AutoCloner

Multiple sequence alignment - TraesCS6B01G045000

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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	TraesCS6B01G045000	chr6B	100.000	3188	0	0	1	3188	26842970	26839783	0.000000e+00	5851.0
1	TraesCS6B01G045000	chr6B	96.791	2244	66	2	945	3188	26856918	26854681	0.000000e+00	3740.0
2	TraesCS6B01G045000	chr6B	89.885	1562	142	8	954	2507	26248000	26249553	0.000000e+00	1995.0
3	TraesCS6B01G045000	chr6B	80.979	1593	263	30	958	2540	26291263	26292825	0.000000e+00	1227.0
4	TraesCS6B01G045000	chr6B	83.736	621	77	16	2572	3188	26249815	26250415	1.660000e-157	566.0
5	TraesCS6B01G045000	chr6B	85.430	453	40	9	314	743	26857578	26857129	6.270000e-122	448.0
6	TraesCS6B01G045000	chr6B	84.429	289	37	5	445	726	26230926	26231213	8.710000e-71	278.0
7	TraesCS6B01G045000	chr6B	83.219	292	34	8	20	310	26230503	26230780	1.470000e-63	254.0
8	TraesCS6B01G045000	chr6B	85.586	222	18	5	860	1080	26007714	26007506	1.490000e-53	220.0
9	TraesCS6B01G045000	chr6B	92.079	101	3	4	787	884	26247880	26247978	1.540000e-28	137.0
10	TraesCS6B01G045000	chr6B	91.398	93	6	2	313	404	26230829	26230920	3.340000e-25	126.0
11	TraesCS6B01G045000	chr6D	84.636	1497	207	16	1055	2540	14422109	14423593	0.000000e+00	1469.0
12	TraesCS6B01G045000	chr6D	81.582	1542	229	30	902	2423	14689357	14687851	0.000000e+00	1223.0
13	TraesCS6B01G045000	chr6D	82.526	1362	207	26	1080	2428	15344780	15343437	0.000000e+00	1168.0
14	TraesCS6B01G045000	chr6D	81.449	1353	227	20	1082	2424	14483761	14485099	0.000000e+00	1086.0
15	TraesCS6B01G045000	chr6D	82.310	1221	198	18	1074	2287	14727274	14726065	0.000000e+00	1042.0
16	TraesCS6B01G045000	chr6D	84.628	631	71	19	2561	3188	14424097	14424704	3.520000e-169	604.0
17	TraesCS6B01G045000	chr6D	95.486	288	13	0	2901	3188	14406005	14406292	8.060000e-126	460.0
18	TraesCS6B01G045000	chr6D	78.218	404	71	13	2560	2953	15346123	15345727	3.180000e-60	243.0
19	TraesCS6B01G045000	chr6A	80.153	1567	241	41	989	2540	15647275	15648786	0.000000e+00	1107.0
20	TraesCS6B01G045000	chr6A	81.536	1354	224	22	1082	2424	15684926	15686264	0.000000e+00	1092.0
21	TraesCS6B01G045000	chr6A	85.243	515	41	15	314	810	15635081	15635578	6.140000e-137	497.0
22	TraesCS6B01G045000	chr6A	88.144	194	22	1	2995	3188	15649259	15649451	2.470000e-56	230.0
23	TraesCS6B01G045000	chr6A	83.902	205	28	3	2563	2763	16616300	16616503	1.170000e-44	191.0
24	TraesCS6B01G045000	chr6A	80.000	190	22	7	625	809	412366276	412366454	3.340000e-25	126.0
25	TraesCS6B01G045000	chr1B	80.521	1381	237	32	1062	2429	48062306	48060945	0.000000e+00	1031.0
26	TraesCS6B01G045000	chrUn	100.000	521	0	0	2668	3188	261310348	261310868	0.000000e+00	963.0
27	TraesCS6B01G045000	chr1D	88.889	171	18	1	3018	3188	82251077	82251246	3.220000e-50	209.0
