AutoCloner

Multiple sequence alignment - TraesCS2B01G565500

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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	TraesCS2B01G565500	chr2B	100.000	2255	0	0	1	2255	757016928	757014674	0.000000e+00	4165.0
1	TraesCS2B01G565500	chr2B	85.088	456	37	8	1791	2220	626991464	626991914	9.560000e-119	436.0
2	TraesCS2B01G565500	chr2B	80.741	540	74	17	763	1288	757394770	757394247	5.840000e-106	394.0
3	TraesCS2B01G565500	chr2B	82.326	430	62	8	876	1299	757453265	757452844	5.920000e-96	361.0
4	TraesCS2B01G565500	chr2B	79.505	444	46	19	1784	2197	644554526	644554954	7.930000e-70	274.0
5	TraesCS2B01G565500	chr2B	79.695	394	53	12	881	1256	757433762	757433378	2.220000e-65	259.0
6	TraesCS2B01G565500	chr2B	79.592	294	41	10	1320	1599	757394167	757393879	2.290000e-45	193.0
7	TraesCS2B01G565500	chr2B	80.859	256	35	7	1362	1605	757452725	757452472	2.960000e-44	189.0
8	TraesCS2B01G565500	chr2B	88.889	99	8	2	770	865	757567308	757567210	3.930000e-23	119.0
9	TraesCS2B01G565500	chrUn	100.000	1161	0	0	1	1161	291049135	291047975	0.000000e+00	2145.0
10	TraesCS2B01G565500	chr2A	88.909	1127	67	24	699	1794	750188675	750189774	0.000000e+00	1336.0
11	TraesCS2B01G565500	chr2A	88.962	453	23	10	1794	2220	1917677	1918128	3.300000e-148	534.0
12	TraesCS2B01G565500	chr2A	83.476	466	39	18	1791	2226	597510185	597509728	1.250000e-107	399.0
13	TraesCS2B01G565500	chr2A	88.186	237	18	4	477	713	750188365	750188591	7.930000e-70	274.0
14	TraesCS2B01G565500	chr2A	76.712	584	77	28	770	1316	750425377	750424816	1.030000e-68	270.0
15	TraesCS2B01G565500	chr2A	76.344	558	74	28	792	1316	750334582	750334050	1.730000e-61	246.0
16	TraesCS2B01G565500	chr7D	92.745	510	26	5	762	1261	498252517	498252009	0.000000e+00	726.0
17	TraesCS2B01G565500	chr7D	81.838	457	46	16	1794	2220	611755069	611755518	1.280000e-92	350.0
18	TraesCS2B01G565500	chr7D	75.896	809	115	47	762	1502	498285478	498284682	7.710000e-90	340.0
19	TraesCS2B01G565500	chr7D	87.458	295	25	5	1290	1572	498252009	498251715	1.670000e-86	329.0
20	TraesCS2B01G565500	chr7D	88.664	247	19	5	1559	1797	498244542	498244297	2.190000e-75	292.0
21	TraesCS2B01G565500	chr7D	93.939	99	5	1	646	744	498252602	498252505	5.020000e-32	148.0
22	TraesCS2B01G565500	chr5B	88.478	460	25	10	1794	2227	13388954	13389411	4.260000e-147	531.0
23	TraesCS2B01G565500	chr5D	88.470	451	35	11	1794	2228	362039300	362039749	1.530000e-146	529.0
24	TraesCS2B01G565500	chr5D	100.000	31	0	0	460	490	9501870	9501840	8.700000e-05	58.4
25	TraesCS2B01G565500	chr5D	100.000	31	0	0	460	490	269578684	269578714	8.700000e-05	58.4
