AutoCloner

Multiple sequence alignment - TraesCS2A01G331700

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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	TraesCS2A01G331700	chr2A	100.000	5174	0	0	1	5174	564611019	564616192	0.000000e+00	9555.0
1	TraesCS2A01G331700	chr2A	80.783	281	41	6	4901	5169	719215605	719215326	1.890000e-49	207.0
2	TraesCS2A01G331700	chr2A	84.545	110	15	2	2284	2392	581567305	581567413	1.970000e-19	108.0
3	TraesCS2A01G331700	chr2A	86.667	90	12	0	2301	2390	676448500	676448411	3.300000e-17	100.0
4	TraesCS2A01G331700	chr2D	92.492	1585	74	19	3214	4763	423861703	423860129	0.000000e+00	2226.0
5	TraesCS2A01G331700	chr2D	96.170	966	24	5	689	1641	423865344	423864379	0.000000e+00	1567.0
6	TraesCS2A01G331700	chr2D	88.148	675	70	5	2420	3085	645316735	645316062	0.000000e+00	795.0
7	TraesCS2A01G331700	chr2D	85.443	632	64	16	2	615	423865979	423865358	2.630000e-177	632.0
8	TraesCS2A01G331700	chr2D	84.420	629	42	27	1638	2226	423864142	423863530	7.520000e-158	568.0
9	TraesCS2A01G331700	chr2D	83.033	389	45	16	2041	2414	423863634	423863252	2.990000e-87	333.0
10	TraesCS2A01G331700	chr2D	88.652	141	8	2	3089	3223	423863244	423863106	1.150000e-36	165.0
11	TraesCS2A01G331700	chr2D	88.060	134	16	0	2281	2414	542064180	542064313	5.360000e-35	159.0
12	TraesCS2A01G331700	chr2D	85.556	90	3	1	4813	4902	423860048	423859969	9.230000e-13	86.1
13	TraesCS2A01G331700	chr2B	95.465	1257	48	7	3214	4464	497801520	497800267	0.000000e+00	1997.0
14	TraesCS2A01G331700	chr2B	94.547	917	26	4	770	1676	497803855	497802953	0.000000e+00	1395.0
15	TraesCS2A01G331700	chr2B	88.850	574	51	6	3228	3798	632387201	632386638	0.000000e+00	693.0
16	TraesCS2A01G331700	chr2B	87.544	570	58	6	3228	3795	98397978	98398536	0.000000e+00	647.0
17	TraesCS2A01G331700	chr2B	81.650	703	85	25	1	692	497805228	497804559	1.270000e-150	544.0
18	TraesCS2A01G331700	chr2B	94.488	127	5	1	1673	1799	497801674	497801550	1.470000e-45	195.0
19	TraesCS2A01G331700	chr2B	80.952	126	24	0	2265	2390	800482891	800483016	3.300000e-17	100.0
20	TraesCS2A01G331700	chr2B	100.000	42	0	0	4815	4856	497800268	497800227	1.540000e-10	78.7
21	TraesCS2A01G331700	chr5D	89.614	674	61	5	2419	3085	62529900	62530571	0.000000e+00	848.0
22	TraesCS2A01G331700	chr5D	87.794	680	72	7	2413	3085	556094176	556093501	0.000000e+00	785.0
23	TraesCS2A01G331700	chr5D	79.381	291	41	13	4895	5170	448662909	448663195	2.460000e-43	187.0
24	TraesCS2A01G331700	chr4A	89.466	674	59	8	2419	3085	717817298	717816630	0.000000e+00	841.0
25	TraesCS2A01G331700	chr4A	91.954	87	7	0	1845	1931	90430857	90430943	7.040000e-24	122.0
26	TraesCS2A01G331700	chr4A	80.000	145	20	7	556	693	552710184	552710042	1.190000e-16	99.0
27	TraesCS2A01G331700	chr4A	83.951	81	12	1	1845	1924	647841707	647841627	5.560000e-10	76.8
