AutoCloner

Multiple sequence alignment - TraesCS5D01G190500

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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	TraesCS5D01G190500	chr5D	100.000	1538	0	0	1	1538	292727490	292725953	0.000000e+00	2841.0
1	TraesCS5D01G190500	chr5D	88.632	1469	153	10	1	1465	354744868	354743410	0.000000e+00	1775.0
2	TraesCS5D01G190500	chr5D	100.000	38	0	0	2245	2282	292725246	292725209	1.130000e-08	71.3
3	TraesCS5D01G190500	chr4D	91.045	1474	120	11	1	1462	398866793	398868266	0.000000e+00	1980.0
4	TraesCS5D01G190500	chr5A	91.905	1396	108	4	1	1391	697889081	697890476	0.000000e+00	1947.0
5	TraesCS5D01G190500	chr5A	90.149	1472	126	15	1	1468	651581872	651580416	0.000000e+00	1897.0
6	TraesCS5D01G190500	chr3D	90.642	1464	130	4	1	1462	134639495	134640953	0.000000e+00	1938.0
7	TraesCS5D01G190500	chr6B	90.366	1474	127	13	1	1465	132658820	132657353	0.000000e+00	1921.0
8	TraesCS5D01G190500	chr4B	89.973	1476	132	14	1	1466	502276037	502277506	0.000000e+00	1892.0
9	TraesCS5D01G190500	chr1B	90.048	1467	131	11	1	1461	414556409	414557866	0.000000e+00	1886.0
10	TraesCS5D01G190500	chr4A	92.081	1326	103	2	1	1324	718008875	718007550	0.000000e+00	1866.0
11	TraesCS5D01G190500	chr4A	86.601	306	28	7	1166	1470	709875349	709875056	2.190000e-85	326.0
12	TraesCS5D01G190500	chr3B	86.020	794	85	10	673	1465	769385940	769385172	0.000000e+00	828.0
13	TraesCS5D01G190500	chr2A	85.572	201	24	3	1275	1471	40955182	40954983	2.970000e-49	206.0
14	TraesCS5D01G190500	chr2A	85.714	105	13	1	1360	1462	23468894	23468998	2.400000e-20	110.0
15	TraesCS5D01G190500	chr2A	96.970	33	1	0	1433	1465	507697386	507697354	3.170000e-04	56.5

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	TraesCS5D01G190500	chr5D	292725209	292727490	2281	True	1456.15	2841	100.000	1	2282	2	chr5D.!!$R2	2281
1	TraesCS5D01G190500	chr5D	354743410	354744868	1458	True	1775.00	1775	88.632	1	1465	1	chr5D.!!$R1	1464
2	TraesCS5D01G190500	chr4D	398866793	398868266	1473	False	1980.00	1980	91.045	1	1462	1	chr4D.!!$F1	1461
3	TraesCS5D01G190500	chr5A	697889081	697890476	1395	False	1947.00	1947	91.905	1	1391	1	chr5A.!!$F1	1390
4	TraesCS5D01G190500	chr5A	651580416	651581872	1456	True	1897.00	1897	90.149	1	1468	1	chr5A.!!$R1	1467
5	TraesCS5D01G190500	chr3D	134639495	134640953	1458	False	1938.00	1938	90.642	1	1462	1	chr3D.!!$F1	1461
