AutoCloner

Multiple sequence alignment - TraesCS4D01G137100

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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	TraesCS4D01G137100	chr4D	100.000	3989	0	0	438	4426	123147206	123143218	0.000000e+00	7367.0
1	TraesCS4D01G137100	chr4D	100.000	91	0	0	1	91	123147643	123147553	7.610000e-38	169.0
2	TraesCS4D01G137100	chr4B	93.931	3625	149	35	835	4426	187732982	187729396	0.000000e+00	5409.0
3	TraesCS4D01G137100	chr4B	91.190	420	16	7	439	851	187734564	187734159	6.470000e-153	551.0
4	TraesCS4D01G137100	chr4B	93.204	103	2	1	4324	4426	187729178	187729081	3.570000e-31	147.0
5	TraesCS4D01G137100	chr4B	100.000	36	0	0	12	47	187734899	187734864	2.860000e-07	67.6
6	TraesCS4D01G137100	chr1B	93.290	3711	168	31	439	4115	173132340	173128677	0.000000e+00	5398.0
7	TraesCS4D01G137100	chr1B	94.444	90	3	1	4318	4405	173126671	173126582	2.150000e-28	137.0
8	TraesCS4D01G137100	chr1B	92.593	81	4	2	4014	4092	583972424	583972344	1.010000e-21	115.0
9	TraesCS4D01G137100	chr4A	94.957	3113	137	10	991	4096	446608848	446611947	0.000000e+00	4861.0
10	TraesCS4D01G137100	chr4A	93.352	361	12	5	439	792	446594803	446595158	1.410000e-144	523.0
11	TraesCS4D01G137100	chr4A	97.619	84	2	0	3	86	446594609	446594692	1.280000e-30	145.0
12	TraesCS4D01G137100	chr1A	96.385	2545	85	5	1393	3934	121135463	121132923	0.000000e+00	4183.0
13	TraesCS4D01G137100	chr1A	89.804	971	57	21	439	1396	121136567	121135626	0.000000e+00	1206.0
14	TraesCS4D01G137100	chr1A	91.979	187	10	4	4207	4392	121132227	121132045	1.580000e-64	257.0
15	TraesCS4D01G137100	chr1A	87.755	147	12	4	3951	4092	121132500	121132355	2.740000e-37	167.0
16	TraesCS4D01G137100	chr1A	92.308	91	4	2	3	91	121136762	121136673	4.650000e-25	126.0
17	TraesCS4D01G137100	chr7D	93.453	1665	87	12	1623	3277	590451994	590450342	0.000000e+00	2451.0
18	TraesCS4D01G137100	chr7D	88.435	882	66	12	765	1621	590518835	590517965	0.000000e+00	1031.0
19	TraesCS4D01G137100	chr7D	88.073	327	23	4	3272	3582	590447425	590447099	1.500000e-99	374.0
20	TraesCS4D01G137100	chr7D	78.723	235	31	10	3870	4092	590446937	590446710	5.970000e-29	139.0
21	TraesCS4D01G137100	chr7D	100.000	34	0	0	3646	3679	590447076	590447043	3.700000e-06	63.9
22	TraesCS4D01G137100	chr5D	82.391	460	47	21	482	920	487291668	487291222	1.940000e-98	370.0
23	TraesCS4D01G137100	chr5D	91.016	256	22	1	1567	1821	119459884	119460139	1.180000e-90	344.0
