AutoCloner

Multiple sequence alignment - TraesCS5A01G021600

Loading Multiple Alignment...

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	TraesCS5A01G021600	chr5A	100.000	3642	0	0	1	3642	17624359	17628000	0.000000e+00	6726
1	TraesCS5A01G021600	chr5A	91.384	1358	92	16	1973	3312	17676239	17674889	0.000000e+00	1836
2	TraesCS5A01G021600	chr5A	92.526	669	50	0	928	1596	17677412	17676744	0.000000e+00	959
3	TraesCS5A01G021600	chr5A	95.205	292	13	1	1686	1976	17676593	17676302	9.210000e-126	460
4	TraesCS5A01G021600	chr5A	94.495	109	5	1	1581	1688	17676728	17676620	2.250000e-37	167
5	TraesCS5A01G021600	chr5D	96.725	1649	30	4	1686	3312	24977764	24976118	0.000000e+00	2724
6	TraesCS5A01G021600	chr5D	96.548	927	29	1	1	927	424050734	424049811	0.000000e+00	1531
7	TraesCS5A01G021600	chr5D	98.688	762	9	1	928	1688	24978553	24977792	0.000000e+00	1351
8	TraesCS5A01G021600	chr5D	91.304	345	15	8	3307	3642	24975655	24975317	1.190000e-124	457
9	TraesCS5A01G021600	chr2A	96.137	932	35	1	1	931	423770369	423771300	0.000000e+00	1520
10	TraesCS5A01G021600	chr2A	84.392	929	127	13	2	915	654864634	654865559	0.000000e+00	896
11	TraesCS5A01G021600	chr3A	95.532	940	29	4	1	927	746539583	746538644	0.000000e+00	1491
12	TraesCS5A01G021600	chr3A	83.387	927	131	16	5	911	36883409	36882486	0.000000e+00	837
13	TraesCS5A01G021600	chr1B	92.349	928	70	1	1	927	676250606	676249679	0.000000e+00	1319
14	TraesCS5A01G021600	chr3B	92.142	929	63	3	1	929	94682741	94683659	0.000000e+00	1303
15	TraesCS5A01G021600	chr3B	85.453	928	118	13	2	915	749283244	749284168	0.000000e+00	950
16	TraesCS5A01G021600	chr3B	93.421	76	5	0	3567	3642	260430891	260430966	2.970000e-21	113
17	TraesCS5A01G021600	chr3B	92.208	77	5	1	3567	3642	140262892	140262816	1.380000e-19	108
18	TraesCS5A01G021600	chr3B	92.105	76	6	0	3567	3642	260445145	260445220	1.380000e-19	108
19	TraesCS5A01G021600	chr4B	89.412	765	76	5	928	1688	35254462	35255225	0.000000e+00	959
20	TraesCS5A01G021600	chr4B	83.603	927	127	21	2	911	656868634	656869552	0.000000e+00	846
21	TraesCS5A01G021600	chr4B	83.607	793	99	21	2043	2820	35255773	35256549	0.000000e+00	715
22	TraesCS5A01G021600	chr4B	91.030	301	23	3	1670	1966	35255233	35255533	1.570000e-108	403
23	TraesCS5A01G021600	chr4B	90.789	76	7	0	3567	3642	653970858	653970933	6.430000e-18	102
24	TraesCS5A01G021600	chr4A	89.281	765	76	6	928	1688	578557528	578556766	0.000000e+00	953
25	TraesCS5A01G021600	chr4A	84.956	791	87	18	2046	2820	578556225	578555451	0.000000e+00	773
26	TraesCS5A01G021600	chr4A	90.879	307	24	3	1670	1972	578556758	578556452	3.390000e-110	409
27	TraesCS5A01G021600	chr4D	89.164	766	75	8	928	1688	23319357	23320119	0.000000e+00	948
28	TraesCS5A01G021600	chr4D	85.075	804	87	18	2032	2820	23320731	23321516	0.000000e+00	789
29	TraesCS5A01G021600	chr4D	91.362	301	22	3	1670	1966	23320127	23320427	3.390000e-110	409