26	TraesCS2B01G565500	chr4D	88.286	461	27	7	1794	2228	18813368	18812909	5.520000e-146	527.0
27	TraesCS2B01G565500	chr4D	100.000	31	0	0	460	490	46178971	46179001	8.700000e-05	58.4
28	TraesCS2B01G565500	chr1A	87.609	460	27	10	1794	2227	362507493	362507948	7.190000e-140	507.0
29	TraesCS2B01G565500	chr1A	84.527	433	48	11	1362	1782	108778404	108778829	5.800000e-111	411.0
30	TraesCS2B01G565500	chr1A	100.000	30	0	0	461	490	576281358	576281387	3.130000e-04	56.5
31	TraesCS2B01G565500	chr1D	86.425	442	29	10	1805	2220	254778346	254778782	2.640000e-124	455.0
32	TraesCS2B01G565500	chr1D	81.111	360	45	14	1400	1744	77450641	77450992	1.330000e-67	267.0
33	TraesCS2B01G565500	chr2D	77.328	741	98	34	876	1570	610757506	610756790	7.610000e-100	374.0
34	TraesCS2B01G565500	chr2D	77.241	580	77	28	770	1316	619312845	619312288	2.830000e-74	289.0
35	TraesCS2B01G565500	chr2D	83.178	214	28	5	1362	1570	619312190	619311980	2.960000e-44	189.0
36	TraesCS2B01G565500	chr2D	82.301	113	13	4	772	880	619252138	619252029	8.580000e-15	91.6
37	TraesCS2B01G565500	chr7A	86.262	313	17	7	1794	2081	671173951	671173640	1.300000e-82	316.0
38	TraesCS2B01G565500	chr7A	90.385	156	7	2	2071	2226	671173252	671173105	4.910000e-47	198.0
39	TraesCS2B01G565500	chr1B	87.342	158	15	4	1362	1514	121012024	121012181	2.300000e-40	176.0
40	TraesCS2B01G565500	chr6A	97.143	35	0	1	460	493	71525509	71525475	8.700000e-05	58.4
41	TraesCS2B01G565500	chr3B	100.000	30	0	0	461	490	687737570	687737541	3.130000e-04	56.5

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	TraesCS2B01G565500	chr2B	757014674	757016928	2254	True	4165.0	4165	100.000000	1	2255	1	chr2B.!!$R1	2254
1	TraesCS2B01G565500	chr2B	757393879	757394770	891	True	293.5	394	80.166500	763	1599	2	chr2B.!!$R4	836
2	TraesCS2B01G565500	chr2B	757452472	757453265	793	True	275.0	361	81.592500	876	1605	2	chr2B.!!$R5	729
3	TraesCS2B01G565500	chrUn	291047975	291049135	1160	True	2145.0	2145	100.000000	1	1161	1	chrUn.!!$R1	1160
4	TraesCS2B01G565500	chr2A	750188365	750189774	1409	False	805.0	1336	88.547500	477	1794	2	chr2A.!!$F2	1317
5	TraesCS2B01G565500	chr2A	750424816	750425377	561	True	270.0	270	76.712000	770	1316	1	chr2A.!!$R3	546
6	TraesCS2B01G565500	chr2A	750334050	750334582	532	True	246.0	246	76.344000	792	1316	1	chr2A.!!$R2	524
7	TraesCS2B01G565500	chr7D	498251715	498252602	887	True	401.0	726	91.380667	646	1572	3	chr7D.!!$R3	926
8	TraesCS2B01G565500	chr7D	498284682	498285478	796	True	340.0	340	75.896000	762	1502	1	chr7D.!!$R2	740
9	TraesCS2B01G565500	chr2D	610756790	610757506	716	True	374.0	374	77.328000	876	1570	1	chr2D.!!$R1	694
