AutoCloner

Multiple sequence alignment - TraesCS1D01G226800

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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	TraesCS1D01G226800	chr1D	100.000	4010	0	0	1	4010	315535621	315539630	0.000000e+00	7406.0
1	TraesCS1D01G226800	chr1D	96.014	577	17	6	147	718	280419506	280418931	0.000000e+00	933.0
2	TraesCS1D01G226800	chr1D	95.329	578	23	4	147	720	137914623	137914046	0.000000e+00	915.0
3	TraesCS1D01G226800	chr1D	96.753	154	5	0	1	154	7941340	7941493	1.430000e-64	257.0
4	TraesCS1D01G226800	chr1D	96.599	147	5	0	1	147	111026203	111026057	1.110000e-60	244.0
5	TraesCS1D01G226800	chr1D	96.599	147	5	0	1	147	329782004	329781858	1.110000e-60	244.0
6	TraesCS1D01G226800	chr1D	94.286	35	1	1	1501	1535	36959395	36959362	7.000000e-03	52.8
7	TraesCS1D01G226800	chr1B	95.981	3309	112	13	719	4010	427216151	427212847	0.000000e+00	5354.0
8	TraesCS1D01G226800	chr1A	95.103	2389	97	13	719	3091	396100272	396102656	0.000000e+00	3746.0
9	TraesCS1D01G226800	chr1A	93.312	927	47	3	3088	4010	396102709	396103624	0.000000e+00	1354.0
10	TraesCS1D01G226800	chr5D	96.335	573	17	4	147	716	98897094	98896523	0.000000e+00	939.0
11	TraesCS1D01G226800	chr5D	94.407	590	25	8	147	731	342065459	342066045	0.000000e+00	900.0
12	TraesCS1D01G226800	chr7D	96.021	578	17	6	147	719	495278014	495277438	0.000000e+00	935.0
13	TraesCS1D01G226800	chr7D	95.345	580	23	4	147	722	258438582	258438003	0.000000e+00	918.0
14	TraesCS1D01G226800	chr3D	95.034	584	24	5	148	726	376175534	376176117	0.000000e+00	913.0
15	TraesCS1D01G226800	chr3D	95.312	576	22	5	147	718	486424201	486424775	0.000000e+00	909.0
16	TraesCS1D01G226800	chr4D	95.147	577	23	5	147	719	131998454	131999029	0.000000e+00	905.0
17	TraesCS1D01G226800	chr4D	96.689	151	4	1	1	151	88499832	88499981	2.390000e-62	250.0
18	TraesCS1D01G226800	chr2D	97.279	147	4	0	1	147	233440640	233440786	2.390000e-62	250.0
19	TraesCS1D01G226800	chr2D	96.575	146	5	0	1	146	233450259	233450404	4.000000e-60	243.0
20	TraesCS1D01G226800	chr6D	96.599	147	5	0	1	147	316524976	316525122	1.110000e-60	244.0
21	TraesCS1D01G226800	chr6D	96.599	147	5	0	1	147	316534206	316534352	1.110000e-60	244.0
22	TraesCS1D01G226800	chr6D	96.575	146	5	0	1	146	316534999	316535144	4.000000e-60	243.0

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	TraesCS1D01G226800	chr1D	315535621	315539630	4009	False	7406.0	7406	100.0000	1	4010	1	chr1D.!!$F2	4009
1	TraesCS1D01G226800	chr1D	280418931	280419506	575	True	933.0	933	96.0140	147	718	1	chr1D.!!$R4	571
