AutoCloner

Multiple sequence alignment - TraesCS5D01G366200

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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	TraesCS5D01G366200	chr5D	100.000	3900	0	0	1	3900	443069780	443065881	0.000000e+00	7203.0
1	TraesCS5D01G366200	chr5D	87.121	132	15	2	1694	1824	95051877	95052007	8.730000e-32	148.0
2	TraesCS5D01G366200	chr5D	90.698	86	4	3	3038	3119	492288318	492288233	1.150000e-20	111.0
3	TraesCS5D01G366200	chr5D	89.130	92	6	3	3032	3119	496216251	496216342	1.150000e-20	111.0
4	TraesCS5D01G366200	chr5B	94.944	3560	112	21	1	3557	539312625	539309131	0.000000e+00	5515.0
5	TraesCS5D01G366200	chr5B	76.989	930	173	22	1901	2805	78135160	78136073	9.730000e-136	494.0
6	TraesCS5D01G366200	chr5B	95.882	170	7	0	3731	3900	539308908	539308739	3.840000e-70	276.0
7	TraesCS5D01G366200	chr5B	90.244	164	7	2	3576	3730	539309143	539308980	5.110000e-49	206.0
8	TraesCS5D01G366200	chr5A	95.589	3106	97	10	1	3084	559095921	559092834	0.000000e+00	4940.0
9	TraesCS5D01G366200	chr5A	93.711	477	30	0	3080	3556	559092723	559092247	0.000000e+00	715.0
10	TraesCS5D01G366200	chr5A	94.643	168	7	1	3733	3900	559091966	559091801	3.870000e-65	259.0
11	TraesCS5D01G366200	chr5A	86.364	132	16	2	1694	1824	89384860	89384990	4.060000e-30	143.0
12	TraesCS5D01G366200	chr5A	89.888	89	5	3	3035	3119	309680265	309680177	1.150000e-20	111.0
13	TraesCS5D01G366200	chr5A	100.000	41	0	0	3690	3730	559092205	559092165	4.180000e-10	76.8
14	TraesCS5D01G366200	chr2D	89.362	94	5	2	3038	3127	61023709	61023801	3.180000e-21	113.0
15	TraesCS5D01G366200	chr2D	90.000	90	5	3	3034	3119	61023798	61023709	3.180000e-21	113.0
16	TraesCS5D01G366200	chr2A	90.698	86	5	1	3038	3120	551817930	551818015	1.150000e-20	111.0
17	TraesCS5D01G366200	chr1A	85.586	111	10	3	3038	3142	568391287	568391177	1.150000e-20	111.0
18	TraesCS5D01G366200	chr1B	86.735	98	7	5	3038	3130	429603126	429603030	1.920000e-18	104.0

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	TraesCS5D01G366200	chr5D	443065881	443069780	3899	True	7203.0	7203	100.00000	1	3900	1	chr5D.!!$R1	3899
1	TraesCS5D01G366200	chr5B	539308739	539312625	3886	True	1999.0	5515	93.69000	1	3900	3	chr5B.!!$R1	3899
2	TraesCS5D01G366200	chr5B	78135160	78136073	913	False	494.0	494	76.98900	1901	2805	1	chr5B.!!$F1	904
3	TraesCS5D01G366200	chr5A	559091801	559095921	4120	True	1497.7	4940	95.98575	1	3900	4	chr5A.!!$R2	3899

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
