AutoCloner

Multiple sequence alignment - TraesCS2D01G237100

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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	TraesCS2D01G237100	chr2D	100.000	2375	0	0	1	2375	239256885	239259259	0.000000e+00	4386.0
1	TraesCS2D01G237100	chr2D	94.024	753	31	8	1555	2300	645235073	645234328	0.000000e+00	1129.0
2	TraesCS2D01G237100	chr7D	95.075	2335	78	15	1	2302	79226608	79228938	0.000000e+00	3640.0
3	TraesCS2D01G237100	chr7D	94.975	1572	52	2	5	1550	51238862	51237292	0.000000e+00	2440.0
4	TraesCS2D01G237100	chr7D	92.469	810	45	10	1497	2299	51237293	51236493	0.000000e+00	1144.0
5	TraesCS2D01G237100	chr6D	94.539	2344	71	28	1	2299	446364396	446362065	0.000000e+00	3567.0
6	TraesCS2D01G237100	chr6D	93.068	2366	90	24	1	2300	297171480	297169123	0.000000e+00	3393.0
7	TraesCS2D01G237100	chr6D	89.598	846	39	8	709	1550	46519952	46519152	0.000000e+00	1029.0
8	TraesCS2D01G237100	chr6D	100.000	76	0	0	2300	2375	112094923	112094848	8.850000e-30	141.0
9	TraesCS2D01G237100	chr6D	98.734	79	1	0	2297	2375	317313632	317313710	8.850000e-30	141.0
10	TraesCS2D01G237100	chr6D	98.734	79	1	0	2297	2375	348263409	348263487	8.850000e-30	141.0
11	TraesCS2D01G237100	chr6D	100.000	76	0	0	2300	2375	391457479	391457404	8.850000e-30	141.0
12	TraesCS2D01G237100	chr6D	80.000	75	12	2	1532	1606	46519114	46519043	4.000000e-03	52.8
13	TraesCS2D01G237100	chr3A	92.129	2363	116	22	1	2303	702240688	702243040	0.000000e+00	3269.0
14	TraesCS2D01G237100	chr3A	94.550	789	31	4	2	784	733879760	733878978	0.000000e+00	1208.0
15	TraesCS2D01G237100	chr3A	94.304	790	33	3	1	784	513304605	513305388	0.000000e+00	1199.0
16	TraesCS2D01G237100	chr5A	92.403	2093	114	25	242	2299	178860401	178858319	0.000000e+00	2942.0
17	TraesCS2D01G237100	chr5A	94.557	790	31	4	1	784	501877060	501877843	0.000000e+00	1210.0
18	TraesCS2D01G237100	chr5A	94.311	791	31	6	1	784	634752684	634753467	0.000000e+00	1199.0
19	TraesCS2D01G237100	chr1D	97.355	1550	41	0	1	1550	336730190	336728641	0.000000e+00	2636.0
20	TraesCS2D01G237100	chr1D	95.819	861	31	2	528	1385	417113548	417114406	0.000000e+00	1386.0
21	TraesCS2D01G237100	chr1D	92.866	827	37	11	1497	2304	336728660	336727837	0.000000e+00	1181.0
22	TraesCS2D01G237100	chr5D	96.679	1566	36	3	1	1550	384512100	384510535	0.000000e+00	2590.0
23	TraesCS2D01G237100	chr5D	94.543	1576	60	6	1	1550	29767669	29766094	0.000000e+00	2410.0
