AutoCloner

Multiple sequence alignment - TraesCS2D01G399000

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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	TraesCS2D01G399000	chr2D	100.000	3001	0	0	1	3001	512044264	512041264	0.000000e+00	5542.0
1	TraesCS2D01G399000	chr2D	87.771	507	50	9	64	560	27499105	27498601	1.550000e-162	582.0
2	TraesCS2D01G399000	chr2D	96.264	348	13	0	2639	2986	533884311	533883964	3.360000e-159	571.0
3	TraesCS2D01G399000	chr2D	95.402	348	16	0	2639	2986	399894553	399894900	3.380000e-154	555.0
4	TraesCS2D01G399000	chr2D	97.635	296	7	0	2163	2458	565529622	565529327	2.670000e-140	508.0
5	TraesCS2D01G399000	chr2A	93.938	1600	49	22	568	2164	655220054	655218500	0.000000e+00	2374.0
6	TraesCS2D01G399000	chr2A	86.252	531	58	11	47	565	11826324	11825797	2.020000e-156	562.0
7	TraesCS2D01G399000	chr2A	92.896	183	6	2	2456	2638	655218502	655218327	2.970000e-65	259.0
8	TraesCS2D01G399000	chr2A	92.683	41	0	2	1974	2014	655218633	655218596	4.180000e-04	56.5
9	TraesCS2D01G399000	chr2B	93.523	1621	53	20	568	2164	601213592	601212000	0.000000e+00	2364.0
10	TraesCS2D01G399000	chr2B	87.698	504	52	8	66	561	556184711	556185212	2.010000e-161	579.0
11	TraesCS2D01G399000	chr2B	87.230	509	56	7	65	565	583385348	583384841	3.360000e-159	571.0
12	TraesCS2D01G399000	chr2B	88.660	194	13	6	2456	2648	601212002	601211817	8.370000e-56	228.0
13	TraesCS2D01G399000	chrUn	88.095	504	51	7	67	562	340151574	340152076	9.270000e-165	590.0
14	TraesCS2D01G399000	chrUn	87.500	504	54	7	70	565	168711223	168710721	9.330000e-160	573.0
15	TraesCS2D01G399000	chrUn	87.500	504	54	7	70	565	168713217	168712715	9.330000e-160	573.0
16	TraesCS2D01G399000	chr5B	87.723	505	52	8	66	562	595340534	595341036	5.580000e-162	580.0
17	TraesCS2D01G399000	chr5B	87.033	509	62	4	57	562	17563293	17562786	3.360000e-159	571.0
18	TraesCS2D01G399000	chr5B	83.598	189	26	5	1032	1216	416851121	416850934	3.980000e-39	172.0
19	TraesCS2D01G399000	chr5B	81.313	198	31	6	1025	1219	417438511	417438705	4.010000e-34	156.0
20	TraesCS2D01G399000	chr3D	96.264	348	13	0	2639	2986	456103771	456103424	3.360000e-159	571.0
21	TraesCS2D01G399000	chr3D	95.402	348	16	0	2639	2986	47242339	47242686	3.380000e-154	555.0
22	TraesCS2D01G399000	chr3D	95.115	348	17	0	2639	2986	313910166	313910513	1.570000e-152	549.0
23	TraesCS2D01G399000	chr3D	89.041	73	8	0	1150	1222	388534334	388534262	1.150000e-14	91.6
24	TraesCS2D01G399000	chr7D	95.977	348	14	0	2639	2986	397988651	397988998	1.560000e-157	566.0
25	TraesCS2D01G399000	chr4D	95.690	348	15	0	2639	2986	14974427	14974080	7.260000e-156	560.0
26	TraesCS2D01G399000	chr4D	74.731	186	41	6	1032	1214	506340126	506339944	8.920000e-11	78.7
27	TraesCS2D01G399000	chr6D	95.402	348	16	0	2639	2986	408657800	408657453	3.380000e-154	555.0
28	TraesCS2D01G399000	chr5D	95.115	348	17	0	2639	2986	480474775	480475122	1.570000e-152	549.0
29	TraesCS2D01G399000	chr5D	83.333	192	27	5	1029	1216	352219256	352219446	3.980000e-39	172.0
30	TraesCS2D01G399000	chr5D	80.808	198	32	6	1025	1219	353478115	353478309	1.860000e-32	150.0
31	TraesCS2D01G399000	chr3B	100.000	297	0	0	2162	2458	581662194	581661898	1.570000e-152	549.0
32	TraesCS2D01G399000	chr6A	98.990	297	3	0	2162	2458	223809933	223809637	1.580000e-147	532.0
33	TraesCS2D01G399000	chr6A	97.306	297	8	0	2163	2459	579017640	579017344	3.450000e-139	505.0
34	TraesCS2D01G399000	chr7A	97.333	300	8	0	2159	2458	410820003	410820302	7.420000e-141	510.0
35	TraesCS2D01G399000	chr3A	97.643	297	6	1	2163	2459	17689761	17690056	2.670000e-140	508.0
36	TraesCS2D01G399000	chr5A	96.711	304	9	1	2160	2462	687280372	687280675	3.450000e-139	505.0
37	TraesCS2D01G399000	chr5A	82.540	189	28	5	1032	1216	453877101	453876914	8.610000e-36	161.0
38	TraesCS2D01G399000	chr5A	79.798	198	34	6	1025	1219	454397162	454397356	4.030000e-29	139.0
39	TraesCS2D01G399000	chr4A	97.000	300	9	0	2159	2458	30695901	30696200	3.450000e-139	505.0
40	TraesCS2D01G399000	chr4A	93.313	329	18	4	2135	2463	569862294	569861970	1.620000e-132	483.0

