AutoCloner

Multiple sequence alignment - TraesCS3A01G440500

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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	TraesCS3A01G440500	chr3A	100.000	2549	0	0	1	2549	683238251	683235703	0.000000e+00	4708.0
1	TraesCS3A01G440500	chr2A	97.010	1973	47	7	578	2549	775967963	775966002	0.000000e+00	3306.0
2	TraesCS3A01G440500	chr2A	95.980	1990	54	8	574	2549	771778414	771780391	0.000000e+00	3208.0
3	TraesCS3A01G440500	chr2A	94.088	1979	77	22	574	2549	744582024	744583965	0.000000e+00	2970.0
4	TraesCS3A01G440500	chr5A	96.638	1993	40	7	573	2549	563443923	563445904	0.000000e+00	3284.0
5	TraesCS3A01G440500	chr5A	84.167	120	16	3	426	543	633855070	633855188	2.070000e-21	113.0
6	TraesCS3A01G440500	chr7A	96.628	1987	45	5	578	2549	49208209	49210188	0.000000e+00	3278.0
7	TraesCS3A01G440500	chr7A	95.628	1990	50	11	576	2549	150203041	150201073	0.000000e+00	3158.0
8	TraesCS3A01G440500	chr7A	95.521	1987	52	8	579	2549	689996369	689994404	0.000000e+00	3142.0
9	TraesCS3A01G440500	chr7A	90.460	2002	116	27	579	2549	622760862	622758905	0.000000e+00	2569.0
10	TraesCS3A01G440500	chr7A	82.090	134	21	3	426	557	547102920	547102788	7.450000e-21	111.0
11	TraesCS3A01G440500	chr7A	80.233	86	16	1	342	427	638849142	638849058	2.120000e-06	63.9
12	TraesCS3A01G440500	chr1A	96.436	1992	51	4	573	2548	50511100	50513087	0.000000e+00	3267.0
13	TraesCS3A01G440500	chr1A	83.562	146	22	2	413	557	452043666	452043810	4.420000e-28	135.0
14	TraesCS3A01G440500	chr6A	96.199	1973	54	9	579	2549	203520912	203518959	0.000000e+00	3208.0
15	TraesCS3A01G440500	chr1D	92.546	1999	91	19	577	2549	17040738	17038772	0.000000e+00	2813.0
16	TraesCS3A01G440500	chr1D	84.962	133	19	1	426	557	351254728	351254860	1.590000e-27	134.0
17	TraesCS3A01G440500	chr1D	88.889	90	10	0	454	543	49592202	49592113	7.450000e-21	111.0
18	TraesCS3A01G440500	chr5D	91.757	1747	94	20	571	2290	114516307	114518030	0.000000e+00	2383.0
19	TraesCS3A01G440500	chr5D	92.412	369	21	5	579	943	357075968	357075603	1.050000e-143	520.0
20	TraesCS3A01G440500	chr5D	82.105	95	6	7	336	427	304213046	304213132	1.270000e-08	71.3
21	TraesCS3A01G440500	chr2D	91.832	1261	54	19	577	1836	435209597	435210809	0.000000e+00	1712.0
22	TraesCS3A01G440500	chr7B	92.288	1167	66	12	570	1734	734145282	734146426	0.000000e+00	1635.0
23	TraesCS3A01G440500	chr7B	83.065	124	18	3	427	548	495340790	495340912	2.680000e-20	110.0
24	TraesCS3A01G440500	chr7B	82.812	64	8	2	351	413	7219723	7219662	1.000000e-03	54.7
25	TraesCS3A01G440500	chr3D	93.995	383	23	0	175	557	546467583	546467201	4.730000e-162	580.0
26	TraesCS3A01G440500	chr3D	96.875	128	3	1	47	174	546467948	546467822	1.990000e-51	213.0
