCS3B01G130600

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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	TraesCS3B01G130600	chr3B	100.000	2228	0	0	1	2228	112904391	112906618	0.000000e+00	4115
1	TraesCS3B01G130600	chr3B	92.222	450	20	9	882	1330	451815307	451814872	6.760000e-175	623
2	TraesCS3B01G130600	chr6B	97.813	1326	25	4	1	1325	163948188	163946866	0.000000e+00	2285
3	TraesCS3B01G130600	chr7A	94.599	1333	66	4	1	1331	538983147	538984475	0.000000e+00	2058
4	TraesCS3B01G130600	chr7A	80.839	715	122	5	1331	2030	213467791	213467077	4.180000e-152	547
5	TraesCS3B01G130600	chr5D	94.715	1192	50	7	145	1330	464404597	464405781	0.000000e+00	1840
6	TraesCS3B01G130600	chr5D	85.489	634	68	5	1333	1950	229334296	229334921	6.710000e-180	640
7	TraesCS3B01G130600	chr1B	93.698	1206	60	7	133	1331	668206897	668208093	0.000000e+00	1792
8	TraesCS3B01G130600	chr1B	90.211	1328	120	7	8	1331	198408484	198407163	0.000000e+00	1724
9	TraesCS3B01G130600	chr1B	89.813	1335	122	7	1	1331	381501750	381500426	0.000000e+00	1700
10	TraesCS3B01G130600	chr3A	90.508	1338	115	9	1	1330	472766261	472764928	0.000000e+00	1757
11	TraesCS3B01G130600	chr1D	90.548	1333	119	5	1	1331	361103095	361101768	0.000000e+00	1757
12	TraesCS3B01G130600	chr4B	90.060	1328	119	6	8	1331	105360398	105359080	0.000000e+00	1709
13	TraesCS3B01G130600	chr4B	85.751	386	43	6	1437	1822	192578724	192578351	4.460000e-107	398
14	TraesCS3B01G130600	chr4B	91.667	84	7	0	1331	1414	192617925	192617842	1.400000e-22	117
15	TraesCS3B01G130600	chr4D	85.222	900	108	8	1331	2225	210235368	210236247	0.000000e+00	902
16	TraesCS3B01G130600	chr4D	83.562	511	52	14	1331	1822	205677653	205678150	1.210000e-122	449
17	TraesCS3B01G130600	chr4D	88.462	338	32	2	1331	1667	304184057	304183726	3.450000e-108	401
18	TraesCS3B01G130600	chr4D	88.525	305	27	5	1331	1632	179710013	179710312	1.630000e-96	363
19	TraesCS3B01G130600	chr1A	84.954	545	78	4	1331	1873	500403572	500403030	1.160000e-152	549
20	TraesCS3B01G130600	chr6D	85.961	406	40	5	1331	1719	138256426	138256021	3.420000e-113	418
21	TraesCS3B01G130600	chr6D	85.961	406	40	5	1331	1719	286023627	286024032	3.420000e-113	418
22	TraesCS3B01G130600	chr6D	85.468	406	42	5	1331	1719	154258479	154258074	7.410000e-110	407
23	TraesCS3B01G130600	chr6D	85.926	135	19	0	1895	2029	286024032	286024166	6.410000e-31	145
