AutoCloner

Multiple sequence alignment - TraesCS5D01G149500

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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	TraesCS5D01G149500	chr5D	100.000	3978	0	0	1	3978	238545485	238549462	0.000000e+00	7347.0
1	TraesCS5D01G149500	chr5D	100.000	36	0	0	246	281	60183721	60183686	2.570000e-07	67.6
2	TraesCS5D01G149500	chr5B	95.123	3998	139	25	1	3978	266520218	266516257	0.000000e+00	6252.0
3	TraesCS5D01G149500	chr5B	79.605	152	27	3	77	227	655020231	655020379	5.440000e-19	106.0
4	TraesCS5D01G149500	chr5A	97.170	3392	86	6	593	3978	316096835	316093448	0.000000e+00	5723.0
5	TraesCS5D01G149500	chr5A	81.934	393	50	11	5	382	316099019	316098633	2.980000e-81	313.0
6	TraesCS5D01G149500	chr5A	82.246	276	27	8	229	495	316098422	316098160	6.690000e-53	219.0
7	TraesCS5D01G149500	chr4D	86.115	1959	214	26	1062	2968	107690748	107692700	0.000000e+00	2058.0
8	TraesCS5D01G149500	chr4B	86.971	1865	190	18	1071	2889	168996642	168994785	0.000000e+00	2049.0
9	TraesCS5D01G149500	chr4A	86.785	1854	193	24	1071	2889	468628966	468627130	0.000000e+00	2019.0
10	TraesCS5D01G149500	chr4A	76.000	175	32	10	112	282	162407645	162407477	9.160000e-12	82.4
11	TraesCS5D01G149500	chr3D	94.078	591	35	0	2260	2850	456924808	456925398	0.000000e+00	898.0
12	TraesCS5D01G149500	chr6B	93.989	549	33	0	2298	2846	642929630	642930178	0.000000e+00	832.0
13	TraesCS5D01G149500	chr6D	79.494	356	56	9	14	356	58670900	58671251	1.850000e-58	237.0
14	TraesCS5D01G149500	chr6D	97.222	36	1	0	246	281	327021784	327021819	1.190000e-05	62.1
15	TraesCS5D01G149500	chr2A	80.447	179	31	3	112	286	632471936	632471758	2.490000e-27	134.0
16	TraesCS5D01G149500	chr3B	79.330	179	27	2	104	281	6971317	6971148	2.510000e-22	117.0
17	TraesCS5D01G149500	chr7B	100.000	35	0	0	247	281	314274150	314274184	9.230000e-07	65.8
18	TraesCS5D01G149500	chr7B	100.000	35	0	0	247	281	314274259	314274293	9.230000e-07	65.8
19	TraesCS5D01G149500	chr7B	100.000	29	0	0	329	357	643267041	643267013	2.000000e-03	54.7
20	TraesCS5D01G149500	chr6A	97.222	36	1	0	246	281	465626242	465626277	1.190000e-05	62.1
21	TraesCS5D01G149500	chr1D	100.000	28	0	0	329	356	143376656	143376629	7.000000e-03	52.8

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	TraesCS5D01G149500	chr5D	238545485	238549462	3977	False	7347	7347	100.000000	1	3978	1	chr5D.!!$F1	3977
1	TraesCS5D01G149500	chr5B	266516257	266520218	3961	True	6252	6252	95.123000	1	3978	1	chr5B.!!$R1	3977
2	TraesCS5D01G149500	chr5A	316093448	316099019	5571	True	2085	5723	87.116667	5	3978	3	chr5A.!!$R1	3973
