AutoCloner

Multiple sequence alignment - TraesCS3D01G381600

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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	TraesCS3D01G381600	chr3D	100.000	2999	0	0	1	2999	497810791	497807793	0.000000e+00	5539.0
1	TraesCS3D01G381600	chr3D	84.032	739	99	14	998	1731	497820428	497819704	0.000000e+00	693.0
2	TraesCS3D01G381600	chr3D	86.126	382	49	4	1341	1720	497825873	497825494	2.780000e-110	409.0
3	TraesCS3D01G381600	chr3D	84.030	263	38	3	1795	2056	497819616	497819357	1.780000e-62	250.0
4	TraesCS3D01G381600	chr3A	91.803	1403	77	15	807	2173	636697722	636699122	0.000000e+00	1919.0
5	TraesCS3D01G381600	chr3A	81.406	1081	156	28	998	2058	636693993	636695048	0.000000e+00	841.0
6	TraesCS3D01G381600	chr3A	86.579	380	47	4	1341	1718	636690395	636690772	1.660000e-112	416.0
7	TraesCS3D01G381600	chr3A	85.526	380	55	0	1338	1717	654236337	654236716	6.020000e-107	398.0
8	TraesCS3D01G381600	chr3A	85.401	137	20	0	1857	1993	654236850	654236986	3.120000e-30	143.0
9	TraesCS3D01G381600	chr3B	91.673	1225	63	19	807	2021	657954507	657953312	0.000000e+00	1661.0
10	TraesCS3D01G381600	chr3B	91.418	839	60	7	2173	2999	640076803	640077641	0.000000e+00	1140.0
11	TraesCS3D01G381600	chr3B	89.150	682	32	19	807	1478	658019892	658019243	0.000000e+00	811.0
12	TraesCS3D01G381600	chr3B	83.264	723	105	11	998	1717	658060160	658059451	0.000000e+00	651.0
13	TraesCS3D01G381600	chr3B	85.302	381	50	6	1341	1718	658063215	658062838	3.630000e-104	388.0
14	TraesCS3D01G381600	chr3B	94.208	259	8	3	550	807	719898276	719898024	3.630000e-104	388.0
15	TraesCS3D01G381600	chr3B	100.000	35	0	0	524	558	719898332	719898298	6.940000e-07	65.8
16	TraesCS3D01G381600	chr5D	98.778	818	8	2	1	816	533536241	533535424	0.000000e+00	1454.0
17	TraesCS3D01G381600	chr5D	98.837	258	3	0	550	807	412253873	412254130	7.570000e-126	460.0
18	TraesCS3D01G381600	chr5D	100.000	35	0	0	524	558	412253818	412253852	6.940000e-07	65.8
19	TraesCS3D01G381600	chr7B	92.096	835	58	5	2173	2999	113206701	113207535	0.000000e+00	1170.0
20	TraesCS3D01G381600	chr7B	91.756	837	60	6	2172	2999	164084143	164083307	0.000000e+00	1155.0
21	TraesCS3D01G381600	chr7B	90.931	838	63	9	2173	2999	742229876	742229041	0.000000e+00	1114.0
22	TraesCS3D01G381600	chr2B	92.048	830	57	6	2173	2994	736388738	736387910	0.000000e+00	1158.0
23	TraesCS3D01G381600	chr2B	91.377	835	64	5	2173	2999	102980073	102979239	0.000000e+00	1136.0
24	TraesCS3D01G381600	chr2B	91.435	829	64	4	2173	2994	719299211	719298383	0.000000e+00	1131.0
25	TraesCS3D01G381600	chr2B	91.466	832	55	9	2173	2994	210267704	210266879	0.000000e+00	1129.0
26	TraesCS3D01G381600	chr2B	93.514	185	6	2	550	734	768576694	768576516	1.370000e-68	270.0