6	TraesCS5D01G190500	chr6B	132657353	132658820	1467	True	1921.00	1921	90.366	1	1465	1	chr6B.!!$R1	1464
7	TraesCS5D01G190500	chr4B	502276037	502277506	1469	False	1892.00	1892	89.973	1	1466	1	chr4B.!!$F1	1465
8	TraesCS5D01G190500	chr1B	414556409	414557866	1457	False	1886.00	1886	90.048	1	1461	1	chr1B.!!$F1	1460
9	TraesCS5D01G190500	chr4A	718007550	718008875	1325	True	1866.00	1866	92.081	1	1324	1	chr4A.!!$R2	1323
10	TraesCS5D01G190500	chr3B	769385172	769385940	768	True	828.00	828	86.020	673	1465	1	chr3B.!!$R1	792

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
298	300	0.247814	CATTGTCCAATGCTCGTCGC	60.248	55.0	7.05	0.0	41.27	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1480	1513	0.25589	GCCCCCACACTCACACATAT	59.744	55.0	0.0	0.0	0.0	1.78	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
66	67	5.906772	AATATGGAGGGAAAATACCGAGT	57.093	39.130	0.00	0.00	0.00	4.18
123	124	7.341030	AGAGCATTATATATGCCATGTGCTTA	58.659	34.615	13.08	6.13	45.59	3.09
176	177	5.451908	TCGCAAAATCATGTGAGAAAGTTC	58.548	37.500	0.00	0.00	35.04	3.01
179	180	6.087291	CGCAAAATCATGTGAGAAAGTTCTTC	59.913	38.462	0.00	0.00	37.73	2.87
272	274	6.016610	GCTTAAACATGTTCCTAGTTTGACCA	60.017	38.462	12.39	0.00	36.29	4.02
290	292	5.968254	TGACCATGAAATCATTGTCCAATG	58.032	37.500	19.21	12.72	44.03	2.82
298	300	0.247814	CATTGTCCAATGCTCGTCGC	60.248	55.000	7.05	0.00	41.27	5.19
346	348	6.430308	CAGCAATAAGATATCAAGCCACTGAT	59.570	38.462	5.32	0.00	39.41	2.90
356	358	4.724399	TCAAGCCACTGATTTAAGGTCAA	58.276	39.130	0.00	0.00	0.00	3.18
372	374	5.353394	AGGTCAACTTTGTCTGAGTTACA	57.647	39.130	0.00	0.00	35.68	2.41
375	377	5.107453	GGTCAACTTTGTCTGAGTTACATCG	60.107	44.000	0.00	0.00	35.68	3.84
411	414	9.605275	CACTGATCCTAAAGATAAAAGTGATGA	57.395	33.333	0.00	0.00	40.33	2.92
538	542	2.165167	CAACCATGTGCATTGACTCCT	58.835	47.619	0.00	0.00	0.00	3.69
615	620	5.359756	GGGTTTTCTTCAAGTTTGAGCATT	58.640	37.500	0.00	0.00	38.61	3.56
660	665	2.618709	GGGAATAGAGCCATTGTTTCCG	59.381	50.000	0.00	0.00	34.72	4.30
666	671	3.012518	AGAGCCATTGTTTCCGATGAAG	58.987	45.455	0.00	0.00	34.81	3.02
689	694	0.982673	CGTGCTACGAGGAAGAAACG	59.017	55.000	3.04	0.00	46.05	3.60
708	713	5.766150	AACGGTTTGATGAAAGTGATTGA	57.234	34.783	0.00	0.00	0.00	2.57
795	800	3.436704	TGGCGATCACTTCTTTGAATGAC	59.563	43.478	0.00	0.00	0.00	3.06
