AutoCloner

Multiple sequence alignment - TraesCS6D01G153500

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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	TraesCS6D01G153500	chr6D	100.000	3346	0	0	1	3346	127381665	127378320	0.000000e+00	6180.0
1	TraesCS6D01G153500	chr6A	92.561	3065	130	40	1	3003	150980004	150983032	0.000000e+00	4307.0
2	TraesCS6D01G153500	chr6A	98.083	313	4	1	3034	3346	150983032	150983342	8.160000e-151	544.0
3	TraesCS6D01G153500	chr6B	90.530	2830	118	60	642	3346	226397679	226394875	0.000000e+00	3603.0
4	TraesCS6D01G153500	chr7D	75.310	725	159	16	1579	2293	515236990	515236276	2.490000e-86	329.0
5	TraesCS6D01G153500	chr7D	74.863	728	157	19	1579	2293	515220784	515220070	1.170000e-79	307.0
6	TraesCS6D01G153500	chr7D	74.760	729	156	21	1579	2293	514093056	514093770	5.430000e-78	302.0
7	TraesCS6D01G153500	chr7D	73.741	278	53	17	1719	1986	514075388	514075655	1.280000e-14	91.6
8	TraesCS6D01G153500	chr7A	74.931	726	160	15	1579	2293	587519180	587519894	2.510000e-81	313.0
9	TraesCS6D01G153500	chr7A	74.932	730	157	19	1579	2293	588739731	588739013	9.010000e-81	311.0
10	TraesCS6D01G153500	chr7A	74.721	716	157	17	1589	2292	586692984	586692281	7.020000e-77	298.0
11	TraesCS6D01G153500	chr7A	74.157	267	55	10	1731	1990	275972784	275972525	7.640000e-17	99.0
12	TraesCS6D01G153500	chr7A	73.741	278	53	16	1719	1986	587365493	587365760	1.280000e-14	91.6
13	TraesCS6D01G153500	chr7B	75.034	725	154	20	1582	2293	544881870	544882580	9.010000e-81	311.0
14	TraesCS6D01G153500	chr7B	74.460	278	51	16	1719	1986	544912285	544912552	5.910000e-18	102.0
15	TraesCS6D01G153500	chr7B	72.222	378	80	19	1731	2097	234913597	234913234	3.550000e-15	93.5
16	TraesCS6D01G153500	chr5D	81.000	200	30	7	1713	1908	519545930	519546125	5.780000e-33	152.0
17	TraesCS6D01G153500	chr2D	73.154	298	62	17	1713	2001	574346175	574345887	1.280000e-14	91.6
18	TraesCS6D01G153500	chr2B	73.154	298	62	17	1713	2001	690211224	690210936	1.280000e-14	91.6
19	TraesCS6D01G153500	chr2A	73.000	300	61	19	1712	2001	712702425	712702136	1.650000e-13	87.9
20	TraesCS6D01G153500	chr4B	80.909	110	13	8	1718	1823	86465879	86465984	2.770000e-11	80.5

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	TraesCS6D01G153500	chr6D	127378320	127381665	3345	True	6180.0	6180	100.000	1	3346	1	chr6D.!!$R1	3345
1	TraesCS6D01G153500	chr6A	150980004	150983342	3338	False	2425.5	4307	95.322	1	3346	2	chr6A.!!$F1	3345
2	TraesCS6D01G153500	chr6B	226394875	226397679	2804	True	3603.0	3603	90.530	642	3346	1	chr6B.!!$R1	2704
3	TraesCS6D01G153500	chr7D	515236276	515236990	714	True	329.0	329	75.310	1579	2293	1	chr7D.!!$R2	714
