AutoCloner

Multiple sequence alignment - TraesCS5D01G108500

Loading Multiple Alignment...

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	TraesCS5D01G108500	chr5D	100.000	4609	0	0	1	4609	122202330	122206938	0.000000e+00	8512.0
1	TraesCS5D01G108500	chr5B	98.020	3081	40	5	1542	4609	134923325	134926397	0.000000e+00	5332.0
2	TraesCS5D01G108500	chr5B	97.245	1488	38	1	2	1486	134921828	134923315	0.000000e+00	2518.0
3	TraesCS5D01G108500	chr5A	95.209	1482	70	1	5	1486	134089857	134091337	0.000000e+00	2342.0
4	TraesCS5D01G108500	chr5A	91.900	1321	63	6	2437	3740	134092166	134093459	0.000000e+00	1807.0
5	TraesCS5D01G108500	chr5A	94.331	688	32	3	1678	2365	134091470	134092150	0.000000e+00	1048.0
6	TraesCS5D01G108500	chr5A	82.665	623	63	21	3946	4530	134094865	134095480	1.140000e-140	510.0
7	TraesCS5D01G108500	chr1A	94.792	96	5	0	1593	1688	530756566	530756661	2.870000e-32	150.0
8	TraesCS5D01G108500	chr2A	95.652	92	3	1	1601	1692	51498554	51498644	3.720000e-31	147.0
9	TraesCS5D01G108500	chr2A	94.681	94	4	1	1600	1693	202840608	202840516	1.340000e-30	145.0
10	TraesCS5D01G108500	chr2D	94.681	94	3	2	1601	1692	534925550	534925457	1.340000e-30	145.0
11	TraesCS5D01G108500	chr6B	95.506	89	4	0	1602	1690	715389936	715389848	4.810000e-30	143.0
12	TraesCS5D01G108500	chr6D	92.079	101	5	3	1588	1688	199210423	199210326	6.220000e-29	139.0
13	TraesCS5D01G108500	chr6D	83.654	104	3	3	2310	2399	429811843	429811946	8.220000e-13	86.1
14	TraesCS5D01G108500	chr6A	92.708	96	7	0	1591	1686	190660445	190660350	6.220000e-29	139.0
15	TraesCS5D01G108500	chr6A	92.708	96	7	0	1591	1686	190738368	190738273	6.220000e-29	139.0
16	TraesCS5D01G108500	chr6A	83.654	104	3	3	2310	2399	53820661	53820558	8.220000e-13	86.1
17	TraesCS5D01G108500	chrUn	83.654	104	3	3	2310	2399	445188177	445188074	8.220000e-13	86.1
18	TraesCS5D01G108500	chrUn	82.692	104	4	3	2310	2399	261568623	261568726	3.820000e-11	80.5
19	TraesCS5D01G108500	chr1D	83.654	104	3	5	2310	2399	254459478	254459375	8.220000e-13	86.1
20	TraesCS5D01G108500	chr4D	82.692	104	4	3	2310	2399	19900795	19900692	3.820000e-11	80.5
21	TraesCS5D01G108500	chr4D	95.745	47	1	1	2354	2399	206908389	206908435	1.780000e-09	75.0
22	TraesCS5D01G108500	chr7D	95.745	47	1	1	2354	2399	225601828	225601874	1.780000e-09	75.0

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	TraesCS5D01G108500	chr5D	122202330	122206938	4608	False	8512.00	8512	100.00000	1	4609	1	chr5D.!!$F1	4608
