AutoCloner

Multiple sequence alignment - TraesCS3A01G087900

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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	TraesCS3A01G087900	chr3A	100.000	3534	0	0	1	3534	56733591	56737124	0.000000e+00	6527.0
1	TraesCS3A01G087900	chr3A	91.445	1239	67	14	1161	2376	56756835	56758057	0.000000e+00	1664.0
2	TraesCS3A01G087900	chr3A	84.548	343	28	8	1	318	641015221	641014879	2.050000e-82	316.0
3	TraesCS3A01G087900	chr3A	83.673	343	31	14	1	318	640954951	640954609	2.060000e-77	300.0
4	TraesCS3A01G087900	chr3A	95.918	49	2	0	3486	3534	661484783	661484831	2.920000e-11	80.5
5	TraesCS3A01G087900	chr3B	88.889	945	70	14	1161	2091	70120962	70121885	0.000000e+00	1131.0
6	TraesCS3A01G087900	chr3B	88.070	855	63	14	1251	2091	70093051	70093880	0.000000e+00	977.0
7	TraesCS3A01G087900	chr3B	84.985	686	58	25	1413	2091	70123440	70124087	0.000000e+00	654.0
8	TraesCS3A01G087900	chr3B	86.712	444	35	10	2123	2551	70095941	70096375	4.130000e-129	472.0
9	TraesCS3A01G087900	chr3B	83.924	423	31	15	768	1166	70092514	70092923	1.550000e-98	370.0
10	TraesCS3A01G087900	chr3B	79.941	339	38	16	8	318	739069073	739068737	4.590000e-54	222.0
11	TraesCS3A01G087900	chr3B	77.509	289	29	21	889	1166	70118968	70119231	1.320000e-29	141.0
12	TraesCS3A01G087900	chr3B	94.382	89	5	0	2092	2180	70121930	70122018	1.710000e-28	137.0
13	TraesCS3A01G087900	chr3B	85.827	127	18	0	355	481	254038381	254038507	6.150000e-28	135.0
14	TraesCS3A01G087900	chr3B	87.379	103	13	0	368	470	450829676	450829778	6.200000e-23	119.0
15	TraesCS3A01G087900	chr3B	97.826	46	1	0	2093	2138	70095335	70095380	2.920000e-11	80.5
16	TraesCS3A01G087900	chr3B	92.308	52	3	1	268	318	792083175	792083124	4.890000e-09	73.1
17	TraesCS3A01G087900	chr3D	93.794	709	37	3	2828	3533	166936736	166937440	0.000000e+00	1059.0
18	TraesCS3A01G087900	chr3D	89.161	858	63	14	1251	2091	44967041	44967885	0.000000e+00	1042.0
19	TraesCS3A01G087900	chr3D	86.982	868	74	18	1161	2020	45011777	45012613	0.000000e+00	941.0
20	TraesCS3A01G087900	chr3D	85.843	445	39	5	2123	2551	44968542	44968978	5.380000e-123	451.0
21	TraesCS3A01G087900	chr3D	85.203	419	25	15	768	1166	44966504	44966905	2.560000e-106	396.0
22	TraesCS3A01G087900	chr4D	94.970	656	33	0	2828	3483	45786218	45785563	0.000000e+00	1029.0
23	TraesCS3A01G087900	chr4D	90.370	135	12	1	185	318	433350936	433350802	3.630000e-40	176.0
24	TraesCS3A01G087900	chr7A	94.970	656	32	1	2828	3483	463720417	463721071	0.000000e+00	1027.0
25	TraesCS3A01G087900	chr7A	91.339	254	21	1	2553	2805	696100083	696099830	2.610000e-91	346.0
26	TraesCS3A01G087900	chr7A	89.344	244	24	2	2566	2807	616328093	616328336	4.430000e-79	305.0
27	TraesCS3A01G087900	chr7A	82.609	184	23	8	73	250	686303287	686303107	1.700000e-33	154.0
28	TraesCS3A01G087900	chr6A	94.970	656	31	2	2828	3483	582937101	582936448	0.000000e+00	1027.0
29	TraesCS3A01G087900	chr6A	95.918	49	2	0	3486	3534	256498807	256498759	2.920000e-11	80.5
30	TraesCS3A01G087900	chr5A	94.665	656	33	1	2828	3483	34894016	34894669	0.000000e+00	1016.0