24	TraesCS4D01G137100	chrUn	91.700	253	20	1	1570	1821	261868755	261869007	2.530000e-92	350.0
25	TraesCS4D01G137100	chr2D	91.700	253	20	1	1570	1821	453710421	453710169	2.530000e-92	350.0
26	TraesCS4D01G137100	chr6D	90.347	259	21	3	1567	1821	285487738	285487996	1.970000e-88	337.0
27	TraesCS4D01G137100	chr2A	81.935	155	18	7	712	866	566598291	566598435	6.010000e-24	122.0
28	TraesCS4D01G137100	chr2A	94.595	74	3	1	4020	4092	24307380	24307453	3.620000e-21	113.0
29	TraesCS4D01G137100	chr2A	100.000	28	0	0	4120	4147	380605753	380605780	8.000000e-03	52.8
30	TraesCS4D01G137100	chr2A	100.000	28	0	0	4120	4147	633296440	633296467	8.000000e-03	52.8
31	TraesCS4D01G137100	chr1D	93.590	78	4	1	4016	4092	47880379	47880456	1.010000e-21	115.0
32	TraesCS4D01G137100	chr3B	94.595	74	3	1	4020	4092	617414966	617415039	3.620000e-21	113.0
33	TraesCS4D01G137100	chr3B	92.500	80	4	2	4013	4092	685059170	685059093	3.620000e-21	113.0
34	TraesCS4D01G137100	chr3B	79.339	121	21	4	804	924	405829894	405830010	1.020000e-11	82.4
35	TraesCS4D01G137100	chr3A	92.500	80	4	2	4013	4092	655640244	655640167	3.620000e-21	113.0
36	TraesCS4D01G137100	chr3A	94.366	71	4	0	4022	4092	703902590	703902660	4.680000e-20	110.0

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	TraesCS4D01G137100	chr4D	123143218	123147643	4425	True	3768.000	7367	100.00000	1	4426	2	chr4D.!!$R1	4425
1	TraesCS4D01G137100	chr4B	187729081	187734899	5818	True	1543.650	5409	94.58125	12	4426	4	chr4B.!!$R1	4414
2	TraesCS4D01G137100	chr1B	173126582	173132340	5758	True	2767.500	5398	93.86700	439	4405	2	chr1B.!!$R2	3966
3	TraesCS4D01G137100	chr4A	446608848	446611947	3099	False	4861.000	4861	94.95700	991	4096	1	chr4A.!!$F1	3105
4	TraesCS4D01G137100	chr4A	446594609	446595158	549	False	334.000	523	95.48550	3	792	2	chr4A.!!$F2	789
5	TraesCS4D01G137100	chr1A	121132045	121136762	4717	True	1187.800	4183	91.64620	3	4392	5	chr1A.!!$R1	4389
6	TraesCS4D01G137100	chr7D	590517965	590518835	870	True	1031.000	1031	88.43500	765	1621	1	chr7D.!!$R1	856
7	TraesCS4D01G137100	chr7D	590446710	590451994	5284	True	756.975	2451	90.06225	1623	4092	4	chr7D.!!$R2	2469

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
926	2138	1.904287	TTTGTTTGTAGCTCCGCCAT	58.096	45.000	0.00	0.00	0.00	4.40	F
1596	2988	0.254178	AGCTCCGGATGCTGTGAAAT	59.746	50.000	22.47	2.63	39.56	2.17	F
