AutoCloner

Multiple sequence alignment - TraesCS3A01G458500

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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	TraesCS3A01G458500	chr3A	100.000	2201	0	0	1	2201	695635727	695633527	0.000000e+00	4065.0
1	TraesCS3A01G458500	chr3A	98.766	1378	17	0	1	1378	695645711	695644334	0.000000e+00	2451.0
2	TraesCS3A01G458500	chr3A	95.364	755	32	3	1447	2199	695627075	695626322	0.000000e+00	1197.0
3	TraesCS3A01G458500	chr3A	91.892	74	6	0	1374	1447	695653365	695653292	1.070000e-18	104.0
4	TraesCS3A01G458500	chr3A	93.846	65	4	0	1379	1443	695615681	695615617	5.000000e-17	99.0
5	TraesCS3A01G458500	chr2A	98.623	1380	17	2	1	1378	726901127	726902506	0.000000e+00	2442.0
6	TraesCS3A01G458500	chr2D	98.550	1379	19	1	1	1378	591991000	591989622	0.000000e+00	2435.0
7	TraesCS3A01G458500	chr2D	98.187	1379	23	2	1	1378	272806922	272808299	0.000000e+00	2407.0
8	TraesCS3A01G458500	chr3B	98.478	1380	19	2	1	1378	201569459	201570838	0.000000e+00	2431.0
9	TraesCS3A01G458500	chr3D	98.333	1380	21	2	1	1378	589258200	589259579	0.000000e+00	2420.0
10	TraesCS3A01G458500	chr3D	95.652	69	3	0	1379	1447	559151400	559151332	6.420000e-21	111.0
11	TraesCS3A01G458500	chr3D	92.754	69	5	0	1379	1447	559155289	559155221	1.390000e-17	100.0
12	TraesCS3A01G458500	chr3D	91.304	69	6	0	1379	1447	559144114	559144046	6.470000e-16	95.3
13	TraesCS3A01G458500	chr7B	98.332	1379	22	1	1	1378	662732241	662730863	0.000000e+00	2418.0
14	TraesCS3A01G458500	chr7B	98.260	1379	23	1	1	1378	663094098	663095476	0.000000e+00	2412.0
15	TraesCS3A01G458500	chr1D	98.261	1380	22	2	1	1378	254530934	254529555	0.000000e+00	2414.0
16	TraesCS3A01G458500	chr1A	95.894	755	25	4	1448	2199	472575543	472574792	0.000000e+00	1218.0
17	TraesCS3A01G458500	chr1A	95.364	755	30	5	1449	2199	83125119	83124366	0.000000e+00	1195.0
18	TraesCS3A01G458500	chr1A	94.716	757	34	5	1447	2198	83118123	83117368	0.000000e+00	1171.0
19	TraesCS3A01G458500	chr6A	95.213	752	34	2	1449	2199	100621161	100620411	0.000000e+00	1188.0
20	TraesCS3A01G458500	chr6A	94.834	755	34	4	1447	2199	552042969	552042218	0.000000e+00	1173.0
21	TraesCS3A01G458500	chr6A	94.591	758	35	5	1447	2201	501469912	501469158	0.000000e+00	1168.0
22	TraesCS3A01G458500	chr7A	95.099	755	33	4	1449	2199	639570856	639570102	0.000000e+00	1186.0
23	TraesCS3A01G458500	chr5A	94.702	755	37	3	1448	2199	489174548	489175302	0.000000e+00	1170.0

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	TraesCS3A01G458500	chr3A	695633527	695635727	2200	True	4065	4065	100.000	1	2201	1	chr3A.!!$R3	2200
1	TraesCS3A01G458500	chr3A	695644334	695645711	1377	True	2451	2451	98.766	1	1378	1	chr3A.!!$R4	1377
