AutoCloner

Multiple sequence alignment - TraesCS1D01G255200

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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	TraesCS1D01G255200	chr1D	100.000	3887	0	0	1	3887	347787883	347783997	0.000000e+00	7179.0
1	TraesCS1D01G255200	chr1B	97.642	2799	48	10	434	3224	469162240	469159452	0.000000e+00	4787.0
2	TraesCS1D01G255200	chr1B	96.409	362	12	1	1	361	469162627	469162266	2.590000e-166	595.0
3	TraesCS1D01G255200	chr1B	89.211	380	22	7	3477	3855	469159179	469158818	1.270000e-124	457.0
4	TraesCS1D01G255200	chr1B	90.361	83	6	2	3144	3224	306072267	306072185	1.480000e-19	108.0
5	TraesCS1D01G255200	chr1A	98.549	2274	31	1	922	3193	448629312	448627039	0.000000e+00	4015.0
6	TraesCS1D01G255200	chr1A	94.503	855	25	3	4	855	448630149	448629314	0.000000e+00	1299.0
7	TraesCS1D01G255200	chr1A	89.620	684	47	12	3224	3887	448626954	448626275	0.000000e+00	848.0
8	TraesCS1D01G255200	chr7B	91.566	83	5	1	3144	3224	576660241	576660159	3.170000e-21	113.0
9	TraesCS1D01G255200	chr7B	88.506	87	8	1	3140	3224	150530398	150530312	1.910000e-18	104.0
10	TraesCS1D01G255200	chr2D	78.495	186	27	11	3383	3560	376691587	376691407	4.110000e-20	110.0
11	TraesCS1D01G255200	chr2D	87.931	58	6	1	3389	3446	340267978	340267922	2.510000e-07	67.6
12	TraesCS1D01G255200	chr7D	77.033	209	35	6	3388	3585	279743774	279743568	1.480000e-19	108.0
13	TraesCS1D01G255200	chr6A	87.778	90	9	1	3137	3224	607089371	607089282	1.910000e-18	104.0
14	TraesCS1D01G255200	chr6A	87.778	90	9	1	3137	3224	607224557	607224468	1.910000e-18	104.0
15	TraesCS1D01G255200	chr2A	88.043	92	6	2	3135	3221	117393000	117393091	1.910000e-18	104.0
16	TraesCS1D01G255200	chr2A	76.136	176	32	6	3383	3551	668277009	668277181	2.490000e-12	84.2
17	TraesCS1D01G255200	chr4B	82.609	115	12	5	3113	3224	640023699	640023590	1.150000e-15	95.3
18	TraesCS1D01G255200	chr3B	88.406	69	8	0	3383	3451	488531255	488531323	2.490000e-12	84.2
19	TraesCS1D01G255200	chr4D	91.379	58	4	1	3389	3446	93611335	93611279	1.160000e-10	78.7
20	TraesCS1D01G255200	chr3D	86.441	59	6	2	3394	3451	374927432	374927489	3.240000e-06	63.9

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	TraesCS1D01G255200	chr1D	347783997	347787883	3886	True	7179.000000	7179	100.000000	1	3887	1	chr1D.!!$R1	3886
1	TraesCS1D01G255200	chr1B	469158818	469162627	3809	True	1946.333333	4787	94.420667	1	3855	3	chr1B.!!$R2	3854
2	TraesCS1D01G255200	chr1A	448626275	448630149	3874	True	2054.000000	4015	94.224000	4	3887	3	chr1A.!!$R1	3883

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
485	487	1.062488	AACCACTGCCAGGAAGAGGT	61.062	55.000	10.91	10.91	39.92	3.85	F
