AutoCloner

Multiple sequence alignment - TraesCS4A01G443700

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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	TraesCS4A01G443700	chr4A	100.000	3714	0	0	1	3714	712444607	712448320	0.000000e+00	6859.0
1	TraesCS4A01G443700	chr4A	99.114	2709	19	2	1	2705	712114104	712111397	0.000000e+00	4865.0
2	TraesCS4A01G443700	chr7D	90.887	2085	131	34	657	2705	21773374	21775435	0.000000e+00	2743.0
3	TraesCS4A01G443700	chr7D	83.051	118	16	3	3287	3402	486943897	486943782	1.820000e-18	104.0
4	TraesCS4A01G443700	chr7D	85.185	81	12	0	359	439	191468877	191468797	2.380000e-12	84.2
5	TraesCS4A01G443700	chr7A	93.703	1731	90	12	994	2705	22197960	22199690	0.000000e+00	2575.0
6	TraesCS4A01G443700	chr7A	88.430	242	16	5	707	939	22197513	22197751	7.850000e-72	281.0
7	TraesCS4A01G443700	chr7A	83.051	118	16	3	3287	3402	653270853	653270738	1.820000e-18	104.0
8	TraesCS4A01G443700	chr1D	90.502	558	32	11	2705	3251	33352545	33351998	0.000000e+00	717.0
9	TraesCS4A01G443700	chr1D	91.361	463	39	1	3252	3714	33351351	33350890	1.880000e-177	632.0
10	TraesCS4A01G443700	chr1D	78.750	320	61	6	7	323	307786280	307786595	1.350000e-49	207.0
11	TraesCS4A01G443700	chr5D	90.734	518	28	10	2745	3251	458212217	458211709	0.000000e+00	673.0
12	TraesCS4A01G443700	chr5D	91.379	464	37	3	3252	3714	458211065	458210604	1.880000e-177	632.0
13	TraesCS4A01G443700	chr1A	91.810	464	35	2	3252	3714	75449011	75449472	0.000000e+00	643.0
14	TraesCS4A01G443700	chr1A	90.261	421	30	6	2841	3251	75447945	75448364	1.170000e-149	540.0
15	TraesCS4A01G443700	chr1A	76.648	364	75	10	75	433	578250448	578250806	3.790000e-45	193.0
16	TraesCS4A01G443700	chr1A	80.435	92	17	1	349	439	572334240	572334149	6.660000e-08	69.4
17	TraesCS4A01G443700	chr2B	79.735	755	123	21	1721	2467	5780828	5780096	1.530000e-143	520.0
18	TraesCS4A01G443700	chr2B	86.253	371	45	3	3252	3621	787512945	787513310	7.470000e-107	398.0
19	TraesCS4A01G443700	chr2B	75.036	685	134	26	1788	2461	17149773	17150431	2.180000e-72	283.0
20	TraesCS4A01G443700	chr2B	73.000	400	96	10	7	401	39792146	39792538	3.010000e-26	130.0
21	TraesCS4A01G443700	chr2B	85.227	88	9	3	667	752	5725094	5725179	1.840000e-13	87.9
22	TraesCS4A01G443700	chr2A	78.519	405	80	7	1	401	13008470	13008069	3.680000e-65	259.0
23	TraesCS4A01G443700	chr2A	74.441	313	73	5	1	311	562727644	562727951	1.080000e-25	128.0
24	TraesCS4A01G443700	chrUn	82.119	302	44	5	2159	2457	32344723	32345017	2.210000e-62	250.0
25	TraesCS4A01G443700	chr5A	79.697	330	62	5	2	328	687161404	687161731	2.230000e-57	233.0
26	TraesCS4A01G443700	chr6B	76.009	446	94	12	1	439	628883654	628883215	6.250000e-53	219.0