2	TraesCS3A01G458500	chr3A	695626322	695627075	753	True	1197	1197	95.364	1447	2199	1	chr3A.!!$R2	752
3	TraesCS3A01G458500	chr2A	726901127	726902506	1379	False	2442	2442	98.623	1	1378	1	chr2A.!!$F1	1377
4	TraesCS3A01G458500	chr2D	591989622	591991000	1378	True	2435	2435	98.550	1	1378	1	chr2D.!!$R1	1377
5	TraesCS3A01G458500	chr2D	272806922	272808299	1377	False	2407	2407	98.187	1	1378	1	chr2D.!!$F1	1377
6	TraesCS3A01G458500	chr3B	201569459	201570838	1379	False	2431	2431	98.478	1	1378	1	chr3B.!!$F1	1377
7	TraesCS3A01G458500	chr3D	589258200	589259579	1379	False	2420	2420	98.333	1	1378	1	chr3D.!!$F1	1377
8	TraesCS3A01G458500	chr7B	662730863	662732241	1378	True	2418	2418	98.332	1	1378	1	chr7B.!!$R1	1377
9	TraesCS3A01G458500	chr7B	663094098	663095476	1378	False	2412	2412	98.260	1	1378	1	chr7B.!!$F1	1377
10	TraesCS3A01G458500	chr1D	254529555	254530934	1379	True	2414	2414	98.261	1	1378	1	chr1D.!!$R1	1377
11	TraesCS3A01G458500	chr1A	472574792	472575543	751	True	1218	1218	95.894	1448	2199	1	chr1A.!!$R3	751
12	TraesCS3A01G458500	chr1A	83124366	83125119	753	True	1195	1195	95.364	1449	2199	1	chr1A.!!$R2	750
13	TraesCS3A01G458500	chr1A	83117368	83118123	755	True	1171	1171	94.716	1447	2198	1	chr1A.!!$R1	751
14	TraesCS3A01G458500	chr6A	100620411	100621161	750	True	1188	1188	95.213	1449	2199	1	chr6A.!!$R1	750
15	TraesCS3A01G458500	chr6A	552042218	552042969	751	True	1173	1173	94.834	1447	2199	1	chr6A.!!$R3	752
16	TraesCS3A01G458500	chr6A	501469158	501469912	754	True	1168	1168	94.591	1447	2201	1	chr6A.!!$R2	754
17	TraesCS3A01G458500	chr7A	639570102	639570856	754	True	1186	1186	95.099	1449	2199	1	chr7A.!!$R1	750
18	TraesCS3A01G458500	chr5A	489174548	489175302	754	False	1170	1170	94.702	1448	2199	1	chr5A.!!$F1	751

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
734	736	1.074889	GAAAGGGACACCAAAGGCCTA	59.925	52.381	5.16	0.0	40.13	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1685	1692	2.290514	CCTTGCTGGATCAAGTTGGAGA	60.291	50.0	2.34	0.0	41.29	3.71	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
571	572	2.091278	CAGGACCTCCCCTACAGTATCA	60.091	54.545	0.00	0.00	34.07	2.15
734	736	1.074889	GAAAGGGACACCAAAGGCCTA	59.925	52.381	5.16	0.00	40.13	3.93
1106	1112	7.497909	GTGGGCTTACTACTTATATGCTTTCAA	59.502	37.037	0.00	0.00	0.00	2.69
1330	1336	0.178903	TGGAACCACCTACAGCTCCT	60.179	55.000	0.00	0.00	39.86	3.69
1378	1384	0.682852	AAACCTTCCCGTCGATGTGA	59.317	50.000	3.52	0.00	0.00	3.58
1379	1385	0.902531	AACCTTCCCGTCGATGTGAT	59.097	50.000	3.52	0.00	0.00	3.06
1380	1386	1.771565	ACCTTCCCGTCGATGTGATA	58.228	50.000	3.52	0.00	0.00	2.15
1381	1387	2.317040	ACCTTCCCGTCGATGTGATAT	58.683	47.619	3.52	0.00	0.00	1.63
1382	1388	3.493334	ACCTTCCCGTCGATGTGATATA	58.507	45.455	3.52	0.00	0.00	0.86