27	TraesCS3D01G381600	chr2B	98.684	76	1	0	731	806	768576280	768576205	5.210000e-28	135.0
28	TraesCS3D01G381600	chr2B	97.500	40	1	0	524	563	768576749	768576710	5.360000e-08	69.4
29	TraesCS3D01G381600	chr6B	91.548	840	62	6	2169	2999	120822098	120822937	0.000000e+00	1149.0
30	TraesCS3D01G381600	chr6B	95.217	230	11	0	92	321	57581841	57582070	6.110000e-97	364.0
31	TraesCS3D01G381600	chr6B	91.346	208	11	4	320	523	57582137	57582341	8.190000e-71	278.0
32	TraesCS3D01G381600	chr6B	82.692	260	36	7	1	254	62404802	62404546	3.890000e-54	222.0
33	TraesCS3D01G381600	chr6B	78.816	321	58	9	1	319	57452744	57453056	1.090000e-49	207.0
34	TraesCS3D01G381600	chr6D	96.904	323	10	0	1	323	30067426	30067104	2.630000e-150	542.0
35	TraesCS3D01G381600	chr6D	91.346	208	14	3	320	523	30067039	30066832	6.330000e-72	281.0
36	TraesCS3D01G381600	chr6D	78.395	324	57	11	1	319	30079025	30078710	6.560000e-47	198.0
37	TraesCS3D01G381600	chr5B	95.349	258	5	3	550	807	608629870	608629620	1.290000e-108	403.0
38	TraesCS3D01G381600	chr5B	100.000	35	0	0	524	558	608629925	608629891	6.940000e-07	65.8
39	TraesCS3D01G381600	chr7A	94.942	257	6	3	550	806	660474119	660473870	2.170000e-106	396.0
40	TraesCS3D01G381600	chr7A	94.141	256	7	4	555	810	16019554	16019307	1.690000e-102	383.0
41	TraesCS3D01G381600	chr7A	100.000	35	0	0	524	558	16019613	16019579	6.940000e-07	65.8
42	TraesCS3D01G381600	chr7A	100.000	35	0	0	524	558	660474174	660474140	6.940000e-07	65.8
43	TraesCS3D01G381600	chr4A	94.694	245	6	3	550	794	718028584	718028347	1.020000e-99	374.0
44	TraesCS3D01G381600	chr4A	95.031	161	5	1	550	710	676213761	676213918	1.780000e-62	250.0
45	TraesCS3D01G381600	chr4A	95.455	110	5	0	698	807	676215485	676215594	3.070000e-40	176.0
46	TraesCS3D01G381600	chr4A	100.000	35	0	0	524	558	718028639	718028605	6.940000e-07	65.8
47	TraesCS3D01G381600	chr6A	83.012	259	37	5	1	254	34178275	34178531	8.360000e-56	228.0
48	TraesCS3D01G381600	chrUn	78.354	328	55	12	1	323	27038695	27039011	6.560000e-47	198.0
49	TraesCS3D01G381600	chrUn	78.395	324	57	10	1	319	27965018	27964703	6.560000e-47	198.0

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	TraesCS3D01G381600	chr3D	497807793	497810791	2998	True	5539.000000	5539	100.0000	1	2999	1	chr3D.!!$R1	2998
1	TraesCS3D01G381600	chr3D	497819357	497820428	1071	True	471.500000	693	84.0310	998	2056	2	chr3D.!!$R3	1058
2	TraesCS3D01G381600	chr3A	636690395	636699122	8727	False	1058.666667	1919	86.5960	807	2173	3	chr3A.!!$F1	1366
3	TraesCS3D01G381600	chr3A	654236337	654236986	649	False	270.500000	398	85.4635	1338	1993	2	chr3A.!!$F2	655
4	TraesCS3D01G381600	chr3B	657953312	657954507	1195	True	1661.000000	1661	91.6730	807	2021	1	chr3B.!!$R1	1214
5	TraesCS3D01G381600	chr3B	640076803	640077641	838	False	1140.000000	1140	91.4180	2173	2999	1	chr3B.!!$F1	826