10	TraesCS2B01G565500	chr2D	619311980	619312845	865	True	239.0	289	80.209500	770	1570	2	chr2D.!!$R3	800
11	TraesCS2B01G565500	chr7A	671173105	671173951	846	True	257.0	316	88.323500	1794	2226	2	chr7A.!!$R1	432

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
1166	1351	1.078759	GACCAGGCGATCGTTGACAG	61.079	60.0	17.81	6.06	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2192	2911	0.398664	AATAGCTCGCCCCCACTACT	60.399	55.0	0.0	0.0	0.0	2.57	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
1166	1351	1.078759	GACCAGGCGATCGTTGACAG	61.079	60.000	17.81	6.06	0.00	3.51
1171	1356	0.804933	GGCGATCGTTGACAGGTACC	60.805	60.000	17.81	2.73	0.00	3.34
1316	1509	4.441415	CGATCTACAGAATTCGTTAGGCAC	59.559	45.833	13.41	7.10	0.00	5.01
1317	1510	5.593010	GATCTACAGAATTCGTTAGGCACT	58.407	41.667	13.41	0.00	46.37	4.40
1335	1576	6.116126	AGGCACTAATAGTTGAACAGGATTC	58.884	40.000	0.00	0.00	36.02	2.52
1357	1598	3.328382	TTGAGTGGGAAACGGACATAG	57.672	47.619	0.00	0.00	0.00	2.23
1358	1599	1.553248	TGAGTGGGAAACGGACATAGG	59.447	52.381	0.00	0.00	0.00	2.57
1359	1600	1.553704	GAGTGGGAAACGGACATAGGT	59.446	52.381	0.00	0.00	0.00	3.08
1429	1700	6.851222	TGATTGAAAGAGTTCTGTCTTGAC	57.149	37.500	1.30	0.00	36.86	3.18
1463	1739	6.139048	TCGATTGTTCATAATCACCGACTA	57.861	37.500	0.00	0.00	36.99	2.59
1524	1804	5.703130	ACCTCTGCAACAACTTTAGAAGATC	59.297	40.000	0.00	0.00	0.00	2.75
1541	1822	9.567776	TTAGAAGATCAGTTTTACAATCCACAA	57.432	29.630	0.00	0.00	0.00	3.33
1605	1889	6.646653	GCCTGAAGAATTTACCCAAGAAAAAG	59.353	38.462	0.00	0.00	0.00	2.27
1634	1920	1.270785	TGAATGCTGACTTGGAGCGAA	60.271	47.619	0.00	0.00	39.47	4.70
1635	1921	1.396301	GAATGCTGACTTGGAGCGAAG	59.604	52.381	0.00	0.00	39.47	3.79
1689	1977	5.545723	TCCTGGGATGCTATTTTTCCAAAAA	59.454	36.000	0.00	0.00	41.59	1.94
1696	1984	7.443879	GGATGCTATTTTTCCAAAAACTCCAAA	59.556	33.333	0.00	0.00	40.33	3.28
1699	1987	8.835439	TGCTATTTTTCCAAAAACTCCAAAATC	58.165	29.630	0.00	0.00	40.33	2.17
1707	2001	3.369546	AAACTCCAAAATCGTGCCAAG	57.630	42.857	0.00	0.00	0.00	3.61
1741	2035	8.740906	TCTTTTAGACTAGAGTACTGAATGTGG	58.259	37.037	0.00	0.00	0.00	4.17
1743	2037	8.418597	TTTAGACTAGAGTACTGAATGTGGTT	57.581	34.615	0.00	0.00	0.00	3.67
1747	2041	4.473477	AGAGTACTGAATGTGGTTAGCC	57.527	45.455	0.00	0.00	0.00	3.93
1843	2140	7.607250	TGCGGGAGTTTGTATGAAATAAAAAT	58.393	30.769	0.00	0.00	38.23	1.82
1894	2191	8.650143	AATGGCTTTACAATTTCTCCTAGAAA	57.350	30.769	4.68	4.68	46.89	2.52
1896	2193	7.458397	TGGCTTTACAATTTCTCCTAGAAAGA	58.542	34.615	8.00	0.00	46.15	2.52