901	906	6.648310	TGAACTTCAAGAATGTTGCACAAAAA	59.352	30.769	0.00	0.00	0.00	1.94
915	920	6.251655	TGCACAAAAATTGCAGAAACTTTT	57.748	29.167	0.00	0.00	45.06	2.27
931	936	9.801873	CAGAAACTTTTTCTCTTAATGGTTCAA	57.198	29.630	0.00	0.00	32.05	2.69
1038	1043	0.532573	TCGGGCATGTGAGAGAAGTC	59.467	55.000	0.00	0.00	0.00	3.01
1094	1099	5.297776	GCATCTTATTTACTGTGCCTGTGAT	59.702	40.000	0.00	0.00	0.00	3.06
1096	1101	4.635765	TCTTATTTACTGTGCCTGTGATGC	59.364	41.667	0.00	0.00	0.00	3.91
1099	1104	1.269958	TACTGTGCCTGTGATGCTCT	58.730	50.000	0.00	0.00	0.00	4.09
1182	1187	5.165961	TGACTCAAGAGAGGTTAAATGGG	57.834	43.478	3.73	0.00	46.44	4.00
1273	1278	5.282055	TGCATCGAGGAATGTTAGAAGAT	57.718	39.130	0.00	0.00	0.00	2.40
1274	1279	5.674525	TGCATCGAGGAATGTTAGAAGATT	58.325	37.500	0.00	0.00	0.00	2.40
1342	1364	4.157656	TGGATGCATTTAAGTGTTACTGGC	59.842	41.667	0.00	0.00	0.00	4.85
1417	1450	7.272978	ACAATGACTTGTATATTAAGGACGCT	58.727	34.615	0.00	0.00	43.77	5.07
1431	1464	7.739498	TTAAGGACGCTCAATTTTTAGTTCT	57.261	32.000	0.00	0.00	0.00	3.01
1494	1527	5.686771	CACGTTAGATATGTGTGAGTGTG	57.313	43.478	0.00	0.00	38.67	3.82
1495	1528	4.562789	CACGTTAGATATGTGTGAGTGTGG	59.437	45.833	0.00	0.00	38.67	4.17
1496	1529	4.112634	CGTTAGATATGTGTGAGTGTGGG	58.887	47.826	0.00	0.00	0.00	4.61
1497	1530	4.442706	GTTAGATATGTGTGAGTGTGGGG	58.557	47.826	0.00	0.00	0.00	4.96
1498	1531	1.839994	AGATATGTGTGAGTGTGGGGG	59.160	52.381	0.00	0.00	0.00	5.40
1499	1532	0.255890	ATATGTGTGAGTGTGGGGGC	59.744	55.000	0.00	0.00	0.00	5.80
1500	1533	2.178876	TATGTGTGAGTGTGGGGGCG	62.179	60.000	0.00	0.00	0.00	6.13
1501	1534	3.936203	GTGTGAGTGTGGGGGCGA	61.936	66.667	0.00	0.00	0.00	5.54
1502	1535	2.927856	TGTGAGTGTGGGGGCGAT	60.928	61.111	0.00	0.00	0.00	4.58
1503	1536	2.436646	GTGAGTGTGGGGGCGATG	60.437	66.667	0.00	0.00	0.00	3.84
1504	1537	3.716195	TGAGTGTGGGGGCGATGG	61.716	66.667	0.00	0.00	0.00	3.51
1505	1538	4.489771	GAGTGTGGGGGCGATGGG	62.490	72.222	0.00	0.00	0.00	4.00
1530	1563	3.590574	GGGAGGGGGTGGCACTTT	61.591	66.667	18.45	0.40	0.00	2.66
1531	1564	2.035783	GGAGGGGGTGGCACTTTC	59.964	66.667	18.45	9.68	0.00	2.62
1532	1565	2.539081	GGAGGGGGTGGCACTTTCT	61.539	63.158	18.45	11.73	0.00	2.52
1533	1566	1.460699	GAGGGGGTGGCACTTTCTT	59.539	57.895	18.45	3.77	0.00	2.52
1534	1567	0.895559	GAGGGGGTGGCACTTTCTTG	60.896	60.000	18.45	0.00	0.00	3.02
