AutoCloner

Multiple sequence alignment - TraesCS3A01G100600

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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	TraesCS3A01G100600	chr3A	100.000	2546	0	0	1	2546	65403253	65400708	0.000000e+00	4702
1	TraesCS3A01G100600	chr3A	98.589	567	8	0	981	1547	65360849	65361415	0.000000e+00	1003
2	TraesCS3A01G100600	chr3A	92.513	187	9	3	752	933	65360666	65360852	1.940000e-66	263
3	TraesCS3A01G100600	chr3A	96.040	101	4	0	668	768	65360545	65360645	5.640000e-37	165
4	TraesCS3A01G100600	chr3D	91.866	2127	115	18	447	2546	54458702	54456607	0.000000e+00	2916
5	TraesCS3A01G100600	chr3D	95.264	908	35	4	648	1547	54393743	54394650	0.000000e+00	1432
6	TraesCS3A01G100600	chr3D	91.339	127	11	0	317	443	54461654	54461528	9.360000e-40	174
7	TraesCS3A01G100600	chr3D	95.745	94	4	0	2	95	54486427	54486334	4.390000e-33	152
8	TraesCS3A01G100600	chr3B	90.677	2156	155	21	2	2124	84877069	84874927	0.000000e+00	2826
9	TraesCS3A01G100600	chr3B	94.601	889	39	4	668	1547	84763207	84764095	0.000000e+00	1367
10	TraesCS3A01G100600	chr3B	87.907	430	47	4	2	430	85054385	85053960	3.780000e-138	501
11	TraesCS3A01G100600	chr3B	86.842	418	28	14	2130	2546	84874885	84874494	2.320000e-120	442
12	TraesCS3A01G100600	chr6D	81.443	97	12	4	108	204	62966157	62966247	9.770000e-10	75

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	TraesCS3A01G100600	chr3A	65400708	65403253	2545	True	4702	4702	100.0000	1	2546	1	chr3A.!!$R1	2545
1	TraesCS3A01G100600	chr3A	65360545	65361415	870	False	477	1003	95.7140	668	1547	3	chr3A.!!$F1	879
2	TraesCS3A01G100600	chr3D	54456607	54461654	5047	True	1545	2916	91.6025	317	2546	2	chr3D.!!$R2	2229
3	TraesCS3A01G100600	chr3D	54393743	54394650	907	False	1432	1432	95.2640	648	1547	1	chr3D.!!$F1	899
4	TraesCS3A01G100600	chr3B	84874494	84877069	2575	True	1634	2826	88.7595	2	2546	2	chr3B.!!$R2	2544
5	TraesCS3A01G100600	chr3B	84763207	84764095	888	False	1367	1367	94.6010	668	1547	1	chr3B.!!$F1	879

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
227	229	0.234884	GAGGGAAAAGTGTTGTCGCG	59.765	55.0	0.0	0.0	0.0	5.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2107	5025	1.137404	CAAACCAGCTATGCCACGC	59.863	57.895	0.0	0.0	0.0	5.34	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
38	39	0.679960	AATAGGGTTCAAGCGCCACC	60.680	55.000	2.29	5.34	0.00	4.61
67	68	1.074167	AGGAGAAGATGGCCCCGAT	60.074	57.895	0.00	0.00	0.00	4.18
70	71	2.049627	GAGAAGATGGCCCCGATGCT	62.050	60.000	0.00	0.00	0.00	3.79
102	103	4.994744	GGCTTTGCCCATCAACAC	57.005	55.556	0.00	0.00	44.06	3.32
104	105	1.734117	GCTTTGCCCATCAACACGC	60.734	57.895	0.00	0.00	33.73	5.34