1993	2312	9.316859	GAAAACAAAACAAAATATGCATAGTGC	57.683	29.630	12.79	0.00	45.29	4.40
2011	2330	3.886505	AGTGCTAGTACTGGAGTATGAGC	59.113	47.826	13.15	6.74	39.50	4.26
2100	2819	1.094785	CGTTGGTGGCTCTTAATGGG	58.905	55.000	0.00	0.00	0.00	4.00
2125	2844	4.660303	AGATCCAATGGCTAATGTAGTCCA	59.340	41.667	0.00	0.00	36.75	4.02
2167	2886	6.602009	GGCTAAACTAATTTAGGTGATGTGGT	59.398	38.462	5.88	0.00	45.15	4.16
2175	2894	4.927267	TTAGGTGATGTGGTTCAAGGAT	57.073	40.909	0.00	0.00	0.00	3.24
2191	2910	7.121907	GGTTCAAGGATAAGCAAGAGAATTCTT	59.878	37.037	9.87	0.00	44.45	2.52
2192	2911	9.167311	GTTCAAGGATAAGCAAGAGAATTCTTA	57.833	33.333	9.87	0.00	41.71	2.10
2193	2912	8.954950	TCAAGGATAAGCAAGAGAATTCTTAG	57.045	34.615	9.87	4.04	41.71	2.18
2194	2913	8.543774	TCAAGGATAAGCAAGAGAATTCTTAGT	58.456	33.333	9.87	0.00	41.71	2.24
2195	2914	9.823647	CAAGGATAAGCAAGAGAATTCTTAGTA	57.176	33.333	9.87	0.00	41.71	1.82
2197	2916	9.207868	AGGATAAGCAAGAGAATTCTTAGTAGT	57.792	33.333	9.87	0.00	41.71	2.73
2204	2923	2.434702	AGAATTCTTAGTAGTGGGGGCG	59.565	50.000	0.88	0.00	0.00	6.13
2220	2939	5.027460	TGGGGGCGAGCTATTTAGATATAA	58.973	41.667	0.00	0.00	0.00	0.98
2221	2940	5.105064	TGGGGGCGAGCTATTTAGATATAAC	60.105	44.000	0.00	0.00	0.00	1.89
2226	2945	8.630917	GGGCGAGCTATTTAGATATAACAGATA	58.369	37.037	0.00	0.00	0.00	1.98
2252	2971	8.771920	ATAGATTATCGTTTTCCATATTCGCA	57.228	30.769	0.00	0.00	0.00	5.10
2253	2972	7.121974	AGATTATCGTTTTCCATATTCGCAG	57.878	36.000	0.00	0.00	0.00	5.18
2254	2973	6.706270	AGATTATCGTTTTCCATATTCGCAGT	59.294	34.615	0.00	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1316	1509	9.442047	ACTCAAAGAATCCTGTTCAACTATTAG	57.558	33.333	0.00	0.00	0.00	1.73
1317	1510	9.219603	CACTCAAAGAATCCTGTTCAACTATTA	57.780	33.333	0.00	0.00	0.00	0.98
1326	1567	4.453480	TTCCCACTCAAAGAATCCTGTT	57.547	40.909	0.00	0.00	0.00	3.16
1335	1576	1.961793	TGTCCGTTTCCCACTCAAAG	58.038	50.000	0.00	0.00	0.00	2.77
1358	1599	6.839134	AGAATGAAGGTATAATTTTGGGGGAC	59.161	38.462	0.00	0.00	0.00	4.46
1359	1600	6.992235	AGAATGAAGGTATAATTTTGGGGGA	58.008	36.000	0.00	0.00	0.00	4.81
1429	1700	9.808808	GATTATGAACAATCGATTCTGAATGAG	57.191	33.333	7.92	2.08	0.00	2.90
1463	1739	5.726980	TTTTTGCTGCCAGTATCATCTTT	57.273	34.783	0.00	0.00	0.00	2.52
1580	1864	5.722021	TTTCTTGGGTAAATTCTTCAGGC	57.278	39.130	0.00	0.00	0.00	4.85
1605	1889	6.855836	TCCAAGTCAGCATTCATGTAATTTC	58.144	36.000	0.00	0.00	0.00	2.17
1609	1893	3.691118	GCTCCAAGTCAGCATTCATGTAA	59.309	43.478	0.00	0.00	36.82	2.41
1618	1904	1.004560	CCTTCGCTCCAAGTCAGCA	60.005	57.895	0.00	0.00	36.61	4.41
1634	1920	2.090267	ATGGAATCCAGAGGAGCTACCT	60.090	50.000	8.40	4.59	43.56	3.08