30	TraesCS5A01G021600	chr5B	88.294	803	76	13	1183	1975	17949215	17950009	0.000000e+00	946
31	TraesCS5A01G021600	chr5B	81.938	454	36	17	1973	2412	17950081	17950502	3.480000e-90	342
32	TraesCS5A01G021600	chr5B	90.000	150	14	1	1044	1193	17948670	17948818	3.710000e-45	193
33	TraesCS5A01G021600	chr7A	82.725	932	141	15	2	915	65493611	65494540	0.000000e+00	811
34	TraesCS5A01G021600	chr1D	88.700	646	66	4	1	642	124104401	124103759	0.000000e+00	782
35	TraesCS5A01G021600	chr1D	92.115	279	20	2	638	915	124095231	124094954	3.410000e-105	392
36	TraesCS5A01G021600	chr1A	90.909	77	7	0	3566	3642	52458240	52458316	1.790000e-18	104
37	TraesCS5A01G021600	chr2D	90.789	76	7	0	3567	3642	540546310	540546385	6.430000e-18	102
38	TraesCS5A01G021600	chr6B	90.667	75	7	0	3567	3641	335346043	335346117	2.310000e-17	100
39	TraesCS5A01G021600	chr7B	87.500	88	8	3	3554	3641	716043164	716043248	8.320000e-17	99

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	TraesCS5A01G021600	chr5A	17624359	17628000	3641	False	6726.000000	6726	100.000000	1	3642	1	chr5A.!!$F1	3641
1	TraesCS5A01G021600	chr5A	17674889	17677412	2523	True	855.500000	1836	93.402500	928	3312	4	chr5A.!!$R1	2384
2	TraesCS5A01G021600	chr5D	424049811	424050734	923	True	1531.000000	1531	96.548000	1	927	1	chr5D.!!$R1	926
3	TraesCS5A01G021600	chr5D	24975317	24978553	3236	True	1510.666667	2724	95.572333	928	3642	3	chr5D.!!$R2	2714
4	TraesCS5A01G021600	chr2A	423770369	423771300	931	False	1520.000000	1520	96.137000	1	931	1	chr2A.!!$F1	930
5	TraesCS5A01G021600	chr2A	654864634	654865559	925	False	896.000000	896	84.392000	2	915	1	chr2A.!!$F2	913
6	TraesCS5A01G021600	chr3A	746538644	746539583	939	True	1491.000000	1491	95.532000	1	927	1	chr3A.!!$R2	926
7	TraesCS5A01G021600	chr3A	36882486	36883409	923	True	837.000000	837	83.387000	5	911	1	chr3A.!!$R1	906
8	TraesCS5A01G021600	chr1B	676249679	676250606	927	True	1319.000000	1319	92.349000	1	927	1	chr1B.!!$R1	926
9	TraesCS5A01G021600	chr3B	94682741	94683659	918	False	1303.000000	1303	92.142000	1	929	1	chr3B.!!$F1	928
10	TraesCS5A01G021600	chr3B	749283244	749284168	924	False	950.000000	950	85.453000	2	915	1	chr3B.!!$F4	913
11	TraesCS5A01G021600	chr4B	656868634	656869552	918	False	846.000000	846	83.603000	2	911	1	chr4B.!!$F2	909
12	TraesCS5A01G021600	chr4B	35254462	35256549	2087	False	692.333333	959	88.016333	928	2820	3	chr4B.!!$F3	1892
13	TraesCS5A01G021600	chr4A	578555451	578557528	2077	True	711.666667	953	88.372000	928	2820	3	chr4A.!!$R1	1892
14	TraesCS5A01G021600	chr4D	23319357	23321516	2159	False	715.333333	948	88.533667	928	2820	3	chr4D.!!$F1	1892
15	TraesCS5A01G021600	chr5B	17948670	17950502	1832	False	493.666667	946	86.744000	1044	2412	3	chr5B.!!$F1	1368
16	TraesCS5A01G021600	chr7A	65493611	65494540	929	False	811.000000	811	82.725000	2	915	1	chr7A.!!$F1	913
17	TraesCS5A01G021600	chr1D	124103759	124104401	642	True	782.000000	782	88.700000	1	642	1	chr1D.!!$R2	641