6	TraesCS3D01G381600	chr3B	658019243	658019892	649	True	811.000000	811	89.1500	807	1478	1	chr3B.!!$R2	671
7	TraesCS3D01G381600	chr3B	658059451	658063215	3764	True	519.500000	651	84.2830	998	1718	2	chr3B.!!$R3	720
8	TraesCS3D01G381600	chr5D	533535424	533536241	817	True	1454.000000	1454	98.7780	1	816	1	chr5D.!!$R1	815
9	TraesCS3D01G381600	chr7B	113206701	113207535	834	False	1170.000000	1170	92.0960	2173	2999	1	chr7B.!!$F1	826
10	TraesCS3D01G381600	chr7B	164083307	164084143	836	True	1155.000000	1155	91.7560	2172	2999	1	chr7B.!!$R1	827
11	TraesCS3D01G381600	chr7B	742229041	742229876	835	True	1114.000000	1114	90.9310	2173	2999	1	chr7B.!!$R2	826
12	TraesCS3D01G381600	chr2B	736387910	736388738	828	True	1158.000000	1158	92.0480	2173	2994	1	chr2B.!!$R4	821
13	TraesCS3D01G381600	chr2B	102979239	102980073	834	True	1136.000000	1136	91.3770	2173	2999	1	chr2B.!!$R1	826
14	TraesCS3D01G381600	chr2B	719298383	719299211	828	True	1131.000000	1131	91.4350	2173	2994	1	chr2B.!!$R3	821
15	TraesCS3D01G381600	chr2B	210266879	210267704	825	True	1129.000000	1129	91.4660	2173	2994	1	chr2B.!!$R2	821
16	TraesCS3D01G381600	chr6B	120822098	120822937	839	False	1149.000000	1149	91.5480	2169	2999	1	chr6B.!!$F2	830
17	TraesCS3D01G381600	chr6B	57581841	57582341	500	False	321.000000	364	93.2815	92	523	2	chr6B.!!$F3	431
18	TraesCS3D01G381600	chr6D	30066832	30067426	594	True	411.500000	542	94.1250	1	523	2	chr6D.!!$R2	522
19	TraesCS3D01G381600	chr4A	676213761	676215594	1833	False	213.000000	250	95.2430	550	807	2	chr4A.!!$F1	257

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
886	7417	0.388649	ACGAGTGGAGTGACGAATGC	60.389	55.0	0.0	0.0	0.0	3.56	F
1086	7629	0.603975	GCTTCTTCAGGTCGTGGCTT	60.604	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1717	8283	0.108041	GGATTTGCCATGGCCAACAG	60.108	55.0	33.44	1.84	41.09	3.16	R
2465	9083	0.109272	GAGTTCGATGGCGTGTCTGA	60.109	55.0	0.00	0.00	38.98	3.27	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
818	7341	6.919115	CGTAAAAGGCCTCTCTTCTTAGTATC	59.081	42.308	5.23	0.00	0.00	2.24
886	7417	0.388649	ACGAGTGGAGTGACGAATGC	60.389	55.000	0.00	0.00	0.00	3.56
930	7461	4.363034	GCCATAAGTAGAGGCGCC	57.637	61.111	21.89	21.89	38.86	6.53
967	7504	2.598787	CCTAACCCAAGCCACCGGA	61.599	63.158	9.46	0.00	0.00	5.14
1076	7619	3.020026	CTGCGCACGGCTTCTTCAG	62.020	63.158	5.66	0.00	44.05	3.02
1086	7629	0.603975	GCTTCTTCAGGTCGTGGCTT	60.604	55.000	0.00	0.00	0.00	4.35
1717	8283	1.516423	GCTCTTGGACGGGAGGTAC	59.484	63.158	0.00	0.00	0.00	3.34
1723	8289	1.189524	TGGACGGGAGGTACTGTTGG	61.190	60.000	0.00	0.00	41.55	3.77
1747	8355	2.324477	CAAATCCGATCGCCGTGC	59.676	61.111	10.32	0.00	36.31	5.34