1383	1389	4.087182	ACCTTCCCGTCGATGTGATATAT	58.913	43.478	3.52	0.00	0.00	0.86
1384	1390	4.082190	ACCTTCCCGTCGATGTGATATATG	60.082	45.833	3.52	0.00	0.00	1.78
1385	1391	4.082190	CCTTCCCGTCGATGTGATATATGT	60.082	45.833	3.52	0.00	0.00	2.29
1386	1392	4.696899	TCCCGTCGATGTGATATATGTC	57.303	45.455	3.52	0.00	0.00	3.06
1387	1393	4.332828	TCCCGTCGATGTGATATATGTCT	58.667	43.478	3.52	0.00	0.00	3.41
1388	1394	5.493809	TCCCGTCGATGTGATATATGTCTA	58.506	41.667	3.52	0.00	0.00	2.59
1389	1395	5.585047	TCCCGTCGATGTGATATATGTCTAG	59.415	44.000	3.52	0.00	0.00	2.43
1390	1396	5.354513	CCCGTCGATGTGATATATGTCTAGT	59.645	44.000	3.52	0.00	0.00	2.57
1391	1397	6.537660	CCCGTCGATGTGATATATGTCTAGTA	59.462	42.308	3.52	0.00	0.00	1.82
1392	1398	7.226918	CCCGTCGATGTGATATATGTCTAGTAT	59.773	40.741	3.52	0.00	0.00	2.12
1393	1399	8.613482	CCGTCGATGTGATATATGTCTAGTATT	58.387	37.037	3.52	0.00	0.00	1.89
1394	1400	9.427127	CGTCGATGTGATATATGTCTAGTATTG	57.573	37.037	0.89	0.00	0.00	1.90
1428	1434	5.203060	GAAAAGATCCATACTAGGCGTCT	57.797	43.478	0.00	0.00	0.00	4.18
1429	1435	5.602628	GAAAAGATCCATACTAGGCGTCTT	58.397	41.667	0.00	0.00	35.94	3.01
1430	1436	4.857509	AAGATCCATACTAGGCGTCTTC	57.142	45.455	0.00	0.00	31.84	2.87
1431	1437	4.107127	AGATCCATACTAGGCGTCTTCT	57.893	45.455	0.00	0.00	0.00	2.85
1432	1438	4.076394	AGATCCATACTAGGCGTCTTCTC	58.924	47.826	0.00	0.00	0.00	2.87
1433	1439	3.292492	TCCATACTAGGCGTCTTCTCA	57.708	47.619	0.00	0.00	0.00	3.27
1434	1440	3.628008	TCCATACTAGGCGTCTTCTCAA	58.372	45.455	0.00	0.00	0.00	3.02
1435	1441	4.021229	TCCATACTAGGCGTCTTCTCAAA	58.979	43.478	0.00	0.00	0.00	2.69
1436	1442	4.649674	TCCATACTAGGCGTCTTCTCAAAT	59.350	41.667	0.00	0.00	0.00	2.32
1437	1443	4.985409	CCATACTAGGCGTCTTCTCAAATC	59.015	45.833	0.00	0.00	0.00	2.17
1438	1444	3.528597	ACTAGGCGTCTTCTCAAATCC	57.471	47.619	0.00	0.00	0.00	3.01
1439	1445	3.100671	ACTAGGCGTCTTCTCAAATCCT	58.899	45.455	0.00	0.00	0.00	3.24
1440	1446	2.393271	AGGCGTCTTCTCAAATCCTG	57.607	50.000	0.00	0.00	0.00	3.86
1441	1447	1.902508	AGGCGTCTTCTCAAATCCTGA	59.097	47.619	0.00	0.00	0.00	3.86
1442	1448	2.003301	GGCGTCTTCTCAAATCCTGAC	58.997	52.381	0.00	0.00	0.00	3.51
1443	1449	2.612972	GGCGTCTTCTCAAATCCTGACA	60.613	50.000	0.00	0.00	0.00	3.58
1444	1450	3.265791	GCGTCTTCTCAAATCCTGACAT	58.734	45.455	0.00	0.00	0.00	3.06
1445	1451	3.686726	GCGTCTTCTCAAATCCTGACATT	59.313	43.478	0.00	0.00	0.00	2.71
1458	1464	3.591527	TCCTGACATTACTGTTGGGGAAT	59.408	43.478	6.43	0.00	35.14	3.01
1539	1545	2.284995	AGGGAGAGGGGAGTGCAC	60.285	66.667	9.40	9.40	0.00	4.57
1564	1570	1.378882	TACCCTTGTAGATCGCGCGT	61.379	55.000	30.98	17.41	0.00	6.01
1629	1635	2.238395	TGATCCAAATCACCGATGACCA	59.762	45.455	0.00	0.00	37.79	4.02
