AutoCloner

Multiple sequence alignment - TraesCS5D01G420900

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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	TraesCS5D01G420900	chr5D	100.000	2273	0	0	1	2273	481290906	481288634	0.000000e+00	4198
1	TraesCS5D01G420900	chr5D	83.589	1304	206	7	5	1304	543342856	543341557	0.000000e+00	1216
2	TraesCS5D01G420900	chr5D	85.987	785	110	0	5	789	541900023	541899239	0.000000e+00	841
3	TraesCS5D01G420900	chr3D	94.781	1303	68	0	2	1304	480855737	480857039	0.000000e+00	2030
4	TraesCS5D01G420900	chr3D	83.978	1111	172	5	195	1303	1289742	1288636	0.000000e+00	1061
5	TraesCS5D01G420900	chr2A	93.774	1301	62	1	1	1301	104772768	104771487	0.000000e+00	1936
6	TraesCS5D01G420900	chr2A	82.588	850	144	3	457	1304	683007860	683007013	0.000000e+00	747
7	TraesCS5D01G420900	chr6B	88.795	1303	144	2	2	1302	610301124	610302426	0.000000e+00	1596
8	TraesCS5D01G420900	chr6A	84.562	1289	197	2	17	1304	189526693	189525406	0.000000e+00	1277
9	TraesCS5D01G420900	chr1D	83.576	1303	209	4	5	1305	12197099	12195800	0.000000e+00	1216
10	TraesCS5D01G420900	chr5A	78.511	1182	239	14	131	1306	330177092	330175920	0.000000e+00	761
11	TraesCS5D01G420900	chr5A	84.459	740	74	23	1305	2011	600360015	600359284	0.000000e+00	691
12	TraesCS5D01G420900	chr5B	89.333	600	53	7	1681	2273	589891491	589890896	0.000000e+00	743
13	TraesCS5D01G420900	chr5B	87.556	225	25	3	2051	2273	88364584	88364361	8.060000e-65	257
14	TraesCS5D01G420900	chr5B	97.802	91	2	0	1541	1631	589891693	589891603	8.410000e-35	158
15	TraesCS5D01G420900	chr5B	92.553	94	6	1	1620	1712	589891584	589891491	1.420000e-27	134

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	TraesCS5D01G420900	chr5D	481288634	481290906	2272	True	4198	4198	100.000000	1	2273	1	chr5D.!!$R1	2272
1	TraesCS5D01G420900	chr5D	543341557	543342856	1299	True	1216	1216	83.589000	5	1304	1	chr5D.!!$R3	1299
2	TraesCS5D01G420900	chr5D	541899239	541900023	784	True	841	841	85.987000	5	789	1	chr5D.!!$R2	784
3	TraesCS5D01G420900	chr3D	480855737	480857039	1302	False	2030	2030	94.781000	2	1304	1	chr3D.!!$F1	1302
4	TraesCS5D01G420900	chr3D	1288636	1289742	1106	True	1061	1061	83.978000	195	1303	1	chr3D.!!$R1	1108
5	TraesCS5D01G420900	chr2A	104771487	104772768	1281	True	1936	1936	93.774000	1	1301	1	chr2A.!!$R1	1300
6	TraesCS5D01G420900	chr2A	683007013	683007860	847	True	747	747	82.588000	457	1304	1	chr2A.!!$R2	847
7	TraesCS5D01G420900	chr6B	610301124	610302426	1302	False	1596	1596	88.795000	2	1302	1	chr6B.!!$F1	1300
8	TraesCS5D01G420900	chr6A	189525406	189526693	1287	True	1277	1277	84.562000	17	1304	1	chr6A.!!$R1	1287