1521	1527	0.615331	TCTCATCAGACCAGGCAACC	59.385	55.000	0.00	0.00	37.17	3.77	F
2217	2223	1.153568	CGGAAGCTTGCGAGATCCA	60.154	57.895	33.47	0.00	45.24	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1821	1827	0.890683	CCAAGCCACTTGAATCACCC	59.109	55.0	8.87	43.42	4.61	R
2552	2558	0.105760	TGAGCTCCATCCTCCTCCTC	60.106	60.0	12.15	0.00	3.71	R
3224	3237	0.679321	CTGCCTTCTCAGCTTTCCCC	60.679	60.0	0.00	0.00	4.81	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
423	425	4.002982	ACGAGCTGCATTAGTTTTCATGA	58.997	39.130	1.02	0.00	0.00	3.07
485	487	1.062488	AACCACTGCCAGGAAGAGGT	61.062	55.000	10.91	10.91	39.92	3.85
1096	1102	1.281867	CTGTCAAGCCAGTGGGGAATA	59.718	52.381	12.15	0.00	40.01	1.75
1101	1107	0.916358	AGCCAGTGGGGAATAGCACT	60.916	55.000	12.15	0.00	40.01	4.40
1317	1323	3.751479	AAGGAAAAATCAACCAGCACC	57.249	42.857	0.00	0.00	0.00	5.01
1320	1326	0.749649	AAAAATCAACCAGCACCGCA	59.250	45.000	0.00	0.00	0.00	5.69
1521	1527	0.615331	TCTCATCAGACCAGGCAACC	59.385	55.000	0.00	0.00	37.17	3.77
1564	1570	2.563179	GGCTGTCTTGAGGAGTCTGTTA	59.437	50.000	0.00	0.00	0.00	2.41
1737	1743	5.357314	GGTAGAAAGGGCTATTGTTTCTTCC	59.643	44.000	2.16	3.49	40.28	3.46
1821	1827	1.929836	GCATCTAAGCCTGAAGTGTCG	59.070	52.381	0.00	0.00	0.00	4.35
1977	1983	3.547054	TTAGTAAATGGTAGTGGCCCG	57.453	47.619	0.00	0.00	0.00	6.13
2217	2223	1.153568	CGGAAGCTTGCGAGATCCA	60.154	57.895	33.47	0.00	45.24	3.41
2244	2250	1.258982	GTAATGCAGCGTCCTCAATCG	59.741	52.381	0.00	0.00	0.00	3.34
2300	2306	4.818005	CCATAGTATGTTTGCATCAGAGCA	59.182	41.667	9.28	0.00	43.99	4.26
2490	2496	1.304879	TGCTAATGGTTGGGGTGGC	60.305	57.895	0.00	0.00	0.00	5.01
2552	2558	2.390599	CGGCACATGGGACGTTCAG	61.391	63.158	17.19	0.00	0.00	3.02
2553	2559	1.003839	GGCACATGGGACGTTCAGA	60.004	57.895	0.00	0.00	0.00	3.27
2554	2560	1.021390	GGCACATGGGACGTTCAGAG	61.021	60.000	0.00	0.00	0.00	3.35
3224	3237	5.461737	TCGCTTTTTAAATTTGTTGAGGCTG	59.538	36.000	0.00	0.00	0.00	4.85
3225	3238	5.333263	CGCTTTTTAAATTTGTTGAGGCTGG	60.333	40.000	0.00	0.00	0.00	4.85
3226	3239	5.049474	GCTTTTTAAATTTGTTGAGGCTGGG	60.049	40.000	0.00	0.00	0.00	4.45
3227	3240	4.615588	TTTAAATTTGTTGAGGCTGGGG	57.384	40.909	0.00	0.00	0.00	4.96
3230	3243	2.397044	ATTTGTTGAGGCTGGGGAAA	57.603	45.000	0.00	0.00	0.00	3.13
3231	3244	1.703411	TTTGTTGAGGCTGGGGAAAG	58.297	50.000	0.00	0.00	0.00	2.62
3232	3245	0.827507	TTGTTGAGGCTGGGGAAAGC	60.828	55.000	0.00	0.00	42.75	3.51
3233	3246	1.075659	GTTGAGGCTGGGGAAAGCT	59.924	57.895	0.00	0.00	43.06	3.74
3237	3313	1.539869	AGGCTGGGGAAAGCTGAGA	60.540	57.895	0.00	0.00	43.06	3.27
3242	3318	1.380302	GGGGAAAGCTGAGAAGGCA	59.620	57.895	0.00	0.00	0.00	4.75
3299	3375	5.887035	AGTATGTAGCTTACTCGAGGTTTCT	59.113	40.000	18.41	10.62	0.00	2.52