3	TraesCS5D01G149500	chr4D	107690748	107692700	1952	False	2058	2058	86.115000	1062	2968	1	chr4D.!!$F1	1906
4	TraesCS5D01G149500	chr4B	168994785	168996642	1857	True	2049	2049	86.971000	1071	2889	1	chr4B.!!$R1	1818
5	TraesCS5D01G149500	chr4A	468627130	468628966	1836	True	2019	2019	86.785000	1071	2889	1	chr4A.!!$R2	1818
6	TraesCS5D01G149500	chr3D	456924808	456925398	590	False	898	898	94.078000	2260	2850	1	chr3D.!!$F1	590
7	TraesCS5D01G149500	chr6B	642929630	642930178	548	False	832	832	93.989000	2298	2846	1	chr6B.!!$F1	548

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
759	2407	0.328258	CCCACCGGAATGTTTCTCCT	59.672	55.000	9.46	0.0	0.0	3.69	F
1016	2665	1.000731	GATCTCCAGCATTCCTCTCCG	59.999	57.143	0.00	0.0	0.0	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2871	4569	2.430465	TGGCATCAAAGCTTCTCTGTC	58.570	47.619	0.0	0.00	34.17	3.51	R
2986	4693	0.317799	GACAACATGGCATGCACCAA	59.682	50.000	26.7	1.71	44.65	3.67	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
45	46	4.720046	TCTGATAAGTCGGCAGATCTAGT	58.280	43.478	0.00	0.00	34.02	2.57
52	53	2.435693	GGCAGATCTAGTGCGGGGT	61.436	63.158	0.00	0.00	42.19	4.95
168	172	2.432628	AACGACTGCGCTAGTGCC	60.433	61.111	24.82	9.22	40.53	5.01
376	762	7.959651	CAGAAATACATACAACAAGAGTCTTGC	59.040	37.037	28.88	10.64	0.00	4.01
378	764	9.151471	GAAATACATACAACAAGAGTCTTGCTA	57.849	33.333	28.88	17.28	0.00	3.49
431	817	3.861113	CCATCAATGAATCAAACGGCTTG	59.139	43.478	0.00	0.00	36.25	4.01
591	2230	8.807948	TTGAGGGGTTTTTGAGATCTTAATAG	57.192	34.615	0.11	0.00	0.00	1.73
603	2242	7.196187	TGAGATCTTAATAGGGGGTATATGCA	58.804	38.462	0.00	0.00	0.00	3.96
733	2380	1.545759	AGTGACGATTACGCATCACG	58.454	50.000	0.00	0.00	44.45	4.35
759	2407	0.328258	CCCACCGGAATGTTTCTCCT	59.672	55.000	9.46	0.00	0.00	3.69
771	2419	4.890158	TGTTTCTCCTCTATGACAAGCA	57.110	40.909	0.00	0.00	0.00	3.91
814	2462	2.725759	CGCGTGTCATCCAATGAAACAG	60.726	50.000	10.12	5.00	45.79	3.16
1015	2664	2.037511	CAGATCTCCAGCATTCCTCTCC	59.962	54.545	0.00	0.00	0.00	3.71
1016	2665	1.000731	GATCTCCAGCATTCCTCTCCG	59.999	57.143	0.00	0.00	0.00	4.63
1017	2666	1.045350	TCTCCAGCATTCCTCTCCGG	61.045	60.000	0.00	0.00	0.00	5.14
1018	2667	2.203126	CCAGCATTCCTCTCCGGC	60.203	66.667	0.00	0.00	0.00	6.13
1019	2668	2.739996	CCAGCATTCCTCTCCGGCT	61.740	63.158	0.00	0.00	34.64	5.52
1105	2758	2.762234	CGCGCCGACTCCTTCTACT	61.762	63.158	0.00	0.00	0.00	2.57
2871	4569	5.049474	TGTCAGTTCTTTCATGATTCGGTTG	60.049	40.000	0.00	0.00	0.00	3.77
