AutoCloner

Multiple sequence alignment - TraesCS6A01G002300

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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	TraesCS6A01G002300	chr6A	100.000	2933	0	0	1	2933	931264	934196	0.000000e+00	5417.0
1	TraesCS6A01G002300	chr6A	85.900	1234	147	16	998	2210	968800	967573	0.000000e+00	1290.0
2	TraesCS6A01G002300	chr6A	81.891	624	82	19	2163	2770	976998	976390	5.640000e-137	497.0
3	TraesCS6A01G002300	chr6A	80.064	622	78	20	2163	2778	967575	966994	1.260000e-113	420.0
4	TraesCS6A01G002300	chr6A	92.857	56	3	1	882	937	968958	968904	2.420000e-11	80.5
5	TraesCS6A01G002300	chr6D	89.996	2519	181	38	1	2466	1759598	1762098	0.000000e+00	3190.0
6	TraesCS6A01G002300	chr6D	91.674	2210	120	28	748	2933	1903646	1901477	0.000000e+00	3003.0
7	TraesCS6A01G002300	chr6D	89.668	1839	130	34	379	2202	1850606	1848813	0.000000e+00	2289.0
8	TraesCS6A01G002300	chr6D	86.960	1227	139	15	999	2210	1799978	1798758	0.000000e+00	1360.0
9	TraesCS6A01G002300	chr6D	85.875	1246	139	22	974	2207	1635715	1636935	0.000000e+00	1291.0
10	TraesCS6A01G002300	chr6D	83.198	988	116	23	1243	2210	1809421	1808464	0.000000e+00	859.0
11	TraesCS6A01G002300	chr6D	87.767	703	76	8	1	699	1911042	1910346	0.000000e+00	813.0
12	TraesCS6A01G002300	chr6D	88.144	641	46	12	2166	2778	1848804	1848166	0.000000e+00	736.0
13	TraesCS6A01G002300	chr6D	95.376	346	13	3	1	344	1851561	1851217	5.530000e-152	547.0
14	TraesCS6A01G002300	chr6D	88.571	385	31	8	78	459	1634912	1635286	3.450000e-124	455.0
15	TraesCS6A01G002300	chr6D	80.480	625	68	23	2163	2778	1636936	1637515	2.090000e-116	429.0
16	TraesCS6A01G002300	chr6D	79.239	631	68	22	2163	2778	1798760	1798178	5.930000e-102	381.0
17	TraesCS6A01G002300	chr6D	91.064	235	8	4	2557	2778	1762102	1762336	3.670000e-79	305.0
18	TraesCS6A01G002300	chr6D	77.209	430	57	21	517	937	1635314	1635711	2.290000e-51	213.0
19	TraesCS6A01G002300	chr6D	90.506	158	13	2	2777	2933	1847981	1847825	1.070000e-49	207.0
20	TraesCS6A01G002300	chr6D	88.571	70	5	2	116	183	1851180	1851112	6.740000e-12	82.4
21	TraesCS6A01G002300	chr6D	92.857	56	3	1	882	937	1800137	1800083	2.420000e-11	80.5
22	TraesCS6A01G002300	chr6B	88.282	2253	189	44	1	2207	4886311	4884088	0.000000e+00	2628.0
23	TraesCS6A01G002300	chr6B	89.505	2020	148	47	211	2207	4855731	4857709	0.000000e+00	2497.0
24	TraesCS6A01G002300	chr6B	91.379	174	15	0	2165	2338	4884085	4883912	3.780000e-59	239.0
25	TraesCS6A01G002300	chr6B	88.172	186	19	3	1	185	4855553	4855736	4.920000e-53	219.0