4	TraesCS6D01G153500	chr7D	515220070	515220784	714	True	307.0	307	74.863	1579	2293	1	chr7D.!!$R1	714
5	TraesCS6D01G153500	chr7D	514093056	514093770	714	False	302.0	302	74.760	1579	2293	1	chr7D.!!$F2	714
6	TraesCS6D01G153500	chr7A	587519180	587519894	714	False	313.0	313	74.931	1579	2293	1	chr7A.!!$F2	714
7	TraesCS6D01G153500	chr7A	588739013	588739731	718	True	311.0	311	74.932	1579	2293	1	chr7A.!!$R3	714
8	TraesCS6D01G153500	chr7A	586692281	586692984	703	True	298.0	298	74.721	1589	2292	1	chr7A.!!$R2	703
9	TraesCS6D01G153500	chr7B	544881870	544882580	710	False	311.0	311	75.034	1582	2293	1	chr7B.!!$F1	711

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
279	280	0.108898	CTCTGGAGTGAGGCTGAACG	60.109	60.0	0.00	0.0	0.0	3.95	F
1507	1562	0.179119	GATCCTCCCCAACGTACGTG	60.179	60.0	23.57	15.4	0.0	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1567	1622	0.518195	TGCATGCACGTGTGATCTTG	59.482	50.0	18.46	9.55	0.00	3.02	R
2889	3051	0.391661	TCGCTTCCATGAGCCAAGAC	60.392	55.0	0.00	0.00	39.51	3.01	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
35	36	0.180642	TAAACAACAGGCACCGGTCA	59.819	50.000	2.59	0.00	0.00	4.02
36	37	1.101049	AAACAACAGGCACCGGTCAG	61.101	55.000	2.59	0.00	0.00	3.51
81	82	2.108952	AGGATGCTCAAGTGGGTTTCTT	59.891	45.455	0.00	0.00	0.00	2.52
147	148	3.683281	GCCCGTTTGGAATGTGGTAGATA	60.683	47.826	0.00	0.00	37.49	1.98
148	149	4.714632	CCCGTTTGGAATGTGGTAGATAT	58.285	43.478	0.00	0.00	37.49	1.63
149	150	4.755123	CCCGTTTGGAATGTGGTAGATATC	59.245	45.833	0.00	0.00	37.49	1.63
156	157	6.815880	TGGAATGTGGTAGATATCTATCCCT	58.184	40.000	18.43	2.63	33.17	4.20
235	236	2.483288	CGGCGCGCCTGTTTAAAT	59.517	55.556	43.60	0.00	0.00	1.40
237	238	2.158330	GGCGCGCCTGTTTAAATGC	61.158	57.895	41.71	11.62	0.00	3.56
253	254	0.744057	ATGCCGTCATGAATGCGACA	60.744	50.000	11.76	4.75	32.02	4.35
279	280	0.108898	CTCTGGAGTGAGGCTGAACG	60.109	60.000	0.00	0.00	0.00	3.95
401	402	2.045926	CCCGCAAAGTCCCTCTGG	60.046	66.667	0.00	0.00	0.00	3.86
405	406	0.593128	CGCAAAGTCCCTCTGGTTTG	59.407	55.000	0.00	0.00	33.09	2.93
408	409	2.930950	CAAAGTCCCTCTGGTTTGTGA	58.069	47.619	0.00	0.00	0.00	3.58
426	427	2.870411	GTGAGGTACCGCATTGGATAAC	59.130	50.000	21.84	2.24	42.00	1.89
464	465	2.695646	GTTCGAACGGATGCGAGC	59.304	61.111	15.49	3.34	37.85	5.03
465	466	2.092291	GTTCGAACGGATGCGAGCA	61.092	57.895	15.49	0.00	37.62	4.26
504	505	4.067896	GTTGACGGCCAAGATGATATCAT	58.932	43.478	18.21	18.21	39.70	2.45
524	525	1.106944	AACGGTTTTGCCCCAGACAG	61.107	55.000	0.00	0.00	0.00	3.51
534	535	1.879575	CCCCAGACAGACCCTATTCA	58.120	55.000	0.00	0.00	0.00	2.57
590	591	9.931210	CAGGATAGTATTTGACCGTTTTATTTC	57.069	33.333	0.00	0.00	0.00	2.17
713	718	1.075374	CCCACCTGTTTTCCATCCTGA	59.925	52.381	0.00	0.00	0.00	3.86