106	107	2.128853	CTTTGCCCATCAACACGCGT	62.129	55.000	5.58	5.58	33.73	6.01
213	215	1.349542	CGAGGAGAGGGAGAGAGGGA	61.350	65.000	0.00	0.00	0.00	4.20
220	222	2.158081	AGAGGGAGAGAGGGAAAAGTGT	60.158	50.000	0.00	0.00	0.00	3.55
222	224	2.373502	AGGGAGAGAGGGAAAAGTGTTG	59.626	50.000	0.00	0.00	0.00	3.33
227	229	0.234884	GAGGGAAAAGTGTTGTCGCG	59.765	55.000	0.00	0.00	0.00	5.87
228	230	1.164041	AGGGAAAAGTGTTGTCGCGG	61.164	55.000	6.13	0.00	0.00	6.46
232	234	0.454196	AAAAGTGTTGTCGCGGCTTT	59.546	45.000	13.81	0.00	0.00	3.51
234	236	2.051345	GTGTTGTCGCGGCTTTGG	60.051	61.111	13.81	0.00	0.00	3.28
259	261	0.322546	ATCCCTCCTTTGCAACCGAC	60.323	55.000	0.00	0.00	0.00	4.79
291	293	0.825840	CCCGTTTGAACACCCCATGT	60.826	55.000	0.00	0.00	46.42	3.21
307	309	4.034742	CCCCATGTGTTTGCGTATAAGTAC	59.965	45.833	0.00	0.00	0.00	2.73
311	313	6.091577	CCATGTGTTTGCGTATAAGTACAAGA	59.908	38.462	0.00	0.00	0.00	3.02
328	330	9.485206	AAGTACAAGATGTTATTTGTCGTAACT	57.515	29.630	0.00	0.00	38.41	2.24
432	434	1.978097	CAACAACGCATGAACATTCGG	59.022	47.619	10.83	0.00	31.92	4.30
443	3267	5.502544	GCATGAACATTCGGCTAGTCTTTAC	60.503	44.000	0.00	0.00	0.00	2.01
445	3269	4.927425	TGAACATTCGGCTAGTCTTTACAC	59.073	41.667	0.00	0.00	0.00	2.90
539	3371	7.725818	AGGTGTGTAGCTTAGTTAAAGAAAC	57.274	36.000	0.00	0.00	37.38	2.78
567	3399	0.950555	ATCATCACGCACGCAACACT	60.951	50.000	0.00	0.00	0.00	3.55
572	3404	3.268603	CGCACGCAACACTCACCA	61.269	61.111	0.00	0.00	0.00	4.17
633	3465	0.324943	ACCTCCCCATTGTTCTGACG	59.675	55.000	0.00	0.00	0.00	4.35
657	3490	3.424829	CGACAATCTCCGAAACAATGTGG	60.425	47.826	0.00	0.00	0.00	4.17
670	3503	1.091537	AATGTGGTCGCCATTAACGG	58.908	50.000	1.90	0.00	35.28	4.44
791	3662	2.672714	CGACAATCTCGGAGACAAACA	58.327	47.619	10.41	0.00	38.87	2.83
853	3735	2.933906	CCGCACGTCTACACCATTTTAT	59.066	45.455	0.00	0.00	0.00	1.40
854	3736	4.114073	CCGCACGTCTACACCATTTTATA	58.886	43.478	0.00	0.00	0.00	0.98
855	3737	4.026310	CCGCACGTCTACACCATTTTATAC	60.026	45.833	0.00	0.00	0.00	1.47
856	3738	4.802039	CGCACGTCTACACCATTTTATACT	59.198	41.667	0.00	0.00	0.00	2.12
857	3739	5.051907	CGCACGTCTACACCATTTTATACTC	60.052	44.000	0.00	0.00	0.00	2.59
858	3740	6.040878	GCACGTCTACACCATTTTATACTCT	58.959	40.000	0.00	0.00	0.00	3.24
1564	4470	4.695455	ACTGATTCGTCCGTTGATTTGAAT	59.305	37.500	0.00	0.00	0.00	2.57
1628	4536	0.171007	GCGCTGCTGCTTTGGATTTA	59.829	50.000	14.03	0.00	36.97	1.40
1634	4542	4.990426	GCTGCTGCTTTGGATTTAAGAAAA	59.010	37.500	8.53	0.00	36.03	2.29
1655	4563	1.321474	TGTGGAGCTTGAAGGCTTTG	58.679	50.000	0.00	0.00	43.20	2.77
1799	4714	4.687018	ACTTCAAACGCATTATACACACGA	59.313	37.500	0.00	0.00	0.00	4.35