3233	4636	1.226379	GCGGCCATCGTTGATTGTG	60.226	57.895	2.24	0.00	41.72	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2306	3709	0.039074	CAGTGAAAGACGGTCGCTCT	60.039	55.0	1.89	0.72	33.59	4.09	R
3388	7716	0.169009	GCTCAAATCGACACCTTGCC	59.831	55.0	0.00	0.00	0.00	4.52	R
4138	8921	0.031449	AAAAATGAACACGCCCACCG	59.969	50.0	0.00	0.00	44.21	4.94	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
88	91	6.255950	GGACAACAAACACTGTTTTCTCTAC	58.744	40.000	4.30	0.00	46.49	2.59
616	620	9.494271	TTGTTTACATTTTATGCAAAGCCATTA	57.506	25.926	0.00	0.00	0.00	1.90
617	621	9.664332	TGTTTACATTTTATGCAAAGCCATTAT	57.336	25.926	0.00	0.00	0.00	1.28
713	726	4.214119	ACTCAATTCGTCTGTGGTTTGATG	59.786	41.667	0.00	0.00	0.00	3.07
767	781	9.990868	AAATAGTCTAATGGGGAAACTGTATTT	57.009	29.630	0.00	0.00	0.00	1.40
826	840	7.807977	ACTCACTTGATCTTGTAACAAATGT	57.192	32.000	0.00	0.00	0.00	2.71
841	855	4.642429	ACAAATGTGAACAGAGGGTACTC	58.358	43.478	0.00	0.00	44.31	2.59
849	2055	4.466370	TGAACAGAGGGTACTCACTAATGG	59.534	45.833	0.00	0.00	46.44	3.16
926	2138	1.904287	TTTGTTTGTAGCTCCGCCAT	58.096	45.000	0.00	0.00	0.00	4.40
970	2193	2.749621	CGGCTTTCTAATCCAGCAGTTT	59.250	45.455	0.00	0.00	35.05	2.66
989	2212	6.650372	CAGTTTGTGTTTCTGCTAAGACTAC	58.350	40.000	0.00	0.00	29.98	2.73
1033	2256	1.595109	CAAGCTGTCCTGTGTCGCA	60.595	57.895	0.00	0.00	0.00	5.10
1058	2281	2.932234	CGGCGAACCTGTCTCCAGT	61.932	63.158	0.00	0.00	36.95	4.00
1142	2365	2.647297	GCCTTTGCAGGTCACAGC	59.353	61.111	0.00	0.00	43.18	4.40
1156	2382	4.777896	AGGTCACAGCCTATCTTCTTACAA	59.222	41.667	0.00	0.00	37.04	2.41
1596	2988	0.254178	AGCTCCGGATGCTGTGAAAT	59.746	50.000	22.47	2.63	39.56	2.17
1864	3258	9.853177	TCGGTATGAGATATATAGATGTCATGT	57.147	33.333	23.28	7.71	39.46	3.21
1983	3377	4.995487	CACCCTTACTTCTGTTGGACTTAC	59.005	45.833	0.00	0.00	0.00	2.34
2000	3394	6.148480	TGGACTTACGACTAAGAGTGACTTAC	59.852	42.308	0.00	0.00	39.72	2.34
2306	3709	3.885901	CAGTGATTCATCTAGTCCGAGGA	59.114	47.826	0.00	0.00	0.00	3.71
2498	3901	2.752030	AGTACATGCTCCAAGGCTAGA	58.248	47.619	0.00	0.00	0.00	2.43
2631	4034	2.091555	ACGGAGGAAGAGGCTCTAGATT	60.092	50.000	19.07	0.87	0.00	2.40
2777	4180	2.928116	CGTCCGTCTATCCAAAGGAAAC	59.072	50.000	0.00	0.00	34.34	2.78
3233	4636	1.226379	GCGGCCATCGTTGATTGTG	60.226	57.895	2.24	0.00	41.72	3.33
3285	7610	3.243877	CGCGATGTATGAAGAACTGAAGG	59.756	47.826	0.00	0.00	0.00	3.46