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	TraesCS2D01G399000	chr2D	512041264	512044264	3000	True	5542.0	5542	100.000000	1	3001	1	chr2D.!!$R2	3000
1	TraesCS2D01G399000	chr2D	27498601	27499105	504	True	582.0	582	87.771000	64	560	1	chr2D.!!$R1	496
2	TraesCS2D01G399000	chr2A	655218327	655220054	1727	True	896.5	2374	93.172333	568	2638	3	chr2A.!!$R2	2070
3	TraesCS2D01G399000	chr2A	11825797	11826324	527	True	562.0	562	86.252000	47	565	1	chr2A.!!$R1	518
4	TraesCS2D01G399000	chr2B	601211817	601213592	1775	True	1296.0	2364	91.091500	568	2648	2	chr2B.!!$R2	2080
5	TraesCS2D01G399000	chr2B	556184711	556185212	501	False	579.0	579	87.698000	66	561	1	chr2B.!!$F1	495
6	TraesCS2D01G399000	chr2B	583384841	583385348	507	True	571.0	571	87.230000	65	565	1	chr2B.!!$R1	500
7	TraesCS2D01G399000	chrUn	340151574	340152076	502	False	590.0	590	88.095000	67	562	1	chrUn.!!$F1	495
8	TraesCS2D01G399000	chrUn	168710721	168713217	2496	True	573.0	573	87.500000	70	565	2	chrUn.!!$R1	495
9	TraesCS2D01G399000	chr5B	595340534	595341036	502	False	580.0	580	87.723000	66	562	1	chr5B.!!$F2	496
10	TraesCS2D01G399000	chr5B	17562786	17563293	507	True	571.0	571	87.033000	57	562	1	chr5B.!!$R1	505

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
541	2549	0.032952	TAGCACCAAACGACGAGCTT	59.967	50.0	0.0	0.0	33.83	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2321	4354	0.035176	ATTGTTGTTGGTGCCATGGC	59.965	50.0	30.54	30.54	42.35	4.4	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
86	88	7.562454	TGTTTATCGAAAAAGTCTTTCACCT	57.438	32.000	0.00	0.00	0.00	4.00
89	91	3.788937	TCGAAAAAGTCTTTCACCTCGT	58.211	40.909	0.00	0.00	0.00	4.18
124	2120	3.119531	GCCATGATCAACAACATTTCGGA	60.120	43.478	0.00	0.00	0.00	4.55
131	2127	3.942115	TCAACAACATTTCGGAACAGACA	59.058	39.130	0.00	0.00	0.00	3.41
174	2180	2.434359	GCGGGATACATAGGCGCC	60.434	66.667	21.89	21.89	36.44	6.53
366	2374	2.047844	CAGGAGCCACACGACAGG	60.048	66.667	0.00	0.00	0.00	4.00
383	2391	1.742880	GGCAATGAGAGCTGCGACA	60.743	57.895	0.00	0.00	39.55	4.35
458	2466	2.732016	GTTTTCACCCCGGCCAAC	59.268	61.111	2.24	0.00	0.00	3.77
508	2516	4.697756	CCACGCCACCCACACGAT	62.698	66.667	0.00	0.00	0.00	3.73
522	2530	4.175337	CGATCATGGCCACCGGGT	62.175	66.667	8.16	0.00	36.17	5.28
531	2539	2.432563	CCACCGGGTAGCACCAAA	59.567	61.111	6.32	0.00	41.02	3.28
537	2545	1.005867	GGGTAGCACCAAACGACGA	60.006	57.895	0.00	0.00	41.02	4.20
541	2549	0.032952	TAGCACCAAACGACGAGCTT	59.967	50.000	0.00	0.00	33.83	3.74
562	2570	2.486504	CCATGAGCAACGCGCAAT	59.513	55.556	5.73	0.00	42.18	3.56
565	2573	0.860203	CATGAGCAACGCGCAATCAG	60.860	55.000	5.73	0.00	42.18	2.90
566	2574	1.300971	ATGAGCAACGCGCAATCAGT	61.301	50.000	5.73	0.00	42.18	3.41
572	2580	0.162933	AACGCGCAATCAGTTACACG	59.837	50.000	5.73	0.00	0.00	4.49
639	2648	7.907214	AAGGAGAGTGTGTCATATAAACAAC	57.093	36.000	0.00	0.00	0.00	3.32
640	2649	6.407202	AGGAGAGTGTGTCATATAAACAACC	58.593	40.000	0.00	0.00	0.00	3.77
677	2686	6.385649	TCTTTGTAGGGTTGCTTAAAACTG	57.614	37.500	0.00	0.00	0.00	3.16
693	2708	8.800031	GCTTAAAACTGAAACAACATCGTAAAA	58.200	29.630	0.00	0.00	0.00	1.52
749	2767	4.351938	CGTCCTTCACGTGGCCGA	62.352	66.667	17.00	5.49	44.07	5.54
750	2768	2.737376	GTCCTTCACGTGGCCGAC	60.737	66.667	17.00	13.94	37.88	4.79
751	2769	2.915659	TCCTTCACGTGGCCGACT	60.916	61.111	17.00	0.00	37.88	4.18
752	2770	2.030562	CCTTCACGTGGCCGACTT	59.969	61.111	17.00	0.00	37.88	3.01

