AutoCloner

Multiple sequence alignment - TraesCS5B01G378300

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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	TraesCS5B01G378300	chr5B	100.000	4769	0	0	1	4769	556640062	556644830	0.000000e+00	8807.0
1	TraesCS5B01G378300	chr7B	96.895	4767	135	9	4	4769	169284865	169280111	0.000000e+00	7971.0
2	TraesCS5B01G378300	chr2B	96.875	4736	142	6	35	4769	571078797	571074067	0.000000e+00	7921.0
3	TraesCS5B01G378300	chr3B	96.708	4709	152	1	64	4769	668321328	668316620	0.000000e+00	7834.0
4	TraesCS5B01G378300	chr3B	96.432	4736	160	5	35	4769	545295206	545290479	0.000000e+00	7801.0
5	TraesCS5B01G378300	chr3B	96.031	4737	182	6	35	4769	413604117	413608849	0.000000e+00	7701.0
6	TraesCS5B01G378300	chr6B	96.288	4741	168	8	32	4769	295370152	295374887	0.000000e+00	7773.0
7	TraesCS5B01G378300	chr1B	94.990	4770	235	4	1	4769	463687537	463692303	0.000000e+00	7481.0
8	TraesCS5B01G378300	chr3D	94.999	4739	232	4	32	4769	372376567	372381301	0.000000e+00	7433.0
9	TraesCS5B01G378300	chr4A	94.721	4736	244	6	35	4769	487349416	487344686	0.000000e+00	7356.0
10	TraesCS5B01G378300	chr2A	95.455	44	2	0	1	44	586820186	586820229	2.380000e-08	71.3
11	TraesCS5B01G378300	chr2A	95.455	44	2	0	1	44	586828506	586828549	2.380000e-08	71.3

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	TraesCS5B01G378300	chr5B	556640062	556644830	4768	False	8807	8807	100.000	1	4769	1	chr5B.!!$F1	4768
1	TraesCS5B01G378300	chr7B	169280111	169284865	4754	True	7971	7971	96.895	4	4769	1	chr7B.!!$R1	4765
2	TraesCS5B01G378300	chr2B	571074067	571078797	4730	True	7921	7921	96.875	35	4769	1	chr2B.!!$R1	4734
3	TraesCS5B01G378300	chr3B	668316620	668321328	4708	True	7834	7834	96.708	64	4769	1	chr3B.!!$R2	4705
4	TraesCS5B01G378300	chr3B	545290479	545295206	4727	True	7801	7801	96.432	35	4769	1	chr3B.!!$R1	4734
5	TraesCS5B01G378300	chr3B	413604117	413608849	4732	False	7701	7701	96.031	35	4769	1	chr3B.!!$F1	4734
6	TraesCS5B01G378300	chr6B	295370152	295374887	4735	False	7773	7773	96.288	32	4769	1	chr6B.!!$F1	4737
7	TraesCS5B01G378300	chr1B	463687537	463692303	4766	False	7481	7481	94.990	1	4769	1	chr1B.!!$F1	4768
8	TraesCS5B01G378300	chr3D	372376567	372381301	4734	False	7433	7433	94.999	32	4769	1	chr3D.!!$F1	4737
9	TraesCS5B01G378300	chr4A	487344686	487349416	4730	True	7356	7356	94.721	35	4769	1	chr4A.!!$R1	4734

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