9	TraesCS5D01G420900	chr1D	12195800	12197099	1299	True	1216	1216	83.576000	5	1305	1	chr1D.!!$R1	1300
10	TraesCS5D01G420900	chr5A	330175920	330177092	1172	True	761	761	78.511000	131	1306	1	chr5A.!!$R1	1175
11	TraesCS5D01G420900	chr5A	600359284	600360015	731	True	691	691	84.459000	1305	2011	1	chr5A.!!$R2	706
12	TraesCS5D01G420900	chr5B	589890896	589891693	797	True	345	743	93.229333	1541	2273	3	chr5B.!!$R2	732

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
333	335	0.482446	TGTGGAAAGCCCTGTGGAAT	59.518	50.0	0.0	0.0	35.38	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1922	2022	0.039798	GTGGCACGAGTCGTTCTACA	60.04	55.0	22.71	13.7	38.32	2.74	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
116	118	5.083533	AGACAGGATTTGATCAGAGACAC	57.916	43.478	0.00	0.00	0.00	3.67
231	233	2.319136	ACTACACTGTGAAAACGGCA	57.681	45.000	15.86	0.00	0.00	5.69
333	335	0.482446	TGTGGAAAGCCCTGTGGAAT	59.518	50.000	0.00	0.00	35.38	3.01
421	423	4.472691	ACAACACTCAAACATCGACATG	57.527	40.909	0.00	0.00	35.92	3.21
433	435	0.604073	TCGACATGTTGCGGAGGTTA	59.396	50.000	8.34	0.00	0.00	2.85
681	684	3.118261	ACCGTATCAAGCATGGTGAAGAT	60.118	43.478	0.00	5.63	33.92	2.40
1018	1021	0.976641	AATGGAAGTGGACTGCTCGA	59.023	50.000	0.00	0.00	0.00	4.04
1072	1075	4.119442	TCTCGTTCTATTGTGGCTTACC	57.881	45.455	0.00	0.00	0.00	2.85
1148	1151	9.967346	TTGTCATGTAAGTAGATCAGCTAATAC	57.033	33.333	0.00	0.00	0.00	1.89
1266	1269	4.624452	GCTGATTGTTCCAAGAATGCTTTC	59.376	41.667	4.20	4.20	30.14	2.62
1320	1324	3.825143	AAAAAGGATATGCATGTGGCC	57.175	42.857	10.16	0.00	43.89	5.36
1328	1332	0.322322	ATGCATGTGGCCTTTGTTGG	59.678	50.000	3.32	0.00	43.89	3.77
1356	1368	1.980844	GCAAATGTGAGCAATGACACG	59.019	47.619	0.00	0.00	39.52	4.49
1363	1375	2.736721	GTGAGCAATGACACGTACACAT	59.263	45.455	0.00	0.00	0.00	3.21
1364	1376	2.736192	TGAGCAATGACACGTACACATG	59.264	45.455	0.00	0.00	0.00	3.21
1365	1377	2.736721	GAGCAATGACACGTACACATGT	59.263	45.455	0.00	0.00	0.00	3.21
1366	1378	2.480037	AGCAATGACACGTACACATGTG	59.520	45.455	24.25	24.25	45.58	3.21
1377	1389	6.907533	CACGTACACATGTGTTTTTCTTTTC	58.092	36.000	34.66	13.42	41.83	2.29
1386	1398	3.308595	GTGTTTTTCTTTTCTTTGCGGGG	59.691	43.478	0.00	0.00	0.00	5.73
1415	1427	5.221461	ACACACGAGTTATCTTCAAGAAGGT	60.221	40.000	9.73	5.44	38.88	3.50
1418	1430	5.346281	CACGAGTTATCTTCAAGAAGGTGAC	59.654	44.000	9.29	9.29	38.04	3.67
1434	1446	4.906618	AGGTGACTGATTAATGTCGGTTT	58.093	39.130	0.00	0.00	41.13	3.27
1438	1450	2.752903	ACTGATTAATGTCGGTTTGGCC	59.247	45.455	0.00	0.00	34.06	5.36
