AutoCloner

Multiple sequence alignment - TraesCS2B01G401200

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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	TraesCS2B01G401200	chr2B	100.000	2648	0	0	1	2648	569484831	569487478	0.000000e+00	4891
1	TraesCS2B01G401200	chr2B	90.341	176	14	3	736	909	569113395	569113221	7.370000e-56	228
2	TraesCS2B01G401200	chr2D	90.382	2017	120	32	44	2017	484833142	484835127	0.000000e+00	2582
3	TraesCS2B01G401200	chr2D	89.989	949	61	16	858	1782	484380815	484381753	0.000000e+00	1195
4	TraesCS2B01G401200	chr2D	88.406	552	31	12	2013	2547	484846525	484847060	3.720000e-178	634
5	TraesCS2B01G401200	chr2D	86.735	98	7	5	2547	2644	484847160	484847251	1.300000e-18	104
6	TraesCS2B01G401200	chr2D	95.238	63	3	0	736	798	484380756	484380818	1.680000e-17	100
7	TraesCS2B01G401200	chr1A	81.971	477	72	7	1	475	507975125	507974661	2.470000e-105	392
8	TraesCS2B01G401200	chr7B	82.030	473	71	7	1	470	465787933	465788394	8.890000e-105	390
9	TraesCS2B01G401200	chr7B	80.804	224	32	5	1	223	508799030	508799243	5.860000e-37	165
10	TraesCS2B01G401200	chr4B	81.917	459	67	8	21	475	434584770	434584324	8.950000e-100	374
11	TraesCS2B01G401200	chr3D	80.802	474	81	6	2	473	477024140	477023675	1.940000e-96	363
12	TraesCS2B01G401200	chr3D	80.705	482	75	13	1	478	438564818	438565285	2.510000e-95	359
13	TraesCS2B01G401200	chr2A	84.334	383	24	15	2188	2547	628701336	628701705	2.520000e-90	342
14	TraesCS2B01G401200	chr3B	79.710	483	77	14	1	473	636266398	636265927	1.960000e-86	329
15	TraesCS2B01G401200	chr3A	79.245	477	83	10	1	476	696398506	696398045	4.250000e-83	318
16	TraesCS2B01G401200	chr3A	79.046	482	82	14	1	478	577556194	577556660	1.980000e-81	313
17	TraesCS2B01G401200	chr7D	79.412	476	69	12	1	474	512737990	512737542	2.560000e-80	309
18	TraesCS2B01G401200	chr6D	78.631	482	74	16	1	475	163147628	163148087	2.580000e-75	292
19	TraesCS2B01G401200	chr5D	82.436	353	44	10	1	349	327645733	327645395	2.580000e-75	292
20	TraesCS2B01G401200	chr6A	83.133	166	27	1	1	165	603787981	603788146	1.640000e-32	150

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	TraesCS2B01G401200	chr2B	569484831	569487478	2647	False	4891.0	4891	100.0000	1	2648	1	chr2B.!!$F1	2647
1	TraesCS2B01G401200	chr2D	484833142	484835127	1985	False	2582.0	2582	90.3820	44	2017	1	chr2D.!!$F1	1973
2	TraesCS2B01G401200	chr2D	484380756	484381753	997	False	647.5	1195	92.6135	736	1782	2	chr2D.!!$F2	1046
3	TraesCS2B01G401200	chr2D	484846525	484847251	726	False	369.0	634	87.5705	2013	2644	2	chr2D.!!$F3	631