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
309	311	3.553597	GTGGTCGACGATCTGATCC	57.446	57.895	9.92	1.19	0.00	3.36	F
593	615	4.722535	AGAGGAAGCGGGGGCAGA	62.723	66.667	0.00	0.00	0.00	4.26	F
1352	1816	3.853355	AGGAAGGCCTCACATTCATAG	57.147	47.619	5.23	0.00	42.19	2.23	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1352	1816	0.035439	TCGGGATGGTCAAAAGGAGC	60.035	55.000	44.35	4.70	R
1684	2182	3.152341	ACAAGAAAGGACAGCCTGAATG	58.848	45.455	46.28	2.67	R
3236	4042	0.690192	TTCCTTGCCATCGTCTCCAA	59.310	50.000	0.00	3.53	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
309	311	3.553597	GTGGTCGACGATCTGATCC	57.446	57.895	9.92	1.19	0.00	3.36
593	615	4.722535	AGAGGAAGCGGGGGCAGA	62.723	66.667	0.00	0.00	0.00	4.26
1152	1208	6.153680	TGACAACACCAGAAAACAAGGTTATT	59.846	34.615	0.00	0.00	32.15	1.40
1322	1786	7.012704	ACGAAGCTCAATCATATGCAAAACTAT	59.987	33.333	0.00	0.00	0.00	2.12
1352	1816	3.853355	AGGAAGGCCTCACATTCATAG	57.147	47.619	5.23	0.00	42.19	2.23
1675	2173	5.251700	ACTGTAACCCTTCTCCAGATTGAAT	59.748	40.000	0.00	0.00	0.00	2.57
1683	2181	7.127955	ACCCTTCTCCAGATTGAATACAATACT	59.872	37.037	0.00	0.00	45.30	2.12
1684	2182	7.659390	CCCTTCTCCAGATTGAATACAATACTC	59.341	40.741	0.00	0.00	45.30	2.59
2083	2861	6.992123	CAGTTCTTGCTGTGGATATTGGTATA	59.008	38.462	0.00	0.00	0.00	1.47
2084	2862	7.663081	CAGTTCTTGCTGTGGATATTGGTATAT	59.337	37.037	0.00	0.00	0.00	0.86
2153	2932	6.889177	TGACATTGCTCAAAAATAGGATGGTA	59.111	34.615	0.00	0.00	0.00	3.25
2731	3527	5.045724	ACATTGTTCCTGTACCGGGTTATTA	60.046	40.000	4.31	0.00	0.00	0.98
2873	3677	7.492524	TGTGTTCTATTCATCATCTGTACTCC	58.507	38.462	0.00	0.00	0.00	3.85
2887	3691	4.163458	TCTGTACTCCTGTGGAAACAGTTT	59.837	41.667	19.42	0.00	42.04	2.66
2910	3714	5.301555	TGAGACCGATTTGTTTGTCATGTA	58.698	37.500	0.00	0.00	0.00	2.29
3156	3961	4.893424	TCTTGTTACTGCAACTGGTTTC	57.107	40.909	0.00	0.00	38.05	2.78
3169	3974	5.729510	CAACTGGTTTCCTTTTCTTTTCCA	58.270	37.500	0.00	0.00	0.00	3.53
3207	4013	1.308998	CTAAACGACATCATGGCCCC	58.691	55.000	0.00	0.00	0.00	5.80
3220	4026	1.302993	GGCCCCGCAAACTTGTAGA	60.303	57.895	0.00	0.00	0.00	2.59
3236	4042	6.885922	ACTTGTAGACCAAACTTGTAGAAGT	58.114	36.000	0.00	0.00	44.79	3.01
3309	4115	3.118992	GGGAAAAGGTGATCATTTCTGCC	60.119	47.826	16.12	8.96	34.34	4.85
3312	4118	3.726557	AAGGTGATCATTTCTGCCTCA	57.273	42.857	0.00	0.00	31.99	3.86
3313	4119	3.278668	AGGTGATCATTTCTGCCTCAG	57.721	47.619	0.00	0.00	0.00	3.35
3329	4603	6.014242	TCTGCCTCAGTTAATATTGATCGGAT	60.014	38.462	0.00	0.00	32.61	4.18
3330	4604	6.166279	TGCCTCAGTTAATATTGATCGGATC	58.834	40.000	11.07	11.07	0.00	3.36
3331	4605	5.582665	GCCTCAGTTAATATTGATCGGATCC	59.417	44.000	15.06	0.00	0.00	3.36
3332	4606	5.807520	CCTCAGTTAATATTGATCGGATCCG	59.192	44.000	28.62	28.62	41.35	4.18
3411	4689	4.954118	TGACGGAGCACCACCCCT	62.954	66.667	0.00	0.00	35.59	4.79
