AutoCloner

Multiple sequence alignment - TraesCS6A01G367500

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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	TraesCS6A01G367500	chr6A	100.000	2873	0	0	1	2873	594504695	594501823	0.000000e+00	5306.0
1	TraesCS6A01G367500	chr6B	93.333	1875	122	2	991	2865	678880757	678878886	0.000000e+00	2767.0
2	TraesCS6A01G367500	chr6B	91.020	1882	146	9	992	2873	678811893	678810035	0.000000e+00	2518.0
3	TraesCS6A01G367500	chr6B	91.274	1845	152	3	1029	2873	678795788	678793953	0.000000e+00	2507.0
4	TraesCS6A01G367500	chr6B	90.237	1055	94	6	1827	2873	679393055	679394108	0.000000e+00	1369.0
5	TraesCS6A01G367500	chr6B	89.867	829	60	6	867	1676	679386550	679387373	0.000000e+00	1044.0
6	TraesCS6A01G367500	chr6B	88.817	778	68	11	19	779	678881817	678881042	0.000000e+00	937.0
7	TraesCS6A01G367500	chr6B	88.761	694	69	6	2187	2873	679530628	679531319	0.000000e+00	841.0
8	TraesCS6A01G367500	chr6B	87.844	617	74	1	1	616	679384847	679385463	0.000000e+00	723.0
9	TraesCS6A01G367500	chr6B	84.158	606	90	6	19	620	678796629	678796026	1.480000e-162	582.0
10	TraesCS6A01G367500	chr6B	83.027	489	65	13	137	618	678807813	678807336	7.360000e-116	427.0
11	TraesCS6A01G367500	chr6B	89.877	326	33	0	1835	2160	679530304	679530629	1.230000e-113	420.0
12	TraesCS6A01G367500	chr6B	82.186	494	59	24	137	617	678876708	678876231	5.770000e-107	398.0
13	TraesCS6A01G367500	chr6B	90.066	151	11	2	629	779	679386283	679386429	2.920000e-45	193.0
14	TraesCS6A01G367500	chr6B	92.000	50	0	2	792	837	679386414	679386463	1.850000e-07	67.6
15	TraesCS6A01G367500	chrUn	90.551	1270	111	6	892	2160	79370460	79371721	0.000000e+00	1672.0
16	TraesCS6A01G367500	chrUn	90.551	1270	111	6	892	2160	79397084	79398345	0.000000e+00	1672.0
17	TraesCS6A01G367500	chrUn	88.583	762	73	4	19	779	79395975	79396723	0.000000e+00	913.0
18	TraesCS6A01G367500	chrUn	88.761	694	69	6	2187	2873	79371720	79372411	0.000000e+00	841.0
19	TraesCS6A01G367500	chrUn	88.329	694	72	6	2187	2873	79398344	79399035	0.000000e+00	824.0
20	TraesCS6A01G367500	chrUn	88.008	492	45	4	289	779	79369621	79370099	1.160000e-158	569.0
21	TraesCS6A01G367500	chr6D	88.636	1144	101	18	837	1975	448041059	448039940	0.000000e+00	1365.0
22	TraesCS6A01G367500	chr6D	91.289	838	73	0	2036	2873	448039948	448039111	0.000000e+00	1144.0
23	TraesCS6A01G367500	chr6D	92.466	438	26	6	286	717	448041665	448041229	1.130000e-173	619.0
