AutoCloner

Multiple sequence alignment - TraesCS3A01G085300

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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	TraesCS3A01G085300	chr3A	100.000	6157	0	0	1	6157	55030272	55036428	0.000000e+00	11370.0
1	TraesCS3A01G085300	chr3A	79.594	1181	167	42	4071	5187	509542599	509543769	0.000000e+00	778.0
2	TraesCS3A01G085300	chr3A	85.714	721	78	12	2945	3654	54937938	54938644	0.000000e+00	737.0
3	TraesCS3A01G085300	chr3A	77.158	1309	233	45	2753	4024	509541343	509542622	0.000000e+00	701.0
4	TraesCS3A01G085300	chr3A	81.728	602	91	13	1922	2518	509540367	509540954	9.280000e-133	484.0
5	TraesCS3A01G085300	chr3A	84.434	212	27	5	235	445	170737609	170737815	2.910000e-48	204.0
6	TraesCS3A01G085300	chr3A	82.328	232	32	6	226	454	700416137	700416362	6.300000e-45	193.0
7	TraesCS3A01G085300	chr3B	92.063	2646	142	20	3554	6157	66875927	66878546	0.000000e+00	3661.0
8	TraesCS3A01G085300	chr3B	87.136	2542	202	51	887	3359	66873179	66875664	0.000000e+00	2767.0
9	TraesCS3A01G085300	chr3B	79.547	1193	171	40	4071	5198	505267340	505268524	0.000000e+00	784.0
10	TraesCS3A01G085300	chr3B	78.411	1070	182	33	2983	4024	505266315	505267363	0.000000e+00	651.0
11	TraesCS3A01G085300	chr3B	79.253	723	123	20	1802	2518	505264913	505265614	4.320000e-131	479.0
12	TraesCS3A01G085300	chr3B	85.714	168	21	2	1007	1174	505263833	505263997	2.280000e-39	174.0
13	TraesCS3A01G085300	chr3D	93.609	2222	93	21	3949	6157	43009274	43011459	0.000000e+00	3271.0
14	TraesCS3A01G085300	chr3D	88.570	2091	151	32	849	2922	43006262	43008281	0.000000e+00	2457.0
15	TraesCS3A01G085300	chr3D	88.100	1000	82	14	2947	3913	43008278	43009273	0.000000e+00	1153.0
16	TraesCS3A01G085300	chr3D	77.515	1312	223	56	2753	4024	388446461	388447740	0.000000e+00	723.0
17	TraesCS3A01G085300	chr3D	84.601	539	76	3	4638	5169	388448335	388448873	4.230000e-146	529.0
18	TraesCS3A01G085300	chr3D	79.778	722	120	20	1802	2518	388445404	388446104	9.210000e-138	501.0
19	TraesCS3A01G085300	chr3D	82.780	482	55	17	4071	4530	388447717	388448192	7.430000e-109	405.0
20	TraesCS3A01G085300	chr3D	84.971	173	20	3	1005	1174	388444393	388444562	2.950000e-38	171.0
21	TraesCS3A01G085300	chr4D	90.312	640	47	6	1383	2018	509552377	509553005	0.000000e+00	824.0
22	TraesCS3A01G085300	chr6B	89.688	640	55	5	1383	2018	139414013	139414645	0.000000e+00	806.0
23	TraesCS3A01G085300	chr6B	85.714	126	13	2	450	570	680740115	680740240	1.800000e-25	128.0
24	TraesCS3A01G085300	chr4B	89.219	640	58	4	1383	2018	488091667	488091035	0.000000e+00	789.0
25	TraesCS3A01G085300	chr4B	89.062	640	59	3	1383	2018	469360682	469360050	0.000000e+00	784.0
26	TraesCS3A01G085300	chr4B	85.714	126	9	4	450	572	55753500	55753619	2.330000e-24	124.0