24	TraesCS2D01G237100	chr5D	93.913	805	31	11	1497	2294	401784148	401784941	0.000000e+00	1199.0
25	TraesCS2D01G237100	chr5D	92.593	810	42	12	1497	2299	384510536	384509738	0.000000e+00	1147.0
26	TraesCS2D01G237100	chr5D	93.278	729	43	4	1575	2299	140951587	140950861	0.000000e+00	1070.0
27	TraesCS2D01G237100	chr5D	100.000	76	0	0	2300	2375	433727544	433727469	8.850000e-30	141.0
28	TraesCS2D01G237100	chr6B	94.684	790	30	4	1	784	703926434	703927217	0.000000e+00	1216.0
29	TraesCS2D01G237100	chr2A	94.578	793	28	7	1	784	15511877	15511091	0.000000e+00	1212.0
30	TraesCS2D01G237100	chr2A	97.647	85	1	1	2292	2375	466543934	466543850	6.840000e-31	145.0
31	TraesCS2D01G237100	chr3B	94.557	790	31	3	1	784	808941806	808941023	0.000000e+00	1210.0
32	TraesCS2D01G237100	chr1A	94.304	790	33	4	1	784	443863425	443864208	0.000000e+00	1199.0
33	TraesCS2D01G237100	chr4D	95.031	161	8	0	1390	1550	125903980	125903820	1.090000e-63	254.0
34	TraesCS2D01G237100	chr4D	98.734	79	1	0	2297	2375	28734240	28734318	8.850000e-30	141.0
35	TraesCS2D01G237100	chr4D	98.734	79	1	0	2297	2375	28736434	28736512	8.850000e-30	141.0
36	TraesCS2D01G237100	chr3D	100.000	76	0	0	2300	2375	348097096	348097021	8.850000e-30	141.0

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	TraesCS2D01G237100	chr2D	239256885	239259259	2374	False	4386.0	4386	100.0000	1	2375	1	chr2D.!!$F1	2374
1	TraesCS2D01G237100	chr2D	645234328	645235073	745	True	1129.0	1129	94.0240	1555	2300	1	chr2D.!!$R1	745
2	TraesCS2D01G237100	chr7D	79226608	79228938	2330	False	3640.0	3640	95.0750	1	2302	1	chr7D.!!$F1	2301
3	TraesCS2D01G237100	chr7D	51236493	51238862	2369	True	1792.0	2440	93.7220	5	2299	2	chr7D.!!$R1	2294
4	TraesCS2D01G237100	chr6D	446362065	446364396	2331	True	3567.0	3567	94.5390	1	2299	1	chr6D.!!$R4	2298
5	TraesCS2D01G237100	chr6D	297169123	297171480	2357	True	3393.0	3393	93.0680	1	2300	1	chr6D.!!$R2	2299
6	TraesCS2D01G237100	chr6D	46519043	46519952	909	True	540.9	1029	84.7990	709	1606	2	chr6D.!!$R5	897
7	TraesCS2D01G237100	chr3A	702240688	702243040	2352	False	3269.0	3269	92.1290	1	2303	1	chr3A.!!$F2	2302
8	TraesCS2D01G237100	chr3A	733878978	733879760	782	True	1208.0	1208	94.5500	2	784	1	chr3A.!!$R1	782
9	TraesCS2D01G237100	chr3A	513304605	513305388	783	False	1199.0	1199	94.3040	1	784	1	chr3A.!!$F1	783
10	TraesCS2D01G237100	chr5A	178858319	178860401	2082	True	2942.0	2942	92.4030	242	2299	1	chr5A.!!$R1	2057