1	TraesCS5D01G108500	chr5B	134921828	134926397	4569	False	3925.00	5332	97.63250	2	4609	2	chr5B.!!$F1	4607
2	TraesCS5D01G108500	chr5A	134089857	134095480	5623	False	1426.75	2342	91.02625	5	4530	4	chr5A.!!$F1	4525

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	End Stability	Orientation
61	62	0.318955	AGCTTTTCACATTGCGGCAC	60.319	50.000	0.05	5.01	F
1326	1330	1.079336	GGTCCGGTTCTGGCTACAC	60.079	63.158	0.00	2.90	F
1760	1783	4.642885	TCCCTTTGCTGAATTATTTACCCG	59.357	41.667	0.00	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1580	1603	0.469917	CAGTCTACAATCCGGGGCAT	59.530	55.000	0.00	0.00	0.00	4.40	R
2214	2237	6.604795	AGCACAACATTAGCAATATTCTTCCT	59.395	34.615	0.00	0.00	0.00	3.36	R
3745	3798	0.527565	CTGGGTAACATGGCAGTTGC	59.472	55.000	11.08	9.79	38.48	4.17	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
31	32	7.820648	AGAATTGAACTGATGTTACATTGACC	58.179	34.615	0.00	0.00	36.39	4.02
47	48	0.332972	GACCTTCCCCATCCAGCTTT	59.667	55.000	0.00	0.00	0.00	3.51
61	62	0.318955	AGCTTTTCACATTGCGGCAC	60.319	50.000	0.05	0.00	0.00	5.01
64	65	2.406130	CTTTTCACATTGCGGCACATT	58.594	42.857	0.05	0.00	0.00	2.71
353	354	5.239306	TCACAAGACATGGCTTCACTAAAAG	59.761	40.000	12.02	0.00	0.00	2.27
432	433	6.415798	AAAAACACACGGGAAATTTTCTTG	57.584	33.333	8.93	6.72	0.00	3.02
515	516	2.721167	GCCGGAAAAATCAGGGGGC	61.721	63.158	5.05	0.00	0.00	5.80
524	525	1.281925	AATCAGGGGGCGTTGAGGAT	61.282	55.000	0.00	0.00	0.00	3.24
542	543	2.329379	GATATCTCGGTGTCAATCGGC	58.671	52.381	0.00	0.00	0.00	5.54
587	588	4.680237	CCGGCAGGACTGTTCGCA	62.680	66.667	0.00	0.00	41.02	5.10
616	617	2.045045	CCTTCCCCTGCGCAATCA	60.045	61.111	13.05	0.00	0.00	2.57
728	729	3.553302	CGTAGAGAGATCTCCTACGCTCA	60.553	52.174	34.81	13.79	43.06	4.26
1272	1273	3.390521	TTCGAGTCCATGGGCGCT	61.391	61.111	18.35	10.91	0.00	5.92
1322	1323	1.415672	TTCAAGGTCCGGTTCTGGCT	61.416	55.000	0.00	0.00	0.00	4.75
1326	1330	1.079336	GGTCCGGTTCTGGCTACAC	60.079	63.158	0.00	0.00	0.00	2.90
1341	1345	6.818644	TCTGGCTACACTTGATTACATTTCTC	59.181	38.462	0.00	0.00	0.00	2.87
1538	1542	9.922305	GTATTGATCAGTCTTGTAATTTAGTGC	57.078	33.333	0.00	0.00	0.00	4.40
1539	1543	6.647212	TGATCAGTCTTGTAATTTAGTGCG	57.353	37.500	0.00	0.00	0.00	5.34
1540	1544	4.921470	TCAGTCTTGTAATTTAGTGCGC	57.079	40.909	0.00	0.00	0.00	6.09
1664	1687	8.954350	ACTAAAGTAGTGATCTAAACGCTCTTA	58.046	33.333	0.00	0.00	37.69	2.10
1682	1705	7.124448	ACGCTCTTATATTCCTTTATAGAGGGG	59.876	40.741	9.36	0.00	37.88	4.79
1760	1783	4.642885	TCCCTTTGCTGAATTATTTACCCG	59.357	41.667	0.00	0.00	0.00	5.28
