AutoCloner

Multiple sequence alignment - TraesCS6D01G317800

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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	TraesCS6D01G317800	chr6D	100.000	6434	0	0	1	6434	426281608	426288041	0.000000e+00	11882.0
1	TraesCS6D01G317800	chr6D	87.455	558	51	12	5322	5877	426333443	426333983	5.480000e-175	625.0
2	TraesCS6D01G317800	chr6D	93.820	178	9	2	4195	4370	104041330	104041153	3.820000e-67	267.0
3	TraesCS6D01G317800	chr6D	93.714	175	10	1	4199	4372	41542650	41542476	1.780000e-65	261.0
4	TraesCS6D01G317800	chr6D	91.489	188	13	3	4179	4366	409753439	409753255	8.280000e-64	255.0
5	TraesCS6D01G317800	chr6D	88.525	122	12	2	4921	5040	426297882	426298003	5.200000e-31	147.0
6	TraesCS6D01G317800	chr6D	86.777	121	13	3	5976	6095	426334111	426334229	1.460000e-26	132.0
7	TraesCS6D01G317800	chr6A	93.260	2359	110	20	1872	4200	571162891	571165230	0.000000e+00	3430.0
8	TraesCS6D01G317800	chr6A	84.258	1118	108	36	895	1966	571161859	571162954	0.000000e+00	1027.0
9	TraesCS6D01G317800	chr6A	88.889	738	42	15	4776	5489	571165832	571166553	0.000000e+00	872.0
10	TraesCS6D01G317800	chr6A	91.509	424	29	5	4360	4780	571165227	571165646	1.560000e-160	577.0
11	TraesCS6D01G317800	chr6A	89.079	467	36	7	5445	5899	571166553	571167016	3.370000e-157	566.0
12	TraesCS6D01G317800	chr6A	81.303	476	64	17	5684	6140	571182235	571181766	4.740000e-96	363.0
13	TraesCS6D01G317800	chr6B	92.368	1926	113	16	1872	3769	641885986	641887905	0.000000e+00	2712.0
14	TraesCS6D01G317800	chr6B	84.215	1077	115	31	5043	6091	641899819	641900868	0.000000e+00	996.0
15	TraesCS6D01G317800	chr6B	90.773	737	35	16	4776	5507	641889002	641889710	0.000000e+00	953.0
16	TraesCS6D01G317800	chr6B	81.943	1019	86	42	1013	1966	641885064	641886049	0.000000e+00	773.0
17	TraesCS6D01G317800	chr6B	97.636	423	8	2	4360	4780	641888417	641888839	0.000000e+00	725.0
18	TraesCS6D01G317800	chr6B	93.793	435	26	1	3767	4200	641887986	641888420	0.000000e+00	652.0
19	TraesCS6D01G317800	chr6B	82.853	624	88	15	5550	6160	641889710	641890327	5.670000e-150	542.0
20	TraesCS6D01G317800	chr6B	90.000	80	8	0	4918	4997	641898597	641898676	3.170000e-18	104.0
21	TraesCS6D01G317800	chr6B	92.857	42	3	0	4999	5040	641898954	641898995	1.940000e-05	62.1
22	TraesCS6D01G317800	chr1D	89.412	255	24	3	3368	3621	395387357	395387105	1.040000e-82	318.0
23	TraesCS6D01G317800	chr1D	89.020	255	25	3	3368	3621	395072818	395072566	4.840000e-81	313.0
24	TraesCS6D01G317800	chr1D	93.889	180	9	2	4189	4368	9218380	9218203	2.960000e-68	270.0