1488	1500	7.541916	ACTACTATGCCTTATTACTCCTTCC	57.458	40.000	0.00	0.00	0.00	3.46
1490	1502	6.176014	ACTATGCCTTATTACTCCTTCCAC	57.824	41.667	0.00	0.00	0.00	4.02
1504	1516	7.511959	ACTCCTTCCACAGAAAAATAAAGTC	57.488	36.000	0.00	0.00	0.00	3.01
1513	1525	7.542130	CCACAGAAAAATAAAGTCCATAACTGC	59.458	37.037	0.00	0.00	38.58	4.40
1520	1532	6.764877	ATAAAGTCCATAACTGCGTATTCG	57.235	37.500	0.00	0.00	38.58	3.34
1666	1711	4.160252	GGATTTGGTATTGCAGGTGTGATT	59.840	41.667	0.00	0.00	0.00	2.57
1792	1870	7.873719	TTCATCTGTGTTGAGTTTAAGGAAA	57.126	32.000	0.00	0.00	0.00	3.13
1807	1887	7.869429	AGTTTAAGGAAATTTCTTGCATGAGTG	59.131	33.333	17.42	0.00	0.00	3.51
1810	1890	5.776744	AGGAAATTTCTTGCATGAGTGTTC	58.223	37.500	17.42	7.32	0.00	3.18
1907	1999	6.926280	TGTGAATCAACGAATAAAATGTGC	57.074	33.333	0.00	0.00	0.00	4.57
1939	2039	1.071567	GCTGTAGAACGACTCGTGCC	61.072	60.000	4.50	0.57	39.99	5.01
1940	2040	0.240145	CTGTAGAACGACTCGTGCCA	59.760	55.000	4.50	0.00	39.99	4.92
1964	2064	8.135529	CCACGAGTAATACATTTCTCTCATACA	58.864	37.037	0.00	0.00	33.61	2.29
1999	2101	3.066064	CGTGGGAAAGAAAATGTGACACA	59.934	43.478	11.41	11.41	0.00	3.72
2013	2115	8.500753	AAATGTGACACATATATTTACGTGGT	57.499	30.769	21.10	0.00	37.97	4.16
2045	2147	3.139077	ACAATGTGGTTTTCTCTCGGTC	58.861	45.455	0.00	0.00	0.00	4.79
2050	2152	0.244178	GGTTTTCTCTCGGTCGCTCT	59.756	55.000	0.00	0.00	0.00	4.09
2065	2167	1.202313	CGCTCTAGAGTAACAGTGCCC	60.202	57.143	20.75	0.00	0.00	5.36
2082	2184	0.039165	CCCAGAGGCGAAAAACAAGC	60.039	55.000	0.00	0.00	0.00	4.01
2102	2204	1.152312	ACACGAGAGGGGTGGTTCT	60.152	57.895	0.00	0.00	40.46	3.01
2104	2206	1.913762	ACGAGAGGGGTGGTTCTGG	60.914	63.158	0.00	0.00	0.00	3.86
2147	2249	4.035102	GCCTCCGGTGGCCTCTTT	62.035	66.667	32.87	0.00	46.82	2.52
2149	2251	2.750350	CTCCGGTGGCCTCTTTGT	59.250	61.111	3.32	0.00	0.00	2.83
2176	2278	1.102978	GGTGGGGGAAATCATCGTTG	58.897	55.000	0.00	0.00	0.00	4.10
2182	2284	1.062587	GGGAAATCATCGTTGACTGCG	59.937	52.381	0.00	0.00	33.85	5.18
2183	2285	1.529826	GGAAATCATCGTTGACTGCGC	60.530	52.381	0.00	0.00	33.85	6.09
2202	2304	0.462789	CGGCCGTGTAGATAGGGTTT	59.537	55.000	19.50	0.00	0.00	3.27
2203	2305	1.805120	CGGCCGTGTAGATAGGGTTTG	60.805	57.143	19.50	0.00	0.00	2.93
2205	2307	2.355412	GGCCGTGTAGATAGGGTTTGTT	60.355	50.000	0.00	0.00	0.00	2.83
2206	2308	3.118665	GGCCGTGTAGATAGGGTTTGTTA	60.119	47.826	0.00	0.00	0.00	2.41
2225	2327	5.488341	TGTTAGGTAGTTTCTCCAAGCATC	58.512	41.667	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	3.254166	GTGAAACAGGTGTCATGCTGATT	59.746	43.478	5.23	0.08	36.32	2.57
116	118	2.479730	GCAGCATCAGAAGCAATGAAGG	60.480	50.000	0.00	0.00	0.00	3.46
