AutoCloner

Multiple sequence alignment - TraesCS1A01G335700

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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	TraesCS1A01G335700	chr1A	100.000	3834	0	0	1	3834	522536884	522533051	0.000000e+00	7081
1	TraesCS1A01G335700	chr1A	83.946	1414	194	22	960	2363	522510855	522509465	0.000000e+00	1323
2	TraesCS1A01G335700	chr1A	83.703	1399	179	31	959	2336	522516329	522514959	0.000000e+00	1275
3	TraesCS1A01G335700	chr1A	88.788	553	43	8	1	545	522879782	522879241	0.000000e+00	660
4	TraesCS1A01G335700	chr1D	97.003	2302	50	10	908	3204	427372375	427370088	0.000000e+00	3851
5	TraesCS1A01G335700	chr1D	82.963	1667	228	40	955	2601	427332244	427330614	0.000000e+00	1454
6	TraesCS1A01G335700	chr1D	82.465	1517	212	37	878	2373	427319596	427318113	0.000000e+00	1279
7	TraesCS1A01G335700	chr1D	86.354	938	115	8	880	1805	427596999	427596063	0.000000e+00	1011
8	TraesCS1A01G335700	chr1D	90.718	571	22	7	3255	3798	427370078	427369512	0.000000e+00	732
9	TraesCS1A01G335700	chr1D	83.658	667	55	20	172	801	427590915	427590266	2.570000e-161	579
10	TraesCS1A01G335700	chr1D	87.500	176	19	3	1	176	427591432	427591260	2.340000e-47	200
11	TraesCS1A01G335700	chr1B	93.745	1311	57	5	1335	2644	579001936	579000650	0.000000e+00	1943
12	TraesCS1A01G335700	chr1B	84.135	1683	208	39	955	2605	577913147	577911492	0.000000e+00	1574
13	TraesCS1A01G335700	chr1B	95.194	978	27	4	374	1331	579002983	579002006	0.000000e+00	1528
14	TraesCS1A01G335700	chr1B	84.535	1442	177	25	955	2371	578045436	578044016	0.000000e+00	1386
15	TraesCS1A01G335700	chr1B	86.652	884	109	8	968	1850	577829257	577828382	0.000000e+00	970
16	TraesCS1A01G335700	chr1B	83.947	760	65	32	3071	3798	579000076	578999342	0.000000e+00	675
17	TraesCS1A01G335700	chr1B	88.225	552	39	16	9	551	579772926	579772392	1.500000e-178	636
18	TraesCS1A01G335700	chr1B	90.141	426	29	9	2650	3069	579000591	579000173	3.370000e-150	542
19	TraesCS1A01G335700	chr1B	91.385	325	23	3	1	325	579003300	579002981	1.260000e-119	440
20	TraesCS1A01G335700	chr1B	87.432	366	42	2	1934	2299	579777841	579777480	5.920000e-113	418
21	TraesCS1A01G335700	chr1B	81.739	345	30	18	3475	3792	578049183	578048845	1.370000e-64	257
22	TraesCS1A01G335700	chr1B	86.512	215	21	8	3227	3438	578049391	578049182	2.980000e-56	230
23	TraesCS1A01G335700	chr5D	84.220	1597	208	28	877	2442	523187663	523186080	0.000000e+00	1513