1812	4727	1.336887	ACACACGAGTAGCGCATTCTT	60.337	47.619	11.47	0.00	46.04	2.52
1821	4736	5.288712	CGAGTAGCGCATTCTTAAAAAGAGA	59.711	40.000	11.47	0.00	39.03	3.10
1884	4799	2.475111	CGCAACGCTTGAGAGAAAGTTA	59.525	45.455	2.51	0.00	31.66	2.24
1902	4817	5.283060	AGTTATGTGCGTGTTTCTTCATC	57.717	39.130	0.00	0.00	0.00	2.92
2062	4979	9.941664	CGCTTCAAACATCTCAAAATAATCTAT	57.058	29.630	0.00	0.00	0.00	1.98
2124	5042	2.398554	CGCGTGGCATAGCTGGTTT	61.399	57.895	14.31	0.00	0.00	3.27
2126	5044	1.586154	GCGTGGCATAGCTGGTTTGT	61.586	55.000	10.09	0.00	0.00	2.83
2235	5194	6.650427	ACTGCTATGACCGTCATATTAGAA	57.350	37.500	24.70	12.09	38.54	2.10
2246	5205	7.382110	ACCGTCATATTAGAAGGAGATTCATG	58.618	38.462	3.02	0.00	39.18	3.07
2263	5222	8.985315	AGATTCATGCATATTTGTCCTTTCTA	57.015	30.769	0.00	0.00	0.00	2.10
2313	5272	1.687628	TTTTGTTATTTTCCGCGCGG	58.312	45.000	42.13	42.13	0.00	6.46
2356	5315	2.295909	TGGCCTTGCACAATTACAGTTC	59.704	45.455	3.32	0.00	0.00	3.01
2377	5336	1.540363	CCTCTGGTTTGCACTACGTGT	60.540	52.381	0.00	0.00	35.75	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	0.325110	TCTTCTCCTCCTGCCCTCTG	60.325	60.000	0.00	0.00	0.00	3.35
46	47	1.385206	GGGGCCATCTTCTCCTCCT	60.385	63.158	4.39	0.00	0.00	3.69
112	113	4.400251	CTCCCTCCTCCCCACCGT	62.400	72.222	0.00	0.00	0.00	4.83
116	117	3.368501	CCTCCTCCCTCCTCCCCA	61.369	72.222	0.00	0.00	0.00	4.96
118	119	2.612251	CTCCTCCTCCCTCCTCCC	59.388	72.222	0.00	0.00	0.00	4.30
123	124	2.612251	CCTCCCTCCTCCTCCCTC	59.388	72.222	0.00	0.00	0.00	4.30
124	125	3.039526	CCCTCCCTCCTCCTCCCT	61.040	72.222	0.00	0.00	0.00	4.20
188	190	4.361971	TCCCTCTCCTCGCACCGT	62.362	66.667	0.00	0.00	0.00	4.83
190	192	2.043852	TCTCCCTCTCCTCGCACC	60.044	66.667	0.00	0.00	0.00	5.01
195	197	0.930726	TTCCCTCTCTCCCTCTCCTC	59.069	60.000	0.00	0.00	0.00	3.71
213	215	0.454196	AAAGCCGCGACAACACTTTT	59.546	45.000	8.23	0.00	0.00	2.27
220	222	1.824329	TTTCCCAAAGCCGCGACAA	60.824	52.632	8.23	0.00	0.00	3.18
222	224	1.862602	ATGTTTCCCAAAGCCGCGAC	61.863	55.000	8.23	0.00	0.00	5.19
234	236	1.923356	TGCAAAGGAGGGATGTTTCC	58.077	50.000	0.00	0.00	41.77	3.13
249	251	2.904866	GGCACTGGTCGGTTGCAA	60.905	61.111	0.00	0.00	0.00	4.08
259	261	1.067915	CAAACGGGTTATTGGCACTGG	60.068	52.381	0.00	0.00	0.00	4.00
291	293	7.661127	AACATCTTGTACTTATACGCAAACA	57.339	32.000	0.00	0.00	33.60	2.83
332	334	9.893305	CAATGTATACATCGTATGTGACTTCTA	57.107	33.333	18.52	0.00	44.60	2.10
334	336	8.480066	CACAATGTATACATCGTATGTGACTTC	58.520	37.037	28.73	0.00	44.60	3.01
432	434	3.320673	ACCAGCAGTGTAAAGACTAGC	57.679	47.619	0.00	0.00	0.00	3.42
443	3267	2.293399	GGACCAGTTTTAACCAGCAGTG	59.707	50.000	0.00	0.00	0.00	3.66