3415	4693	2.592308	GGAGCACCACCCCTCATC	59.408	66.667	0.00	0.00	35.97	2.92
3422	4700	0.830648	ACCACCCCTCATCGTGTATG	59.169	55.000	0.00	0.00	36.88	2.39
3433	4713	5.920840	CCTCATCGTGTATGTGTATAACTGG	59.079	44.000	0.00	0.00	36.89	4.00
3509	4791	3.927142	ACGCTGCAATAAGAACTACAGTC	59.073	43.478	0.00	0.00	0.00	3.51
3522	4804	5.944599	AGAACTACAGTCGTAAATCTCCTCA	59.055	40.000	0.00	0.00	0.00	3.86
3539	4821	4.451900	TCCTCACTTGTTTGTCTCTTTCC	58.548	43.478	0.00	0.00	0.00	3.13
3544	4826	6.852664	TCACTTGTTTGTCTCTTTCCTTTTC	58.147	36.000	0.00	0.00	0.00	2.29
3579	4861	3.245193	ACAGTAACTTACTCCCTCCGTCT	60.245	47.826	0.00	0.00	36.76	4.18
3607	4889	9.982651	ATAATATAAGAACGCTGTTGACACTAT	57.017	29.630	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
179	181	2.415491	CGTCAGTATCGCAACCTCAAGA	60.415	50.000	0.00	0.00	0.00	3.02
309	311	0.250038	CCATGTATGCCACCCTCTCG	60.250	60.000	0.00	0.00	0.00	4.04
349	351	1.889530	AACAGCCAGTACCTCGAGCC	61.890	60.000	6.99	0.00	0.00	4.70
1322	1786	2.596851	GGCCTTCCTCCTCACAGCA	61.597	63.158	0.00	0.00	0.00	4.41
1352	1816	0.035439	TCGGGATGGTCAAAAGGAGC	60.035	55.000	0.00	0.00	44.35	4.70
1675	2173	4.716784	AGGACAGCCTGAATGAGTATTGTA	59.283	41.667	0.00	0.00	44.90	2.41
1683	2181	3.181440	ACAAGAAAGGACAGCCTGAATGA	60.181	43.478	0.00	0.00	46.28	2.57
1684	2182	3.152341	ACAAGAAAGGACAGCCTGAATG	58.848	45.455	0.00	0.00	46.28	2.67
2129	2908	6.212888	ACCATCCTATTTTTGAGCAATGTC	57.787	37.500	0.00	0.00	0.00	3.06
2153	2932	5.312079	ACAAACTGCAGAGCTAGAATTTCT	58.688	37.500	23.35	4.03	0.00	2.52
2260	3053	3.701040	ACATATCCTGTGCCCATGAAAAC	59.299	43.478	0.00	0.00	36.48	2.43
2887	3691	4.133820	ACATGACAAACAAATCGGTCTCA	58.866	39.130	0.00	0.00	0.00	3.27
2977	3781	3.510388	TGTACTCGAGCAGGATTTCTG	57.490	47.619	13.61	0.00	46.03	3.02
3200	4005	0.965363	CTACAAGTTTGCGGGGCCAT	60.965	55.000	4.39	0.00	0.00	4.40
3207	4013	3.963383	AGTTTGGTCTACAAGTTTGCG	57.037	42.857	0.00	0.00	40.82	4.85
3236	4042	0.690192	TTCCTTGCCATCGTCTCCAA	59.310	50.000	0.00	0.00	0.00	3.53
3309	4115	6.621613	TCGGATCCGATCAATATTAACTGAG	58.378	40.000	32.59	0.00	44.01	3.35
3329	4603	9.458727	CTAAACAATATATACTACTCCCTCGGA	57.541	37.037	0.00	0.00	0.00	4.55
3330	4604	9.458727	TCTAAACAATATATACTACTCCCTCGG	57.541	37.037	0.00	0.00	0.00	4.63
3384	4658	1.226717	GCTCCGTCATCTCCGTCAC	60.227	63.158	0.00	0.00	0.00	3.67
3411	4689	5.221362	CCCCAGTTATACACATACACGATGA	60.221	44.000	0.00	0.00	39.06	2.92
3415	4693	3.128349	GCCCCAGTTATACACATACACG	58.872	50.000	0.00	0.00	0.00	4.49
3422	4700	2.572290	GGTCATGCCCCAGTTATACAC	58.428	52.381	0.00	0.00	0.00	2.90
3492	4774	8.408743	AGATTTACGACTGTAGTTCTTATTGC	57.591	34.615	0.00	0.00	0.00	3.56
3509	4791	5.696724	AGACAAACAAGTGAGGAGATTTACG	59.303	40.000	0.00	0.00	0.00	3.18
3522	4804	6.834168	TGAAAAGGAAAGAGACAAACAAGT	57.166	33.333	0.00	0.00	0.00	3.16
3579	4861	7.979537	AGTGTCAACAGCGTTCTTATATTATGA	59.020	33.333	0.00	0.00	0.00	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.