AutoCloner

Multiple sequence alignment - TraesCS6D01G019800

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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	TraesCS6D01G019800	chr6D	100.000	2867	0	0	1	2867	7961501	7964367	0.000000e+00	5295.0
1	TraesCS6D01G019800	chr6D	87.818	1732	156	34	101	1811	7885469	7887166	0.000000e+00	1978.0
2	TraesCS6D01G019800	chr6D	88.177	1201	136	6	350	1548	7678761	7679957	0.000000e+00	1426.0
3	TraesCS6D01G019800	chr6D	85.077	1233	160	18	449	1666	7901336	7902559	0.000000e+00	1236.0
4	TraesCS6D01G019800	chr6D	74.718	1859	350	65	460	2269	25300789	25299002	0.000000e+00	719.0
5	TraesCS6D01G019800	chr6D	90.147	477	31	8	101	571	7873897	7874363	8.790000e-170	606.0
6	TraesCS6D01G019800	chr6D	86.189	391	18	12	101	487	7694803	7695161	9.630000e-105	390.0
7	TraesCS6D01G019800	chr6D	81.281	406	57	12	2470	2867	7888425	7888819	7.710000e-81	311.0
8	TraesCS6D01G019800	chr6D	87.879	264	30	2	1464	1725	7414887	7414624	2.770000e-80	309.0
9	TraesCS6D01G019800	chr6D	81.416	226	35	4	2648	2867	7414340	7414116	8.160000e-41	178.0
10	TraesCS6D01G019800	chr6D	97.222	36	1	0	217	252	7678645	7678680	8.580000e-06	62.1
11	TraesCS6D01G019800	chr6A	89.485	1788	134	34	101	1875	8170210	8171956	0.000000e+00	2211.0
12	TraesCS6D01G019800	chr6A	82.753	1751	225	46	449	2156	8175045	8176761	0.000000e+00	1489.0
13	TraesCS6D01G019800	chr6A	77.094	1122	227	24	444	1546	10544440	10543330	3.140000e-174	621.0
14	TraesCS6D01G019800	chr6A	80.000	405	64	11	2470	2867	8173167	8173561	1.680000e-72	283.0
15	TraesCS6D01G019800	chr6A	81.388	317	47	10	1956	2269	23229506	23229813	6.130000e-62	248.0
16	TraesCS6D01G019800	chr6A	88.889	198	21	1	1953	2149	572389383	572389186	2.850000e-60	243.0
17	TraesCS6D01G019800	chr3B	88.582	1559	141	11	356	1902	761047766	761046233	0.000000e+00	1858.0
18	TraesCS6D01G019800	chr6B	86.463	1507	158	30	317	1811	14399920	14398448	0.000000e+00	1611.0
19	TraesCS6D01G019800	chr6B	97.430	934	23	1	1934	2867	14360603	14359671	0.000000e+00	1591.0
20	TraesCS6D01G019800	chr6B	83.735	1537	205	31	209	1719	13934254	13932737	0.000000e+00	1411.0
21	TraesCS6D01G019800	chr6B	84.444	1350	164	24	218	1548	54422413	54421091	0.000000e+00	1288.0
22	TraesCS6D01G019800	chr6B	85.188	1276	159	15	300	1548	14303193	14304465	0.000000e+00	1282.0
23	TraesCS6D01G019800	chr6B	85.565	1240	154	18	350	1571	14323488	14324720	0.000000e+00	1275.0
24	TraesCS6D01G019800	chr6B	83.831	1305	175	28	354	1632	14455067	14453773	0.000000e+00	1208.0
25	TraesCS6D01G019800	chr6B	84.408	1225	173	11	350	1559	39311039	39312260	0.000000e+00	1188.0
26	TraesCS6D01G019800	chr6B	94.527	201	2	6	101	299	14402684	14402491	4.640000e-78	302.0
27	TraesCS6D01G019800	chr6B	80.688	378	55	13	2473	2841	14387433	14387065	7.820000e-71	278.0
28	TraesCS6D01G019800	chr6B	82.129	263	43	3	2007	2269	40790737	40790479	3.720000e-54	222.0