1535	1568	2.574018	GGGGGTGGCACTTTCTTGC	61.574	63.158	18.45	0.00	42.18	4.01
1536	1569	2.644992	GGGTGGCACTTTCTTGCG	59.355	61.111	18.45	0.00	44.00	4.85
1537	1570	2.644992	GGTGGCACTTTCTTGCGG	59.355	61.111	18.45	0.00	44.00	5.69
2264	2297	3.780804	CCAACATTATATGGTCGGGGA	57.219	47.619	0.00	0.00	33.60	4.81
2265	2298	4.093472	CCAACATTATATGGTCGGGGAA	57.907	45.455	0.00	0.00	33.60	3.97
2266	2299	4.072131	CCAACATTATATGGTCGGGGAAG	58.928	47.826	0.00	0.00	33.60	3.46
2267	2300	4.072131	CAACATTATATGGTCGGGGAAGG	58.928	47.826	0.00	0.00	33.60	3.46
2268	2301	3.593942	ACATTATATGGTCGGGGAAGGA	58.406	45.455	0.00	0.00	33.60	3.36
2269	2302	3.977999	ACATTATATGGTCGGGGAAGGAA	59.022	43.478	0.00	0.00	33.60	3.36
2270	2303	4.041691	ACATTATATGGTCGGGGAAGGAAG	59.958	45.833	0.00	0.00	33.60	3.46
2271	2304	2.489528	ATATGGTCGGGGAAGGAAGA	57.510	50.000	0.00	0.00	0.00	2.87
2272	2305	1.789523	TATGGTCGGGGAAGGAAGAG	58.210	55.000	0.00	0.00	0.00	2.85
2273	2306	0.983378	ATGGTCGGGGAAGGAAGAGG	60.983	60.000	0.00	0.00	0.00	3.69
2274	2307	2.368011	GGTCGGGGAAGGAAGAGGG	61.368	68.421	0.00	0.00	0.00	4.30
2275	2308	2.040606	TCGGGGAAGGAAGAGGGG	59.959	66.667	0.00	0.00	0.00	4.79
2276	2309	3.090532	CGGGGAAGGAAGAGGGGG	61.091	72.222	0.00	0.00	0.00	5.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	9.429109	TCATATCAAGTAACCTAGATTGTACCA	57.571	33.333	0.00	0.00	0.00	3.25
123	124	8.076910	ACAAAGAGTGAGATTGAGACTATGAT	57.923	34.615	0.00	0.00	0.00	2.45
154	155	5.455392	AGAACTTTCTCACATGATTTTGCG	58.545	37.500	0.00	0.00	29.94	4.85
229	230	2.820330	AGCAAAACATTCCACCGTTTG	58.180	42.857	0.00	0.00	35.57	2.93
233	235	4.965042	GTTTAAGCAAAACATTCCACCG	57.035	40.909	9.17	0.00	45.72	4.94
272	274	4.400251	ACGAGCATTGGACAATGATTTCAT	59.600	37.500	24.76	7.90	46.10	2.57
298	300	7.410942	GCTGTAACACTTTTGATTCTACTCTCG	60.411	40.741	0.00	0.00	0.00	4.04
346	348	7.825270	TGTAACTCAGACAAAGTTGACCTTAAA	59.175	33.333	0.00	0.00	37.52	1.52
356	358	3.741344	GCACGATGTAACTCAGACAAAGT	59.259	43.478	0.00	0.00	0.00	2.66
372	374	2.417924	GGATCAGTGTCAGAAGCACGAT	60.418	50.000	0.00	0.00	41.36	3.73
375	377	2.758736	AGGATCAGTGTCAGAAGCAC	57.241	50.000	0.00	0.00	37.13	4.40
411	414	7.095691	CGACCAAGTGCATCAAATAATGTTTTT	60.096	33.333	0.00	0.00	0.00	1.94
416	419	3.792956	GCGACCAAGTGCATCAAATAATG	59.207	43.478	0.00	0.00	0.00	1.90
615	620	6.389091	CATTTCAGTTGCAATACCTTTAGCA	58.611	36.000	0.59	0.00	34.79	3.49