Showing 1 to 25 of 537 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	9.268268	AGACTTTTTCGATAAACATGTAACTGA	57.732	29.630	0.00	0.00	0.00	3.41
54	55	9.878599	AAGACTTTTTCGATAAACATGTAACTG	57.121	29.630	0.00	0.00	0.00	3.16
68	70	3.788937	ACGAGGTGAAAGACTTTTTCGA	58.211	40.909	21.27	0.00	0.00	3.71
83	85	9.959721	ATCATGGCTTTATATATAAAACGAGGT	57.040	29.630	16.69	5.63	32.39	3.85
104	106	5.459768	TGTTCCGAAATGTTGTTGATCATG	58.540	37.500	0.00	0.00	0.00	3.07
124	2120	0.908910	TGTGGTGGAGTGTGTCTGTT	59.091	50.000	0.00	0.00	0.00	3.16
131	2127	0.326595	TGTGTGTTGTGGTGGAGTGT	59.673	50.000	0.00	0.00	0.00	3.55
174	2180	1.130613	GTGTAGTTTGCTGCGCTCG	59.869	57.895	9.73	0.00	35.43	5.03
188	2195	5.227908	GTTGCTCTTGTAGTGCTAAGTGTA	58.772	41.667	0.00	0.00	35.86	2.90
191	2198	3.665190	GGTTGCTCTTGTAGTGCTAAGT	58.335	45.455	0.00	0.00	35.86	2.24
193	2200	2.611971	CCGGTTGCTCTTGTAGTGCTAA	60.612	50.000	0.00	0.00	35.86	3.09
366	2374	0.179205	GTTGTCGCAGCTCTCATTGC	60.179	55.000	0.00	0.00	36.97	3.56
383	2391	1.605753	GTTCCCTTCTTGAAGGCGTT	58.394	50.000	20.71	0.00	38.63	4.84
424	2432	4.162320	TGAAAACCTGCTCTATCTTCGGAT	59.838	41.667	0.00	0.00	38.39	4.18
458	2466	2.444624	CGTTCGATGGCGGTGAGTG	61.445	63.158	0.00	0.00	38.28	3.51
489	2497	4.302509	CGTGTGGGTGGCGTGGTA	62.303	66.667	0.00	0.00	0.00	3.25
498	2506	2.272146	GGCCATGATCGTGTGGGT	59.728	61.111	13.81	0.00	36.00	4.51
508	2516	3.792736	GCTACCCGGTGGCCATGA	61.793	66.667	14.86	0.00	33.94	3.07
522	2530	0.032952	AAGCTCGTCGTTTGGTGCTA	59.967	50.000	0.00	0.00	0.00	3.49
531	2539	2.034879	CATGGGCAAAGCTCGTCGT	61.035	57.895	0.00	0.00	0.00	4.34
554	2562	1.779061	CGTGTAACTGATTGCGCGT	59.221	52.632	8.43	0.00	45.69	6.01
562	2570	5.517411	CAGACACACTAAAACGTGTAACTGA	59.483	40.000	16.81	0.00	46.06	3.41
565	2573	5.707411	ACAGACACACTAAAACGTGTAAC	57.293	39.130	0.00	0.00	46.06	2.50
566	2574	5.868258	TGAACAGACACACTAAAACGTGTAA	59.132	36.000	0.00	0.00	46.06	2.41
572	2580	4.565564	ACGAGTGAACAGACACACTAAAAC	59.434	41.667	0.00	0.00	45.54	2.43

Showing 1 to 25 of 506 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.