AutoCloner

Multiple sequence alignment - TraesCS1B01G225200

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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	TraesCS1B01G225200	chr1B	100.000	3005	0	0	651	3655	404302538	404299534	0.000000e+00	5550
1	TraesCS1B01G225200	chr1B	94.667	450	22	1	3208	3655	342054620	342055069	0.000000e+00	697
2	TraesCS1B01G225200	chr1B	100.000	231	0	0	1	231	404303188	404302958	9.380000e-116	427
3	TraesCS1B01G225200	chr1A	90.363	2480	144	43	651	3066	374169549	374167101	0.000000e+00	3168
4	TraesCS1B01G225200	chr1D	94.514	1276	65	3	651	1923	299811783	299810510	0.000000e+00	1964
5	TraesCS1B01G225200	chr1D	88.860	1167	69	30	1922	3068	299810479	299809354	0.000000e+00	1378
6	TraesCS1B01G225200	chr1D	97.835	231	5	0	1	231	203441230	203441460	2.040000e-107	399
7	TraesCS1B01G225200	chr1D	94.631	149	7	1	3060	3208	381069329	381069476	2.840000e-56	230
8	TraesCS1B01G225200	chr6B	93.527	448	26	1	3208	3655	349655929	349656373	0.000000e+00	664
9	TraesCS1B01G225200	chr6B	93.333	450	24	3	3208	3655	349679762	349680207	0.000000e+00	660
10	TraesCS1B01G225200	chr5D	92.489	466	31	2	3194	3655	205628037	205628502	0.000000e+00	664
11	TraesCS1B01G225200	chr5D	98.268	231	4	0	1	231	503998830	503999060	4.390000e-109	405
12	TraesCS1B01G225200	chr5D	96.943	229	7	0	1	229	84891658	84891430	5.730000e-103	385
13	TraesCS1B01G225200	chr4A	93.172	454	24	6	3193	3644	254842066	254842514	0.000000e+00	660
14	TraesCS1B01G225200	chr7D	92.625	461	28	4	3193	3649	350065233	350065691	0.000000e+00	658
15	TraesCS1B01G225200	chr7A	93.096	449	29	1	3198	3644	452730343	452729895	0.000000e+00	656
16	TraesCS1B01G225200	chr7A	90.833	480	30	11	3184	3655	240672305	240671832	6.660000e-177	630
17	TraesCS1B01G225200	chr7A	85.052	582	70	15	3068	3644	286503547	286502978	8.800000e-161	577
18	TraesCS1B01G225200	chr7A	97.183	142	4	0	3067	3208	442001232	442001091	1.310000e-59	241
19	TraesCS1B01G225200	chr2B	93.126	451	23	5	3208	3655	332285837	332285392	0.000000e+00	654
20	TraesCS1B01G225200	chr2B	96.479	142	3	2	3069	3210	798011296	798011435	2.190000e-57	233
21	TraesCS1B01G225200	chr6D	92.889	450	30	1	3197	3644	69587649	69588098	0.000000e+00	652
22	TraesCS1B01G225200	chr6D	97.143	140	3	1	3069	3208	461322427	461322289	6.100000e-58	235
23	TraesCS1B01G225200	chr6D	94.079	152	8	1	3058	3208	6044521	6044370	2.840000e-56	230
24	TraesCS1B01G225200	chr2D	92.291	454	31	3	3198	3649	236439783	236440234	3.080000e-180	641
25	TraesCS1B01G225200	chr2D	98.701	231	3	0	1	231	434348184	434348414	9.450000e-111	411
26	TraesCS1B01G225200	chr2D	97.403	231	6	0	1	231	217473891	217473661	9.510000e-106	394
27	TraesCS1B01G225200	chr2D	93.548	155	7	3	3055	3208	395317641	395317489	1.020000e-55	228
28	TraesCS1B01G225200	chr4D	91.649	467	32	6	3194	3655	419535753	419535289	1.110000e-179	640
29	TraesCS1B01G225200	chr6A	100.000	231	0	0	1	231	614592080	614591850	9.380000e-116	427
30	TraesCS1B01G225200	chr7B	99.567	231	1	0	1	231	6906632	6906402	4.360000e-114	422
31	TraesCS1B01G225200	chr7B	96.970	231	7	0	1	231	23069702	23069932	4.430000e-104	388
32	TraesCS1B01G225200	chr7B	97.163	141	4	0	3068	3208	450912086	450911946	4.720000e-59	239
33	TraesCS1B01G225200	chr4B	96.970	231	7	0	1	231	614049376	614049606	4.430000e-104	388
34	TraesCS1B01G225200	chr5A	89.764	254	16	7	3068	3313	308506768	308506517	2.120000e-82	316