26	TraesCS6A01G002300	chr3D	83.769	918	119	19	1019	1931	582909598	582908706	0.000000e+00	843.0
27	TraesCS6A01G002300	chr3D	83.856	861	109	19	1019	1874	582922020	582921185	0.000000e+00	793.0

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	TraesCS6A01G002300	chr6A	931264	934196	2932	False	5417.000000	5417	100.000000	1	2933	1	chr6A.!!$F1	2932
1	TraesCS6A01G002300	chr6A	966994	968958	1964	True	596.833333	1290	86.273667	882	2778	3	chr6A.!!$R2	1896
2	TraesCS6A01G002300	chr6A	976390	976998	608	True	497.000000	497	81.891000	2163	2770	1	chr6A.!!$R1	607
3	TraesCS6A01G002300	chr6D	1901477	1903646	2169	True	3003.000000	3003	91.674000	748	2933	1	chr6D.!!$R2	2185
4	TraesCS6A01G002300	chr6D	1759598	1762336	2738	False	1747.500000	3190	90.530000	1	2778	2	chr6D.!!$F2	2777
5	TraesCS6A01G002300	chr6D	1808464	1809421	957	True	859.000000	859	83.198000	1243	2210	1	chr6D.!!$R1	967
6	TraesCS6A01G002300	chr6D	1910346	1911042	696	True	813.000000	813	87.767000	1	699	1	chr6D.!!$R3	698
7	TraesCS6A01G002300	chr6D	1847825	1851561	3736	True	772.280000	2289	90.453000	1	2933	5	chr6D.!!$R5	2932
8	TraesCS6A01G002300	chr6D	1798178	1800137	1959	True	607.166667	1360	86.352000	882	2778	3	chr6D.!!$R4	1896
9	TraesCS6A01G002300	chr6D	1634912	1637515	2603	False	597.000000	1291	83.033750	78	2778	4	chr6D.!!$F1	2700
10	TraesCS6A01G002300	chr6B	4883912	4886311	2399	True	1433.500000	2628	89.830500	1	2338	2	chr6B.!!$R1	2337
11	TraesCS6A01G002300	chr6B	4855553	4857709	2156	False	1358.000000	2497	88.838500	1	2207	2	chr6B.!!$F1	2206
12	TraesCS6A01G002300	chr3D	582908706	582909598	892	True	843.000000	843	83.769000	1019	1931	1	chr3D.!!$R1	912
13	TraesCS6A01G002300	chr3D	582921185	582922020	835	True	793.000000	793	83.856000	1019	1874	1	chr3D.!!$R2	855

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
955	1680	0.106708	CGGTCGGTCATCCATCCAAT	59.893	55.0	0.0	0.0	0.0	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2279	3115	0.180642	TTGGTGGCCGTTGTCTAACA	59.819	50.0	0.0	0.0	36.58	2.41	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
37	38	0.515127	TTATGTGGCTTGACGCAACG	59.485	50.000	0.00	0.00	46.04	4.10
76	79	1.139989	CTAGTTGACACGGTGCACAG	58.860	55.000	20.43	18.06	0.00	3.66
293	328	3.056035	AGGAGTAACGAGGACAATGGAAC	60.056	47.826	0.00	0.00	0.00	3.62
304	339	3.435671	GGACAATGGAACGGAGTAAAGTG	59.564	47.826	0.00	0.00	45.00	3.16
329	364	4.044571	AGTTGAAAAGGATGGGGAGATCAA	59.955	41.667	0.00	0.00	0.00	2.57