27	TraesCS3A01G440500	chr3D	94.366	71	3	1	357	427	546467332	546467263	9.640000e-20	108.0
28	TraesCS3A01G440500	chr3D	97.368	38	1	0	1	38	546468009	546467972	5.890000e-07	65.8
29	TraesCS3A01G440500	chr3B	95.912	318	9	3	47	361	723498613	723498297	1.750000e-141	512.0
30	TraesCS3A01G440500	chr3B	97.368	38	1	0	1	38	723498673	723498636	5.890000e-07	65.8
31	TraesCS3A01G440500	chr7D	83.582	134	18	4	427	557	63561557	63561425	3.440000e-24	122.0
32	TraesCS3A01G440500	chr1B	85.246	122	14	4	440	557	69830300	69830179	3.440000e-24	122.0

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	TraesCS3A01G440500	chr3A	683235703	683238251	2548	True	4708.0	4708	100.000	1	2549	1	chr3A.!!$R1	2548
1	TraesCS3A01G440500	chr2A	775966002	775967963	1961	True	3306.0	3306	97.010	578	2549	1	chr2A.!!$R1	1971
2	TraesCS3A01G440500	chr2A	771778414	771780391	1977	False	3208.0	3208	95.980	574	2549	1	chr2A.!!$F2	1975
3	TraesCS3A01G440500	chr2A	744582024	744583965	1941	False	2970.0	2970	94.088	574	2549	1	chr2A.!!$F1	1975
4	TraesCS3A01G440500	chr5A	563443923	563445904	1981	False	3284.0	3284	96.638	573	2549	1	chr5A.!!$F1	1976
5	TraesCS3A01G440500	chr7A	49208209	49210188	1979	False	3278.0	3278	96.628	578	2549	1	chr7A.!!$F1	1971
6	TraesCS3A01G440500	chr7A	150201073	150203041	1968	True	3158.0	3158	95.628	576	2549	1	chr7A.!!$R1	1973
7	TraesCS3A01G440500	chr7A	689994404	689996369	1965	True	3142.0	3142	95.521	579	2549	1	chr7A.!!$R5	1970
8	TraesCS3A01G440500	chr7A	622758905	622760862	1957	True	2569.0	2569	90.460	579	2549	1	chr7A.!!$R3	1970
9	TraesCS3A01G440500	chr1A	50511100	50513087	1987	False	3267.0	3267	96.436	573	2548	1	chr1A.!!$F1	1975
10	TraesCS3A01G440500	chr6A	203518959	203520912	1953	True	3208.0	3208	96.199	579	2549	1	chr6A.!!$R1	1970
11	TraesCS3A01G440500	chr1D	17038772	17040738	1966	True	2813.0	2813	92.546	577	2549	1	chr1D.!!$R1	1972
12	TraesCS3A01G440500	chr5D	114516307	114518030	1723	False	2383.0	2383	91.757	571	2290	1	chr5D.!!$F1	1719
13	TraesCS3A01G440500	chr2D	435209597	435210809	1212	False	1712.0	1712	91.832	577	1836	1	chr2D.!!$F1	1259
14	TraesCS3A01G440500	chr7B	734145282	734146426	1144	False	1635.0	1635	92.288	570	1734	1	chr7B.!!$F2	1164
15	TraesCS3A01G440500	chr3D	546467201	546468009	808	True	241.7	580	95.651	1	557	4	chr3D.!!$R1	556

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
892	1197	0.323816	AGTGACCATGGCGAGAGAGA	60.324	55.0	13.04	0.0	0.0	3.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2062	2557	0.752009	TTTGGCACCTGGCGTAAACA	60.752	50.0	0.0	0.0	46.16	2.83	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
45	46	7.281324	TCAACCAATTATGAATAACAGTACCGG	59.719	37.037	0.00	0.00	0.00	5.28
50	66	8.926710	CAATTATGAATAACAGTACCGGAGATC	58.073	37.037	9.46	0.00	0.00	2.75