29	TraesCS6D01G019800	chr6B	86.550	171	19	4	2101	2269	40657029	40656861	4.880000e-43	185.0
30	TraesCS6D01G019800	chr6B	98.077	52	1	0	30	81	14402728	14402677	1.090000e-14	91.6
31	TraesCS6D01G019800	chr4A	86.694	1210	138	11	342	1532	667425287	667426492	0.000000e+00	1321.0
32	TraesCS6D01G019800	chr4A	86.337	1215	150	9	345	1548	667380007	667381216	0.000000e+00	1310.0
33	TraesCS6D01G019800	chr7B	79.141	978	126	40	1318	2274	623950161	623949241	3.160000e-169	604.0
34	TraesCS6D01G019800	chr7A	81.197	585	80	13	1318	1897	657023643	657023084	7.290000e-121	444.0
35	TraesCS6D01G019800	chr7A	87.500	328	35	3	1953	2274	123426700	123426373	9.700000e-100	374.0
36	TraesCS6D01G019800	chr7A	92.045	88	7	0	2187	2274	657023053	657022966	1.080000e-24	124.0
37	TraesCS6D01G019800	chr7D	78.603	687	59	31	1621	2274	568370001	568369370	9.700000e-100	374.0

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	TraesCS6D01G019800	chr6D	7961501	7964367	2866	False	5295.000000	5295	100.000000	1	2867	1	chr6D.!!$F4	2866
1	TraesCS6D01G019800	chr6D	7901336	7902559	1223	False	1236.000000	1236	85.077000	449	1666	1	chr6D.!!$F3	1217
2	TraesCS6D01G019800	chr6D	7885469	7888819	3350	False	1144.500000	1978	84.549500	101	2867	2	chr6D.!!$F6	2766
3	TraesCS6D01G019800	chr6D	7678645	7679957	1312	False	744.050000	1426	92.699500	217	1548	2	chr6D.!!$F5	1331
4	TraesCS6D01G019800	chr6D	25299002	25300789	1787	True	719.000000	719	74.718000	460	2269	1	chr6D.!!$R1	1809
5	TraesCS6D01G019800	chr6D	7414116	7414887	771	True	243.500000	309	84.647500	1464	2867	2	chr6D.!!$R2	1403
6	TraesCS6D01G019800	chr6A	8170210	8176761	6551	False	1327.666667	2211	84.079333	101	2867	3	chr6A.!!$F2	2766
7	TraesCS6D01G019800	chr6A	10543330	10544440	1110	True	621.000000	621	77.094000	444	1546	1	chr6A.!!$R1	1102
8	TraesCS6D01G019800	chr3B	761046233	761047766	1533	True	1858.000000	1858	88.582000	356	1902	1	chr3B.!!$R1	1546
9	TraesCS6D01G019800	chr6B	14359671	14360603	932	True	1591.000000	1591	97.430000	1934	2867	1	chr6B.!!$R2	933
10	TraesCS6D01G019800	chr6B	13932737	13934254	1517	True	1411.000000	1411	83.735000	209	1719	1	chr6B.!!$R1	1510
11	TraesCS6D01G019800	chr6B	54421091	54422413	1322	True	1288.000000	1288	84.444000	218	1548	1	chr6B.!!$R7	1330
12	TraesCS6D01G019800	chr6B	14303193	14304465	1272	False	1282.000000	1282	85.188000	300	1548	1	chr6B.!!$F1	1248
13	TraesCS6D01G019800	chr6B	14323488	14324720	1232	False	1275.000000	1275	85.565000	350	1571	1	chr6B.!!$F2	1221
14	TraesCS6D01G019800	chr6B	14453773	14455067	1294	True	1208.000000	1208	83.831000	354	1632	1	chr6B.!!$R4	1278
15	TraesCS6D01G019800	chr6B	39311039	39312260	1221	False	1188.000000	1188	84.408000	350	1559	1	chr6B.!!$F3	1209
16	TraesCS6D01G019800	chr6B	14398448	14402728	4280	True	668.200000	1611	93.022333	30	1811	3	chr6B.!!$R8	1781