11	TraesCS2D01G237100	chr5A	501877060	501877843	783	False	1210.0	1210	94.5570	1	784	1	chr5A.!!$F1	783
12	TraesCS2D01G237100	chr5A	634752684	634753467	783	False	1199.0	1199	94.3110	1	784	1	chr5A.!!$F2	783
13	TraesCS2D01G237100	chr1D	336727837	336730190	2353	True	1908.5	2636	95.1105	1	2304	2	chr1D.!!$R1	2303
14	TraesCS2D01G237100	chr1D	417113548	417114406	858	False	1386.0	1386	95.8190	528	1385	1	chr1D.!!$F1	857
15	TraesCS2D01G237100	chr5D	29766094	29767669	1575	True	2410.0	2410	94.5430	1	1550	1	chr5D.!!$R1	1549
16	TraesCS2D01G237100	chr5D	384509738	384512100	2362	True	1868.5	2590	94.6360	1	2299	2	chr5D.!!$R4	2298
17	TraesCS2D01G237100	chr5D	401784148	401784941	793	False	1199.0	1199	93.9130	1497	2294	1	chr5D.!!$F1	797
18	TraesCS2D01G237100	chr5D	140950861	140951587	726	True	1070.0	1070	93.2780	1575	2299	1	chr5D.!!$R2	724
19	TraesCS2D01G237100	chr6B	703926434	703927217	783	False	1216.0	1216	94.6840	1	784	1	chr6B.!!$F1	783
20	TraesCS2D01G237100	chr2A	15511091	15511877	786	True	1212.0	1212	94.5780	1	784	1	chr2A.!!$R1	783
21	TraesCS2D01G237100	chr3B	808941023	808941806	783	True	1210.0	1210	94.5570	1	784	1	chr3B.!!$R1	783
22	TraesCS2D01G237100	chr1A	443863425	443864208	783	False	1199.0	1199	94.3040	1	784	1	chr1A.!!$F1	783

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
61	62	0.107508	CTGACGGATGGTGAATGGCT	60.108	55.0	0.0	0.0	0.0	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2052	2308	0.325933	TCAGATCCACAGTGGCAAGG	59.674	55.0	15.64	4.85	37.47	3.61	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
36	37	3.008049	AGTCAGCATTAAGTCTCCGGTTT	59.992	43.478	0.00	0.00	0.00	3.27
61	62	0.107508	CTGACGGATGGTGAATGGCT	60.108	55.000	0.00	0.00	0.00	4.75
218	220	7.805071	GTGTCGAACAAGATGAATCAAGAAAAT	59.195	33.333	0.00	0.00	0.00	1.82
440	442	1.715019	TAAGGCCACCCACAACAGCT	61.715	55.000	5.01	0.00	0.00	4.24
509	511	0.899720	CATGCTTTGTCCATGCCCTT	59.100	50.000	0.00	0.00	34.34	3.95
614	654	6.822667	TGATGCTGTTTGATAGTTCAACAT	57.177	33.333	0.00	0.00	41.50	2.71
795	835	6.152323	TGTCTCCAGGTCACATAAGTTACTAC	59.848	42.308	0.00	0.00	0.00	2.73
974	1017	8.917414	AAATAGATCTCCCACTAATGCCTATA	57.083	34.615	0.00	0.00	0.00	1.31
1109	1152	3.057033	GTCAAGCAAAGCACATTCCTCAT	60.057	43.478	0.00	0.00	0.00	2.90
1423	1466	4.155280	TGTGATCTGATGCAGTTTGTCATG	59.845	41.667	0.00	0.00	32.61	3.07
1508	1603	1.610522	CTTTGCAAGTGAACCTGGGAG	59.389	52.381	0.00	0.00	0.00	4.30