2011	8619	5.954335	AGAAGATTTGACGGCCTTAAATTG	58.046	37.500	0.00	0.00	0.00	2.32
2016	8624	4.920640	TTGACGGCCTTAAATTGTTTGA	57.079	36.364	0.00	0.00	0.00	2.69
2021	8629	3.987220	CGGCCTTAAATTGTTTGAGTTGG	59.013	43.478	0.00	0.00	0.00	3.77
2023	8631	5.230182	GGCCTTAAATTGTTTGAGTTGGAG	58.770	41.667	0.00	0.00	0.00	3.86
2038	8649	7.016153	TGAGTTGGAGTAATAGATTGGTTGT	57.984	36.000	0.00	0.00	0.00	3.32
2097	8711	5.713792	ATATCTAGGACATCGACTTGTGG	57.286	43.478	0.00	0.00	0.00	4.17
2167	8781	0.926155	CATCTCCTCACGCATTCACG	59.074	55.000	0.00	0.00	39.50	4.35
2271	8885	9.736023	ACAAAACTGAAAAGATAACAGAACATC	57.264	29.630	0.00	0.00	35.85	3.06
2273	8887	7.730364	AACTGAAAAGATAACAGAACATCGT	57.270	32.000	0.00	0.00	35.85	3.73
2332	8950	0.323725	ACCATAGCAGCCACCAAAGG	60.324	55.000	0.00	0.00	0.00	3.11
2363	8981	0.684805	GATCACCTCCTCACCCGAGT	60.685	60.000	0.00	0.00	37.59	4.18
2365	8983	0.406750	TCACCTCCTCACCCGAGTTA	59.593	55.000	0.00	0.00	37.59	2.24
2456	9074	1.792006	GTTGAACGAATCAGACCGGT	58.208	50.000	6.92	6.92	39.77	5.28
2475	9093	2.607892	GCAACACCTCAGACACGCC	61.608	63.158	0.00	0.00	0.00	5.68
2494	9112	2.801342	GCCATCGAACTCCAGATCTGAC	60.801	54.545	24.62	8.63	0.00	3.51
2514	9132	1.069513	CACCCCACAACGACTAAGACA	59.930	52.381	0.00	0.00	0.00	3.41
2593	9211	0.746659	TCCAGATGTCGTCGATGCAT	59.253	50.000	0.00	0.00	0.00	3.96
2624	9243	1.410004	CATCCGCTCCCAACTACCTA	58.590	55.000	0.00	0.00	0.00	3.08
2634	9253	3.012047	TCCCAACTACCTACCAAGCTCTA	59.988	47.826	0.00	0.00	0.00	2.43
2655	9274	2.505777	CGACGCTGGAGCAGACAG	60.506	66.667	0.00	0.00	42.21	3.51
2704	9325	0.606401	CCACCACAAAGATGCCGTCT	60.606	55.000	0.00	0.00	39.43	4.18
2732	9353	2.503765	TGATATCCCCGCTTGAACAGAA	59.496	45.455	0.00	0.00	0.00	3.02
2755	9376	1.743394	GTTCCCAAATCCATCACCGAC	59.257	52.381	0.00	0.00	0.00	4.79
2760	9381	3.550820	CCAAATCCATCACCGACCATAA	58.449	45.455	0.00	0.00	0.00	1.90
2762	9383	4.400884	CCAAATCCATCACCGACCATAAAA	59.599	41.667	0.00	0.00	0.00	1.52
2770	9391	4.509616	TCACCGACCATAAAAACGATCAT	58.490	39.130	0.00	0.00	0.00	2.45
2809	9430	4.880120	TCTGGAGCTTCTTTATTCAGCATG	59.120	41.667	0.00	0.00	35.88	4.06
2853	9475	6.599437	CCAAGACGTCAAACGATCTAAAAAT	58.401	36.000	19.50	0.00	46.05	1.82
2936	9560	1.008194	CTCACGACCGACGACCAAA	60.008	57.895	0.00	0.00	45.77	3.28
2947	9574	2.613506	CGACCAAAAGGTCACCGGC	61.614	63.158	14.38	0.00	38.68	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
818	7341	1.156736	GTGTCGTGTTGGATTGGAGG	58.843	55.000	0.00	0.00	0.00	4.30
866	7397	1.340658	CATTCGTCACTCCACTCGTG	58.659	55.000	0.00	0.00	0.00	4.35
886	7417	0.175760	ATGGTCGTTGATGGAGGTCG	59.824	55.000	0.00	0.00	0.00	4.79
967	7504	2.426023	GTGCACGGTGAGACCCTT	59.574	61.111	13.29	0.00	33.75	3.95
992	7533	3.925630	AAGGTGTCCATGGCGGCTG	62.926	63.158	11.43	5.98	33.14	4.85