3309	3385	4.345854	ACTCGAGGTTTCTAGTCCAATCT	58.654	43.478	18.41	0.00	0.00	2.40
3338	3414	3.246699	CGTTTACGAAGGTTGAGAAAGCA	59.753	43.478	0.00	0.00	43.02	3.91
3371	3447	3.290948	TTTTGGATCCAGGTAATCCCG	57.709	47.619	15.53	0.00	41.78	5.14
3372	3448	2.184088	TTGGATCCAGGTAATCCCGA	57.816	50.000	15.53	0.00	41.78	5.14
3381	3457	4.013728	CCAGGTAATCCCGAAATGTTTGA	58.986	43.478	0.00	0.00	38.74	2.69
3383	3459	5.047660	CCAGGTAATCCCGAAATGTTTGAAA	60.048	40.000	0.00	0.00	38.74	2.69
3384	3460	6.451393	CAGGTAATCCCGAAATGTTTGAAAA	58.549	36.000	0.00	0.00	38.74	2.29
3388	3464	7.600752	GGTAATCCCGAAATGTTTGAAAATTGA	59.399	33.333	0.00	0.00	0.00	2.57
3389	3465	8.983724	GTAATCCCGAAATGTTTGAAAATTGAA	58.016	29.630	0.00	0.00	0.00	2.69
3391	3467	5.460419	TCCCGAAATGTTTGAAAATTGAACG	59.540	36.000	0.00	0.00	0.00	3.95
3438	3528	3.430374	GCGAGGATGGCAAGTTTAGTAGA	60.430	47.826	0.00	0.00	40.68	2.59
3445	3535	6.017852	GGATGGCAAGTTTAGTAGATAAGCAC	60.018	42.308	0.00	0.00	0.00	4.40
3451	3541	5.484715	AGTTTAGTAGATAAGCACGGCAAA	58.515	37.500	0.00	0.00	0.00	3.68
3453	3543	6.258068	AGTTTAGTAGATAAGCACGGCAAATC	59.742	38.462	0.00	1.75	0.00	2.17
3454	3544	3.467803	AGTAGATAAGCACGGCAAATCC	58.532	45.455	0.00	0.00	0.00	3.01
3476	3567	0.175302	CTGTGGTTTGCTTGTTGCCA	59.825	50.000	0.00	0.00	42.00	4.92
3513	3604	2.287608	ACTAAAGTTGCCTCTTTTGCGC	60.288	45.455	0.00	0.00	38.40	6.09
3518	3609	0.038343	TTGCCTCTTTTGCGCCAATC	60.038	50.000	4.18	0.00	0.00	2.67
3582	3674	7.646548	AGCCTAACTTTTGGGATTTATCTTC	57.353	36.000	0.00	0.00	32.08	2.87
3732	3825	0.399519	GGGGCTGCCTACCTACCTAA	60.400	60.000	19.68	0.00	0.00	2.69
3760	3853	3.537206	AAAGTGCGGCGCTCTTCCT	62.537	57.895	38.46	26.33	40.70	3.36
3776	3869	5.128991	GCTCTTCCTTAGCTAAAAGGTCCTA	59.871	44.000	13.80	0.00	45.37	2.94
3856	3949	1.468914	GAAGACATTTCCGTCCCTTGC	59.531	52.381	0.00	0.00	36.52	4.01
3871	3964	2.797866	CTTGCGCCAAAGCTCTGCAG	62.798	60.000	7.63	7.63	34.89	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	2.598394	GCAAGGCTGACCCAAGCA	60.598	61.111	0.00	0.00	45.43	3.91
239	240	6.530181	GCAACCTTTTTCCATTTTATCTACGG	59.470	38.462	0.00	0.00	0.00	4.02
402	404	4.604843	TCATGAAAACTAATGCAGCTCG	57.395	40.909	0.00	0.00	0.00	5.03
423	425	3.598019	AAGCGGATGCATGTCAAAAAT	57.402	38.095	2.46	0.00	46.23	1.82
485	487	7.328277	ACATTCAAACTGTTGCAACTAAGTA	57.672	32.000	28.61	11.09	34.50	2.24
580	582	5.957771	AAGTATTCAGCTGACCCAATAGA	57.042	39.130	18.03	0.00	0.00	1.98
1101	1107	7.228590	AGAGGTTATTAAAAGTACTTGCACCA	58.771	34.615	9.34	0.00	0.00	4.17
1317	1323	2.179517	GAGTCCACTCGAGGTGCG	59.820	66.667	18.41	1.86	44.08	5.34
1521	1527	4.253685	CCTCGTTATGTATAAGGGCCATG	58.746	47.826	6.18	0.00	0.00	3.66
1564	1570	4.342092	GCCATCAAAATTACATAGCCAGGT	59.658	41.667	0.00	0.00	0.00	4.00