24	TraesCS3B01G130600	chr6D	85.185	135	20	0	1895	2029	154258074	154257940	2.980000e-29	139
25	TraesCS3B01G130600	chr3D	90.132	304	26	3	1331	1632	543349983	543349682	2.070000e-105	392
26	TraesCS3B01G130600	chr5A	80.974	431	82	0	1596	2026	280629537	280629967	2.120000e-90	342

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	TraesCS3B01G130600	chr3B	112904391	112906618	2227	False	4115.0	4115	100.0000	1	2228	1	chr3B.!!$F1	2227
1	TraesCS3B01G130600	chr6B	163946866	163948188	1322	True	2285.0	2285	97.8130	1	1325	1	chr6B.!!$R1	1324
2	TraesCS3B01G130600	chr7A	538983147	538984475	1328	False	2058.0	2058	94.5990	1	1331	1	chr7A.!!$F1	1330
3	TraesCS3B01G130600	chr7A	213467077	213467791	714	True	547.0	547	80.8390	1331	2030	1	chr7A.!!$R1	699
4	TraesCS3B01G130600	chr5D	464404597	464405781	1184	False	1840.0	1840	94.7150	145	1330	1	chr5D.!!$F2	1185
5	TraesCS3B01G130600	chr5D	229334296	229334921	625	False	640.0	640	85.4890	1333	1950	1	chr5D.!!$F1	617
6	TraesCS3B01G130600	chr1B	668206897	668208093	1196	False	1792.0	1792	93.6980	133	1331	1	chr1B.!!$F1	1198
7	TraesCS3B01G130600	chr1B	198407163	198408484	1321	True	1724.0	1724	90.2110	8	1331	1	chr1B.!!$R1	1323
8	TraesCS3B01G130600	chr1B	381500426	381501750	1324	True	1700.0	1700	89.8130	1	1331	1	chr1B.!!$R2	1330
9	TraesCS3B01G130600	chr3A	472764928	472766261	1333	True	1757.0	1757	90.5080	1	1330	1	chr3A.!!$R1	1329
10	TraesCS3B01G130600	chr1D	361101768	361103095	1327	True	1757.0	1757	90.5480	1	1331	1	chr1D.!!$R1	1330
11	TraesCS3B01G130600	chr4B	105359080	105360398	1318	True	1709.0	1709	90.0600	8	1331	1	chr4B.!!$R1	1323
12	TraesCS3B01G130600	chr4D	210235368	210236247	879	False	902.0	902	85.2220	1331	2225	1	chr4D.!!$F3	894
13	TraesCS3B01G130600	chr1A	500403030	500403572	542	True	549.0	549	84.9540	1331	1873	1	chr1A.!!$R1	542
14	TraesCS3B01G130600	chr6D	286023627	286024166	539	False	281.5	418	85.9435	1331	2029	2	chr6D.!!$F1	698
15	TraesCS3B01G130600	chr6D	154257940	154258479	539	True	273.0	407	85.3265	1331	2029	2	chr6D.!!$R2	698

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
417	418	1.184322	TGTTGGAAATGGGCGCACAT	61.184	50.0	22.04	22.04	0.0	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1400	1414	0.040958	GGTCGCTTCAGCAGTTGTTG	60.041	55.0	0.0	0.0	42.21	3.33	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
59	60	1.521681	GAGTGCTGGGCGTATGGTC	60.522	63.158	0.00	0.00	0.00	4.02