993	7534	3.628646	GAAGGTGTCCATGGCGGCT	62.629	63.158	11.43	0.00	33.14	5.52
994	7535	3.134127	GAAGGTGTCCATGGCGGC	61.134	66.667	6.96	0.00	33.14	6.53
995	7536	1.002134	AAGAAGGTGTCCATGGCGG	60.002	57.895	6.96	0.00	0.00	6.13
1059	7602	3.043713	CTGAAGAAGCCGTGCGCA	61.044	61.111	5.66	5.66	41.38	6.09
1372	7934	3.635268	CTTGGTCCTCCTGGCCAGC	62.635	68.421	28.39	13.08	39.46	4.85
1703	8265	0.682852	CAACAGTACCTCCCGTCCAA	59.317	55.000	0.00	0.00	0.00	3.53
1717	8283	0.108041	GGATTTGCCATGGCCAACAG	60.108	55.000	33.44	1.84	41.09	3.16
1723	8289	1.283793	CGATCGGATTTGCCATGGC	59.716	57.895	30.54	30.54	42.35	4.40
1747	8355	7.865385	TCAATTTAGGAACAAAAACGATCAAGG	59.135	33.333	0.00	0.00	0.00	3.61
1799	8407	4.824166	CGTCGTCGTACCTGGCCG	62.824	72.222	0.00	0.00	0.00	6.13
2011	8619	7.923414	ACCAATCTATTACTCCAACTCAAAC	57.077	36.000	0.00	0.00	0.00	2.93
2016	8624	6.151144	GCAACAACCAATCTATTACTCCAACT	59.849	38.462	0.00	0.00	0.00	3.16
2021	8629	7.320443	TCATGCAACAACCAATCTATTACTC	57.680	36.000	0.00	0.00	0.00	2.59
2023	8631	6.318648	TCCTCATGCAACAACCAATCTATTAC	59.681	38.462	0.00	0.00	0.00	1.89
2038	8649	2.039480	AGAAGTTCAGCTCCTCATGCAA	59.961	45.455	5.50	0.00	0.00	4.08
2075	8689	5.141182	ACCACAAGTCGATGTCCTAGATAT	58.859	41.667	0.00	0.00	0.00	1.63
2097	8711	2.813754	TGCTTTAGCCAATCTGTGTGAC	59.186	45.455	0.00	0.00	41.18	3.67
2190	8804	8.413229	TGATCTTTATGATATGAACGAGACACA	58.587	33.333	0.00	0.00	35.14	3.72
2271	8885	1.595794	ACGTTGGTGTCAAGCTTAACG	59.404	47.619	21.99	21.99	44.35	3.18
2273	8887	2.215196	GGACGTTGGTGTCAAGCTTAA	58.785	47.619	0.00	0.00	40.72	1.85
2363	8981	2.411701	CGATGGAGCCGCGTCTAA	59.588	61.111	4.92	0.00	0.00	2.10
2456	9074	1.887242	GCGTGTCTGAGGTGTTGCA	60.887	57.895	0.00	0.00	0.00	4.08
2465	9083	0.109272	GAGTTCGATGGCGTGTCTGA	60.109	55.000	0.00	0.00	38.98	3.27
2467	9085	1.215647	GGAGTTCGATGGCGTGTCT	59.784	57.895	0.00	0.00	38.98	3.41
2475	9093	3.443037	GTGTCAGATCTGGAGTTCGATG	58.557	50.000	22.42	0.00	0.00	3.84
2494	9112	1.069513	TGTCTTAGTCGTTGTGGGGTG	59.930	52.381	0.00	0.00	0.00	4.61
2514	9132	3.197116	CAGGTATGGTTTCCTACTTCGGT	59.803	47.826	0.00	0.00	32.26	4.69
2593	9211	2.548707	GGAGCGGATGCAGATTGTGATA	60.549	50.000	0.00	0.00	46.23	2.15
2704	9325	2.954684	GCGGGGATATCATGGCGGA	61.955	63.158	4.83	0.00	0.00	5.54
2770	9391	0.741326	CAGATTCTTCTCCGGCGAGA	59.259	55.000	9.30	6.72	43.62	4.04
2786	9407	4.558226	TGCTGAATAAAGAAGCTCCAGA	57.442	40.909	0.00	0.00	37.82	3.86
2823	9445	0.234884	GTTTGACGTCTTGGCTTCGG	59.765	55.000	17.92	0.00	0.00	4.30
2853	9475	6.382925	AGGTTTAGAGCCCTAATAGCTTAGA	58.617	40.000	0.00	0.00	41.75	2.10
2916	9540	3.360340	GGTCGTCGGTCGTGAGGT	61.360	66.667	0.00	0.00	40.80	3.85
2936	9560	3.382832	CTCTCCGCCGGTGACCTT	61.383	66.667	18.79	0.00	0.00	3.50

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.