28	TraesCS6B01G045000	chr1D	80.597	201	25	4	614	810	78966822	78967012	3.310000e-30	143.0
29	TraesCS6B01G045000	chr4A	80.193	207	25	7	607	809	595044968	595044774	1.190000e-29	141.0
30	TraesCS6B01G045000	chr2B	79.612	206	28	5	608	809	45740947	45740752	5.550000e-28	135.0
31	TraesCS6B01G045000	chr2B	87.719	57	6	1	754	809	775168128	775168184	7.380000e-07	65.8
32	TraesCS6B01G045000	chr7D	79.365	189	25	6	625	809	611352732	611352554	1.200000e-24	124.0
33	TraesCS6B01G045000	chr7B	75.806	186	38	7	630	810	97937747	97937564	4.350000e-19	106.0
34	TraesCS6B01G045000	chr7B	81.579	114	17	4	633	743	708856966	708857078	1.220000e-14	91.6
35	TraesCS6B01G045000	chr1A	74.725	182	43	3	630	809	363692918	363692738	2.620000e-16	97.1
36	TraesCS6B01G045000	chr3D	78.146	151	21	3	661	809	502893374	502893234	5.670000e-13	86.1

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	TraesCS6B01G045000	chr6B	26839783	26842970	3187	True	5851.000000	5851	100.000000	1	3188	1	chr6B.!!$R2	3187
1	TraesCS6B01G045000	chr6B	26854681	26857578	2897	True	2094.000000	3740	91.110500	314	3188	2	chr6B.!!$R3	2874
2	TraesCS6B01G045000	chr6B	26291263	26292825	1562	False	1227.000000	1227	80.979000	958	2540	1	chr6B.!!$F1	1582
3	TraesCS6B01G045000	chr6B	26247880	26250415	2535	False	899.333333	1995	88.566667	787	3188	3	chr6B.!!$F3	2401
4	TraesCS6B01G045000	chr6B	26230503	26231213	710	False	219.333333	278	86.348667	20	726	3	chr6B.!!$F2	706
5	TraesCS6B01G045000	chr6D	14687851	14689357	1506	True	1223.000000	1223	81.582000	902	2423	1	chr6D.!!$R1	1521
6	TraesCS6B01G045000	chr6D	14483761	14485099	1338	False	1086.000000	1086	81.449000	1082	2424	1	chr6D.!!$F2	1342
7	TraesCS6B01G045000	chr6D	14726065	14727274	1209	True	1042.000000	1042	82.310000	1074	2287	1	chr6D.!!$R2	1213
8	TraesCS6B01G045000	chr6D	14422109	14424704	2595	False	1036.500000	1469	84.632000	1055	3188	2	chr6D.!!$F3	2133
9	TraesCS6B01G045000	chr6D	15343437	15346123	2686	True	705.500000	1168	80.372000	1080	2953	2	chr6D.!!$R3	1873
10	TraesCS6B01G045000	chr6A	15684926	15686264	1338	False	1092.000000	1092	81.536000	1082	2424	1	chr6A.!!$F2	1342
11	TraesCS6B01G045000	chr6A	15647275	15649451	2176	False	668.500000	1107	84.148500	989	3188	2	chr6A.!!$F5	2199
12	TraesCS6B01G045000	chr1B	48060945	48062306	1361	True	1031.000000	1031	80.521000	1062	2429	1	chr1B.!!$R1	1367
13	TraesCS6B01G045000	chrUn	261310348	261310868	520	False	963.000000	963	100.000000	2668	3188	1	chrUn.!!$F1	520

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
920	1081	0.173708	CTCACTAGCGACCTTCACCC	59.826	60.0	0.0	0.0	0.00	4.61	F
1585	1866	0.668401	GCTGAAGCCCAATGTTGTGC	60.668	55.0	0.0	0.0	34.31	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2055	2336	1.153628	CTCGGCCCTCTTAACCACG	60.154	63.158	0.00	0.0	0.0	4.94	R
2641	3430	2.158667	ACAACCAGTGACCGGAAGAAAT	60.159	45.455	9.46	0.0	0.0	2.17	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