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	TraesCS1B01G225200	chr1B	404299534	404303188	3654	True	2988.5	5550	100.000	1	3655	2	chr1B.!!$R1	3654
1	TraesCS1B01G225200	chr1A	374167101	374169549	2448	True	3168.0	3168	90.363	651	3066	1	chr1A.!!$R1	2415
2	TraesCS1B01G225200	chr1D	299809354	299811783	2429	True	1671.0	1964	91.687	651	3068	2	chr1D.!!$R1	2417
3	TraesCS1B01G225200	chr7A	286502978	286503547	569	True	577.0	577	85.052	3068	3644	1	chr7A.!!$R2	576

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
25	26	0.030369	CCGGGTTTATCGAGGAGACG	59.970	60.0	0.00	0.00	0.00	4.18	F
65	66	0.040425	ACGGCGTCATGTTTTTGAGC	60.040	50.0	6.77	0.00	0.00	4.26	F
66	67	0.040514	CGGCGTCATGTTTTTGAGCA	60.041	50.0	0.00	0.00	0.00	4.26	F
142	143	0.167251	GCCAACGTACGATGGTTTGG	59.833	55.0	35.50	29.25	39.80	3.28	F
143	144	0.167251	CCAACGTACGATGGTTTGGC	59.833	55.0	30.26	0.00	33.98	4.52	F
1302	1315	0.806102	CTGGGCAGGTGACGTTATCG	60.806	60.0	0.00	0.00	43.34	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1284	1297	1.216977	CGATAACGTCACCTGCCCA	59.783	57.895	34.56	5.36	R
1288	1301	1.520787	GGGGCGATAACGTCACCTG	60.521	63.158	46.58	4.00	R
1906	1930	1.623542	AAGTATGGGGGAGTGCGTCC	61.624	60.000	46.10	4.79	R
2139	2196	1.375523	GGACAGAACGTGCGGGAAT	60.376	57.895	0.00	3.01	R
2140	2197	2.029964	GGACAGAACGTGCGGGAA	59.970	61.111	0.00	3.97	R
3206	3317	0.034337	TTGAGGTCGGGTTGCTACAC	59.966	55.000	0.00	2.90	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	Hairpin	End Stability
17	18	3.095032	CGTTGGCCGGGTTTATCG	58.905	61.111	2.18	0.00	2.92
18	19	1.448189	CGTTGGCCGGGTTTATCGA	60.448	57.895	2.18	0.00	3.59
19	20	1.426041	CGTTGGCCGGGTTTATCGAG	61.426	60.000	2.18	0.00	4.04
20	21	1.093496	GTTGGCCGGGTTTATCGAGG	61.093	60.000	2.18	0.00	4.63
21	22	1.266160	TTGGCCGGGTTTATCGAGGA	61.266	55.000	2.18	0.00	3.71
22	23	1.069258	GGCCGGGTTTATCGAGGAG	59.931	63.158	2.18	0.00	3.69
23	24	1.397390	GGCCGGGTTTATCGAGGAGA	61.397	60.000	2.18	0.00	3.71
24	25	0.249363	GCCGGGTTTATCGAGGAGAC	60.249	60.000	2.18	0.00	3.36
25	26	0.030369	CCGGGTTTATCGAGGAGACG	59.970	60.000	0.00	0.00	4.18
26	27	1.019673	CGGGTTTATCGAGGAGACGA	58.980	55.000	0.00	46.04	4.20
27	28	1.402968	CGGGTTTATCGAGGAGACGAA	59.597	52.381	0.00	45.16	3.85
28	29	2.541178	CGGGTTTATCGAGGAGACGAAG	60.541	54.545	0.00	45.16	3.79
29	30	2.686915	GGGTTTATCGAGGAGACGAAGA	59.313	50.000	0.00	45.16	2.87
30	31	3.243134	GGGTTTATCGAGGAGACGAAGAG	60.243	52.174	0.00	45.16	2.85
31	32	3.243134	GGTTTATCGAGGAGACGAAGAGG	60.243	52.174	0.00	45.16	3.69
32	33	1.595466	TATCGAGGAGACGAAGAGGC	58.405	55.000	0.00	45.16	4.70
33	34	0.106918	ATCGAGGAGACGAAGAGGCT	60.107	55.000	0.00	45.16	4.58
34	35	0.540454	TCGAGGAGACGAAGAGGCTA	59.460	55.000	0.00	39.26	3.93
35	36	1.141254	TCGAGGAGACGAAGAGGCTAT	59.859	52.381	0.00	39.26	2.97
36	37	1.950909	CGAGGAGACGAAGAGGCTATT	59.049	52.381	0.00	39.26	1.73
37	38	2.287308	CGAGGAGACGAAGAGGCTATTG	60.287	54.545	0.00	39.26	1.90
38	39	1.410882	AGGAGACGAAGAGGCTATTGC	59.589	52.381	0.00	39.26	3.56
39	40	1.137086	GGAGACGAAGAGGCTATTGCA	59.863	52.381	0.00	39.26	4.08
40	41	2.224161	GGAGACGAAGAGGCTATTGCAT	60.224	50.000	0.00	39.26	3.96
41	42	2.799412	GAGACGAAGAGGCTATTGCATG	59.201	50.000	0.00	39.26	4.06