512	517	5.392380	GCAGACATAATCCAGTTTCTTGTGG	60.392	44.0	0.00	0.0	34.87	4.17	F
2030	2040	0.031857	CCAGTCCAGCTCTAGCATCG	59.968	60.0	4.54	0.0	45.16	3.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2417	2433	1.356624	GCGAAATCTGGGAATGCCG	59.643	57.895	0.0	0.0	33.83	5.69	R
3425	3575	0.322975	AATCAACGACCTGCTCAGCT	59.677	50.000	0.0	0.0	0.00	4.24	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
512	517	5.392380	GCAGACATAATCCAGTTTCTTGTGG	60.392	44.000	0.00	0.00	34.87	4.17
937	944	6.041523	GCAAGACCTATCTTCCAGAATACTCT	59.958	42.308	0.00	0.00	43.69	3.24
976	983	8.087982	TGCAGATTGTAGAGTAAACTTGAAAG	57.912	34.615	0.00	0.00	0.00	2.62
1024	1031	7.560991	ACATGGAGAATAAACCAATTGAGCATA	59.439	33.333	7.12	0.00	39.69	3.14
1244	1251	4.396166	AGGCGTAATTGTTTCTCATTCCTG	59.604	41.667	0.00	0.00	0.00	3.86
1355	1362	6.851836	AGGAGGTGAATCAAAGGGATATTCTA	59.148	38.462	0.00	0.00	34.28	2.10
1632	1642	4.278419	GCCAAGAAATAGTGGTTCAGTTGT	59.722	41.667	0.00	0.00	0.00	3.32
1633	1643	5.221244	GCCAAGAAATAGTGGTTCAGTTGTT	60.221	40.000	0.00	0.00	0.00	2.83
1634	1644	6.208644	CCAAGAAATAGTGGTTCAGTTGTTG	58.791	40.000	0.00	0.00	0.00	3.33
1827	1837	9.613428	TTCTAAGAACCAGTGTTATTCATATGG	57.387	33.333	2.13	0.00	37.17	2.74
1963	1973	0.463295	ATCGAAGCAGTGGCATGGAG	60.463	55.000	0.00	0.00	44.61	3.86
2030	2040	0.031857	CCAGTCCAGCTCTAGCATCG	59.968	60.000	4.54	0.00	45.16	3.84
2179	2189	3.857010	GCCGACTTCCAACATTTCAAAGG	60.857	47.826	0.00	0.00	0.00	3.11
2333	2349	5.399858	CAAGTGAGAATGCATCAAAGGAAG	58.600	41.667	0.00	0.00	0.00	3.46
2364	2380	2.545946	ACAGAAAGAAGCTGCGAAACTC	59.454	45.455	0.00	0.00	36.86	3.01
2400	2416	5.593909	TCACCATGAAGAAATCACAAGTGTT	59.406	36.000	0.00	0.00	41.93	3.32
2417	2433	5.000012	AGTGTTACCGAGTCATGAGAATC	58.000	43.478	0.00	0.00	35.60	2.52
2524	2540	0.911769	AAGATTCTCACCGCCCATCA	59.088	50.000	0.00	0.00	0.00	3.07
2565	2581	2.281070	CGCAGACAGCACACCCTT	60.281	61.111	0.00	0.00	46.13	3.95
2585	2601	0.610687	GAGCAAGGGTGTAGCTGACT	59.389	55.000	0.00	0.00	39.02	3.41
2827	2861	1.372307	GCATTGGTTTGCTGGCCTT	59.628	52.632	3.32	0.00	39.57	4.35
2909	2943	0.029300	GAAGCTTTGACGCTGCAACA	59.971	50.000	0.00	0.00	40.79	3.33
2935	2969	3.691498	GAAACCAAAGACTGTGTTTCCG	58.309	45.455	0.00	0.00	38.24	4.30
2937	2971	3.208747	ACCAAAGACTGTGTTTCCGAT	57.791	42.857	0.00	0.00	0.00	4.18
3107	3257	8.993121	ACTAAATCAGCGACAATTAATATGGAG	58.007	33.333	0.00	0.00	0.00	3.86
3134	3284	5.221864	GGGGGAGTAAGAAGTTTCAGAGAAA	60.222	44.000	0.00	0.00	0.00	2.52