2214	2237	3.936653	CAAAGCGTGCTGTCGAGA	58.063	55.556	0.00	0.00	0.00	4.04
2282	2305	4.994852	CGGATTGAGGTTAGTGAACTCAAA	59.005	41.667	18.23	3.83	36.83	2.69
2284	2307	6.017440	CGGATTGAGGTTAGTGAACTCAAAAA	60.017	38.462	18.23	0.00	36.83	1.94
2430	2466	4.516698	CGCTGGAGGTAGCAATATCAAAAT	59.483	41.667	0.00	0.00	43.87	1.82
2537	2573	7.041916	CCTGATCTGATTCTTGAGTTCTAATGC	60.042	40.741	0.38	0.00	0.00	3.56
3693	3746	4.740934	GCAGAACCAGCTTAATCCGATAGT	60.741	45.833	0.00	0.00	0.00	2.12
3745	3798	4.024133	TGACATGTGGTTTGAATCTGTTCG	60.024	41.667	1.15	0.00	37.15	3.95
3881	4745	5.794894	TCTAAGCTTACCAAACTTCTGAGG	58.205	41.667	0.86	0.00	0.00	3.86
3929	4793	2.455674	TGTGCCTACAGTGTAAGCTG	57.544	50.000	21.45	3.28	41.92	4.24
4561	5911	0.681733	ACTCGAGAGAAAGCAAGGCA	59.318	50.000	21.68	0.00	41.32	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	1.821136	GTGAAAAGCTGGATGGGGAAG	59.179	52.381	0.00	0.00	0.00	3.46
47	48	3.650070	TTAAATGTGCCGCAATGTGAA	57.350	38.095	0.00	0.00	0.00	3.18
64	65	7.327214	GGGCACACATTTTAGGATTTCATTAA	58.673	34.615	0.00	0.00	0.00	1.40
353	354	6.595772	AATTCGATCTAACTCTGTGATTGC	57.404	37.500	0.00	0.00	0.00	3.56
432	433	4.508124	CAGGTGAGACACTTGTGAAGTTAC	59.492	45.833	7.83	0.80	40.46	2.50
515	516	2.357952	TGACACCGAGATATCCTCAACG	59.642	50.000	0.00	0.00	42.06	4.10
524	525	0.030235	CGCCGATTGACACCGAGATA	59.970	55.000	0.00	0.00	0.00	1.98
607	608	0.307453	GTGACAAGTGTGATTGCGCA	59.693	50.000	5.66	5.66	33.28	6.09
616	617	3.243839	GGAATTTGGCATGTGACAAGTGT	60.244	43.478	1.07	0.00	44.95	3.55
833	834	0.039256	TCGTTACAAGAACCGACCGG	60.039	55.000	6.94	6.94	42.03	5.28
1322	1323	8.375506	AGGAAGTGAGAAATGTAATCAAGTGTA	58.624	33.333	0.00	0.00	0.00	2.90
1341	1345	5.336372	GGCTGATCTACTGCTATAGGAAGTG	60.336	48.000	1.04	0.00	41.95	3.16
1441	1445	6.815089	AGACTAGTCAATGATCTGAACCATC	58.185	40.000	24.44	0.00	0.00	3.51
1512	1516	9.922305	GCACTAAATTACAAGACTGATCAATAC	57.078	33.333	0.00	0.00	0.00	1.89
1513	1517	8.817100	CGCACTAAATTACAAGACTGATCAATA	58.183	33.333	0.00	0.00	0.00	1.90
1514	1518	7.677276	GCGCACTAAATTACAAGACTGATCAAT	60.677	37.037	0.30	0.00	0.00	2.57
1515	1519	6.402118	GCGCACTAAATTACAAGACTGATCAA	60.402	38.462	0.30	0.00	0.00	2.57
1516	1520	5.063438	GCGCACTAAATTACAAGACTGATCA	59.937	40.000	0.30	0.00	0.00	2.92
1517	1521	5.292101	AGCGCACTAAATTACAAGACTGATC	59.708	40.000	11.47	0.00	0.00	2.92
1518	1522	5.178797	AGCGCACTAAATTACAAGACTGAT	58.821	37.500	11.47	0.00	0.00	2.90
1519	1523	4.566004	AGCGCACTAAATTACAAGACTGA	58.434	39.130	11.47	0.00	0.00	3.41