27	TraesCS3A01G085300	chr1B	89.219	640	58	4	1383	2018	546249155	546249787	0.000000e+00	789.0
28	TraesCS3A01G085300	chr1B	85.345	232	28	2	4296	4524	428108897	428109125	1.030000e-57	235.0
29	TraesCS3A01G085300	chr1B	85.227	176	22	3	3757	3928	428108494	428108669	1.760000e-40	178.0
30	TraesCS3A01G085300	chr5B	89.097	642	57	6	1383	2018	327987338	327987972	0.000000e+00	785.0
31	TraesCS3A01G085300	chr5B	89.062	640	54	5	1383	2018	245728699	245729326	0.000000e+00	780.0
32	TraesCS3A01G085300	chr5B	84.360	211	30	3	235	445	659301312	659301519	2.910000e-48	204.0
33	TraesCS3A01G085300	chr6A	78.214	459	89	10	3571	4021	148530817	148530362	3.630000e-72	283.0
34	TraesCS3A01G085300	chr6A	80.548	365	44	14	3016	3361	148531394	148531038	7.920000e-64	255.0
35	TraesCS3A01G085300	chr6A	83.673	245	32	7	4287	4528	148530190	148529951	2.230000e-54	224.0
36	TraesCS3A01G085300	chr6A	83.412	211	32	2	235	445	558457703	558457496	6.300000e-45	193.0
37	TraesCS3A01G085300	chr6A	83.412	211	32	2	235	445	558461023	558460816	6.300000e-45	193.0
38	TraesCS3A01G085300	chr6A	95.122	41	1	1	152	192	580790022	580789983	5.150000e-06	63.9
39	TraesCS3A01G085300	chr1D	86.207	232	26	2	4296	4524	316010132	316010360	4.770000e-61	246.0
40	TraesCS3A01G085300	chr1D	84.434	212	28	3	235	445	18864560	18864767	2.910000e-48	204.0
41	TraesCS3A01G085300	chr1D	84.181	177	22	5	3757	3928	316009722	316009897	3.820000e-37	167.0
42	TraesCS3A01G085300	chr2B	84.112	214	32	2	235	448	174594124	174593913	8.090000e-49	206.0
43	TraesCS3A01G085300	chr2B	83.796	216	26	6	235	446	626881475	626881265	4.870000e-46	196.0
44	TraesCS3A01G085300	chrUn	83.491	212	31	3	235	445	171112599	171112391	1.750000e-45	195.0
45	TraesCS3A01G085300	chr1A	83.708	178	21	6	3757	3928	396450857	396451032	1.780000e-35	161.0

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	TraesCS3A01G085300	chr3A	55030272	55036428	6156	False	11370.000000	11370	100.000000	1	6157	1	chr3A.!!$F2	6156
1	TraesCS3A01G085300	chr3A	54937938	54938644	706	False	737.000000	737	85.714000	2945	3654	1	chr3A.!!$F1	709
2	TraesCS3A01G085300	chr3A	509540367	509543769	3402	False	654.333333	778	79.493333	1922	5187	3	chr3A.!!$F5	3265
3	TraesCS3A01G085300	chr3B	66873179	66878546	5367	False	3214.000000	3661	89.599500	887	6157	2	chr3B.!!$F1	5270
4	TraesCS3A01G085300	chr3B	505263833	505268524	4691	False	522.000000	784	80.731250	1007	5198	4	chr3B.!!$F2	4191
5	TraesCS3A01G085300	chr3D	43006262	43011459	5197	False	2293.666667	3271	90.093000	849	6157	3	chr3D.!!$F1	5308
6	TraesCS3A01G085300	chr3D	388444393	388448873	4480	False	465.800000	723	81.929000	1005	5169	5	chr3D.!!$F2	4164
7	TraesCS3A01G085300	chr4D	509552377	509553005	628	False	824.000000	824	90.312000	1383	2018	1	chr4D.!!$F1	635