57	58	6.601741	TTGAAAGATGCACCAACATTTTTC	57.398	33.333	11.48	11.48	44.93	2.29
59	60	6.601741	GAAAGATGCACCAACATTTTTCAA	57.398	33.333	12.83	0.00	44.48	2.69
82	83	8.300286	TCAACACAACATAAACTTGTCTTCAAA	58.700	29.630	0.00	0.00	32.87	2.69
202	203	8.857694	TCGAAAGGACTAATAAGGAAACAAAT	57.142	30.769	0.00	0.00	0.00	2.32
207	208	8.934023	AGGACTAATAAGGAAACAAATGAACA	57.066	30.769	0.00	0.00	0.00	3.18
219	220	7.253256	GGAAACAAATGAACAAAATGCAAAACG	60.253	33.333	0.00	0.00	0.00	3.60
220	221	5.027099	ACAAATGAACAAAATGCAAAACGC	58.973	33.333	0.00	0.00	42.89	4.84
254	255	4.883354	GGCCAGCCCATTCCTCGG	62.883	72.222	0.00	0.00	0.00	4.63
262	263	1.750399	CCATTCCTCGGCCACCTTG	60.750	63.158	2.24	0.00	0.00	3.61
481	533	3.727387	GCAGAGGGCCTAGTTGGA	58.273	61.111	5.73	0.00	38.35	3.53
527	579	5.838531	TCCCAACGAACTAAAATGTTTGT	57.161	34.783	0.00	0.00	43.96	2.83
538	590	6.074648	ACTAAAATGTTTGTGAGGGGATTCA	58.925	36.000	0.00	0.00	0.00	2.57
562	614	4.988540	TCGTAGAGAACCAAACATTCACAG	59.011	41.667	0.00	0.00	0.00	3.66
580	633	3.399181	TGACCTCCCCATGGCGTC	61.399	66.667	6.09	9.18	33.52	5.19
628	695	7.634671	TTGACTCCACTATAAATCTGACGTA	57.365	36.000	0.00	0.00	0.00	3.57
729	797	1.269448	GCAAATCCGCCTCAGTTCAAA	59.731	47.619	0.00	0.00	0.00	2.69
738	806	4.358851	CGCCTCAGTTCAAATTTTGTCAA	58.641	39.130	8.89	0.00	0.00	3.18
739	807	4.803088	CGCCTCAGTTCAAATTTTGTCAAA	59.197	37.500	8.89	0.00	0.00	2.69
740	808	5.290643	CGCCTCAGTTCAAATTTTGTCAAAA	59.709	36.000	12.97	12.97	34.41	2.44
741	809	6.183360	CGCCTCAGTTCAAATTTTGTCAAAAA	60.183	34.615	14.47	0.34	39.53	1.94
770	838	4.149346	TGCCGTGCTTGCAAACTA	57.851	50.000	0.00	0.00	35.40	2.24
771	839	2.409399	TGCCGTGCTTGCAAACTAA	58.591	47.368	0.00	0.00	35.40	2.24
775	843	2.799978	GCCGTGCTTGCAAACTAAATTT	59.200	40.909	0.00	0.00	0.00	1.82
787	855	6.399204	CAAACTAAATTTGCCATCTTGAGC	57.601	37.500	0.00	0.00	41.30	4.26
884	1045	2.282180	GCCGAAACCTCAGCCCAA	60.282	61.111	0.00	0.00	0.00	4.12
889	1050	2.555199	CGAAACCTCAGCCCAATAGAG	58.445	52.381	0.00	0.00	0.00	2.43
896	1057	2.437281	CTCAGCCCAATAGAGTCCACAT	59.563	50.000	0.00	0.00	0.00	3.21
900	1061	2.548067	GCCCAATAGAGTCCACATACCG	60.548	54.545	0.00	0.00	0.00	4.02
908	1069	2.025155	AGTCCACATACCGCTCACTAG	58.975	52.381	0.00	0.00	0.00	2.57
920	1081	0.173708	CTCACTAGCGACCTTCACCC	59.826	60.000	0.00	0.00	0.00	4.61
921	1082	1.153823	CACTAGCGACCTTCACCCG	60.154	63.158	0.00	0.00	0.00	5.28
923	1084	0.683504	ACTAGCGACCTTCACCCGAT	60.684	55.000	0.00	0.00	0.00	4.18
1024	1193	4.615815	ATCTCCGGCAGCGCATCC	62.616	66.667	11.47	9.26	0.00	3.51
1031	1200	3.521796	GCAGCGCATCCTTTCCCC	61.522	66.667	11.47	0.00	0.00	4.81
1090	1355	1.229625	ACCACCTCTGCCATCTCCA	60.230	57.895	0.00	0.00	0.00	3.86
1248	1525	4.760047	CACCTCAAGTCCCCCGCG	62.760	72.222	0.00	0.00	0.00	6.46
