AutoCloner

Multiple sequence alignment - TraesCS3B01G272800

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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	TraesCS3B01G272800	chr3B	100.000	2240	0	0	1	2240	439335559	439333320	0.000000e+00	4137.0
1	TraesCS3B01G272800	chr3B	92.551	1329	95	2	1	1329	448775769	448777093	0.000000e+00	1903.0
2	TraesCS3B01G272800	chr3B	75.758	198	43	3	1827	2023	90858382	90858575	6.590000e-16	95.3
3	TraesCS3B01G272800	chr5B	96.319	1331	48	1	1	1331	330791348	330792677	0.000000e+00	2185.0
4	TraesCS3B01G272800	chr5A	95.639	1330	58	0	1	1330	328959221	328960550	0.000000e+00	2135.0
5	TraesCS3B01G272800	chr4D	92.916	1327	91	3	1	1327	488794749	488793426	0.000000e+00	1927.0
6	TraesCS3B01G272800	chr4B	92.551	1329	98	1	1	1329	173350417	173351744	0.000000e+00	1905.0
7	TraesCS3B01G272800	chr3D	91.660	1331	108	3	1	1330	496689292	496690620	0.000000e+00	1840.0
8	TraesCS3B01G272800	chr3D	97.345	791	18	1	1453	2240	340416104	340415314	0.000000e+00	1341.0
9	TraesCS3B01G272800	chr3D	75.758	198	43	3	1827	2023	58080799	58080992	6.590000e-16	95.3
10	TraesCS3B01G272800	chr5D	91.454	1334	112	2	1	1332	271704698	271706031	0.000000e+00	1831.0
11	TraesCS3B01G272800	chr1A	91.491	1328	113	0	1	1328	179528453	179527126	0.000000e+00	1827.0
12	TraesCS3B01G272800	chr1A	80.800	375	55	11	1839	2206	562784804	562785168	6.090000e-71	278.0
13	TraesCS3B01G272800	chr2B	89.425	1286	130	4	1	1284	313414243	313412962	0.000000e+00	1616.0
14	TraesCS3B01G272800	chr3A	94.737	836	24	7	1406	2240	464319429	464320245	0.000000e+00	1282.0
15	TraesCS3B01G272800	chr3A	75.635	197	42	4	1828	2023	66907967	66908158	2.370000e-15	93.5
16	TraesCS3B01G272800	chr1B	80.990	384	56	11	1830	2206	649368730	649369103	2.810000e-74	289.0
17	TraesCS3B01G272800	chr1D	80.260	385	57	13	1830	2206	469587034	469587407	2.830000e-69	272.0

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	TraesCS3B01G272800	chr3B	439333320	439335559	2239	True	4137	4137	100.000	1	2240	1	chr3B.!!$R1	2239
1	TraesCS3B01G272800	chr3B	448775769	448777093	1324	False	1903	1903	92.551	1	1329	1	chr3B.!!$F2	1328
2	TraesCS3B01G272800	chr5B	330791348	330792677	1329	False	2185	2185	96.319	1	1331	1	chr5B.!!$F1	1330
3	TraesCS3B01G272800	chr5A	328959221	328960550	1329	False	2135	2135	95.639	1	1330	1	chr5A.!!$F1	1329
4	TraesCS3B01G272800	chr4D	488793426	488794749	1323	True	1927	1927	92.916	1	1327	1	chr4D.!!$R1	1326
5	TraesCS3B01G272800	chr4B	173350417	173351744	1327	False	1905	1905	92.551	1	1329	1	chr4B.!!$F1	1328
6	TraesCS3B01G272800	chr3D	496689292	496690620	1328	False	1840	1840	91.660	1	1330	1	chr3D.!!$F2	1329