25	TraesCS6D01G317800	chr1D	81.974	233	26	10	3400	3621	395093440	395093213	3.960000e-42	183.0
26	TraesCS6D01G317800	chr1D	83.333	198	28	3	4007	4204	395490517	395490325	1.840000e-40	178.0
27	TraesCS6D01G317800	chr3D	89.020	255	24	4	3368	3621	57052711	57052962	4.840000e-81	313.0
28	TraesCS6D01G317800	chr1A	87.843	255	25	4	3368	3621	489387766	489387517	1.750000e-75	294.0
29	TraesCS6D01G317800	chr1A	92.350	183	12	1	4184	4366	493208161	493207981	6.400000e-65	259.0
30	TraesCS6D01G317800	chr1A	85.388	219	25	6	3977	4194	489402044	489401832	3.020000e-53	220.0
31	TraesCS6D01G317800	chr1A	95.726	117	5	0	382	498	466906334	466906450	8.520000e-44	189.0
32	TraesCS6D01G317800	chr1A	89.899	99	5	3	4362	4460	489339254	489339161	8.760000e-24	122.0
33	TraesCS6D01G317800	chr2B	84.106	302	39	2	3395	3696	250519015	250518723	3.800000e-72	283.0
34	TraesCS6D01G317800	chr4D	95.833	168	7	0	4199	4366	93336684	93336851	8.220000e-69	272.0
35	TraesCS6D01G317800	chr5D	94.798	173	9	0	4194	4366	42949729	42949557	2.960000e-68	270.0
36	TraesCS6D01G317800	chr3A	94.767	172	9	0	4194	4365	477708161	477708332	1.060000e-67	268.0
37	TraesCS6D01G317800	chr2D	94.253	174	10	0	4199	4372	609886791	609886964	3.820000e-67	267.0
38	TraesCS6D01G317800	chr4B	80.844	308	44	5	3389	3696	78600198	78599906	1.800000e-55	228.0
39	TraesCS6D01G317800	chr7D	97.297	111	3	0	391	501	598013058	598012948	8.520000e-44	189.0
40	TraesCS6D01G317800	chr5A	97.297	111	3	0	392	502	16500061	16499951	8.520000e-44	189.0
41	TraesCS6D01G317800	chr5A	96.491	114	4	0	389	502	69844897	69844784	8.520000e-44	189.0
42	TraesCS6D01G317800	chr5A	95.652	115	5	0	388	502	299768208	299768322	1.100000e-42	185.0
43	TraesCS6D01G317800	chr2A	95.690	116	4	1	389	504	448553183	448553069	1.100000e-42	185.0
44	TraesCS6D01G317800	chr2A	94.215	121	6	1	383	503	78333700	78333819	3.960000e-42	183.0
45	TraesCS6D01G317800	chr7A	92.742	124	9	0	375	498	674301181	674301058	5.130000e-41	180.0
46	TraesCS6D01G317800	chr3B	91.538	130	8	2	373	501	41023202	41023075	6.630000e-40	176.0

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	TraesCS6D01G317800	chr6D	426281608	426288041	6433	False	11882.000000	11882	100.000000	1	6434	1	chr6D.!!$F1	6433
1	TraesCS6D01G317800	chr6D	426333443	426334229	786	False	378.500000	625	87.116000	5322	6095	2	chr6D.!!$F3	773
2	TraesCS6D01G317800	chr6A	571161859	571167016	5157	False	1294.400000	3430	89.399000	895	5899	5	chr6A.!!$F1	5004