1585	1866	0.668401	GCTGAAGCCCAATGTTGTGC	60.668	55.000	0.00	0.00	34.31	4.57
1634	1915	3.689161	TGTGATATTGCCAAGCTGTGTAC	59.311	43.478	0.00	0.00	0.00	2.90
1785	2066	1.446272	GGAGAAGGTCGCCGACAAG	60.446	63.158	20.08	0.00	33.68	3.16
1856	2137	1.276421	TGCTCTGTCTAAGGCTCCAAC	59.724	52.381	0.00	0.00	0.00	3.77
2055	2336	2.621998	TCGCAACCTGAGCTACTATACC	59.378	50.000	0.00	0.00	0.00	2.73
2666	3455	1.384525	TCCGGTCACTGGTTGTTTTG	58.615	50.000	1.45	0.00	0.00	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	4.874970	AGAGCAAATGTTCGAAAAATGCT	58.125	34.783	24.18	24.18	44.61	3.79
3	4	4.681025	TGAGAGCAAATGTTCGAAAAATGC	59.319	37.500	17.35	17.35	0.00	3.56
5	6	6.272318	TGTTGAGAGCAAATGTTCGAAAAAT	58.728	32.000	0.00	0.00	35.42	1.82
6	7	5.645624	TGTTGAGAGCAAATGTTCGAAAAA	58.354	33.333	0.00	0.00	35.42	1.94
7	8	5.242069	TGTTGAGAGCAAATGTTCGAAAA	57.758	34.783	0.00	0.00	35.42	2.29
8	9	4.891627	TGTTGAGAGCAAATGTTCGAAA	57.108	36.364	0.00	0.00	35.42	3.46
9	10	5.437289	AATGTTGAGAGCAAATGTTCGAA	57.563	34.783	0.00	0.00	35.42	3.71
10	11	5.437289	AAATGTTGAGAGCAAATGTTCGA	57.563	34.783	0.00	0.00	35.42	3.71
11	12	6.515043	AAAAATGTTGAGAGCAAATGTTCG	57.485	33.333	0.00	0.00	35.42	3.95
36	37	6.036953	TGTTGAAAAATGTTGGTGCATCTTTC	59.963	34.615	0.00	0.00	36.73	2.62
40	41	4.569966	TGTGTTGAAAAATGTTGGTGCATC	59.430	37.500	0.00	0.00	0.00	3.91
41	42	4.511527	TGTGTTGAAAAATGTTGGTGCAT	58.488	34.783	0.00	0.00	0.00	3.96
57	58	8.372521	GTTTGAAGACAAGTTTATGTTGTGTTG	58.627	33.333	3.39	0.00	40.42	3.33
59	60	7.826690	AGTTTGAAGACAAGTTTATGTTGTGT	58.173	30.769	0.00	0.00	38.26	3.72
173	174	9.122779	TGTTTCCTTATTAGTCCTTTCGAAAAA	57.877	29.630	12.41	3.22	0.00	1.94
174	175	8.680039	TGTTTCCTTATTAGTCCTTTCGAAAA	57.320	30.769	12.41	0.00	0.00	2.29
175	176	8.680039	TTGTTTCCTTATTAGTCCTTTCGAAA	57.320	30.769	10.71	10.71	0.00	3.46
176	177	8.680039	TTTGTTTCCTTATTAGTCCTTTCGAA	57.320	30.769	0.00	0.00	0.00	3.71
177	178	8.726988	CATTTGTTTCCTTATTAGTCCTTTCGA	58.273	33.333	0.00	0.00	0.00	3.71
194	195	7.590548	CGTTTTGCATTTTGTTCATTTGTTTC	58.409	30.769	0.00	0.00	0.00	2.78
220	221	0.594796	GCCCAGTTGCACTTTTCGTG	60.595	55.000	0.00	0.00	46.58	4.35
254	255	1.739067	GTATCTGTGGTCAAGGTGGC	58.261	55.000	0.00	0.00	0.00	5.01
262	263	0.721718	GCAAGTGCGTATCTGTGGTC	59.278	55.000	0.00	0.00	0.00	4.02
292	293	2.157640	AATTCCGATGGGATTTGCCA	57.842	45.000	0.00	0.00	43.41	4.92
293	294	3.541996	AAAATTCCGATGGGATTTGCC	57.458	42.857	2.90	0.00	43.41	4.52
321	368	9.807921	TTCTTTTGGTCATTTAAAGATCTAGGT	57.192	29.630	0.00	0.00	37.63	3.08
433	482	1.273041	GCCCAACTCCCCCTTTTACAT	60.273	52.381	0.00	0.00	0.00	2.29
476	528	2.258726	GCACGAACCCCACTCCAAC	61.259	63.158	0.00	0.00	0.00	3.77
477	529	2.112297	GCACGAACCCCACTCCAA	59.888	61.111	0.00	0.00	0.00	3.53
510	562	4.277423	CCCCTCACAAACATTTTAGTTCGT	59.723	41.667	0.00	0.00	0.00	3.85