3388	7716	1.404717	CCTTATGGATGCCTCGGATCG	60.405	57.143	0.00	0.00	34.57	3.69
3680	8028	5.086104	TCAAGTGCTATTTCTAGTGTCCC	57.914	43.478	0.00	0.00	0.00	4.46
3684	8032	5.876357	AGTGCTATTTCTAGTGTCCCAAAA	58.124	37.500	0.00	0.00	0.00	2.44
3685	8033	6.485171	AGTGCTATTTCTAGTGTCCCAAAAT	58.515	36.000	0.00	0.00	0.00	1.82
3764	8113	0.604578	CTGGTGAGTTTTGCATGGGG	59.395	55.000	0.00	0.00	0.00	4.96
3820	8170	4.204370	GCGTACTTTGCTTTGTTTCTCAAC	59.796	41.667	0.00	0.00	35.61	3.18
3905	8267	2.288666	GTGACTGGTGTCTGCTGAAAA	58.711	47.619	0.00	0.00	43.29	2.29
3991	8760	4.212636	CCGTTTGTCAACTTTTCCGAGTAT	59.787	41.667	0.00	0.00	0.00	2.12
4020	8789	6.749923	AGAATTAGGATGCTGAAAACTGTC	57.250	37.500	0.00	0.00	0.00	3.51
4082	8857	1.959226	CTTGTGGTCGTGGGTTCGG	60.959	63.158	0.00	0.00	0.00	4.30
4084	8859	3.932483	GTGGTCGTGGGTTCGGGT	61.932	66.667	0.00	0.00	0.00	5.28
4099	8874	4.612412	GGTCCCACGGCGTGTTCA	62.612	66.667	34.74	17.63	0.00	3.18
4126	8909	6.597832	TTTATTAACCACCATTGTCTTGGG	57.402	37.500	0.00	0.00	41.35	4.12
4127	8910	3.603965	TTAACCACCATTGTCTTGGGT	57.396	42.857	0.00	0.00	41.35	4.51
4129	8912	1.995376	ACCACCATTGTCTTGGGTTC	58.005	50.000	0.00	0.00	41.35	3.62
4130	8913	0.881118	CCACCATTGTCTTGGGTTCG	59.119	55.000	0.00	0.00	41.35	3.95
4131	8914	1.544537	CCACCATTGTCTTGGGTTCGA	60.545	52.381	0.00	0.00	41.35	3.71
4132	8915	1.806542	CACCATTGTCTTGGGTTCGAG	59.193	52.381	0.00	0.00	41.35	4.04
4133	8916	0.804989	CCATTGTCTTGGGTTCGAGC	59.195	55.000	0.00	0.00	32.80	5.03
4134	8917	0.804989	CATTGTCTTGGGTTCGAGCC	59.195	55.000	10.28	10.28	36.00	4.70
4152	8935	4.920112	CCACGGTGGGCGTGTTCA	62.920	66.667	19.63	0.00	35.79	3.18
4193	9831	1.629043	TCCTGTGCTTAGAGAACGGT	58.371	50.000	0.00	0.00	27.37	4.83
4195	9833	2.367567	TCCTGTGCTTAGAGAACGGTTT	59.632	45.455	0.00	0.00	27.37	3.27
4196	9834	2.480419	CCTGTGCTTAGAGAACGGTTTG	59.520	50.000	0.00	0.00	27.37	2.93
4197	9835	3.131396	CTGTGCTTAGAGAACGGTTTGT	58.869	45.455	0.00	0.00	0.00	2.83
4199	9837	3.311322	TGTGCTTAGAGAACGGTTTGTTG	59.689	43.478	0.00	0.00	42.09	3.33
4200	9838	2.289547	TGCTTAGAGAACGGTTTGTTGC	59.710	45.455	0.00	0.00	42.09	4.17
4201	9839	2.661979	GCTTAGAGAACGGTTTGTTGCG	60.662	50.000	0.00	0.00	42.09	4.85
4202	9840	2.228138	TAGAGAACGGTTTGTTGCGT	57.772	45.000	0.00	0.00	42.09	5.24
4203	9841	0.655733	AGAGAACGGTTTGTTGCGTG	59.344	50.000	0.00	0.00	42.09	5.34