24	TraesCS6A01G367500	chr6D	96.094	256	10	0	1	256	448041921	448041666	4.430000e-113	418.0
25	TraesCS6A01G367500	chr6D	85.846	325	36	6	142	458	448510532	448510854	1.280000e-88	337.0
26	TraesCS6A01G367500	chr4B	76.895	1359	260	40	1008	2344	580530054	580531380	0.000000e+00	721.0
27	TraesCS6A01G367500	chr4B	74.872	784	156	29	1069	1838	579887213	579887969	4.620000e-83	318.0
28	TraesCS6A01G367500	chr4D	73.939	1343	265	54	1023	2344	464170471	464171749	2.020000e-126	462.0

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	TraesCS6A01G367500	chr6A	594501823	594504695	2872	True	5306.000000	5306	100.000000	1	2873	1	chr6A.!!$R1	2872
1	TraesCS6A01G367500	chr6B	678793953	678796629	2676	True	1544.500000	2507	87.716000	19	2873	2	chr6B.!!$R1	2854
2	TraesCS6A01G367500	chr6B	678807336	678811893	4557	True	1472.500000	2518	87.023500	137	2873	2	chr6B.!!$R2	2736
3	TraesCS6A01G367500	chr6B	679393055	679394108	1053	False	1369.000000	1369	90.237000	1827	2873	1	chr6B.!!$F1	1046
4	TraesCS6A01G367500	chr6B	678876231	678881817	5586	True	1367.333333	2767	88.112000	19	2865	3	chr6B.!!$R3	2846
5	TraesCS6A01G367500	chr6B	679530304	679531319	1015	False	630.500000	841	89.319000	1835	2873	2	chr6B.!!$F3	1038
6	TraesCS6A01G367500	chr6B	679384847	679387373	2526	False	506.900000	1044	89.944250	1	1676	4	chr6B.!!$F2	1675
7	TraesCS6A01G367500	chrUn	79395975	79399035	3060	False	1136.333333	1672	89.154333	19	2873	3	chrUn.!!$F2	2854
8	TraesCS6A01G367500	chrUn	79369621	79372411	2790	False	1027.333333	1672	89.106667	289	2873	3	chrUn.!!$F1	2584
9	TraesCS6A01G367500	chr6D	448039111	448041921	2810	True	886.500000	1365	92.121250	1	2873	4	chr6D.!!$R1	2872
10	TraesCS6A01G367500	chr4B	580530054	580531380	1326	False	721.000000	721	76.895000	1008	2344	1	chr4B.!!$F2	1336
11	TraesCS6A01G367500	chr4B	579887213	579887969	756	False	318.000000	318	74.872000	1069	1838	1	chr4B.!!$F1	769
12	TraesCS6A01G367500	chr4D	464170471	464171749	1278	False	462.000000	462	73.939000	1023	2344	1	chr4D.!!$F1	1321

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
282	312	0.596341	AAAACGTCGCAAACATGGGC	60.596	50.0	0.0	0.0	0.0	5.36	F
1026	2324	0.039074	GATCAGATACCAGGGTCGCG	60.039	60.0	0.0	0.0	0.0	5.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1614	2930	0.182775	GGGGGATTACCTTGTGCGAT	59.817	55.0	0.00	0.0	40.03	4.58	R