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
837	852	0.040425	CCAACGCGAACCTTTTCCAG	60.04	55.0	15.93	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2499	2576	0.037326	TGAGGAATCGACAGCCACAC	60.037	55.0	0.0	0.0	0.0	3.82	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
19	20	2.804697	TTCATCGAACAAGTGTCGGA	57.195	45.000	0.00	0.00	0.00	4.55
20	21	2.060326	TCATCGAACAAGTGTCGGAC	57.940	50.000	0.00	0.00	0.00	4.79
21	22	1.338655	TCATCGAACAAGTGTCGGACA	59.661	47.619	6.76	6.76	0.00	4.02
22	23	2.029380	TCATCGAACAAGTGTCGGACAT	60.029	45.455	14.78	0.00	0.00	3.06
23	24	1.778334	TCGAACAAGTGTCGGACATG	58.222	50.000	14.78	11.82	0.00	3.21
24	25	0.790207	CGAACAAGTGTCGGACATGG	59.210	55.000	14.78	9.28	0.00	3.66
25	26	1.872237	CGAACAAGTGTCGGACATGGT	60.872	52.381	14.78	8.10	0.00	3.55
26	27	2.608506	CGAACAAGTGTCGGACATGGTA	60.609	50.000	14.78	0.00	0.00	3.25
27	28	2.743636	ACAAGTGTCGGACATGGTAG	57.256	50.000	14.78	5.89	0.00	3.18
28	29	1.968493	ACAAGTGTCGGACATGGTAGT	59.032	47.619	14.78	6.49	0.00	2.73
29	30	3.159472	ACAAGTGTCGGACATGGTAGTA	58.841	45.455	14.78	0.00	0.00	1.82
30	31	3.767673	ACAAGTGTCGGACATGGTAGTAT	59.232	43.478	14.78	0.00	0.00	2.12
31	32	4.951715	ACAAGTGTCGGACATGGTAGTATA	59.048	41.667	14.78	0.00	0.00	1.47
32	33	5.067413	ACAAGTGTCGGACATGGTAGTATAG	59.933	44.000	14.78	0.00	0.00	1.31
33	34	3.568853	AGTGTCGGACATGGTAGTATAGC	59.431	47.826	14.78	0.00	40.09	2.97
42	43	3.497103	TGGTAGTATAGCAGTAGCGGA	57.503	47.619	0.00	0.00	45.27	5.54
53	54	1.069258	GTAGCGGATGGTACCTGGC	59.931	63.158	14.36	10.81	42.02	4.85
54	55	1.382009	TAGCGGATGGTACCTGGCA	60.382	57.895	14.36	0.00	0.00	4.92
55	56	0.978667	TAGCGGATGGTACCTGGCAA	60.979	55.000	14.36	0.00	0.00	4.52
65	66	3.691342	CCTGGCAAGACGGTCGGA	61.691	66.667	1.89	0.00	0.00	4.55
84	85	2.747686	GAGAGGGGTTGAACGGCA	59.252	61.111	0.00	0.00	0.00	5.69
97	98	2.224523	TGAACGGCAATGGAGAAGAAGT	60.225	45.455	0.00	0.00	0.00	3.01
137	138	1.606601	CCTGGAGGTGACGGAGACA	60.607	63.158	0.00	0.00	0.00	3.41
154	155	1.227674	CATAGAGTTCCGGCAGGGC	60.228	63.158	2.05	0.00	38.33	5.19
155	156	1.383248	ATAGAGTTCCGGCAGGGCT	60.383	57.895	2.05	1.54	38.33	5.19

Showing 1 to 25 of 161 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.223852	TGTCCGACACTTGTTCGATGAA	60.224	45.455	0.00	0.00	0.00	2.57
1	2	1.338655	TGTCCGACACTTGTTCGATGA	59.661	47.619	0.00	0.00	0.00	2.92
2	3	1.778334	TGTCCGACACTTGTTCGATG	58.222	50.000	0.00	0.00	0.00	3.84
3	4	2.337583	CATGTCCGACACTTGTTCGAT	58.662	47.619	2.57	0.00	0.00	3.59
4	5	1.604438	CCATGTCCGACACTTGTTCGA	60.604	52.381	2.57	0.00	0.00	3.71
5	6	0.790207	CCATGTCCGACACTTGTTCG	59.210	55.000	2.57	0.00	0.00	3.95
6	7	1.878953	ACCATGTCCGACACTTGTTC	58.121	50.000	2.57	0.00	0.00	3.18
7	8	2.367567	ACTACCATGTCCGACACTTGTT	59.632	45.455	2.57	0.00	0.00	2.83
8	9	1.968493	ACTACCATGTCCGACACTTGT	59.032	47.619	2.57	4.20	0.00	3.16
9	10	2.743636	ACTACCATGTCCGACACTTG	57.256	50.000	2.57	0.00	0.00	3.16
10	11	4.037684	GCTATACTACCATGTCCGACACTT	59.962	45.833	2.57	0.00	0.00	3.16
11	12	3.568853	GCTATACTACCATGTCCGACACT	59.431	47.826	2.57	0.00	0.00	3.55
12	13	3.317149	TGCTATACTACCATGTCCGACAC	59.683	47.826	2.57	0.00	0.00	3.67
13	14	3.558033	TGCTATACTACCATGTCCGACA	58.442	45.455	3.10	3.10	0.00	4.35
14	15	3.568853	ACTGCTATACTACCATGTCCGAC	59.431	47.826	0.00	0.00	0.00	4.79
15	16	3.828921	ACTGCTATACTACCATGTCCGA	58.171	45.455	0.00	0.00	0.00	4.55
16	17	4.379603	GCTACTGCTATACTACCATGTCCG	60.380	50.000	0.00	0.00	36.03	4.79
17	18	4.379603	CGCTACTGCTATACTACCATGTCC	60.380	50.000	0.00	0.00	36.97	4.02
18	19	4.379603	CCGCTACTGCTATACTACCATGTC	60.380	50.000	0.00	0.00	36.97	3.06
19	20	3.506455	CCGCTACTGCTATACTACCATGT	59.494	47.826	0.00	0.00	36.97	3.21
20	21	3.756963	TCCGCTACTGCTATACTACCATG	59.243	47.826	0.00	0.00	36.97	3.66
21	22	4.030314	TCCGCTACTGCTATACTACCAT	57.970	45.455	0.00	0.00	36.97	3.55
22	23	3.497103	TCCGCTACTGCTATACTACCA	57.503	47.619	0.00	0.00	36.97	3.25
23	24	3.128938	CCATCCGCTACTGCTATACTACC	59.871	52.174	0.00	0.00	36.97	3.18
24	25	3.757493	ACCATCCGCTACTGCTATACTAC	59.243	47.826	0.00	0.00	36.97	2.73

Showing 1 to 25 of 157 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.