31	TraesCS3A01G087900	chr5A	94.512	656	34	2	2828	3483	352478036	352477383	0.000000e+00	1011.0
32	TraesCS3A01G087900	chr5A	81.081	185	29	6	66	246	374905519	374905701	3.680000e-30	143.0
33	TraesCS3A01G087900	chr5A	94.737	76	4	0	3404	3479	681766936	681766861	6.200000e-23	119.0
34	TraesCS3A01G087900	chr5D	94.521	657	34	1	2827	3483	281493692	281494346	0.000000e+00	1013.0
35	TraesCS3A01G087900	chr5D	88.333	180	20	1	1	179	436938356	436938177	7.680000e-52	215.0
36	TraesCS3A01G087900	chr5D	81.283	187	27	6	71	252	408654089	408653906	1.020000e-30	145.0
37	TraesCS3A01G087900	chr5D	88.235	51	5	1	497	547	378052157	378052108	3.810000e-05	60.2
38	TraesCS3A01G087900	chr2A	94.512	656	36	0	2828	3483	729252590	729251935	0.000000e+00	1013.0
39	TraesCS3A01G087900	chr6D	92.362	707	43	7	2828	3534	62817566	62818261	0.000000e+00	996.0
40	TraesCS3A01G087900	chr6D	80.597	335	38	14	8	316	351928724	351929057	2.120000e-57	233.0
41	TraesCS3A01G087900	chrUn	82.173	589	81	10	1312	1885	103768761	103768182	5.300000e-133	484.0
42	TraesCS3A01G087900	chrUn	79.249	559	96	12	1339	1884	103726365	103725814	4.310000e-99	372.0
43	TraesCS3A01G087900	chrUn	83.721	344	30	16	1	318	244965953	244965610	5.730000e-78	302.0
44	TraesCS3A01G087900	chrUn	84.821	112	17	0	355	466	225200884	225200995	2.880000e-21	113.0
45	TraesCS3A01G087900	chr6B	86.159	289	34	4	1597	1885	55597020	55596738	1.230000e-79	307.0
46	TraesCS3A01G087900	chr6B	77.515	338	47	11	8	318	90959904	90959569	3.630000e-40	176.0
47	TraesCS3A01G087900	chr6B	90.566	53	3	2	3483	3533	289825981	289825929	6.330000e-08	69.4
48	TraesCS3A01G087900	chr6B	91.489	47	2	2	3489	3533	289772078	289772032	2.950000e-06	63.9
49	TraesCS3A01G087900	chr7D	88.976	254	16	6	2553	2805	561605432	561605190	1.590000e-78	303.0
50	TraesCS3A01G087900	chr7D	81.667	240	38	5	71	306	546050450	546050687	1.000000e-45	195.0
51	TraesCS3A01G087900	chr7D	86.087	115	16	0	356	470	157664105	157663991	1.330000e-24	124.0
52	TraesCS3A01G087900	chr7B	83.721	344	30	12	1	318	687896779	687896436	5.730000e-78	302.0
53	TraesCS3A01G087900	chr7B	85.965	171	22	2	149	318	83987639	83987470	7.790000e-42	182.0
54	TraesCS3A01G087900	chr1B	80.516	349	36	13	1	317	280986718	280987066	4.560000e-59	239.0
55	TraesCS3A01G087900	chr1B	100.000	29	0	0	502	530	463525472	463525444	2.000000e-03	54.7
56	TraesCS3A01G087900	chr2D	80.290	345	34	15	1	318	388483455	388483118	2.740000e-56	230.0
57	TraesCS3A01G087900	chr2D	81.622	185	28	5	71	252	44184774	44184593	7.900000e-32	148.0
58	TraesCS3A01G087900	chr5B	78.635	337	44	8	8	318	601422127	601422461	7.740000e-47	198.0
59	TraesCS3A01G087900	chr5B	86.429	140	19	0	355	494	710225012	710225151	1.700000e-33	154.0
60	TraesCS3A01G087900	chr5B	95.918	49	2	0	3486	3534	166669509	166669461	2.920000e-11	80.5
61	TraesCS3A01G087900	chr4A	86.364	176	18	5	8	179	531236380	531236207	1.680000e-43	187.0
62	TraesCS3A01G087900	chr4B	93.878	49	3	0	3486	3534	406686483	406686435	1.360000e-09	75.0

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	TraesCS3A01G087900	chr3A	56733591	56737124	3533	False	6527.000000	6527	100.000000	1	3534	1	chr3A.!!$F1	3533