4204	9842	0.375803	GAGAACGGTTTGTTGCGTGT	59.624	50.000	0.00	0.00	42.09	4.49
4205	9843	0.098025	AGAACGGTTTGTTGCGTGTG	59.902	50.000	0.00	0.00	42.09	3.82
4268	10000	1.615392	GAACATTCCCAGCTGCAGTTT	59.385	47.619	16.64	0.77	0.00	2.66
4304	10036	4.463891	CAGGCCATTACTTTTCCTGTCAAT	59.536	41.667	5.01	0.00	39.45	2.57
4310	10042	7.533426	CCATTACTTTTCCTGTCAATTCTCAG	58.467	38.462	0.83	0.83	0.00	3.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.850098	CTGGTCAGGTGGTGTGGCC	62.850	68.421	0.00	0.00	40.38	5.36
1	2	2.281761	CTGGTCAGGTGGTGTGGC	60.282	66.667	0.00	0.00	0.00	5.01
10	11	0.447801	GTTGCGTTATGCTGGTCAGG	59.552	55.000	0.00	0.00	46.63	3.86
616	620	7.867403	CAGAACAATGCCTAAACTGTAAACAAT	59.133	33.333	0.00	0.00	0.00	2.71
617	621	7.147983	ACAGAACAATGCCTAAACTGTAAACAA	60.148	33.333	0.00	0.00	35.77	2.83
618	622	6.320164	ACAGAACAATGCCTAAACTGTAAACA	59.680	34.615	0.00	0.00	35.77	2.83
662	675	3.281727	TGATACCTGCCAAACTGGATC	57.718	47.619	0.00	0.00	40.96	3.36
676	689	9.046296	AGACGAATTGAGTGAATTATTGATACC	57.954	33.333	0.00	0.00	34.18	2.73
713	726	3.507622	AGCCATTACAAAAGCTTGGAGAC	59.492	43.478	0.00	0.00	36.82	3.36
794	808	9.856488	GTTACAAGATCAAGTGAGTAGACATAA	57.144	33.333	0.00	0.00	0.00	1.90
795	809	9.020731	TGTTACAAGATCAAGTGAGTAGACATA	57.979	33.333	0.00	0.00	0.00	2.29
796	810	7.896811	TGTTACAAGATCAAGTGAGTAGACAT	58.103	34.615	0.00	0.00	0.00	3.06
797	811	7.284919	TGTTACAAGATCAAGTGAGTAGACA	57.715	36.000	0.00	0.00	0.00	3.41
798	812	8.589335	TTTGTTACAAGATCAAGTGAGTAGAC	57.411	34.615	0.00	0.00	0.00	2.59
799	813	9.208022	CATTTGTTACAAGATCAAGTGAGTAGA	57.792	33.333	0.00	0.00	33.00	2.59
826	840	4.466370	CCATTAGTGAGTACCCTCTGTTCA	59.534	45.833	0.00	0.00	38.61	3.18
841	855	4.944962	TTCTGAATCGTTGCCATTAGTG	57.055	40.909	0.00	0.00	0.00	2.74
870	2076	3.128349	AGCTACAGAAGAACGCGAAAAA	58.872	40.909	15.93	0.00	0.00	1.94
886	2092	4.733542	TTGGGCGGGCCAAGCTAC	62.734	66.667	29.82	14.09	37.98	3.58
926	2138	2.127042	GCGTTGATTTCGCCGCAA	60.127	55.556	8.27	0.00	46.61	4.85
970	2193	5.531122	ACTGTAGTCTTAGCAGAAACACA	57.469	39.130	0.00	0.00	34.60	3.72
989	2212	1.645034	CCGCCACATCTTCACTACTG	58.355	55.000	0.00	0.00	0.00	2.74
1058	2281	4.682334	CACCACCAGCCCATGCCA	62.682	66.667	0.00	0.00	38.69	4.92
1142	2365	6.534079	CCCACGTAAAGTTGTAAGAAGATAGG	59.466	42.308	0.00	0.00	0.00	2.57
1276	2502	3.286694	ATTGCCACCATCGCCACCT	62.287	57.895	0.00	0.00	0.00	4.00