1014	1042	4.096003	AAGATGGTGACGGCGGGG	62.096	66.667	13.24	0.00	0.00	5.73
1405	1460	1.565156	GATGCGCGTGGACAACTTCA	61.565	55.000	6.97	0.00	0.00	3.02
1424	1479	4.101790	CATCAACGGCCACGGCAC	62.102	66.667	10.83	0.00	46.48	5.01
1507	1562	0.179119	GATCCTCCCCAACGTACGTG	60.179	60.000	23.57	15.40	0.00	4.49
1511	1566	4.317444	CCCCAACGTACGTGCCCA	62.317	66.667	23.57	0.00	0.00	5.36
1514	1569	3.045492	CAACGTACGTGCCCACCC	61.045	66.667	23.57	0.00	0.00	4.61
1529	1584	0.962356	CACCCACCCACTCTTGCATC	60.962	60.000	0.00	0.00	0.00	3.91
1566	1621	5.080337	ACCAAAACCAAAACCAAAACCAAT	58.920	33.333	0.00	0.00	0.00	3.16
1567	1622	5.184096	ACCAAAACCAAAACCAAAACCAATC	59.816	36.000	0.00	0.00	0.00	2.67
1568	1623	5.183904	CCAAAACCAAAACCAAAACCAATCA	59.816	36.000	0.00	0.00	0.00	2.57
1569	1624	6.294731	CCAAAACCAAAACCAAAACCAATCAA	60.295	34.615	0.00	0.00	0.00	2.57
1570	1625	6.507958	AAACCAAAACCAAAACCAATCAAG	57.492	33.333	0.00	0.00	0.00	3.02
1572	1627	6.000246	ACCAAAACCAAAACCAATCAAGAT	58.000	33.333	0.00	0.00	0.00	2.40
1573	1628	6.054941	ACCAAAACCAAAACCAATCAAGATC	58.945	36.000	0.00	0.00	0.00	2.75
1574	1629	6.054295	CCAAAACCAAAACCAATCAAGATCA	58.946	36.000	0.00	0.00	0.00	2.92
1577	1632	5.200368	ACCAAAACCAATCAAGATCACAC	57.800	39.130	0.00	0.00	0.00	3.82
1634	1722	2.785105	GAACAACGCGACGATCCGG	61.785	63.158	15.93	0.00	0.00	5.14
2349	2437	1.588403	CTCGCATGCCTCTGACTCG	60.588	63.158	13.15	0.00	0.00	4.18
2457	2560	9.458374	CCTATCATACGTTTGTTTTCAGTTTTT	57.542	29.630	5.89	0.00	0.00	1.94
2489	2595	4.673403	TGGTGTAAGCAGCTGACG	57.327	55.556	20.43	0.00	40.88	4.35
2497	2603	1.797025	AAGCAGCTGACGGTTAACTC	58.203	50.000	20.43	0.00	0.00	3.01
2524	2630	7.484007	GTCAATGATAGCAAGTGTCTGATTTTG	59.516	37.037	0.00	0.00	0.00	2.44
2575	2704	4.323553	GTGATAGTTAGCTACCACCCAG	57.676	50.000	0.00	0.00	36.03	4.45
2613	2744	2.323580	GCGTTGCTCTTGCTCAGCT	61.324	57.895	0.00	0.00	40.48	4.24
2683	2814	1.593196	CGGTGTTGCAGAGGAGAAAA	58.407	50.000	0.00	0.00	0.00	2.29
2741	2888	4.972201	GATATCATCGAGGAAGTACCGAC	58.028	47.826	2.91	0.00	44.74	4.79
2742	2889	2.414994	TCATCGAGGAAGTACCGACT	57.585	50.000	0.00	0.00	44.74	4.18
2747	2894	2.421424	TCGAGGAAGTACCGACTAAAGC	59.579	50.000	0.00	0.00	44.74	3.51
2766	2913	9.182214	ACTAAAGCAATCAAGTTATCACATCAT	57.818	29.630	0.00	0.00	0.00	2.45
2767	2914	9.661187	CTAAAGCAATCAAGTTATCACATCATC	57.339	33.333	0.00	0.00	0.00	2.92
2769	2916	7.024340	AGCAATCAAGTTATCACATCATCAC	57.976	36.000	0.00	0.00	0.00	3.06
2770	2917	6.827251	AGCAATCAAGTTATCACATCATCACT	59.173	34.615	0.00	0.00	0.00	3.41
2771	2918	7.989170	AGCAATCAAGTTATCACATCATCACTA	59.011	33.333	0.00	0.00	0.00	2.74
2772	2919	8.281194	GCAATCAAGTTATCACATCATCACTAG	58.719	37.037	0.00	0.00	0.00	2.57