17	TraesCS6D01G019800	chr4A	667425287	667426492	1205	False	1321.000000	1321	86.694000	342	1532	1	chr4A.!!$F2	1190
18	TraesCS6D01G019800	chr4A	667380007	667381216	1209	False	1310.000000	1310	86.337000	345	1548	1	chr4A.!!$F1	1203
19	TraesCS6D01G019800	chr7B	623949241	623950161	920	True	604.000000	604	79.141000	1318	2274	1	chr7B.!!$R1	956
20	TraesCS6D01G019800	chr7A	657022966	657023643	677	True	284.000000	444	86.621000	1318	2274	2	chr7A.!!$R2	956
21	TraesCS6D01G019800	chr7D	568369370	568370001	631	True	374.000000	374	78.603000	1621	2274	1	chr7D.!!$R1	653

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
602	3240	0.689623	AAGCTCTCCCACCTCAAGTG	59.31	55.0	0.0	0.0	46.83	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1895	9434	0.034767	TGAGATTTCAGCCTGGCAGG	60.035	55.0	29.44	29.44	38.8	4.85	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
19	20	2.930826	AACGAGACCCTCATTGTTGT	57.069	45.000	0.00	0.00	0.00	3.32
21	22	3.594603	ACGAGACCCTCATTGTTGTAG	57.405	47.619	0.00	0.00	0.00	2.74
22	23	2.271800	CGAGACCCTCATTGTTGTAGC	58.728	52.381	0.00	0.00	0.00	3.58
23	24	2.093973	CGAGACCCTCATTGTTGTAGCT	60.094	50.000	0.00	0.00	0.00	3.32
24	25	3.130516	CGAGACCCTCATTGTTGTAGCTA	59.869	47.826	0.00	0.00	0.00	3.32
25	26	4.202161	CGAGACCCTCATTGTTGTAGCTAT	60.202	45.833	0.00	0.00	0.00	2.97
26	27	5.009710	CGAGACCCTCATTGTTGTAGCTATA	59.990	44.000	0.00	0.00	0.00	1.31
27	28	6.294787	CGAGACCCTCATTGTTGTAGCTATAT	60.295	42.308	0.00	0.00	0.00	0.86
28	29	6.763355	AGACCCTCATTGTTGTAGCTATATG	58.237	40.000	0.00	0.00	0.00	1.78
51	52	0.958822	ACACTCCGTGAAAATTGCCC	59.041	50.000	0.38	0.00	36.96	5.36
81	82	5.810074	GCATCCCACCATTTTACAATACAAC	59.190	40.000	0.00	0.00	0.00	3.32
314	2877	2.616330	CCACACACCACACCATCGC	61.616	63.158	0.00	0.00	0.00	4.58
396	3008	2.731571	GGGCGTCATGCTCCACCTA	61.732	63.158	0.00	0.00	45.43	3.08
416	3034	4.838486	GCACCGCGTCCTCTCTCG	62.838	72.222	4.92	0.00	0.00	4.04
472	3092	2.607750	TCCTCCCTTTCCAGCGCT	60.608	61.111	2.64	2.64	0.00	5.92
602	3240	0.689623	AAGCTCTCCCACCTCAAGTG	59.310	55.000	0.00	0.00	46.83	3.16
607	3245	3.579302	CCCACCTCAAGTGCCCCA	61.579	66.667	0.00	0.00	45.83	4.96
724	3362	2.283529	GGCGTGGAGAGAACCCTGA	61.284	63.158	0.00	0.00	0.00	3.86
729	3367	1.229529	GGAGAGAACCCTGACCCCA	60.230	63.158	0.00	0.00	0.00	4.96
1169	3820	4.411256	TGAAGAAGACGTTTAGGTGGTT	57.589	40.909	0.00	0.00	0.00	3.67
1482	4136	3.982241	GCTGCACCACACCTTGCC	61.982	66.667	0.00	0.00	38.00	4.52
1592	8731	3.502920	TGTACGGTGCAACAAAGTTTTG	58.497	40.909	0.98	3.17	43.62	2.44
1673	8814	1.833630	TCCACTCTGTTAGATGCTGGG	59.166	52.381	0.00	0.00	0.00	4.45
1755	8998	9.256228	TCTTAGTGTATCATTTGGTAGAGAAGT	57.744	33.333	0.00	0.00	0.00	3.01
1764	9007	7.861629	TCATTTGGTAGAGAAGTAATCATGGT	58.138	34.615	0.00	0.00	0.00	3.55
1765	9008	7.987458	TCATTTGGTAGAGAAGTAATCATGGTC	59.013	37.037	0.00	0.00	0.00	4.02