2766	4111	0.251474	CCATGGGGTATGCTGGATGG	60.251	60.0	2.85	0.0	35.37	3.51	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
118	119	5.104527	ACAGACTTGCCATACTTATAGCCAA	60.105	40.000	0.00	0.00	0.00	4.52
263	293	4.973055	CCGTGGCGTCGGGACAAA	62.973	66.667	12.07	0.00	45.88	2.83
264	294	2.968156	CGTGGCGTCGGGACAAAA	60.968	61.111	0.00	0.00	33.40	2.44
265	295	2.535788	CGTGGCGTCGGGACAAAAA	61.536	57.895	0.00	0.00	33.40	1.94
281	311	1.846541	AAAAACGTCGCAAACATGGG	58.153	45.000	0.00	0.00	0.00	4.00
282	312	0.596341	AAAACGTCGCAAACATGGGC	60.596	50.000	0.00	0.00	0.00	5.36
283	313	1.452145	AAACGTCGCAAACATGGGCT	61.452	50.000	0.00	0.00	0.00	5.19
284	314	1.452145	AACGTCGCAAACATGGGCTT	61.452	50.000	0.00	0.00	0.00	4.35
492	522	1.658717	GATCTCACGGATGGCGTCG	60.659	63.158	0.00	0.00	34.33	5.12
549	580	4.305769	CCGTCTCATCCATCTTTGATCTC	58.694	47.826	0.00	0.00	0.00	2.75
560	591	6.554228	TCCATCTTTGATCTCTAGCTTGATCT	59.446	38.462	18.37	3.42	39.63	2.75
565	596	3.496507	TGATCTCTAGCTTGATCTCGTCG	59.503	47.826	18.37	0.00	39.63	5.12
566	597	1.600013	TCTCTAGCTTGATCTCGTCGC	59.400	52.381	0.00	0.00	0.00	5.19
567	598	1.332065	CTCTAGCTTGATCTCGTCGCA	59.668	52.381	0.00	0.00	0.00	5.10
650	1505	1.722011	AACTAAGTTGCGTCCCGATG	58.278	50.000	0.00	0.00	0.00	3.84
705	1560	3.443045	GCCGGTCCAGCATGTTGG	61.443	66.667	21.77	21.77	39.70	3.77
767	1641	4.847757	GCGGACCAATTTTTAGTACGAAAC	59.152	41.667	0.14	0.00	40.32	2.78
768	1642	5.384787	CGGACCAATTTTTAGTACGAAACC	58.615	41.667	0.14	0.00	40.32	3.27
769	1643	5.049543	CGGACCAATTTTTAGTACGAAACCA	60.050	40.000	0.14	0.00	40.32	3.67
770	1644	6.144854	GGACCAATTTTTAGTACGAAACCAC	58.855	40.000	0.14	0.00	0.00	4.16
771	1645	6.238703	GGACCAATTTTTAGTACGAAACCACA	60.239	38.462	0.14	0.00	0.00	4.17
772	1646	7.098074	ACCAATTTTTAGTACGAAACCACAA	57.902	32.000	0.14	0.00	0.00	3.33
773	1647	7.718525	ACCAATTTTTAGTACGAAACCACAAT	58.281	30.769	0.14	0.00	0.00	2.71
774	1648	8.198778	ACCAATTTTTAGTACGAAACCACAATT	58.801	29.630	0.14	2.58	0.00	2.32
775	1649	9.680315	CCAATTTTTAGTACGAAACCACAATTA	57.320	29.630	0.14	0.00	0.00	1.40
854	1908	1.594862	GCAGATAGATGTTGGCGACAC	59.405	52.381	10.35	4.61	42.04	3.67
875	1929	2.596904	ATCCTACCCAAACACGATCG	57.403	50.000	14.88	14.88	0.00	3.69
897	1951	0.678048	AAGCCACCTCTCAAATCCGC	60.678	55.000	0.00	0.00	0.00	5.54
940	2226	6.658816	CACCCATCATCGATCCCATAAAAATA	59.341	38.462	0.00	0.00	0.00	1.40
952	2238	5.045213	TCCCATAAAAATACCTGCTCAGACA	60.045	40.000	0.00	0.00	0.00	3.41