24	TraesCS1A01G335700	chr5D	84.178	1599	205	29	877	2442	523314852	523313269	0.000000e+00	1507
25	TraesCS1A01G335700	chrUn	84.233	704	86	17	1494	2182	199131473	199132166	0.000000e+00	662

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	TraesCS1A01G335700	chr1A	522533051	522536884	3833	True	7081.000000	7081	100.0000	1	3834	1	chr1A.!!$R3	3833
1	TraesCS1A01G335700	chr1A	522509465	522510855	1390	True	1323.000000	1323	83.9460	960	2363	1	chr1A.!!$R1	1403
2	TraesCS1A01G335700	chr1A	522514959	522516329	1370	True	1275.000000	1275	83.7030	959	2336	1	chr1A.!!$R2	1377
3	TraesCS1A01G335700	chr1A	522879241	522879782	541	True	660.000000	660	88.7880	1	545	1	chr1A.!!$R4	544
4	TraesCS1A01G335700	chr1D	427369512	427372375	2863	True	2291.500000	3851	93.8605	908	3798	2	chr1D.!!$R4	2890
5	TraesCS1A01G335700	chr1D	427330614	427332244	1630	True	1454.000000	1454	82.9630	955	2601	1	chr1D.!!$R2	1646
6	TraesCS1A01G335700	chr1D	427318113	427319596	1483	True	1279.000000	1279	82.4650	878	2373	1	chr1D.!!$R1	1495
7	TraesCS1A01G335700	chr1D	427596063	427596999	936	True	1011.000000	1011	86.3540	880	1805	1	chr1D.!!$R3	925
8	TraesCS1A01G335700	chr1D	427590266	427591432	1166	True	389.500000	579	85.5790	1	801	2	chr1D.!!$R5	800
9	TraesCS1A01G335700	chr1B	577911492	577913147	1655	True	1574.000000	1574	84.1350	955	2605	1	chr1B.!!$R2	1650
10	TraesCS1A01G335700	chr1B	578999342	579003300	3958	True	1025.600000	1943	90.8824	1	3798	5	chr1B.!!$R6	3797
11	TraesCS1A01G335700	chr1B	577828382	577829257	875	True	970.000000	970	86.6520	968	1850	1	chr1B.!!$R1	882
12	TraesCS1A01G335700	chr1B	579772392	579772926	534	True	636.000000	636	88.2250	9	551	1	chr1B.!!$R3	542
13	TraesCS1A01G335700	chr1B	578044016	578049391	5375	True	624.333333	1386	84.2620	955	3792	3	chr1B.!!$R5	2837
14	TraesCS1A01G335700	chr5D	523186080	523187663	1583	True	1513.000000	1513	84.2200	877	2442	1	chr5D.!!$R1	1565
15	TraesCS1A01G335700	chr5D	523313269	523314852	1583	True	1507.000000	1507	84.1780	877	2442	1	chr5D.!!$R2	1565
16	TraesCS1A01G335700	chrUn	199131473	199132166	693	False	662.000000	662	84.2330	1494	2182	1	chrUn.!!$F1	688

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
484	843	1.483595	TTGCTAGCCACCTGTGCTCT	61.484	55.0	13.29	0.0	40.23	4.09	F
1452	4529	0.313987	CGTCCCTGTTCAAAAAGGCC	59.686	55.0	0.00	0.0	31.71	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2365	5490	1.143183	ACCATACTAGGCCAACGCG	59.857	57.895	5.01	3.53	35.02	6.01	R