69	85	4.219507	AGATCCGTGCAATACCTATCTCAG	59.780	45.833	0.00	0.00	0.00	3.35
97	113	6.767902	GGTTGCATAGTGGAAAAGAGATCATA	59.232	38.462	0.00	0.00	26.96	2.15
187	441	3.320826	TCGCCTTAGTATAAGATGCAGCA	59.679	43.478	4.07	0.00	0.00	4.41
227	481	7.770433	AGCTATGCAAATAACACTGAAGTCATA	59.230	33.333	0.00	0.00	0.00	2.15
237	491	9.897744	ATAACACTGAAGTCATACATTTTTGTG	57.102	29.630	0.00	0.00	0.00	3.33
288	542	8.507524	AATTCAACTTTAAGTATGACCCTAGC	57.492	34.615	0.00	0.00	0.00	3.42
328	582	8.633408	CATTTCGACTTGCTAATTTGAGAAAAG	58.367	33.333	0.00	0.00	0.00	2.27
347	601	7.298374	AGAAAAGGAAAACAACTAATCCCTCT	58.702	34.615	0.00	0.00	32.15	3.69
361	615	9.614792	AACTAATCCCTCTGTTCACAAATATAC	57.385	33.333	0.00	0.00	0.00	1.47
374	628	8.818057	GTTCACAAATATACGATGCTCTTAACT	58.182	33.333	0.00	0.00	0.00	2.24
405	659	6.422100	GCGATTCAGATGTACATAGACATGTT	59.578	38.462	8.71	0.00	42.98	2.71
420	674	5.057149	AGACATGTTTTAGTGTGTCTGTCC	58.943	41.667	0.00	0.00	46.80	4.02
439	693	6.552725	TCTGTCCACTCATATAAGATGCTCTT	59.447	38.462	4.26	4.26	40.35	2.85
450	704	9.455847	CATATAAGATGCTCTTAACTTTTTGCC	57.544	33.333	8.92	0.00	41.72	4.52
455	709	4.545610	TGCTCTTAACTTTTTGCCATTCG	58.454	39.130	0.00	0.00	0.00	3.34
461	715	3.302365	ACTTTTTGCCATTCGGATGTG	57.698	42.857	2.31	0.00	0.00	3.21
466	720	1.596603	TGCCATTCGGATGTGCATAG	58.403	50.000	13.81	0.00	35.75	2.23
480	734	5.295431	TGTGCATAGACATGTTTTAGTGC	57.705	39.130	0.00	6.94	34.40	4.40
497	751	1.461127	GTGCGTCTGTCCACTCATTTC	59.539	52.381	0.00	0.00	0.00	2.17
504	758	1.691976	TGTCCACTCATTTCAGTCCGT	59.308	47.619	0.00	0.00	0.00	4.69
517	771	8.593679	TCATTTCAGTCCGTATGTAATCCATAT	58.406	33.333	0.00	0.00	38.29	1.78
557	811	8.642869	ACATCCTATATTTATAAGGGAGGGAGA	58.357	37.037	0.00	0.00	0.00	3.71
558	812	8.929487	CATCCTATATTTATAAGGGAGGGAGAC	58.071	40.741	0.00	0.00	0.00	3.36
559	813	8.019537	TCCTATATTTATAAGGGAGGGAGACA	57.980	38.462	5.46	0.00	0.00	3.41
560	814	8.123130	TCCTATATTTATAAGGGAGGGAGACAG	58.877	40.741	5.46	0.00	0.00	3.51
561	815	7.345914	CCTATATTTATAAGGGAGGGAGACAGG	59.654	44.444	0.00	0.00	0.00	4.00
562	816	3.346146	TTATAAGGGAGGGAGACAGGG	57.654	52.381	0.00	0.00	0.00	4.45
563	817	1.330155	ATAAGGGAGGGAGACAGGGA	58.670	55.000	0.00	0.00	0.00	4.20
564	818	0.637195	TAAGGGAGGGAGACAGGGAG	59.363	60.000	0.00	0.00	0.00	4.30
565	819	1.456518	AAGGGAGGGAGACAGGGAGT	61.457	60.000	0.00	0.00	0.00	3.85
566	820	0.555369	AGGGAGGGAGACAGGGAGTA	60.555	60.000	0.00	0.00	0.00	2.59
567	821	0.563672	GGGAGGGAGACAGGGAGTAT	59.436	60.000	0.00	0.00	0.00	2.12
568	822	1.062044	GGGAGGGAGACAGGGAGTATT	60.062	57.143	0.00	0.00	0.00	1.89
598	852	5.126384	TCAAGGGTTAATTATCCTTTTGCCG	59.874	40.000	14.44	6.85	38.70	5.69
601	855	4.496840	GGGTTAATTATCCTTTTGCCGTCG	60.497	45.833	11.51	0.00	0.00	5.12
892	1197	0.323816	AGTGACCATGGCGAGAGAGA	60.324	55.000	13.04	0.00	0.00	3.10