386	997	4.096382	GGTGCTCGTGTCCAAATAATGAAT	59.904	41.667	0.00	0.00	0.00	2.57
425	1038	1.138247	GGGTCTACGTCGCGACATT	59.862	57.895	35.71	24.78	31.88	2.71
438	1051	1.502990	CGACATTGGTGACCGTTGCA	61.503	55.000	0.00	0.00	0.00	4.08
446	1059	1.609580	GGTGACCGTTGCATGGTAAGA	60.610	52.381	10.85	0.00	37.69	2.10
493	1136	8.970020	AGTCCATATGCATAGTTTCAAAATCAA	58.030	29.630	12.79	0.00	0.00	2.57
498	1141	9.941325	ATATGCATAGTTTCAAAATCAAAACCA	57.059	25.926	12.79	0.00	36.29	3.67
595	1238	7.511028	TGGTTTCTTTGGTACCAAATTAAGGAT	59.489	33.333	34.40	0.00	43.78	3.24
618	1261	4.230502	TCAATAAAGGCTTGGGAGAGGATT	59.769	41.667	0.00	0.00	0.00	3.01
630	1273	2.305927	GGAGAGGATTTGAAGGACACCA	59.694	50.000	0.00	0.00	0.00	4.17
641	1284	1.153549	GGACACCAAGCTAGGCGAG	60.154	63.158	0.00	0.00	0.00	5.03
679	1322	6.924060	TGGTTTGTTTGGTACCAAATTAATCG	59.076	34.615	36.07	0.00	45.90	3.34
729	1413	7.119116	CACGCCATATATTTAGCAGGATACAAA	59.881	37.037	0.00	0.00	41.41	2.83
731	1415	7.475840	GCCATATATTTAGCAGGATACAAAGC	58.524	38.462	0.00	0.00	41.41	3.51
737	1421	9.964354	ATATTTAGCAGGATACAAAGCATATGA	57.036	29.630	6.97	0.00	41.41	2.15
738	1422	8.874744	ATTTAGCAGGATACAAAGCATATGAT	57.125	30.769	6.97	0.00	41.41	2.45
739	1423	7.677454	TTAGCAGGATACAAAGCATATGATG	57.323	36.000	6.97	4.54	41.41	3.07
740	1424	5.628130	AGCAGGATACAAAGCATATGATGT	58.372	37.500	6.97	10.26	41.41	3.06
741	1425	6.772605	AGCAGGATACAAAGCATATGATGTA	58.227	36.000	6.97	12.05	41.41	2.29
743	1427	7.720957	AGCAGGATACAAAGCATATGATGTAAA	59.279	33.333	6.97	0.00	41.41	2.01
744	1428	8.352201	GCAGGATACAAAGCATATGATGTAAAA	58.648	33.333	6.97	0.00	41.41	1.52
821	1518	3.011566	TGTGAAACCAAGCAAGGAAGA	57.988	42.857	1.01	0.00	34.36	2.87
880	1587	5.392380	GCACCTCATTAAACATTGACCAGAG	60.392	44.000	0.00	0.00	0.00	3.35
954	1679	1.520192	CGGTCGGTCATCCATCCAA	59.480	57.895	0.00	0.00	0.00	3.53
955	1680	0.106708	CGGTCGGTCATCCATCCAAT	59.893	55.000	0.00	0.00	0.00	3.16
956	1681	1.873903	CGGTCGGTCATCCATCCAATC	60.874	57.143	0.00	0.00	0.00	2.67
1320	2087	1.134670	GTCTACATCGAGCCTGGCTTT	60.135	52.381	24.26	8.29	39.88	3.51
1704	2476	6.920210	TCTTCGTATCATTGATGTCTGATGAC	59.080	38.462	9.46	0.00	43.20	3.06
1761	2536	1.149174	CTGTGTGGTGAGGGTGCTT	59.851	57.895	0.00	0.00	0.00	3.91
1836	2611	1.677966	AGAGGCGGTCGTGAAGCTA	60.678	57.895	0.00	0.00	0.00	3.32
1940	2716	2.490148	CCGTCGCCTAGCCAGATCA	61.490	63.158	0.00	0.00	0.00	2.92
2008	2789	1.202698	AGCCAGATCTACCGGATTTGC	60.203	52.381	9.46	0.00	35.84	3.68