2	TraesCS1D01G226800	chr1D	137914046	137914623	577	True	915.0	915	95.3290	147	720	1	chr1D.!!$R3	573
3	TraesCS1D01G226800	chr1B	427212847	427216151	3304	True	5354.0	5354	95.9810	719	4010	1	chr1B.!!$R1	3291
4	TraesCS1D01G226800	chr1A	396100272	396103624	3352	False	2550.0	3746	94.2075	719	4010	2	chr1A.!!$F1	3291
5	TraesCS1D01G226800	chr5D	98896523	98897094	571	True	939.0	939	96.3350	147	716	1	chr5D.!!$R1	569
6	TraesCS1D01G226800	chr5D	342065459	342066045	586	False	900.0	900	94.4070	147	731	1	chr5D.!!$F1	584
7	TraesCS1D01G226800	chr7D	495277438	495278014	576	True	935.0	935	96.0210	147	719	1	chr7D.!!$R2	572
8	TraesCS1D01G226800	chr7D	258438003	258438582	579	True	918.0	918	95.3450	147	722	1	chr7D.!!$R1	575
9	TraesCS1D01G226800	chr3D	376175534	376176117	583	False	913.0	913	95.0340	148	726	1	chr3D.!!$F1	578
10	TraesCS1D01G226800	chr3D	486424201	486424775	574	False	909.0	909	95.3120	147	718	1	chr3D.!!$F2	571
11	TraesCS1D01G226800	chr4D	131998454	131999029	575	False	905.0	905	95.1470	147	719	1	chr4D.!!$F2	572
12	TraesCS1D01G226800	chr6D	316534206	316535144	938	False	243.5	244	96.5870	1	147	2	chr6D.!!$F2	146

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
981	1366	1.383456	CCATACACCACAATGGGCCG	61.383	60.0	0.0	0.0	43.37	6.13	F
1836	2225	0.389948	AGTTCGAGACGATGGTTGCC	60.390	55.0	0.0	0.0	35.23	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2351	2740	0.036010	CATCTCCTCAAACCACCGCT	60.036	55.000	0.0	0.0	0.0	5.52	R
3373	3830	1.133575	CAGTATCGGTCTAGGGGTCCA	60.134	57.143	0.0	0.0	0.0	4.02	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
103	104	4.602259	CCGTGGTGACGTGGCACT	62.602	66.667	16.72	2.45	44.54	4.40
107	108	1.519408	GTGGTGACGTGGCACTATTT	58.481	50.000	16.72	0.00	38.78	1.40
118	119	2.939460	GCACTATTTGCGTGGGATTT	57.061	45.000	0.00	0.00	42.79	2.17
156	157	2.572290	GGGCGTTACAAGGCTGAATAT	58.428	47.619	6.60	0.00	39.58	1.28
211	457	2.292267	GAGGATGGTGTGCATTGTAGG	58.708	52.381	0.00	0.00	0.00	3.18
275	522	4.979943	TCAACTGCAATTTCAGTGTTCA	57.020	36.364	11.60	0.00	45.77	3.18
292	539	5.003804	GTGTTCATGTCTGGAATTACCTGT	58.996	41.667	0.00	0.00	39.86	4.00
517	820	7.549134	TGCAATATAGGATTAAATCTGCCTACG	59.451	37.037	0.00	0.00	35.95	3.51
549	852	5.413309	TTCTCAAGTGGATCTCTTTCCTC	57.587	43.478	0.00	0.00	36.68	3.71
612	916	6.156429	CCCTCCTCTCCTTTTAGTTTAGCTTA	59.844	42.308	0.00	0.00	0.00	3.09
693	999	4.244862	GTTTTGATATGCTGTGGGGTTTG	58.755	43.478	0.00	0.00	0.00	2.93