27	TraesCS4A01G443700	chr3D	76.451	293	61	7	9	294	522200898	522200607	6.420000e-33	152.0
28	TraesCS4A01G443700	chr6A	75.633	316	62	13	1	311	472952434	472952129	3.870000e-30	143.0
29	TraesCS4A01G443700	chr7B	73.210	377	96	5	66	439	714556253	714556627	8.370000e-27	132.0
30	TraesCS4A01G443700	chr7B	75.595	168	38	3	22	187	675422093	675421927	3.070000e-11	80.5
31	TraesCS4A01G443700	chr3A	77.128	188	34	5	337	515	123284404	123284217	2.360000e-17	100.0
32	TraesCS4A01G443700	chr3A	71.722	389	96	12	1	384	728351651	728352030	3.050000e-16	97.1
33	TraesCS4A01G443700	chr4B	71.988	332	69	16	6	329	104340388	104340073	3.980000e-10	76.8

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	TraesCS4A01G443700	chr4A	712444607	712448320	3713	False	6859.0	6859	100.0000	1	3714	1	chr4A.!!$F1	3713
1	TraesCS4A01G443700	chr4A	712111397	712114104	2707	True	4865.0	4865	99.1140	1	2705	1	chr4A.!!$R1	2704
2	TraesCS4A01G443700	chr7D	21773374	21775435	2061	False	2743.0	2743	90.8870	657	2705	1	chr7D.!!$F1	2048
3	TraesCS4A01G443700	chr7A	22197513	22199690	2177	False	1428.0	2575	91.0665	707	2705	2	chr7A.!!$F1	1998
4	TraesCS4A01G443700	chr1D	33350890	33352545	1655	True	674.5	717	90.9315	2705	3714	2	chr1D.!!$R1	1009
5	TraesCS4A01G443700	chr5D	458210604	458212217	1613	True	652.5	673	91.0565	2745	3714	2	chr5D.!!$R1	969
6	TraesCS4A01G443700	chr1A	75447945	75449472	1527	False	591.5	643	91.0355	2841	3714	2	chr1A.!!$F2	873
7	TraesCS4A01G443700	chr2B	5780096	5780828	732	True	520.0	520	79.7350	1721	2467	1	chr2B.!!$R1	746
8	TraesCS4A01G443700	chr2B	17149773	17150431	658	False	283.0	283	75.0360	1788	2461	1	chr2B.!!$F2	673

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
595	596	1.69973	TCTCTCTCGTTTCCACCACA	58.300	50.000	0.0	0.0	0.00	4.17	F
2678	2908	6.81664	TGCTATCTTGTGTAGTTGATGTAACC	59.183	38.462	0.0	0.0	40.24	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2423	2638	0.238553	GCGGAAAGTGGCTTCTTCAC	59.761	55.0	0.0	0.0	35.51	3.18	R
3489	4377	0.039035	GACCTGGGGTTGCCACATTA	59.961	55.0	0.0	0.0	35.80	1.90	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
35	36	6.207691	TCTTCATCGATCATGACAGTACAA	57.792	37.500	0.00	0.00	41.56	2.41
42	43	6.090783	TCGATCATGACAGTACAACTAACAC	58.909	40.000	0.00	0.00	0.00	3.32
46	47	5.303333	TCATGACAGTACAACTAACACCAGA	59.697	40.000	0.00	0.00	0.00	3.86
148	149	2.926242	ACCCCTTCTTCGCCGGAA	60.926	61.111	5.05	0.00	0.00	4.30
179	180	6.780706	AAACTTGTTACAGTAGACAATCGG	57.219	37.500	8.08	2.60	35.44	4.18
376	377	2.919971	GAGACACACCTCCACAAGC	58.080	57.895	0.00	0.00	0.00	4.01
407	408	1.826024	CTAGAAGCGCCACCAGGAT	59.174	57.895	2.29	0.00	36.89	3.24
595	596	1.699730	TCTCTCTCGTTTCCACCACA	58.300	50.000	0.00	0.00	0.00	4.17
2678	2908	6.816640	TGCTATCTTGTGTAGTTGATGTAACC	59.183	38.462	0.00	0.00	40.24	2.85