1685	1692	2.353406	CGTACGGTTGGGAAGATGTCTT	60.353	50.000	7.57	0.00	39.23	3.01
1715	1722	1.216427	GATCCAGCAAGGGGAAAGGAT	59.784	52.381	0.00	0.00	38.09	3.24
2165	2184	1.676014	CGAAAACCTTCTCGATGGCCT	60.676	52.381	3.32	0.00	37.23	5.19
2170	2189	1.906574	ACCTTCTCGATGGCCTAAACA	59.093	47.619	3.32	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
528	529	2.090760	TGCAAAATAGCTCGATGCCAA	58.909	42.857	10.13	0.00	44.23	4.52
571	572	3.259876	TGGTTAAACTCTACTGCGGTGAT	59.740	43.478	8.92	0.00	0.00	3.06
734	736	3.052186	GGATAGATAGAGAGGGAGGGCAT	60.052	52.174	0.00	0.00	0.00	4.40
1106	1112	1.853963	AGTGCGGAGAGGATAACTGT	58.146	50.000	0.00	0.00	0.00	3.55
1251	1257	1.067776	GGGTTCAGAACGTCGTGAGAT	60.068	52.381	7.22	0.00	45.19	2.75
1389	1395	9.788960	GGATCTTTTCCTTCATTTGTACAATAC	57.211	33.333	9.56	0.00	41.78	1.89
1390	1396	9.527157	TGGATCTTTTCCTTCATTTGTACAATA	57.473	29.630	9.56	1.09	45.68	1.90
1391	1397	8.421249	TGGATCTTTTCCTTCATTTGTACAAT	57.579	30.769	9.56	0.00	45.68	2.71
1392	1398	7.831691	TGGATCTTTTCCTTCATTTGTACAA	57.168	32.000	3.59	3.59	45.68	2.41
1393	1399	8.956426	GTATGGATCTTTTCCTTCATTTGTACA	58.044	33.333	0.00	0.00	45.68	2.90
1394	1400	9.178758	AGTATGGATCTTTTCCTTCATTTGTAC	57.821	33.333	0.00	0.00	45.68	2.90
1396	1402	9.401058	CTAGTATGGATCTTTTCCTTCATTTGT	57.599	33.333	0.00	0.00	45.68	2.83
1397	1403	8.844244	CCTAGTATGGATCTTTTCCTTCATTTG	58.156	37.037	0.00	0.00	45.68	2.32
1398	1404	7.503902	GCCTAGTATGGATCTTTTCCTTCATTT	59.496	37.037	0.00	0.00	45.68	2.32
1399	1405	7.001073	GCCTAGTATGGATCTTTTCCTTCATT	58.999	38.462	0.00	0.00	45.68	2.57
1400	1406	6.538263	GCCTAGTATGGATCTTTTCCTTCAT	58.462	40.000	0.00	0.00	45.68	2.57
1401	1407	5.453339	CGCCTAGTATGGATCTTTTCCTTCA	60.453	44.000	0.00	0.00	45.68	3.02
1402	1408	4.991687	CGCCTAGTATGGATCTTTTCCTTC	59.008	45.833	0.00	0.00	45.68	3.46
1403	1409	4.409247	ACGCCTAGTATGGATCTTTTCCTT	59.591	41.667	0.00	0.00	45.68	3.36
1404	1410	3.967987	ACGCCTAGTATGGATCTTTTCCT	59.032	43.478	0.00	0.00	45.68	3.36
1405	1411	4.039366	AGACGCCTAGTATGGATCTTTTCC	59.961	45.833	0.00	0.00	45.69	3.13
1406	1412	5.203060	AGACGCCTAGTATGGATCTTTTC	57.797	43.478	0.00	0.00	0.00	2.29
1407	1413	5.364157	AGAAGACGCCTAGTATGGATCTTTT	59.636	40.000	0.00	0.00	35.55	2.27
1408	1414	4.896482	AGAAGACGCCTAGTATGGATCTTT	59.104	41.667	0.00	0.00	35.55	2.52
1409	1415	4.475345	AGAAGACGCCTAGTATGGATCTT	58.525	43.478	0.00	0.00	37.03	2.40
1410	1416	4.076394	GAGAAGACGCCTAGTATGGATCT	58.924	47.826	0.00	0.00	0.00	2.75
1411	1417	3.821600	TGAGAAGACGCCTAGTATGGATC	59.178	47.826	0.00	0.00	0.00	3.36
1412	1418	3.833732	TGAGAAGACGCCTAGTATGGAT	58.166	45.455	0.00	0.00	0.00	3.41
1413	1419	3.292492	TGAGAAGACGCCTAGTATGGA	57.708	47.619	0.00	0.00	0.00	3.41
1414	1420	4.386867	TTTGAGAAGACGCCTAGTATGG	57.613	45.455	0.00	0.00	0.00	2.74