2905	4606	3.312718	GCCATGTGCTTGCCCCAA	61.313	61.111	0.00	0.00	36.87	4.12
2968	4675	7.181125	AGGCTTGTTCTCTCTAAATAAAGGAGA	59.819	37.037	0.00	0.00	35.25	3.71
2986	4693	3.054802	GGAGATTGACTGGTTGAGGATGT	60.055	47.826	0.00	0.00	0.00	3.06
3150	4857	5.147032	CCCCATTAGCAAAGGATAATCCAA	58.853	41.667	0.00	0.00	39.61	3.53
3333	5041	5.861787	GTGTCAAGTTTTTAGTGTGCAAACT	59.138	36.000	15.35	15.35	41.50	2.66
3457	5165	8.328758	AGTTCCATACCATTCTTACAATGAGAA	58.671	33.333	0.00	0.00	37.52	2.87
3474	5182	7.496591	ACAATGAGAACAAGCAATTTTGAACAT	59.503	29.630	0.00	0.00	0.00	2.71
3504	5212	5.765510	TGTTACAGAGGGCCAATTTATCAT	58.234	37.500	6.18	0.00	0.00	2.45
3534	5243	0.475906	AGGGCTATGGATGAACTGCC	59.524	55.000	0.00	0.00	39.61	4.85
3548	5257	0.971386	ACTGCCATTTTTCTGCCCAG	59.029	50.000	0.00	0.00	0.00	4.45
3583	5292	8.994429	ACATGTAAATAGTCTGAACTCTGAAG	57.006	34.615	0.00	0.00	36.92	3.02
3697	5407	6.811665	CAGTGATTTGATTCATTCATGTGCTT	59.188	34.615	0.00	0.00	33.34	3.91
3704	5414	7.263100	TGATTCATTCATGTGCTTGTATACC	57.737	36.000	0.00	0.00	0.00	2.73
3789	5499	6.231258	TCATAGATCTTTGATGAGTGTGCT	57.769	37.500	11.36	0.00	0.00	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	0.101399	CGCACTAGATCTGCCGACTT	59.899	55.000	5.18	0.00	0.00	3.01
52	53	1.118965	TTGAGTGAAGGAGGCGGACA	61.119	55.000	0.00	0.00	0.00	4.02
92	96	4.141287	CAGAGATAAGATGAGAGACGGGT	58.859	47.826	0.00	0.00	0.00	5.28
147	151	0.859232	CACTAGCGCAGTCGTTGTTT	59.141	50.000	11.47	0.00	34.26	2.83
151	155	2.432628	GGCACTAGCGCAGTCGTT	60.433	61.111	11.47	0.00	43.41	3.85
213	217	6.817270	TCGCCGTATCTAATTTTCTACAAC	57.183	37.500	0.00	0.00	0.00	3.32
217	221	6.365247	GCATCTTCGCCGTATCTAATTTTCTA	59.635	38.462	0.00	0.00	0.00	2.10
230	235	2.311294	GCAATAGCATCTTCGCCGT	58.689	52.632	0.00	0.00	41.58	5.68
281	286	2.943033	CAAGACCCGTGTTGAACTCTTT	59.057	45.455	0.00	0.00	36.09	2.52
282	287	2.093128	ACAAGACCCGTGTTGAACTCTT	60.093	45.455	11.29	0.00	37.30	2.85
284	289	1.949465	ACAAGACCCGTGTTGAACTC	58.051	50.000	11.29	0.00	37.30	3.01
294	380	3.369546	AATTTTCTGCAACAAGACCCG	57.630	42.857	0.00	0.00	0.00	5.28
297	383	9.346725	CTCCTTTATAATTTTCTGCAACAAGAC	57.653	33.333	0.00	0.00	0.00	3.01
361	747	3.134458	GCTGTAGCAAGACTCTTGTTGT	58.866	45.455	18.16	7.81	41.59	3.32
376	762	5.390991	GGATCGTTTCTCCTTTTTGCTGTAG	60.391	44.000	0.00	0.00	0.00	2.74
378	764	3.253432	GGATCGTTTCTCCTTTTTGCTGT	59.747	43.478	0.00	0.00	0.00	4.40
392	778	3.007940	TGATGGAGTTGTCTGGATCGTTT	59.992	43.478	0.00	0.00	0.00	3.60
431	817	1.373121	GTAAGATCCGCCGGCTAGC	60.373	63.158	26.68	15.54	0.00	3.42