828	835	2.507058	TGGAGCAAGAGTATGGCTTCAT	59.493	45.455	0.0	0.0	38.21	2.57	F
2330	2338	0.833287	AGTGCTCTGTGTGACTTGGT	59.167	50.000	0.0	0.0	0.00	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2514	2522	1.771255	ACAGCCTCACTTTTGTCCTCT	59.229	47.619	0.0	0.0	0.0	3.69	R
3866	3876	3.864789	TGGCTATCTTGGAGAAATCCC	57.135	47.619	0.0	0.0	0.0	3.85	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
49	50	4.000325	TGTGATGTCTGAACCATTTACCG	59.000	43.478	0.00	0.00	0.00	4.02
68	69	7.979115	TTACCGTTGCTGCATATTATTTTTC	57.021	32.000	1.84	0.00	0.00	2.29
170	171	4.338682	GTGCTTCGAAGTTCTAGATCCCTA	59.661	45.833	25.24	0.00	0.00	3.53
178	179	6.072175	CGAAGTTCTAGATCCCTATGGAGAAG	60.072	46.154	0.56	0.00	46.08	2.85
206	208	2.807392	TCCGTAGTTTGGGCGTAAAAAG	59.193	45.455	0.00	0.00	0.00	2.27
414	418	8.579850	TTACAGGAAATTGTCTTATGCTTCAT	57.420	30.769	0.00	0.00	32.56	2.57
418	422	7.500227	CAGGAAATTGTCTTATGCTTCATCCTA	59.500	37.037	0.00	0.00	31.52	2.94
496	503	5.237344	AGAAGAGAGAATCAAACACGGTTTG	59.763	40.000	18.01	18.01	37.82	2.93
508	515	2.687935	ACACGGTTTGAAGTTGCTGAAT	59.312	40.909	0.00	0.00	0.00	2.57
545	552	8.152898	TCAAGAAGAAGAAAAGATGTCTGATCA	58.847	33.333	0.00	0.00	0.00	2.92
778	785	2.924290	GTTTCACCGAGTGCTATCAGAC	59.076	50.000	0.00	0.00	32.98	3.51
828	835	2.507058	TGGAGCAAGAGTATGGCTTCAT	59.493	45.455	0.00	0.00	38.21	2.57
996	1003	7.332678	GCATGGCAAAGATTCAACTCTTTAATT	59.667	33.333	0.00	0.00	42.21	1.40
1089	1096	2.069273	ACCAGAGCTTTTGTCGATTCG	58.931	47.619	0.00	0.00	0.00	3.34
1120	1127	4.739793	AGGAGGAATCATGAACAAAACCA	58.260	39.130	0.00	0.00	0.00	3.67
1179	1187	4.400251	TCTCATCATTTCCAATGGTCAAGC	59.600	41.667	0.00	0.00	0.00	4.01
1200	1208	1.745653	GAAAGAGCAATAGCACCACCC	59.254	52.381	0.00	0.00	45.49	4.61
1406	1414	3.763360	TCAGCAATTGGATCATCGGTTTT	59.237	39.130	7.72	0.00	0.00	2.43
1448	1456	4.792068	AGTCAAGGTCCATTCTCAAACAA	58.208	39.130	0.00	0.00	0.00	2.83
1668	1676	7.177216	AGCAAGATGACAAATGAAGTTAATGGA	59.823	33.333	0.00	0.00	0.00	3.41
1729	1737	7.060421	GGATAGTATGGTGGGAGAAAATGAAA	58.940	38.462	0.00	0.00	0.00	2.69
1730	1738	7.559897	GGATAGTATGGTGGGAGAAAATGAAAA	59.440	37.037	0.00	0.00	0.00	2.29
1789	1797	3.010027	TCACTGTGGGGCAATATCTTCAA	59.990	43.478	8.11	0.00	0.00	2.69
1792	1800	5.593909	CACTGTGGGGCAATATCTTCAATTA	59.406	40.000	0.00	0.00	0.00	1.40
1930	1938	9.277783	CATCAGAGAAACTAAAGGAGAAAGAAA	57.722	33.333	0.00	0.00	0.00	2.52