666	671	1.868251	CTTCCTCGTAGCACGACGC	60.868	63.158	7.20	0.00	46.73	5.19
689	694	6.738114	TCTTGTCAATCACTTTCATCAAACC	58.262	36.000	0.00	0.00	0.00	3.27
708	713	8.682936	TCTCAGCTTCTAAAATTTCTTCTTGT	57.317	30.769	0.00	0.00	0.00	3.16
901	906	8.424133	ACCATTAAGAGAAAAAGTTTCTGCAAT	58.576	29.630	7.93	2.72	0.00	3.56
931	936	9.632638	AATAAGATTGCATACCTCAACATTAGT	57.367	29.630	0.00	0.00	0.00	2.24
934	939	9.193806	AGAAATAAGATTGCATACCTCAACATT	57.806	29.630	0.00	0.00	0.00	2.71
1004	1009	2.297701	GCCCGAAAATCTCCATAGCAA	58.702	47.619	0.00	0.00	0.00	3.91
1038	1043	8.607459	GCAATGGAGATATTAGGATAACAATCG	58.393	37.037	0.00	0.00	0.00	3.34
1094	1099	2.865119	TCTTTTGGCTGATGAGAGCA	57.135	45.000	0.00	0.00	41.08	4.26
1096	1101	3.345414	AGCTTCTTTTGGCTGATGAGAG	58.655	45.455	0.00	0.00	37.41	3.20
1099	1104	4.942761	AAAAGCTTCTTTTGGCTGATGA	57.057	36.364	0.00	0.00	38.91	2.92
1104	1109	5.089970	ACTTCAAAAAGCTTCTTTTGGCT	57.910	34.783	18.86	4.24	43.48	4.75
1182	1187	4.058124	TCTCGATGCATAATGTAGCCAAC	58.942	43.478	0.00	0.00	0.00	3.77
1300	1306	6.566564	GCATCCAAAATCGGTATGTGTATCAG	60.567	42.308	0.00	0.00	0.00	2.90
1313	1320	6.949578	AACACTTAAATGCATCCAAAATCG	57.050	33.333	0.00	0.00	0.00	3.34
1413	1446	3.756963	GGGGAGAACTAAAAATTGAGCGT	59.243	43.478	0.00	0.00	0.00	5.07
1415	1448	3.128764	CCGGGGAGAACTAAAAATTGAGC	59.871	47.826	0.00	0.00	0.00	4.26
1417	1450	3.692690	CCCGGGGAGAACTAAAAATTGA	58.307	45.455	14.71	0.00	0.00	2.57
1471	1504	5.161358	CACACTCACACATATCTAACGTGT	58.839	41.667	0.00	0.00	44.45	4.49
1472	1505	4.562789	CCACACTCACACATATCTAACGTG	59.437	45.833	0.00	0.00	36.70	4.49
1473	1506	4.381612	CCCACACTCACACATATCTAACGT	60.382	45.833	0.00	0.00	0.00	3.99
1474	1507	4.112634	CCCACACTCACACATATCTAACG	58.887	47.826	0.00	0.00	0.00	3.18
1475	1508	4.442706	CCCCACACTCACACATATCTAAC	58.557	47.826	0.00	0.00	0.00	2.34
1476	1509	3.454447	CCCCCACACTCACACATATCTAA	59.546	47.826	0.00	0.00	0.00	2.10
1477	1510	3.038280	CCCCCACACTCACACATATCTA	58.962	50.000	0.00	0.00	0.00	1.98
1478	1511	1.839994	CCCCCACACTCACACATATCT	59.160	52.381	0.00	0.00	0.00	1.98
1479	1512	1.747206	GCCCCCACACTCACACATATC	60.747	57.143	0.00	0.00	0.00	1.63
1480	1513	0.255890	GCCCCCACACTCACACATAT	59.744	55.000	0.00	0.00	0.00	1.78
1481	1514	1.682849	GCCCCCACACTCACACATA	59.317	57.895	0.00	0.00	0.00	2.29
1482	1515	2.436109	GCCCCCACACTCACACAT	59.564	61.111	0.00	0.00	0.00	3.21