3146	3296	6.169800	AGTTTCAGAGAAATGAGGAACTAGC	58.830	40.000	0.00	0.00	41.55	3.42
3149	3299	3.454082	CAGAGAAATGAGGAACTAGCCCT	59.546	47.826	4.10	4.10	41.55	5.19
3184	3334	0.249398	ATTGCGGGCTCTAGAAACGT	59.751	50.000	10.73	0.00	0.00	3.99
3192	3342	4.677250	CGGGCTCTAGAAACGTAAACATCT	60.677	45.833	0.00	0.00	0.00	2.90
3334	3484	0.795735	GCATGTTGACAGCGTGATGC	60.796	55.000	14.95	6.52	46.98	3.91
3425	3575	7.230510	AGCTGTCATTTGTGGTATACTTTTCAA	59.769	33.333	2.25	1.49	0.00	2.69
3448	3598	2.346803	TGAGCAGGTCGTTGATTAAGC	58.653	47.619	0.00	0.00	0.00	3.09
3548	3698	9.725019	TCACTTAAGCAATTTTGAGATAGAAGA	57.275	29.630	1.29	0.00	0.00	2.87
3555	3705	9.678260	AGCAATTTTGAGATAGAAGAAGTATGT	57.322	29.630	0.00	0.00	0.00	2.29
3594	3744	6.449830	AGGGGAAGAAGTATGTTGTAAGTT	57.550	37.500	0.00	0.00	0.00	2.66
3652	3804	1.622725	GGGGTCCTACTGACATCTGGT	60.623	57.143	0.00	0.00	46.38	4.00
3662	3814	4.820744	CATCTGGTTGGGCCGGGG	62.821	72.222	2.18	0.00	43.94	5.73
3803	4158	1.686052	GGGACACTTGTTGCCATCAAA	59.314	47.619	0.00	0.00	33.37	2.69
3880	4235	3.822940	ACAAAACCTACGGATGACCAAA	58.177	40.909	0.00	0.00	35.59	3.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
512	517	2.180276	TCCAGCCAAGAGTCCTTAGAC	58.820	52.381	0.00	0.00	43.89	2.59
937	944	1.005037	CTGCAAGTGGCCGAGTACA	60.005	57.895	0.00	0.00	43.89	2.90
976	983	5.105554	TGTGTTATGATAACCACCAATTGCC	60.106	40.000	12.39	0.00	0.00	4.52
1024	1031	5.636543	GTGTTACTGTGAAGCGGTTACTAAT	59.363	40.000	0.00	0.00	37.04	1.73
1244	1251	9.977762	CTATAAATAAAGGTGTCAAAACCGTAC	57.022	33.333	0.00	0.00	45.53	3.67
1355	1362	9.986157	AGATGGTAATGAATATGATATGGCTTT	57.014	29.630	0.00	0.00	0.00	3.51
1431	1438	4.518970	TGAATTTTCCAGAAGGTTTCCTCG	59.481	41.667	0.00	0.00	35.89	4.63
1552	1559	5.062308	CACATCATCATCACTATCATCTGCG	59.938	44.000	0.00	0.00	0.00	5.18
1632	1642	5.312895	TGCTAAGCTTCAGATTTGTACCAA	58.687	37.500	0.00	0.00	0.00	3.67
1633	1643	4.905429	TGCTAAGCTTCAGATTTGTACCA	58.095	39.130	0.00	0.00	0.00	3.25
1634	1644	6.094048	TCAATGCTAAGCTTCAGATTTGTACC	59.906	38.462	0.00	0.00	0.00	3.34
1935	1945	3.873952	GCCACTGCTTCGATCTAGAAAAT	59.126	43.478	0.00	0.00	33.53	1.82
1963	1973	2.423538	AGTTTTCTTGTGTGTGAGCCAC	59.576	45.455	0.00	0.00	44.78	5.01
2030	2040	4.098349	TGCTGCAAATATTCCTGGATTGAC	59.902	41.667	11.05	4.37	0.00	3.18
2146	2156	1.424493	GAAGTCGGCCATTCTGAGCG	61.424	60.000	2.24	0.00	0.00	5.03
2179	2189	3.466836	TGATGAATGAAGGCGGTGATAC	58.533	45.455	0.00	0.00	0.00	2.24
2333	2349	2.550180	GCTTCTTTCTGTCCCACAAGAC	59.450	50.000	0.00	0.00	37.28	3.01