2075	2858	8.066612	TGGAGCCAAATTAGGAGAAATTAAAG	57.933	34.615	0.00	0.00	0.00	1.85
2103	2888	4.799564	TGACAAAAAGTTTGTTGCTCCT	57.200	36.364	7.72	0.00	31.96	3.69
2110	2896	3.692791	AGTTTGTTGCTCCTTTCGTTC	57.307	42.857	0.00	0.00	0.00	3.95
2243	3078	0.390124	TAGACAGAACAAACGGGCGT	59.610	50.000	0.00	0.00	0.00	5.68
2247	3082	1.896660	AGAACAAACGGGCGTGCAT	60.897	52.632	0.00	0.00	0.00	3.96
2256	3091	0.802494	CGGGCGTGCATAAGTTCTTT	59.198	50.000	0.00	0.00	0.00	2.52
2303	3139	1.152860	ACAACGGCCACCAATGTCA	60.153	52.632	2.24	0.00	0.00	3.58
2311	3147	2.164219	GGCCACCAATGTCACAACATAG	59.836	50.000	0.00	0.00	45.48	2.23
2366	3203	5.944135	TGGATATTGATCTCCTTCATGCAA	58.056	37.500	0.00	0.00	32.47	4.08
2374	3212	3.273434	TCTCCTTCATGCAATTTCCTCG	58.727	45.455	0.00	0.00	0.00	4.63
2774	3664	6.620678	TGCATATGCTTTCTCTTACCAAAAC	58.379	36.000	27.13	0.00	42.66	2.43
2834	3910	6.588719	TGTAACATGAAAATTCCCTTCAGG	57.411	37.500	0.00	2.35	39.76	3.86
2848	3924	0.469705	TTCAGGTGGCATGGCAAGTT	60.470	50.000	25.11	9.52	0.00	2.66
2849	3925	0.403655	TCAGGTGGCATGGCAAGTTA	59.596	50.000	25.11	7.52	0.00	2.24
2860	3936	1.210722	TGGCAAGTTATCGGCATGGTA	59.789	47.619	0.00	0.00	32.00	3.25
2905	3981	2.025981	AGTCTGCCAATTGTCCATGCTA	60.026	45.455	4.43	0.00	0.00	3.49
2929	4005	1.818060	TCATGGCAATCTCCAAAACCG	59.182	47.619	0.00	0.00	39.96	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.060479	AGCCACATAAGGAGATACCCA	57.940	47.619	0.00	0.00	40.05	4.51
14	15	1.009829	GCGTCAAGCCACATAAGGAG	58.990	55.000	0.00	0.00	40.81	3.69
48	50	4.451096	CACCGTGTCAACTAGTAAAGCAAT	59.549	41.667	0.00	0.00	0.00	3.56
76	79	9.888878	GTTATAGGTTTTGGTTTACACTTCTTC	57.111	33.333	0.00	0.00	0.00	2.87
215	249	0.616891	GGGACCCATGTACCGTTTCT	59.383	55.000	5.33	0.00	35.18	2.52
293	328	5.526111	TCCTTTTCAACTTCACTTTACTCCG	59.474	40.000	0.00	0.00	0.00	4.63
304	339	4.034285	TCTCCCCATCCTTTTCAACTTC	57.966	45.455	0.00	0.00	0.00	3.01
329	364	1.464722	CCAACCATGGTCCCACCTT	59.535	57.895	20.07	0.00	42.18	3.50
386	997	1.305633	CTGCACTCCCCTCCTCTGA	60.306	63.158	0.00	0.00	0.00	3.27
425	1038	0.108774	TTACCATGCAACGGTCACCA	59.891	50.000	14.05	0.00	37.99	4.17
463	1105	6.191657	TGAAACTATGCATATGGACTCCAT	57.808	37.500	15.18	15.18	46.99	3.41
464	1106	5.628797	TGAAACTATGCATATGGACTCCA	57.371	39.130	6.92	0.00	38.19	3.86
465	1107	6.942532	TTTGAAACTATGCATATGGACTCC	57.057	37.500	6.92	0.00	0.00	3.85
466	1108	8.623903	TGATTTTGAAACTATGCATATGGACTC	58.376	33.333	6.92	1.31	0.00	3.36
493	1136	2.393764	CGCGCAAAGATTCTTTGGTTT	58.606	42.857	30.55	1.99	0.00	3.27