957	2243	4.833478	AAATACCTGCTCAGACACAGAT	57.167	40.909	0.00	0.00	35.90	2.90
972	2258	2.029288	AGATCGGCAACACGCACAG	61.029	57.895	0.00	0.00	45.17	3.66
985	2283	1.683917	ACGCACAGATCAGATCTACCC	59.316	52.381	12.88	3.42	37.58	3.69
986	2284	1.000283	CGCACAGATCAGATCTACCCC	60.000	57.143	12.88	1.77	37.58	4.95
989	2287	2.556189	CACAGATCAGATCTACCCCTCG	59.444	54.545	12.88	1.65	37.58	4.63
1015	2313	5.221322	CCGAGAACAATGACTGGATCAGATA	60.221	44.000	1.59	0.00	41.91	1.98
1026	2324	0.039074	GATCAGATACCAGGGTCGCG	60.039	60.000	0.00	0.00	0.00	5.87
1060	2375	0.253044	GCCCACCATAACAGAGCTGA	59.747	55.000	4.21	0.00	0.00	4.26
1107	2422	1.374758	CAGCCTCGACACAAGGGTC	60.375	63.158	0.00	0.00	42.62	4.46
1255	2571	4.927782	AGCACGCCAACTTCGCCA	62.928	61.111	0.00	0.00	0.00	5.69
1371	2687	1.298340	CATGTACCAGGCCGTTCCA	59.702	57.895	0.00	0.00	37.29	3.53
1725	3045	1.885887	ACTTATGCATGCGTGTGGTTT	59.114	42.857	22.77	0.00	0.00	3.27
1816	3146	2.989909	TCACTTGCATCAATGGATCGT	58.010	42.857	0.00	0.00	0.00	3.73
2021	3357	0.953471	CTTTCGGACGATGGTTGGCA	60.953	55.000	0.00	0.00	0.00	4.92
2134	3470	6.907212	CGGTAACTCATCAATAATGAACTTGC	59.093	38.462	0.00	0.00	43.78	4.01
2299	3637	2.719739	CTGAATTGGATGACCACTGCT	58.280	47.619	0.00	0.00	46.80	4.24
2307	3645	0.773644	ATGACCACTGCTCCCACTTT	59.226	50.000	0.00	0.00	0.00	2.66
2344	3682	4.833478	AAGTATCTGAGCAACACTCCAT	57.167	40.909	0.00	0.00	45.61	3.41
2372	3710	3.433274	TGACTGATTTTACGAGCAAGCAG	59.567	43.478	8.30	8.30	41.29	4.24
2645	3989	2.274542	TGGGAGTCATGTTGGGTATGT	58.725	47.619	0.00	0.00	0.00	2.29
2709	4053	1.673626	CCATTGCAGCATCAACCAACC	60.674	52.381	0.00	0.00	0.00	3.77
2737	4082	2.167693	CCTAACTCGGTACATCTTGCCA	59.832	50.000	0.00	0.00	0.00	4.92
2766	4111	0.734889	CATCAGGTCCAATGAACGCC	59.265	55.000	0.00	0.00	31.67	5.68
2796	4141	0.777446	ACCCCATGGTTAACACAGCT	59.223	50.000	11.73	0.00	44.75	4.24
2819	4164	3.213506	CCCTTGGACGAATTATGCATCA	58.786	45.455	0.19	0.00	0.00	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	71	0.877071	CATCTGGCCGTATGCAATCC	59.123	55.000	0.00	0.00	43.89	3.01
118	119	1.303888	TCTCCCCGAACGTAGCTGT	60.304	57.895	0.00	0.00	0.00	4.40
182	183	4.578898	ACGCGTGCAACCTCGACA	62.579	61.111	12.93	0.00	34.18	4.35
262	292	1.846541	CCCATGTTTGCGACGTTTTT	58.153	45.000	0.00	0.00	0.00	1.94
263	293	0.596341	GCCCATGTTTGCGACGTTTT	60.596	50.000	0.00	0.00	0.00	2.43
264	294	1.007849	GCCCATGTTTGCGACGTTT	60.008	52.632	0.00	0.00	0.00	3.60