231	233	2.447443	TGAGTCACAAGAGAGCGGTAT	58.553	47.619	0.00	0.00	0.00	2.73
264	266	1.770294	CCGTCCCTTCTTCTAGAGCT	58.230	55.000	0.00	0.00	0.00	4.09
273	275	2.758737	CCGGTAGCCGTCCCTTCT	60.759	66.667	6.82	0.00	46.80	2.85
365	367	1.668294	CCACGAAGCACTCTCCACT	59.332	57.895	0.00	0.00	0.00	4.00
421	423	1.130561	GCATTGACTAACCTCCGCAAC	59.869	52.381	0.00	0.00	0.00	4.17
433	435	6.090898	GTCGTTAGACATACTTTGCATTGACT	59.909	38.462	0.00	0.00	46.32	3.41
1018	1021	3.864789	ATTCCAGAGTGTCACCAACTT	57.135	42.857	0.00	0.00	0.00	2.66
1072	1075	8.049117	ACTGAGCTCTCCTATCTCATCTAATAG	58.951	40.741	16.19	0.00	36.41	1.73
1147	1150	3.161450	ACATAGATGCGCCGGGGT	61.161	61.111	20.83	0.00	0.00	4.95
1148	1151	2.666190	CACATAGATGCGCCGGGG	60.666	66.667	15.40	15.40	0.00	5.73
1266	1269	7.597743	GGCAAATTGGAGAGCTTTATTCATATG	59.402	37.037	0.00	0.00	0.00	1.78
1320	1324	4.404654	GCTCCGCCGCCAACAAAG	62.405	66.667	0.00	0.00	0.00	2.77
1328	1332	3.386867	CTCACATTTGCTCCGCCGC	62.387	63.158	0.00	0.00	0.00	6.53
1330	1334	1.865788	TTGCTCACATTTGCTCCGCC	61.866	55.000	0.00	0.00	0.00	6.13
1332	1336	1.469703	TCATTGCTCACATTTGCTCCG	59.530	47.619	0.00	0.00	0.00	4.63
1356	1368	7.897800	GCAAAGAAAAGAAAAACACATGTGTAC	59.102	33.333	30.75	20.61	44.13	2.90
1363	1375	3.929610	CCCGCAAAGAAAAGAAAAACACA	59.070	39.130	0.00	0.00	0.00	3.72
1364	1376	3.308595	CCCCGCAAAGAAAAGAAAAACAC	59.691	43.478	0.00	0.00	0.00	3.32
1365	1377	3.195825	TCCCCGCAAAGAAAAGAAAAACA	59.804	39.130	0.00	0.00	0.00	2.83
1366	1378	3.554324	GTCCCCGCAAAGAAAAGAAAAAC	59.446	43.478	0.00	0.00	0.00	2.43
1367	1379	3.735514	CGTCCCCGCAAAGAAAAGAAAAA	60.736	43.478	0.00	0.00	0.00	1.94
1368	1380	2.223618	CGTCCCCGCAAAGAAAAGAAAA	60.224	45.455	0.00	0.00	0.00	2.29
1369	1381	1.335496	CGTCCCCGCAAAGAAAAGAAA	59.665	47.619	0.00	0.00	0.00	2.52
1370	1382	0.948678	CGTCCCCGCAAAGAAAAGAA	59.051	50.000	0.00	0.00	0.00	2.52
1371	1383	0.179040	ACGTCCCCGCAAAGAAAAGA	60.179	50.000	0.00	0.00	37.70	2.52
1372	1384	1.196127	GTACGTCCCCGCAAAGAAAAG	59.804	52.381	0.00	0.00	37.70	2.27
1373	1385	1.228533	GTACGTCCCCGCAAAGAAAA	58.771	50.000	0.00	0.00	37.70	2.29
1377	1389	1.301087	TGTGTACGTCCCCGCAAAG	60.301	57.895	0.00	0.00	37.70	2.77
1394	1406	5.346281	GTCACCTTCTTGAAGATAACTCGTG	59.654	44.000	11.53	8.92	0.00	4.35
1396	1408	5.574830	CAGTCACCTTCTTGAAGATAACTCG	59.425	44.000	11.53	0.00	0.00	4.18
1398	1410	6.672266	TCAGTCACCTTCTTGAAGATAACT	57.328	37.500	11.53	8.27	0.00	2.24
1412	1424	4.553330	AACCGACATTAATCAGTCACCT	57.447	40.909	6.71	0.00	34.48	4.00
1415	1427	3.438781	GCCAAACCGACATTAATCAGTCA	59.561	43.478	6.71	0.00	34.48	3.41
1418	1430	2.752354	TGGCCAAACCGACATTAATCAG	59.248	45.455	0.61	0.00	43.94	2.90