2916	6124	3.173151	ACCTGAAAAATGGGTCCATTCC	58.827	45.455	14.80	8.61	44.86	3.01	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	89	7.038154	TGCAAACAAAATCTAGTTAAGCTGT	57.962	32.000	0.00	0.00	33.07	4.40
94	95	8.015409	ACAAAATCTAGTTAAGCTGTTACGTC	57.985	34.615	0.00	0.00	0.00	4.34
95	96	7.871463	ACAAAATCTAGTTAAGCTGTTACGTCT	59.129	33.333	0.00	0.00	0.00	4.18
117	118	7.305475	CGTCTCGATTCAATGTATGTCTGTTAC	60.305	40.741	0.00	0.00	0.00	2.50
331	681	8.578308	TCAATGAAAGCTTGTCTTTTATGTTG	57.422	30.769	0.00	0.00	44.58	3.33
362	712	7.981789	TGAGTATCAGACATGTAAAATCCTGAC	59.018	37.037	13.17	4.83	42.56	3.51
370	720	6.842163	ACATGTAAAATCCTGACATCGAAAC	58.158	36.000	0.00	0.00	31.44	2.78
372	722	6.869315	TGTAAAATCCTGACATCGAAACAA	57.131	33.333	0.00	0.00	0.00	2.83
440	791	8.956014	GTTAGCTCTCGTAGTACAATACAAATC	58.044	37.037	0.38	0.00	0.00	2.17
442	793	8.447924	AGCTCTCGTAGTACAATACAAATCTA	57.552	34.615	0.38	0.00	0.00	1.98
443	794	8.561212	AGCTCTCGTAGTACAATACAAATCTAG	58.439	37.037	0.38	0.00	0.00	2.43
444	795	8.344098	GCTCTCGTAGTACAATACAAATCTAGT	58.656	37.037	0.38	0.00	0.00	2.57
460	818	9.362151	ACAAATCTAGTTAAGATAGGAGAGAGG	57.638	37.037	0.00	0.00	44.56	3.69
477	835	2.310052	AGAGGATTTTTGCTAGCCACCT	59.690	45.455	13.29	11.14	0.00	4.00
478	836	2.424956	GAGGATTTTTGCTAGCCACCTG	59.575	50.000	13.29	0.00	0.00	4.00
484	843	1.483595	TTGCTAGCCACCTGTGCTCT	61.484	55.000	13.29	0.00	40.23	4.09
560	949	3.710209	AACTCATTGTTCCCCAGAGAG	57.290	47.619	0.00	0.00	32.63	3.20
804	1205	9.003658	AGTAAATAGGCTTCCATGAATAATTCG	57.996	33.333	0.00	0.00	0.00	3.34
1452	4529	0.313987	CGTCCCTGTTCAAAAAGGCC	59.686	55.000	0.00	0.00	31.71	5.19
1689	4766	2.355108	CGTGTTGGATCTCCCTCATGTT	60.355	50.000	0.00	0.00	35.38	2.71
1878	4970	3.000727	AGTGTGTATTTAGCCGCTTGTC	58.999	45.455	0.00	0.00	0.00	3.18
2338	5461	5.163703	TGTTGTATGTTCATAAACGGGCATC	60.164	40.000	0.00	0.00	38.28	3.91
2498	5649	4.010349	GCAGCTGGGTCTATACTTTGTTT	58.990	43.478	17.12	0.00	0.00	2.83
2499	5650	4.095036	GCAGCTGGGTCTATACTTTGTTTC	59.905	45.833	17.12	0.00	0.00	2.78
2500	5651	5.491982	CAGCTGGGTCTATACTTTGTTTCT	58.508	41.667	5.57	0.00	0.00	2.52
2501	5652	5.352569	CAGCTGGGTCTATACTTTGTTTCTG	59.647	44.000	5.57	0.00	0.00	3.02
2602	5754	3.259064	CGTCCGTACCTTTGTGAATCAT	58.741	45.455	0.00	0.00	0.00	2.45
2637	5789	3.394674	TTGTGCTCATGAGGTCGTTAA	57.605	42.857	23.89	2.98	0.00	2.01
2793	5999	4.278170	TCATTGACTTGCAACTTTACAGGG	59.722	41.667	0.00	0.00	39.78	4.45
2846	6052	6.995091	GGATCCATTTTAGTAAGACTGCATCT	59.005	38.462	6.95	0.00	40.46	2.90