28	TraesCS2A01G331700	chr4D	88.690	672	69	4	2420	3085	354114869	354115539	0.000000e+00	813.0
29	TraesCS2A01G331700	chr4D	92.771	83	6	0	3112	3194	39358775	39358693	2.530000e-23	121.0
30	TraesCS2A01G331700	chr4D	80.952	105	16	4	3089	3191	431556767	431556665	4.290000e-11	80.5
31	TraesCS2A01G331700	chr6D	88.444	675	65	9	2419	3085	5070215	5069546	0.000000e+00	802.0
32	TraesCS2A01G331700	chr6D	89.530	468	43	5	3227	3693	178681509	178681971	5.770000e-164	588.0
33	TraesCS2A01G331700	chr6D	91.597	119	10	0	3730	3848	178681966	178682084	1.150000e-36	165.0
34	TraesCS2A01G331700	chr5A	88.571	665	69	3	2416	3073	288257694	288258358	0.000000e+00	800.0
35	TraesCS2A01G331700	chr3D	88.473	668	64	9	2417	3076	156891112	156890450	0.000000e+00	795.0
36	TraesCS2A01G331700	chr3D	91.667	48	3	1	1884	1930	290858782	290858829	1.200000e-06	65.8
37	TraesCS2A01G331700	chr3B	88.201	678	65	11	2415	3085	775734316	775734985	0.000000e+00	795.0
38	TraesCS2A01G331700	chr3B	82.595	316	39	12	4466	4769	809182268	809182579	1.100000e-66	265.0
39	TraesCS2A01G331700	chr3B	77.273	176	27	8	530	692	540686427	540686252	1.980000e-14	91.6
40	TraesCS2A01G331700	chr3B	79.259	135	17	8	567	692	734164130	734164262	3.320000e-12	84.2
41	TraesCS2A01G331700	chr3B	91.667	48	3	1	1884	1930	383707095	383707142	1.200000e-06	65.8
42	TraesCS2A01G331700	chr3B	91.111	45	4	0	1845	1889	5070822	5070866	1.560000e-05	62.1
43	TraesCS2A01G331700	chr5B	87.895	570	53	8	3228	3795	491817466	491818021	0.000000e+00	656.0
44	TraesCS2A01G331700	chr5B	82.540	315	44	9	4466	4772	36079473	36079162	3.070000e-67	267.0
45	TraesCS2A01G331700	chr1D	87.566	571	55	9	3228	3795	211946003	211945446	0.000000e+00	647.0
46	TraesCS2A01G331700	chr1D	87.544	570	57	7	3228	3795	291784534	291785091	0.000000e+00	647.0
47	TraesCS2A01G331700	chr1D	84.874	119	16	2	2276	2394	452253796	452253680	9.100000e-23	119.0
48	TraesCS2A01G331700	chr6B	88.889	468	46	5	3227	3693	169156353	169156815	5.810000e-159	571.0
49	TraesCS2A01G331700	chr6B	83.333	312	43	8	4466	4772	701069525	701069218	3.950000e-71	279.0
50	TraesCS2A01G331700	chr6B	83.013	312	44	8	4466	4772	701071330	701071023	1.840000e-69	274.0
51	TraesCS2A01G331700	chr6B	82.748	313	38	12	4466	4769	528908220	528908525	1.100000e-66	265.0
52	TraesCS2A01G331700	chr3A	86.408	309	24	11	4472	4776	612766453	612766747	6.460000e-84	322.0
53	TraesCS2A01G331700	chr3A	84.177	158	24	1	2257	2414	625566154	625565998	8.970000e-33	152.0
54	TraesCS2A01G331700	chr3A	75.745	235	48	7	462	693	66178093	66177865	5.480000e-20	110.0
55	TraesCS2A01G331700	chr3A	88.889	54	6	0	1845	1898	7130576	7130523	3.340000e-07	67.6
56	TraesCS2A01G331700	chr3A	89.583	48	4	1	1884	1930	383694462	383694509	5.600000e-05	60.2
57	TraesCS2A01G331700	chr7B	81.586	353	49	12	4463	4803	481349017	481348669	1.420000e-70	278.0