766	1145	5.646606	TGACGGGTGAAGAAAAAGAAAAAG	58.353	37.500	0.00	0.00	0.00	2.27
768	1147	4.142026	ACGGGTGAAGAAAAAGAAAAAGGG	60.142	41.667	0.00	0.00	0.00	3.95
828	1208	5.178067	TGTCTCATGTGCATAATAAGCATCG	59.822	40.000	0.00	0.00	44.79	3.84
833	1213	7.924940	TCATGTGCATAATAAGCATCGTAAAA	58.075	30.769	0.00	0.00	44.79	1.52
933	1317	9.842775	ACTGATGCTATTTAATCAATGAAGAGA	57.157	29.630	0.00	0.00	32.60	3.10
945	1329	8.553459	AATCAATGAAGAGACGTATTTGACTT	57.447	30.769	0.00	0.00	0.00	3.01
972	1357	4.281898	AGAAACTACCACCATACACCAC	57.718	45.455	0.00	0.00	0.00	4.16
981	1366	1.383456	CCATACACCACAATGGGCCG	61.383	60.000	0.00	0.00	43.37	6.13
1053	1441	2.501881	GCAACAAAACCATACTACGCG	58.498	47.619	3.53	3.53	0.00	6.01
1222	1611	2.437897	CCTTGCCTGGTGCTCCTT	59.562	61.111	6.34	0.00	42.00	3.36
1306	1695	2.105128	GTCGGCCACCTCATCTCG	59.895	66.667	2.24	0.00	0.00	4.04
1340	1729	2.512515	GCCACATCTGACCTCCGC	60.513	66.667	0.00	0.00	0.00	5.54
1430	1819	1.756950	CGAGATCCCGTTCCCTCCA	60.757	63.158	0.00	0.00	0.00	3.86
1722	2111	1.308069	ATCACGCACACAAGCCATCC	61.308	55.000	0.00	0.00	0.00	3.51
1836	2225	0.389948	AGTTCGAGACGATGGTTGCC	60.390	55.000	0.00	0.00	35.23	4.52
1960	2349	2.166459	GTGTTCGAGATGATGAGGGTGA	59.834	50.000	0.00	0.00	0.00	4.02
2351	2740	2.178580	GGGAAAGATGGACATGGCAAA	58.821	47.619	0.00	0.00	0.00	3.68
2358	2747	2.568090	GACATGGCAAAGCGGTGG	59.432	61.111	0.00	0.00	0.00	4.61
2373	2762	1.881925	CGGTGGTTTGAGGAGATGCAA	60.882	52.381	0.00	0.00	0.00	4.08
2562	2951	3.439476	GGAATATGCCAGATGATGCAGTC	59.561	47.826	0.00	0.00	41.46	3.51
2633	3022	8.843262	CCATACATACAACATGATGATGAAGTT	58.157	33.333	10.29	0.00	33.36	2.66
2644	3033	8.680903	ACATGATGATGAAGTTGTATTTCCTTC	58.319	33.333	0.00	0.00	36.09	3.46
2646	3035	6.878923	TGATGATGAAGTTGTATTTCCTTCGT	59.121	34.615	0.00	0.00	37.90	3.85
2651	3040	3.671716	AGTTGTATTTCCTTCGTGGGAC	58.328	45.455	0.00	0.00	34.78	4.46
2682	3071	3.660111	GGTTGCGCAGTGTGGGAC	61.660	66.667	11.31	3.49	31.21	4.46
2719	3108	2.420022	GGGATTTGTCCTGATGTGAACG	59.580	50.000	0.00	0.00	0.00	3.95
2835	3224	5.122396	GGCTCCACAAATAGACTACAACAAG	59.878	44.000	0.00	0.00	0.00	3.16
2974	3363	0.390472	GAGAAGTCGGGTCAAGCAGG	60.390	60.000	0.00	0.00	0.00	4.85
3016	3405	4.933400	GGAGCAGGACGTTGTAAGATTAAA	59.067	41.667	0.00	0.00	0.00	1.52
3017	3406	5.063564	GGAGCAGGACGTTGTAAGATTAAAG	59.936	44.000	0.00	0.00	0.00	1.85
3018	3407	5.790593	AGCAGGACGTTGTAAGATTAAAGA	58.209	37.500	0.00	0.00	0.00	2.52
3025	3425	8.287503	GGACGTTGTAAGATTAAAGATGTTTGT	58.712	33.333	0.00	0.00	0.00	2.83