1	TraesCS3A01G087900	chr3A	56756835	56758057	1222	False	1664.000000	1664	91.445000	1161	2376	1	chr3A.!!$F2	1215
2	TraesCS3A01G087900	chr3B	70118968	70124087	5119	False	515.750000	1131	86.441250	889	2180	4	chr3B.!!$F4	1291
3	TraesCS3A01G087900	chr3B	70092514	70096375	3861	False	474.875000	977	89.133000	768	2551	4	chr3B.!!$F3	1783
4	TraesCS3A01G087900	chr3D	166936736	166937440	704	False	1059.000000	1059	93.794000	2828	3533	1	chr3D.!!$F2	705
5	TraesCS3A01G087900	chr3D	45011777	45012613	836	False	941.000000	941	86.982000	1161	2020	1	chr3D.!!$F1	859
6	TraesCS3A01G087900	chr3D	44966504	44968978	2474	False	629.666667	1042	86.735667	768	2551	3	chr3D.!!$F3	1783
7	TraesCS3A01G087900	chr4D	45785563	45786218	655	True	1029.000000	1029	94.970000	2828	3483	1	chr4D.!!$R1	655
8	TraesCS3A01G087900	chr7A	463720417	463721071	654	False	1027.000000	1027	94.970000	2828	3483	1	chr7A.!!$F1	655
9	TraesCS3A01G087900	chr6A	582936448	582937101	653	True	1027.000000	1027	94.970000	2828	3483	1	chr6A.!!$R2	655
10	TraesCS3A01G087900	chr5A	34894016	34894669	653	False	1016.000000	1016	94.665000	2828	3483	1	chr5A.!!$F1	655
11	TraesCS3A01G087900	chr5A	352477383	352478036	653	True	1011.000000	1011	94.512000	2828	3483	1	chr5A.!!$R1	655
12	TraesCS3A01G087900	chr5D	281493692	281494346	654	False	1013.000000	1013	94.521000	2827	3483	1	chr5D.!!$F1	656
13	TraesCS3A01G087900	chr2A	729251935	729252590	655	True	1013.000000	1013	94.512000	2828	3483	1	chr2A.!!$R1	655
14	TraesCS3A01G087900	chr6D	62817566	62818261	695	False	996.000000	996	92.362000	2828	3534	1	chr6D.!!$F1	706
15	TraesCS3A01G087900	chrUn	103768182	103768761	579	True	484.000000	484	82.173000	1312	1885	1	chrUn.!!$R2	573
16	TraesCS3A01G087900	chrUn	103725814	103726365	551	True	372.000000	372	79.249000	1339	1884	1	chrUn.!!$R1	545

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
451	452	0.033642	TATCAACGTGTGTGGGCGAA	59.966	50.0	0.00	0.0	0.00	4.70	F
643	644	0.250901	GCTGTTCCAGGGAGCAAAGA	60.251	55.0	6.33	0.0	35.07	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2376	6482	0.586319	ACTTCCGCAACAACACGATG	59.414	50.000	0.0	0.0	0.0	3.84	R
2582	7504	2.978978	TCCCTCTCCATGTGAAGTTTGA	59.021	45.455	0.0	0.0	0.0	2.69	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
23	24	4.118995	CGGTACTGGCCGCGTGTA	62.119	66.667	4.92	0.00	45.47	2.90
24	25	2.497770	GGTACTGGCCGCGTGTAT	59.502	61.111	4.92	0.00	0.00	2.29
25	26	1.153509	GGTACTGGCCGCGTGTATT	60.154	57.895	4.92	0.00	0.00	1.89
26	27	0.741927	GGTACTGGCCGCGTGTATTT	60.742	55.000	4.92	0.00	0.00	1.40
27	28	1.471327	GGTACTGGCCGCGTGTATTTA	60.471	52.381	4.92	0.00	0.00	1.40
28	29	2.270047	GTACTGGCCGCGTGTATTTAA	58.730	47.619	4.92	0.00	0.00	1.52
29	30	1.810959	ACTGGCCGCGTGTATTTAAA	58.189	45.000	4.92	0.00	0.00	1.52
30	31	1.465777	ACTGGCCGCGTGTATTTAAAC	59.534	47.619	4.92	0.00	0.00	2.01
31	32	0.443088	TGGCCGCGTGTATTTAAACG	59.557	50.000	4.92	0.00	42.61	3.60
32	33	0.720590	GGCCGCGTGTATTTAAACGA	59.279	50.000	4.92	0.00	42.32	3.85
33	34	1.328374	GGCCGCGTGTATTTAAACGAT	59.672	47.619	4.92	0.00	42.32	3.73
34	35	2.539274	GGCCGCGTGTATTTAAACGATA	59.461	45.455	4.92	0.00	42.32	2.92