1737	1743	2.432510	AGCCTTTTCTAGATCACCCTCG	59.567	50.000	0.00	0.00	0.00	4.63
1821	1827	0.890683	CCAAGCCACTTGAATCACCC	59.109	55.000	8.87	0.00	43.42	4.61
1977	1983	3.889538	ACCCTTTAACTGCAGGTTCTTTC	59.110	43.478	19.93	0.00	39.17	2.62
2084	2090	2.846206	ACATAAGGAGCTGATGGAACCA	59.154	45.455	0.00	0.00	0.00	3.67
2217	2223	2.233922	AGGACGCTGCATTACAACTACT	59.766	45.455	0.00	0.00	0.00	2.57
2300	2306	4.044065	TCATGTACCATTCCCTTGAAGGTT	59.956	41.667	10.82	0.00	35.23	3.50
2490	2496	1.925455	ACCTCCAGGACCCCATGTG	60.925	63.158	0.00	0.00	38.94	3.21
2552	2558	0.105760	TGAGCTCCATCCTCCTCCTC	60.106	60.000	12.15	0.00	0.00	3.71
2553	2559	0.567182	ATGAGCTCCATCCTCCTCCT	59.433	55.000	12.15	0.00	0.00	3.69
2554	2560	0.975887	GATGAGCTCCATCCTCCTCC	59.024	60.000	12.15	0.00	44.59	4.30
2937	2946	7.420800	ACAAGAACAGAAACAAATGACATCTC	58.579	34.615	0.00	0.00	0.00	2.75
3202	3215	5.049474	CCCAGCCTCAACAAATTTAAAAAGC	60.049	40.000	0.00	0.00	0.00	3.51
3203	3216	5.469760	CCCCAGCCTCAACAAATTTAAAAAG	59.530	40.000	0.00	0.00	0.00	2.27
3224	3237	0.679321	CTGCCTTCTCAGCTTTCCCC	60.679	60.000	0.00	0.00	0.00	4.81
3225	3238	2.865492	CTGCCTTCTCAGCTTTCCC	58.135	57.895	0.00	0.00	0.00	3.97
3261	3337	5.045869	AGCTACATACTGGCCAGTTCTTTTA	60.046	40.000	41.69	24.25	42.54	1.52
3299	3375	8.394971	TCGTAAACGGATAATAGATTGGACTA	57.605	34.615	2.24	0.00	40.29	2.59
3309	3385	7.099266	TCTCAACCTTCGTAAACGGATAATA	57.901	36.000	2.24	0.00	40.29	0.98
3322	3398	2.159599	GCATCTGCTTTCTCAACCTTCG	60.160	50.000	0.00	0.00	38.21	3.79
3367	3443	5.460419	CGTTCAATTTTCAAACATTTCGGGA	59.540	36.000	0.00	0.00	0.00	5.14
3368	3444	5.233263	ACGTTCAATTTTCAAACATTTCGGG	59.767	36.000	0.00	0.00	0.00	5.14
3372	3448	9.884465	TGAAAAACGTTCAATTTTCAAACATTT	57.116	22.222	18.69	4.44	46.70	2.32
3381	3457	8.250538	AGTTGACATGAAAAACGTTCAATTTT	57.749	26.923	0.00	0.00	31.55	1.82
3383	3459	7.826260	AAGTTGACATGAAAAACGTTCAATT	57.174	28.000	0.00	0.00	31.55	2.32
3384	3460	7.826260	AAAGTTGACATGAAAAACGTTCAAT	57.174	28.000	0.00	0.00	31.55	2.57
3451	3541	1.238439	CAAGCAAACCACAGACGGAT	58.762	50.000	0.00	0.00	0.00	4.18
3453	3543	0.738389	AACAAGCAAACCACAGACGG	59.262	50.000	0.00	0.00	0.00	4.79
3454	3544	1.826327	CAACAAGCAAACCACAGACG	58.174	50.000	0.00	0.00	0.00	4.18
3582	3674	5.530915	TCCAGCAATCCAAAATAATACGGAG	59.469	40.000	0.00	0.00	0.00	4.63
3732	3825	1.079127	CCGCACTTTCCGATCACCT	60.079	57.895	0.00	0.00	0.00	4.00
3760	3853	4.643784	CCGAGTCTAGGACCTTTTAGCTAA	59.356	45.833	0.86	0.86	32.18	3.09
3776	3869	1.890041	CTCGAGCGATCCCGAGTCT	60.890	63.158	14.83	0.00	44.99	3.24
3856	3949	3.324099	CTGCTGCAGAGCTTTGGCG	62.324	63.158	24.88	0.00	46.39	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.