1483	1516	4.248842	CGCCCCCACACTCACACA	62.249	66.667	0.00	0.00	0.00	3.72
1484	1517	3.254024	ATCGCCCCCACACTCACAC	62.254	63.158	0.00	0.00	0.00	3.82
1485	1518	2.927856	ATCGCCCCCACACTCACA	60.928	61.111	0.00	0.00	0.00	3.58
1486	1519	2.436646	CATCGCCCCCACACTCAC	60.437	66.667	0.00	0.00	0.00	3.51
1487	1520	3.716195	CCATCGCCCCCACACTCA	61.716	66.667	0.00	0.00	0.00	3.41
1488	1521	4.489771	CCCATCGCCCCCACACTC	62.490	72.222	0.00	0.00	0.00	3.51
1513	1546	3.585525	GAAAGTGCCACCCCCTCCC	62.586	68.421	0.00	0.00	0.00	4.30
1514	1547	2.035783	GAAAGTGCCACCCCCTCC	59.964	66.667	0.00	0.00	0.00	4.30
1515	1548	0.895559	CAAGAAAGTGCCACCCCCTC	60.896	60.000	0.00	0.00	0.00	4.30
1516	1549	1.153756	CAAGAAAGTGCCACCCCCT	59.846	57.895	0.00	0.00	0.00	4.79
1517	1550	2.574018	GCAAGAAAGTGCCACCCCC	61.574	63.158	0.00	0.00	38.66	5.40
1518	1551	2.919494	CGCAAGAAAGTGCCACCCC	61.919	63.158	0.00	0.00	41.73	4.95
1519	1552	2.644992	CGCAAGAAAGTGCCACCC	59.355	61.111	0.00	0.00	41.73	4.61
1520	1553	2.644992	CCGCAAGAAAGTGCCACC	59.355	61.111	0.00	0.00	41.73	4.61
2244	2277	3.780804	TCCCCGACCATATAATGTTGG	57.219	47.619	4.86	4.86	39.02	3.77
2245	2278	4.072131	CCTTCCCCGACCATATAATGTTG	58.928	47.826	0.00	0.00	0.00	3.33
2246	2279	3.977999	TCCTTCCCCGACCATATAATGTT	59.022	43.478	0.00	0.00	0.00	2.71
2247	2280	3.593942	TCCTTCCCCGACCATATAATGT	58.406	45.455	0.00	0.00	0.00	2.71
2248	2281	4.286032	TCTTCCTTCCCCGACCATATAATG	59.714	45.833	0.00	0.00	0.00	1.90
2249	2282	4.499472	TCTTCCTTCCCCGACCATATAAT	58.501	43.478	0.00	0.00	0.00	1.28
2250	2283	3.901844	CTCTTCCTTCCCCGACCATATAA	59.098	47.826	0.00	0.00	0.00	0.98
2251	2284	3.507411	CTCTTCCTTCCCCGACCATATA	58.493	50.000	0.00	0.00	0.00	0.86
2252	2285	2.330216	CTCTTCCTTCCCCGACCATAT	58.670	52.381	0.00	0.00	0.00	1.78
2253	2286	1.691482	CCTCTTCCTTCCCCGACCATA	60.691	57.143	0.00	0.00	0.00	2.74
2254	2287	0.983378	CCTCTTCCTTCCCCGACCAT	60.983	60.000	0.00	0.00	0.00	3.55
2255	2288	1.612442	CCTCTTCCTTCCCCGACCA	60.612	63.158	0.00	0.00	0.00	4.02
2256	2289	2.368011	CCCTCTTCCTTCCCCGACC	61.368	68.421	0.00	0.00	0.00	4.79
2257	2290	2.368011	CCCCTCTTCCTTCCCCGAC	61.368	68.421	0.00	0.00	0.00	4.79
2258	2291	2.040606	CCCCTCTTCCTTCCCCGA	59.959	66.667	0.00	0.00	0.00	5.14
2259	2292	3.090532	CCCCCTCTTCCTTCCCCG	61.091	72.222	0.00	0.00	0.00	5.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.