2916	6124	9.903682	AATTCTGAATTTCAGTAAACATGTGAG	57.096	29.630	22.44	0.00	44.58	3.51
3009	6220	2.083002	TGCAGCAATTGTGAAGCGATA	58.917	42.857	7.40	0.00	0.00	2.92
3031	6242	7.280652	CGATAATGGCATCCATATTGTGACATA	59.719	37.037	0.00	0.00	44.40	2.29
3134	6441	5.957132	AGAAGCATATATTGTCCCCAACAT	58.043	37.500	0.00	0.00	37.82	2.71
3138	6445	5.898972	AGCATATATTGTCCCCAACATTTGT	59.101	36.000	0.00	0.00	37.82	2.83
3175	6482	3.538591	TGATCTTGTGCTGGATGTCATC	58.461	45.455	4.06	4.06	0.00	2.92
3176	6483	3.054948	TGATCTTGTGCTGGATGTCATCA	60.055	43.478	14.72	0.67	0.00	3.07
3177	6484	3.639672	TCTTGTGCTGGATGTCATCAT	57.360	42.857	14.72	0.00	36.95	2.45
3228	6535	5.016051	TGCAAGTCTTTAGATAGCTCTGG	57.984	43.478	0.00	0.00	32.66	3.86
3308	6615	5.021458	AGGTAATAGTTCTCTTTCACCGGA	58.979	41.667	9.46	0.00	0.00	5.14
3316	6623	4.150897	TCTCTTTCACCGGATTTATGGG	57.849	45.455	9.46	0.00	0.00	4.00
3317	6624	3.778075	TCTCTTTCACCGGATTTATGGGA	59.222	43.478	9.46	0.00	0.00	4.37
3425	6734	9.599866	TTTATATGAATGACGTGATCTTCTTGT	57.400	29.630	0.00	0.00	0.00	3.16
3516	6825	6.096423	AGTTCCAAAAGTCACCTAAAAGTTCC	59.904	38.462	0.00	0.00	0.00	3.62
3545	6854	8.010733	ACATTCATGACCACTTTTATATTGGG	57.989	34.615	0.00	0.00	34.41	4.12
3627	6938	8.553459	TTTAAATTTGCAAGGACACTTTTTGA	57.447	26.923	0.00	0.00	33.81	2.69
3666	7000	8.718102	TTTTAGACTGTTGAGCATATCCTAAC	57.282	34.615	0.00	0.00	0.00	2.34
3833	7171	9.838339	CTGAGGGATTCTATTAAACATAAGTGT	57.162	33.333	0.00	0.00	41.28	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	81	5.050644	TGAATCGAGACGTAACAGCTTAA	57.949	39.130	0.00	0.00	0.00	1.85
88	89	6.691388	CAGACATACATTGAATCGAGACGTAA	59.309	38.462	0.00	0.00	0.00	3.18
94	95	6.472486	ACGTAACAGACATACATTGAATCGAG	59.528	38.462	0.00	0.00	0.00	4.04
95	96	6.327154	ACGTAACAGACATACATTGAATCGA	58.673	36.000	0.00	0.00	0.00	3.59
117	118	8.892887	TTAAACGGGCATACTTTATAAAAACG	57.107	30.769	0.00	0.00	0.00	3.60
156	157	8.969267	CAAGGAGCTTAGTATATACTGAAAACG	58.031	37.037	23.09	6.49	37.10	3.60
357	707	4.216257	ACTCCAAATTGTTTCGATGTCAGG	59.784	41.667	0.00	0.00	0.00	3.86
362	712	7.447430	GCAAATAACTCCAAATTGTTTCGATG	58.553	34.615	0.00	0.00	0.00	3.84
370	720	4.858692	CACCTCGCAAATAACTCCAAATTG	59.141	41.667	0.00	0.00	0.00	2.32
372	722	4.079253	ACACCTCGCAAATAACTCCAAAT	58.921	39.130	0.00	0.00	0.00	2.32
442	793	7.990314	GCAAAAATCCTCTCTCCTATCTTAACT	59.010	37.037	0.00	0.00	0.00	2.24
443	794	7.990314	AGCAAAAATCCTCTCTCCTATCTTAAC	59.010	37.037	0.00	0.00	0.00	2.01