1509	1604	0.823356	TTGCAAGTGAACCTGGGAGC	60.823	55.000	0.00	0.00	0.00	4.70
1510	1605	1.228245	GCAAGTGAACCTGGGAGCA	60.228	57.895	0.00	0.00	0.00	4.26
1842	2087	3.704100	GCTGTGGCCCAAAACAATT	57.296	47.368	0.00	0.00	0.00	2.32
1850	2095	2.158827	GGCCCAAAACAATTGTGGACTT	60.159	45.455	12.82	0.00	34.05	3.01
1989	2245	2.257409	CTTGGCCCATGTAGACGGCT	62.257	60.000	0.00	0.00	42.58	5.52
1995	2251	2.484770	GCCCATGTAGACGGCTGAAATA	60.485	50.000	0.00	0.00	39.70	1.40
2052	2308	2.095919	GGTTGTAATTCTGCCACGTCAC	60.096	50.000	0.00	0.00	0.00	3.67
2061	2317	2.111043	CCACGTCACCTTGCCACT	59.889	61.111	0.00	0.00	0.00	4.00
2072	2328	1.064906	CCTTGCCACTGTGGATCTGAT	60.065	52.381	30.23	0.00	40.96	2.90
2207	2468	0.037590	ACGGCCAGCTTTTGACCATA	59.962	50.000	2.24	0.00	0.00	2.74
2210	2471	1.410153	GGCCAGCTTTTGACCATATGG	59.590	52.381	20.68	20.68	42.17	2.74
2254	2515	6.582295	CACAAAAGGAAAACTATGACCATTCG	59.418	38.462	0.00	0.00	0.00	3.34
2303	2564	2.493278	ACATATTTCTTGCAGTGGTGGC	59.507	45.455	0.00	0.00	0.00	5.01
2304	2565	1.164411	TATTTCTTGCAGTGGTGGCG	58.836	50.000	0.00	0.00	0.00	5.69
2305	2566	0.823356	ATTTCTTGCAGTGGTGGCGT	60.823	50.000	0.00	0.00	0.00	5.68
2306	2567	1.034838	TTTCTTGCAGTGGTGGCGTT	61.035	50.000	0.00	0.00	0.00	4.84
2307	2568	1.034838	TTCTTGCAGTGGTGGCGTTT	61.035	50.000	0.00	0.00	0.00	3.60
2308	2569	1.034838	TCTTGCAGTGGTGGCGTTTT	61.035	50.000	0.00	0.00	0.00	2.43
2309	2570	0.594796	CTTGCAGTGGTGGCGTTTTC	60.595	55.000	0.00	0.00	0.00	2.29
2310	2571	2.010582	TTGCAGTGGTGGCGTTTTCC	62.011	55.000	0.00	0.00	0.00	3.13
2311	2572	2.485795	GCAGTGGTGGCGTTTTCCA	61.486	57.895	0.00	0.00	0.00	3.53
2312	2573	2.010582	GCAGTGGTGGCGTTTTCCAA	62.011	55.000	0.00	0.00	37.96	3.53
2313	2574	0.457851	CAGTGGTGGCGTTTTCCAAA	59.542	50.000	0.00	0.00	37.96	3.28
2314	2575	0.744281	AGTGGTGGCGTTTTCCAAAG	59.256	50.000	0.00	0.00	37.96	2.77
2315	2576	0.458260	GTGGTGGCGTTTTCCAAAGT	59.542	50.000	0.00	0.00	37.96	2.66
2316	2577	1.134936	GTGGTGGCGTTTTCCAAAGTT	60.135	47.619	0.00	0.00	37.96	2.66
2317	2578	1.550976	TGGTGGCGTTTTCCAAAGTTT	59.449	42.857	0.00	0.00	37.96	2.66
2318	2579	1.930503	GGTGGCGTTTTCCAAAGTTTG	59.069	47.619	8.73	8.73	37.96	2.93
2319	2580	1.326245	GTGGCGTTTTCCAAAGTTTGC	59.674	47.619	10.25	0.00	37.96	3.68
2320	2581	1.066858	TGGCGTTTTCCAAAGTTTGCA	60.067	42.857	10.25	0.00	32.18	4.08
2321	2582	2.003301	GGCGTTTTCCAAAGTTTGCAA	58.997	42.857	10.25	0.00	0.00	4.08
2322	2583	2.416893	GGCGTTTTCCAAAGTTTGCAAA	59.583	40.909	8.05	8.05	0.00	3.68