2719	2949	3.949842	AGTAAACTAGTCGTCAACCCC	57.050	47.619	0.00	0.00	0.00	4.95
2743	2973	0.756903	ATTCGCACGGGTTAGCCTAT	59.243	50.000	0.00	0.00	34.45	2.57
2808	3038	8.773033	AAATTCATCAAGTGGCCTTCTATTAT	57.227	30.769	3.32	0.00	0.00	1.28
2822	3052	9.247861	GGCCTTCTATTATCATGGTTATTCATT	57.752	33.333	0.00	0.00	0.00	2.57
2962	3194	8.825667	TTAGCCTACATTGTTGGAAATTTTTC	57.174	30.769	19.60	1.21	36.46	2.29
3032	3270	7.384358	ACGTTTTCAATTACCAAATCGTTTC	57.616	32.000	6.85	0.00	35.45	2.78
3092	3333	5.673337	TCTCTCTGTTTTGTATGCACAAC	57.327	39.130	5.94	5.94	44.28	3.32
3252	3494	8.997621	TTTATGTAGTAGACTTTCATGTCACC	57.002	34.615	0.00	0.00	39.27	4.02
3253	3495	5.401531	TGTAGTAGACTTTCATGTCACCC	57.598	43.478	0.00	0.00	39.27	4.61
3255	3497	4.974645	AGTAGACTTTCATGTCACCCAA	57.025	40.909	0.00	0.00	39.27	4.12
3256	3498	5.505181	AGTAGACTTTCATGTCACCCAAT	57.495	39.130	0.00	0.00	39.27	3.16
3257	3499	5.248640	AGTAGACTTTCATGTCACCCAATG	58.751	41.667	0.00	0.00	39.27	2.82
3258	3500	3.424703	AGACTTTCATGTCACCCAATGG	58.575	45.455	0.00	0.00	39.27	3.16
3447	4334	6.763303	AACAAAAGAACACACAACTTCAAC	57.237	33.333	0.00	0.00	0.00	3.18
3449	4336	6.149633	ACAAAAGAACACACAACTTCAACTC	58.850	36.000	0.00	0.00	0.00	3.01
3506	4394	1.756538	GAATAATGTGGCAACCCCAGG	59.243	52.381	0.00	0.00	46.54	4.45
3509	4397	2.730129	AATGTGGCAACCCCAGGTCC	62.730	60.000	0.00	0.00	46.54	4.46
3528	4416	2.034053	TCCAACCTGTTGTTCGCAATTC	59.966	45.455	9.03	0.00	39.55	2.17
3562	4450	6.351711	CCTTCTGGACTCTGAACTGTATGAAT	60.352	42.308	0.00	0.00	34.57	2.57
3574	4462	4.122776	ACTGTATGAATCGATGCACCTTC	58.877	43.478	8.66	0.00	0.00	3.46
3597	4485	0.538584	ATGACAGAGGCGCAGATCAA	59.461	50.000	10.83	0.00	0.00	2.57
3620	4508	4.003648	GGTGCTTGAGTAACTGCTTGTAT	58.996	43.478	0.00	0.00	0.00	2.29
3668	4556	6.016024	CCATTTATGTCATGGTCAGGTTATGG	60.016	42.308	0.00	0.00	37.07	2.74
3690	4578	4.379652	GAGTTGGTGCCAAATTGATTGTT	58.620	39.130	5.09	0.00	37.70	2.83
3691	4579	4.379652	AGTTGGTGCCAAATTGATTGTTC	58.620	39.130	5.09	0.00	37.70	3.18
3693	4581	4.620589	TGGTGCCAAATTGATTGTTCAT	57.379	36.364	0.00	0.00	37.32	2.57
3708	4596	7.380536	TGATTGTTCATGTTAGTAACCGTAGT	58.619	34.615	10.51	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	2.093075	AGGTGGTCTGCAGATCTGATTG	60.093	50.000	26.71	14.21	0.00	2.67
63	64	1.876849	AGGTGGTCTGCAGATCTGAT	58.123	50.000	26.71	10.20	0.00	2.90
65	66	1.202510	GCTAGGTGGTCTGCAGATCTG	60.203	57.143	26.71	18.84	0.00	2.90
103	104	2.813908	CGCGTTTTCGGCTAGCCT	60.814	61.111	30.55	0.00	44.29	4.58
148	149	6.537660	GTCTACTGTAACAAGTTTTGTCTGGT	59.462	38.462	0.00	0.00	44.59	4.00
179	180	2.952310	GGGCATTAACATGGAGACTTCC	59.048	50.000	0.00	0.00	44.31	3.46
376	377	1.337635	GCTTCTAGCATCATCGGAGGG	60.338	57.143	0.00	0.00	41.89	4.30