7	TraesCS3B01G272800	chr3D	340415314	340416104	790	True	1341	1341	97.345	1453	2240	1	chr3D.!!$R1	787
8	TraesCS3B01G272800	chr5D	271704698	271706031	1333	False	1831	1831	91.454	1	1332	1	chr5D.!!$F1	1331
9	TraesCS3B01G272800	chr1A	179527126	179528453	1327	True	1827	1827	91.491	1	1328	1	chr1A.!!$R1	1327
10	TraesCS3B01G272800	chr2B	313412962	313414243	1281	True	1616	1616	89.425	1	1284	1	chr2B.!!$R1	1283
11	TraesCS3B01G272800	chr3A	464319429	464320245	816	False	1282	1282	94.737	1406	2240	1	chr3A.!!$F2	834

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
940	943	0.250124	ATGTCGTTTCACCCTTCGCA	60.25	50.0	0.0	0.0	0.0	5.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2052	2059	3.017581	AGGATGTGGGCCTGGACC	61.018	66.667	13.16	13.16	33.59	4.46	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
367	369	1.677637	TATGGGCACGCCATGTACGA	61.678	55.000	10.83	0.00	37.98	3.43
392	394	4.664150	AGGAAAAAGATTTGTTTGCGGA	57.336	36.364	0.00	0.00	31.10	5.54
414	416	1.472728	GCCACTATAGTCACGGTTGGG	60.473	57.143	1.26	0.00	0.00	4.12
505	507	6.825721	ACCTGACATCTTTGATCTATCCAAAC	59.174	38.462	0.00	0.00	31.13	2.93
537	539	0.652592	CGGTCCAGCAAGCTTTATCG	59.347	55.000	0.00	0.00	0.00	2.92
583	585	2.099098	GACATTTCCAATGGCCTAACCG	59.901	50.000	3.32	0.00	43.94	4.44
632	634	1.549203	TGGGAAAAGATTGCTCAGGC	58.451	50.000	0.00	0.00	39.26	4.85
901	904	1.806542	GCAAGCAAAGTCAGGAATCGA	59.193	47.619	0.00	0.00	0.00	3.59
940	943	0.250124	ATGTCGTTTCACCCTTCGCA	60.250	50.000	0.00	0.00	0.00	5.10
1001	1004	2.158769	TCAATACCGCAGCTTGGATGAT	60.159	45.455	8.75	0.00	0.00	2.45
1034	1037	0.995024	AGGGAATGGTGGACAGGAAG	59.005	55.000	0.00	0.00	0.00	3.46
1240	1243	1.385528	TGTAATGGCGCGAGAGTAGA	58.614	50.000	12.10	0.00	0.00	2.59
1284	1287	4.082136	TGTGGCGTTGTTTAAACCTTCTTT	60.082	37.500	15.59	0.00	0.00	2.52
1291	1294	9.027129	GCGTTGTTTAAACCTTCTTTCTTAATT	57.973	29.630	15.59	0.00	0.00	1.40
1344	1347	1.358759	AAAAAGTTCTGCACGGCCG	59.641	52.632	26.86	26.86	0.00	6.13
1345	1348	1.381165	AAAAAGTTCTGCACGGCCGT	61.381	50.000	28.70	28.70	0.00	5.68
1346	1349	1.381165	AAAAGTTCTGCACGGCCGTT	61.381	50.000	32.11	9.86	0.00	4.44
1347	1350	2.058829	AAAGTTCTGCACGGCCGTTG	62.059	55.000	32.11	24.32	0.00	4.10
1348	1351	4.683334	GTTCTGCACGGCCGTTGC	62.683	66.667	32.27	32.27	0.00	4.17
1357	1360	2.746277	GGCCGTTGCGTGGAGATT	60.746	61.111	0.00	0.00	38.85	2.40
1358	1361	2.750888	GGCCGTTGCGTGGAGATTC	61.751	63.158	0.00	0.00	38.85	2.52
1359	1362	1.741770	GCCGTTGCGTGGAGATTCT	60.742	57.895	0.00	0.00	0.00	2.40
1360	1363	1.696832	GCCGTTGCGTGGAGATTCTC	61.697	60.000	5.03	5.03	0.00	2.87
1361	1364	1.413767	CCGTTGCGTGGAGATTCTCG	61.414	60.000	7.57	0.00	0.00	4.04