2323	2584	3.120165	GGCGTTTTCCAAAGTTTGCAAAA	60.120	39.130	14.67	12.41	0.00	2.44
2324	2585	4.467735	GCGTTTTCCAAAGTTTGCAAAAA	58.532	34.783	16.96	16.84	0.00	1.94
2325	2586	5.092105	GCGTTTTCCAAAGTTTGCAAAAAT	58.908	33.333	16.96	2.58	31.28	1.82
2326	2587	5.570973	GCGTTTTCCAAAGTTTGCAAAAATT	59.429	32.000	16.96	9.21	31.28	1.82
2327	2588	6.452220	GCGTTTTCCAAAGTTTGCAAAAATTG	60.452	34.615	16.96	22.24	31.28	2.32
2348	2609	4.880886	GCAGTGGCATTTTTCAAAGTTT	57.119	36.364	0.00	0.00	40.72	2.66
2349	2610	4.590226	GCAGTGGCATTTTTCAAAGTTTG	58.410	39.130	9.44	9.44	40.72	2.93
2350	2611	4.496175	GCAGTGGCATTTTTCAAAGTTTGG	60.496	41.667	15.47	0.00	40.72	3.28
2351	2612	4.874966	CAGTGGCATTTTTCAAAGTTTGGA	59.125	37.500	15.47	3.83	0.00	3.53
2352	2613	5.353678	CAGTGGCATTTTTCAAAGTTTGGAA	59.646	36.000	15.47	10.54	0.00	3.53
2353	2614	5.942826	AGTGGCATTTTTCAAAGTTTGGAAA	59.057	32.000	16.59	16.59	36.38	3.13
2354	2615	6.602803	AGTGGCATTTTTCAAAGTTTGGAAAT	59.397	30.769	20.26	18.72	37.93	2.17
2355	2616	7.122501	AGTGGCATTTTTCAAAGTTTGGAAATT	59.877	29.630	20.26	14.79	37.93	1.82
2356	2617	7.220491	GTGGCATTTTTCAAAGTTTGGAAATTG	59.780	33.333	26.17	26.17	37.93	2.32
2359	2620	8.330302	CATTTTTCAAAGTTTGGAAATTGCAG	57.670	30.769	22.21	10.09	37.93	4.41
2360	2621	7.446001	TTTTTCAAAGTTTGGAAATTGCAGT	57.554	28.000	20.26	0.00	37.93	4.40
2361	2622	6.419980	TTTCAAAGTTTGGAAATTGCAGTG	57.580	33.333	15.47	0.00	0.00	3.66
2362	2623	4.440880	TCAAAGTTTGGAAATTGCAGTGG	58.559	39.130	15.47	0.00	0.00	4.00
2363	2624	2.531522	AGTTTGGAAATTGCAGTGGC	57.468	45.000	0.00	0.00	41.68	5.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	2.143876	TCACCATCCGTCAGATCTGA	57.856	50.000	21.67	21.67	37.24	3.27
61	62	1.273267	ACCACATCTCCACCAGAGCTA	60.273	52.381	0.00	0.00	42.90	3.32
218	220	4.546570	CAGTTCTCTGATTGTACACGACA	58.453	43.478	0.00	0.00	43.76	4.35
253	255	1.142474	GGCAAAAATGTGAGCTGTGC	58.858	50.000	0.00	0.00	0.00	4.57
440	442	0.680618	TCCGAAAACCCGTGCTTCTA	59.319	50.000	0.00	0.00	0.00	2.10
479	481	3.686726	GGACAAAGCATGGAGTGACTTAG	59.313	47.826	0.00	0.00	0.00	2.18
509	511	3.384146	TCAAAGCTGGCTGTGAATCAAAA	59.616	39.130	12.47	0.00	37.36	2.44
614	654	6.968263	AGCTACAGCAAGTTCTGATATCTA	57.032	37.500	3.98	0.00	45.16	1.98
974	1017	8.220559	TCTTAAGCTAGCATATGGAGGAAAATT	58.779	33.333	18.83	0.00	0.00	1.82
1109	1152	0.770499	TGACTGGAGCCCAACATTCA	59.230	50.000	0.00	0.00	30.80	2.57