1797	9041	7.522073	GCTTGTTATGAACTTGTTCATCCTGAA	60.522	37.037	26.09	15.44	41.50	3.02
1852	9101	2.949177	AGTGTGACAACAGGCCATTA	57.051	45.000	5.01	0.00	36.84	1.90
1888	9410	9.801873	TTAAAATTTCTATGCTGGCTTACATTC	57.198	29.630	0.00	0.00	0.00	2.67
1891	9430	8.752005	AATTTCTATGCTGGCTTACATTCTTA	57.248	30.769	0.00	0.00	0.00	2.10
1893	9432	7.969536	TTCTATGCTGGCTTACATTCTTATC	57.030	36.000	0.00	0.00	0.00	1.75
1894	9433	6.159293	TCTATGCTGGCTTACATTCTTATCG	58.841	40.000	0.00	0.00	0.00	2.92
1895	9434	2.872245	TGCTGGCTTACATTCTTATCGC	59.128	45.455	0.00	0.00	0.00	4.58
1896	9435	2.224314	GCTGGCTTACATTCTTATCGCC	59.776	50.000	0.00	0.00	36.64	5.54
1898	9437	3.466836	TGGCTTACATTCTTATCGCCTG	58.533	45.455	0.00	0.00	37.01	4.85
1901	9440	3.466836	CTTACATTCTTATCGCCTGCCA	58.533	45.455	0.00	0.00	0.00	4.92
1999	9572	2.714259	TGCTTGGCGCAGTAAGTTT	58.286	47.368	10.83	0.00	45.47	2.66
2004	9577	0.030101	TGGCGCAGTAAGTTTGCAAC	59.970	50.000	10.83	0.00	41.59	4.17
2022	9595	0.663153	ACCTTTGTTTCAGTGCGCTC	59.337	50.000	9.73	4.74	0.00	5.03
2091	9665	6.036735	GCTAGTTTGGTCATTGCTAACGATTA	59.963	38.462	0.00	0.00	0.00	1.75
2101	9679	8.006590	GTCATTGCTAACGATTAATGAAGCTAG	58.993	37.037	0.00	0.00	40.14	3.42
2364	10197	7.645058	ATTACTTACAGGCAATGCTTTATGT	57.355	32.000	4.82	8.02	0.00	2.29
2424	10380	7.333672	GGACGTTATTCAGAATTTTACTGTCCT	59.666	37.037	21.01	0.00	36.81	3.85
2456	10412	9.338291	CTGATCACTGAACATATTTTGAACAAG	57.662	33.333	0.00	0.00	0.00	3.16
2463	10419	9.232082	CTGAACATATTTTGAACAAGTTTTCGA	57.768	29.630	0.00	0.00	0.00	3.71
2630	10587	7.577303	TCTGCAAAATCCCTTCTCTGTATATT	58.423	34.615	0.00	0.00	0.00	1.28
2641	10598	6.037610	CCTTCTCTGTATATTGTTGTTGCCTC	59.962	42.308	0.00	0.00	0.00	4.70
2790	10753	3.699038	AGGCTACTTGTTTGTCTTGCAAA	59.301	39.130	0.00	0.00	44.05	3.68
2861	10824	2.849096	ATCTGTGGCCATGCACCTGG	62.849	60.000	9.72	1.68	39.45	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.930826	ACAACAATGAGGGTCTCGTT	57.069	45.000	0.00	0.00	39.93	3.85
3	4	3.618690	AGCTACAACAATGAGGGTCTC	57.381	47.619	0.00	0.00	0.00	3.36
4	5	6.742644	GCATATAGCTACAACAATGAGGGTCT	60.743	42.308	0.00	0.00	41.15	3.85
5	6	5.409826	GCATATAGCTACAACAATGAGGGTC	59.590	44.000	0.00	0.00	41.15	4.46
6	7	5.163205	TGCATATAGCTACAACAATGAGGGT	60.163	40.000	0.00	0.00	45.94	4.34
7	8	5.180117	GTGCATATAGCTACAACAATGAGGG	59.820	44.000	0.00	0.00	45.94	4.30
8	9	5.759763	TGTGCATATAGCTACAACAATGAGG	59.240	40.000	0.00	0.00	45.94	3.86
9	10	6.258507	TGTGTGCATATAGCTACAACAATGAG	59.741	38.462	0.00	0.00	45.94	2.90
10	11	6.037062	GTGTGTGCATATAGCTACAACAATGA	59.963	38.462	0.00	0.00	45.94	2.57
11	12	6.037500	AGTGTGTGCATATAGCTACAACAATG	59.962	38.462	0.00	0.00	45.94	2.82
12	13	6.115446	AGTGTGTGCATATAGCTACAACAAT	58.885	36.000	0.00	0.00	45.94	2.71
13	14	5.487433	AGTGTGTGCATATAGCTACAACAA	58.513	37.500	0.00	0.00	45.94	2.83
14	15	5.084818	AGTGTGTGCATATAGCTACAACA	57.915	39.130	0.00	0.00	45.94	3.33