89	90	4.451150	GTCCTCACGGCCATCGCA	62.451	66.667	2.24	0.00	43.89	5.10
110	111	4.693283	CAATTTATCACCTCACGCCTCTA	58.307	43.478	0.00	0.00	0.00	2.43
187	188	1.265905	GGCGGGTACAGACAAAGTTTG	59.734	52.381	14.13	14.13	0.00	2.93
417	418	1.184322	TGTTGGAAATGGGCGCACAT	61.184	50.000	22.04	22.04	0.00	3.21
852	861	3.897122	TCGGGGCTGGCCAAACTT	61.897	61.111	22.68	0.00	37.98	2.66
1000	1010	1.939934	CTTGGCAAACAGTGACTTCGA	59.060	47.619	0.00	0.00	35.56	3.71
1360	1374	6.873997	TGTTTTCTCCATCATGTCTACGTAT	58.126	36.000	0.00	0.00	0.00	3.06
1400	1414	1.900498	AACAGCCAGCCTTGCTCAC	60.900	57.895	0.00	0.00	36.40	3.51
1478	1522	6.015434	CCTTGTTTTCCAATGGTAGTAGCTTT	60.015	38.462	0.00	0.00	31.20	3.51
1496	1540	3.379452	CTTTCCATCAGACCTAGGGAGT	58.621	50.000	14.81	0.00	0.00	3.85
1499	1543	2.520120	TCCATCAGACCTAGGGAGTCAT	59.480	50.000	14.81	0.00	36.68	3.06
1509	1553	3.328931	CCTAGGGAGTCATGCCATAATGT	59.671	47.826	0.00	0.00	40.01	2.71
1525	1569	7.148086	TGCCATAATGTTTGTTTCTCATACTCC	60.148	37.037	0.00	0.00	0.00	3.85
1529	1573	4.312443	TGTTTGTTTCTCATACTCCGACC	58.688	43.478	0.00	0.00	0.00	4.79
1552	1596	0.792640	CACGTCTTGTTGCTAGCAGG	59.207	55.000	18.45	9.73	0.00	4.85
1563	1607	0.752054	GCTAGCAGGTCAGCAGATCT	59.248	55.000	10.63	0.00	37.73	2.75
1670	1715	1.063642	TGGTTTGGTCACCCATCACAA	60.064	47.619	0.00	0.00	41.49	3.33
1685	1730	0.883833	CACAAAGGAAATCAGGCGCT	59.116	50.000	7.64	0.00	0.00	5.92
1690	1735	1.153429	GGAAATCAGGCGCTACGGT	60.153	57.895	7.64	0.00	0.00	4.83
1693	1738	0.178068	AAATCAGGCGCTACGGTGAT	59.822	50.000	7.64	5.68	0.00	3.06
1761	1806	0.819259	GTGAGAGCAGTGGTTTGGCA	60.819	55.000	0.00	0.00	0.00	4.92
1765	1810	1.799258	GAGCAGTGGTTTGGCACAGG	61.799	60.000	0.00	0.00	42.39	4.00
1792	1837	2.358247	GAAAGCGAGGCGGGTCAA	60.358	61.111	0.00	0.00	0.00	3.18
1836	1881	1.905512	GGGTTGACGAGGCTATGGT	59.094	57.895	0.00	0.00	0.00	3.55
1886	1931	2.143594	GAACGACACGAGGCAGAGGT	62.144	60.000	0.00	0.00	0.00	3.85
1901	1946	0.108520	GAGGTACATCGCCGGAAACA	60.109	55.000	5.05	0.00	0.00	2.83
1906	1951	0.802494	ACATCGCCGGAAACATGAAC	59.198	50.000	5.05	0.00	0.00	3.18
1985	2030	3.865929	CTTGACGGCTGCCACGAGT	62.866	63.158	20.29	8.16	34.93	4.18
2001	2046	2.189191	GAGTCCATGGCTGTGGCTCA	62.189	60.000	6.96	0.00	39.79	4.26
2038	2083	1.220206	CAGAGCGGCAACTCAGGAT	59.780	57.895	1.45	0.00	39.26	3.24
2041	2086	0.878086	GAGCGGCAACTCAGGATAGC	60.878	60.000	1.45	0.00	36.65	2.97