8	TraesCS3A01G085300	chr6B	139414013	139414645	632	False	806.000000	806	89.688000	1383	2018	1	chr6B.!!$F1	635
9	TraesCS3A01G085300	chr4B	488091035	488091667	632	True	789.000000	789	89.219000	1383	2018	1	chr4B.!!$R2	635
10	TraesCS3A01G085300	chr4B	469360050	469360682	632	True	784.000000	784	89.062000	1383	2018	1	chr4B.!!$R1	635
11	TraesCS3A01G085300	chr1B	546249155	546249787	632	False	789.000000	789	89.219000	1383	2018	1	chr1B.!!$F1	635
12	TraesCS3A01G085300	chr1B	428108494	428109125	631	False	206.500000	235	85.286000	3757	4524	2	chr1B.!!$F2	767
13	TraesCS3A01G085300	chr5B	327987338	327987972	634	False	785.000000	785	89.097000	1383	2018	1	chr5B.!!$F2	635
14	TraesCS3A01G085300	chr5B	245728699	245729326	627	False	780.000000	780	89.062000	1383	2018	1	chr5B.!!$F1	635
15	TraesCS3A01G085300	chr6A	148529951	148531394	1443	True	254.000000	283	80.811667	3016	4528	3	chr6A.!!$R2	1512
16	TraesCS3A01G085300	chr1D	316009722	316010360	638	False	206.500000	246	85.194000	3757	4524	2	chr1D.!!$F2	767

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
433	434	0.034670	AGCATGGGAAGAGAACAGGC	60.035	55.000	0.0	0.0	41.70	4.85	F
1401	1416	0.030638	TGCTCGCAAGGTTCTTTTGC	59.969	50.000	0.1	0.1	45.64	3.68	F
1908	2332	0.593128	ATTCGTCACAGCAACCAAGC	59.407	50.000	0.0	0.0	0.00	4.01	F
2608	3066	2.368439	GCATACTGCAATCACCCAGAA	58.632	47.619	0.0	0.0	44.26	3.02	F
2811	3523	0.248907	GCAGTCATGTGCCATGCATC	60.249	55.000	0.0	0.0	41.91	3.91	F
4692	5717	0.029267	ATCCCTGCCTCCTCCAGATT	60.029	55.000	0.0	0.0	32.03	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1429	1445	0.106521	CCAGCAAAACCACCCAAAGG	59.893	55.000	40.04	3.11	R
2730	3210	0.258774	AACAAGTCACCAGGCAACCT	59.741	50.000	37.17	3.50	R
2731	3211	0.668535	GAACAAGTCACCAGGCAACC	59.331	55.000	37.17	3.77	R
4381	5370	0.878961	GCCAATGGGGACGACGATAC	60.879	60.000	40.01	2.24	R
4782	5810	0.617413	AGGATCTGAGCTGTGGGTTG	59.383	55.000	0.00	3.77	R
5516	6581	1.066858	TGCTGGTTCCTAGAGAAAGCG	60.067	52.381	40.01	4.68	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	Hairpin	End Stability
31	32	6.935741	TCGTGTTATTTATGAAATGGAGGG	57.064	37.500	32.38	4.30
32	33	6.654959	TCGTGTTATTTATGAAATGGAGGGA	58.345	36.000	32.38	4.20
33	34	6.540914	TCGTGTTATTTATGAAATGGAGGGAC	59.459	38.462	32.38	4.46
34	35	6.317642	CGTGTTATTTATGAAATGGAGGGACA	59.682	38.462	32.38	4.02
35	36	7.013274	CGTGTTATTTATGAAATGGAGGGACAT	59.987	37.037	32.38	3.06
36	37	8.137437	GTGTTATTTATGAAATGGAGGGACATG	58.863	37.037	32.38	3.21
37	38	7.287466	TGTTATTTATGAAATGGAGGGACATGG	59.713	37.037	32.38	3.66
38	39	5.464588	TTTATGAAATGGAGGGACATGGA	57.535	39.130	0.00	3.41
39	40	5.464588	TTATGAAATGGAGGGACATGGAA	57.535	39.130	0.00	3.53
40	41	3.370840	TGAAATGGAGGGACATGGAAG	57.629	47.619	0.00	3.46