3135	3592	7.660208	TGTCTCCTGTTTGTTAGACCTAAAATC	59.340	37.037	0.00	0.00	38.04	2.17
3139	3596	6.349363	CCTGTTTGTTAGACCTAAAATCTGCC	60.349	42.308	0.00	0.00	0.00	4.85
3165	3622	9.014297	CCCAAGTCATGATTAAGTTCTAGTTTT	57.986	33.333	0.00	0.00	0.00	2.43
3245	3702	1.031571	TGTAGGTACCGTAGTGGCCG	61.032	60.000	6.18	0.00	43.94	6.13
3258	3715	0.177141	GTGGCCGAGTATGCACCTTA	59.823	55.000	0.00	0.00	0.00	2.69
3276	3733	8.162746	TGCACCTTACATTGGATCAATCATATA	58.837	33.333	0.00	0.00	31.05	0.86
3385	3842	8.667592	ATTTAGACTAATATGGACCCCTAGAC	57.332	38.462	0.00	0.00	0.00	2.59
3404	3861	6.819649	CCTAGACCGATACTGATACTCCTTAG	59.180	46.154	0.00	0.00	0.00	2.18
3408	3865	5.004448	CCGATACTGATACTCCTTAGCAGA	58.996	45.833	3.67	0.00	45.65	4.26
3616	4073	9.017509	ACCAAATTATATGTAGCTTGATGGATG	57.982	33.333	0.00	0.00	0.00	3.51
3699	4160	3.562557	TGGTGTTTAGCGGAAGTTCTTTC	59.437	43.478	2.25	0.00	34.93	2.62
3765	4226	2.824689	TTGCCACATGGTCCATACAT	57.175	45.000	3.38	0.00	37.57	2.29
3806	4267	7.907389	AGTCCACTCTAATACAGTGATTTGAA	58.093	34.615	0.00	0.00	43.54	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	104	5.373222	AGCTACATAAATCCCACGCAAATA	58.627	37.500	0.00	0.00	0.00	1.40
107	108	2.942376	CAAGCTACATAAATCCCACGCA	59.058	45.455	0.00	0.00	0.00	5.24
118	119	3.368013	CGCCCGGATAATCAAGCTACATA	60.368	47.826	0.73	0.00	0.00	2.29
119	120	2.612972	CGCCCGGATAATCAAGCTACAT	60.613	50.000	0.73	0.00	0.00	2.29
156	157	5.044476	TGCCTTCTTTCCACCATATCCTTTA	60.044	40.000	0.00	0.00	0.00	1.85
275	522	9.479549	AATCAATTTACAGGTAATTCCAGACAT	57.520	29.630	0.00	0.00	39.02	3.06
292	539	2.109774	CCCTGCAGGCCAATCAATTTA	58.890	47.619	28.39	0.00	0.00	1.40
517	820	2.834549	TCCACTTGAGAAGGTCATCCTC	59.165	50.000	0.00	0.00	44.35	3.71
589	893	9.674068	AAATAAGCTAAACTAAAAGGAGAGGAG	57.326	33.333	0.00	0.00	0.00	3.69
671	976	4.244862	CAAACCCCACAGCATATCAAAAC	58.755	43.478	0.00	0.00	0.00	2.43
693	999	1.989706	TTTTACTGGGAACTGTGGGC	58.010	50.000	0.00	0.00	42.98	5.36
951	1335	3.649023	TGTGGTGTATGGTGGTAGTTTCT	59.351	43.478	0.00	0.00	0.00	2.52
952	1336	4.010667	TGTGGTGTATGGTGGTAGTTTC	57.989	45.455	0.00	0.00	0.00	2.78
972	1357	3.127030	GTCTTAAAAGAGTCGGCCCATTG	59.873	47.826	0.00	0.00	35.32	2.82
981	1366	4.691216	ACCATTCTGCGTCTTAAAAGAGTC	59.309	41.667	0.00	0.00	35.32	3.36
1053	1441	1.248101	AATGTTGGGTTAGCGGCACC	61.248	55.000	1.45	1.19	0.00	5.01
1222	1611	2.276116	GGCGATGAGGGCGAGGATA	61.276	63.158	0.00	0.00	0.00	2.59
1722	2111	3.121030	CACTGGAAGAAGCGGCGG	61.121	66.667	9.78	0.00	37.43	6.13