1362	1365	0.732880	CGTTGCGTGGAGATTCTCGT	60.733	55.000	7.57	0.00	0.00	4.18
1363	1366	0.716108	GTTGCGTGGAGATTCTCGTG	59.284	55.000	7.57	1.50	0.00	4.35
1364	1367	0.317160	TTGCGTGGAGATTCTCGTGT	59.683	50.000	7.57	0.00	0.00	4.49
1365	1368	0.388520	TGCGTGGAGATTCTCGTGTG	60.389	55.000	7.57	0.00	0.00	3.82
1366	1369	1.687494	GCGTGGAGATTCTCGTGTGC	61.687	60.000	7.57	5.53	0.00	4.57
1367	1370	1.406219	CGTGGAGATTCTCGTGTGCG	61.406	60.000	7.57	4.17	39.92	5.34
1368	1371	0.109272	GTGGAGATTCTCGTGTGCGA	60.109	55.000	7.57	0.00	45.79	5.10
1369	1372	0.109272	TGGAGATTCTCGTGTGCGAC	60.109	55.000	7.57	0.00	42.81	5.19
1370	1373	0.802607	GGAGATTCTCGTGTGCGACC	60.803	60.000	7.57	0.00	42.81	4.79
1371	1374	1.134530	GAGATTCTCGTGTGCGACCG	61.135	60.000	0.00	0.00	42.81	4.79
1372	1375	2.789203	GATTCTCGTGTGCGACCGC	61.789	63.158	7.53	7.53	42.81	5.68
1394	1397	2.125310	CGCTCCCGCACACCATTA	60.125	61.111	0.00	0.00	35.30	1.90
1395	1398	1.743623	CGCTCCCGCACACCATTAA	60.744	57.895	0.00	0.00	35.30	1.40
1396	1399	1.302383	CGCTCCCGCACACCATTAAA	61.302	55.000	0.00	0.00	35.30	1.52
1397	1400	1.102978	GCTCCCGCACACCATTAAAT	58.897	50.000	0.00	0.00	35.78	1.40
1398	1401	1.065551	GCTCCCGCACACCATTAAATC	59.934	52.381	0.00	0.00	35.78	2.17
1399	1402	2.364632	CTCCCGCACACCATTAAATCA	58.635	47.619	0.00	0.00	0.00	2.57
1400	1403	2.951642	CTCCCGCACACCATTAAATCAT	59.048	45.455	0.00	0.00	0.00	2.45
1401	1404	2.948979	TCCCGCACACCATTAAATCATC	59.051	45.455	0.00	0.00	0.00	2.92
1402	1405	2.687425	CCCGCACACCATTAAATCATCA	59.313	45.455	0.00	0.00	0.00	3.07
1403	1406	3.489059	CCCGCACACCATTAAATCATCAC	60.489	47.826	0.00	0.00	0.00	3.06
1404	1407	3.353524	CGCACACCATTAAATCATCACG	58.646	45.455	0.00	0.00	0.00	4.35
1435	1438	3.332034	ACGCACCATTAACCTTACTCAC	58.668	45.455	0.00	0.00	0.00	3.51
1436	1439	2.347452	CGCACCATTAACCTTACTCACG	59.653	50.000	0.00	0.00	0.00	4.35
1437	1440	2.095372	GCACCATTAACCTTACTCACGC	59.905	50.000	0.00	0.00	0.00	5.34
1438	1441	3.331150	CACCATTAACCTTACTCACGCA	58.669	45.455	0.00	0.00	0.00	5.24
1439	1442	3.749088	CACCATTAACCTTACTCACGCAA	59.251	43.478	0.00	0.00	0.00	4.85
1440	1443	4.394920	CACCATTAACCTTACTCACGCAAT	59.605	41.667	0.00	0.00	0.00	3.56
1441	1444	4.394920	ACCATTAACCTTACTCACGCAATG	59.605	41.667	0.00	0.00	0.00	2.82
1442	1445	4.342772	CATTAACCTTACTCACGCAATGC	58.657	43.478	0.00	0.00	0.00	3.56
1443	1446	1.890876	AACCTTACTCACGCAATGCA	58.109	45.000	5.91	0.00	0.00	3.96
1444	1447	1.156736	ACCTTACTCACGCAATGCAC	58.843	50.000	5.91	0.00	0.00	4.57
1445	1448	1.270839	ACCTTACTCACGCAATGCACT	60.271	47.619	5.91	0.00	0.00	4.40
1446	1449	1.394917	CCTTACTCACGCAATGCACTC	59.605	52.381	5.91	0.00	0.00	3.51