2048	2093	1.320344	AACTCAGGATAGCGACCGCA	61.320	55.000	16.97	3.29	44.88	5.69
2051	2096	4.271816	AGGATAGCGACCGCAGCG	62.272	66.667	16.97	8.18	44.88	5.18
2063	2108	2.126071	GCAGCGGCGACAAGTAGA	60.126	61.111	12.98	0.00	0.00	2.59
2065	2110	1.956620	GCAGCGGCGACAAGTAGAAC	61.957	60.000	12.98	0.00	0.00	3.01
2068	2113	0.739813	GCGGCGACAAGTAGAACCAT	60.740	55.000	12.98	0.00	0.00	3.55
2075	2120	1.278127	ACAAGTAGAACCATGGGGACG	59.722	52.381	18.09	0.00	38.05	4.79
2076	2121	1.553248	CAAGTAGAACCATGGGGACGA	59.447	52.381	18.09	0.19	38.05	4.20
2077	2122	1.192428	AGTAGAACCATGGGGACGAC	58.808	55.000	18.09	12.52	38.05	4.34
2079	2124	1.553704	GTAGAACCATGGGGACGACTT	59.446	52.381	18.09	0.00	38.05	3.01
2080	2125	0.324943	AGAACCATGGGGACGACTTG	59.675	55.000	18.09	0.00	38.05	3.16
2081	2126	0.323629	GAACCATGGGGACGACTTGA	59.676	55.000	18.09	0.00	38.05	3.02
2093	2138	1.352156	CGACTTGAAGTAGTGGCGGC	61.352	60.000	0.00	0.00	0.00	6.53
2143	2191	0.385473	GTGATGCCGGTGAAAACGTG	60.385	55.000	1.90	0.00	0.00	4.49
2144	2192	1.209127	GATGCCGGTGAAAACGTGG	59.791	57.895	1.90	0.00	0.00	4.94
2145	2193	2.796245	GATGCCGGTGAAAACGTGGC	62.796	60.000	1.90	3.98	45.91	5.01
2146	2194	4.676586	GCCGGTGAAAACGTGGCG	62.677	66.667	1.90	0.00	35.77	5.69
2147	2195	4.020378	CCGGTGAAAACGTGGCGG	62.020	66.667	0.00	0.00	0.00	6.13
2148	2196	4.676586	CGGTGAAAACGTGGCGGC	62.677	66.667	0.00	0.00	0.00	6.53
2149	2197	3.284449	GGTGAAAACGTGGCGGCT	61.284	61.111	11.43	0.00	0.00	5.52
2150	2198	2.251371	GTGAAAACGTGGCGGCTC	59.749	61.111	11.43	5.59	0.00	4.70
2151	2199	2.110213	TGAAAACGTGGCGGCTCT	59.890	55.556	11.43	0.00	0.00	4.09
2152	2200	2.250939	TGAAAACGTGGCGGCTCTG	61.251	57.895	11.43	5.96	0.00	3.35
2153	2201	2.966309	GAAAACGTGGCGGCTCTGG	61.966	63.158	11.43	0.00	0.00	3.86
2154	2202	3.469863	AAAACGTGGCGGCTCTGGA	62.470	57.895	11.43	0.00	0.00	3.86
2155	2203	3.883744	AAACGTGGCGGCTCTGGAG	62.884	63.158	11.43	0.00	0.00	3.86
2191	2239	2.876550	ACGAGGCTGTAGAAACAAAACC	59.123	45.455	0.00	0.00	34.49	3.27
2192	2240	2.096417	CGAGGCTGTAGAAACAAAACCG	60.096	50.000	0.00	0.00	34.49	4.44
2193	2241	2.876550	GAGGCTGTAGAAACAAAACCGT	59.123	45.455	0.00	0.00	34.49	4.83
2195	2243	2.287368	GGCTGTAGAAACAAAACCGTGG	60.287	50.000	0.00	0.00	34.49	4.94
2197	2245	1.677052	TGTAGAAACAAAACCGTGGCC	59.323	47.619	0.00	0.00	30.91	5.36
2198	2246	0.945813	TAGAAACAAAACCGTGGCCG	59.054	50.000	0.00	0.00	0.00	6.13
2225	2273	2.439156	AATGGCAGAAGGGCTCGC	60.439	61.111	0.00	0.00	43.83	5.03