436	822	0.527817	GTCTGTGTAAGATCCGCCGG	60.528	60.000	0.00	0.00	37.23	6.13
440	826	2.631418	ACGTGTCTGTGTAAGATCCG	57.369	50.000	0.00	0.00	37.23	4.18
561	2200	5.840693	AGATCTCAAAAACCCCTCAAACAAT	59.159	36.000	0.00	0.00	0.00	2.71
563	2202	4.803452	AGATCTCAAAAACCCCTCAAACA	58.197	39.130	0.00	0.00	0.00	2.83
564	2203	5.791336	AAGATCTCAAAAACCCCTCAAAC	57.209	39.130	0.00	0.00	0.00	2.93
591	2230	2.047061	TGTGAGACTGCATATACCCCC	58.953	52.381	0.00	0.00	0.00	5.40
603	2242	2.760650	TCCAGCGTATGATTGTGAGACT	59.239	45.455	0.00	0.00	0.00	3.24
679	2318	0.250513	CTGGGCTGGTTCTGACCTAC	59.749	60.000	0.00	0.00	46.66	3.18
733	2380	0.538746	ACATTCCGGTGGGTTGTTCC	60.539	55.000	0.00	0.00	30.16	3.62
759	2407	1.220749	GGGGCGTGCTTGTCATAGA	59.779	57.895	0.00	0.00	0.00	1.98
771	2419	4.715523	CACATTCCGGTGGGGCGT	62.716	66.667	0.00	0.00	35.13	5.68
1015	2664	3.775654	GTGGAGGTGGGAGAGCCG	61.776	72.222	0.00	0.00	33.83	5.52
1016	2665	3.403558	GGTGGAGGTGGGAGAGCC	61.404	72.222	0.00	0.00	0.00	4.70
1017	2666	3.775654	CGGTGGAGGTGGGAGAGC	61.776	72.222	0.00	0.00	0.00	4.09
1018	2667	1.192146	TTTCGGTGGAGGTGGGAGAG	61.192	60.000	0.00	0.00	0.00	3.20
1019	2668	0.765135	TTTTCGGTGGAGGTGGGAGA	60.765	55.000	0.00	0.00	0.00	3.71
1553	3245	3.733960	CACGGAGGTGCTCGTCGA	61.734	66.667	0.00	0.00	37.35	4.20
2871	4569	2.430465	TGGCATCAAAGCTTCTCTGTC	58.570	47.619	0.00	0.00	34.17	3.51
2968	4675	3.181429	ACCAACATCCTCAACCAGTCAAT	60.181	43.478	0.00	0.00	0.00	2.57
2986	4693	0.317799	GACAACATGGCATGCACCAA	59.682	50.000	26.70	1.71	44.65	3.67
3150	4857	4.897509	TCAGGTTGACATCTGAATCTGT	57.102	40.909	6.56	0.00	37.11	3.41
3333	5041	5.582269	ACATAGAGTAGAGTAACGCGTGTTA	59.418	40.000	14.98	17.24	39.54	2.41
3435	5143	7.864108	TGTTCTCATTGTAAGAATGGTATGG	57.136	36.000	0.00	0.00	35.35	2.74
3457	5165	6.477688	CAGAAGTCATGTTCAAAATTGCTTGT	59.522	34.615	0.00	0.00	0.00	3.16
3474	5182	1.623811	GGCCCTCTGTAACAGAAGTCA	59.376	52.381	0.00	0.00	40.18	3.41
3504	5212	1.338674	CCATAGCCCTGTGAACGACAA	60.339	52.381	0.00	0.00	32.80	3.18
3534	5243	4.219070	TCAGAACATCTGGGCAGAAAAATG	59.781	41.667	7.47	0.00	44.39	2.32
3566	5275	6.268847	ACTTGTTCCTTCAGAGTTCAGACTAT	59.731	38.462	0.00	0.00	35.88	2.12
3583	5292	4.820894	AGTACCCTATGACACTTGTTCC	57.179	45.455	0.00	0.00	0.00	3.62
3697	5407	8.086522	GCTAAGGATTTCTATCAACGGTATACA	58.913	37.037	5.01	0.00	32.09	2.29
3704	5414	4.804139	ACACGCTAAGGATTTCTATCAACG	59.196	41.667	0.00	0.00	32.09	4.10
3789	5499	3.490439	ACACCATGTGTTGACATCTCA	57.510	42.857	0.00	0.00	45.08	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.