527	579	3.595190	TCTCTACGATGAATCCCCTCA	57.405	47.619	0.00	0.00	0.00	3.86
538	590	5.547465	TGTGAATGTTTGGTTCTCTACGAT	58.453	37.500	0.00	0.00	0.00	3.73
562	614	3.682292	GACGCCATGGGGAGGTCAC	62.682	68.421	33.50	13.56	38.47	3.67
628	695	8.206189	AGTTTGATTTGTCATGGTCAAAATCTT	58.794	29.630	16.37	5.11	40.85	2.40
754	822	2.064573	ATTTAGTTTGCAAGCACGGC	57.935	45.000	16.04	0.00	0.00	5.68
765	833	5.011943	TGGCTCAAGATGGCAAATTTAGTTT	59.988	36.000	0.00	0.00	37.05	2.66
766	834	4.527816	TGGCTCAAGATGGCAAATTTAGTT	59.472	37.500	0.00	0.00	37.05	2.24
768	836	4.724074	TGGCTCAAGATGGCAAATTTAG	57.276	40.909	0.00	0.00	37.05	1.85
775	843	6.982160	AATTTATATTGGCTCAAGATGGCA	57.018	33.333	0.00	0.00	38.22	4.92
776	844	6.583806	CGAAATTTATATTGGCTCAAGATGGC	59.416	38.462	0.00	0.00	0.00	4.40
777	845	7.874940	TCGAAATTTATATTGGCTCAAGATGG	58.125	34.615	0.00	0.00	0.00	3.51
778	846	9.338291	CATCGAAATTTATATTGGCTCAAGATG	57.662	33.333	0.00	0.00	0.00	2.90
780	848	8.675705	TCATCGAAATTTATATTGGCTCAAGA	57.324	30.769	0.00	0.00	0.00	3.02
781	849	9.734620	TTTCATCGAAATTTATATTGGCTCAAG	57.265	29.630	0.00	0.00	0.00	3.02
784	852	9.515020	TGTTTTCATCGAAATTTATATTGGCTC	57.485	29.630	0.00	0.00	31.34	4.70
785	853	9.868277	TTGTTTTCATCGAAATTTATATTGGCT	57.132	25.926	0.00	0.00	31.34	4.75
884	1045	2.623889	GTGAGCGGTATGTGGACTCTAT	59.376	50.000	0.00	0.00	0.00	1.98
889	1050	1.536284	GCTAGTGAGCGGTATGTGGAC	60.536	57.143	0.00	0.00	39.39	4.02
900	1061	0.458716	GGTGAAGGTCGCTAGTGAGC	60.459	60.000	24.49	24.49	46.00	4.26
908	1069	1.665161	CGTATATCGGGTGAAGGTCGC	60.665	57.143	0.00	0.00	35.71	5.19
915	1076	0.589708	CGAGTGCGTATATCGGGTGA	59.410	55.000	3.70	0.00	40.26	4.02
920	1081	1.058590	GACGGCGAGTGCGTATATCG	61.059	60.000	16.62	6.70	44.10	2.92
921	1082	0.040692	TGACGGCGAGTGCGTATATC	60.041	55.000	16.62	0.00	44.10	1.63
923	1084	0.170784	TTTGACGGCGAGTGCGTATA	59.829	50.000	16.62	0.00	44.10	1.47
1024	1193	2.782341	AGGAGGAGATGATTGGGGAAAG	59.218	50.000	0.00	0.00	0.00	2.62
1031	1200	0.034616	GGCGGAGGAGGAGATGATTG	59.965	60.000	0.00	0.00	0.00	2.67
1248	1525	2.281276	AGGACGGCGTTGGGTTTC	60.281	61.111	16.19	0.00	0.00	2.78
1309	1587	2.355481	GTCTTTGGCGACGACGGT	60.355	61.111	9.67	0.00	40.15	4.83
1648	1929	3.977244	CGGGTTGGTTGCCAGCAC	61.977	66.667	4.52	0.00	36.44	4.40
1691	1972	2.094894	CGCACACCTAATCTTTCAGCAG	59.905	50.000	0.00	0.00	0.00	4.24
1785	2066	6.148811	TGAACGTCTTCTTCAAATAATCCACC	59.851	38.462	0.00	0.00	0.00	4.61
1856	2137	4.155099	TCTCTCTAGACTTCTTCAGCAACG	59.845	45.833	0.00	0.00	0.00	4.10
2055	2336	1.153628	CTCGGCCCTCTTAACCACG	60.154	63.158	0.00	0.00	0.00	4.94
2425	2727	7.179516	AGGAATAAAATTACCCGGAAAACACAT	59.820	33.333	0.73	0.00	0.00	3.21
2641	3430	2.158667	ACAACCAGTGACCGGAAGAAAT	60.159	45.455	9.46	0.00	0.00	2.17
2666	3455	2.162408	GCAGGTGCAGATTTCAGTAACC	59.838	50.000	0.00	0.00	41.59	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.