58	TraesCS2A01G331700	chr7B	91.045	134	9	2	2281	2414	399171572	399171702	1.480000e-40	178.0
59	TraesCS2A01G331700	chr7B	80.952	147	15	9	554	693	434828370	434828510	2.550000e-18	104.0
60	TraesCS2A01G331700	chr4B	83.067	313	41	11	4465	4769	633150028	633150336	1.840000e-69	274.0
61	TraesCS2A01G331700	chr4B	93.827	81	5	0	3114	3194	57794322	57794402	7.040000e-24	122.0
62	TraesCS2A01G331700	chr4B	77.665	197	34	10	474	663	2466818	2467011	1.520000e-20	111.0
63	TraesCS2A01G331700	chr4B	82.308	130	20	3	2264	2392	567002512	567002639	5.480000e-20	110.0
64	TraesCS2A01G331700	chr4B	83.784	111	14	4	3086	3194	427262525	427262633	9.170000e-18	102.0
65	TraesCS2A01G331700	chr1B	81.272	283	38	8	4901	5170	106767543	106767263	1.130000e-51	215.0
66	TraesCS2A01G331700	chr1B	81.481	243	33	4	1846	2085	566280878	566280645	6.840000e-44	189.0
67	TraesCS2A01G331700	chr1B	87.273	55	6	1	1845	1898	14186155	14186101	1.560000e-05	62.1
68	TraesCS2A01G331700	chr1B	84.746	59	8	1	1845	1902	573066742	573066684	2.010000e-04	58.4
69	TraesCS2A01G331700	chrUn	87.963	108	13	0	3086	3193	69778908	69779015	1.510000e-25	128.0
70	TraesCS2A01G331700	chrUn	77.358	212	25	13	503	693	112606812	112606603	2.550000e-18	104.0
71	TraesCS2A01G331700	chr7D	80.220	182	27	7	503	677	418919352	418919531	1.510000e-25	128.0
72	TraesCS2A01G331700	chr7A	91.667	48	4	0	1845	1892	589243136	589243089	3.340000e-07	67.6

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	TraesCS2A01G331700	chr2A	564611019	564616192	5173	False	9555.000000	9555	100.000000	1	5174	1	chr2A.!!$F1	5173
1	TraesCS2A01G331700	chr2D	423859969	423865979	6010	True	796.728571	2226	87.966571	2	4902	7	chr2D.!!$R2	4900
2	TraesCS2A01G331700	chr2D	645316062	645316735	673	True	795.000000	795	88.148000	2420	3085	1	chr2D.!!$R1	665
3	TraesCS2A01G331700	chr2B	497800227	497805228	5001	True	841.940000	1997	93.230000	1	4856	5	chr2B.!!$R2	4855
4	TraesCS2A01G331700	chr2B	632386638	632387201	563	True	693.000000	693	88.850000	3228	3798	1	chr2B.!!$R1	570
5	TraesCS2A01G331700	chr2B	98397978	98398536	558	False	647.000000	647	87.544000	3228	3795	1	chr2B.!!$F1	567
6	TraesCS2A01G331700	chr5D	62529900	62530571	671	False	848.000000	848	89.614000	2419	3085	1	chr5D.!!$F1	666
7	TraesCS2A01G331700	chr5D	556093501	556094176	675	True	785.000000	785	87.794000	2413	3085	1	chr5D.!!$R1	672
8	TraesCS2A01G331700	chr4A	717816630	717817298	668	True	841.000000	841	89.466000	2419	3085	1	chr4A.!!$R3	666
9	TraesCS2A01G331700	chr4D	354114869	354115539	670	False	813.000000	813	88.690000	2420	3085	1	chr4D.!!$F1	665
10	TraesCS2A01G331700	chr6D	5069546	5070215	669	True	802.000000	802	88.444000	2419	3085	1	chr6D.!!$R1	666
11	TraesCS2A01G331700	chr6D	178681509	178682084	575	False	376.500000	588	90.563500	3227	3848	2	chr6D.!!$F1	621