407	408	0.621571	ATTCTCCCTGCCTAGCACCA	60.622	55.000	0.00	0.00	33.79	4.17
595	596	5.801947	GCAATGTTGTTCGAAGCTTCATAAT	59.198	36.000	25.47	6.61	0.00	1.28
2423	2638	0.238553	GCGGAAAGTGGCTTCTTCAC	59.761	55.000	0.00	0.00	35.51	3.18
2678	2908	4.268405	ACTTAATTATACGCCGGAAACACG	59.732	41.667	5.05	0.00	35.80	4.49
2781	3011	5.904362	AGAAGGCCACTTGATGAATTTAC	57.096	39.130	5.01	0.00	36.97	2.01
2793	3023	5.653255	AACCATGATAATAGAAGGCCACT	57.347	39.130	5.01	6.61	0.00	4.00
2843	3073	9.681062	ACCAGCAAGTTATATTTGTGTATAGTT	57.319	29.630	0.00	0.00	0.00	2.24
2901	3133	9.287373	AGTCCATCATTTTTATGTGCAATTTTT	57.713	25.926	0.00	0.00	0.00	1.94
2904	3136	7.879160	ACAAGTCCATCATTTTTATGTGCAATT	59.121	29.630	0.00	0.00	0.00	2.32
2922	3154	9.914834	AATGTAGGCTAATATTTAACAAGTCCA	57.085	29.630	0.00	0.00	0.00	4.02
2956	3188	8.816894	TGGAGACTGAGTAGTGATAAGAAAAAT	58.183	33.333	0.00	0.00	37.25	1.82
2962	3194	6.516739	TGTTGGAGACTGAGTAGTGATAAG	57.483	41.667	0.00	0.00	37.25	1.73
3032	3270	0.942410	GCATTGTGTTGGTGCAGCAG	60.942	55.000	19.25	6.69	38.68	4.24
3107	3348	3.438087	CAGTCACCTTTCCTATTGTGCTG	59.562	47.826	0.00	0.00	31.63	4.41
3180	3421	9.651913	TTAATTTTGATGGTAAGGATTGCTTTC	57.348	29.630	0.00	0.00	0.00	2.62
3282	4169	2.513897	GCAGGATACCGTGGCACC	60.514	66.667	12.86	0.00	37.17	5.01
3341	4228	6.228258	TCGCCAGTCAACTATTAGAAGTTTT	58.772	36.000	0.00	0.00	37.61	2.43
3404	4291	9.474920	TTTTGTTTCTTATTGAAGTGCCATAAG	57.525	29.630	0.00	0.00	35.89	1.73
3447	4334	7.014230	TGGAATTTTTAAACCAGAAGGACAGAG	59.986	37.037	0.00	0.00	38.69	3.35
3449	4336	7.049799	TGGAATTTTTAAACCAGAAGGACAG	57.950	36.000	0.00	0.00	38.69	3.51
3487	4375	1.078656	ACCTGGGGTTGCCACATTATT	59.921	47.619	0.00	0.00	35.80	1.40
3489	4377	0.039035	GACCTGGGGTTGCCACATTA	59.961	55.000	0.00	0.00	35.80	1.90
3506	4394	0.736053	TTGCGAACAACAGGTTGGAC	59.264	50.000	15.84	8.46	44.45	4.02
3509	4397	2.043411	CGAATTGCGAACAACAGGTTG	58.957	47.619	10.45	10.45	44.57	3.77
3528	4416	0.534412	AGTCCAGAAGGAGCATGTCG	59.466	55.000	0.00	0.00	46.92	4.35
3562	4450	2.495669	TGTCATAGTGAAGGTGCATCGA	59.504	45.455	0.00	0.00	0.00	3.59
3574	4462	0.457443	TCTGCGCCTCTGTCATAGTG	59.543	55.000	4.18	0.00	0.00	2.74
3597	4485	2.158755	ACAAGCAGTTACTCAAGCACCT	60.159	45.455	0.00	0.00	0.00	4.00
3620	4508	5.410439	GGAGACAAAGTTATACGAAAAGGCA	59.590	40.000	0.00	0.00	0.00	4.75
3650	4538	3.181329	ACTCCATAACCTGACCATGACA	58.819	45.455	0.00	0.00	0.00	3.58
3655	4543	2.039746	CACCAACTCCATAACCTGACCA	59.960	50.000	0.00	0.00	0.00	4.02
3668	4556	3.993920	ACAATCAATTTGGCACCAACTC	58.006	40.909	0.45	0.00	39.80	3.01
3690	4578	5.981088	TTCCACTACGGTTACTAACATGA	57.019	39.130	0.00	0.00	35.57	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.