1423	1466	1.704641	AACTTCCCAGCCTTCAAACC	58.295	50.000	0.00	0.00	0.00	3.27
1508	1603	1.168714	GATCCCAGGTTCACAAGTGC	58.831	55.000	0.00	0.00	0.00	4.40
1509	1604	2.816087	CAAGATCCCAGGTTCACAAGTG	59.184	50.000	0.00	0.00	0.00	3.16
1510	1605	2.443255	ACAAGATCCCAGGTTCACAAGT	59.557	45.455	0.00	0.00	0.00	3.16
1665	1905	6.463995	TTTTGCAGTCCAACTCAATTTAGT	57.536	33.333	0.00	0.00	31.97	2.24
1989	2245	2.771943	AGAATCAGCCCGGTCTATTTCA	59.228	45.455	0.00	0.00	0.00	2.69
1995	2251	3.933861	AAAATAGAATCAGCCCGGTCT	57.066	42.857	0.00	0.00	0.00	3.85
2052	2308	0.325933	TCAGATCCACAGTGGCAAGG	59.674	55.000	15.64	4.85	37.47	3.61
2061	2317	1.003464	CCACACCACATCAGATCCACA	59.997	52.381	0.00	0.00	0.00	4.17
2072	2328	2.282110	CAATCCGCCCACACCACA	60.282	61.111	0.00	0.00	0.00	4.17
2294	2555	0.457851	TTTGGAAAACGCCACCACTG	59.542	50.000	0.00	0.00	37.75	3.66
2327	2588	4.496175	CCAAACTTTGAAAAATGCCACTGC	60.496	41.667	2.87	0.00	38.26	4.40
2328	2589	4.874966	TCCAAACTTTGAAAAATGCCACTG	59.125	37.500	2.87	0.00	0.00	3.66
2329	2590	5.096443	TCCAAACTTTGAAAAATGCCACT	57.904	34.783	2.87	0.00	0.00	4.00
2330	2591	5.809719	TTCCAAACTTTGAAAAATGCCAC	57.190	34.783	2.87	0.00	0.00	5.01
2331	2592	7.256286	CAATTTCCAAACTTTGAAAAATGCCA	58.744	30.769	2.87	0.00	31.07	4.92
2332	2593	6.198778	GCAATTTCCAAACTTTGAAAAATGCC	59.801	34.615	12.80	6.14	31.07	4.40
2333	2594	6.750963	TGCAATTTCCAAACTTTGAAAAATGC	59.249	30.769	15.62	15.62	31.07	3.56
2334	2595	7.969508	ACTGCAATTTCCAAACTTTGAAAAATG	59.030	29.630	2.87	0.43	31.07	2.32
2335	2596	7.969508	CACTGCAATTTCCAAACTTTGAAAAAT	59.030	29.630	2.87	6.16	31.56	1.82
2336	2597	7.303998	CACTGCAATTTCCAAACTTTGAAAAA	58.696	30.769	2.87	4.27	0.00	1.94
2337	2598	6.128063	CCACTGCAATTTCCAAACTTTGAAAA	60.128	34.615	2.87	0.00	0.00	2.29
2338	2599	5.353678	CCACTGCAATTTCCAAACTTTGAAA	59.646	36.000	2.87	3.11	0.00	2.69
2339	2600	4.874966	CCACTGCAATTTCCAAACTTTGAA	59.125	37.500	2.87	0.00	0.00	2.69
2340	2601	4.440880	CCACTGCAATTTCCAAACTTTGA	58.559	39.130	2.87	0.00	0.00	2.69
2341	2602	3.002553	GCCACTGCAATTTCCAAACTTTG	59.997	43.478	0.00	0.00	37.47	2.77
2342	2603	3.205338	GCCACTGCAATTTCCAAACTTT	58.795	40.909	0.00	0.00	37.47	2.66
2343	2604	2.170187	TGCCACTGCAATTTCCAAACTT	59.830	40.909	0.00	0.00	46.66	2.66
2344	2605	1.761784	TGCCACTGCAATTTCCAAACT	59.238	42.857	0.00	0.00	46.66	2.66
2345	2606	2.237393	TGCCACTGCAATTTCCAAAC	57.763	45.000	0.00	0.00	46.66	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.