2226	2274	4.845580	ATGGCAGAAGGGCTCGCG	62.846	66.667	0.00	0.00	43.83	5.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	1.446272	GAGGACCGCTTTGACGAGG	60.446	63.158	0.00	0.00	34.06	4.63
89	90	3.914426	AGAGGCGTGAGGTGATAAATT	57.086	42.857	0.00	0.00	0.00	1.82
110	111	1.639635	GCACCTCCATGGGGATGTCT	61.640	60.000	15.22	0.00	43.63	3.41
187	188	6.536224	CCAATTAATCTTGCATTTTCCACCTC	59.464	38.462	0.00	0.00	0.00	3.85
340	341	2.280389	CGGTGCATGGAGATCCCG	60.280	66.667	0.00	0.00	37.93	5.14
417	418	1.623311	TGGCGAGTTCCAGAATCTTGA	59.377	47.619	0.00	0.00	0.00	3.02
852	861	4.503296	GCTTACAAAGAGGACAGAGACCAA	60.503	45.833	0.00	0.00	0.00	3.67
1000	1010	1.681166	GCTGTTCCACCATGCTCTCAT	60.681	52.381	0.00	0.00	0.00	2.90
1245	1257	2.544903	GCCACAAAGCGGCTAAAAGAAA	60.545	45.455	1.35	0.00	46.56	2.52
1246	1258	1.000717	GCCACAAAGCGGCTAAAAGAA	60.001	47.619	1.35	0.00	46.56	2.52
1247	1259	0.596082	GCCACAAAGCGGCTAAAAGA	59.404	50.000	1.35	0.00	46.56	2.52
1347	1361	8.301720	AGTTTGTGAGTTTATACGTAGACATGA	58.698	33.333	0.00	0.00	0.00	3.07
1400	1414	0.040958	GGTCGCTTCAGCAGTTGTTG	60.041	55.000	0.00	0.00	42.21	3.33
1478	1522	1.930204	TGACTCCCTAGGTCTGATGGA	59.070	52.381	8.29	0.00	35.04	3.41
1496	1540	6.587206	TGAGAAACAAACATTATGGCATGA	57.413	33.333	10.98	1.24	0.00	3.07
1499	1543	7.148086	GGAGTATGAGAAACAAACATTATGGCA	60.148	37.037	0.00	0.00	0.00	4.92
1509	1553	3.307199	GGGGTCGGAGTATGAGAAACAAA	60.307	47.826	0.00	0.00	0.00	2.83
1525	1569	0.944311	CAACAAGACGTGAGGGGTCG	60.944	60.000	0.00	0.00	39.38	4.79
1529	1573	1.714794	CTAGCAACAAGACGTGAGGG	58.285	55.000	0.00	0.00	0.00	4.30
1600	1645	6.802608	TCAAAAGGAGTATAGTACATGGACG	58.197	40.000	1.41	0.00	0.00	4.79
1670	1715	0.462047	CCGTAGCGCCTGATTTCCTT	60.462	55.000	2.29	0.00	0.00	3.36
1685	1730	0.392461	GGCCTCTGCAAATCACCGTA	60.392	55.000	0.00	0.00	40.13	4.02
1690	1735	0.612732	CCCAAGGCCTCTGCAAATCA	60.613	55.000	5.23	0.00	40.13	2.57
1693	1738	2.601367	GCCCAAGGCCTCTGCAAA	60.601	61.111	5.23	0.00	44.06	3.68
1745	1790	0.820891	CTGTGCCAAACCACTGCTCT	60.821	55.000	0.00	0.00	36.68	4.09
1746	1791	1.656441	CTGTGCCAAACCACTGCTC	59.344	57.895	0.00	0.00	36.68	4.26
1761	1806	0.536006	GCTTTCTCACCTGCACCTGT	60.536	55.000	0.00	0.00	0.00	4.00
1765	1810	1.294659	CCTCGCTTTCTCACCTGCAC	61.295	60.000	0.00	0.00	0.00	4.57
1808	1853	2.418356	GTCAACCCGTCGTGTCCA	59.582	61.111	0.00	0.00	0.00	4.02