1447	1450	1.394917	CTTACTCACGCAATGCACTCC	59.605	52.381	5.91	0.00	0.00	3.85
1448	1451	0.735978	TACTCACGCAATGCACTCCG	60.736	55.000	5.91	0.00	0.00	4.63
1471	1474	1.202510	GCATTGCGGCCCATTTCATTA	60.203	47.619	0.00	0.00	0.00	1.90
1493	1496	2.088763	CGCACAGCATCGTCTCGTT	61.089	57.895	0.00	0.00	0.00	3.85
1636	1640	0.811915	CGTCGGCCTCCCTATATCAG	59.188	60.000	0.00	0.00	0.00	2.90
1652	1656	3.246112	AGCCAACACTACCCGCCA	61.246	61.111	0.00	0.00	0.00	5.69
1678	1685	0.739813	GATCACACGCACTACCACCC	60.740	60.000	0.00	0.00	0.00	4.61
1700	1707	1.548357	GCTCTCTCCTGCAACCTCCA	61.548	60.000	0.00	0.00	0.00	3.86
1764	1771	3.071459	GAGCGGCATTGTCGTCGTG	62.071	63.158	12.79	0.00	31.29	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
160	161	2.513666	CCAAAGATAGGCGCGGCA	60.514	61.111	34.94	20.49	0.00	5.69
367	369	5.064579	CCGCAAACAAATCTTTTTCCTTGTT	59.935	36.000	0.00	0.00	42.30	2.83
392	394	2.158957	CCAACCGTGACTATAGTGGCAT	60.159	50.000	10.90	0.00	0.00	4.40
505	507	1.532868	CTGGACCGAGCAGTTTTTCTG	59.467	52.381	0.00	0.00	46.12	3.02
622	624	0.178981	ACAAGTGTGGCCTGAGCAAT	60.179	50.000	3.32	0.00	42.56	3.56
632	634	4.194640	CTCCATATCCTCAACAAGTGTGG	58.805	47.826	0.00	0.00	41.50	4.17
901	904	2.590114	GGAACAGTAGGTGGGCCGT	61.590	63.158	0.00	0.00	40.50	5.68
940	943	4.708421	CCACTGGAGAATTTCATTCCACAT	59.292	41.667	3.82	0.00	40.13	3.21
1001	1004	2.037367	CCCTCACCGAGACCCTCA	59.963	66.667	0.00	0.00	0.00	3.86
1034	1037	3.307242	GGATTCGCTACGGATATGAATGC	59.693	47.826	0.00	0.00	31.83	3.56
1240	1243	4.202212	ACAAAGCGGCAAGAAAATAAAGGT	60.202	37.500	1.45	0.00	0.00	3.50
1296	1299	7.984050	TGAAACAAGGCAAAAGATTTGTCATTA	59.016	29.630	9.76	0.00	32.97	1.90
1331	1334	4.683334	GCAACGGCCGTGCAGAAC	62.683	66.667	34.95	13.95	0.00	3.01
1340	1343	2.746277	AATCTCCACGCAACGGCC	60.746	61.111	0.00	0.00	36.38	6.13
1341	1344	1.696832	GAGAATCTCCACGCAACGGC	61.697	60.000	0.00	0.00	0.00	5.68
1342	1345	1.413767	CGAGAATCTCCACGCAACGG	61.414	60.000	4.47	0.00	0.00	4.44
1343	1346	0.732880	ACGAGAATCTCCACGCAACG	60.733	55.000	4.47	0.00	0.00	4.10
1344	1347	0.716108	CACGAGAATCTCCACGCAAC	59.284	55.000	4.47	0.00	0.00	4.17
1345	1348	0.317160	ACACGAGAATCTCCACGCAA	59.683	50.000	4.47	0.00	0.00	4.85
1346	1349	0.388520	CACACGAGAATCTCCACGCA	60.389	55.000	4.47	0.00	0.00	5.24
1347	1350	1.687494	GCACACGAGAATCTCCACGC	61.687	60.000	4.47	0.00	0.00	5.34
1348	1351	1.406219	CGCACACGAGAATCTCCACG	61.406	60.000	4.47	0.00	43.93	4.94
1349	1352	0.109272	TCGCACACGAGAATCTCCAC	60.109	55.000	4.47	0.00	45.12	4.02
1350	1353	2.263153	TCGCACACGAGAATCTCCA	58.737	52.632	4.47	0.00	45.12	3.86
1379	1382	2.364632	TGATTTAATGGTGTGCGGGAG	58.635	47.619	0.00	0.00	0.00	4.30
1380	1383	2.498644	TGATTTAATGGTGTGCGGGA	57.501	45.000	0.00	0.00	0.00	5.14