1635	1921	1.794714	TGGAATCCAGAGGAGCTACC	58.205	55.000	0.00	0.00	34.05	3.18
1652	1940	1.053264	CCCAGGAGGAGTGGAGATGG	61.053	65.000	0.00	0.00	37.23	3.51
1689	1977	1.981256	ACTTGGCACGATTTTGGAGT	58.019	45.000	0.00	0.00	0.00	3.85
1696	1984	9.191995	CTAAAAGAAAAATTACTTGGCACGATT	57.808	29.630	0.00	0.00	0.00	3.34
1699	1987	7.860872	AGTCTAAAAGAAAAATTACTTGGCACG	59.139	33.333	0.00	0.00	0.00	5.34
1814	2111	0.729116	CATACAAACTCCCGCAGCAG	59.271	55.000	0.00	0.00	0.00	4.24
1817	2114	5.811399	TTATTTCATACAAACTCCCGCAG	57.189	39.130	0.00	0.00	0.00	5.18
1821	2118	9.150348	CCACATTTTTATTTCATACAAACTCCC	57.850	33.333	0.00	0.00	0.00	4.30
1843	2140	7.172342	AGCTTGGTTTATTAGTTCATACCACA	58.828	34.615	0.00	0.00	35.55	4.17
1849	2146	7.716612	GCCATTAGCTTGGTTTATTAGTTCAT	58.283	34.615	6.32	0.00	39.11	2.57
1993	2312	2.226912	GCGGCTCATACTCCAGTACTAG	59.773	54.545	0.00	0.00	32.72	2.57
2034	2353	7.389330	TGATGCCTAAAGAGTGTTTTAATCGAA	59.611	33.333	0.00	0.00	0.00	3.71
2036	2355	7.072177	TGATGCCTAAAGAGTGTTTTAATCG	57.928	36.000	0.00	0.00	0.00	3.34
2052	2371	6.406288	GCAGTGCATATAGTAGATGATGCCTA	60.406	42.308	11.09	0.00	43.26	3.93
2054	2373	4.569966	GCAGTGCATATAGTAGATGATGCC	59.430	45.833	11.09	0.99	43.26	4.40
2100	2819	6.166982	GGACTACATTAGCCATTGGATCTAC	58.833	44.000	6.95	0.00	0.00	2.59
2125	2844	5.717078	TTAGCCGTTGGATATACTCGATT	57.283	39.130	5.03	0.00	0.00	3.34
2167	2886	9.388506	CTAAGAATTCTCTTGCTTATCCTTGAA	57.611	33.333	8.78	0.00	42.11	2.69
2175	2894	7.364762	CCCCACTACTAAGAATTCTCTTGCTTA	60.365	40.741	8.78	0.00	42.11	3.09
2191	2910	0.481567	ATAGCTCGCCCCCACTACTA	59.518	55.000	0.00	0.00	0.00	1.82
2192	2911	0.398664	AATAGCTCGCCCCCACTACT	60.399	55.000	0.00	0.00	0.00	2.57
2193	2912	0.468648	AAATAGCTCGCCCCCACTAC	59.531	55.000	0.00	0.00	0.00	2.73
2194	2913	1.968493	CTAAATAGCTCGCCCCCACTA	59.032	52.381	0.00	0.00	0.00	2.74
2195	2914	0.759346	CTAAATAGCTCGCCCCCACT	59.241	55.000	0.00	0.00	0.00	4.00
2196	2915	0.756903	TCTAAATAGCTCGCCCCCAC	59.243	55.000	0.00	0.00	0.00	4.61
2197	2916	1.729586	ATCTAAATAGCTCGCCCCCA	58.270	50.000	0.00	0.00	0.00	4.96
2226	2945	9.214957	TGCGAATATGGAAAACGATAATCTATT	57.785	29.630	0.00	0.00	0.00	1.73
2227	2946	8.771920	TGCGAATATGGAAAACGATAATCTAT	57.228	30.769	0.00	0.00	0.00	1.98
2228	2947	7.870954	ACTGCGAATATGGAAAACGATAATCTA	59.129	33.333	0.00	0.00	0.00	1.98
2229	2948	6.706270	ACTGCGAATATGGAAAACGATAATCT	59.294	34.615	0.00	0.00	0.00	2.40
2230	2949	6.888430	ACTGCGAATATGGAAAACGATAATC	58.112	36.000	0.00	0.00	0.00	1.75
2231	2950	6.861065	ACTGCGAATATGGAAAACGATAAT	57.139	33.333	0.00	0.00	0.00	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.