444	795	8.095452	AGCAAAAATCCTCTCTCCTATCTTAA	57.905	34.615	0.00	0.00	0.00	1.85
460	818	2.672195	GCACAGGTGGCTAGCAAAAATC	60.672	50.000	18.24	0.00	0.00	2.17
477	835	0.610174	GGGACAGATCACAGAGCACA	59.390	55.000	0.00	0.00	0.00	4.57
478	836	0.610174	TGGGACAGATCACAGAGCAC	59.390	55.000	0.00	0.00	31.41	4.40
484	843	3.024547	GCTACTAGTGGGACAGATCACA	58.975	50.000	5.39	0.00	41.80	3.58
653	1054	5.668558	AAACACAGTCCGACACTTAAATC	57.331	39.130	0.40	0.00	30.26	2.17
657	1058	8.089597	TCATAATTAAACACAGTCCGACACTTA	58.910	33.333	0.40	0.00	30.26	2.24
803	1204	5.158494	TGCAGACAGTACAAATACACTACG	58.842	41.667	0.00	0.00	33.30	3.51
804	1205	7.596749	ATTGCAGACAGTACAAATACACTAC	57.403	36.000	0.00	0.00	33.30	2.73
1452	4529	2.558359	CTCCCAAAAGTTAAGGCTGTGG	59.442	50.000	0.00	0.00	0.00	4.17
1640	4717	1.823610	TCATTTGCGGGAATGCATTCA	59.176	42.857	34.08	17.51	45.78	2.57
1689	4766	4.406972	ACATCACTAGGAGCTTCTGCAATA	59.593	41.667	4.19	0.00	42.74	1.90
1853	4937	5.470777	ACAAGCGGCTAAATACACACTTTAA	59.529	36.000	1.35	0.00	0.00	1.52
2365	5490	1.143183	ACCATACTAGGCCAACGCG	59.857	57.895	5.01	3.53	35.02	6.01
2637	5789	7.173218	ACAGTATCACATCGAATGAACAGTTTT	59.827	33.333	6.81	0.00	0.00	2.43
2916	6124	3.173151	ACCTGAAAAATGGGTCCATTCC	58.827	45.455	14.80	8.61	44.86	3.01
3009	6220	6.779049	AGTTATGTCACAATATGGATGCCATT	59.221	34.615	4.03	0.00	42.23	3.16
3020	6231	6.816640	GCCAGTACTCAAGTTATGTCACAATA	59.183	38.462	0.00	0.00	0.00	1.90
3088	6394	6.001449	TCTTTATCTCCATTGATCCGGTTT	57.999	37.500	0.00	0.00	0.00	3.27
3134	6441	6.388100	AGATCAGAATTATCTCCAGGGACAAA	59.612	38.462	0.00	0.00	32.03	2.83
3138	6445	5.907662	ACAAGATCAGAATTATCTCCAGGGA	59.092	40.000	0.00	0.00	32.48	4.20
3225	6532	3.251004	GTGAAACACCTGAAAGCTACCAG	59.749	47.826	7.98	7.98	36.32	4.00
3228	6535	4.574828	TGAAGTGAAACACCTGAAAGCTAC	59.425	41.667	0.00	0.00	41.43	3.58
3281	6588	6.310711	CGGTGAAAGAGAACTATTACCTGAAC	59.689	42.308	0.00	0.00	0.00	3.18
3296	6603	4.150897	TCCCATAAATCCGGTGAAAGAG	57.849	45.455	0.00	0.00	0.00	2.85
3297	6604	4.788925	ATCCCATAAATCCGGTGAAAGA	57.211	40.909	0.00	0.00	0.00	2.52
3298	6605	5.852282	AAATCCCATAAATCCGGTGAAAG	57.148	39.130	0.00	0.00	0.00	2.62
3367	6674	7.867305	TGTCACAAAACAAGGATAGTAAACA	57.133	32.000	0.00	0.00	0.00	2.83
3608	6918	4.527509	TGTCAAAAAGTGTCCTTGCAAA	57.472	36.364	0.00	0.00	0.00	3.68
3807	7145	9.838339	ACACTTATGTTTAATAGAATCCCTCAG	57.162	33.333	0.00	0.00	34.46	3.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.