3	TraesCS6D01G317800	chr6B	641885064	641890327	5263	False	1059.500000	2712	89.894333	1013	6160	6	chr6B.!!$F1	5147
4	TraesCS6D01G317800	chr6B	641898597	641900868	2271	False	387.366667	996	89.024000	4918	6091	3	chr6B.!!$F2	1173

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
708	709	0.026674	CACTGCGCACCGTTATCATG	59.973	55.000	5.66	0.00	0.00	3.07	F
742	743	0.028505	GCGGCTGCAATGACATAGTG	59.971	55.000	14.08	0.00	42.15	2.74	F
1790	1871	0.036010	ATTCTCCTTGGCGTCAGTGG	60.036	55.000	4.96	4.96	0.00	4.00	F
1927	2040	0.992072	CGTCATGCCAACTACTGTCG	59.008	55.000	0.00	0.00	0.00	4.35	F
2952	3097	1.153958	GCCAAAGATGCTTGCGGAC	60.154	57.895	0.00	0.00	0.00	4.79	F
3815	4046	0.322546	AGAAACGGTTCCATCTGGCC	60.323	55.000	10.19	0.00	33.92	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2110	2254	0.251033	TTCAGTGCCTGCTTGCAGAT	60.251	50.0	22.5	4.34	43.02	2.90	R
2337	2481	0.880278	CCTAACCCGATGTCATGCGG	60.880	60.0	13.6	13.60	46.80	5.69	R
3234	3382	0.803117	CACTGGAAGCAGAGCATGTG	59.197	55.0	0.0	0.00	37.60	3.21	R
3374	3522	2.095263	CCCGACAAGCACCTGTAAATTG	60.095	50.0	0.0	0.00	0.00	2.32	R
4196	4428	0.115745	TTGGGAACGGAGGGAGTACT	59.884	55.0	0.0	0.00	0.00	2.73	R
5512	7110	0.322906	GGGGAAAAGGCTCAGGACAG	60.323	60.0	0.0	0.00	0.00	3.51	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	2.974698	GCATCTGGGCGATTCCGG	60.975	66.667	0.00	0.00	36.06	5.14
28	29	2.281070	CATCTGGGCGATTCCGGG	60.281	66.667	0.00	0.00	36.06	5.73
29	30	2.445845	ATCTGGGCGATTCCGGGA	60.446	61.111	0.00	0.00	36.06	5.14
30	31	2.070039	ATCTGGGCGATTCCGGGAA	61.070	57.895	12.67	12.67	36.06	3.97
31	32	1.418908	ATCTGGGCGATTCCGGGAAT	61.419	55.000	21.89	21.89	34.71	3.01
32	33	1.598130	CTGGGCGATTCCGGGAATC	60.598	63.158	31.21	31.21	43.31	2.52
33	34	2.281553	GGGCGATTCCGGGAATCC	60.282	66.667	33.31	26.65	43.70	3.01
34	35	2.508928	GGCGATTCCGGGAATCCA	59.491	61.111	33.31	6.40	43.70	3.41
35	36	1.892391	GGCGATTCCGGGAATCCAC	60.892	63.158	33.31	26.91	43.70	4.02
36	37	1.892391	GCGATTCCGGGAATCCACC	60.892	63.158	33.31	22.08	43.70	4.61
43	44	3.873812	GGGAATCCACCGGCCGAT	61.874	66.667	30.73	6.36	0.00	4.18
44	45	2.192175	GGAATCCACCGGCCGATT	59.808	61.111	30.73	18.78	0.00	3.34
45	46	1.892391	GGAATCCACCGGCCGATTC	60.892	63.158	30.73	25.63	42.36	2.52
46	47	2.203015	AATCCACCGGCCGATTCG	60.203	61.111	30.73	12.89	0.00	3.34
47	48	2.638330	GAATCCACCGGCCGATTCGA	62.638	60.000	30.73	16.54	36.18	3.71
48	49	2.918230	AATCCACCGGCCGATTCGAC	62.918	60.000	30.73	0.00	0.00	4.20
54	55	4.487412	GGCCGATTCGACCGTCGT	62.487	66.667	19.89	2.10	41.35	4.34