41	42	2.025037	TGAAATGGAGGGACATGGAAGG	60.025	50.000	0.00	3.46
42	43	1.686236	AATGGAGGGACATGGAAGGT	58.314	50.000	0.00	3.50
43	44	0.921896	ATGGAGGGACATGGAAGGTG	59.078	55.000	0.00	4.00
44	45	1.077429	GGAGGGACATGGAAGGTGC	60.077	63.158	38.61	5.01
45	46	1.685224	GAGGGACATGGAAGGTGCA	59.315	57.895	42.20	4.57
46	47	0.393537	GAGGGACATGGAAGGTGCAG	60.394	60.000	42.20	4.41
47	48	1.136329	AGGGACATGGAAGGTGCAGT	61.136	55.000	42.20	4.40
48	49	0.678048	GGGACATGGAAGGTGCAGTC	60.678	60.000	42.20	3.51
49	50	0.036732	GGACATGGAAGGTGCAGTCA	59.963	55.000	39.37	3.41
50	51	1.545428	GGACATGGAAGGTGCAGTCAA	60.545	52.381	39.37	3.18
51	52	2.229792	GACATGGAAGGTGCAGTCAAA	58.770	47.619	0.00	2.69
52	53	2.821969	GACATGGAAGGTGCAGTCAAAT	59.178	45.455	0.00	2.32
53	54	4.009675	GACATGGAAGGTGCAGTCAAATA	58.990	43.478	0.00	1.40
54	55	4.603131	ACATGGAAGGTGCAGTCAAATAT	58.397	39.130	0.00	1.28
55	56	4.400251	ACATGGAAGGTGCAGTCAAATATG	59.600	41.667	0.00	1.78

Showing 1 to 25 of 652 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
5	6	8.413229	CCCTCCATTTCATAAATAACACGATTT	58.587	33.333	33.60	2.17
6	7	7.777910	TCCCTCCATTTCATAAATAACACGATT	59.222	33.333	0.00	3.34
7	8	7.228706	GTCCCTCCATTTCATAAATAACACGAT	59.771	37.037	0.00	3.73
8	9	6.540914	GTCCCTCCATTTCATAAATAACACGA	59.459	38.462	0.00	4.35
9	10	6.317642	TGTCCCTCCATTTCATAAATAACACG	59.682	38.462	0.00	4.49
10	11	7.639113	TGTCCCTCCATTTCATAAATAACAC	57.361	36.000	0.00	3.32
11	12	7.287466	CCATGTCCCTCCATTTCATAAATAACA	59.713	37.037	0.00	2.41
12	13	7.505585	TCCATGTCCCTCCATTTCATAAATAAC	59.494	37.037	0.00	1.89
13	14	7.590907	TCCATGTCCCTCCATTTCATAAATAA	58.409	34.615	0.00	1.40
14	15	7.160457	TCCATGTCCCTCCATTTCATAAATA	57.840	36.000	0.00	1.40
15	16	6.029492	TCCATGTCCCTCCATTTCATAAAT	57.971	37.500	0.00	1.40
16	17	5.464588	TCCATGTCCCTCCATTTCATAAA	57.535	39.130	0.00	1.40
17	18	5.448654	CTTCCATGTCCCTCCATTTCATAA	58.551	41.667	0.00	1.90
18	19	4.141181	CCTTCCATGTCCCTCCATTTCATA	60.141	45.833	0.00	2.15
19	20	3.373438	CCTTCCATGTCCCTCCATTTCAT	60.373	47.826	0.00	2.57
20	21	2.025037	CCTTCCATGTCCCTCCATTTCA	60.025	50.000	0.00	2.69
21	22	2.024941	ACCTTCCATGTCCCTCCATTTC	60.025	50.000	0.00	2.17
22	23	2.003072	ACCTTCCATGTCCCTCCATTT	58.997	47.619	0.00	2.32
23	24	1.285962	CACCTTCCATGTCCCTCCATT	59.714	52.381	0.00	3.16
24	25	0.921896	CACCTTCCATGTCCCTCCAT	59.078	55.000	0.00	3.41
25	26	1.852157	GCACCTTCCATGTCCCTCCA	61.852	60.000	0.00	3.86
26	27	1.077429	GCACCTTCCATGTCCCTCC	60.077	63.158	0.00	4.30
27	28	0.393537	CTGCACCTTCCATGTCCCTC	60.394	60.000	0.00	4.30
28	29	1.136329	ACTGCACCTTCCATGTCCCT	61.136	55.000	0.00	4.20
29	30	0.678048	GACTGCACCTTCCATGTCCC	60.678	60.000	0.00	4.46

Showing 1 to 25 of 661 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.