265	295	1.452145	AAGCCCATGTTTGCGACGTT	61.452	50.000	0.00	0.00	0.00	3.99
266	296	1.852067	GAAGCCCATGTTTGCGACGT	61.852	55.000	0.00	0.00	0.00	4.34
267	297	1.154225	GAAGCCCATGTTTGCGACG	60.154	57.895	0.00	0.00	0.00	5.12
268	298	1.212751	GGAAGCCCATGTTTGCGAC	59.787	57.895	0.00	0.00	0.00	5.19
269	299	1.976474	GGGAAGCCCATGTTTGCGA	60.976	57.895	0.00	0.00	44.65	5.10
270	300	2.573340	GGGAAGCCCATGTTTGCG	59.427	61.111	0.00	0.00	44.65	4.85
279	309	3.327404	TTCCGGACAGGGAAGCCC	61.327	66.667	1.83	0.00	45.90	5.19
283	313	3.373226	CGACTTCCGGACAGGGAA	58.627	61.111	1.83	0.00	43.66	3.97
534	564	6.744175	TCAAGCTAGAGATCAAAGATGGAT	57.256	37.500	0.00	0.00	0.00	3.41
549	580	1.332065	TCTGCGACGAGATCAAGCTAG	59.668	52.381	0.00	0.00	0.00	3.42
566	597	4.868635	CGTCCAGCTACACAGACGTCTG	62.869	59.091	37.50	37.50	45.25	3.51
567	598	0.882474	GTCCAGCTACACAGACGTCT	59.118	55.000	13.58	13.58	0.00	4.18
573	610	1.066303	GATCCTCGTCCAGCTACACAG	59.934	57.143	0.00	0.00	0.00	3.66
578	615	0.468648	TCTCGATCCTCGTCCAGCTA	59.531	55.000	0.00	0.00	41.35	3.32
650	1505	6.239036	GGAAACCACAATTTATAGCTGGATCC	60.239	42.308	4.20	4.20	0.00	3.36
717	1572	4.054455	CGGTGAACAACGCGACGG	62.054	66.667	15.93	3.63	33.50	4.79
726	1600	0.108992	GCGAGTATGGACGGTGAACA	60.109	55.000	0.00	0.00	0.00	3.18
781	1655	3.922171	AATTGTGGTTCCCTGCAAAAA	57.078	38.095	0.00	0.00	0.00	1.94
782	1656	3.964031	ACTAATTGTGGTTCCCTGCAAAA	59.036	39.130	0.00	0.00	0.00	2.44
783	1657	3.571590	ACTAATTGTGGTTCCCTGCAAA	58.428	40.909	0.00	0.00	0.00	3.68
784	1658	3.237268	ACTAATTGTGGTTCCCTGCAA	57.763	42.857	0.00	0.00	0.00	4.08
785	1659	2.969821	ACTAATTGTGGTTCCCTGCA	57.030	45.000	0.00	0.00	0.00	4.41
786	1660	3.057526	GTGAACTAATTGTGGTTCCCTGC	60.058	47.826	13.97	0.00	42.87	4.85
787	1661	3.506067	GGTGAACTAATTGTGGTTCCCTG	59.494	47.826	13.97	0.00	42.87	4.45
788	1662	3.763057	GGTGAACTAATTGTGGTTCCCT	58.237	45.455	13.97	0.00	42.87	4.20
789	1663	2.486592	CGGTGAACTAATTGTGGTTCCC	59.513	50.000	13.97	13.16	42.87	3.97
790	1664	2.486592	CCGGTGAACTAATTGTGGTTCC	59.513	50.000	13.97	8.33	42.87	3.62
791	1665	2.095415	GCCGGTGAACTAATTGTGGTTC	60.095	50.000	1.90	11.33	43.58	3.62
792	1666	1.883926	GCCGGTGAACTAATTGTGGTT	59.116	47.619	1.90	0.00	0.00	3.67
793	1667	1.073284	AGCCGGTGAACTAATTGTGGT	59.927	47.619	1.90	0.00	0.00	4.16
850	1904	2.482721	CGTGTTTGGGTAGGATTGTGTC	59.517	50.000	0.00	0.00	0.00	3.67
854	1908	2.607635	CGATCGTGTTTGGGTAGGATTG	59.392	50.000	7.03	0.00	0.00	2.67