1438	1450	0.960364	AGGCAACACGGGCATACTTG	60.960	55.000	0.00	0.00	41.41	3.16
1488	1500	7.271223	CGCAGTTATGGACTTTATTTTTCTGTG	59.729	37.037	0.00	0.00	36.10	3.66
1490	1502	7.305474	ACGCAGTTATGGACTTTATTTTTCTG	58.695	34.615	0.00	0.00	37.78	3.02
1500	1512	4.380841	TCGAATACGCAGTTATGGACTT	57.619	40.909	0.00	0.00	37.78	3.01
1501	1513	4.585955	ATCGAATACGCAGTTATGGACT	57.414	40.909	0.00	0.00	37.78	3.85
1639	1683	5.302568	CACACCTGCAATACCAAATCCATAT	59.697	40.000	0.00	0.00	0.00	1.78
1643	1687	3.088532	TCACACCTGCAATACCAAATCC	58.911	45.455	0.00	0.00	0.00	3.01
1792	1870	5.437289	TTTCGAACACTCATGCAAGAAAT	57.563	34.783	0.00	0.00	0.00	2.17
1817	1900	9.528018	ACACATTTTGTTCGTTGATTAGATTTT	57.472	25.926	0.00	0.00	33.09	1.82
1820	1903	6.582295	GCACACATTTTGTTCGTTGATTAGAT	59.418	34.615	0.00	0.00	35.67	1.98
1822	1905	5.914635	AGCACACATTTTGTTCGTTGATTAG	59.085	36.000	0.00	0.00	35.67	1.73
1907	1999	8.182881	AGTCGTTCTACAGCTTTACTTGTATAG	58.817	37.037	0.00	0.00	0.00	1.31
1922	2022	0.039798	GTGGCACGAGTCGTTCTACA	60.040	55.000	22.71	13.70	38.32	2.74
1939	2039	9.516314	TTGTATGAGAGAAATGTATTACTCGTG	57.484	33.333	0.00	0.00	34.98	4.35
1940	2040	9.517609	GTTGTATGAGAGAAATGTATTACTCGT	57.482	33.333	0.00	0.00	34.98	4.18
2013	2115	4.330944	AACCACATTGTCGTGTCTTCTA	57.669	40.909	0.00	0.00	34.98	2.10
2029	2131	0.319641	AGCGACCGAGAGAAAACCAC	60.320	55.000	0.00	0.00	0.00	4.16
2045	2147	1.202313	GGGCACTGTTACTCTAGAGCG	60.202	57.143	19.97	5.94	32.34	5.03
2050	2152	2.457598	CCTCTGGGCACTGTTACTCTA	58.542	52.381	0.00	0.00	0.00	2.43
2065	2167	0.586319	TCGCTTGTTTTTCGCCTCTG	59.414	50.000	0.00	0.00	0.00	3.35
2080	2182	3.374402	CACCCCTCTCGTGTCGCT	61.374	66.667	0.00	0.00	0.00	4.93
2082	2184	2.488087	GAACCACCCCTCTCGTGTCG	62.488	65.000	0.00	0.00	0.00	4.35
2140	2242	2.747855	CTCCCGGCACAAAGAGGC	60.748	66.667	0.00	0.00	0.00	4.70
2153	2255	0.186143	GATGATTTCCCCCACCTCCC	59.814	60.000	0.00	0.00	0.00	4.30
2166	2268	1.695893	CCGCGCAGTCAACGATGATT	61.696	55.000	8.75	0.00	38.01	2.57
2168	2270	2.809174	CCGCGCAGTCAACGATGA	60.809	61.111	8.75	0.00	0.00	2.92
2182	2284	2.024590	AACCCTATCTACACGGCCGC	62.025	60.000	28.58	0.00	0.00	6.53
2183	2285	0.462789	AAACCCTATCTACACGGCCG	59.537	55.000	26.86	26.86	0.00	6.13
2202	2304	4.967084	TGCTTGGAGAAACTACCTAACA	57.033	40.909	0.00	0.00	0.00	2.41
2203	2305	4.567159	CGATGCTTGGAGAAACTACCTAAC	59.433	45.833	0.00	0.00	0.00	2.34
2205	2307	3.132289	CCGATGCTTGGAGAAACTACCTA	59.868	47.826	0.00	0.00	0.00	3.08
2206	2308	2.093447	CCGATGCTTGGAGAAACTACCT	60.093	50.000	0.00	0.00	0.00	3.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.