35	36	3.362304	GGCCGCGTGTATTTAAACGATAG	60.362	47.826	4.92	0.00	42.32	2.08
54	55	7.525688	CGATAGTTGACATGTGTGATAAACT	57.474	36.000	1.15	6.04	33.62	2.66
55	56	8.628882	CGATAGTTGACATGTGTGATAAACTA	57.371	34.615	1.15	7.98	35.13	2.24
56	57	8.532341	CGATAGTTGACATGTGTGATAAACTAC	58.468	37.037	1.15	0.00	34.35	2.73
57	58	9.587772	GATAGTTGACATGTGTGATAAACTACT	57.412	33.333	1.15	1.17	34.35	2.57
58	59	9.944376	ATAGTTGACATGTGTGATAAACTACTT	57.056	29.630	1.15	0.00	34.35	2.24
59	60	8.087982	AGTTGACATGTGTGATAAACTACTTG	57.912	34.615	1.15	0.00	30.15	3.16
60	61	6.480524	TGACATGTGTGATAAACTACTTGC	57.519	37.500	1.15	0.00	0.00	4.01
61	62	5.411361	TGACATGTGTGATAAACTACTTGCC	59.589	40.000	1.15	0.00	0.00	4.52
62	63	4.700213	ACATGTGTGATAAACTACTTGCCC	59.300	41.667	0.00	0.00	0.00	5.36
63	64	4.634012	TGTGTGATAAACTACTTGCCCT	57.366	40.909	0.00	0.00	0.00	5.19
64	65	5.748670	TGTGTGATAAACTACTTGCCCTA	57.251	39.130	0.00	0.00	0.00	3.53
65	66	5.484715	TGTGTGATAAACTACTTGCCCTAC	58.515	41.667	0.00	0.00	0.00	3.18

Showing 1 to 25 of 687 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	0.741927	AAATACACGCGGCCAGTACC	60.742	55.000	12.47	0.00	0.00	3.34
8	9	1.925229	TAAATACACGCGGCCAGTAC	58.075	50.000	12.47	0.00	0.00	2.73
9	10	2.669300	TTAAATACACGCGGCCAGTA	57.331	45.000	12.47	8.26	0.00	2.74
10	11	1.465777	GTTTAAATACACGCGGCCAGT	59.534	47.619	12.47	6.00	0.00	4.00
11	12	1.528198	CGTTTAAATACACGCGGCCAG	60.528	52.381	12.47	0.00	0.00	4.85
12	13	0.443088	CGTTTAAATACACGCGGCCA	59.557	50.000	12.47	0.00	0.00	5.36
13	14	0.720590	TCGTTTAAATACACGCGGCC	59.279	50.000	12.47	0.00	36.32	6.13
14	15	2.724744	ATCGTTTAAATACACGCGGC	57.275	45.000	12.47	0.00	36.32	6.53
15	16	5.004630	TCAACTATCGTTTAAATACACGCGG	59.995	40.000	12.47	1.27	36.32	6.46
16	17	5.887288	GTCAACTATCGTTTAAATACACGCG	59.113	40.000	3.53	3.53	36.32	6.01
17	18	6.754206	TGTCAACTATCGTTTAAATACACGC	58.246	36.000	0.00	0.00	36.32	5.34
18	19	8.377681	ACATGTCAACTATCGTTTAAATACACG	58.622	33.333	0.00	0.00	37.77	4.49
19	20	9.472995	CACATGTCAACTATCGTTTAAATACAC	57.527	33.333	0.00	0.00	0.00	2.90
20	21	9.210329	ACACATGTCAACTATCGTTTAAATACA	57.790	29.630	0.00	0.00	0.00	2.29
21	22	9.472995	CACACATGTCAACTATCGTTTAAATAC	57.527	33.333	0.00	0.00	0.00	1.89
22	23	9.425577	TCACACATGTCAACTATCGTTTAAATA	57.574	29.630	0.00	0.00	0.00	1.40
23	24	8.317891	TCACACATGTCAACTATCGTTTAAAT	57.682	30.769	0.00	0.00	0.00	1.40
24	25	7.716768	TCACACATGTCAACTATCGTTTAAA	57.283	32.000	0.00	0.00	0.00	1.52
25	26	7.899178	ATCACACATGTCAACTATCGTTTAA	57.101	32.000	0.00	0.00	0.00	1.52
26	27	8.989653	TTATCACACATGTCAACTATCGTTTA	57.010	30.769	0.00	0.00	0.00	2.01
27	28	7.899178	TTATCACACATGTCAACTATCGTTT	57.101	32.000	0.00	0.00	0.00	3.60
28	29	7.602644	AGTTTATCACACATGTCAACTATCGTT	59.397	33.333	0.00	0.00	0.00	3.85
29	30	7.097192	AGTTTATCACACATGTCAACTATCGT	58.903	34.615	0.00	0.00	0.00	3.73
30	31	7.525688	AGTTTATCACACATGTCAACTATCG	57.474	36.000	0.00	0.00	0.00	2.92
31	32	9.587772	AGTAGTTTATCACACATGTCAACTATC	57.412	33.333	0.00	0.00	31.45	2.08

Showing 1 to 25 of 752 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.