Showing 1 to 25 of 287 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	1.426041	CTCGATAAACCCGGCCAACG	61.426	60.000	2.24	43.80	4.10
1	2	1.093496	CCTCGATAAACCCGGCCAAC	61.093	60.000	2.24	0.00	3.77
2	3	1.222387	CCTCGATAAACCCGGCCAA	59.778	57.895	2.24	0.00	4.52
3	4	1.682451	CTCCTCGATAAACCCGGCCA	61.682	60.000	2.24	0.00	5.36
4	5	1.069258	CTCCTCGATAAACCCGGCC	59.931	63.158	0.00	0.00	6.13
5	6	0.249363	GTCTCCTCGATAAACCCGGC	60.249	60.000	0.00	0.00	6.13
6	7	0.030369	CGTCTCCTCGATAAACCCGG	59.970	60.000	0.00	0.00	5.73
7	8	1.019673	TCGTCTCCTCGATAAACCCG	58.980	55.000	0.00	34.85	5.28
8	9	2.686915	TCTTCGTCTCCTCGATAAACCC	59.313	50.000	0.00	39.57	4.11
9	10	3.243134	CCTCTTCGTCTCCTCGATAAACC	60.243	52.174	0.00	39.57	3.27
10	11	3.792794	GCCTCTTCGTCTCCTCGATAAAC	60.793	52.174	0.00	39.57	2.01
11	12	2.358267	GCCTCTTCGTCTCCTCGATAAA	59.642	50.000	0.00	39.57	1.40
12	13	1.948145	GCCTCTTCGTCTCCTCGATAA	59.052	52.381	0.00	39.57	1.75
13	14	1.141254	AGCCTCTTCGTCTCCTCGATA	59.859	52.381	0.00	39.57	2.92
14	15	0.106918	AGCCTCTTCGTCTCCTCGAT	60.107	55.000	0.00	39.57	3.59
15	16	0.540454	TAGCCTCTTCGTCTCCTCGA	59.460	55.000	0.00	38.08	4.04
16	17	1.600023	ATAGCCTCTTCGTCTCCTCG	58.400	55.000	0.00	0.00	4.63
17	18	2.544903	GCAATAGCCTCTTCGTCTCCTC	60.545	54.545	0.00	33.58	3.71
18	19	1.410882	GCAATAGCCTCTTCGTCTCCT	59.589	52.381	0.00	33.58	3.69
19	20	1.137086	TGCAATAGCCTCTTCGTCTCC	59.863	52.381	0.00	41.13	3.71
20	21	2.586258	TGCAATAGCCTCTTCGTCTC	57.414	50.000	0.00	41.13	3.36
21	22	2.484417	CCATGCAATAGCCTCTTCGTCT	60.484	50.000	0.00	41.13	4.18
22	23	1.869767	CCATGCAATAGCCTCTTCGTC	59.130	52.381	0.00	41.13	4.20
23	24	1.486310	TCCATGCAATAGCCTCTTCGT	59.514	47.619	0.00	41.13	3.85
24	25	2.141517	CTCCATGCAATAGCCTCTTCG	58.858	52.381	0.00	41.13	3.79

Showing 1 to 25 of 300 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.