445	3269	2.863809	AGGACCAGTTTTAACCAGCAG	58.136	47.619	0.00	0.00	0.00	4.24
567	3399	8.215736	AGACATGATCTGATAATGATTTGGTGA	58.784	33.333	19.67	0.00	35.81	4.02
633	3465	1.153353	TTGTTTCGGAGATTGTCGGC	58.847	50.000	0.00	0.00	35.04	5.54
657	3490	0.580104	CGGATTCCGTTAATGGCGAC	59.420	55.000	17.08	2.60	42.73	5.19
670	3503	2.477863	CGGCACCAAAGATTTCGGATTC	60.478	50.000	0.00	0.00	0.00	2.52
791	3662	0.978146	AATGGCCTACGTGAGAGCCT	60.978	55.000	17.24	4.61	42.73	4.58
819	3701	4.488136	TGCGGCCATGTAGCTGGG	62.488	66.667	2.24	0.00	39.66	4.45
823	3705	2.622903	TAGACGTGCGGCCATGTAGC	62.623	60.000	2.24	0.00	41.15	3.58
853	3735	0.335361	GTGAGGGGTCAGGGAGAGTA	59.665	60.000	0.00	0.00	0.00	2.59
854	3736	1.079438	GTGAGGGGTCAGGGAGAGT	59.921	63.158	0.00	0.00	0.00	3.24
855	3737	1.687493	GGTGAGGGGTCAGGGAGAG	60.687	68.421	0.00	0.00	0.00	3.20
856	3738	2.177518	AGGTGAGGGGTCAGGGAGA	61.178	63.158	0.00	0.00	0.00	3.71
857	3739	1.992277	CAGGTGAGGGGTCAGGGAG	60.992	68.421	0.00	0.00	0.00	4.30
858	3740	2.122729	CAGGTGAGGGGTCAGGGA	59.877	66.667	0.00	0.00	0.00	4.20
890	3774	2.758979	AGGCGTCGGGTTCATATATAGG	59.241	50.000	0.00	0.00	0.00	2.57
1628	4536	4.502087	GCCTTCAAGCTCCACAATTTTCTT	60.502	41.667	0.00	0.00	0.00	2.52
1634	4542	2.298163	CAAAGCCTTCAAGCTCCACAAT	59.702	45.455	0.00	0.00	44.11	2.71
1737	4652	2.635427	ACTTGTCCAAGGAAGAGGTCTC	59.365	50.000	11.45	0.00	42.53	3.36
1799	4714	7.982354	ACTATCTCTTTTTAAGAATGCGCTACT	59.018	33.333	9.73	1.99	37.02	2.57
1812	4727	9.773328	CGAATCAAAATGCACTATCTCTTTTTA	57.227	29.630	0.00	0.00	0.00	1.52
1821	4736	6.595326	TCTCAAGACGAATCAAAATGCACTAT	59.405	34.615	0.00	0.00	0.00	2.12
1884	4799	5.940192	TTAAGATGAAGAAACACGCACAT	57.060	34.783	0.00	0.00	0.00	3.21
1955	4870	2.493414	TGTGATGTCCATGTGATGCA	57.507	45.000	0.00	0.00	0.00	3.96
1966	4881	9.912634	TTTTCTTTTTAAGATGGATGTGATGTC	57.087	29.630	0.00	0.00	37.38	3.06
2031	4947	5.545658	TTTGAGATGTTTGAAGCGATACC	57.454	39.130	0.00	0.00	0.00	2.73
2035	4951	8.044060	AGATTATTTTGAGATGTTTGAAGCGA	57.956	30.769	0.00	0.00	0.00	4.93
2087	5005	4.124351	CGCATGCTGGTTGGCTGG	62.124	66.667	17.13	0.00	0.00	4.85
2107	5025	1.137404	CAAACCAGCTATGCCACGC	59.863	57.895	0.00	0.00	0.00	5.34
2201	5159	5.986135	ACGGTCATAGCAGTTATTGAGATTC	59.014	40.000	0.00	0.00	0.00	2.52
2235	5194	5.950023	AGGACAAATATGCATGAATCTCCT	58.050	37.500	10.16	10.03	0.00	3.69
2310	5269	1.332375	TGTGTGCAACTTTAGTTCCGC	59.668	47.619	0.00	0.00	38.04	5.54
2333	5292	0.595588	TGTAATTGTGCAAGGCCACG	59.404	50.000	5.01	0.00	38.55	4.94
2356	5315	0.034896	ACGTAGTGCAAACCAGAGGG	59.965	55.000	0.00	0.00	42.51	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.