2029	2037	8.672815	CAATAACAACCAACAACATTCCTTTTT	58.327	29.630	0.00	0.00	0.00	1.94
2164	2172	8.819974	CAATGTATGCCAAATATTTCAAGGAAC	58.180	33.333	7.13	3.30	0.00	3.62
2174	2182	9.132521	CAAATATTTCAAGGAACTGCTAACAAG	57.867	33.333	0.00	0.00	40.86	3.16
2249	2257	6.044046	GTGCAATAATTCAGAATTCCATGCA	58.956	36.000	24.96	24.96	39.42	3.96
2330	2338	0.833287	AGTGCTCTGTGTGACTTGGT	59.167	50.000	0.00	0.00	0.00	3.67
2419	2427	3.519510	AGCCATAACTCTTCAGTTAGCCA	59.480	43.478	1.42	0.00	46.20	4.75
2514	2522	7.423199	CGGTTGACTTTGTAGTGCTAGATATA	58.577	38.462	0.00	0.00	33.84	0.86
2686	2694	6.490040	AGGAGAAAAGCACTGCTACAAAATTA	59.510	34.615	3.33	0.00	38.25	1.40
2842	2850	2.776536	AGGCCACTAGAGAAGATGCAAT	59.223	45.455	5.01	0.00	0.00	3.56
2939	2947	7.395489	GCCAATTATCATGAATAGGGAGTTGAT	59.605	37.037	0.00	0.00	0.00	2.57
3123	3131	2.109128	TCCCCATTTGCAAGAGGTTGTA	59.891	45.455	15.51	0.00	35.92	2.41
3653	3662	4.454728	TGAATAATTTGGCAGCAGTTCC	57.545	40.909	0.00	0.00	0.00	3.62
3766	3775	6.546484	TCTGAAAGAGGAATTGAGGTTGATT	58.454	36.000	0.00	0.00	38.67	2.57
3866	3876	8.370940	TGCTGGGTTCTATAGAAGATTCATAAG	58.629	37.037	15.58	6.48	34.27	1.73
3907	3917	4.101741	CCAAACCCCTCACTAATCTCCTAG	59.898	50.000	0.00	0.00	0.00	3.02
3967	3977	6.096705	TGAAAAATCCTTCAACTTGCTCAAGA	59.903	34.615	15.74	0.00	35.15	3.02
4416	4426	7.060383	AGACTCCTTACCTATCAATGATGTG	57.940	40.000	5.91	0.00	0.00	3.21
4421	4431	8.319057	TCCTTACCTATCAATGATGTGTTACT	57.681	34.615	5.91	0.00	0.00	2.24
4630	4640	0.320334	TGTTCGAAGATGCTTGCCGA	60.320	50.000	0.00	0.00	35.04	5.54
4673	4683	5.014860	TGATCTATCATTGCCATTCATCCCT	59.985	40.000	0.00	0.00	0.00	4.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.951037	ACACACAACTCAAGCAACCAATA	59.049	39.130	0.00	0.00	0.00	1.90
12	13	3.181497	ACATCACACACAACTCAAGCAAC	60.181	43.478	0.00	0.00	0.00	4.17
17	18	4.135747	TCAGACATCACACACAACTCAA	57.864	40.909	0.00	0.00	0.00	3.02
22	23	3.274095	TGGTTCAGACATCACACACAA	57.726	42.857	0.00	0.00	0.00	3.33
68	69	7.617041	AGCAATTACTAGAGCAAGGTAAAAG	57.383	36.000	0.00	0.00	0.00	2.27
210	212	9.345517	CGCCAAAATGATCATTTGTAATATAGG	57.654	33.333	29.52	20.63	40.57	2.57
414	418	8.713971	TCAAATGGCTCTAGTGAATATTTAGGA	58.286	33.333	0.00	0.00	0.00	2.94
418	422	8.000709	TGGATCAAATGGCTCTAGTGAATATTT	58.999	33.333	0.00	0.00	0.00	1.40
778	785	9.618890	TCTCAAGGAAAATGGAAATAGTGATAG	57.381	33.333	0.00	0.00	0.00	2.08
828	835	3.760151	CCTTCAGATGTTCAGGCAATGAA	59.240	43.478	0.00	0.00	45.79	2.57