498	1141	0.313672	TTGGCGCGCAAAGATTCTTT	59.686	45.000	34.42	5.82	0.00	2.52
595	1238	3.189606	TCCTCTCCCAAGCCTTTATTGA	58.810	45.455	0.00	0.00	0.00	2.57
618	1261	1.271379	GCCTAGCTTGGTGTCCTTCAA	60.271	52.381	15.85	0.00	0.00	2.69
630	1273	3.435275	TGATGATATCCTCGCCTAGCTT	58.565	45.455	0.00	0.00	0.00	3.74
641	1284	7.330262	ACCAAACAAACCATTTGATGATATCC	58.670	34.615	8.24	0.00	43.26	2.59
700	1368	4.072131	CCTGCTAAATATATGGCGTGGTT	58.928	43.478	0.00	0.00	0.00	3.67
762	1453	9.562583	TGTAATTCGTTTTACATCCTAAAATGC	57.437	29.630	8.27	0.00	37.20	3.56
784	1475	8.696374	TGGTTTCACATCCTATTTTGTTTGTAA	58.304	29.630	0.00	0.00	0.00	2.41
796	1493	3.073798	TCCTTGCTTGGTTTCACATCCTA	59.926	43.478	0.00	0.00	0.00	2.94
880	1587	1.750193	TGGGTATTTGTAGCTGCTGC	58.250	50.000	13.43	12.15	40.05	5.25
995	1728	2.765807	CCGACCCCTCCATGCTCT	60.766	66.667	0.00	0.00	0.00	4.09
996	1729	4.554036	GCCGACCCCTCCATGCTC	62.554	72.222	0.00	0.00	0.00	4.26
1320	2087	1.072505	GTCCTGGTGGAAGGCGAAA	59.927	57.895	0.00	0.00	45.18	3.46
1506	2273	3.330405	TGGAGAAGGTGATGAACATGGAA	59.670	43.478	0.00	0.00	0.00	3.53
1704	2476	2.761767	TCCATCCATGACAAATTGCCAG	59.238	45.455	0.00	0.00	0.00	4.85
1761	2536	0.738975	CGCCTGTCGTCTTCTCCATA	59.261	55.000	0.00	0.00	0.00	2.74
1940	2716	5.301835	AGACGATGATTGATTCCTGGATT	57.698	39.130	0.00	0.00	0.00	3.01
2075	2858	5.668621	GCAACAAACTTTTTGTCAAGCAGTC	60.669	40.000	4.82	0.00	0.00	3.51
2103	2888	7.903995	ATGGTTTATTTAGTACCGAACGAAA	57.096	32.000	0.00	0.00	37.15	3.46
2110	2896	8.145767	TGTCCTCATATGGTTTATTTAGTACCG	58.854	37.037	2.13	0.00	34.62	4.02
2274	3110	2.292292	GTGGCCGTTGTCTAACATTTGT	59.708	45.455	0.00	0.00	36.58	2.83
2279	3115	0.180642	TTGGTGGCCGTTGTCTAACA	59.819	50.000	0.00	0.00	36.58	2.41
2366	3203	1.064685	GGGACCATGGTTCGAGGAAAT	60.065	52.381	20.85	0.00	0.00	2.17
2374	3212	0.748005	CGGTGATGGGACCATGGTTC	60.748	60.000	20.85	18.19	36.70	3.62
2511	3370	1.753848	CCGGCATGGGAGCATGAAA	60.754	57.895	0.00	0.00	34.66	2.69
2689	3551	2.892852	TGAGGCTTGACCCAATGAAAAG	59.107	45.455	0.00	0.00	40.58	2.27
2774	3664	1.750778	AGAATTGCCATGCCCTAAACG	59.249	47.619	0.00	0.00	0.00	3.60
2834	3910	0.381801	CCGATAACTTGCCATGCCAC	59.618	55.000	0.00	0.00	0.00	5.01
2848	3924	4.950475	TGGTGAAAATTTACCATGCCGATA	59.050	37.500	8.48	0.00	41.80	2.92
2849	3925	3.766591	TGGTGAAAATTTACCATGCCGAT	59.233	39.130	8.48	0.00	41.80	4.18
2905	3981	4.322953	GGTTTTGGAGATTGCCATGATTGT	60.323	41.667	0.00	0.00	37.86	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.