2811	2973	8.581578	CCCAATTTTATTACTATTTACCGCCAT	58.418	33.333	0.00	0.00	0.00	4.40
2889	3051	1.765314	AGAACTGAAGATCATCCCCCG	59.235	52.381	0.00	0.00	0.00	5.73
2995	3157	3.630312	TGCCATCAAGATCACACATCATG	59.370	43.478	0.00	0.00	0.00	3.07
3004	3166	8.042515	TCAAGATCACACATCATGTCATCTTTA	58.957	33.333	11.28	4.41	40.64	1.85
3084	3249	6.978080	CGATGGAAAAGAAAAGAAAAAGGACA	59.022	34.615	0.00	0.00	0.00	4.02
3085	3250	7.653311	CGATGGAAAAGAAAAGAAAAAGGACAT	59.347	33.333	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.647611	CCTGTTGTTTATACCTGACCACA	58.352	43.478	0.00	0.00	0.00	4.17
134	135	7.147637	GGGAAGGGATAGATATCTACCACATTC	60.148	44.444	22.33	20.70	33.28	2.67
147	148	1.152271	ACGGGATGGGAAGGGATAGAT	59.848	52.381	0.00	0.00	0.00	1.98
148	149	0.566176	ACGGGATGGGAAGGGATAGA	59.434	55.000	0.00	0.00	0.00	1.98
149	150	0.977395	GACGGGATGGGAAGGGATAG	59.023	60.000	0.00	0.00	0.00	2.08
173	174	1.447838	GCCGGAGCAACGAGATTGA	60.448	57.895	5.05	0.00	41.23	2.57
221	222	1.867373	CGGCATTTAAACAGGCGCG	60.867	57.895	20.18	0.00	44.06	6.86
235	236	1.375268	TGTCGCATTCATGACGGCA	60.375	52.632	15.75	11.93	38.71	5.69
237	238	1.715585	GGTGTCGCATTCATGACGG	59.284	57.895	0.00	0.00	37.94	4.79
264	265	2.435059	GCCGTTCAGCCTCACTCC	60.435	66.667	0.00	0.00	0.00	3.85
279	280	0.604578	AGTTGCCACACATTCATGCC	59.395	50.000	0.00	0.00	0.00	4.40
363	364	3.403057	CCGAACCGCTGTCACACG	61.403	66.667	0.00	0.00	0.00	4.49
365	366	2.028484	GTCCGAACCGCTGTCACA	59.972	61.111	0.00	0.00	0.00	3.58
386	387	0.593128	CAAACCAGAGGGACTTTGCG	59.407	55.000	0.00	0.00	41.55	4.85
401	402	1.199097	CCAATGCGGTACCTCACAAAC	59.801	52.381	6.75	0.00	0.00	2.93
405	406	2.870411	GTTATCCAATGCGGTACCTCAC	59.130	50.000	6.75	0.00	35.57	3.51
408	409	3.637911	TTGTTATCCAATGCGGTACCT	57.362	42.857	10.90	0.00	35.57	3.08
464	465	2.271173	GGCCGGACCCCTAAACTG	59.729	66.667	5.05	0.00	0.00	3.16
465	466	3.396570	CGGCCGGACCCCTAAACT	61.397	66.667	20.10	0.00	33.26	2.66
504	505	0.183014	TGTCTGGGGCAAAACCGTTA	59.817	50.000	0.00	0.00	40.62	3.18
534	535	8.517878	GCTGCCAAATCATATTCATTACTGTAT	58.482	33.333	0.00	0.00	0.00	2.29
590	591	1.726791	CAGTGCTAAGTGCTAACGTGG	59.273	52.381	0.00	0.00	43.37	4.94
1014	1042	2.486966	GTGGCGGCATTGCTTCTC	59.513	61.111	17.19	0.00	34.52	2.87
1507	1562	3.580319	AAGAGTGGGTGGGTGGGC	61.580	66.667	0.00	0.00	0.00	5.36
1511	1566	1.380302	GATGCAAGAGTGGGTGGGT	59.620	57.895	0.00	0.00	0.00	4.51
1514	1569	2.401766	GGCGATGCAAGAGTGGGTG	61.402	63.158	0.00	0.00	0.00	4.61
1529	1584	3.248841	GGTTTTGGTTTTGGTTAATGGCG	59.751	43.478	0.00	0.00	0.00	5.69
1566	1621	0.798159	GCATGCACGTGTGATCTTGA	59.202	50.000	18.38	0.00	0.00	3.02
1567	1622	0.518195	TGCATGCACGTGTGATCTTG	59.482	50.000	18.46	9.55	0.00	3.02