996	1003	5.698741	AACCATGATGAGGACACATTCTA	57.301	39.130	0.00	0.00	0.00	2.10
1089	1096	0.620556	TGATTCCTCCTCCAACAGCC	59.379	55.000	0.00	0.00	0.00	4.85
1120	1127	6.821160	TCAATCAATGCAAATGCTTCATCAAT	59.179	30.769	6.97	0.00	42.66	2.57
1179	1187	1.398390	GGTGGTGCTATTGCTCTTTCG	59.602	52.381	0.00	0.00	40.48	3.46
1361	1369	9.219603	CTGAATAGAAGGTACATTCTGTTGAAA	57.780	33.333	29.09	16.74	39.74	2.69
1406	1414	7.011499	TGACTTTGGGCATAACTTACTTCTA	57.989	36.000	0.00	0.00	0.00	2.10
1668	1676	9.686683	ACAAGCATCTTAACAGTATCCTTTAAT	57.313	29.630	0.00	0.00	0.00	1.40
1789	1797	5.877012	CACTCCTTGTAGTCACTGCATTAAT	59.123	40.000	0.00	0.00	0.00	1.40
1792	1800	3.557898	CCACTCCTTGTAGTCACTGCATT	60.558	47.826	0.00	0.00	0.00	3.56
1930	1938	8.110860	ACTTCAGTTTCAATTCGGTTATCAAT	57.889	30.769	0.00	0.00	0.00	2.57
2164	2172	4.836125	TGCTTCTTTTCCTTGTTAGCAG	57.164	40.909	0.00	0.00	33.64	4.24
2174	2182	2.163211	GGCTCAGACATGCTTCTTTTCC	59.837	50.000	0.00	0.00	0.00	3.13
2330	2338	5.601583	TGGTAACACACTAACACTTGAGA	57.398	39.130	0.00	0.00	46.17	3.27
2419	2427	6.659242	CCAACAGGTTTCCTATATGTTCTGTT	59.341	38.462	0.00	0.00	42.58	3.16
2514	2522	1.771255	ACAGCCTCACTTTTGTCCTCT	59.229	47.619	0.00	0.00	0.00	3.69
2561	2569	4.220693	ACATCAATAAGTGCACCAGCTA	57.779	40.909	14.63	0.36	42.74	3.32
2686	2694	7.450074	TCTTCCACACATTTCTGTAGTGTATT	58.550	34.615	0.00	0.00	44.02	1.89
2842	2850	7.725251	AGTTGTTTCATTTCTATTTGCCTTGA	58.275	30.769	0.00	0.00	0.00	3.02
2939	2947	3.247162	AGCCCTTTTATTTGCCTTTCCA	58.753	40.909	0.00	0.00	0.00	3.53
3557	3566	7.206789	TCCACTTTGGTTCCTATCATATCAA	57.793	36.000	0.00	0.00	39.03	2.57
3572	3581	4.286297	TCTATGAACACCTCCACTTTGG	57.714	45.455	0.00	0.00	39.43	3.28
3866	3876	3.864789	TGGCTATCTTGGAGAAATCCC	57.135	47.619	0.00	0.00	0.00	3.85
3907	3917	9.683069	ATCAAAGTTGAACTTAACATCATTGTC	57.317	29.630	11.43	0.00	37.47	3.18
4184	4194	6.547141	CCCTACAAGATATTGCCTGAATTTGA	59.453	38.462	0.00	0.00	0.00	2.69
4416	4426	5.611374	TGCATAAGATTGCTCCCTAGTAAC	58.389	41.667	0.00	0.00	43.18	2.50
4421	4431	4.164030	TCACTTGCATAAGATTGCTCCCTA	59.836	41.667	0.00	0.00	43.18	3.53
4630	4640	4.164843	TCACACCTTTAGCTTCACCTTT	57.835	40.909	0.00	0.00	0.00	3.11
4645	4655	4.823442	TGAATGGCAATGATAGATCACACC	59.177	41.667	0.00	0.00	40.03	4.16
4673	4683	5.435686	AGTACTTGCATGACCTCCATAAA	57.564	39.130	6.60	0.00	33.31	1.40
4716	4726	2.166254	CCAGTAAAATCCCGCTTGCAAT	59.834	45.455	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.