15	16	4.508124	GGAGTGTGTGCATATAGCTACAAC	59.492	45.833	0.00	0.00	45.94	3.32
16	17	4.693283	GGAGTGTGTGCATATAGCTACAA	58.307	43.478	0.00	0.00	45.94	2.41
17	18	3.243401	CGGAGTGTGTGCATATAGCTACA	60.243	47.826	0.00	0.00	45.94	2.74
18	19	3.243434	ACGGAGTGTGTGCATATAGCTAC	60.243	47.826	0.00	0.00	42.51	3.58
19	20	2.956333	ACGGAGTGTGTGCATATAGCTA	59.044	45.455	0.00	0.00	42.51	3.32
20	21	1.757118	ACGGAGTGTGTGCATATAGCT	59.243	47.619	0.00	0.00	42.51	3.32
21	22	2.225068	ACGGAGTGTGTGCATATAGC	57.775	50.000	0.00	0.00	42.51	2.97
51	52	2.442236	AAATGGTGGGATGCTACAGG	57.558	50.000	2.62	0.00	0.00	4.00
92	93	6.935741	AAGTACAGTTGTATTGCTGTCAAA	57.064	33.333	0.18	0.00	43.91	2.69
93	94	6.935741	AAAGTACAGTTGTATTGCTGTCAA	57.064	33.333	0.18	0.00	43.91	3.18
94	95	6.935741	AAAAGTACAGTTGTATTGCTGTCA	57.064	33.333	0.18	0.00	43.91	3.58
314	2877	3.939837	ATGCGGCGTGTGTCTCCTG	62.940	63.158	9.37	0.00	0.00	3.86
378	2986	2.731571	TAGGTGGAGCATGACGCCC	61.732	63.158	0.00	0.00	44.04	6.13
416	3034	3.894947	GAGCGGCGGAGAGGAGAC	61.895	72.222	9.78	0.00	0.00	3.36
751	3389	2.031163	AGCTTGTGACAGGCCGAC	59.969	61.111	16.37	0.00	37.15	4.79
1368	4019	2.618241	ACGCTTGAGCAATCTGTTTTCA	59.382	40.909	3.65	0.00	42.21	2.69
1482	4136	1.326852	CAAGCAGCTGCATAGTCTTCG	59.673	52.381	38.24	11.01	45.16	3.79
1592	8731	5.163652	GGAATTACCAGCTTACCACACAATC	60.164	44.000	0.00	0.00	38.79	2.67
1673	8814	2.097466	CCAACCGTTAGCAATGACCATC	59.903	50.000	0.00	0.00	0.00	3.51
1755	8998	4.032960	ACAAGCCAACAGACCATGATTA	57.967	40.909	0.00	0.00	0.00	1.75
1764	9007	4.887071	ACAAGTTCATAACAAGCCAACAGA	59.113	37.500	0.00	0.00	0.00	3.41
1765	9008	5.186996	ACAAGTTCATAACAAGCCAACAG	57.813	39.130	0.00	0.00	0.00	3.16
1797	9041	9.407380	TCAATATCTGTGTTAAATAACATGGCT	57.593	29.630	9.06	1.32	46.56	4.75
1840	9089	2.206750	GCATTGCATAATGGCCTGTTG	58.793	47.619	3.32	0.00	43.12	3.33
1895	9434	0.034767	TGAGATTTCAGCCTGGCAGG	60.035	55.000	29.44	29.44	38.80	4.85
1896	9435	1.093159	GTGAGATTTCAGCCTGGCAG	58.907	55.000	22.65	13.84	32.98	4.85
1898	9437	1.742268	GAAGTGAGATTTCAGCCTGGC	59.258	52.381	11.65	11.65	32.98	4.85
1999	9572	1.468908	CGCACTGAAACAAAGGTTGCA	60.469	47.619	0.00	0.00	40.34	4.08
2004	9577	0.384725	CGAGCGCACTGAAACAAAGG	60.385	55.000	11.47	0.00	0.00	3.11
2022	9595	1.009829	GGTCAGCATCTTGTTAGGCG	58.990	55.000	0.00	0.00	0.00	5.52
2364	10197	5.188948	TCTGTTAATGCCTAGCTCTGGTTTA	59.811	40.000	0.00	0.00	0.00	2.01
2424	10380	8.724229	CAAAATATGTTCAGTGATCAGTTCTCA	58.276	33.333	9.63	0.88	0.00	3.27
2456	10412	8.568732	TGGAAGAAAAACAATGTATCGAAAAC	57.431	30.769	0.00	0.00	0.00	2.43
2463	10419	7.734942	ACAACCATGGAAGAAAAACAATGTAT	58.265	30.769	21.47	0.00	0.00	2.29
2630	10587	0.453793	CAACCAACGAGGCAACAACA	59.546	50.000	0.00	0.00	43.14	3.33
2790	10753	2.170012	TATAGCAAGGGAGGACGGTT	57.830	50.000	0.00	0.00	0.00	4.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.