12	TraesCS2A01G331700	chr5A	288257694	288258358	664	False	800.000000	800	88.571000	2416	3073	1	chr5A.!!$F1	657
13	TraesCS2A01G331700	chr3D	156890450	156891112	662	True	795.000000	795	88.473000	2417	3076	1	chr3D.!!$R1	659
14	TraesCS2A01G331700	chr3B	775734316	775734985	669	False	795.000000	795	88.201000	2415	3085	1	chr3B.!!$F4	670
15	TraesCS2A01G331700	chr5B	491817466	491818021	555	False	656.000000	656	87.895000	3228	3795	1	chr5B.!!$F1	567
16	TraesCS2A01G331700	chr1D	211945446	211946003	557	True	647.000000	647	87.566000	3228	3795	1	chr1D.!!$R1	567
17	TraesCS2A01G331700	chr1D	291784534	291785091	557	False	647.000000	647	87.544000	3228	3795	1	chr1D.!!$F1	567
18	TraesCS2A01G331700	chr6B	701069218	701071330	2112	True	276.500000	279	83.173000	4466	4772	2	chr6B.!!$R1	306

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
318	332	0.318699	TACTCGCATATGTCGGCTGC	60.319	55.0	16.01	0.00	0.00	5.25	F
492	510	0.447801	CGAGTTCAAATGCTTCCCGG	59.552	55.0	0.00	0.00	0.00	5.73	F
2122	4337	1.045911	GGGGAGGAGTAGCTGACAGG	61.046	65.0	4.26	0.00	0.00	4.00	F
2133	4348	1.297456	GCTGACAGGAGCAGAAGCAC	61.297	60.0	4.26	0.00	45.49	4.40	F
3795	7546	0.762842	TGATTCCCCGGACCGATGAT	60.763	55.0	17.49	3.52	0.00	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2104	4319	0.033011	TCCTGTCAGCTACTCCTCCC	60.033	60.0	0.00	0.0	0.00	4.30	R
2397	4699	0.182775	AAAATCCTCCGGCGCCTATT	59.817	50.0	26.68	12.8	0.00	1.73	R
3170	5495	0.179054	GGCCAACTCTAACCGATCCC	60.179	60.0	0.00	0.0	0.00	3.85	R
4011	7762	0.409484	AGCCAGTAAACCCAGCCATT	59.591	50.0	0.00	0.0	0.00	3.16	R
4983	10604	0.034670	AAGCACCTGCCTTGAGGATC	60.035	55.0	0.06	0.0	43.38	3.36	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
40	41	5.416083	GGTAAGTGGACAAATAATTTGGGC	58.584	41.667	0.00	0.00	44.81	5.36
51	52	5.675684	AATAATTTGGGCCAGTCGATTTT	57.324	34.783	6.23	0.00	0.00	1.82
102	103	5.437060	GGTCATATGGCTTTCTTCAACCTA	58.563	41.667	7.36	0.00	0.00	3.08
121	122	4.589374	ACCTAGTATTCATCTTCTTCCCCG	59.411	45.833	0.00	0.00	0.00	5.73
132	134	2.204013	TTCCCCGACCACCCATGA	60.204	61.111	0.00	0.00	0.00	3.07
146	148	1.467678	CCATGAACCACCGGCCAAAA	61.468	55.000	0.00	0.00	0.00	2.44
222	227	1.531748	CACCCTTACCGCCATCCAT	59.468	57.895	0.00	0.00	0.00	3.41
262	276	1.760613	CCCGACCATGCCTCTAAACTA	59.239	52.381	0.00	0.00	0.00	2.24
306	320	5.856126	AATCGTCAAATTTCTTACTCGCA	57.144	34.783	0.00	0.00	0.00	5.10
314	328	5.907197	AATTTCTTACTCGCATATGTCGG	57.093	39.130	16.01	10.89	0.00	4.79
318	332	0.318699	TACTCGCATATGTCGGCTGC	60.319	55.000	16.01	0.00	0.00	5.25
319	333	1.300465	CTCGCATATGTCGGCTGCT	60.300	57.895	16.01	0.00	33.75	4.24
390	408	1.202964	TCGTCACCTACTTCTCCACCA	60.203	52.381	0.00	0.00	0.00	4.17
402	420	6.844097	ACTTCTCCACCAAAACAACTAAAA	57.156	33.333	0.00	0.00	0.00	1.52
455	473	2.573941	AACCGACACCTAATACTCGC	57.426	50.000	0.00	0.00	0.00	5.03