875	1929	2.637947	GGATTTGAGAGGTGGCTTCTC	58.362	52.381	1.93	1.93	41.14	2.87
897	1951	4.778143	CGCAGGGAGAAACCGGGG	62.778	72.222	6.32	0.00	40.11	5.73
904	2182	3.329542	GATGGGTGCGCAGGGAGAA	62.330	63.158	12.22	0.00	0.00	2.87
940	2226	0.529833	CGATCTGTGTCTGAGCAGGT	59.470	55.000	8.65	2.79	33.81	4.00
952	2238	2.030412	TGCGTGTTGCCGATCTGT	59.970	55.556	0.00	0.00	45.60	3.41
957	2243	2.027073	GATCTGTGCGTGTTGCCGA	61.027	57.895	0.00	0.00	45.60	5.54
972	2258	0.892063	GCCGAGGGGTAGATCTGATC	59.108	60.000	9.65	9.65	34.97	2.92
985	2283	1.084370	GTCATTGTTCTCGGCCGAGG	61.084	60.000	45.31	31.42	42.20	4.63
986	2284	0.108615	AGTCATTGTTCTCGGCCGAG	60.109	55.000	42.89	42.89	43.21	4.63
989	2287	0.036388	TCCAGTCATTGTTCTCGGCC	60.036	55.000	0.00	0.00	0.00	6.13
1142	2458	1.871772	CCTTTGCTTGTCTCGGCTG	59.128	57.895	0.00	0.00	0.00	4.85
1614	2930	0.182775	GGGGGATTACCTTGTGCGAT	59.817	55.000	0.00	0.00	40.03	4.58
1725	3045	4.974438	AGGCCGGGAAGTGGGACA	62.974	66.667	2.18	0.00	31.98	4.02
1866	3196	1.102154	CCACCGCAATGCCTTATTCA	58.898	50.000	0.00	0.00	0.00	2.57
1870	3200	2.034843	TGCCACCGCAATGCCTTA	59.965	55.556	0.00	0.00	43.74	2.69
2021	3357	4.265056	GAACACGGCACCCCCTGT	62.265	66.667	0.00	0.00	0.00	4.00
2033	3369	5.357878	ACCAATATGTCATCACCATGAACAC	59.642	40.000	0.00	0.00	40.90	3.32
2077	3413	1.402107	CCAAGCCCAGCCAACAAAGT	61.402	55.000	0.00	0.00	0.00	2.66
2103	3439	2.851263	TTGATGAGTTACCGGCAGTT	57.149	45.000	0.00	0.00	0.00	3.16
2109	3445	6.907212	GCAAGTTCATTATTGATGAGTTACCG	59.093	38.462	0.00	0.00	45.15	4.02
2134	3470	1.212935	CAGGGTGGGGAAAGATGGTAG	59.787	57.143	0.00	0.00	0.00	3.18
2299	3637	0.923358	AACACACAGGGAAAGTGGGA	59.077	50.000	2.19	0.00	42.98	4.37
2307	3645	2.799126	ACTTTGACAACACACAGGGA	57.201	45.000	0.00	0.00	0.00	4.20
2344	3682	5.053811	TGCTCGTAAAATCAGTCACAAAGA	58.946	37.500	0.00	0.00	0.00	2.52
2372	3710	2.450609	TTCGGTTACAGTTCCAGAGC	57.549	50.000	0.00	0.00	0.00	4.09
2645	3989	0.867746	GTCTGAGCGTGTGCAATCAA	59.132	50.000	0.00	0.00	46.23	2.57
2709	4053	3.947910	TGTACCGAGTTAGGTTGGAAG	57.052	47.619	0.00	0.00	43.00	3.46
2737	4082	2.837947	TGGACCTGATGAGATCCAACT	58.162	47.619	0.00	0.00	38.30	3.16
2766	4111	0.251474	CCATGGGGTATGCTGGATGG	60.251	60.000	2.85	0.00	35.37	3.51
2796	4141	1.340502	TGCATAATTCGTCCAAGGGCA	60.341	47.619	0.00	0.00	0.00	5.36
2819	4164	3.518590	CGGTAGTTATTCAGCGGAAACT	58.481	45.455	2.68	6.29	36.43	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.