2364	2380	4.388773	TCTTCATGGTGATTTTCTTCGTCG	59.611	41.667	0.00	0.00	0.00	5.12
2417	2433	1.356624	GCGAAATCTGGGAATGCCG	59.643	57.895	0.00	0.00	33.83	5.69
2565	2581	0.321671	GTCAGCTACACCCTTGCTCA	59.678	55.000	0.00	0.00	34.51	4.26
2827	2861	1.300963	GCTCTCCCCTGATGTTGCA	59.699	57.895	0.00	0.00	0.00	4.08
2909	2943	3.606687	ACACAGTCTTTGGTTTCGAACT	58.393	40.909	0.00	0.00	0.00	3.01
2935	2969	4.913924	CGCTATGCTTGAATTGGCTTTATC	59.086	41.667	0.00	0.00	0.00	1.75
2937	2971	3.944650	TCGCTATGCTTGAATTGGCTTTA	59.055	39.130	0.00	0.00	0.00	1.85
3146	3296	5.692204	CGCAATAGAGTTGTGAACTATAGGG	59.308	44.000	4.43	0.00	43.03	3.53
3149	3299	5.597806	CCCGCAATAGAGTTGTGAACTATA	58.402	41.667	3.14	0.00	43.03	1.31
3192	3342	9.760077	TTGTTGTAAAACAAAGGTAACAAGAAA	57.240	25.926	8.82	0.00	40.15	2.52
3215	3365	6.983906	AAGAAATCCTGAACCAGAATTTGT	57.016	33.333	0.00	0.00	32.44	2.83
3243	3393	8.598075	GGTGATATTCAAACAAAGCATTCATTC	58.402	33.333	0.00	0.00	0.00	2.67
3260	3410	2.032178	GCACTCAAAGGCGGTGATATTC	59.968	50.000	0.00	0.00	33.32	1.75
3325	3475	1.939974	ACATAACATCGCATCACGCT	58.060	45.000	0.00	0.00	43.23	5.07
3334	3484	4.853196	CCAGCAACTCAAAACATAACATCG	59.147	41.667	0.00	0.00	0.00	3.84
3425	3575	0.322975	AATCAACGACCTGCTCAGCT	59.677	50.000	0.00	0.00	0.00	4.24
3448	3598	2.354203	GGTTCAACCACCTCTAGCAGAG	60.354	54.545	0.01	6.28	38.99	3.35
3462	3612	5.672819	GCTCCAATACGTTGTATGGTTCAAC	60.673	44.000	0.00	0.00	40.89	3.18
3513	3663	9.624697	TCAAAATTGCTTAAGTGATACATGAAC	57.375	29.630	0.00	0.00	0.00	3.18
3566	3716	9.292195	CTTACAACATACTTCTTCCCCTAAAAA	57.708	33.333	0.00	0.00	0.00	1.94
3567	3717	8.442374	ACTTACAACATACTTCTTCCCCTAAAA	58.558	33.333	0.00	0.00	0.00	1.52
3568	3718	7.981142	ACTTACAACATACTTCTTCCCCTAAA	58.019	34.615	0.00	0.00	0.00	1.85
3569	3719	7.563724	ACTTACAACATACTTCTTCCCCTAA	57.436	36.000	0.00	0.00	0.00	2.69
3570	3720	7.236019	TGAACTTACAACATACTTCTTCCCCTA	59.764	37.037	0.00	0.00	0.00	3.53
3571	3721	6.043938	TGAACTTACAACATACTTCTTCCCCT	59.956	38.462	0.00	0.00	0.00	4.79
3572	3722	6.235664	TGAACTTACAACATACTTCTTCCCC	58.764	40.000	0.00	0.00	0.00	4.81
3573	3723	6.935208	ACTGAACTTACAACATACTTCTTCCC	59.065	38.462	0.00	0.00	0.00	3.97
3574	3724	7.964604	ACTGAACTTACAACATACTTCTTCC	57.035	36.000	0.00	0.00	0.00	3.46
3662	3814	3.066814	CAGAAGCCCAGCCCAAGC	61.067	66.667	0.00	0.00	40.32	4.01
3803	4158	4.023291	TGGAAAAAGCTCACCAAAACTCT	58.977	39.130	0.00	0.00	0.00	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.