1914	2303	0.580578	CTGCATTCTTGATCTCGCCG	59.419	55.000	0.00	0.00	0.00	6.46
1960	2349	0.039618	ACCCCATCATCAAAGCCGTT	59.960	50.000	0.00	0.00	0.00	4.44
2351	2740	0.036010	CATCTCCTCAAACCACCGCT	60.036	55.000	0.00	0.00	0.00	5.52
2358	2747	3.340814	TCCTCTTGCATCTCCTCAAAC	57.659	47.619	0.00	0.00	0.00	2.93
2373	2762	3.415087	GGCTGGCACCCATCCTCT	61.415	66.667	0.00	0.00	36.90	3.69
2577	2966	5.602561	GGGTTCAAGCCCCTTATTTATCATT	59.397	40.000	0.00	0.00	42.89	2.57
2604	2993	8.782339	TCATCATCATGTTGTATGTATGGATC	57.218	34.615	3.76	0.00	0.00	3.36
2633	3022	2.373540	CGTCCCACGAAGGAAATACA	57.626	50.000	0.00	0.00	46.05	2.29
2644	3033	1.327460	CATTGCATAGTTCGTCCCACG	59.673	52.381	0.00	0.00	44.19	4.94
2646	3035	1.408127	CCCATTGCATAGTTCGTCCCA	60.408	52.381	0.00	0.00	0.00	4.37
2682	3071	1.301244	CCCCTTCCGATGCATCTCG	60.301	63.158	23.73	13.69	38.37	4.04
2719	3108	7.696453	GTGACCATTAATAAACACAGTGTATGC	59.304	37.037	6.63	0.00	0.00	3.14
2835	3224	1.597742	TGGAGAAGTCTGCAGCAAAC	58.402	50.000	9.47	1.80	39.44	2.93
2974	3363	3.567397	TCCTAGTCTGATTAGGGACAGC	58.433	50.000	21.75	0.00	38.57	4.40
3016	3405	9.846248	GAGCACATTCTAAAATTACAAACATCT	57.154	29.630	0.00	0.00	0.00	2.90
3017	3406	9.076596	GGAGCACATTCTAAAATTACAAACATC	57.923	33.333	0.00	0.00	0.00	3.06
3018	3407	8.806146	AGGAGCACATTCTAAAATTACAAACAT	58.194	29.630	0.00	0.00	0.00	2.71
3025	3425	8.752005	AATAGCAGGAGCACATTCTAAAATTA	57.248	30.769	0.00	0.00	45.49	1.40
3135	3592	3.624777	ACTTAATCATGACTTGGGGCAG	58.375	45.455	0.00	0.00	0.00	4.85
3139	3596	8.567285	AAACTAGAACTTAATCATGACTTGGG	57.433	34.615	0.00	0.00	0.00	4.12
3165	3622	2.564771	CAGCTCACCTGAGTTTCACAA	58.435	47.619	4.26	0.00	44.64	3.33
3245	3702	5.368145	TGATCCAATGTAAGGTGCATACTC	58.632	41.667	0.00	0.00	0.00	2.59
3276	3733	5.189180	GTTGAGCCACTGGAAGATAGAAAT	58.811	41.667	0.00	0.00	37.43	2.17
3373	3830	1.133575	CAGTATCGGTCTAGGGGTCCA	60.134	57.143	0.00	0.00	0.00	4.02
3385	3842	5.004448	TCTGCTAAGGAGTATCAGTATCGG	58.996	45.833	0.00	0.00	36.25	4.18
3404	3861	4.244066	CCTACATATCAGCATCACTCTGC	58.756	47.826	0.00	0.00	42.62	4.26
3408	3865	4.970860	AAGCCTACATATCAGCATCACT	57.029	40.909	0.00	0.00	0.00	3.41
3636	4097	9.956720	GCATGCATTATTTCTAACTTTCTACAT	57.043	29.630	14.21	0.00	0.00	2.29
3699	4160	3.544356	TCGCTACAAGATAGCATCGAG	57.456	47.619	6.73	0.00	40.39	4.04
3765	4226	7.568349	AGAGTGGACTCAATAAATATGAGCAA	58.432	34.615	9.43	0.00	46.56	3.91
3840	4301	8.261492	ACAAGAGATAGTAATGCAGAAAACTG	57.739	34.615	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.