477	495	1.202200	GCGAAGTATGTGCTCTCGAGT	60.202	52.381	13.13	0.00	0.00	4.18
487	505	2.481952	GTGCTCTCGAGTTCAAATGCTT	59.518	45.455	13.13	0.00	0.00	3.91
492	510	0.447801	CGAGTTCAAATGCTTCCCGG	59.552	55.000	0.00	0.00	0.00	5.73
506	524	4.282195	TGCTTCCCGGTGAACAATAAAATT	59.718	37.500	0.00	0.00	0.00	1.82
575	594	8.772705	TGTTCTTGCAAAAATTATCATGAAACC	58.227	29.630	0.00	0.00	0.00	3.27
590	609	4.974368	TGAAACCACATTCGTGAAAGTT	57.026	36.364	0.00	0.00	46.80	2.66
592	611	2.774439	ACCACATTCGTGAAAGTTGC	57.226	45.000	0.00	0.00	46.80	4.17
639	658	7.798596	TGCTATTTTTGAAAGCATTTTGGAA	57.201	28.000	0.00	0.00	39.27	3.53
640	659	8.393671	TGCTATTTTTGAAAGCATTTTGGAAT	57.606	26.923	0.00	0.00	39.27	3.01
720	821	2.208431	CTGTTCATCCCGAGCTCATTC	58.792	52.381	15.40	0.00	0.00	2.67

Showing 1 to 25 of 272 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	2.030805	GTCTATTTTGCATCGGATGGCC	60.031	50.000	18.96	0.00	0.00	5.36
61	62	3.131396	GACCGTCTATTTTGCATCGGAT	58.869	45.455	8.35	0.00	40.90	4.18
64	65	5.389830	CCATATGACCGTCTATTTTGCATCG	60.390	44.000	3.65	0.00	0.00	3.84
74	75	4.404394	TGAAGAAAGCCATATGACCGTCTA	59.596	41.667	3.65	0.00	0.00	2.59
102	103	3.388350	GGTCGGGGAAGAAGATGAATACT	59.612	47.826	0.00	0.00	0.00	2.12
121	122	1.674322	CGGTGGTTCATGGGTGGTC	60.674	63.158	0.00	0.00	0.00	4.02
132	134	0.684805	TGACTTTTTGGCCGGTGGTT	60.685	50.000	1.90	0.00	0.00	3.67
146	148	0.106149	GTGGACGAGGTGGTTGACTT	59.894	55.000	0.00	0.00	0.00	3.01
205	209	1.837090	GATGGATGGCGGTAAGGGT	59.163	57.895	0.00	0.00	0.00	4.34
244	249	2.474816	GCTAGTTTAGAGGCATGGTCG	58.525	52.381	0.00	0.00	0.00	4.79
326	340	3.423154	GGCCAAGAACGAGCCACG	61.423	66.667	0.00	0.00	46.34	4.94
367	381	0.179169	GGAGAAGTAGGTGACGACGC	60.179	60.000	0.00	0.00	41.32	5.19
375	389	4.079958	AGTTGTTTTGGTGGAGAAGTAGGT	60.080	41.667	0.00	0.00	0.00	3.08
402	420	5.691754	GTCACTCGCCTGAATTTTCAATTTT	59.308	36.000	0.00	0.00	36.64	1.82
455	473	1.202973	CGAGAGCACATACTTCGCGG	61.203	60.000	6.13	0.00	0.00	6.46
477	495	1.611491	GTTCACCGGGAAGCATTTGAA	59.389	47.619	6.32	0.33	35.82	2.69
513	531	9.778741	TGTCAAGTTTGATACTAAAGAACAGAT	57.221	29.630	0.00	0.00	39.73	2.90
514	532	9.607988	TTGTCAAGTTTGATACTAAAGAACAGA	57.392	29.630	0.00	0.00	39.73	3.41
605	624	7.498570	TGCTTTCAAAAATAGCATTTTTGGAGT	59.501	29.630	27.67	7.76	44.86	3.85
692	711	5.741011	AGCTCGGGATGAACAGTAAAATTA	58.259	37.500	0.00	0.00	0.00	1.40
720	821	2.290122	ATCTTCTGCTCCTCCGCACG	62.290	60.000	0.00	0.00	35.74	5.34
725	826	4.116238	CGAAAGTTATCTTCTGCTCCTCC	58.884	47.826	0.00	0.00	32.90	4.30
740	841	4.287766	AGGAGAGTATTTGGCGAAAGTT	57.712	40.909	0.00	0.00	0.00	2.66
797	1442	2.490903	CCAAATGGCAGTCAAGAGAAGG	59.509	50.000	0.00	0.00	0.00	3.46
932	1578	1.738099	CGGAGTGGTTCGAAGCAGG	60.738	63.158	28.94	15.08	37.04	4.85

Showing 1 to 25 of 295 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.