1381	1384	2.687425	TGATGATTTAATGGTGTGCGGG	59.313	45.455	0.00	0.00	0.00	6.13
1382	1385	3.694734	GTGATGATTTAATGGTGTGCGG	58.305	45.455	0.00	0.00	0.00	5.69
1383	1386	3.063316	TCGTGATGATTTAATGGTGTGCG	59.937	43.478	0.00	0.00	0.00	5.34
1384	1387	4.342772	GTCGTGATGATTTAATGGTGTGC	58.657	43.478	0.00	0.00	0.00	4.57
1385	1388	4.328712	TCGTCGTGATGATTTAATGGTGTG	59.671	41.667	0.00	0.00	0.00	3.82
1386	1389	4.500127	TCGTCGTGATGATTTAATGGTGT	58.500	39.130	0.00	0.00	0.00	4.16
1387	1390	5.610338	CGATCGTCGTGATGATTTAATGGTG	60.610	44.000	7.03	0.00	37.47	4.17
1388	1391	4.444388	CGATCGTCGTGATGATTTAATGGT	59.556	41.667	7.03	0.00	37.47	3.55
1389	1392	4.143326	CCGATCGTCGTGATGATTTAATGG	60.143	45.833	15.09	1.50	38.40	3.16
1390	1393	4.444388	ACCGATCGTCGTGATGATTTAATG	59.556	41.667	15.09	0.00	38.40	1.90
1391	1394	4.617959	ACCGATCGTCGTGATGATTTAAT	58.382	39.130	15.09	0.00	38.40	1.40
1392	1395	4.036567	ACCGATCGTCGTGATGATTTAA	57.963	40.909	15.09	0.00	38.40	1.52
1393	1396	3.703286	ACCGATCGTCGTGATGATTTA	57.297	42.857	15.09	0.00	38.40	1.40
1394	1397	2.579207	ACCGATCGTCGTGATGATTT	57.421	45.000	15.09	0.00	38.40	2.17
1395	1398	2.601504	CGTACCGATCGTCGTGATGATT	60.602	50.000	15.09	0.00	38.40	2.57
1396	1399	1.070108	CGTACCGATCGTCGTGATGAT	60.070	52.381	15.09	4.28	38.40	2.45
1397	1400	0.302589	CGTACCGATCGTCGTGATGA	59.697	55.000	15.09	0.00	38.40	2.92
1398	1401	1.260198	GCGTACCGATCGTCGTGATG	61.260	60.000	15.09	0.00	38.40	3.07
1399	1402	1.010350	GCGTACCGATCGTCGTGAT	60.010	57.895	15.09	0.00	38.40	3.06
1400	1403	2.389809	TGCGTACCGATCGTCGTGA	61.390	57.895	15.09	4.75	38.40	4.35
1401	1404	2.098871	TGCGTACCGATCGTCGTG	59.901	61.111	15.09	0.49	38.40	4.35
1402	1405	2.099062	GTGCGTACCGATCGTCGT	59.901	61.111	15.09	8.31	38.40	4.34
1403	1406	2.649975	GGTGCGTACCGATCGTCG	60.650	66.667	15.09	15.78	37.19	5.12
1448	1451	3.668980	AAATGGGCCGCAATGCAGC	62.669	57.895	4.61	4.61	0.00	5.25
1461	1464	2.787723	GCTGTGCGACGTAATGAAATGG	60.788	50.000	0.00	0.00	0.00	3.16
1471	1474	2.805353	GACGATGCTGTGCGACGT	60.805	61.111	11.73	11.73	42.66	4.34
1493	1496	1.447140	GGAATGTGCGCTACGACCA	60.447	57.895	9.73	0.00	0.00	4.02
1561	1564	2.126189	GTCTGACGGTGCGTACCC	60.126	66.667	17.62	4.49	44.53	3.69
1636	1640	2.045340	ATGGCGGGTAGTGTTGGC	60.045	61.111	0.00	0.00	0.00	4.52
1652	1656	0.530744	AGTGCGTGTGATCGGTACAT	59.469	50.000	0.00	0.00	0.00	2.29
1678	1685	2.125350	GTTGCAGGAGAGAGCGGG	60.125	66.667	0.00	0.00	0.00	6.13
1700	1707	1.531423	CTGGTGCTGCTCTGAACAAT	58.469	50.000	0.00	0.00	0.00	2.71
2052	2059	3.017581	AGGATGTGGGCCTGGACC	61.018	66.667	13.16	13.16	33.59	4.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.