1415	1421	4.985409	GGATTTGAGAAGACGCCTAGTATG	59.015	45.833	0.00	0.00	0.00	2.39
1416	1422	4.896482	AGGATTTGAGAAGACGCCTAGTAT	59.104	41.667	0.00	0.00	0.00	2.12
1417	1423	4.098044	CAGGATTTGAGAAGACGCCTAGTA	59.902	45.833	0.00	0.00	0.00	1.82
1418	1424	3.100671	AGGATTTGAGAAGACGCCTAGT	58.899	45.455	0.00	0.00	0.00	2.57
1419	1425	3.131223	TCAGGATTTGAGAAGACGCCTAG	59.869	47.826	0.00	0.00	0.00	3.02
1420	1426	3.096852	TCAGGATTTGAGAAGACGCCTA	58.903	45.455	0.00	0.00	0.00	3.93
1421	1427	1.902508	TCAGGATTTGAGAAGACGCCT	59.097	47.619	0.00	0.00	0.00	5.52
1422	1428	2.003301	GTCAGGATTTGAGAAGACGCC	58.997	52.381	0.00	0.00	36.21	5.68
1423	1429	2.688507	TGTCAGGATTTGAGAAGACGC	58.311	47.619	0.00	0.00	36.21	5.19
1424	1430	6.035435	CAGTAATGTCAGGATTTGAGAAGACG	59.965	42.308	0.00	0.00	36.21	4.18
1425	1431	6.876257	ACAGTAATGTCAGGATTTGAGAAGAC	59.124	38.462	0.00	0.00	36.21	3.01
1426	1432	7.009179	ACAGTAATGTCAGGATTTGAGAAGA	57.991	36.000	0.00	0.00	36.21	2.87
1427	1433	7.361542	CCAACAGTAATGTCAGGATTTGAGAAG	60.362	40.741	8.58	0.00	36.21	2.85
1428	1434	6.430925	CCAACAGTAATGTCAGGATTTGAGAA	59.569	38.462	8.58	0.00	36.21	2.87
1429	1435	5.939883	CCAACAGTAATGTCAGGATTTGAGA	59.060	40.000	8.58	0.00	36.21	3.27
1430	1436	5.124457	CCCAACAGTAATGTCAGGATTTGAG	59.876	44.000	14.24	0.00	36.21	3.02
1431	1437	5.009631	CCCAACAGTAATGTCAGGATTTGA	58.990	41.667	14.24	0.00	0.00	2.69
1432	1438	4.158394	CCCCAACAGTAATGTCAGGATTTG	59.842	45.833	14.24	0.04	0.00	2.32
1433	1439	4.044065	TCCCCAACAGTAATGTCAGGATTT	59.956	41.667	14.24	0.00	0.00	2.17
1434	1440	3.591527	TCCCCAACAGTAATGTCAGGATT	59.408	43.478	14.24	0.00	0.00	3.01
1435	1441	3.189606	TCCCCAACAGTAATGTCAGGAT	58.810	45.455	14.24	0.00	0.00	3.24
1436	1442	2.626785	TCCCCAACAGTAATGTCAGGA	58.373	47.619	14.24	9.75	0.00	3.86
1437	1443	3.433306	TTCCCCAACAGTAATGTCAGG	57.567	47.619	0.00	1.91	0.00	3.86
1438	1444	4.335416	ACATTCCCCAACAGTAATGTCAG	58.665	43.478	0.00	0.00	37.91	3.51
1439	1445	4.380843	ACATTCCCCAACAGTAATGTCA	57.619	40.909	0.00	0.00	37.91	3.58
1440	1446	4.335594	GCTACATTCCCCAACAGTAATGTC	59.664	45.833	0.00	0.00	40.67	3.06
1441	1447	4.263727	TGCTACATTCCCCAACAGTAATGT	60.264	41.667	0.00	0.00	43.17	2.71
1442	1448	4.269183	TGCTACATTCCCCAACAGTAATG	58.731	43.478	0.00	0.00	35.83	1.90
1443	1449	4.227300	TCTGCTACATTCCCCAACAGTAAT	59.773	41.667	0.00	0.00	0.00	1.89
1444	1450	3.585289	TCTGCTACATTCCCCAACAGTAA	59.415	43.478	0.00	0.00	0.00	2.24
1445	1451	3.178046	TCTGCTACATTCCCCAACAGTA	58.822	45.455	0.00	0.00	0.00	2.74
1685	1692	2.290514	CCTTGCTGGATCAAGTTGGAGA	60.291	50.000	2.34	0.00	41.29	3.71
1715	1722	3.432749	GCTGCTGGATCTTCATCAACCTA	60.433	47.826	0.00	0.00	0.00	3.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.