1568	1623	0.518636	GTGCATGCACGTGTGATCTT	59.481	50.000	33.20	0.00	37.19	2.40
1569	1624	2.165380	GTGCATGCACGTGTGATCT	58.835	52.632	33.20	0.00	37.19	2.75
1570	1625	4.751539	GTGCATGCACGTGTGATC	57.248	55.556	33.20	9.99	37.19	2.92
1832	1920	1.079503	GGATCTTGACGTGCTTGGTC	58.920	55.000	0.00	0.00	34.99	4.02
2045	2133	1.553704	GGGTAGGAGACGTTGTCCATT	59.446	52.381	17.55	3.53	36.43	3.16
2415	2515	8.850452	CGTATGATAGGAAGCAAAAAGAAAAAC	58.150	33.333	0.00	0.00	0.00	2.43
2417	2517	8.106247	ACGTATGATAGGAAGCAAAAAGAAAA	57.894	30.769	0.00	0.00	0.00	2.29
2419	2519	7.681939	AACGTATGATAGGAAGCAAAAAGAA	57.318	32.000	0.00	0.00	0.00	2.52
2420	2520	7.174253	ACAAACGTATGATAGGAAGCAAAAAGA	59.826	33.333	0.00	0.00	0.00	2.52
2421	2521	7.305474	ACAAACGTATGATAGGAAGCAAAAAG	58.695	34.615	0.00	0.00	0.00	2.27
2457	2560	8.453238	TGCTTACACCAGTTGATTTAAGTAAA	57.547	30.769	0.00	0.00	0.00	2.01
2458	2561	7.308348	GCTGCTTACACCAGTTGATTTAAGTAA	60.308	37.037	0.00	0.00	32.93	2.24
2459	2562	6.148811	GCTGCTTACACCAGTTGATTTAAGTA	59.851	38.462	0.00	0.00	32.93	2.24
2489	2595	5.581085	ACTTGCTATCATTGACGAGTTAACC	59.419	40.000	0.88	0.00	0.00	2.85
2497	2603	4.176271	TCAGACACTTGCTATCATTGACG	58.824	43.478	0.00	0.00	0.00	4.35
2524	2630	1.830477	TGCATGGGCCAATTCTTAACC	59.170	47.619	11.89	0.00	40.13	2.85
2575	2704	2.464865	CAGACGCTAGGTAGATTGTGC	58.535	52.381	0.00	0.00	0.00	4.57
2613	2744	6.043411	CCGAAGTAAATTTTGTTGGGTTTCA	58.957	36.000	0.00	0.00	0.00	2.69
2683	2814	6.033966	GTGTGTCATTTCGTTTTCTTCCTTT	58.966	36.000	0.00	0.00	0.00	3.11
2704	2835	5.700846	GATGATATCGTGATTCTACCGTGT	58.299	41.667	1.08	0.00	0.00	4.49
2736	2883	6.092259	GTGATAACTTGATTGCTTTAGTCGGT	59.908	38.462	0.00	0.00	0.00	4.69
2738	2885	7.060600	TGTGATAACTTGATTGCTTTAGTCG	57.939	36.000	0.00	0.00	0.00	4.18
2740	2887	8.565896	TGATGTGATAACTTGATTGCTTTAGT	57.434	30.769	0.00	0.00	0.00	2.24
2741	2888	9.661187	GATGATGTGATAACTTGATTGCTTTAG	57.339	33.333	0.00	0.00	0.00	1.85
2742	2889	9.176460	TGATGATGTGATAACTTGATTGCTTTA	57.824	29.630	0.00	0.00	0.00	1.85
2747	2894	8.771766	CCTAGTGATGATGTGATAACTTGATTG	58.228	37.037	0.00	0.00	0.00	2.67
2807	2969	1.135721	CTTGAAGGGCTTAGCAATGGC	59.864	52.381	6.53	0.00	41.61	4.40
2811	2973	4.568072	TGTATCTTGAAGGGCTTAGCAA	57.432	40.909	6.53	0.00	0.00	3.91
2889	3051	0.391661	TCGCTTCCATGAGCCAAGAC	60.392	55.000	0.00	0.00	39.51	3.01
3031	3193	6.788684	TTATCGGTCTTGAAAATTTCGACA	57.211	33.333	13.13	0.00	0.00	4.35
3032	3194	7.241376	ACATTATCGGTCTTGAAAATTTCGAC	58.759	34.615	0.97	3.62	0.00	4.20
3084	3249	4.460263	TGTTGCAAGGTTCAGTGAACTAT	58.540	39.130	29.89	18.82	41.70	2.12
3085	3250	3.876914	CTGTTGCAAGGTTCAGTGAACTA	59.123	43.478	29.89	12.69	41.70	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.