1812	1857	2.430244	CCTCGTCAACCCGTCGTG	60.430	66.667	0.00	0.00	0.00	4.35
1822	1867	0.106167	AGCCTACCATAGCCTCGTCA	60.106	55.000	0.00	0.00	0.00	4.35
1841	1886	4.344865	GTCTTTGAGCCGGGCCCA	62.345	66.667	24.92	7.44	0.00	5.36
1862	1907	1.664965	GCCTCGTGTCGTTCAAGCT	60.665	57.895	0.00	0.00	0.00	3.74
1886	1931	2.004017	GTTCATGTTTCCGGCGATGTA	58.996	47.619	9.30	0.00	0.00	2.29
1969	2014	4.357947	GACTCGTGGCAGCCGTCA	62.358	66.667	7.03	0.00	0.00	4.35
1985	2030	2.672908	CTGAGCCACAGCCATGGA	59.327	61.111	18.40	0.00	43.02	3.41
2021	2066	0.749649	CTATCCTGAGTTGCCGCTCT	59.250	55.000	6.26	0.00	36.51	4.09
2030	2075	1.729470	CTGCGGTCGCTATCCTGAGT	61.729	60.000	16.36	0.00	42.51	3.41
2048	2093	1.080025	GGTTCTACTTGTCGCCGCT	60.080	57.895	0.00	0.00	0.00	5.52
2051	2096	1.369625	CCATGGTTCTACTTGTCGCC	58.630	55.000	2.57	0.00	0.00	5.54
2052	2097	1.369625	CCCATGGTTCTACTTGTCGC	58.630	55.000	11.73	0.00	0.00	5.19
2053	2098	1.553248	TCCCCATGGTTCTACTTGTCG	59.447	52.381	11.73	0.00	0.00	4.35
2055	2100	1.278127	CGTCCCCATGGTTCTACTTGT	59.722	52.381	11.73	0.00	0.00	3.16
2057	2102	1.553704	GTCGTCCCCATGGTTCTACTT	59.446	52.381	11.73	0.00	0.00	2.24
2058	2103	1.192428	GTCGTCCCCATGGTTCTACT	58.808	55.000	11.73	0.00	0.00	2.57
2060	2105	1.553248	CAAGTCGTCCCCATGGTTCTA	59.447	52.381	11.73	0.00	0.00	2.10
2061	2106	0.324943	CAAGTCGTCCCCATGGTTCT	59.675	55.000	11.73	0.00	0.00	3.01
2062	2107	0.323629	TCAAGTCGTCCCCATGGTTC	59.676	55.000	11.73	0.00	0.00	3.62
2063	2108	0.768622	TTCAAGTCGTCCCCATGGTT	59.231	50.000	11.73	0.00	0.00	3.67
2065	2110	0.324943	ACTTCAAGTCGTCCCCATGG	59.675	55.000	4.14	4.14	0.00	3.66
2068	2113	1.616865	CACTACTTCAAGTCGTCCCCA	59.383	52.381	0.00	0.00	0.00	4.96
2075	2120	1.019805	GGCCGCCACTACTTCAAGTC	61.020	60.000	3.91	0.00	0.00	3.01
2076	2121	1.003718	GGCCGCCACTACTTCAAGT	60.004	57.895	3.91	0.00	0.00	3.16
2077	2122	0.392998	ATGGCCGCCACTACTTCAAG	60.393	55.000	16.16	0.00	35.80	3.02
2079	2124	1.078497	CATGGCCGCCACTACTTCA	60.078	57.895	16.16	0.00	35.80	3.02
2080	2125	0.811616	CTCATGGCCGCCACTACTTC	60.812	60.000	16.16	0.00	35.80	3.01
2081	2126	1.221840	CTCATGGCCGCCACTACTT	59.778	57.895	16.16	0.00	35.80	2.24
2125	2173	1.511318	CCACGTTTTCACCGGCATCA	61.511	55.000	0.00	0.00	0.00	3.07
2128	2176	3.587933	GCCACGTTTTCACCGGCA	61.588	61.111	0.00	0.00	37.74	5.69
2178	2226	1.334329	CGGCCACGGTTTTGTTTCTAC	60.334	52.381	2.24	0.00	36.18	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.