930	1311	2.579201	GCGGGAAGCTAGCTGTGA	59.421	61.111	20.16	0.00	44.04	3.58
1137	1519	1.486310	CCGAGGAACCAGAATCATCCA	59.514	52.381	0.00	0.00	34.30	3.41
1749	2181	3.246403	GCTCTCTGCTCTGCCTTTT	57.754	52.632	0.00	0.00	38.95	2.27
1788	2220	2.881403	GCTCTTGGGCCAAATTCAGAGA	60.881	50.000	28.21	16.60	0.00	3.10
1998	2493	7.026631	TGGAGCTGTTAATTAATCCAATTCG	57.973	36.000	13.50	0.00	37.93	3.34
2062	2557	1.118838	GTGCCTCAGCTCTGGTAGAT	58.881	55.000	3.75	0.00	40.80	1.98
2226	2724	1.671054	GTGTTTAGGGCTGCGCTGA	60.671	57.895	27.01	17.69	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	4.218635	TGAGATAGGTATTGCACGGATCTC	59.781	45.833	10.86	10.86	41.76	2.75
50	66	4.302455	CTTCTGAGATAGGTATTGCACGG	58.698	47.826	0.00	0.00	0.00	4.94
63	79	3.776969	TCCACTATGCAACCTTCTGAGAT	59.223	43.478	0.00	0.00	0.00	2.75
69	85	5.003804	TCTCTTTTCCACTATGCAACCTTC	58.996	41.667	0.00	0.00	0.00	3.46
97	113	2.756760	CCAGTTCCATATGCAGCAGTTT	59.243	45.455	0.00	0.00	0.00	2.66
187	441	1.860950	CATAGCTTGCTCGCATTACGT	59.139	47.619	0.00	0.00	44.19	3.57
328	582	5.768164	TGAACAGAGGGATTAGTTGTTTTCC	59.232	40.000	0.00	0.00	32.58	3.13
340	594	6.479972	TCGTATATTTGTGAACAGAGGGAT	57.520	37.500	0.00	0.00	0.00	3.85
347	601	8.600625	GTTAAGAGCATCGTATATTTGTGAACA	58.399	33.333	0.00	0.00	42.67	3.18
439	693	4.804108	CACATCCGAATGGCAAAAAGTTA	58.196	39.130	0.00	0.00	37.19	2.24
450	704	3.811497	ACATGTCTATGCACATCCGAATG	59.189	43.478	0.00	0.00	37.85	2.67
455	709	6.489675	CACTAAAACATGTCTATGCACATCC	58.510	40.000	0.00	0.00	37.85	3.51
461	715	4.330074	AGACGCACTAAAACATGTCTATGC	59.670	41.667	0.00	4.70	37.85	3.14
466	720	3.120649	GGACAGACGCACTAAAACATGTC	60.121	47.826	0.00	0.00	36.06	3.06
480	734	2.989840	GACTGAAATGAGTGGACAGACG	59.010	50.000	0.00	0.00	33.53	4.18
557	811	6.800890	ACCCTTGAAATTTAATACTCCCTGT	58.199	36.000	0.00	0.00	0.00	4.00
558	812	7.718334	AACCCTTGAAATTTAATACTCCCTG	57.282	36.000	0.00	0.00	0.00	4.45
598	852	0.884704	AGCACATGAACACCACCGAC	60.885	55.000	0.00	0.00	0.00	4.79
601	855	0.877071	CTGAGCACATGAACACCACC	59.123	55.000	0.00	0.00	0.00	4.61
892	1197	0.748005	GCCGTGCTCTCTCTCTCTCT	60.748	60.000	0.00	0.00	0.00	3.10
1045	1427	2.042259	CAGGCATGTCCACACGCAT	61.042	57.895	0.00	0.00	36.69	4.73
1046	1428	2.669229	CAGGCATGTCCACACGCA	60.669	61.111	0.00	0.00	36.69	5.24
1137	1519	0.526211	TCTCGCTGCACACGTAGAAT	59.474	50.000	0.00	0.00	0.00	2.40
1650	2079	9.277565	CATATTTAAATGTTGGTCACTTCTTCG	57.722	33.333	11.05	0.00	0.00	3.79
1788	2220	1.298014	GCCTGCACTTGGCTCTACT	59.702	57.895	8.16	0.00	46.38	2.57
2062	2557	0.752009	TTTGGCACCTGGCGTAAACA	60.752	50.000	0.00	0.00	46.16	2.83
2226	2724	1.344763	GCCATCTGTCCTAGCGGTTAT	59.655	52.381	0.00	0.00	0.00	1.89

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.