1520	1524	4.627467	AGAGCGCACTAAATTACAAGACTG	59.373	41.667	11.47	0.00	0.00	3.51
1521	1525	4.822026	AGAGCGCACTAAATTACAAGACT	58.178	39.130	11.47	0.00	0.00	3.24
1522	1526	5.107065	ACAAGAGCGCACTAAATTACAAGAC	60.107	40.000	11.47	0.00	0.00	3.01
1523	1527	4.994852	ACAAGAGCGCACTAAATTACAAGA	59.005	37.500	11.47	0.00	0.00	3.02
1524	1528	5.283060	ACAAGAGCGCACTAAATTACAAG	57.717	39.130	11.47	0.00	0.00	3.16
1525	1529	5.682943	AACAAGAGCGCACTAAATTACAA	57.317	34.783	11.47	0.00	0.00	2.41
1526	1530	6.160684	TCTAACAAGAGCGCACTAAATTACA	58.839	36.000	11.47	0.00	0.00	2.41
1527	1531	6.642683	TCTAACAAGAGCGCACTAAATTAC	57.357	37.500	11.47	0.00	0.00	1.89
1528	1532	7.843490	AATCTAACAAGAGCGCACTAAATTA	57.157	32.000	11.47	7.59	0.00	1.40
1529	1533	6.743575	AATCTAACAAGAGCGCACTAAATT	57.256	33.333	11.47	6.78	0.00	1.82
1530	1534	6.743575	AAATCTAACAAGAGCGCACTAAAT	57.256	33.333	11.47	0.50	0.00	1.40
1531	1535	6.554334	AAAATCTAACAAGAGCGCACTAAA	57.446	33.333	11.47	0.00	0.00	1.85
1532	1536	6.370593	CAAAAATCTAACAAGAGCGCACTAA	58.629	36.000	11.47	0.00	0.00	2.24
1533	1537	5.616866	GCAAAAATCTAACAAGAGCGCACTA	60.617	40.000	11.47	0.00	0.00	2.74
1534	1538	4.787598	CAAAAATCTAACAAGAGCGCACT	58.212	39.130	11.47	5.59	0.00	4.40
1535	1539	3.361940	GCAAAAATCTAACAAGAGCGCAC	59.638	43.478	11.47	2.25	0.00	5.34
1536	1540	3.004210	TGCAAAAATCTAACAAGAGCGCA	59.996	39.130	11.47	0.00	0.00	6.09
1537	1541	3.564511	TGCAAAAATCTAACAAGAGCGC	58.435	40.909	0.00	0.00	0.00	5.92
1538	1542	6.546395	AGTATGCAAAAATCTAACAAGAGCG	58.454	36.000	0.00	0.00	0.00	5.03
1579	1602	1.134098	CAGTCTACAATCCGGGGCATT	60.134	52.381	0.00	0.00	0.00	3.56
1580	1603	0.469917	CAGTCTACAATCCGGGGCAT	59.530	55.000	0.00	0.00	0.00	4.40
1581	1604	1.622607	CCAGTCTACAATCCGGGGCA	61.623	60.000	0.00	0.00	0.00	5.36
1664	1687	9.475013	AAAAGTACCCCCTCTATAAAGGAATAT	57.525	33.333	0.00	0.00	38.87	1.28
1669	1692	6.570654	TCAAAAGTACCCCCTCTATAAAGG	57.429	41.667	0.00	0.00	36.08	3.11
1675	1698	2.574824	GGCTTCAAAAGTACCCCCTCTA	59.425	50.000	0.00	0.00	0.00	2.43
1682	1705	2.558359	ACTGCATGGCTTCAAAAGTACC	59.442	45.455	0.00	0.00	0.00	3.34
2214	2237	6.604795	AGCACAACATTAGCAATATTCTTCCT	59.395	34.615	0.00	0.00	0.00	3.36
2430	2466	6.703607	GCAAATCTTTCCGAATCTATCTCTCA	59.296	38.462	0.00	0.00	0.00	3.27
3655	3708	3.126343	GGTTCTGCGTCGTTTATCCATTT	59.874	43.478	0.00	0.00	0.00	2.32
3745	3798	0.527565	CTGGGTAACATGGCAGTTGC	59.472	55.000	11.08	9.79	38.48	4.17
4457	5807	5.329035	AGTGTTATTGACATTTCATGGCC	57.671	39.130	0.00	0.00	41.10	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.