55	56	3.245315	GCCGATTCGACCGTCGTG	61.245	66.667	19.89	9.01	41.35	4.35
56	57	3.245315	CCGATTCGACCGTCGTGC	61.245	66.667	19.89	9.88	41.35	5.34
57	58	3.594827	CGATTCGACCGTCGTGCG	61.595	66.667	19.89	16.75	41.35	5.34
58	59	2.503375	GATTCGACCGTCGTGCGT	60.503	61.111	19.89	5.49	41.35	5.24
59	60	2.774951	GATTCGACCGTCGTGCGTG	61.775	63.158	19.89	0.00	41.35	5.34
97	98	3.862402	CTCCGACGTCCGACCGAG	61.862	72.222	10.58	3.65	41.76	4.63
105	106	2.362503	TCCGACCGAGGACAGCAT	60.363	61.111	0.00	0.00	34.92	3.79
106	107	1.077285	TCCGACCGAGGACAGCATA	60.077	57.895	0.00	0.00	34.92	3.14

Showing 1 to 25 of 956 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.974698	CCGGAATCGCCCAGATGC	60.975	66.667	0.00	0.00	40.02	3.91
11	12	2.281070	CCCGGAATCGCCCAGATG	60.281	66.667	0.73	0.00	40.02	2.90
12	13	1.418908	ATTCCCGGAATCGCCCAGAT	61.419	55.000	0.73	0.00	42.43	2.90
13	14	2.040009	GATTCCCGGAATCGCCCAGA	62.040	60.000	21.75	0.00	38.91	3.86
14	15	1.598130	GATTCCCGGAATCGCCCAG	60.598	63.158	21.75	0.00	38.91	4.45
15	16	2.508928	GATTCCCGGAATCGCCCA	59.491	61.111	21.75	0.00	38.91	5.36
16	17	2.281553	GGATTCCCGGAATCGCCC	60.282	66.667	26.86	15.05	46.47	6.13
17	18	1.892391	GTGGATTCCCGGAATCGCC	60.892	63.158	26.86	18.58	46.47	5.54
18	19	1.892391	GGTGGATTCCCGGAATCGC	60.892	63.158	26.86	22.13	46.47	4.58
19	20	1.594293	CGGTGGATTCCCGGAATCG	60.594	63.158	26.86	16.36	46.47	3.34
20	21	4.456806	CGGTGGATTCCCGGAATC	57.543	61.111	26.33	26.33	45.26	2.52
26	27	3.415650	AATCGGCCGGTGGATTCCC	62.416	63.158	27.83	0.00	0.00	3.97
27	28	1.892391	GAATCGGCCGGTGGATTCC	60.892	63.158	27.83	15.30	41.57	3.01
28	29	2.244651	CGAATCGGCCGGTGGATTC	61.245	63.158	27.83	26.56	43.13	2.52
29	30	2.203015	CGAATCGGCCGGTGGATT	60.203	61.111	27.83	17.75	35.67	3.01
30	31	3.151710	TCGAATCGGCCGGTGGAT	61.152	61.111	27.83	8.53	0.00	3.41
31	32	4.137872	GTCGAATCGGCCGGTGGA	62.138	66.667	27.83	17.19	0.00	4.02
38	39	3.245315	CACGACGGTCGAATCGGC	61.245	66.667	34.40	11.51	43.74	5.54
39	40	3.245315	GCACGACGGTCGAATCGG	61.245	66.667	34.40	18.50	43.74	4.18
40	41	3.594827	CGCACGACGGTCGAATCG	61.595	66.667	34.40	26.43	43.74	3.34
80	81	3.862402	CTCGGTCGGACGTCGGAG	61.862	72.222	24.25	14.59	39.77	4.63
83	84	4.157958	GTCCTCGGTCGGACGTCG	62.158	72.222	9.92	5.26	43.56	5.12
88	89	0.467474	ATATGCTGTCCTCGGTCGGA	60.467	55.000	0.00	0.00	0.00	4.55
89	90	0.319040	CATATGCTGTCCTCGGTCGG	60.319	60.000	0.00	0.00	0.00	4.79
90	91	0.941463	GCATATGCTGTCCTCGGTCG	60.941	60.000	20.64	0.00	38.21	4.79

Showing 1 to 25 of 918 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.