1740	3133	5.003160	CACTCAAGAATGACATTACCACCA	58.997	41.667	0.00	0.00	0.00	4.17
1864	3258	4.164822	GCATCTAGCAAAACAAAGAGCA	57.835	40.909	0.00	0.00	44.79	4.26
2011	3405	6.602803	TGCAAAGGCTCAATGTGATATTAAGA	59.397	34.615	0.00	0.00	41.91	2.10
2306	3709	0.039074	CAGTGAAAGACGGTCGCTCT	60.039	55.000	1.89	0.72	33.59	4.09
2498	3901	5.168569	TCACTATCTTCAGCGTTCGAAAAT	58.831	37.500	0.00	0.00	0.00	1.82
2631	4034	1.018840	TCTTCCCCCTCCTCATCTGA	58.981	55.000	0.00	0.00	0.00	3.27
2777	4180	0.827368	GGGCTACCTCCTCTTGTCTG	59.173	60.000	0.00	0.00	0.00	3.51
3233	4636	5.418840	TCCCTCTTCATCTATTTTGTTTGCC	59.581	40.000	0.00	0.00	0.00	4.52
3285	7610	0.606673	GGAACACCTTGCACTCTCCC	60.607	60.000	0.00	0.00	0.00	4.30
3388	7716	0.169009	GCTCAAATCGACACCTTGCC	59.831	55.000	0.00	0.00	0.00	4.52
3739	8088	2.294074	TGCAAAACTCACCAGTACACC	58.706	47.619	0.00	0.00	30.14	4.16
3764	8113	3.686726	CAGTCAAGTTCTTGGTGATAGGC	59.313	47.826	11.82	0.00	0.00	3.93
3905	8267	2.035832	AGTTGCTTAACTTTGGCGCAAT	59.964	40.909	10.83	0.00	41.84	3.56
3953	8721	5.591067	TGACAAACGGTGACCTAAATTCTTT	59.409	36.000	0.00	0.00	0.00	2.52
3991	8760	8.543774	AGTTTTCAGCATCCTAATTCTTCTCTA	58.456	33.333	0.00	0.00	0.00	2.43
4020	8789	0.459237	CTGAGCTAGACGGGCTTGTG	60.459	60.000	0.00	0.00	40.40	3.33
4082	8857	3.894547	ATGAACACGCCGTGGGACC	62.895	63.158	22.60	7.73	37.94	4.46
4084	8859	0.820074	AAAATGAACACGCCGTGGGA	60.820	50.000	22.60	4.84	37.94	4.37
4106	8888	4.126520	ACCCAAGACAATGGTGGTTAAT	57.873	40.909	0.00	0.00	38.91	1.40
4109	8891	2.316108	GAACCCAAGACAATGGTGGTT	58.684	47.619	0.00	0.00	38.91	3.67
4116	8899	3.249687	GGCTCGAACCCAAGACAAT	57.750	52.632	0.00	0.00	0.00	2.71
4138	8921	0.031449	AAAAATGAACACGCCCACCG	59.969	50.000	0.00	0.00	44.21	4.94
4139	8922	3.978460	AAAAATGAACACGCCCACC	57.022	47.368	0.00	0.00	0.00	4.61
4202	9840	0.667487	GCGAGCTCTAGTGTTGCACA	60.667	55.000	12.85	0.00	36.74	4.57
4203	9841	0.667487	TGCGAGCTCTAGTGTTGCAC	60.667	55.000	12.85	0.00	34.10	4.57
4204	9842	0.389037	CTGCGAGCTCTAGTGTTGCA	60.389	55.000	12.85	10.84	0.00	4.08
4205	9843	0.389166	ACTGCGAGCTCTAGTGTTGC	60.389	55.000	16.74	9.56	0.00	4.17
4268	10000	0.189574	TGGCCTGGTGGATCCAAAAA	59.810	50.000	18.20	3.93	46.59	1.94
4304	10036	4.956075	TGTATGTAGATGGACAGCTGAGAA	59.044	41.667	23.35	4.98	31.51	2.87
4310	10042	8.260818	ACCAATATATGTATGTAGATGGACAGC	58.739	37.037	4.63	0.00	31.51	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.